To see the other types of publications on this topic, follow the link: Eukaryotic gene; Genes; Chromosomal domain.
Journal articles on the topic 'Eukaryotic gene; Genes; Chromosomal domain'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Eukaryotic gene; Genes; Chromosomal domain.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Nützmann, Hans-Wilhelm, Daniel Doerr, América Ramírez-Colmenero, Jesús Emiliano Sotelo-Fonseca, Eva Wegel, Marco Di Stefano, Steven W. Wingett, et al. "Active and repressed biosynthetic gene clusters have spatially distinct chromosome states." Proceedings of the National Academy of Sciences 117, no. 24 (June 3, 2020): 13800–13809. http://dx.doi.org/10.1073/pnas.1920474117.
Full textAbstract:
While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes inArabidopsis thaliana. Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.
2
Shopland, Lindsay S., Carol V. Johnson, Meg Byron, John McNeil, and Jeanne B. Lawrence. "Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains." Journal of Cell Biology 162, no. 6 (September 15, 2003): 981–90. http://dx.doi.org/10.1083/jcb.200303131.
Full textAbstract:
Typically, eukaryotic nuclei contain 10–30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain “choice” appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3–4 subregions of the chromosome periphery that contact a domain. Most importantly, visualization of six individual chromosome bands showed that large genomic segments (∼5 Mb) have striking differences in organization relative to domains. Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not. All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences. Similarly, late-replicating DNA generally avoids SC-35 domains. These findings suggest a functional rationale for gene clustering in chromosomal bands, which relates to nuclear clustering of genes with SC-35 domains. Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic “neighborhoods.”
3
LaSalle, Janine M., and Marc Lalande. "Domain organization of allele-specific DNA replication within the GABAA receptor gene cluster." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 766–67. http://dx.doi.org/10.1017/s0424820100140208.
Full textAbstract:
Parental imprinting is a gamete-specific modification that distinguishes the paternal and maternal chromosomes in higher eukaryotes, resulting in allele-specific changes in chromatin organization, transcription and replication. One example of parental imprinting in humans is revealed by two distinct genetic diseases, Prader-Willi syndrome (PWS) and Angelman syndrome (AS) which both map to chromosome 15q11-13. PWS is caused by the absence of a paternal contribution to 15q11-13, while AS results from the lack of a maternal copy of the region. Within this chromosomal subregion lies a cluster of GABAA receptor β3 and α5 subunit genes (GABRB3 and GABRA5) which are separated by about 100 kb and arranged in opposite transcritional orientations (Figure 1). Allele-specific asynchronous DNA replication has previously been found to be associated with imprinted chromosomal regions.In order to further study the association between DNA replication and imprinting, allele-specific replication was assayed by fluorescence in situ hybridization (FISH). Biotin-labeled phage probes detected by FITC hybridized to each chromosome as either a singlet (unreplicated state) or a doublet (replicated state). Cells demonstrating asynchronous replication (one singlet and one doublet) for each probe are shown in Figure 2.
4
Orlov, Y. L., O. Thierry, A. G. Bogomolov, A. V. Tsukanov, E. V. Kulakova, E. R. Galieva, A. O. Bragin, and G. Li. "Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data." Biomeditsinskaya Khimiya 63, no. 5 (2017): 418–22. http://dx.doi.org/10.18097/pbmc20176305418.
Full textAbstract:
The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research. The technique of chromatin immunoprecipitation and subsequent sequencing (ChIP-seq) make possible to determine binding sites of transcription factors that regulate expression of eukaryotic genes; genome transcription factors binding maps have been. The ChIA-PET technology allows exploring not only target protein binding sites, but also pairs of such sites on proximally located and interacting with each other chromosomes co-located in three-dimensional space of the cell nucleus. Here we discuss the principles of the construction of genomic maps and matrices of chromosome contacts according to ChIA-PET and Hi-C data that capture the chromosome conformation and overview existing software for 3D genome analysis including in house programs of gene location analysis in topological domains.
5
Schiklenk, Christoph, Boryana Petrova, Marc Kschonsak, Markus Hassler, Carlo Klein, Toby J. Gibson, and Christian H. Haering. "Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1." Journal of Cell Biology 217, no. 7 (May 7, 2018): 2383–401. http://dx.doi.org/10.1083/jcb.201711097.
Full textAbstract:
Although the formation of rod-shaped chromosomes is vital for the correct segregation of eukaryotic genomes during cell divisions, the molecular mechanisms that control the chromosome condensation process have remained largely unknown. Here, we identify the C2H2 zinc-finger transcription factor Zas1 as a key regulator of mitotic condensation dynamics in a quantitative live-cell microscopy screen of the fission yeast Schizosaccharomyces pombe. By binding to specific DNA target sequences in their promoter regions, Zas1 controls expression of the Cnd1 subunit of the condensin protein complex and several other target genes, whose combined misregulation in zas1 mutants results in defects in chromosome condensation and segregation. Genetic and biochemical analysis reveals an evolutionarily conserved transactivation domain motif in Zas1 that is pivotal to its function in gene regulation. Our results suggest that this motif, together with the Zas1 C-terminal helical domain to which it binds, creates a cis/trans switch module for transcriptional regulation of genes that control chromosome condensation.
6
Landis, G., and J. Tower. "The Drosophila chiffon gene is required for chorion gene amplification, and is related to the yeast Dbf4 regulator of DNA replication and cell cycle." Development 126, no. 19 (October 1, 1999): 4281–93. http://dx.doi.org/10.1242/dev.126.19.4281.
Full textAbstract:
The Drosophila chorion genes encode the major protein components of the chorion (eggshell) and are arranged in two clusters in the genome. To meet the demand for rapid chorion synthesis, Drosophila ovary follicle cells amplify the chorion gene clusters approximately 80-fold. Amplification proceeds through repeated firing of one or more DNA replication origins located near the center of each gene cluster. Hypomorphic mutant alleles of the chiffon gene cause thin, fragile chorions and female sterility, and were found to eliminate chorion gene amplification. Null alleles of chiffon had the additional phenotypes of rough eyes and thin thoracic bristles: phenotypes often associated with disruption of normal cell cycle. The chiffon locus was cloned by chromosomal walking from the nearby cactus locus. A 6.5 kb transcript was identified and confirmed to be chiffon by sequencing of mutant alleles and by phenotypic rescue with genomic transformation constructs. The protein predicted by translation of the 5.1 kb chiffon ORF contains two domains related to the S. cerevisiae Dbf4 regulator of DNA replication origin firing and cell cycle progression: a 44 residue domain designated CDDN1 (43% identical) and a 41 residue domain designated CDDN2 (12% identical). The CDDN domains were also found in the S. pombe homolog of Dbf4, Dfp1, as well as in the proteins predicted by translation of the Aspergillus nimO gene and specific human and mouse clones. The data suggest a family of eukaryotic proteins related to Dbf4 and involved in initiation of DNA replication.
7
Kellum, R., and P. Schedl. "A group of scs elements function as domain boundaries in an enhancer-blocking assay." Molecular and Cellular Biology 12, no. 5 (May 1992): 2424–31. http://dx.doi.org/10.1128/mcb.12.5.2424.
Full textAbstract:
Chromosomes of higher eukaryotes are thought to be organized into a series of discrete and topologically independent higher-order domains. In addition to providing a mechanism for chromatin compaction, these higher-order domains are thought to define independent units of gene activity. Implicit in most models for the folding of the chromatin fiber are special nucleoprotein structures, the domain boundaries, which serve to delimit each higher-order chromosomal domain. We have used an "enhancer-blocking assay" to test putative domain boundaries for boundary function in vivo. This assay is based on the notion that in delimiting independent units of gene activity, domain boundaries should be able to restrict the scope of activity of enhancer elements to genes which reside within the same domain. In this case, interposing a boundary between an enhancer and a promoter should block the action of the enhancer. In the experiments reported here, we have used the yolk protein-1 enhancer element and an hsp70 promoter:lacZ fusion gene to test putative boundary DNA segments for enhancer-blocking activity. We have found that several scs-like elements are capable of blocking the action of the yp-1 enhancer when placed between it and the hsp70 promoter. In contrast, a MAR/SAR DNA segment and another spacer DNA segment had no apparent effect on enhancer activity.
8
Kellum, R., and P. Schedl. "A group of scs elements function as domain boundaries in an enhancer-blocking assay." Molecular and Cellular Biology 12, no. 5 (May 1992): 2424–31. http://dx.doi.org/10.1128/mcb.12.5.2424-2431.1992.
Full textAbstract:
Chromosomes of higher eukaryotes are thought to be organized into a series of discrete and topologically independent higher-order domains. In addition to providing a mechanism for chromatin compaction, these higher-order domains are thought to define independent units of gene activity. Implicit in most models for the folding of the chromatin fiber are special nucleoprotein structures, the domain boundaries, which serve to delimit each higher-order chromosomal domain. We have used an "enhancer-blocking assay" to test putative domain boundaries for boundary function in vivo. This assay is based on the notion that in delimiting independent units of gene activity, domain boundaries should be able to restrict the scope of activity of enhancer elements to genes which reside within the same domain. In this case, interposing a boundary between an enhancer and a promoter should block the action of the enhancer. In the experiments reported here, we have used the yolk protein-1 enhancer element and an hsp70 promoter:lacZ fusion gene to test putative boundary DNA segments for enhancer-blocking activity. We have found that several scs-like elements are capable of blocking the action of the yp-1 enhancer when placed between it and the hsp70 promoter. In contrast, a MAR/SAR DNA segment and another spacer DNA segment had no apparent effect on enhancer activity.
9
Shazadee, Hamna, Nadeem Khan, Jingjing Wang, Chencan Wang, Jianguo Zeng, Zhongyi Huang, and Xinyu Wang. "Identification and Expression Profiling of Protein Phosphatases (PP2C) Gene Family in Gossypium hirsutum L." International Journal of Molecular Sciences 20, no. 6 (March 20, 2019): 1395. http://dx.doi.org/10.3390/ijms20061395.
