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1
Martín, Victoria, Miguel A. Rodríguez-Gabriel, W. Hayes McDonald, Stephen Watt, John R. Yates, Jürg Bähler, and Paul Russell. "Cip1 and Cip2 Are Novel RNA-Recognition-Motif Proteins That Counteract Csx1 Function during Oxidative Stress." Molecular Biology of the Cell 17, no. 3 (March 2006): 1176–83. http://dx.doi.org/10.1091/mbc.e05-09-0847.
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Eukaryotic cells reprogram their global patterns of gene expression in response to stress. Recent studies in Schizosaccharomyces pombe showed that the RNA-binding protein Csx1 plays a central role in controlling gene expression during oxidative stress. It does so by stabilizing atf1+ mRNA, which encodes a subunit of a bZIP transcription factor required for gene expression during oxidative stress. Here, we describe two related proteins, Cip1 and Cip2, that were identified by multidimensional protein identification technology (MudPIT) as proteins that coprecipitate with Csx1. Cip1 and Cip2 are cytoplasmic proteins that have RNA recognition motifs (RRMs). Neither protein is essential for viability, but a cip1Δ cip2Δ strain grows poorly and has altered cellular morphology. Genetic epistasis studies and whole genome expression profiling show that Cip1 and Cip2 exert posttranscriptional control of gene expression in a manner that is counteracted by Csx1. Notably, the sensitivity of csx1Δ cells to oxidative stress and their inability to induce expression of Atf1-dependent genes are partially rescued by cip1Δ and cip2Δ mutations. This study emphasizes the importance of a modulated mRNA stability in the eukaryotic stress response pathways and adds new information to the role of RNA-binding proteins in the oxidative stress response.
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Yao, Yunping, Changsheng Ouyang, Lu Jiang, Xiaoguang Liu, Qing Hao, Guozhong Zhao, and Bin Zeng. "Specificity of acyl-CoA binding protein to acyl-CoAs: influence on the lipid metabolism in Aspergillus oryzae." RSC Advances 6, no. 97 (2016): 94859–65. http://dx.doi.org/10.1039/c6ra20532a.
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Acyl-CoA binding protein (ACBP) is involved in lipid metabolism and regulation of gene expression in eukaryotic cells, however, the specific functional roles of this important class of proteins remain to be elucidated.
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de Koning, Bart, Fabian Blombach, Hao Wu, Stan J. J. Brouns, and John van der Oost. "Role of multiprotein bridging factor 1 in archaea: bridging the domains?" Biochemical Society Transactions 37, no. 1 (January 20, 2009): 52–57. http://dx.doi.org/10.1042/bst0370052.
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MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 (Bombyx mori regulator of fushi tarazu). MBF1 was demonstrated to enhance transcription by forming a bridge between distinct regulatory DNA-binding proteins and the TATA-box-binding protein. MBF1 consists of two parts: a C-terminal part that contains a highly conserved helix–turn–helix, and an N-terminal part that shows a clear divergence: in eukaryotes, it is a weakly conserved flexible domain, whereas, in archaea, it is a conserved zinc-ribbon domain. Although its function in archaea remains elusive, its function as a transcriptional co-activator has been deduced from thorough studies of several eukaryotic proteins, often indicating a role in stress response. In addition, MBF1 was found to influence translation fidelity in yeast. Genome context analysis of mbf1 in archaea revealed conserved clustering in the crenarchaeal branch together with genes generally involved in gene expression. It points to a role of MBF1 in transcription and/or translation. Experimental data are required to allow comparison of the archaeal MBF1 with its eukaryotic counterpart.
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Patrick, Ryan M., Jessica C. H. Lee, Jade R. J. Teetsel, Soo-Hyun Yang, Grace S. Choy, and Karen S. Browning. "Discovery and characterization of conserved binding of eIF4E 1 (CBE1), a eukaryotic translation initiation factor 4E–binding plant protein." Journal of Biological Chemistry 293, no. 44 (September 13, 2018): 17240–47. http://dx.doi.org/10.1074/jbc.ra118.003945.
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In many eukaryotes, translation initiation is regulated by proteins that bind to the mRNA cap–binding protein eukaryotic translation initiation factor 4E (eIF4E). These proteins commonly prevent association of eIF4E with eIF4G or form repressive messenger ribonucleoproteins that exclude the translation machinery. Such gene-regulatory mechanisms in plants, and even the presence of eIF4E-interacting proteins other than eIF4G (and the plant-specific isoform eIFiso4G, which binds eIFiso4E), are unknown. Here, we report the discovery of a plant-specific protein, conserved binding of eIF4E 1 (CBE1). We found that CBE1 has an evolutionarily conserved eIF4E-binding motif in its N-terminal domain and binds eIF4E or eIFiso4E in vitro. CBE1 thereby forms cap-binding complexes and is an eIF4E-dependent constituent of these complexes in vivo. Of note, plant mutants lacking CBE1 exhibited dysregulation of cell cycle–related transcripts and accumulated higher levels of mRNAs encoding proteins involved in mitosis than did WT plants. Our findings indicate that CBE1 is a plant protein that can form mRNA cap–binding complexes having the potential for regulating gene expression. Because mammalian translation factors are known regulators of cell cycle progression, we propose that CBE1 may represent such first translation factor–associated plant-specific cell cycle regulator.
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Xu, Ming-yan, Ju-li Liu, Ren-li Zhang, and Yu-cai Fu. "Isolation of a novel ras gene from Trichomonas vaginalis: a possible evolutionary ancestor of the Ras and Rap genes of higher eukaryotesThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process." Biochemistry and Cell Biology 85, no. 2 (April 2007): 239–45. http://dx.doi.org/10.1139/o07-008.
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The Ras subfamily proteins are small, monomeric GTP-binding proteins with vital roles in regulating eukaryotic signal transduction pathways. Gene duplication and divergence have been postulated as the mechanism by which such family members have evolved their specific functions. A cDNA clone of TvRsp was isolated and sequenced from a cDNA expression library of the primitive eukaryote Trichomonas vaginalis . The genomic DNA corresponding to the cDNA sequence was amplified by PCR and sequenced. Sequence analysis suggested that TvRsp was an intronless gene. This gene encoded a protein of 181 amino acids and contained the 5 conserved G domains that designated it as a Ras or Rap subfamily member. However, the deduced amino acid sequence shared only 34%–37% overall identity with other Ras subfamily members of different species, and the presence of motifs characteristic of both the Ras and Rap families of GTPase confused the familial classification of this gene. Phylogenetic analysis showed its origins at the divergence point of the Ras/Rap families and suggested that TvRsp was a possible evolutionary ancestral gene of the ras/rap genes of higher eukaryotes. This information was of importance not only from the perspective of understanding the evolution and diversity of eukaryotic signal transduction pathways but also in providing a framework by which to understand protein processing in the growth and differentiation of single-celled microorganisms.
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Harvey, Robert, Veronica Dezi, Mariavittoria Pizzinga, and Anne E. Willis. "Post-transcriptional control of gene expression following stress: the role of RNA-binding proteins." Biochemical Society Transactions 45, no. 4 (July 14, 2017): 1007–14. http://dx.doi.org/10.1042/bst20160364.
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The ability of mammalian cells to modulate global protein synthesis in response to cellular stress is essential for cell survival. While control of protein synthesis is mediated by the regulation of eukaryotic initiation and elongation factors, RNA-binding proteins (RBPs) provide a crucial additional layer to post-transcriptional regulation. RBPs bind specific RNA through conserved RNA-binding domains and ensure that the information contained within the genome and transcribed in the form of RNA is exported to the cytoplasm, chemically modified, and translated prior to folding into a functional protein. Thus, this group of proteins, through mediating translational reprogramming, spatial reorganisation, and chemical modification of RNA molecules, have a major influence on the robust cellular response to external stress and toxic injury.
