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Relevant bibliographies by topics / Nucleoid Proteins

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Academic literature on the topic 'Nucleoid Proteins'

Author: Grafiati

Published: 6 September 2023

Last updated: 7 September 2023

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Journal articles on the topic "Nucleoid Proteins"

1

Hayat, M. A., and Denise A. Mancarella. "Nucleoid proteins." Micron 26, no. 5 (January 1995): 461–80. http://dx.doi.org/10.1016/0968-4328(95)00022-4.

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Oetke, Svenja, Axel J. Scheidig, and Karin Krupinska. "WHIRLY1 of Barley and Maize Share a PRAPP Motif Conferring Nucleoid Compaction." Plant and Cell Physiology 63, no. 2 (November 11, 2021): 234–47. http://dx.doi.org/10.1093/pcp/pcab164.

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Abstract WHIRLY1 in barley was shown to be a major architect of plastid nucleoids. Its accumulation in cells of Escherichia coli coincided with an induction of nucleoid compaction and growth retardation. While WHIRLY1 of maize had similar effects on E. coli cells, WHIRLY1 proteins of Arabidopsis and potato as well as WHIRLY2 proteins had no impact on nucleoid compaction in E. coli. By mutagenesis of HvWHIRLY1 the PRAPP motif at the N-terminus preceding the highly conserved WHIRLY domain was identified to be responsible for the nucleoid compacting activity of HvWHIRLY1 in bacteria. This motif is found in WHIRLY1 proteins of most members of the Poaceae family, but neither in the WHIRLY2 proteins of the family nor in any WHIRLY protein of eudicot species such as Arabidopsis thaliana. This finding indicates that a subset of the monocot WHIRLY1 proteins has acquired a specific function as nucleoid compacters by sequence variation in the N-terminal part preceding the conserved WHIRLY domain and that in different groups of higher plants the compaction of nucleoids is mediated by other proteins.

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Dillon, Shane C., and Charles J. Dorman. "Bacterial nucleoid-associated proteins, nucleoid structure and gene expression." Nature Reviews Microbiology 8, no. 3 (February 8, 2010): 185–95. http://dx.doi.org/10.1038/nrmicro2261.

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Driessen, Rosalie P. C., and Remus Th Dame. "Nucleoid-associated proteins in Crenarchaea." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 116–21. http://dx.doi.org/10.1042/bst0390116.

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Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.

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Ragkousi, Katerina, Ann E. Cowan, Margery A. Ross, and Peter Setlow. "Analysis of Nucleoid Morphology during Germination and Outgrowth of Spores of Bacillus Species." Journal of Bacteriology 182, no. 19 (October 1, 2000): 5556–62. http://dx.doi.org/10.1128/jb.182.19.5556-5562.2000.

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ABSTRACT After a few minutes of germination, nucleoids in the great majority of spores of Bacillus subtilis and Bacillus megaterium were ring shaped. The major spore DNA binding proteins, the α/β-type small, acid-soluble proteins (SASP), colocalized to these nucleoid rings early in spore germination, as did the B. megaterium homolog of the major B. subtilis chromosomal protein HBsu. The percentage of ring-shaped nucleoids was decreased in germinated spores with lower levels of α/β-type SASP. As spore outgrowth proceeded, the ring-shaped nucleoids disappeared and the nucleoid became more compact. This change took place after degradation of most of the spores' pool of major α/β-type SASP and was delayed when α/β-type SASP degradation was delayed. Later in spore outgrowth, the shape of the nucleoid reverted to the diffuse lobular shape seen in growing cells.

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K Davies, John. "Control of transcription by nucleoid proteins." Microbiology Australia 27, no. 3 (2006): 112. http://dx.doi.org/10.1071/ma06112.

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Although not confined to a membrane-bound organelle such as the eukaryotic nucleus, the chromosome(s) of bacterial cells are compacted into a DNA-protein complex termed the nucleoid. Many different proteins appear to be associated with the nucleoid, but we understand the function of just a few of these.

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Rimsky, Sylvie, and Andrew Travers. "Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins." Current Opinion in Microbiology 14, no. 2 (April 2011): 136–41. http://dx.doi.org/10.1016/j.mib.2011.01.003.