Full textAbstract:
The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypium arboreum), 147 (Gossypium barbadense), 181 (Gossypium hirsutum), and 99 (Gossypium raimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C gene family in cotton, such as gene structure organization, gene duplications, expression profiling, chromosomal mapping, protein motif organization, and phylogenetic relationships of each species. Phylogenetic analysis further categorized PP2C genes into 12 subgroups based on conserved domain composition analysis. Moreover, we observed a strong signature of purifying selection among duplicated pairs (i.e., segmental and dispersed) of Gossypium hirsutum. We also observed the tissue-specific response of GhPP2C genes in organ and fiber development by comparing the RNA-sequence (RNA-seq) data reported on different organs. The qRT-PCR validation of 30 GhPP2C genes suggested their critical role in cotton by exposure to heat, cold, drought, and salt stress treatments. Hence, our findings provide an overview of the PP2C gene family in cotton based on various bioinformatic tools that demonstrated their critical role in organ and fiber development, and abiotic stress tolerance, thereby contributing to the genetic improvement of cotton for the resistant cultivar.
10
Howe, Kerstin, Philipp H. Schiffer, Julia Zielinski, Thomas Wiehe, Gavin K. Laird, John C. Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. "Structure and evolutionary history of a large family of NLR proteins in the zebrafish." Open Biology 6, no. 4 (April 2016): 160009. http://dx.doi.org/10.1098/rsob.160009.
Full textAbstract:
Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system.
11
Wiese, Oliver, Davide Marenduzzo, and Chris A. Brackley. "Nucleosome positions alone can be used to predict domains in yeast chromosomes." Proceedings of the National Academy of Sciences 116, no. 35 (August 15, 2019): 17307–15. http://dx.doi.org/10.1073/pnas.1817829116.
Full textAbstract:
We use molecular dynamics simulations based on publicly available micrococcal nuclease sequencing data for nucleosome positions to predict the 3D structure of chromatin in the yeast genome. Our main aim is to shed light on the mechanism underlying the formation of chromosomal interaction domains, chromosome regions of around 0.5 to 10 kbp which show enriched self-interactions, which were experimentally observed in recent MicroC experiments (importantly these are at a different length scale from the 100- to 1,000-kbp–sized domains observed in higher eukaryotes). We show that the sole input of nucleosome positioning data is already sufficient to determine the patterns of chromatin interactions and domain boundaries seen experimentally to a high degree of accuracy. Since the nucleosome spacing so strongly affects the larger-scale domain structure, we next examine the genome-wide linker-length distribution in more detail, finding that it is highly irregular and varies in different genomic regions such as gene bodies, promoters, and active and inactive genes. Finally we use our simple simulation model to characterize in more detail how irregular nucleosome spacing may affect local chromatin structure.
12
Kuhn, Emily J., Craig M. Hart, and Pamela K. Geyer. "Studies of the Role of the Drosophila scs and scs′ Insulators in Defining Boundaries of a Chromosome Puff." Molecular and Cellular Biology 24, no. 4 (February 15, 2004): 1470–80. http://dx.doi.org/10.1128/mcb.24.4.1470-1480.2004.
Full textAbstract:
ABSTRACT Insulators are DNA elements that establish independent transcriptional domains within eukaryotic genomes. The Drosophila scs and scs′ insulators localize near the borders of a structural domain in the polytene chromosomes, known as a puff, produced by transcription of the 87A heat shock protein (hsp) genes. It has been suggested that scs and scs′ are boundary elements that delimit this decondensed chromatin domain, reflecting the mechanism by which these sequences act to constrain regulatory interactions. This model was tested using transposons that carried a yellow gene to assess enhancer blocking and an hsp70-lacZ gene to examine the structure of a heat shock puff in the presence and absence of insulators. We found that although scs and scs′ blocked enhancer function, these sequences did not prevent the spread of decondensation resulting from hsp70-lacZ transcription. Further analysis of the endogenous 87A locus demonstrated that scs and scs′ reside within, not at, the borders of the puff. Taken together, our studies suggest that scs and scs′ are not boundary elements that block the propagation of an altered chromatin state associated with puff formation. We propose that these insulators may have a direct role in limiting regulatory interactions in the gene-dense 87A region.
13
Weber, V., M. Harata, H. Hauser, and U. Wintersberger. "The actin-related protein Act3p of Saccharomyces cerevisiae is located in the nucleus." Molecular Biology of the Cell 6, no. 10 (October 1995): 1263–70. http://dx.doi.org/10.1091/mbc.6.10.1263.
Full textAbstract:
Actin-related proteins, a group of protein families that exhibit about 50% sequence identity among each other and to conventional actin, have been found in a variety of eukaryotic organisms. In the budding yeast Saccharomyces cerevisiae, genes for one conventional actin (ACT1) and for three actin-related proteins (ACT2, ACT3, and ACT5) are known. ACT3, which we recently discovered, is an essential gene coding for a polypeptide of 489 amino acids (Act3p), with a calculated molecular mass of 54.8 kDa. Besides its homology to conventional actin, Act3p possesses a domain exhibiting weak similarity to the chromosomal protein HMG-14 as well as a potential nuclear localization signal. An antiserum prepared against a specific segment of the ACT3 gene product recognizes a polypeptide band of approximately 55 kDa in yeast extract. Indirect immunofluorescence experiments with this antiserum revealed that Act3p is located in the nucleus. Nuclear staining was observed in all cells regardless of the stage of the cell cycle. Independently, immunoblotting experiments with subcellular fractions showed that Act3p is indeed highly enriched in the nuclear fraction. We suggest that Act3p is an essential constituent of yeast chromatin.
14
Li, Chaoqiong, Xiaoli Li, Hongzhan Liu, Xueqin Wang, Weifeng Li, Mao-Sheng Chen, and Long-Jian Niu. "Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly." Plant and Cell Physiology 61, no. 5 (March 10, 2020): 978–87. http://dx.doi.org/10.1093/pcp/pcaa026.
Full textAbstract:
Abstract Eukaryotic chromatin is tightly packed into hierarchical structures, allowing appropriate gene transcription in response to environmental and developmental cues. Here, we provide a chromosome-scale de novo genome assembly of sesame with a total length of 292.3 Mb and a scaffold N50 of 20.5 Mb, containing estimated 28,406 coding genes using Pacific Biosciences long reads combined with a genome-wide chromosome conformation capture (Hi-C) approach. Based on this high-quality reference genome, we detected changes in chromatin architectures between normal growth and dark-treated sesame seedlings. Gene expression level was significantly higher in ‘A’ compartment and topologically associated domain (TAD) boundary regions than in ‘B’ compartment and TAD interior regions, which is coincident with the enrichment of H4K3me3 modification in these regions. Moreover, differentially expressed genes (DEGs) induced by dark treated were enriched in the changed TAD-related regions and genomic differential contact regions. Gene Ontology (GO) enrichment analysis of DEGs showed that genes related to ‘response to stress’ and ‘photosynthesis’ functional categories were enriched, which corresponds to dark treatment. These results suggested that chromatin organization is associated with gene transcription in response to dark treatment in sesame. Our results will facilitate the understanding of regulatory mechanisms in response to environmental cues in plants.
15
Formaggioni, Alessandro, Andrea Luchetti, and Federico Plazzi. "Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence." Life 11, no. 7 (July 6, 2021): 663. http://dx.doi.org/10.3390/life11070663.
Full textAbstract:
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.
16
PEÑA-DÍAZ, Javier, Andrea MONTALVETTI, Ana CAMACHO, Claribel GALLEGO, Luis M. RUIZ-PEREZ, and Dolores GONZALEZ-PACANOWSKA. "A soluble 3-hydroxy-3-methylglutaryl-CoA reductase in the protozoan Trypanosoma cruzi." Biochemical Journal 324, no. 2 (June 1, 1997): 619–26. http://dx.doi.org/10.1042/bj3240619.
Full textAbstract:
We report the isolation and characterization of a genomic clone containing the open reading frame sequence for 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase from Trypanosoma cruzi, the causative agent of Chagas' disease. The protozoan gene encoded for a smaller polypeptide than the rest of the genes described from eukaryotic organisms and the deduced amino acid sequence could be aligned with the C-terminal half of animal and plant reductases exhibiting pronounced similarity to other eukaryotic counterparts. Further examination of the 5′ flanking region by cDNA analysis and establishment of the splice acceptor sites clearly indicated that the corresponding mRNA apparently lacks sequences encoding a membrane N-terminal domain. The reductase gene is a single copy and is located on a chromosome of 1.36 Mb as determined by contour-clamped homogeneous electric field electrophoresis. The overall cellular distribution of enzymic activity was investigated after differential centrifugation of Trypanosoma cell extracts. Reductase activity was primarily associated with the cellular soluble fraction because 95% of the total cellular activity was recovered in the supernatant and was particularly sensitive to proteolytic inactivation. Furthermore the enzyme can be efficiently overexpressed in a highly active form by using the expression vector pET-11c. Thus Trypanosoma cruziHMG-CoA reductase is unique in the sense that it totally lacks the membrane-spanning sequences present in all eukaryotic HMG-CoA reductases so far characterized.
17
Naito, Mizue, Joseph B. Morton, and Teresa E. Pawlowska. "Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota." Proceedings of the National Academy of Sciences 112, no. 25 (May 11, 2015): 7791–96. http://dx.doi.org/10.1073/pnas.1501676112.