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Das, Aparajita, and Vijayakumar Boggaram. "Proteasome dysfunction inhibits surfactant protein gene expression in lung epithelial cells: mechanism of inhibition of SP-B gene expression." American Journal of Physiology-Lung Cellular and Molecular Physiology 292, no. 1 (January 2007): L74—L84. http://dx.doi.org/10.1152/ajplung.00103.2006.
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Surfactant proteins maintain lung function through their actions to reduce alveolar surface tension and control of innate immune responses in the lung. The ubiquitin proteasome pathway is responsible for the degradation of majority of intracellular proteins in eukaryotic cells, and proteasome dysfunction has been linked to the development of neurodegenerative, cardiac, and other diseases. Proteasome function is impaired in interstitial lung diseases associated with surfactant protein C (SP-C) mutation mapping to the BRICHOS domain located in the proSP-C protein. In this study we determined the effects of proteasome inhibition on surfactant protein expression in H441 and MLE-12 lung epithelial cells to understand the relationship between proteasome dysfunction and surfactant protein gene expression. Proteasome inhibitors lactacystin and MG132 reduced the levels of SP-A, SP-B, and SP-C mRNAs in a concentration-dependent manner in H441 and MLE-12 cells. In H441 cells, lactacystin and MG132 inhibition of SP-B mRNA was associated with similar decreases in SP-B protein, and the inhibition was due to inhibition of gene transcription. Proteasome inhibitors decreased thyroid transcription factor-1 (TTF-1)/Nkx2.1 DNA binding activity, and the reduced TTF-1 DNA binding activity was due to reduced expression levels of TTF-1 protein. These data indicated that the ubiquitin proteasome pathway is essential for the maintenance of surfactant protein gene expression and that disruption of this pathway inhibits surfactant protein gene expression via reduced expression of TTF-1 protein.
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Corry, Gareth N., and D. Alan Underhill. "Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression." Biochemistry and Cell Biology 83, no. 4 (August 1, 2005): 535–47. http://dx.doi.org/10.1139/o05-062.
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To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.
9
Pacheco, Almudena, and Encarnacion Martinez-Salas. "Insights into the Biology of IRES Elements through Riboproteomic Approaches." Journal of Biomedicine and Biotechnology 2010 (2010): 1–12. http://dx.doi.org/10.1155/2010/458927.
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Translation initiation is a highly regulated process that exerts a strong influence on the posttranscriptional control of gene expression. Two alternative mechanisms govern translation initiation in eukaryotic mRNAs, the cap-dependent initiation mechanism operating in most mRNAs, and the internal ribosome entry site (IRES)-dependent mechanism, first discovered in picornaviruses. IRES elements are highly structured RNA sequences that, in most instances, require specific proteins for recruitment of the translation machinery. Some of these proteins are eukaryotic initiation factors. In addition, RNA-binding proteins (RBPs) play a key role in internal initiation control. RBPs are pivotal regulators of gene expression in response to numerous stresses, including virus infection. This review discusses recent advances on riboproteomic approaches to identify IRES transacting factors (ITAFs) and the relationship between RNA-protein interaction and IRES activity, highlighting the most relevant features on picornavirus and hepatitis C virus IRESs.
10
Kamenska, Anastasiia, Clare Simpson, and Nancy Standart. "eIF4E-binding proteins: new factors, new locations, new roles." Biochemical Society Transactions 42, no. 4 (August 1, 2014): 1238–45. http://dx.doi.org/10.1042/bst20140063.
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The cap-binding translation initiation factor eIF4E (eukaryotic initiation factor 4E) is central to protein synthesis in eukaryotes. As an integral component of eIF4F, a complex also containing the large bridging factor eIF4G and eIF4A RNA helicase, eIF4E enables the recruitment of the small ribosomal subunit to the 5′ end of mRNAs. The interaction between eIF4E and eIF4G via a YXXXXLϕ motif is regulated by small eIF4E-binding proteins, 4E-BPs, which use the same sequence to competitively bind eIF4E thereby inhibiting cap-dependent translation. Additional eIF4E-binding proteins have been identified in the last 10–15 years, characterized by the YXXXXLϕ motif, and by interactions (many of which remain to be detailed) with RNA-binding proteins, or other factors in complexes that recognize the specific mRNAs. In the present article, we focus on the metazoan 4E-T (4E-transporter)/Cup family of eIF4E-binding proteins, and also discuss very recent examples in yeast, fruitflies and humans, some of which predictably inhibit translation, while others may result in mRNA decay or even enhance translation; altogether considerably expanding our understanding of the roles of eIF4E-binding proteins in gene expression regulation.
11
Gonatopoulos-Pournatzis, Thomas, and Victoria H. Cowling. "Cap-binding complex (CBC)." Biochemical Journal 457, no. 2 (December 20, 2013): 231–42. http://dx.doi.org/10.1042/bj20131214.
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The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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Wildeman, Alan G. "Regulation of SV40 early gene expression." Biochemistry and Cell Biology 66, no. 6 (June 1, 1988): 567–77. http://dx.doi.org/10.1139/o88-067.
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The early promoter of the simian virus 40 (SV40) has been used as a model eukaryotic promoter for the study of DN A sequence elements and cellular factors that are involved in transcriptional control and initiation. Site-directed mutagenesis and cell-free transcription systems have enabled the dissection of the functional domains within the 21 bp upstream sequence element and the 72 bp enhancer, and a number of protein factors that bind to various "motifs" within these domains have been identified. This article summarizes recent observations that have led to the conclusion that the SV40 promoter, and particularly, the enhancer region, is composed of multiple sequence elements. Some of these elements are present in cellular genes, and may exhibit tissue-specificity in their action. Furthermore, the proteins that are being identified (e.g., Sp1) may have binding sites within these elements that are sufficiently specific to ensure that only certain sets of genes will be selectively expressed.
13
Searle, S., M. V. McCrossan, and D. F. Smith. "Expression of a mitochondrial stress protein in the protozoan parasite Leishmania major." Journal of Cell Science 104, no. 4 (April 1, 1993): 1091–100. http://dx.doi.org/10.1242/jcs.104.4.1091.
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The DNA sequence has been determined of a gene from Leishmania major that shares sequence identity with members of the eukaryotic heat shock protein (hsp) 70 gene family. The deduced open reading frame for translation shares a number of features common to hsp70 stress proteins, including conserved amino acids implicated in ATP binding and a putative calmodulin-binding site. In addition, the protein has an N-terminal sequence characteristic of a mitochondrial targeting signal. Specific antibodies to this protein, generated by the use of recombinant fusion peptides, recognise a 65 kDa molecule of pI 6.7. This molecule is constitutively expressed and localises to the mitochondrion in all stages of the parasite life cycle. These features suggest a role for this protein as a molecular chaperone in Leishmania.
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Han, W., Y. Yu, N. Altan, and L. Pick. "Multiple proteins interact with the fushi tarazu proximal enhancer." Molecular and Cellular Biology 13, no. 9 (September 1993): 5549–59. http://dx.doi.org/10.1128/mcb.13.9.5549.
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The expression of the Drosophila segmentation gene fushi tarazu (ftz) is controlled at the level of transcription. The proximal enhancer, located approximately 3.4 kb upstream of the transcription start site, directs lacZ fusion gene expression in a ftz-like seven-stripe pattern in transgenic fly embryos. We have taken a biochemical approach to identify DNA-binding proteins that regulate ftz gene expression through the proximal enhancer. DNase I footprinting and methylation interference experiments with staged Drosophila embryo nuclear extracts identified nine protein binding sites in the proximal enhancer. Ten different sequence-specific DNA-binding complexes that interact with eight of these sites were identified. Some interact with multiple sites, while others bind to single sites in the enhancer. Two of the complexes that interact with multiple sites appear to contain the previously described ftz regulators, FTZ-F1 and TTK/FTZ-F2. These in vitro studies allowed us to narrow down the proximal enhancer to a 323-bp DNA fragment that contains all of the protein binding sites. Expression directed by this minimal enhancer element in seven ftz-like stripes in transgenic embryos is identical to that directed by the full-length enhancer. Internal deletions of several sites abolish reporter gene expression in vivo. Thus, the ftz proximal enhancer, like other cell-type-specific eukaryotic enhancers, interacts with an array of proteins that are expected to mediate the establishment, maintenance, and repression of transcription of the ftz gene in seven stripes in the developing embryo.