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McLeod, Sarah M., and Reid C. Johnson. "Control of transcription by nucleoid proteins." Current Opinion in Microbiology 4, no. 2 (April 2001): 152–59. http://dx.doi.org/10.1016/s1369-5274(00)00181-8.

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Miyakawa, Isamu, Akira Okamuro, Slavomir Kinsky, Katarina Visacka, Lubomir Tomaska, and Jozef Nosek. "Mitochondrial nucleoids from the yeast Candida parapsilosis: expansion of the repertoire of proteins associated with mitochondrial DNA." Microbiology 155, no. 5 (May 1, 2009): 1558–68. http://dx.doi.org/10.1099/mic.0.027474-0.

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Molecules of mitochondrial DNA (mtDNA) are packed into nucleic acid–protein complexes termed mitochondrial nucleoids (mt-nucleoids). In this study, we analysed mt-nucleoids of the yeast Candida parapsilosis, which harbours a linear form of the mitochondrial genome. To identify conserved as well as specific features of mt-nucleoids in this species, we employed two strategies for analysis of their components. First, we investigated the protein composition of mt-nucleoids isolated from C. parapsilosis mitochondria, determined N-terminal amino acid sequences of 14 proteins associated with the mt-nucleoids and identified corresponding genes. Next, we complemented the list of mt-nucleoid components with additional candidates identified in the complete genome sequence of C. parapsilosis as homologues of Saccharomyces cerevisiae mt-nucleoid proteins. Our approach revealed several known mt-nucleoid proteins as well as additional components that expand the repertoire of proteins associated with these cytological structures. In particular, we identified and purified the protein Gcf1, which is abundant in the mt-nucleoids and exhibits structural features in common with the mtDNA packaging protein Abf2 from S. cerevisiae. We demonstrate that Gcf1p co-localizes with mtDNA, has DNA-binding activity in vitro, and is able to stabilize mtDNA in the S. cerevisiae Δabf2 mutant, all of which points to a role in the maintenance of the C. parapsilosis mitochondrial genome. Importantly, in contrast to Abf2p, in silico analysis of Gcf1p predicted the presence of a coiled-coil domain and a single high-mobility group (HMG) box, suggesting that it represents a novel type of mitochondrial HMG protein.

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Zhao, Haiqing. "Self-assembled nucleoid proteins scaffold bacterial DNA." Biophysical Journal 120, no. 5 (March 2021): 754–55. http://dx.doi.org/10.1016/j.bpj.2021.02.001.

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Dissertations / Theses on the topic "Nucleoid Proteins"

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Boyd-Kirkup, Jerome Douglas. "Characterising putative mammalian mitochondrial nucleoid proteins." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608921.

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Cao, Wei, and 曹威. "Structural studies of two nucleoid-associated proteins : histone-like nucleoid-structuring protein H-NS and α-hemolysin expression-modulating protein Hha." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208420.

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In prokaryotic cells, the nucleoid contains almost all the genetic materials as well as a number of nucleoid structuring factors. The nucleoid-associated proteins (NAPs) are known to have low molecular weight and the ability to form dimer or oligomer, and most of them can bind to DNA for regulation of gene expression. The Histone-like nucleoid structuring protein H-NS, well studied as one of the NAPs, acts as a global transcriptional repressor. It has independent functional N-terminal domain for oligomerization and C-terminal domain for DNA binding, joined by a flexible linker. H-NS contributes to horizontal genes transfer and responses to environmental factors like temperature or pH, which would influence the oligomerization ability of H-NS and DNA binding. The α-hemolysin expression-modulating protein Hha is a member of the Hha-YmoA family, expressed only in Gram-negative Enterobacteriaceae as a modulator of virulence factors expression. In E. coli, the binding of Hha to H-NS can modulate the expression of α-hemolysin operon, which is essential for the H-NS-regulated gene expression. In this study, both Hha and the oligomerization domain of H-NS (H-NS64) were expressed in E. coli and the purified proteins were crystallized. The Hha crystals diffracted to 2.2 Å; and the HhA/H-NS complex crystals diffracted to 1.8 Å. Both structures were successfully determined by molecular replacement method. Comparisons were carried out between the published apo Hha and H-NS structures and our complex structures. The structures showed the binding details between H-NS and Hha and also conformational changes of each protein, which may indicate how Hha regulates gene expressions through H-NS.
published_or_final_version
Physiology
Master
Master of Philosophy

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Bradshaw, Elizabeth Helen. "Nucleoid-associated proteins of Streptomyces coelicolor : discovery and functions." Thesis, University of East Anglia, 2013. https://ueaeprints.uea.ac.uk/44850/.