Full textAbstract:
Arbuscular mycorrhizal fungi (AMF, Glomeromycota) colonize roots of the majority of terrestrial plants. They provide essential minerals to their plant hosts and receive photosynthates in return. All major lineages of AMF harbor endobacteria classified as Mollicutes, and known as mycoplasma-related endobacteria (MRE). Except for their substantial intrahost genetic diversity and ability to transmit vertically, virtually nothing is known about the life history of these endobacteria. To understand MRE biology, we sequenced metagenomes of three MRE populations, each associated with divergent AMF hosts. We found that each AMF species harbored a genetically distinct group of MRE. Despite vertical transmission, all MRE populations showed extensive chromosomal rearrangements, which we attributed to genetic recombination, activity of mobile elements, and a history of plectroviral invasion. The MRE genomes are characterized by a highly reduced gene content, indicating metabolic dependence on the fungal host, with the mechanism of energy production remaining unclear. Several MRE genes encode proteins with domains involved in protein–protein interactions with eukaryotic hosts. In addition, the MRE genomes harbor genes horizontally acquired from AMF. Some of these genes encode small ubiquitin-like modifier (SUMO) proteases specific to the SUMOylation systems of eukaryotes, which MRE likely use to manipulate their fungal host. The extent of MRE genome plasticity and reduction, along with the large number of horizontally acquired host genes, suggests a high degree of adaptation to the fungal host. These features, together with the ubiquity of the MRE–Glomeromycota associations, emphasize the significance of MRE in the biology of Glomeromycota.
18
Shi, Liang, and Weiwen Zhang. "Comparative analysis of eukaryotic-type protein phosphatases in two streptomycete genomes." Microbiology 150, no. 7 (July 1, 2004): 2247–56. http://dx.doi.org/10.1099/mic.0.27057-0.
Full textAbstract:
Inspection of the genomes of Streptomyces coelicolor A3(2) and Streptomyces avermitilis reveals that each contains 55 putative eukaryotic-type protein phosphatases (PPs), the largest number ever identified from any single prokaryotic organism. Unlike most other prokaryotic genomes that have only one or two superfamilies of eukaryotic-type PPs, the streptomycete genomes possess the eukaryotic-type PPs that belong to four superfamilies: 2 phosphoprotein phosphatases and 2 low-molecular-mass protein tyrosine phosphatases in each species, 49 Mg2+- or Mn2+-dependent protein phosphatases (PPMs) and 2 conventional protein tyrosine phosphatases (CPTPs) in S. coelicolor A3(2), and 48 PPMs and 3 CPTPs in S. avermitilis. Sixty-four percent of the PPs found in S. coelicolor A3(2) have orthologues in S. avermitilis, indicating that they originated from a common ancestor and might be involved in the regulation of more conserved metabolic activities. The genes of eukaryotic-type PP unique to each surveyed streptomycete genome are mainly located in two arms of the linear chromosomes and their evolution might be involved in gene acquisition or duplication to adapt to the extremely variable soil environments where these organisms live. In addition, 56 % of the PPs from S. coelicolor A3(2) and 65 % of the PPs from S. avermitilis possess at least one additional domain having a putative biological function. These include the domains involved in the detection of redox potential, the binding of cyclic nucleotides, mRNA, DNA and ATP, and the catalysis of phosphorylation reactions. Because they contained multiple functional domains, most of them were assigned functions other than PPs in previous annotations. Although few studies have been conducted on the physiological functions of the PPs in streptomycetes, the existence of large numbers of putative PPs in these two streptomycete genomes strongly suggests that eukaryotic-type PPs play important regulatory roles in primary or secondary metabolic pathways. The identification and analysis of such a large number of putative eukaryotic-type PPs from S. coelicolor A3(2) and S. avermitilis constitute a basis for further exploration of the signal transduction pathways mediated by these phosphatases in industrially important strains of streptomycetes.
19
Masson, J. Y., and D. Ramotar. "The Saccharomyces cerevisiae IMP2 gene encodes a transcriptional activator that mediates protection against DNA damage caused by bleomycin and other oxidants." Molecular and Cellular Biology 16, no. 5 (May 1996): 2091–100. http://dx.doi.org/10.1128/mcb.16.5.2091.
Full textAbstract:
Bleomycin belongs to a class of antitumor drugs that damage cellular DNA through the production of free radicals. The molecular basis by which eukaryotic cells provide resistance to the lethal effects of bleomycin is not clear. Using the yeast Saccharomyces cerevisiae as a model with which to study the effect of bleomycin damage on cellular DNA, we isolated several mutants that display hypersensitivity to bleomycin. A DNA clone containing the IMP2 gene that complemented the most sensitive bleomycin mutant was identified. A role for IMP2 in defense against the toxic effects of bleomycin has not been previously reported. imp2 null mutants were constructed and were found to be 15-fold more sensitive to bleomycin than wild-type strains. The imp2 null mutants were also hypersensitive to several oxidants but displayed parental resistance to UV light and methyl methane sulfonate. Exposure of mutants to either bleomycin or hydrogen peroxide resulted in the accumulation of strand breaks in the chromosomal DNA, which remained even after 6 h postchallenge, but not in the wild type. These results suggest that the oxidant hypersensitivity of the imp2 mutant results from a defect in the repair of oxidative DNA lesions. Molecular analysis of IMP2 indicates that it encodes a transcriptional activator that can activate a reporter gene via an acidic domain located at the N terminus. Imp2 lacks a DNA binding motif, but it possesses a C-terminal leucine-rich repeat. With these data taken together, we propose that Imp2 prevents oxidative damage by regulating the expression of genes that are directly required to repair DNA damage.
20
MacQueen, Alice, Dacheng Tian, Wenhan Chang, Eric Holub, Martin Kreitman, and Joy Bergelson. "Population Genetics of the Highly Polymorphic RPP8 Gene Family." Genes 10, no. 9 (September 8, 2019): 691. http://dx.doi.org/10.3390/genes10090691.
Full textAbstract:
Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.
21
Fort, Rafael Sebastián, and María Ana Duhagon. "Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology." F1000Research 10 (June 9, 2021): 182. http://dx.doi.org/10.12688/f1000research.28510.2.
Full textAbstract:
Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue. VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA chromatin status cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.
22
Fort, Rafael Sebastián, and María Ana Duhagon. "Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology." F1000Research 10 (March 5, 2021): 182. http://dx.doi.org/10.12688/f1000research.28510.1.
Full textAbstract:
Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. Although the vtRNAs are co-regulated by transcription factors related to viral infection, vtRNA2-1 is the most independently regulated homologue. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA expression cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.
23
Aparicio, Jennifer G., Christopher J. Viggiani, Daniel G. Gibson, and Oscar M. Aparicio. "The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae." Molecular and Cellular Biology 24, no. 11 (June 1, 2004): 4769–80. http://dx.doi.org/10.1128/mcb.24.11.4769-4780.2004.
Full textAbstract:
ABSTRACT The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins or a late-firing, telomere-proximal origin. By delaying initiation relative to the earliest origins, Rpd3 enables regulation of late origins by the intra-S replication checkpoint. RPD3 deletion suppresses the slow S phase of clb5Δ cells by enabling late origins to fire earlier, suggesting that Rpd3 modulates the initiation timing of many origins throughout the genome. Examination of factors such as Ume6 that function together with Rpd3 in transcriptional repression indicates that Rpd3 regulates origin initiation timing independently of its role in transcriptional repression. This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked.
24
Kalendar, Ruslan, Olga Raskina, Alexander Belyayev, and Alan H. Schulman. "Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants." International Journal of Molecular Sciences 21, no. 8 (April 22, 2020): 2931. http://dx.doi.org/10.3390/ijms21082931.
Full textAbstract:
Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.
25
Baiamonte, Elena, Rosalia Di Stefano, Melania Lo Iacono, Barbara Spina, Angela Vitrano, Rosario Di Maggio, Massimiliano Sacco, et al. "The Sea Urchin sns5 Chromatin Insulator Improves the Likelihood of Lentiviral Vectors in Erythroid Milieu By Organizing an Independent Chromatin Domain at the Integration Site." Blood 126, no. 23 (December 3, 2015): 4414. http://dx.doi.org/10.1182/blood.v126.23.4414.4414.
Full textAbstract:
Abstract Retroviral vectors are currently the most suitable vehicles for therapeutic gene transfer in hematopoietic stem cells. However, these vectors are known to integrate rather randomly throughout the genome, suffering the so called chromosomal position effects (PE). Such a critical occurrence most probably depends upon the ability of heterochromatin to spread in the inserted vector sequences. Moreover, the use of transgenes imply genotoxicity effects, since the cis-regulatory sequences harbored by the vector can disturb the proper transcription of the resident genes neighboring the integration site, potentially leading to malignant transformation. Due to their enhancer blocker activity, the incorporation of chromatin insulators in flanking position to the transferred unit can reduce the mentioned dangerous effects. Moreover, by acting as barriers to the spread of heterochromatin, chromatin insulators can also mitigate vector silencing. We have previously shown that the sea urchin sns5 chromatin insulator activity is conserved in mouse and human erythroid milieu: it blocks the βglobin-LCR-HS2 enhancer/globin promoter interaction when placed between them. In addition, when placed in flanking location of a γ-retrovirus vector, sns5 impedes PE variegation and improves vector-specific expression following integration in the erythroid genome. Importantly, by binding both erythroid-specific and ubiquitous factors, sns5 favors the accumulation inside the provirus locus of epigenetic marks commonly associated to an euchromatic state (Acuto S. et al., BCMD 2005; D'Apolito D. et al., 2009; Di Caro D. et al., J Mol Biol 2004; Cavalieri V. et al., NAR 2009). In this study we extend these findings, demonstrating that sns5 works as chromatin insulator also when placed in flanking position of a GFP transgene contained in a lentivirus vector (LV-GFP). A large panel of mouse erythroleukemic clones (MELC) was generated after transduction with uninsulated and sns5 -insulated LV-GFP. Individual clones were screened for single vector integrants (by Q-PCR), and for GFP-expression (by cytofluorimetry). Our results shown that the inclusion of the sns5 element in a forward orientation increased the fraction of vector expressing cells (89% for the insulated vector vs 42% for the uninsulated ones). The clonal variegation of expression, assessed as frequency of clones that showed a percentage of GFP-negative cells in the progeny, decreased in clones transduced with the insulated vectors (7.4% vs 13,9%). It has been suggested that chromatin insulators could shape the architecture of topologically independent chromosome domains. High resolution mapping of chromosomal domains in drosophila and higher eukaryotes highlighted that chromatin insulators play a critical role in shaping the architectural genome organization both in a local chromosome environment and in long range chromosomal interaction. Intriguingly, by using the Chromosome Conformation Capture (3C) technology, we demonstrated that the sns5 -flanked LV-GFP integrated at a single copy in the erythroid cell genome is organized into an independent chromatin loop at the integration site. Worth to mention, no looping was detected in the absence of sns5, indicating that the two flanking copies of sns5 are specifically involved in the reorganization of the chromatin structure at the provirus locus. In conclusion our results not only confirm the conserved and striking boundary function of sns5, but also provide a new clue concerning the molecular mechanism that allows this function to occur. On these basis, our findings reassure the use of sns5 to improve both efficacy and safety of lentiviral vectors for gene therapy. This work was funded by the Assessorato Regionale della Salute, Regione Siciliana (PO FESR 4.1.1.1 RIMEDRI) Disclosures No relevant conflicts of interest to declare.