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Han, W., Y. Yu, N. Altan, and L. Pick. "Multiple proteins interact with the fushi tarazu proximal enhancer." Molecular and Cellular Biology 13, no. 9 (September 1993): 5549–59. http://dx.doi.org/10.1128/mcb.13.9.5549-5559.1993.
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The expression of the Drosophila segmentation gene fushi tarazu (ftz) is controlled at the level of transcription. The proximal enhancer, located approximately 3.4 kb upstream of the transcription start site, directs lacZ fusion gene expression in a ftz-like seven-stripe pattern in transgenic fly embryos. We have taken a biochemical approach to identify DNA-binding proteins that regulate ftz gene expression through the proximal enhancer. DNase I footprinting and methylation interference experiments with staged Drosophila embryo nuclear extracts identified nine protein binding sites in the proximal enhancer. Ten different sequence-specific DNA-binding complexes that interact with eight of these sites were identified. Some interact with multiple sites, while others bind to single sites in the enhancer. Two of the complexes that interact with multiple sites appear to contain the previously described ftz regulators, FTZ-F1 and TTK/FTZ-F2. These in vitro studies allowed us to narrow down the proximal enhancer to a 323-bp DNA fragment that contains all of the protein binding sites. Expression directed by this minimal enhancer element in seven ftz-like stripes in transgenic embryos is identical to that directed by the full-length enhancer. Internal deletions of several sites abolish reporter gene expression in vivo. Thus, the ftz proximal enhancer, like other cell-type-specific eukaryotic enhancers, interacts with an array of proteins that are expected to mediate the establishment, maintenance, and repression of transcription of the ftz gene in seven stripes in the developing embryo.
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Liu, Yilei, and David J. Elliott. "Coupling genetics and post-genomic approaches to decipher the cellular splicing code at a systems-wide level." Biochemical Society Transactions 38, no. 1 (January 19, 2010): 237–41. http://dx.doi.org/10.1042/bst0380237.
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Nuclear RNA processing is a critical stage in eukaryotic gene expression, and is controlled in part by the expression and concentration of nuclear RNA-binding proteins. Different nuclear RNA-binding proteins are differentially expressed in different cells, helping the spliceosome to decode pre-mRNAs into alternatively spliced mRNAs. Recent post-genomic technology has exposed the complexity of nuclear RNA processing, and is starting to reveal the mechanisms and rules through which networks of RNA-binding proteins can regulate multiple parallel pathways. Identification of multiple parallel processing pathways regulated by nuclear RNA-binding proteins is leading to a systems-wide understanding of the rules and consequences of alternative nuclear RNA processing.
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Hintz, William E., Inge Kalsner, Ewa Plawinski, Zimin Guo, and Peter A. Lagosky. "Improved gene expression in Aspergillus nidulans." Canadian Journal of Botany 73, S1 (December 31, 1995): 876–84. http://dx.doi.org/10.1139/b95-334.
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A variety of gene expression systems have been developed that utilize the promoter and transcriptional regulatory sequences derived from carbon-catabolite repressed genes for the expression of heterologous genes. The alcA expression system of Aspergillus nidulans utilizes the promoter and regulatory sequences derived from the alcohol dehydrogenase I (alcA) gene. Expression of the alcA gene is repressed by a DNA-binding protein (CreA) in the presence of glucose and induced by ethanol under glucose-depleted conditions. One problem encountered during the expression of therapeutic proteins in A. nidulans is the coexpression of secreted proteases at the time of maximal secretion of heterologous product. To avoid the proteases we created an alcA promoter variant that is no longer sensitive to glucose repression hence could drive expression at earlier time points during the fermentation. The use of this promoter variant in the expression of recombinant interleukin-6 is discussed. A second problem encountered during the expression of high-quality human therapeutic proteins in Aspergillus is aberrant glycosylation. Lower eukaryotic systems, such as Aspergillus, tend to add highly branched mannosidic chains to heterologous secreted protein products. N-Glycans can be important for both the structure and function of specific glycoproteins, hence efforts are being made to in vivo alter the type and complexity of N-glycans substituted by A. nidulans. Key words: Aspergillus, gene expression, alcohol dehydrogenase, glycosylation.
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O'Brien, R. M., N. Halmi, P. E. Stromstedt, R. L. Printz, and D. K. Granner. "Expression cloning of a zinc-finger cyclic AMP-response-element-binding protein." Biochemical Journal 312, no. 1 (November 15, 1995): 17–21. http://dx.doi.org/10.1042/bj3120017.
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In response to specific extracellular signals, intracellular cyclic AMP levels increase, leading to a variety of responses including the alteration of transcription of many eukaryotic genes. This transcriptional effect is frequently mediated through the cyclic AMP-response element (CRE) motif T(T/G)ACGTCA. Using an expression screening approach we have cloned a yeast gene, MSN2, that encodes a 78 kDa protein that recognizes this consensus CRE motif. Phosphorylation of the MSN2 protein by the catalytic subunit of protein kinase A stimulates DNA binding in vitro. Two putative Cys2His2-type zinc fingers present in the C-terminal 79 amino acids of the MSN2 protein are sufficient to confer CRE-binding specificity. Therefore, MSN2 represents a novel CRE-binding protein distinct from the multiple previously characterized basic region-leucine zipper repeat CRE-binding proteins.
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Brachner, Andreas, and Roland Foisner. "Evolvement of LEM proteins as chromatin tethers at the nuclear periphery." Biochemical Society Transactions 39, no. 6 (November 21, 2011): 1735–41. http://dx.doi.org/10.1042/bst20110724.
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The nuclear envelope in eukaryotic cells has important roles in chromatin organization. The inner nuclear membrane contains over 60 transmembrane proteins. LEM [LAP2 (lamina-associated polypeptide 2)/emerin/MAN1] domain-containing proteins of the inner nuclear membrane are involved in tethering chromatin to the nuclear envelope and affect gene expression. They contain a common structural, bihelical motif, the so-called LEM domain, which mediates binding to a conserved chromatin protein, BAF (barrier to autointegration factor). Interestingly, this domain is highly related to other bihelical motifs, termed HeH (helix–extension–helix) and SAP {SAF (scaffold attachment factor)/acinus/PIAS [protein inhibitor of activated STAT (signal transducer and activator of transcription)]} motifs, which are directly linked to DNA. In the present paper, we summarize evidence that the LEM motif evolved from the HeH and SAP domains concomitantly with BAF. In addition, we discuss the potential evolution of HeH/SAP and LEM domain-containing proteins and their role in chromatin tethering and gene regulation from unicellular eukaryotes to mammals.
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Weising, Kurt, and Günter Kahl. "Towards an Understanding of Plant Gene Regulation: The Action of Nuclear Factors." Zeitschrift für Naturforschung C 46, no. 1-2 (February 1, 1991): 1–11. http://dx.doi.org/10.1515/znc-1991-1-202.
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Abstract Over the last decade an intensive research on the regulation of gene expression in viral and animal systems has led to the discovery of cis-acting regulatory sequences, the identification of sequence-specific DNA -binding proteins (trans-acting factors), the characterization of protein domains involved in DNA -protein recognition and binding as well as in protein -protein interactions, and the cloning and sequencing of genes encoding regulatory proteins. The tremendous progress in this field is now being complemented by advances in our understanding of how plant genes are regulated. A wealth of data has accumulated in the past few years witnessing basic similarities in the transcriptional regulation of various eukaryotic genes, but also specific features of plant genes. This article collects presently available data, focusses on DNA -protein interactions in plant genes, particularly in light-regulated and “constitutively expressed” genes, reports on the isolation of plant genes encoding regulatory proteins, an dismeant to induce further activities in plant gene research.