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The regulation of gene expression from biosynthetic gene clusters is a key concern in natural product discovery as these clusters are often transcriptionally silent (“cryptic”) under normal laboratory conditions, making the initial characterisation and heterologous expression of the products they encode problematic. The role of the architectural nucleoid-associated proteins (NAPs) in regulation of the expression of these products has been neglected within the Actinomycetes. NAPs are small, highly abundant proteins which govern both gene expression and nucleoid structure on a genome-wide scale. A method for surveying the proteome of the S. coelicolor nucleoid was developed which generated a list of 25 proteins with a high probability of being NAPs. This list included known NAPs such as HupA, HupS, Lsr2 and sIHF and the known global regulators CRP and BldD, as well as a number of interesting novel NAP candidates from a variety of protein classes suitable for further investigation. One of these proteins, SCO5592, was investigated as a candidate global RNA-binding regulator. It was found to comprise a KH domain with an N-terminal extension and formed oligomers of 10 - 12 subunits in solution. The mutant phenotypes of both S. coelicolor paralogs of HU (HupA and HupS) were examined and showed opposite effects on growth, spore formation and actinorhodin production. The mutant phenotypes of both S. coelicolor paralogs of the H-NS-like proteins Lsr2 (SCO3375 and SCO4076) were milder and showed a greater degree of overlap than the HU mutants, however both showed a moderate abnormality in spore morphology, suggesting that they have a role in spore nucleoid segregation. Phylogenetic analysis of the HU and Lsr2 proteins revealed that the lysine-rich tail domain of HupS was acquired after the HupA and HupS core domains had begun to diverge and that lysine-rich sequences have evolved multiple times.

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Ono, Shusuke. "The biophysical characterisation of the Enterobacterial nucleoid proteins H-NS and StpA." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1445757/.

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H-NS is a major protein component of the nucleoid, found in many Gram-negative bacterial species. H-NS is involved in the modulation of expression of a wide range of genes, as well as contributing towards nucleoid structure. There are two structur ally independent domains in H-NS, one involved in protein-protein interactions (the N-terminal oligomerisation domain), and the other involved in DNA-binding (C- terminal). These are joined via a flexible linker sequence. H-NS both self-associates and interacts with other nucleoid-associated proteins to form specific oligomeric complexes that bind DNA, allowing a precise level of control in gene expression. The protein StpA, a paralogue of H-NS with 58% sequence identity, was originally identified by its RNA chaperone activity. Subsequent studies have suggested struc tural similarities between H-NS and StpA, with a degree of overlap in their function in vivo. StpA self-associates in a similar manner to H-NS, and has been shown to in teract with H-NS. Whilst small differences in the properties of H-NS and StpA have been identified, no clear distinctions have been made between the two proteins. This work investigates several key issues regarding the properties of the StpA protein. A number of biophysical techniques have been used to investigate the interaction of H-NS and StpA. The results of these experiments are consistent with a model whereby StpA self-associates via a 'head-to-taif interaction. Furthermore, StpA ex hibits a different affinity and kinetic behaviour of association in comparison to H-NS. The properties of self-association and interaction of H-NS and StpA are fully consis tent with studies that highlight the intimate relationship between the two proteins in vivo. Two independent structures of the N-terminal oligomerisation domain of H-NS have been reported. These structures were derived at different temperatures (i.e. 25 C and 35 C). To investigate the implications of these model structures on the thermoregula tory functions of H-NS, the oligomerisation properties of H-NS were investigated over a temperature range. Both the oligomerisation and DNA-binding properties of H-NS were found to vary within a physiologically relevant range of temperatures. To characterise the interaction of StpA with DNA and to allow comparison with H- NS, the solution structure of the C-terminal domain of StpA was determined, solved by NMR. The interaction of DNA with this domain was characterised using both NMR and calorimetric methods. Statement The work described in this thesis was carried out in the Department of Biochemistry and Molecular Biology, University College London between 2000 and 2004. The NMR spectra were acquired with the assistance of Dr. M. Williams, Dr. R. Harris or J. Taylor. All experiments involving H-NS 1.39 were conducted with the assistance of T. Olsson. All other work was carried out by the author. This project was funded by the Biotechnology and Biological Sciences Research Council (BBSRC). Some of the work detailed in this thesis has been published elsewhere: Esposito, D., Petrovic, A., Harris, R., Ono, S., Eccleston, J. F., Mbabaali, A., Haq, I., Higgins, C. F., Hinton, J. C, Driscoll, P. C, and Ladbury, J. E. (2002) H-NS oli gomerisation domain structure reveals the mechanism for high order self-association of the intact protein. J Mol. Biol. 324, 841-850.