26
Yang, Qing, ShengNan Wang, ChuanBao Wu, QiuLei Zhang, Yi Zhang, QiuJu Chen, Yang Li, et al. "Malus domestica ADF1 severs actin filaments in growing pollen tubes." Functional Plant Biology 44, no. 4 (2017): 455. http://dx.doi.org/10.1071/fp16360.
Full textAbstract:
A dynamic actin cytoskeleton is essential for pollen tube growth and germination. However, the molecular mechanism that determines the organisation of the actin cytoskeleton in pollen remains poorly understood. ADF modulates the structure and dynamics of actin filaments and influences the higher-order organisation of the actin cytoskeleton in eukaryotic cells. Members of the ADF family have been shown to have important functions in pollen tube growth. However, the role of this gene family remains largely unknown in apple (Malus domestica Borkh.). In this study, we identified seven ADFs in the apple genome. Phylogenetic analysis showed that MdADF1 clusters with Arabidopsis thaliana (L.) Heynh. AtADF7, ADF8, ADF10 and AtADF11. We performed sequence alignments and analysed the domain structures of the seven MdADF proteins and identified the chromosome locations of the encoding genes. We cloned the gene encoding MdADF1 from ‘Ralls Janet’ apple and found that it was strongly expressed in pollen. Biochemical assays revealed that MdADF1 directly bound to and severed F-actin under low Ca2+ conditions. We demonstrated that knockdown of MdADF1 inhibited pollen tube growth and reduced the pollen germination rate, but rendered the pollen insensitive to treatment with Latrunculin B, an actin depolymerising agent. Taken together, our results provide insight into the function of MdADF1 and serve as a reference for studies of ADF in other plants.
27
Yokoyama, Akihiko, and Hiroshi Okuda. "The Molecular Mechanism of Transcriptional Activation By MLL-AEP Fusion Proteins." Blood 126, no. 23 (December 3, 2015): 2435. http://dx.doi.org/10.1182/blood.v126.23.2435.2435.
Full textAbstract:
Abstract Chromosomal translocations generate a variety of mixed lineage leukemia (MLL) fusion genes, which cause aggressive leukemia. Although >70 different fusion partners have been identified, the majority of the cases are caused by the chimeric genes of MLL and a component of the AEP co-activator complex (hereafter referred to as AEP), which comprises of AF4 family proteins (e.g. AF4, AF5Q31), ENL family proteins (e.g. ENL, AF9), and the P-TEFb elongation factor. MLL-AEP fusion proteins constitutively activate their target genes by recruiting AEP components to their target chromatin, whereas wild-type MLL recruits AEP in a context-dependent manner. In the hematopoietic lineage, MLL fusion proteins aberrantly activate a subset of genes implicated in the hematopoietic stem cell (HSC) program, such as HOXA9 and MEIS1. Constitutive expression of these HSC program genes in hematopoietic progenitors has been shown to induce leukemia in a mouse model. It has been speculated that MLL-AEP activates transcription of those HSC program genes by aberrantly activating transcription elongation. However, it is largely unclear how AEP activates transcription. Using an extensive structure/function analysis, we revealed that a serine-rich domain of the AF4 family proteins, termed pSER, is an essential functional component of MLL-AEP-dependent gene activation and leukemic transformation. Through biochemical purification, we have identified Selectivity Factor 1 (SL1) as a novel factor associated with the pSER domain. SL1 comprises TBP and four TBP-associated factors (TAF1A, TAF1B, TAF1C, TAF1D), and is known as a core component of the pre-initiation complex (PIC) of RNA polymerase I (RNAP1). In the presence of UBF, SL1 forms a PIC on the promoters of ribosomal RNA genes, to drive RNAP1-dependent transcription. However, its role in RNAP2-dependent transcription was unknown. The initiation of RNAP2-dependent transcription in eukaryotes occurs through the loading of TBP to the promoter, via a direct association with the TATA element or through as-yet-unidentified mechanisms. Our results demonstrate that AEP facilitates the initiation of RNAP2-dependent transcription via the loading of TBP onto the TATA element, through SL1 activity. MLL-AEP fusion proteins utilize this TBP-loading function to activate transcription initiation in leukemic transformation. The wild-type AEP complex activates gene expression in the same manner in the physiological conditions. Taken together, our results unveil a novel role of SL1 as a TBP-loading factor in RNAP2-dependent gene activation, and a previously unknown transcription initiation mechanism involving AEP, which is more important than its transcription elongation activities for leukemic transformation. These findings greatly advance our understanding of the molecular mechanism of MLL fusion-dependent leukemic transformation, which was previously interpreted simply as mis-regulated transcription elongation. Disclosures Yokoyama: Dainipon Sumitomo Pharma Co., Ltd.: Research Funding.
28
Li, Huiyu, Xiaomei Chen, Wei Xiong, Fang Liu, and Shiang Huang. "The Regulation of Zinc Finger Proteins by Mirnas Enriched in ALL-Microvesicles." Blood 120, no. 21 (November 16, 2012): 1448. http://dx.doi.org/10.1182/blood.v120.21.1448.1448.
Full textAbstract:
Abstract Abstract 1448 Microvesicles (MVs) are submicrometric membrane fragments and they can “hijack” membrane components and engulf cytoplasmic contents from their cellular origin. MVs are enriched in various bioactive molecules of their parental cells, such as proteins, DNA, mRNA and miRNAs. Microvesicles (MVs) released by leukemia cells constitute an important part of the leukemia microenvironment. As a cell-to-cell communication tool, MVs transfer microRNA (miRNA) between cells. MVs miRNAs may also provide an insight in the role of miRNAs playing in the underlying of pathophysiologic processes of various leukemia. We determined the miRNA expression profiles of ALL-derived MVs using Agilent miRNA microarray analysis. The five miRNAs obtained by microarray profiling were validated using real-time PCR. The putative target genes were predicted by bioformation software. We identified 182 and 166 dysregulated miRNAs in MVs derived from Nalm 6 cells and from Jurkat cells, respectively. Both up regulated (123/182 in Nalm 6-MVs and 114/166 in Jurkat- MVs) and down regulated (59/182 in Nalm 6-MVs and 52/166 in Jurkat- MVs) expressions were observed compared with MVs from normal peripheral blood the MVs normal control. When we analyzed those miRNA with bioinformatic tools (TargetScan), we found an interesting phenomenon that presence of 111 zinc fingers genes were regulated by 52 miRNAs, indicating that the ALL-microvesicles were enriched with miRNAs regulating zinc finger proteins. They encompassed zinc fingers and homeoboxes 2, zinc finger, ZZ-type containing 3, zinc finger, SWIM-type containing 1, zinc finger, RAN-binding domain containing 3, zinc finger, NFX1-type containing 1, zinc finger, MYM-type 4, zinc finger, FYVE domain containing 1 and their 5 subtypes; zinc finger, DHHC-type containing16, and other subtypes; zinc finger, CCHC domain containing 14 and 7A, zinc finger, BED-type containing 4; zinc finger protein, X-linked; zinc finger protein, multitype 2; zinc finger protein 81, and their 55 subtypes; zinc finger and SCAN domain containing 18, zinc finger and BTB domain containing 9. ALL-microvesicles were enriched with expression changes of distinct sets of miRNAs regulating zinc finger proteins. This provides clues that genes commonly function together. It is worth noting that 52 miRNA regulating above zinc finger protein genes were up-expressed, suggeting that miRNA regulating zinc fingers were active in ALL-MVs. Zinc finger proteins are important transcriptions in eukaryotes and play roles in regulating gene. Some members of the Zinc finger family have close relationaship with tumour. Zinc finger X-chromosomal protein (Zfx) is a protein that in humans is encoded by the ZFX gene. The level of Zfx expression correlates with aggressiveness and severity in many cancer types, including prostate cancer, breast cancer, gastric tumoural tissues, and leukemia. [1,2]. Zinc finger and homeoboxes 2 (ZHX2) was target gene of miRNA-1260. The role of miRNA are negatively regulated host gene expressions. ZHX2 inhibits HCC cell proliferation by preventing expression of Cyclins A and E, and reduces growth of xenograft tumors. Loss of nuclear ZHX2 might be an early step in the development of HCC[3]. In our study, the miRNA-1260 were 9 fold higher in ALL MVs. In leukeima microenvironment, ALL-MVs may transfer aberantly expressed miRNAs to their target cell lead to abnormally regulated the zinc finger proteins that may play roles in ALL. In this study, we demonstrated that ALL-microvesicles were enriched with expression changes of distinct sets of miRNAs regulating zinc finger proteins. Futhermore, Zinc fingers were active in ALL-MVs and commonly function together. Disclosures: No relevant conflicts of interest to declare.
29
Dong, Chongmei, Ryan Whitford, and Peter Langridge. "A DNA mismatch repair gene links to the Ph2 locus in wheat." Genome 45, no. 1 (February 1, 2002): 116–24. http://dx.doi.org/10.1139/g01-126.