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Willkomm, Sarah, Benedikt Moissl, Henri Michel, and Dina Grohmann. "Die erstaunliche Vielseitigkeit der Argonauten-Crew." BIOspektrum 26, no. 6 (October 14, 2020): 603–5. http://dx.doi.org/10.1007/s12268-020-1453-8.
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Abstract Cellular nucleic acid levels are specifically regulated by Argonaute (Ago) proteins. Eukaryotic (e)Ago participates mainly in posttranscriptional regulation of gene expression. In contrast, prokaryotic (p)Ago proteins are involved in defense processes. Our work adds to the understanding of pAgo function and elucidates dynamic aspects of Ago-mediated substrate binding thereby highlighting mechanistic differences between eAgo and pAgo proteins.
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Dahan, Sivan, Stuart Knutton, Robert K. Shaw, Valerie F. Crepin, Gordon Dougan, and Gad Frankel. "Transcriptome of Enterohemorrhagic Escherichia coli O157 Adhering to Eukaryotic Plasma Membranes." Infection and Immunity 72, no. 9 (September 2004): 5452–59. http://dx.doi.org/10.1128/iai.72.9.5452-5459.2004.
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ABSTRACT Using a DNA microarray, we determined changes in enterohemorrhagic Escherichia coli O157:H7 gene expression during binding to plasma membranes. Analysis of the complete transcriptomes of the bound bacteria revealed increased levels of stress-associated mRNAs and decreased levels of mRNA encoding proteins involved in translation and type III secretion.
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Takai, Yoshimi, Takuya Sasaki, and Takashi Matozaki. "Small GTP-Binding Proteins." Physiological Reviews 81, no. 1 (January 1, 2001): 153–208. http://dx.doi.org/10.1152/physrev.2001.81.1.153.
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Small GTP-binding proteins (G proteins) exist in eukaryotes from yeast to human and constitute a superfamily consisting of more than 100 members. This superfamily is structurally classified into at least five families: the Ras, Rho, Rab, Sar1/Arf, and Ran families. They regulate a wide variety of cell functions as biological timers (biotimers) that initiate and terminate specific cell functions and determine the periods of time for the continuation of the specific cell functions. They furthermore play key roles in not only temporal but also spatial determination of specific cell functions. The Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. Many upstream regulators and downstream effectors of small G proteins have been isolated, and their modes of activation and action have gradually been elucidated. Cascades and cross-talks of small G proteins have also been clarified. In this review, functions of small G proteins and their modes of activation and action are described.
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Morozova, Olga V., Elena I. Isaeva, and Dmitry V. Klinov. "Protein Nanoparticles with Enzymatic and Antigen-Binding Activities Induce Th1 Cytokine Gene Expression." Materials Science Forum 995 (June 2020): 109–13. http://dx.doi.org/10.4028/www.scientific.net/msf.995.109.
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To improve protein stability and membrane permeability the protein nanoparticles (NP) were fabricated from enzymes or virus-specific antibodies by nanoprecipitation. Lysozyme NP destroyed bacterial cellular walls. RNase-based NP hydrolyzed RNA. Lipase, catalase and horseradish peroxidase activities were also registered for corresponding protein NP. NP from polyclonal antibodies against the influenza A virus and monoclonal antibodies against hemagglutinin H1, H3; proteins NS and NP could interact with their specific antigens. NP from monoclonal antibodies against the hepatitis B surface antigen bound with the antigen as shown by ELISA. The protein NP were stable in water at 4°C for several months and in the presence of blood sera or saliva for more than 5 days. The protein NP were not toxic for human cells and mice. The protein NP could penetrate and accumulate in cells in 2 hours with maximum after 2 days and subsequent gradual decline until background values. Entry of foreign protein NP into the eukaryotic cells induced cytokine gene expression. RNA of interferon (IFN) a, b and l but not IFN g were detected by reverse transcription with real time PCR. Polarization index (Th2:Th1 cytokine RNA) was near 0. Accordingly, cellular uptake of non-toxic protein NP induced Th1 polarization of immune response.
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Chen, Meng, and John M. Lopes. "Multiple Basic Helix-Loop-Helix Proteins Regulate Expression of the ENO1 Gene of Saccharomyces cerevisiae." Eukaryotic Cell 6, no. 5 (March 9, 2007): 786–96. http://dx.doi.org/10.1128/ec.00383-06.
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ABSTRACT The basic helix-loop-helix (bHLH) eukaryotic transcription factors have the ability to form multiple dimer combinations. This property, together with limited DNA-binding specificity for the E box (CANNTG), makes them ideally suited for combinatorial control of gene expression. We tested the ability of all nine Saccharomyces cerevisiae bHLH proteins to regulate the enolase-encoding gene ENO1. ENO1 was known to be activated by the bHLH protein Sgc1p. Here we show that expression of an ENO1-lacZ reporter was also regulated by the other eight bHLH proteins, namely, Ino2p, Ino4p, Cbf1p, Rtg1p, Rtg3p, Pho4p, Hms1p, and Ygr290wp. ENO1-lacZ expression was also repressed by growth in inositol-choline-containing medium. Epistatic analysis and chromatin immunoprecipitation experiments showed that regulation by Sgc1p, Ino2p, Ino4p, and Cbf1p and repression by inositol-choline required three distal E boxes, E1, E2, and E3. The pattern of bHLH binding to the three E boxes and experiments with two dominant-negative mutant alleles of INO4 and INO2 support the model that bHLH dimer selection affects ENO1-lacZ expression. These results support the general model that bHLH proteins can coordinate different biological pathways via multiple mechanisms.
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Maloney, Christopher A., and William D. Rees. "Gene-nutrient interactions during fetal development." Reproduction 130, no. 4 (October 2005): 401–10. http://dx.doi.org/10.1530/rep.1.00523.
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Eukaryotic cells have evolved a complex series of nutrient sensors that protect them from damage caused by acute deficiencies and also mediate adaptive responses to prolonged excess or deficiency of particular nutrients. In adults gene expression is regulated by nutrients interacting with pathways involving mammalian target of rapamycin (mTOR), CCAAT/ enhancer-binding proteins (C/EBPs) and peroxisome proliferator activator proteins (PPARs). These systems are also present in key cells of the developing oocyte, embryo and fetus. In this review we will consider the role of interactions between genes and nutrients during reproduction with a particular emphasis on their possible involvement in the prenatal programming of glucose metabolism in the adult.
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Liu, Changying, Panpan Zhu, Wei Fan, Yang Feng, Min Kou, Jie Hu, and Aichun Zhao. "Functional analysis of drought and salt tolerance mechanisms of mulberry RACK1 gene." Tree Physiology 39, no. 12 (November 14, 2019): 2055–69. http://dx.doi.org/10.1093/treephys/tpz108.
Full textAbstract:
Abstract The receptor for activated C kinase 1 (RACK1) protein acts as a central hub for the integration of many physiological processes in eukaryotic organisms. Plant RACK1 is implicated in abiotic stress responses, but the underlying molecular mechanisms of stress adaptation remain largely unknown. Here, the overexpression of the mulberry (Morus alba L.) RACK1 gene in Arabidopsis decreased tolerance to drought and salt stresses and MaRACK1 overexpression changed expression levels of genes in response to stress and stimuli. We developed a simple and efficient transient transformation system in mulberry, and the mulberry seedlings transiently expressing MaRACK1 were hypersensitive to drought and salt stresses. The expression levels of guanine nucleotide-binding protein (G-protein) encoding genes in mulberry and Arabidopsis were not affected by MaRACK1 overexpression. The interactions between RACK1 and G-proteins were confirmed, and the RACK1 proteins from mulberry and Arabidopsis could not interact with their respective G-proteins, which indicated that RACK1 may regulate stress responses independently of G-proteins. Additionally, MaRACK1 may regulate drought and salt stress tolerances by interacting with a fructose 1, 6-bisphosphate aldolase. Our findings provide new insights into the mechanisms underlying RACK1 functions in abiotic stress responses and important information for their further characterization.