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Mahajan, Shikha. "Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4139.

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Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various diseases. An important challenge in modern protein profiling approaches is to reduce the complexity of the samples by limiting the number of proteins that need to be evaluated for distinction in the expression between normal and deceased cells. In this research, an affinity based approach for the enrichment of nucleotide and nucleoside binding proteins from a complex cell proteome has been developed. To achieve this goal, new N6-biotinylated-8-azido-adenosine probes (AdoRs) have been designed and synthesized to photolabel the nucleotide and nucleoside binding proteins. These probes contain a reactive group that forms a covalent bond with the target proteins, as well as a biotin tag for affinity enrichment using avidin chromatography. Further, a mass spectrometric protein profiling approach is employed to quantitatively identify small variations in expression of nucleoside and nucleotide binding proteins in samples of interest. Mouse neuroblastoma N18TG2 cell proteome has been used as a model system for the development of the LC-MS/MS based proteomic analysis of these affinity enriched protein fractions. Upon enrichment, the photolabeled proteome exhibited an approximately four-fold abundance of nucleoside and nucleotide binding proteins over nonlabeled proteome. The approach was extended to compare the proteomic profiles of nucleotide and nucleoside binding proteins in cancerous (Hey) and non-cancerous (T-80) human ovarian cell proteome. Certain proteins that were not detected in cell lysate were also identified in labeled proteome, thereby demonstrating the strength of our approach in enriching low abundant proteins. To substantiate the qualitative analysis, we have employed the Stable Isotope Labeling in Amino Acid Cell Culture (SILAC) for the quantitative study of the protein expression in cancerous and non-cancerous human ovarian cells. A modest panel of proteins with differential expressions in these cell lines was identified, a few of which have been correlated to various forms of cancer. Vimentin, stress induced phosphoprotein-1, and heat shock protein 90 that were identified to have altered expressions in these cell lines are among some of the proteins associated with ovarian cancer.

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Johansson, Monika. "The role of nucleoside diphosphate kinase in plant mitochondria /." Uppsala : Dept. of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/200674.pdf.

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Wallis, Anne Elizabeth. "Identification of Leishmania genes encoding proteins containing tandemly repeating peptides." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/29447.

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In order to identify Leishmania proteins which may be immunologically relevant or may play a role in interactions between Leishmania and its mammalian host, a Leishmania major genomic DNA library was constructed in the vector λgt11 and screened with antibodies raised to Leishmania major promastigote membranes. Two recombinant DNA clones were identified which encoded repetitive sequences (Clone 20 and Clone 39). Clone 20 encoded a repetitive peptide of 14 amino acids and clone 39 encoded an unrelated repetitive peptide of 10 amino acids. Analysis of one of these clones, Clone 20, indicated that there were two RNA transcripts of 9500 and 5200 nucleotides expressed which corresponded to this clone in Leishmania major and Leishmania donovani and this expression was not stage-specific. The results of genomic DNA analysis and isolation of additional clones encoding Clone 20 sequences indicated that there were two genes which corresponded to Clone 20 in both Leishmania major and Leishmania donovani and that these genes differed from one another with respect to the number of repeats which they contained. Antibodies against the fusion protein produced by Clone 20 recognized a series of Leishmania major proteins of apparent mol wt 250,000. Analysis of Clone 39 indicated that there was a single transcript of 7500 nucleotides expressed which corresponded to this clone in both Leishmania major and Leishmania donovani and that there was a single gene (or two identical genes) which encoded this transcript. The genomes of many protozoan parasites exhibit a high degree of plasticity with respect to chromosome size and number. The presence of highly repetitive regions within their DNA may be involved in maintaining this plasticity, allowing the parasite to evolve rapidly under selective pressure. Repetitive regions have been identified within many Plasmodia antigens and have been implicated in the ability of this parasite to evade the host immune system. The presence of Leishmania genes encoding proteins containing tandemly repeating peptides may indicate that these proteins play a similar role in evading the host immune system during the course of Leishmania infections. The possible evolution and functions of repetitive proteins in protozoan parasites is discussed.
Medicine, Faculty of
Medical Genetics, Department of
Graduate