Full textAbstract:
DNA mismatch repair is an essential system for maintaining genetic stability in bacteria and higher eukaryotes. Based on the conserved regions of the bacterial MutS gene and its homologues in yeast and human, a wheat cDNA homologue of MSH6, designated TaMSH7, was isolated by RTPCR. The deduced amino acid sequence of TaMSH7 shows conserved domains characteristic of other MSH6 genes, with highest similarity to maize MSH7 and Arabidopsis MSH7. TaMSH7 is expressed in meristem tissue associated with a high level of mitotic and meiotic activity, with maximum expression in the reproductive organs of young flower spikes. TaMSH7 is located on the short arms of chromosomes 3A, 3B, and 3D and has been mapped within barley chromosome 3HS. The copy on 3DS is located within the region deleted in the wheat mutant ph2a, which shows altered recombination frequency in the interspecific hybrids. The relationship between the ph2a mutant and TaMSH7 gene function is discussed.Key words: wheat, DNA mismatch repair gene, expression, chromosomal location, Ph2.
30
Hennig, Wolfgang, Reindert C. Brand, Johannes Hackstein, Ron Hochstenbach, Hannie Kremer, Dirk-Henner Lankenau, Susanne Lankenau, Koos Miedema, and Andy Pötgens. "Y chromosomal fertility genes of Drosophila: a new type of eukaryotic genes." Genome 31, no. 2 (January 15, 1989): 561–71. http://dx.doi.org/10.1139/g89-105.
Full textAbstract:
The Y chromosomal fertility genes of Drosophila are required for sperm differentiation. They are active only in primary spermatocytes where they form giant lampbrush loops. The molecular structure of these genes was investigated and revealed an unusual composition of DNA. Short, tandemly repeated sequence clusters are interrupted by longer and more heterogeneous sequences, which probably all represent transposable elements. No indication of the presence of protein-coding regions has been found within the fertility genes. However, the lampbrush loops bind site-specific proteins recognized by immunofluorescence techniques. This, together with other experimental data, led to the hypothesis that the Y chromosomal genes have a function in binding chromosomal proteins. The data and arguments in support of this gene model are summarized in this paper.Key words: Y chromosome, Drosophila, fertility genes, gene structure, lampbrush loops, spermatogenesis.
31
Ross, Benjamin D., Leah Rosin, Andreas W. Thomae, Mary Alice Hiatt, Danielle Vermaak, Aida Flor A. de la Cruz, Axel Imhof, Barbara G. Mellone, and Harmit S. Malik. "Stepwise Evolution of Essential Centromere Function in a Drosophila Neogene." Science 340, no. 6137 (June 6, 2013): 1211–14. http://dx.doi.org/10.1126/science.1234393.
Full textAbstract:
Evolutionarily young genes that serve essential functions represent a paradox; they must perform a function that either was not required until after their birth or was redundant with another gene. How young genes rapidly acquire essential function is largely unknown. We traced the evolutionary steps by which the Drosophila gene Umbrea acquired an essential role in chromosome segregation in D. melanogaster since the gene's origin less than 15 million years ago. Umbrea neofunctionalization occurred via loss of an ancestral heterochromatin-localizing domain, followed by alterations that rewired its protein interaction network and led to species-specific centromere localization. Our evolutionary cell biology approach provides temporal and mechanistic detail about how young genes gain essential function. Such innovations may constantly alter the repertoire of centromeric proteins in eukaryotes.
32
Yang, Yan-Qing, and Yun-Hai Lu. "Genome-wide survey, characterization, and expression analysis of RING finger protein genes in Brassica oleracea and their syntenic comparison to Brassica rapa and Arabidopsis thaliana." Genome 61, no. 9 (September 2018): 685–97. http://dx.doi.org/10.1139/gen-2018-0046.
Full textAbstract:
The ubiquitin-mediated post-translational regulatory pathway regulates a broad range of cell functions in all eukaryotes. It requires the involvement of a large number of E3 ligases, of which more than one third belongs to the RING protein family as in Arabidopsis thaliana. In this study, a total of 756 RING domains in 734 predicted proteins were identified in Brassica oleracea. Their encoding genes were characterized by RING domain type, additional domain, and expression pattern, and mapped on the nine chromosomes of B. oleracea. Comparison of these results with B. rapa and A. thaliana revealed some common as well as species-specific features. Our results showed that the differential gene loss following the whole genome triplication has largely contributed to the RING protein gene number variation among these species, although other factors such as tandem duplication, RING domain loss, or modification had also contributed to this variation. Analysis of RNA-seq data showed that these RING protein genes were functionally diversified and involved in all the stages of plant growth and development, and that the triplicated members were also diverged in expression with one member often more dominantly expressed over the two others in the majority of cases. Our study lays the foundation for further functional determination of each RING protein gene among species of the genus Brassica.
33
Shi, Wei, Therese Vu, Glen Boyle, Fares Al-Ejeh, Tej Pandita, Krzysztof Ginalski, Maga Rowicka, Steven W. Lane, and Kum Kum Khanna. "SSB1/NABP2 and SSB2/NABP1 Have Essential and Overlapping Roles in Maintaining Hematopoietic Stem and Progenitor Cells." Blood 126, no. 23 (December 3, 2015): 2405. http://dx.doi.org/10.1182/blood.v126.23.2405.2405.
Full textAbstract:
Abstract Single-stranded DNA binding (SSB) proteins are essential for a variety of DNA metabolic processes and the maintenance of genomic stability. SSB1 and its homolog SSB2, share greater sequence and domain homology to the archaeal and bacterial SSBs than eukaryotic RPA. They form complexes with two other proteins, C9Orf80 and INTS3, and play roles in mediating transcription and DNA repair. SSB1 (also known as OBFC2B or NABP2) is recurrently mutated in various cancers, however the precise function in normal development is incompletely understood. We have previously shown that Ssb1 is required for skeletogenesis, telomeric homeostasis and genomic stability in vivo while Ssb2 knockout mice are viable and grow normally without any detectable phenotype. Interestingly, we observed pronounced upregulation of Ssb2 in response to Ssb1 deletion and modest up-regulation of Ssb1 in response to Ssb2 deletion, suggesting that Ssb1 and Ssb2 may have some overlapping functions. To investigate the specific roles of both Ssb1 and Ssb2 in adult tissue homeostasis, we generated conditional double-knockout (DKO) mouse models of both genes. DKO in adult mice was achieved by using a tamoxifen-inducible Cre (Ssb1fl/fl Ssb2fl/fl R26-CreERT2), in which Ssb1 and Ssb2 are conditionally deleted by the administration of tamoxifen. Induced DKO mice become moribund within seven days featured with pancytopenia and dramatic loss of hematopoietic stem and progenitor cells (HSPCs), suggesting that Ssb1 and Ssb2 are required for the maintenance of haematopoietic stem and progenitors cells (HSPCs). DKO bone marrow was markedly hypocellular with reduction in all lineages of haematopoietic development. Functionally, HSPCs in DKO mice show decreased quiescence at the early stage followed by decreased proliferation and increased cell loss due to apoptotic cell death at the later stage, suggesting the imbalanced bone marrow homeostasis upon DKO may eventually result in exhaustion of the stem cell pool in DKO mice. Furthermore, bona fide HSPC intrinsic functional deficiency caused by DKO was confirmed by competitive bone marrow transplant, where DKO bone marrows showed abolished differentiation capacity and failed to repopulate the bone marrows of recipient mice after induction of DKO in the established engraftments from the Ssb1fl/fl Ssb2fl/fl R26-CreERT2 donors. Gene expression of DKO HSPCs demonstrated an exacerbated p53/p21 DNA damage response and pronounced interferon response. Validating these findings, stabilization of p53 and increased apoptotic cell death were observed in DKO bone marrows and HSPCs and induction of cell cycle and expression of interferon target genes was confirmed by QPCR. DKO HSPCs have increased expression of IFN induced surface markers such as Sca1. The IFN response was intrinsic to HSPCs. Mechanistically, DKO HSPCs manifest a profile of stalled replication forks on DNA combing analysis, unrepaired double strand breaks (increased gammaH2Ax foci and alkaline comet tail moment) and telomeric loss resulting in widespread chromosomal instability. DKO HSPC showed aberrant cytoplasmic accumulation of single stranded DNAs, with R-loop formation (DNA:RNA hybrid), driving this genetic instability and cell-intrinsic interferon response. Altogether, these data provide strong evidence that Ssb1 and Ssb2 have essential functions in regulating haematopoiesis through repairing replication associated DNA damage as well as resolution of R-loop generated during transcription, to maintain genomic stability during normal HSPC homeostasis. Disclosures No relevant conflicts of interest to declare.
34
Runyen-Janecky, L. J., and S. M. Payne. "Identification of Chromosomal Shigella flexneri Genes Induced by the Eukaryotic Intracellular Environment." Infection and Immunity 70, no. 8 (August 2002): 4379–88. http://dx.doi.org/10.1128/iai.70.8.4379-4388.2002.
Full textAbstract:
ABSTRACT Upon entry into the eukaryotic cytosol, the facultative intracellular bacterium Shigella flexneri is exposed to an environment that may necessitate the expression of particular genes for it to survive and grow intracellularly. To identify genes that are induced in response to the intracellular environment, we screened a library containing fragments of the S. flexneri chromosome fused to a promoterless green fluorescent protein gene (gfp). Bacteria containing promoter fusions that had a higher level of gfp expression when S. flexneri was intracellular (in Henle cells) than when S. flexneri was extracellular (in Luria-Bertani broth) were isolated by using fluorescence-activated cell sorting. Nine different genes with increased expression in Henle cells were identified. Several genes (uhpT, bioA, and lysA) were involved in metabolic processes. The uhpT gene, which encoded a sugar phosphate transporter, was the most frequently isolated gene and was induced by glucose-6-phosphate in vitro. Two of the intracellularly induced genes (pstS and phoA) encode proteins involved in phosphate acquisition and were induced by phosphate limitation in vitro. Additionally, three iron-regulated genes (sufA, sitA, and fhuA) were identified. The sufA promoter was derepressed in iron-limiting media and was also induced by oxidative stress. To determine whether intracellularly induced genes are required for survival or growth in the intracellular environment, we constructed mutations in the S. flexneri uhpT and pstS genes by allelic exchange. The uhpT mutant could not use glucose-6-phosphate as a sole carbon source in vitro but exhibited normal plaque formation on Henle cell monolayers. The pstS mutant had no apparent growth defect in low-phosphate media in vitro but formed smaller plaques on Henle cell monolayers than the parent strain. Both mutants were as effective as the parent strain in inducing apoptosis in a macrophage cell line.