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Baier, LJ, MC Hannibal, EW Hanley, and GJ Nabel. "Lymphoid expression and TATAA binding of a human protein containing an Antennapedia homeodomain." Blood 78, no. 4 (August 15, 1991): 1047–55. http://dx.doi.org/10.1182/blood.v78.4.1047.1047.
Full textAbstract:
Abstract In an effort to identify human proteins that bind to the TATAA box, a lambda gt-11 expression library was screened with a radiolabeled DNA probe containing 12 copies of the TATAA sequence. A cDNA encoding a specific TATAA binding protein was isolated and found to contain a homeobox domain identical at 59 of 60 residues to the Drosophila Antennapedia (Antp) homeodomain, as well as another conserved motif found in homeotic genes, the homeo-specific pentapeptide. Although this and other Antp-like homeobox proteins have been described previously in neuronal cells and fibroblasts, we report the expression of this gene in lymphoid cells. This cDNA, isolated from a B-cell library, hybridizes to a 1.6-kb messenger RNA in several T- and B-cell lines, and the expected protein was identified in Jurkat T-lymphoid cells by Western blot analysis. The DNA binding specificity of this human Antp clone was analyzed using single-base mutations of the TATAA sequence. The first thymidine, as well as the last three bases (TAA), were important for homeobox binding. Finally, the function of the highly conserved homeospecific pentapeptide protein region was investigated in both the human and Drosophila Antp proteins. The homeospecific pentapeptide region was not required for DNA binding, and Drosophila Antp proteins mutated in the pentapeptide region were able to transactivate the Ubx promoter in Schneider L2 cells, in contrast to a homeodomain mutation, suggesting an alternative function for the homeospecific pentapeptide in homeotic genes. Because the human Antp TATAA binding protein is expressed in both lymphoid and non-lymphoid cells, we suggest that this homeobox gene has evolved a more general transcriptional regulatory function in higher eukaryotic cells.
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Baier, LJ, MC Hannibal, EW Hanley, and GJ Nabel. "Lymphoid expression and TATAA binding of a human protein containing an Antennapedia homeodomain." Blood 78, no. 4 (August 15, 1991): 1047–55. http://dx.doi.org/10.1182/blood.v78.4.1047.bloodjournal7841047.
Full textAbstract:
In an effort to identify human proteins that bind to the TATAA box, a lambda gt-11 expression library was screened with a radiolabeled DNA probe containing 12 copies of the TATAA sequence. A cDNA encoding a specific TATAA binding protein was isolated and found to contain a homeobox domain identical at 59 of 60 residues to the Drosophila Antennapedia (Antp) homeodomain, as well as another conserved motif found in homeotic genes, the homeo-specific pentapeptide. Although this and other Antp-like homeobox proteins have been described previously in neuronal cells and fibroblasts, we report the expression of this gene in lymphoid cells. This cDNA, isolated from a B-cell library, hybridizes to a 1.6-kb messenger RNA in several T- and B-cell lines, and the expected protein was identified in Jurkat T-lymphoid cells by Western blot analysis. The DNA binding specificity of this human Antp clone was analyzed using single-base mutations of the TATAA sequence. The first thymidine, as well as the last three bases (TAA), were important for homeobox binding. Finally, the function of the highly conserved homeospecific pentapeptide protein region was investigated in both the human and Drosophila Antp proteins. The homeospecific pentapeptide region was not required for DNA binding, and Drosophila Antp proteins mutated in the pentapeptide region were able to transactivate the Ubx promoter in Schneider L2 cells, in contrast to a homeodomain mutation, suggesting an alternative function for the homeospecific pentapeptide in homeotic genes. Because the human Antp TATAA binding protein is expressed in both lymphoid and non-lymphoid cells, we suggest that this homeobox gene has evolved a more general transcriptional regulatory function in higher eukaryotic cells.
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Akıl, Caner, Linh T. Tran, Magali Orhant-Prioux, Yohendran Baskaran, Edward Manser, Laurent Blanchoin, and Robert C. Robinson. "Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea." Proceedings of the National Academy of Sciences 117, no. 33 (August 3, 2020): 19904–13. http://dx.doi.org/10.1073/pnas.2009167117.
Full textAbstract:
Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical for providing force and structure in many processes, including membrane remodeling. In general, Asgard genomes encode two classes of actin-regulating proteins from sequence analysis, profilins and gelsolins. Asgard profilins were demonstrated to regulate actin filament nucleation. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryotic-like actin depolymerization cycle, and indicate complex actin cytoskeleton regulation in Asgard organisms. Thor gelsolins have homologs in other Asgard archaea and comprise one or two copies of the prototypical gelsolin domain. This appears to be a record of an initial preeukaryotic gene duplication event, since eukaryotic gelsolins are generally comprise three to six domains. X-ray structures of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin or cofilin with actin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for a calcium-controlled Asgard actin cytoskeleton, indicating that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled actin filaments are responsible for shaping filopodia and microvilli. By correlation, we hypothesize that the formation of the protrusions observed from Lokiarchaeota cell bodies may involve the gelsolin-regulated actin structures.
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Majumder, Mrinmoyee, and Viswanathan Palanisamy. "Compendium of Methods to Uncover RNA-Protein Interactions In Vivo." Methods and Protocols 4, no. 1 (March 19, 2021): 22. http://dx.doi.org/10.3390/mps4010022.
Full textAbstract:
Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.
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Amiruddin, Nadzirah, Pek-Lan Chan, Norazah Azizi, Priscilla Elizabeth Morris, Kuang-Lim Chan, Pei Wen Ong, Rozana Rosli, et al. "Characterization of Oil Palm Acyl-CoA-Binding Proteins and Correlation of Their Gene Expression with Oil Synthesis." Plant and Cell Physiology 61, no. 4 (December 27, 2019): 735–47. http://dx.doi.org/10.1093/pcp/pcz237.
Full textAbstract:
Abstract Acyl-CoA-binding proteins (ACBPs) are involved in binding and trafficking acyl-CoA esters in eukaryotic cells. ACBPs contain a well-conserved acyl-CoA-binding domain. Their various functions have been characterized in the model plant Arabidopsis and, to a lesser extent, in rice. In this study, genome-wide detection and expression analysis of ACBPs were performed on Elaeis guineensis (oil palm), the most important oil crop in the world. Seven E. guineensis ACBPs were identified and classified into four groups according to their deduced amino acid domain organization. Phylogenetic analysis showed conservation of this family with other higher plants. All seven EgACBPs were expressed in most tissues while their differential expression suggests various functions in specific tissues. For example, EgACBP3 had high expression in inflorescences and stalks while EgACBP1 showed strong expression in leaves. Because of the importance of E. guineensis as an oil crop, expression of EgACBPs was specifically examined during fruit development. EgACBP3 showed high expression throughout mesocarp development, while EgACBP1 had enhanced expression during rapid oil synthesis. In endosperm, both EgACBP1 and EgACBP3 exhibited increased expression during seed development. These results provide important information for further investigations on the biological functions of EgACBPs in various tissues and, in particular, their roles in oil synthesis.
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Manuell, A., M. V. Beligni, K. Yamaguchi, and S. P. Mayfield. "Regulation of chloroplast translation: interactions of RNA elements, RNA-binding proteins and the plastid ribosome." Biochemical Society Transactions 32, no. 4 (August 1, 2004): 601–5. http://dx.doi.org/10.1042/bst0320601.