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8

Hamilton, Tatyana. "Protein-nucleic acid interactions of Wilms' tumor and TFIIIA zinc finger proteins." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ34266.pdf.

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Bramble, Sharyl Elizabeth. "Guanine nucleotide binding properties and attempted immunopurification of ras protein from dictyostelium discoideum." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/26172.

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One purpose of this study was to determine whether the ras protein from Dictyostelium discoideum (p23) binds guanine nucleotides like the ras proteins from mammals (p21) and yeast. The other purpose of this investigation was to purify or enrich for p23ras from D. discoideum by immunoaffinity chromatography. A number of different approaches were used to determine guanine nucleotide binding by p23RAS . A simple filter binding assay, binding to Western blots, and photoaffinity labeling all failed to demonstrate specific binding with lysates of D. discoideum cells. In contrast p21RAS from transformed NIH-3T3 cell lysate was successfully photoaffinity labeled in the presence of ³²P-α-guanosine 5¹-triphosphate (GTP) suggesting that the technique had been performed correctly. It was concluded that either p23RAS has a very low affinity for guanine nucleotides such that GTP binding was not detectable in these experiments or that the ras protein from D. discoideum simply does not bind guanine nucleotides. The purification of p23RAS from D. discoideum cells was attempted in order to provide a purified protein preparation for guanine nucleotide binding and for reconstitution studies. An anti-ras monoclonal antibody (Y13-259) was used as the ligand for the immunoaffinity chromatography. This approach was not successful in that the ras protein could not be enriched relative to other proteins because the immunoaffinity columns did not bind p23RAS.
Science, Faculty of
Microbiology and Immunology, Department of
Graduate

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Pérez, González Daniel Cibrán. "Single-molecule studies of nucleic acid folding and nucleic acid-protein interactions." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/12039.

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Nucleic acids and proteins, some of the building blocks of life, are not static structures but highly dynamic entities that need to interact with one another to meet cellular demands. The work presented in this thesis focuses on the application of highly sensitive fluorescence methods, both at ensemble and single-molecule level, to determine the dynamics and structure of specific biomolecular interactions with nanometer resolution and in temporal scales from nanoseconds to minutes, which includes most biologically relevant processes. The main aims of my PhD can be classified in three areas: i) exploring new fluorescent sensors with increased specificity for certain nucleic acid structures; ii) understanding how some of these nucleic acids sense the presence of small molecules in the cellular environment and trigger gene regulation by altering their structure; and iii) understanding how certain molecular machines, such as helicase proteins, are able to unwind the DNA double helix by using chemical energy in the form of ATP hydrolysis.

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Books on the topic "Nucleoid Proteins"

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McDermott, Paul. The nucleoid proteins H-NS and STPA: Structure/function relationships and the modulation of gene expression. Oxford: Oxford Brookes University, 2003.

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A, Rice Phoebe, and Correll Carl C, eds. Protein-nucleic acid interactions: Structural biology. Cambridge: RSC Pub., 2008.

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A, Ducruix, and Giegé R, eds. Crystallization of nucleic acids and proteins: A practical approach. 2nd ed. Oxford: Oxford University Press, 1999.

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1948-, Walker John M., ed. New protein techniques. Clifton, N.J: Humana Press, 1998.