35
Calestagne-Morelli, Alison, and Juan Ausió. "Long-range histone acetylation: biological significance, structural implications, and mechanismsThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 84, no. 4 (August 2006): 518–27. http://dx.doi.org/10.1139/o06-067.
Full textAbstract:
Genomic characterization of various euchromatic regions in higher eukaryotes has revealed that domain-wide hyperacetylation (over several kb) occurs at a range of loci, including individual genes, gene family clusters, compound clusters, and more general clusters of unrelated genes. Patterns of long-range histone hyperacetylation are strictly conserved within each unique cellular system studied and they reflect biological variability in gene regulation. Domain-wide histone acetylation consists generally of nonuniform peaks of enriched hyperacetylation of specific core histones, histone isoforms, and (or) histone variants against a backdrop of nonspecific acetylation across the domain in question. Here we review the characteristics of long-range histone acetylation in some higher eukaryotes and draw special attention to recent literature on the multiple effects that histone hyperacetylation has on chromatin’s structural integrity and how they affect transcription. These include the thermal, ionic, cumulative, and isoform-specific (H4 K16) consequences of acetylation that result in a more dynamic core complex and chromatin fiber.
36
Tejera Nevado, Paloma, Eugenia Bifeld, Katharina Höhn, and Joachim Clos. "A Telomeric Cluster of Antimony Resistance Genes on Chromosome 34 of Leishmania infantum." Antimicrobial Agents and Chemotherapy 60, no. 9 (June 20, 2016): 5262–75. http://dx.doi.org/10.1128/aac.00544-16.
Full textAbstract:
ABSTRACTThe mechanisms underlying the drug resistance ofLeishmaniaspp. are manifold and not completely identified. Apart from the highly conserved multidrug resistance gene family known from higher eukaryotes,Leishmaniaspp. also possess genus-specific resistance marker genes. One of them, ARM58, was first identified inLeishmania braziliensisusing a functional cloning approach, and its domain structure was characterized inL. infantum. Here we report thatL. infantumARM58 is part of a gene cluster at the telomeric end of chromosome 34 also comprising the neighboring genes ARM56 and HSP23. We show that overexpression of all three genes can confer antimony resistance to intracellular amastigotes. Upon overexpression inL. donovani, ARM58 and ARM56 are secreted via exosomes, suggesting a scavenger/secretion mechanism of action. Using a combination of functional cloning and next-generation sequencing, we found that the gene cluster was selected only under antimonyl tartrate challenge and weakly under Cu2+challenge but not under sodium arsenite, Cd2+, or miltefosine challenge. The selective advantage is less pronounced in intracellular amastigotes treated with the sodium stibogluconate, possibly due to the known macrophage-stimulatory activity of this drug, against which these resistance markers may not be active. Our data point to the specificity of these three genes for antimony resistance.
37
ZHENG, Jiarui, Yongling LIAO, Feng XU, Xian ZHOU, Jiabao YE, Mingyue FU, Xiaomeng LIU, Zhengyan CAO, and Weiwei ZHANG. "Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 49, no. 2 (June 18, 2021): 12086. http://dx.doi.org/10.15835/nbha49212086.
Full textAbstract:
The WD40 transcription factor family is a superfamily found in eukaryotes and implicated in regulating growth and development. In this study, 167 WD40 family genes are identified in the Ginkgo biloba genome. They are divided into 5 clusters and 16 subfamilies based on the difference analysis of a phylogenetic tree and domain structures. The distribution of WD40 genes in chromosomes, gene structures, and motifs is analyzed. Promoter analysis shows that five GbWD40 gene promoters contain the MYB binding site participating in the regulation of flavonoid metabolism, suggesting that these five genes may participate in the regulation of flavonoid synthesis in G. biloba. The correlation analysis is carried out based on FPKM value of WD40 gene and flavonoid content in 8 tissues of G. biloba. Six GbWD40 genes that may participate in flavonoid metabolism are screened. The biological functions of the WD40 family genes in G. biloba are systematically analyzed, providing a foundation for further elucidating their regulatory mechanisms. A number of WD40 candidate genes involved in the biosynthesis and metabolism of G. biloba also predicted. This study presents an important basis and direction for conducting further research on the regulatory network of flavonoid synthesis and metabolism.
38
Shoja, Valia, T. M. Murali, and Liqing Zhang. "Expression Divergence of Tandemly Arrayed Genes in Human and Mouse." Comparative and Functional Genomics 2007 (2007): 1–8. http://dx.doi.org/10.1155/2007/60964.
Full textAbstract:
Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship between gene orientation and expression similarity. We also found that downstream TAG members do not show significantly narrower expression breadth than upstream members, contrary to what we predict based on TAG expression divergence hypothesis that we propose. Finally, we show that both chromosomal proximity and expression correlation in TAGs do not differ significantly from their neighboring non-TAG gene pairs, suggesting that tandem duplication is unlikely to be the cause for the higher-than-random expression association between neighboring genes on a chromosome in human and mouse.
39
Dundr, Miroslav, Jason K. Ospina, Myong-Hee Sung, Sam John, Madhvi Upender, Thomas Ried, Gordon L. Hager, and A. Gregory Matera. "Actin-dependent intranuclear repositioning of an active gene locus in vivo." Journal of Cell Biology 179, no. 6 (December 10, 2007): 1095–103. http://dx.doi.org/10.1083/jcb.200710058.
Full textAbstract:
Although bulk chromatin is thought to have limited mobility within the interphase eukaryotic nucleus, directed long-distance chromosome movements are not unknown. Cajal bodies (CBs) are nuclear suborganelles that nonrandomly associate with small nuclear RNA (snRNA) and histone gene loci in human cells during interphase. However, the mechanism responsible for this association is uncertain. In this study, we present an experimental system to probe the dynamic interplay of CBs with a U2 snRNA target gene locus during transcriptional activation in living cells. Simultaneous four-dimensional tracking of CBs and U2 genes reveals that target loci are recruited toward relatively stably positioned CBs by long-range chromosomal motion. In the presence of a dominant-negative mutant of β-actin, the repositioning of activated U2 genes is markedly inhibited. This supports a model in which nuclear actin is required for these rapid, long-range chromosomal movements.
40
Heusipp, Gerhard, Glenn M. Young, and Virginia L. Miller. "HreP, an In Vivo-Expressed Protease of Yersinia enterocolitica, Is a New Member of the Family of Subtilisin/Kexin-Like Proteases." Journal of Bacteriology 183, no. 12 (June 15, 2001): 3556–63. http://dx.doi.org/10.1128/jb.183.12.3556-3563.2001.
Full textAbstract:
ABSTRACT The role of proteases in pathogenesis is well established for several microorganisms but has not been described for Yersinia enterocolitica. Previously, we identified a gene,hreP, which showed significant similarity to proteases in a screen for chromosomal genes of Y. enterocoliticathat were exclusively expressed during an infection of mice. We cloned this gene by chromosome capture and subsequently determined its nucleotide sequence. Like inv, the gene encoding the invasin protein of Y. enterocolitica,hreP is located in a cluster of flagellum biosynthesis and chemotaxis genes. The genomic organization of this chromosomal region is different in Escherichia coli, Salmonella, andYersinia pestis than in Y. enterocolitica. Analysis of the distribution ofhreP between different Yersinia isolates and the relatively low G+C content of the gene suggests acquisition by horizontal gene transfer. Sequence analysis also revealed that HreP belongs to a family of eukaryotic subtilisin/kexin-like proteases. Together with the calcium-dependent protease PrcA of Anabaena variabilis, HreP forms a new subfamily of bacterial subtilisin/kexin-like proteases which might have originated from a common eukaryotic ancestor. Like other proteases of this family, HreP is expressed with an N-terminal prosequence. Expression of an HreP-His6 tag fusion protein in E. coli revealed that HreP undergoes autocatalytic processing at a consensus cleavage site of subtilisin/kexin-like proteases, thereby releasing the proprotein.
41
Harris, P. V., O. M. Mazina, E. A. Leonhardt, R. B. Case, J. B. Boyd, and K. C. Burtis. "Molecular cloning of Drosophila mus308, a gene involved in DNA cross-link repair with homology to prokaryotic DNA polymerase I genes." Molecular and Cellular Biology 16, no. 10 (October 1996): 5764–71. http://dx.doi.org/10.1128/mcb.16.10.5764.
Full textAbstract:
Mutations in the Drosophila mus308 gene confer specific hypersensitivity to DNA-cross-linking agents as a consequence of defects in DNA repair. The mus308 gene is shown here to encode a 229-kDa protein in which the amino-terminal domain contains the seven conserved motifs characteristic of DNA and RNA helicases and the carboxy-terminal domain shares over 55% sequence similarity with the polymerase domains of prokaryotic DNA polymerase I-like enzymes. This is the first reported member of this family of DNA polymerases in a eukaryotic organism, as well as the first example of a single polypeptide with homology to both DNA polymerase and helicase motifs. Identification of a closely related gene in the genome of Caenorhabditis elegans suggests that this novel polypeptide may play an evolutionarily conserved role in the repair of DNA damage in eukaryotic organisms.
42
Huang, Y. J., R. Stoffel, H. Tobler, and F. Mueller. "A newly formed telomere in Ascaris suum does not exert a telomere position effect on a nearby gene." Molecular and Cellular Biology 16, no. 1 (January 1996): 130–34. http://dx.doi.org/10.1128/mcb.16.1.130.