Full textAbstract:
Chloroplast gene expression is primarily controlled during the translation of plastid mRNAs into proteins, and genetic studies have identified cis-acting RNA elements and trans-acting protein factors required for chloroplast translation. Biochemical analysis has identified both general and specific mRNA-binding proteins as components of the regulation of chloroplast translation, and has revealed that chloroplast translation is related to bacterial translation but is more complex. Utilizing proteomic and bioinformatic analyses, we have identified the proteins that function in chloroplast translation, including a complete set of chloroplast ribosomal proteins, and homologues of the 70 S initiation, elongation and termination factors. These analyses show that the translational apparatus of chloroplasts is related to that of bacteria, but has adopted a number of eukaryotic mechanisms to facilitate and regulate chloroplast translation.
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Das, Anish, Qing Zhang, Jennifer B. Palenchar, Bithi Chatterjee, George A. M. Cross, and Vivian Bellofatto. "Trypanosomal TBP Functions with the Multisubunit Transcription Factor tSNAP To Direct Spliced-Leader RNA Gene Expression." Molecular and Cellular Biology 25, no. 16 (August 15, 2005): 7314–22. http://dx.doi.org/10.1128/mcb.25.16.7314-7322.2005.
Full textAbstract:
ABSTRACT Protein-coding genes of trypanosomes are mainly transcribed polycistronically and cleaved into functional mRNAs in a process that requires trans splicing of a capped 39-nucleotide RNA derived from a short transcript, the spliced-leader (SL) RNA. SL RNA genes are individually transcribed from the only identified trypanosome RNA polymerase II promoter. We have purified and characterized a sequence-specific SL RNA promoter-binding complex, tSNAPc, from the pathogenic parasite Trypanosoma brucei, which induces robust transcriptional activity within the SL RNA gene. Two tSNAPc subunits resemble essential components of the metazoan transcription factor SNAPc, which directs small nuclear RNA transcription. A third subunit is unrelated to any eukaryotic protein and identifies tSNAPc as a unique trypanosomal transcription factor. Intriguingly, the unusual trypanosome TATA-binding protein (TBP) tightly associates with tSNAPc and is essential for SL RNA gene transcription. These findings provide the first view of the architecture of a transcriptional complex that assembles at an RNA polymerase II-dependent gene promoter in a highly divergent eukaryote.
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Michelotti, G. A., E. F. Michelotti, A. Pullner, R. C. Duncan, D. Eick, and D. Levens. "Multiple single-stranded cis elements are associated with activated chromatin of the human c-myc gene in vivo." Molecular and Cellular Biology 16, no. 6 (June 1996): 2656–69. http://dx.doi.org/10.1128/mcb.16.6.2656.
Full textAbstract:
Transcription activation and repression of eukaryotic genes are associated with conformational and topological changes of the DNA and chromatin, altering the spectrum of proteins associated with an active gene. Segments of the human c-myc gene possessing non-B structure in vivo located with enzymatic and chemical probes. Sites hypertensive to cleavage with single-strand-specific S1 nuclease or the single-strand-selective agent potassium permanganate included the major promoters P1 and P2 as well as the far upstream sequence element (FUSE) and CT elements, which bind, respectively, the single-strand-specific factors FUSE-binding protein and heterogeneous nuclear ribonucleoprotein K in vitro. Active and inactive c-myc genes yielded different patterns of S1 nuclease and permanganate sensitivity, indicating alternative chromatin configurations of active and silent genes. The melting of specific cis elements of active c-myc genes in vivo suggested that transcriptionally associated torsional strain might assist strand separation and facilitate factor binding. Therefore, the interaction of FUSE-binding protein and heterogeneous nuclear ribonucleoprotein K with supercoiled DNA was studied. Remarkably, both proteins recognize their respective elements torsionally strained but not as liner duplexes. Single-strand- or supercoil-dependent gene regulatory proteins may directly link alterations in DNA conformation and topology with changes in gene expression.
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Laurent, B. C., X. Yang, and M. Carlson. "An essential Saccharomyces cerevisiae gene homologous to SNF2 encodes a helicase-related protein in a new family." Molecular and Cellular Biology 12, no. 4 (April 1992): 1893–902. http://dx.doi.org/10.1128/mcb.12.4.1893.
Full textAbstract:
The Saccharomyces cerevisiae SNF2 gene affects the expression of many diversely regulated genes and has been implicated in transcriptional activation. We report here the cloning and characterization of STH1, a gene that is homologous to SNF2. STH1 is essential for mitotic growth and is functionally distinct from SNF2. A bifunctional STH1-beta-galactosidase protein is located in the nucleus. The predicted 155,914-Da STH1 protein is 72% identical to SNF2 over 661 amino acids and 46% identical over another stretch of 66 amino acids. Both STH1 and SNF2 contain a putative nucleoside triphosphate-binding site and sequences resembling the consensus helicase motifs. The large region of homology shared by STH1 and SNF2 is conserved among other eukaryotic proteins, and STH1 and SNF2 appear to define a novel family of proteins related to helicases.
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Laurent, B. C., X. Yang, and M. Carlson. "An essential Saccharomyces cerevisiae gene homologous to SNF2 encodes a helicase-related protein in a new family." Molecular and Cellular Biology 12, no. 4 (April 1992): 1893–902. http://dx.doi.org/10.1128/mcb.12.4.1893-1902.1992.
Full textAbstract:
The Saccharomyces cerevisiae SNF2 gene affects the expression of many diversely regulated genes and has been implicated in transcriptional activation. We report here the cloning and characterization of STH1, a gene that is homologous to SNF2. STH1 is essential for mitotic growth and is functionally distinct from SNF2. A bifunctional STH1-beta-galactosidase protein is located in the nucleus. The predicted 155,914-Da STH1 protein is 72% identical to SNF2 over 661 amino acids and 46% identical over another stretch of 66 amino acids. Both STH1 and SNF2 contain a putative nucleoside triphosphate-binding site and sequences resembling the consensus helicase motifs. The large region of homology shared by STH1 and SNF2 is conserved among other eukaryotic proteins, and STH1 and SNF2 appear to define a novel family of proteins related to helicases.
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Clerch, L. B., A. Wright, D. J. Chung, and D. Massaro. "Early divergent lung antioxidant enzyme expression in response to lipopolysaccharide." American Journal of Physiology-Lung Cellular and Molecular Physiology 271, no. 6 (December 1, 1996): L949—L954. http://dx.doi.org/10.1152/ajplung.1996.271.6.l949.
Full textAbstract:
Lipopolysaccharide (LPS), a component of the cell wall of Gram-negative bacteria, interacts with eukaryotic cells, causing changes in gene expression and a rapid increase in the formation of superoxide and H2O2. We now report that, within 6 h of treating rats with LPS, there was a divergent response in the lung of manganese superoxide dismutase (Mn-SOD) and catalase expression without a change in expression of copper-zinc superoxide dismutase or glutathione peroxidase. The activity and mRNA concentration of Mn-SOD increased during the time catalase mRNA concentration and activity decreased. These divergent changes and activation of nuclear factor-kappa B (NF-kappa B) were preceded by a fall, 1 h after LPS treatment, in the RNA binding activity of two redox-sensitive proteins: Mn-SOD RNA binding protein and catalase RNA binding protein. The rapid onset of these changes, the bacteriostatic properties of H2O2, and the signaling function of NF-kappa B suggest that the divergent expression of Mn-SOD and catalase is a coordinated component of the acute phase reaction to bacterial invasion.
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Naro, Chiara, and Claudio Sette. "Phosphorylation-Mediated Regulation of Alternative Splicing in Cancer." International Journal of Cell Biology 2013 (2013): 1–15. http://dx.doi.org/10.1155/2013/151839.
Full textAbstract:
Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted bycis-acting RNA sequence elements andtrans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.
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Williams, Simon C., Erin K. Patterson, Nancy L. Carty, John A. Griswold, Abdul N. Hamood, and Kendra P. Rumbaugh. "Pseudomonas aeruginosa Autoinducer Enters and Functions in Mammalian Cells." Journal of Bacteriology 186, no. 8 (April 15, 2004): 2281–87. http://dx.doi.org/10.1128/jb.186.8.2281-2287.2004.