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Bosch, L., B. Kraal, and A. Parmeggiani, eds. The Guanine — Nucleotide Binding Proteins. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-2037-2.

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Brändén, Carl-Ivar. Introduction to protein structure. 2nd ed. New York, NY: Garland Pub., 2009.

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John, Tooze, ed. Introduction to protein structure. New York: Garland Pub., 1991.

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John, Tooze, ed. Introduction to protein structure. 2nd ed. New York: Garland Pub., 1999.

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Lilley, David M. J. 1948-, ed. DNA-protein: Structural interactions. Oxford: IRL Press at Oxford University Press, 1995.

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A, Jurnak Frances, and McPherson Alexander 1944-, eds. Nucleic acids and interactive proteins. New York: Wiley, 1985.

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Book chapters on the topic "Nucleoid Proteins"

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Pul, Ümit, and Rolf Wagner. "Nucleoid-Associated Proteins: Structural Properties." In Bacterial Chromatin, 149–73. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3473-1_8.

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Singh, Parul, and Aswin Sai Narain Seshasayee. "Nucleoid-Associated Proteins: Genome Level Occupancy and Expression Analysis." In The Bacterial Nucleoid, 85–97. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7098-8_8.

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Mehandziska, Sanja, Alexander M. Petrescu, and Georgi Muskhelishvili. "Isolation and Analysis of RNA Polymerase Supramolecular Complex with Associated Proteins." In The Bacterial Nucleoid, 101–16. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7098-8_9.

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van der Valk, Ramon A., Niels Laurens, and Remus T. Dame. "Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins." In The Bacterial Nucleoid, 127–43. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7098-8_11.

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Hégarat, F. Le, V. Salti, and L. Hirschbein. "Characterization of Bacillus subtilis Nucleoid DNA-Binding Proteins." In Proceedings in Life Sciences, 155–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-71266-1_12.

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Spahn, Christoph, Mathilda Glaesmann, Yunfeng Gao, Yong Hwee Foo, Marko Lampe, Linda J. Kenney, and Mike Heilemann. "Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells." In The Bacterial Nucleoid, 269–89. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7098-8_20.

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Spahn, Christoph, Mathilda Glaesmann, Yunfeng Gao, Yong Hwee Foo, Marko Lampe, Linda J. Kenney, and Mike Heilemann. "Erratum to: Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells." In The Bacterial Nucleoid, E1. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7098-8_25.

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Maruyama, Hugo, Nicholas A. Kent, Hiromi Nishida, and Taku Oshima. "Functions of Archaeal Nucleoid Proteins: Archaeal Silencers are Still Missing." In DNA Traffic in the Environment, 29–45. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-3411-5_2.

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Aaltonen, Mari J., and Hana Antonicka. "Identification of Proximity Interactors of Mammalian Nucleoid Proteins by BioID." In Methods in Molecular Biology, 153–72. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2922-2_12.

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Browning, Douglas F., David C. Grainger, Meng Xu, and Stephen J. W. Busby. "Transcriptional Regulation by Nucleoid-Associated Proteins at Complex Promoters in Escherichia coli." In Bacterial Chromatin, 419–43. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3473-1_18.

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Conference papers on the topic "Nucleoid Proteins"

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Liao, Jung-Chi, and George Oster. "The Engines of Biomolecular Motors." In ASME 2004 3rd Integrated Nanosystems Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/nano2004-46094.

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The majority of biomolecular motors are powered by nucleoside triphosphate (NTP), especially adenosine triphosphate (ATP). These motors consist of a β-sheet with highly conserved motifs and the nucleotide binding domain around it. The highly conserved protein folds are the engines of these motors, which convert the energy of NTP hydrolysis cycle to mechanical work. Although functions of molecular motors are widely diverse, (including cargo movement, DNA unwinding, protein degradation, ion pumping, etc), the nucleotide binding domains are very similar. In the binding site, NTP undergoes a hydrolysis cycle E+NTP⇄E·NTP⇄E•NTP⇄E•NDP•Pi⇄E•NDP+Pi⇄E+NDP+Pi where E is the enzyme (motor protein), the small dot represents the docking of NTP, and the large dot represents the tightly-bound states. The hydrogen bond network formed in the NTP binding step, as shown in Figure 1 [1], deforms the β-sheet and adjacent structures. The local deformation propagates to conformational changes of functional residues to do mechanical work or to change the affinity to the substrate [2]. For multimeric motor proteins, we must also consider the stress paths among subunits which control the sequence and the activity of the protein. Stress trajectories emanating from a binding site either passes through a circumferential stress loop or a stress loop through the substrate.