Full textAbstract:
During the process of chromatin diminution in Ascaris suum (formerly named Ascaris lumbricoides var. suum), developmentally regulated chromosomal fragmentation and new telomere addition occur within specific chromosomal breakage regions (CBRs). The DNA sequences flanking one of these CBRs (CBR-1) were analyzed, and two protein-encoding genes were found on either side. The noneliminated gene, agp-1, whose AUG start codon is located within approximately 2 kb of the boundary of CBR-1, encodes a putative GTP-binding protein which is structurally related to eukaryotic and prokaryotic elongation factors. Northern (RNA) blot analyses revealed that transcripts of this gene are present at all developmental stages, suggesting that the massive chromosomal rearrangements associated with the process of chromatin diminution have no influence on agp-1 expression. This demonstrates that addition of new telomeres in CBR-1 does not result in a telomeric position effect, a phenomenon previously described in Saccharomyces cerevisiae.
43
Richards, Thomas A., Joel B. Dacks, Samantha A. Campbell, Jeffrey L. Blanchard, Peter G. Foster, Rima McLeod, and Craig W. Roberts. "Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements." Eukaryotic Cell 5, no. 9 (September 2006): 1517–31. http://dx.doi.org/10.1128/ec.00106-06.
Full textAbstract:
ABSTRACT Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been an important process in eukaryote genome evolution.
44
Li, Bin, Shin Kurihara, Sok Ho Kim, Jue Liang, and Anthony J. Michael. "A polyamine-independent role for S-adenosylmethionine decarboxylase." Biochemical Journal 476, no. 18 (September 20, 2019): 2579–94. http://dx.doi.org/10.1042/bcj20190561.
Full textAbstract:
Abstract The only known function of S-adenosylmethionine decarboxylase (AdoMetDC) is to supply, with its partner aminopropyltransferase enzymes such as spermidine synthase (SpdSyn), the aminopropyl donor for polyamine biosynthesis. Polyamine spermidine is probably essential for the growth of all eukaryotes, most archaea and many bacteria. Two classes of AdoMetDC exist, the prokaryotic class 1a and 1b forms, and the eukaryotic class 2 enzyme, which is derived from an ancient fusion of two prokaryotic class 1b genes. Herein, we show that ‘eukaryotic' class 2 AdoMetDCs are found in bacteria and are enzymatically functional. However, the bacterial AdoMetDC class 2 genes are phylogenetically limited and were likely acquired from a eukaryotic source via transdomain horizontal gene transfer, consistent with the class 2 form of AdoMetDC being a eukaryotic invention. We found that some class 2 and thousands of class 1b AdoMetDC homologues are present in bacterial genomes that also encode a gene fusion of an N-terminal membrane protein of the Major Facilitator Superfamily (MFS) class of transporters and a C-terminal SpdSyn-like domain. Although these AdoMetDCs are enzymatically functional, spermidine is absent, and an entire fusion protein or its SpdSyn-like domain only, does not biochemically complement a SpdSyn deletion strain of E. coli. This suggests that the fusion protein aminopropylates a substrate other than putrescine, and has a role outside of polyamine biosynthesis. Another integral membrane protein found clustered with these genes is DUF350, which is also found in other gene clusters containing a homologue of the glutathionylspermidine synthetase family and occasionally other polyamine biosynthetic enzymes.
45
Lawrence, Jeanne B., and Christine M. Clemson. "Gene associations: true romance or chance meeting in a nuclear neighborhood?" Journal of Cell Biology 182, no. 6 (September 22, 2008): 1035–38. http://dx.doi.org/10.1083/jcb.200808121.
Full textAbstract:
Many recent studies have raised interest in the nuclear associations of coregulated genes from different chromosomes, often evoking interpretations of gene–gene interactions, communication, and even “romance.” However, in some cases, the associations may be indirect and infrequent and may reflect the segregation of active and inactive genes into different nuclear compartments. The study by Brown et al. (see p. 1083 of this issue) reports that the apparent association of erythroid genes is not a direct interaction nor colocalization to one tiny transcription factory but arises as a result of the known clustering of many active genes with larger splicing factor–rich speckles (a.k.a., SC35-defined domains). This clustering appears largely stochastic but is impacted by the chromosomal neighborhood of the gene as well as its transcriptional status. The study adds a new twist by examining the same gene in a foreign chromosomal context, providing evidence that this impacts a gene's propensity to form gene–domain (or apparent gene–gene) associations within nuclei.
46
Glover, D. M. "New doors to open…and so many!" Journal of Cell Science 113, no. 3 (February 1, 2000): 359–60. http://dx.doi.org/10.1242/jcs.113.3.359.
Full textAbstract:
The pursuit of science is a wonderful journey of discovery along which there are a myriad of avenues to be explored. There have always been so many objects of fascination, so many questions to ask along the way, so many possibilities to understand new principles, that making the decision about which problem to address and then having the self-discipline to explore it in depth challenge all who practice the art. How then are we, as cell biologists, to cope with the mountain of information that is accumulating as we enter the twenty-first century? We now have the potential to decipher the primary sequences of every single cellular protein for several model organisms. Just how are we to put this information into an intelligible framework for understanding cell physiology? The turn of a century is a time at which we can permit ourselves the luxury of looking backwards as well as forwards. Where were we a century ago, what were the challenges that faced us then and how do these questions relate to our future goals? As a cell biologist standing on the threshold of the twentieth century, one must have had a similar feeling of elation and expectation to that which we have at the present time. The Theory of Cells had been established by Schleiden and Schwan in 1838–1839, and in the following fifty years it had led to unifying ideas about the nature of plants and animals, an understanding of embryonic development, and the mysteries of the fertilisation of the egg and genetic continuity in terms of ‘cellular immortality’. These were truly halcyon days. By the end of the nineteenth century many of the central principles of cell biology were firmly established. Virchow had maintained in 1855 that every cell is the offspring of a pre-existing parent cell, but the realisation that the cell nucleus is essential for this continuity had to wait another 30 years. By this time, Miecher had already made in 1871 his famous discovery of nuclein, a phosphorus-rich substance extracted from preparations of nuclei from sperm and pus cells, and over the next twenty years a spectrum of sophisticated dyes became available that facilitated the visualisation of not only nuclein but also asters, spindle fibres, and microsomal components of cytoplasm in fixed preparations of cells. The centrosome, discovered independently by Flemming in 1875 and Van Beneden in 1876, and named by Boveri in 1888, was already considered to be an autonomous organelle with a central role in cell division. The behaviour of chromosomes, centrosomes, astral fibres and spindle fibres throughout mitosis and meiosis had been described in exquisite detail. Galeotti had even concluded by 1893 that the unequal distribution of chromatin in cancer cells correlates with an inequality of the centrosomes and the development of abnormal spindles - a conclusion reinforced by others over a century later (Pihan et al., 1998; Lingle et al., 1998). It had taken 200 years following Leuwenhoek's first observation of sperm to Hertwig's demonstration in 1875 that fertilisation of the egg is accomplished by its union with one spermatozoon. This demonstration was rapidly followed by Van Beneden's discovery - eventually to unify genetics and cell biology - that the nuclei of germ cells each contain one half the number of chromosomes characteristic of body cells. By 1902, both Sutton and Boveri had realised that the behaviour of chromosomes in meiosis precisely parallels the behaviour of Mendel's genetic particles described some 35 years earlier. In many ways we have witnessed during the past 50 years, and particularly in the last quarter century, a series of exciting breakthroughs in establishing an understanding of genetic function and continuity that are comparable to those of the previous century in demonstrating cellular function and continuity. The determination of the structure of DNA in 1953 and the elucidation of the genetic code throughout the 1960s led to the rapid realisation of the code's universality. The parallel development of sophisticated techniques for studying the genetics of the model bacterium Escherichia coli and its plasmids and viruses paved the way for a new era in biology. We were soon to construct recombinant DNA molecules in vitro, propagate them and eventually express them in E. coli, taking full advantage of the universality of the code. The principles of cloning DNA molecules had been clearly enunciated by Berg and Hogness in the early 1970s, and I myself had the great fortune as a young post-doc to share in this excitement and participate in putting some of these principles into their early practice. By the end of that decade, genes had been cloned from a multitude of eukaryotes and, moreover, technologies had been developed by Maxam and Gilbert and by Sanger that enabled these cloned genes to be sequenced. The accelerating accumulation of knowledge enabled by these simple technical breakthroughs has been astounding, leading to the determination of the complete genome sequences of budding yeast, the nematode Caenorhabditis elegans and the fruit fly, Drosophila melanogaster, and the prospect of the complete human sequence within a few years. To date we have managed this accumulating wealth reasonably well. Cloned genes have allowed cell biologists access to the encoded proteins, and as a consequence we have a working knowledge of many cellular processes. The sub-cellular meanderings of molecules have been charted with increasing accuracy, and gene products have been positioned in regulatory pathways. The concerted application of genetic and molecular approaches has given new insights into cell biology. This is particularly evident from work on the yeasts, which have come into their own as model systems with our realisation of the extent to which cell biological processes have been conserved. Nevertheless, the resulting regulatory pathways that emerge from our current ways of looking at the cell are rather unidimensional, gene products being placed into linear pathways as a result of either molecular or genetic analyses. Our current views are often blind to the fact that the cell is a multidimensional structure whose components are arranged in space, have multiple contacts that change with time and can respond simultaneously to a multitude of signals. Glimpses of such complexity are emerging from studies in which microarrays of all the identified open reading frames (ORFs) from the complete budding yeast genome have been screened for changes in patterns of gene expression throughout the cell cycle or upon sporulation. Cell-cycle-dependent periodicity was found for 416 of the 6220 monitored ORFs, and over 25% of these genes were found to be clustered at particular chromosomal sites, which suggesting there are global chromosomal responses in transcriptional control (Cho et al., 1998). The study of sporulation is perhaps the first example of the application of this type of technology to a developmental process. It revealed that, of the 6220 genes, about 500 undergo repression and 500 induction in seven temporally distinct patterns during the sporulation process, identifying potential functions for many previously uncharacterised genes (Chu et al., 1998). These studies already reveal layers of complexity in the regulation of the levels of transcripts as cells prepare for and pass through the different stages of meiosis. How much more complex are these patterns likely to be when viewed in terms of proteins, and