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ABSTRACT Quorum sensing (QS) is a cell density-dependent signaling mechanism used by many bacteria to control gene expression. Several recent reports indicate that the signaling molecules (autoinducers) that mediate QS in Pseudomonas aeruginosa may also modulate gene expression in host cells; however, the mechanisms are largely unknown. Here we show that two P. aeruginosa autoinducers, N-3-oxododecanoyl-homoserine lactone and N-butyryl-homoserine lactone, can both enter eukaryotic cells and activate artificial chimeric transcription factors based on their cognate transcriptional activators, LasR and RhlR, respectively. The autoinducers promoted nuclear localization of chimeric proteins containing the full LasR or RhlR coding region, and the LasR-based proteins were capable of activating transcription of a LasR-dependent luciferase gene. Responsiveness to autoinducer required the N-terminal autoinducer-binding domains of LasR and RhlR. Truncated proteins consisting of only the C-terminal helix-turn-helix DNA-binding domains of both proteins attached to a nuclear localization signal efficiently translocated to the nucleus in the absence of autoinducer, and truncated LasR-based proteins functioned as constitutively active transcription factors. Chimeric LasR proteins were only activated by their cognate autoinducer ligand and not by N-butyryl-l-homoserine lactone. These data provide evidence that autoinducer molecules from human pathogens can enter mammalian cells and suggest that autoinducers may influence gene expression in host cells by interacting with and activating as-yet-unidentified endogenous proteins.
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Tahmasebi, Soroush, Seyed Mehdi Jafarnejad, Ingrid S. Tam, Thomas Gonatopoulos-Pournatzis, Edna Matta-Camacho, Yoshinori Tsukumo, Akiko Yanagiya, et al. "Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2." Proceedings of the National Academy of Sciences 113, no. 44 (October 24, 2016): 12360–67. http://dx.doi.org/10.1073/pnas.1615540113.
Full textAbstract:
Translational control of gene expression plays a key role during the early phases of embryonic development. Here we describe a transcriptional regulator of mouse embryonic stem cells (mESCs), Yin-yang 2 (YY2), that is controlled by the translation inhibitors, Eukaryotic initiation factor 4E-binding proteins (4E-BPs). YY2 plays a critical role in regulating mESC functions through control of key pluripotency factors, including Octamer-binding protein 4 (Oct4) and Estrogen-related receptor-β (Esrrb). Importantly, overexpression of YY2 directs the differentiation of mESCs into cardiovascular lineages. We show that the splicing regulator Polypyrimidine tract-binding protein 1 (PTBP1) promotes the retention of an intron in the 5′-UTR of Yy2 mRNA that confers sensitivity to 4E-BP–mediated translational suppression. Thus, we conclude that YY2 is a major regulator of mESC self-renewal and lineage commitment and document a multilayer regulatory mechanism that controls its expression.
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Albers, S. V., M. Jonuscheit, S. Dinkelaker, T. Urich, A. Kletzin, R. Tampé, A. J. M. Driessen, and C. Schleper. "Production of Recombinant and Tagged Proteins in the Hyperthermophilic Archaeon Sulfolobus solfataricus." Applied and Environmental Microbiology 72, no. 1 (January 2006): 102–11. http://dx.doi.org/10.1128/aem.72.1.102-111.2006.
Full textAbstract:
ABSTRACT Many systems are available for the production of recombinant proteins in bacterial and eukaryotic model organisms, which allow us to study proteins in their native hosts and to identify protein-protein interaction partners. In contrast, only a few transformation systems have been developed for archaea, and no system for high-level gene expression existed for hyperthermophilic organisms. Recently, a virus-based shuttle vector with a reporter gene was developed for the crenarchaeote Sulfolobus solfataricus, a model organism of hyperthermophilic archaea that grows optimally at 80°C (M. Jonuscheit, E. Martusewitsch, K. M. Stedman, and C. Schleper, Mol. Microbiol. 48:1241-1252, 2003). Here we have refined this system for high-level gene expression in S. solfataricus with the help of two different promoters, the heat-inducible promoter of the major chaperonin, thermophilic factor 55, and the arabinose-inducible promoter of the arabinose-binding protein AraS. Functional expression of heterologous and homologous genes was demonstrated, including production of the cytoplasmic sulfur oxygenase reductase from Acidianus ambivalens, an Fe-S protein of the ABC class from S. solfataricus, and two membrane-associated ATPases potentially involved in the secretion of proteins. Single-step purification of the proteins was obtained via fused His or Strep tags. To our knowledge, these are the first examples of the application of an expression vector system to produce large amounts of recombinant and also tagged proteins in a hyperthermophilic archaeon.
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Nocero, M., T. Isshiki, M. Yamamoto, and C. S. Hoffman. "Glucose repression of fbp1 transcription of Schizosaccharomyces pombe is partially regulated by adenylate cyclase activation by a G protein alpha subunit encoded by gpa2 (git8)." Genetics 138, no. 1 (September 1, 1994): 39–45. http://dx.doi.org/10.1093/genetics/138.1.39.
Full textAbstract:
Abstract In the fission yeast Schizosaccharomyces pombe, genetic studies have identified genes that are required for glucose repression of fbp1 transcription. The git2 gene, also known as cyr1, encodes adenylate cyclase. Adenylate cyclase converts ATP into the second messenger cAMP as part of many eukaryotic signal transduction pathways. The git1, git3, git5, git7, git8 and git10 genes act upstream of adenylate cyclase, presumably encoding an adenylate cyclase activation pathway. In mammalian cells, adenylate cyclase enzymatic activity is regulated by heterotrimeric guanine nucleotide-binding proteins (G proteins). In the budding yeast Saccharomyces cerevisiae, adenylate cyclase enzymatic activity is regulated by monomeric, guanine nucleotide-binding Ras proteins. We show here that git8 is identical to the gpa2 gene that encodes a protein homologous to the alpha subunit of a G protein. Mutations in two additional genes, git3 and git5 are suppressed by gpa2+ in high copy number. Furthermore, a mutation in either git3 or git5 has an additive effect in strains deleted for gpa2 (git8), as it significantly increases expression of an fbp1-lacZ reporter gene. Therefore, git3 and git5 appear to act either in concert with or independently from gpa2 (git8) to regulate adenylate cyclase activity.
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Borriello, Giorgia, Veronica Russo, Rubina Paradiso, Marita Georgia Riccardi, Daniela Criscuolo, Gaetano Verde, Rosangela Marasco, Paolo Vincenzo Pedone, Giorgio Galiero, and Ilaria Baglivo. "Different Impacts of MucR Binding to the babR and virB Promoters on Gene Expression in Brucella abortus 2308." Biomolecules 10, no. 5 (May 19, 2020): 788. http://dx.doi.org/10.3390/biom10050788.
Full textAbstract:
The protein MucR from Brucella abortus has been described as a transcriptional regulator of many virulence genes. It is a member of the Ros/MucR family comprising proteins that control the expression of genes important for the successful interaction of α-proteobacteria with their eukaryotic hosts. Despite clear evidence of the role of MucR in repressing virulence genes, no study has been carried out so far demonstrating the direct interaction of this protein with the promoter of its target gene babR encoding a LuxR-like regulator repressing virB genes. In this study, we show for the first time the ability of MucR to bind the promoter of babR in electrophoretic mobility shift assays demonstrating a direct role of MucR in repressing this gene. Furthermore, we demonstrate that MucR can bind the virB gene promoter. Analyses by RT-qPCR showed no significant differences in the expression level of virB genes in Brucella abortus CC092 lacking MucR compared to the wild-type Brucella abortus strain, indicating that MucR binding to the virB promoter has little impact on virB gene expression in B. abortus 2308. The MucR modality to bind the two promoters analyzed supports our previous hypothesis that this is a histone-like protein never found before in Brucella.