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Tseng, Fan-Gang. "From High Performance Protein Micro Chip Toward Ultra High Sensitive Single Molecule Nano Array." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82291.

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Protein microarrays have been employed to screen tens to thousands of proteins simultaneously for the observation of the biochemical activities in the protein-protein, protein-nucleic acid and small molecule interactions. This technology allows high throughput analysis and holds great potential for basic molecular biology research, disease marker identification, toxicological response profiling and pharmaceutical target screening. However, proteins easily malfunction in harsh environments so that they are hardly preserved before the application because of their complex and fragile structures. On the other hand, identify scarce amount of proteins less than fM range is very important and challenge for disease diagnosis at very early stage. As a result, the procedures for protein micro array formation are very important for preserving protein functionality to ensure useful protein assays, as well as the improvement of the detection sensitivity up to single molecule event but with high dynamic range for disease early detection. Therefore, this paper provides a novel view from the preparation of high efficient protein micro chip toward ultra high sensitive single protein nano array through the technology integration of BioMEMS and Bio-Nanotechnology.

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Stenflo, J., A.-K. öhlin, Å. Lundvall, and B. Dahlback. "β-HYDROXY ASPARTIC ACID AND ft-HYDROXYASPARAGINE IN THEEGF-HOMOLOGY REGIONS OF PROTEIN C AND PROTEINS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643995.

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The amino acid sequence has been determined for all of the vitamin K-dependent proteins and the gene structure is known for some of them. These findings have shown the proteins to consist of four clearly discernible domains, except protein S which has six domains. The protein domains seem to be coded on separate exons (Foster, D. C. et. al. 1985 Proc. Natl. Acad. Sci. USA 82,4673). The vitamin K-dependent γ-carboxyglutamic acid (Gla) containing domain isthe common structural denominator of the members of this protein family. In addition, all of these proteins except prothrombin contain domains that are homologous to the precursor of the epidermal growth factor (EGF). Such domains arealso found in proteins that are not vitamin K-dependent, such as the low density lipoprotein receptor, thrombomodulin, factor XII, plasminogen, the tissue type plasminogen activator, urokinase and the complement protein Clr. The vitamin K-dependent proteins can be dividedinto three groups. Factors VII, IX, X, protein C and protein Z form one group, which in addition to the Gla-region have two EGF-homology regions and one domain that is homologous to the serine proteases. Prothrombin has two 'kringle' structures and a serine protease domain and constitutes a group of its own. Protein S is also unique in that it has four EGF-homology regions and a COOH-terminal region that is homologous to the sexual hormone binding globulin (see poster by Edenbrand et. al.).Recently a posttranslationally modified amino acid, B-hydroxyaspatic acid (Hya), was identified in position 71 in the NH2-terminal EGF-homology region ofbovine protein C. The amino acid is formed by hydroxylation of aspartic acid. It has also been identified in the corresponding positions in factors VII, IX,X and protein Z (i. e. proteins which like protein C have two EGF-homology regions each). In protein S the N2-terminal of four EGF-homology regions has hydroxy lated aspartic acid .whereas the following three EGF-like domains have B-hydroxyasparagine. The nucleotide sequence codes for asparagine in the three latter positions. Neither vitamin K nor vitamin C seem to be involvedin the formation of the two hydroxylated amino acids. Recently, Hya was identified in acid hydrolysates of the complement protein Clr. Hya and Hyn have onlybeen found in domains that are homologous to the EGF precursor. In an attempt to identify the structural requirement of the hydroxylating enzyme, we have compared the sequences of EGF-homology regions that contain Hya or Hyn with the corresponding sequences that have been shown not to contain the modified amino acids. The domains that have Hya or Hyn have the consensus sequence Cx xxxx xCxC. This sequence has been found in three EGF-like domains in the EGF-precursor, in two in the LDL-receptor and in two in thrombomodulin. Furthermore, the neurogenic Notch locus in Drosophila melanogaster codes for 36 EGF-homolgy regions, 22 of which contain the consensussequence, whereas the Lin-12 locus in Caenorhabditis elegans codes for at least 11 EGF-like repeats, two of which comply with the consensus sequence. Whether any of these proteins contain Hya orHyn is not yet known with certainty.It has been hypothesized that Hya isinvolved in the Gla independent Ca2+binding of factors IX, X and protein C. In an attempt to resolve this issue, we have isolated the EGF-homology region from human protein C and been able to demonstrate that it binds Ca2+ (see poster by öhlin and Stenflo). However, we do not yet know whether Hya is directly involved in the Ca2+binding.