their interactions, locations and functions within the cell? It seems clear, however, that a wonderful molecular description of the events of meiosis that can match the cytological understanding revealed by the work of Van Beneden and Boveri one hundred years ago is within our grasp. The cataloguing of all cellular proteins is now feasible through a combination of 2D-gel analysis and mass spectrometry, from which molecular mass data can be correlated with the fragment sizes of peptides predicted from whole genome sequence data (the emerging field of proteomics). It is not an easy task, but it seems just a matter of time before we have all this information at our fingertips. Yet how can we know the functions of all these proteins and have a full 3D picture of how they interact within a cell and the dynamics with which they do so? Yeast may be the first eukaryote for which some of these problems can be approached. Its genome is six-times smaller than that of C. elegans and 200 times smaller than the human genome, and has the further advantage that the genes can be easily disrupted through homologous recombination. Thus the prospect of systematic gene deletion to study the function of the 3700 novel ORFs identified in the whole genome sequence is feasible for this organism (Winzeler et al., 1999). One group in particular has devised a multifaceted approach for doing this: the affected gene is simultaneously tagged with an in-frame transcriptional reporter and further modified to epitope tag the affected protein, which thus allows the latter to be immunolocalised within cells (Ross-MacDonald et al., 1999). We can thus see the glimmerings of a holistic, genome-wide, cell-wide unravelling of cellular physiology. Some of these approaches will be easily adaptable to higher organisms. We will soon have read-outs of RNA expression patterns in cells undergoing a variety of developmental and physiological programmes in normal and diseased states. The analysis of function and the identification of ORFs in higher eukaryotes are likely to be more problematic. However, solutions for the rapid assessment of the functions of novel genes are already emerging. New insights are coming from labs using double-stranded RNA to interfere with cellular processes in C. elegans. It was originally found in this organism that the injection of double-stranded RNA corresponding to part of the mRNA of a gene prevents the expression of that gene through a mechanism that currently remains mysterious (Fire, 1999). The technique works extremely well in the nematode and even in the fruit fly, but doubts had been cast as to whether it would ever be valuable in mammals. The recent finding that the technique does indeed work in the mouse may well accelerate programmes to identify gene function by circumventing the particularly lengthy procedures for disruption of mouse genes (Wianny and Zernicka-Goetz, 2000). The multiple layers of complexity revealed by these emerging studies give some indication of the computational power that will be needed to model the cell. Is it now time for a new breed of mathematical biologists to emerge? Our present generation of cellular and molecular biologists have lost sight of some of the basic principles of physical chemistry, and quantitative analyses are done poorly if at all. Should the quantification of reaction kinetics now come out of the traditional domain of enzymology and be applied to multiple cellular processes - if we are truly to understand the dynamics of the living cell? If the yeast cell is complex, then how much greater complexity will we find in multicellular eukaryotes, given all the potential for cell-cell interactions? These problems are perhaps most alluring in the field of development, in which many phenomena are now demanding attention at the cellular level. In recent decades we have seen classical embryological approaches supplemented by genetic analyses to define the components of many developmental signalling pathways. This has demonstrated the existence of a conserved collection of molecular switches that can be used in a variety of different developmental circumstances. We are perhaps reaching the limits at which conventional genetic analyses can interpret these processes: often the precise relationships between components of regulatory pathways is not clear. We require a better grasp of how the molecules within the pathways interact, which will require the concerted application of sub-cellular fractionation, to identify molecular complexes, and proteomics. This has to be achieved in a way that allows us to interpret the consequences of multiple signalling events between different cell types. In the introduction to his famous text The Cell in Development and Inheritance, E. B. Wilson wrote almost a century ago: ‘It has only recently become possible adequately to formulate the great problems of development and heredity in terms of cellular biology - indeed we can as yet do little more than so formulate them.’ Has our perspective changed during the past one hundred years? Are not these the same challenges that lie ahead for the twenty-first century? It is now rather like being Alice in Wonderland in a room with many doors, each of which marks the onset of a new journey. Undoubtedly, any of the doors will lead to remarkable opportunities, but to what extent can we, as Alice, rely upon drinking from the bottle, or eating the biscuit, that happens to be at hand? We will have to use the existing resources, but it will be fascinating to see what new ingenuities we can bring to bear to help us on our journey through Wonderland. I have the feeling that we are to witness conceptual challenges to the way we think about cell biology that we cannot yet begin to appreciate…but what I would give to be around in one hundred years time to witness the progress we have made on our journeys!
47
Subramaniam, Chandra, Paul Veazey, Seth Redmond, Jamie Hayes-Sinclair, Emma Chambers, Mark Carrington, Keith Gull, Keith Matthews, David Horn, and Mark C. Field. "Chromosome-Wide Analysis of Gene Function by RNA Interference in the African Trypanosome." Eukaryotic Cell 5, no. 9 (September 2006): 1539–49. http://dx.doi.org/10.1128/ec.00141-06.
Full textAbstract:
ABSTRACT Trypanosomatids of the order Kinetoplastida are major contributors to global disease and morbidity, and understanding their basic biology coupled with the development of new drug targets represents a critical need. Additionally, trypanosomes are among the more accessible divergent eukaryote experimental systems. The genome of Trypanosoma brucei contains 8,131 predicted open reading frames (ORFs), of which over half have no known homologues beyond the Kinetoplastida and a substantial number of others are poorly defined by in silico analysis. Thus, a major challenge following completion of the T. brucei genome sequence is to obtain functional data for all trypanosome ORFs. As T. brucei is more experimentally tractable than the related Trypanosoma cruzi and Leishmania spp. and shares >75% of their genes, functional analysis of T. brucei has the potential to inform a range of parasite biology. Here, we report methods for systematic mRNA ablation by RNA interference (RNAi) and for phenotypic analysis, together with online data dissemination. This represents the first systematic analysis of gene function in a parasitic organism. In total, 210 genes have been targeted in the bloodstream form parasite, representing an essentially complete phenotypic catalogue of chromosome I together with a validation set. Over 30% of the chromosome I genes generated a phenotype when targeted by RNAi; most commonly, this affected cell growth, viability, and/or cell cycle progression. RNAi against approximately 12% of ORFs was lethal, and an additional 11% had growth defects but retained short-term viability in culture. Although we found no evidence for clustering or a bias towards widely evolutionarily conserved genes within the essential ORF cohort, the putative chromosome I centromere is adjacent to a domain containing genes with no associated phenotype. Involvement of such a large proportion of genes in robust growth in vitro indicates that a high proportion of the expressed trypanosome genome is required for efficient propagation; many of these gene products represent potential drug targets.
48
Bi, Xin. "Domains of Gene Silencing Near the Left End of Chromosome III inSaccharomyces cerevisiae." Genetics 160, no. 4 (April 1, 2002): 1401–7. http://dx.doi.org/10.1093/genetics/160.4.1401.
Full textAbstract:
AbstractIn Saccharomyces cerevisiae the HM loci and regions adjacent to the telomeres are transcriptionally silent. HML is situated 11 kb from the left telomere of chromosome III. I have systematically examined gene silencing along this 11-kb chromosomal region. I found that silencing extends at least 1.1 kb beyond HML, indicating that the HML E silencer acts on both sides. Moreover, I obtained evidence indicating that a 0.71-kb sequence near the E silencer acts as a barrier to the spread of silencing and coincides with the left boundary of the silent HML domain. I also showed that silencing at the telomere is limited to an ~2-kb domain. On the other hand, an ~7-kb region between HML and the telomere is not silenced by HML or the telomere. These results provide a clear example of organization of the eukaryotic genome into interspersed domains with distinct potentials for gene expression.
49
Meijer, Harold J. G., and Francine Govers. "Genomewide Analysis of Phospholipid Signaling Genes in Phytophthora spp.: Novelties and a Missing Link." Molecular Plant-Microbe Interactions® 19, no. 12 (December 2006): 1337–47. http://dx.doi.org/10.1094/mpmi-19-1337.
Full textAbstract:
Phospholipids are cellular membrane components in eukaryotic cells that execute many important roles in signaling. Genes encoding enzymes required for phospholipid signaling and metabolism have been characterized in several organisms, but only a few have been described for oomycetes. In this study, the genome sequences of Phytophthora sojae and P. ramorum were explored to construct a comprehensive genomewide inventory of genes involved in the most universal phospholipid signaling pathways. Several genes and gene families were annotated, including those encoding phosphatidylinositol synthase (PIS), phosphatidy-linositol (phosphate) kinase (PI[P]K), diacylglycerol kinase (DAG), and phospholipase D (PLD). The most obvious missing link is a gene encoding phospholipase C (PLC). In all eukaryotic genomes sequenced to date, PLC genes are annotated based on certain conserved features; however, these genes seem to be absent in Phytophthora spp. Analysis of the structural and regulatory domains and domain organization of the predicted isoforms of PIS, PIK, PIPK, DAG, and PLD revealed many novel features compared with characterized representatives in other eukaryotes. Examples are transmembrane proteins with a C-terminal catalytic PLD domain, secreted PLD-like proteins, and PIPKs that have an N-terminal G-protein-coupled receptor-transmembrane signature. Compared with other sequenced eukaryotes, the genus Phytophthora clearly has several exceptional features in its phospholipid-modifying enzymes.
50
Brickner, Jason. "Genetic and epigenetic control of the spatial organization of the genome." Molecular Biology of the Cell 28, no. 3 (February 2017): 364–69. http://dx.doi.org/10.1091/mbc.e16-03-0149.
Full textAbstract:
Eukaryotic genomes are spatially organized within the nucleus by chromosome folding, interchromosomal contacts, and interaction with nuclear structures. This spatial organization is observed in diverse organisms and both reflects and contributes to gene expression and differentiation. This leads to the notion that the arrangement of the genome within the nucleus has been shaped and conserved through evolutionary processes and likely plays an adaptive function. Both DNA-binding proteins and changes in chromatin structure influence the positioning of genes and larger domains within the nucleus. This suggests that the spatial organization of the genome can be genetically encoded by binding sites for DNA-binding proteins and can also involve changes in chromatin structure, potentially through nongenetic mechanisms. Here I briefly discuss the results that support these ideas and their implications for how genomes encode spatial organization.