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Falb, D., and T. Maniatis. "Drosophila transcriptional repressor protein that binds specifically to negative control elements in fat body enhancers." Molecular and Cellular Biology 12, no. 9 (September 1992): 4093–103. http://dx.doi.org/10.1128/mcb.12.9.4093.
Full textAbstract:
Expression of the Drosophila melanogaster Adh gene in adults requires a fat body-specific enhancer called the Adh adult enhancer (AAE). We have identified a protein in Drosophila nuclear extracts that binds specifically to a site within the AAE (adult enhancer factor 1 [AEF-1]). In addition, we have shown that AEF-1 binds specifically to two other Drosophila fat body enhancers. Base substitutions in the AEF-1 binding site that disrupt AEF-1 binding in vitro result in a significant increase in the level of Adh expression in vivo. Thus, the AEF-1 binding site is a negative regulatory element within the AAE. A cDNA encoding the AEF-1 protein was isolated and shown to act as a repressor of the AAE in cotransfection studies. The AEF-1 protein contains four zinc fingers and an alanine-rich sequence. The latter motif is found in other eukaryotic proteins known to be transcriptional repressors.
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Falb, D., and T. Maniatis. "Drosophila transcriptional repressor protein that binds specifically to negative control elements in fat body enhancers." Molecular and Cellular Biology 12, no. 9 (September 1992): 4093–103. http://dx.doi.org/10.1128/mcb.12.9.4093-4103.1992.
Full textAbstract:
Expression of the Drosophila melanogaster Adh gene in adults requires a fat body-specific enhancer called the Adh adult enhancer (AAE). We have identified a protein in Drosophila nuclear extracts that binds specifically to a site within the AAE (adult enhancer factor 1 [AEF-1]). In addition, we have shown that AEF-1 binds specifically to two other Drosophila fat body enhancers. Base substitutions in the AEF-1 binding site that disrupt AEF-1 binding in vitro result in a significant increase in the level of Adh expression in vivo. Thus, the AEF-1 binding site is a negative regulatory element within the AAE. A cDNA encoding the AEF-1 protein was isolated and shown to act as a repressor of the AAE in cotransfection studies. The AEF-1 protein contains four zinc fingers and an alanine-rich sequence. The latter motif is found in other eukaryotic proteins known to be transcriptional repressors.
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Espeso, Eduardo A., and Herbert N. Arst. "On the Mechanism by which Alkaline pH Prevents Expression of an Acid-Expressed Gene." Molecular and Cellular Biology 20, no. 10 (May 15, 2000): 3355–63. http://dx.doi.org/10.1128/mcb.20.10.3355-3363.2000.
Full textAbstract:
ABSTRACT Previous work has shown that zinc finger transcription factor PacC mediates the regulation of gene expression by ambient pH in the fungusAspergillus nidulans. This regulation ensures that the syntheses of molecules functioning in the external environment, such as permeases, secreted enzymes, and exported metabolites, are tailored to the pH of the growth environment. A direct role for PacC in activating the expression of an alkaline-expressed gene has previously been demonstrated, but the mechanism by which alkaline ambient pH prevents the expression of any eukaryotic acid-expressed gene has never been reported. Here we show that a double PacC binding site in the promoter of the acid-expressed gabA gene, encoding γ-aminobutyrate (GABA) permease, overlaps the binding site for the transcriptional activator IntA, which mediates ω-amino acid induction. Using bacterially expressed fusion proteins, we have shown that PacC competes with IntA for DNA binding in vitro at this site. Thus, PacC repression of GABA permease synthesis is direct and occurs by blocking induction. A swap of IntA sites between promoters for gabA andamdS, a gene not subject to pH regulation, makesgabA expression pH independent and amdS acid expressed.
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Stronach, B. E., S. E. Siegrist, and M. C. Beckerle. "Two muscle-specific LIM proteins in Drosophila." Journal of Cell Biology 134, no. 5 (September 1, 1996): 1179–95. http://dx.doi.org/10.1083/jcb.134.5.1179.
Full textAbstract:
The LIM domain defines a zinc-binding motif found in a growing number of eukaryotic proteins that regulate cell growth and differentiation during development. Members of the cysteine-rich protein (CRP) family of LIM proteins have been implicated in muscle differentiation in vertebrates. Here we report the identification and characterization of cDNA clones encoding two members of the CRP family in Drosophila, referred to as muscle LIM proteins (Mlp). Mlp60A encodes a protein with a single LIM domain linked to a glycine-rich region. Mlp84B encodes a protein with five tandem LIM-glycine modules. In the embryo, Mlp gene expression is spatially restricted to somatic, visceral, and pharyngeal muscles. Within the somatic musculature, Mlp84B transcripts are enriched at the terminal ends of muscle fibers, whereas Mlp60A transcripts are found throughout the muscle fibers. The distributions of the Mlp60A and Mlp84B proteins mirror their respective mRNA localizations, with Mlp84B enrichment occurring at sites of muscle attachment. Northern blot analysis revealed that Mlp gene expression is developmentally regulated, showing a biphasic pattern over the course of the Drosophila life cycle. Peaks of expression occur late in embryogenesis and during metamorphosis, when the musculature is differentiating. Drosophila Mlp60A and Mlp84B, like vertebrate members of the CRP family, have the ability to associate with the actin cytoskeleton when expressed in rat fibroblast cells. The temporal expression and spatial distribution of muscle LIM proteins in Drosophila are consistent with a role for Mlps in myogenesis, late in the differentiation pathway.
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Ray, Swagat, Pól Ó. Catnaigh, and Emma C. Anderson. "Post-transcriptional regulation of gene expression by Unr." Biochemical Society Transactions 43, no. 3 (June 1, 2015): 323–27. http://dx.doi.org/10.1042/bst20140271.
Full textAbstract:
Unr (upstream of N-ras) is a eukaryotic RNA-binding protein that has a number of roles in the post-transcriptional regulation of gene expression. Originally identified as an activator of internal initiation of picornavirus translation, it has since been shown to act as an activator and inhibitor of cellular translation and as a positive and negative regulator of mRNA stability, regulating cellular processes such as mitosis and apoptosis. The different post-transcriptional functions of Unr depend on the identity of its mRNA and protein partners and can vary with cell type and changing cellular conditions. Recent high-throughput analyses of RNA–protein interactions indicate that Unr binds to a large subset of cellular mRNAs, suggesting that Unr may play a wider role in translational responses to cellular signals than previously thought.
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Belostotsky, Dmitry A. "Unexpected Complexity of Poly(A)-Binding Protein Gene Families in Flowering Plants: Three Conserved Lineages That Are at Least 200 Million Years Old and Possible Auto- and Cross-Regulation." Genetics 163, no. 1 (January 1, 2003): 311–19. http://dx.doi.org/10.1093/genetics/163.1.311.
Full textAbstract:
Abstract Eukaryotic poly(A)-binding protein (PABP) is a ubiquitous, essential factor involved in mRNA biogenesis, translation, and turnover. Most eukaryotes examined have only one or a few PABPs. In contrast, eight expressed PABP genes are present in Arabidopsis thaliana. These genes fall into three distinct classes, based on highly concordant results of (i) phylogenetic analysis of the amino acid sequences of the encoded proteins, (ii) analysis of the intron number and placement, and (iii) surveys of gene expression patterns. Representatives of each of the three classes also exist in the rice genome, suggesting that the diversification of the plant PABP genes has occurred prior to the split of monocots and dicots ≥200 MYA. Experiments with the recombinant PAB3 protein suggest the possibility of a negative feedback regulation, as well as of cross-regulation between the Arabidopsis PABPs that belong to different classes but are simultaneously expressed in the same cell type. Such a high complexity of the plant PABPs might enable a very fine regulation of organismal growth and development at the post-transcriptional level, compared with PABPs of other eukaryotes.