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Brass, L. F., D. R. Manning, and M. J. Woolkalis. "G PROTEIN REGULATORS OF PHOSPHOLIPASE C AND ADENYLATE CYCLASE IN PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644630.

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The hydrolysis of polyphosphoinositides (PI) by phospholipase C during platelet activation produces two key intracellular messengers, inositol triphosphate and diacylglycerol. This process is thought to be regulated by a guanine nucleotide binding protein referred to as Gp. Although the evidence that Gp exists is compelling, to date it has not been isolated. Uncertainty about its identity has been compounded by variations between tissues in the susceptibility of Gp to pertussis toxin and by reconstitution studies which show that pertussis toxin-inhibited PI hydrolysis can be restored by purified Gi, the pertussis toxin-sensitive G protein which inhibits adenylate cyclase. Therefore, it remains unclear whether Gp represents a new G protein or a second role for Gj. When platelets permeabilized with saponin were incubated with pertussis toxin and 32P-NAD, a single 42 kDa protein was 32P-ADP-ribosylated which co-migrated with the purified a subunit of Gi. Preincubating the platelets with an agonist inhibited labeling of this protein by dissociating the G protein into subunits. The extent of inhibition correlated with the number of toxin-sensitive functions caused by the agonist. Labeling was abolished by thrombin, which inhibited cAMP formation and caused toxin-inhibitable PI hydrolysis. Labeling was partially inhibited by vasopressin and platelet activating factor, which caused toxin-inhibitable PI hydrolysis, but had no effect on cAMP formation and by epinephrine, which inhibited cAMP formation, but did not cause PI hydrolysis. Labeling was unaffected by the TxA2 analog U46619, which neither caused toxin-sensitive PI hydrolysis nor inhibited cAMP formation. These observations suggest that the 42 kDa band may contain a subunits from both Gp and Gi and, in fact, 2D electrophoresis resolved the 42 kDa protein band into two proteins with distinct pi. However, those agonists linked functionally only to Gp or only to Gi decreased the labeling of both proteins. Therefore, our data suggest (1) that Gj and Gp are the same protein and (2) that whether a aiven platelet agonist affects adenylate cyclase or phospholipase C or both depends upon factors extrinsic to the G protein.

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"Nucleotide excision repair proteins and PARP1/PAR interplay regulats protein assembly on damaged DNA." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-366.

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6

Fojta, Miroslav, Luděk Havran, Petra Horáková, Hana Pivoňková, Pavel Kostečka, Hana Macíčková, Veronika Raindlová, Milan Vrabel, and Michal Hocek. "Redox labelling of nucleic acids for analyzing nucleotide sequences and monitoring DNA-protein interactions." In XVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2011. http://dx.doi.org/10.1135/css201112155.

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7

Jakobs, K. H., P. Gierschik, and R. Grandt. "THE ROLE OF GTP-BINDING PROTEINS EXHIBITING GTPase ACTIVITY IN PLATELET ACTIVATION." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644773.

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Activation of platelets by agonists acting via cell surface-located receptors apparently involves as an early event in transmembrane signalling an interaction of the agonist-occupied receptor with a guanine nucleotide-binding regulatory protein (G-protein). The activated G-protein, then, transduces the information to the effector molecule, being responsible for the changes in intracellular second messengers. At least two changes in intracellular signal molecules are often found to be associated with platelet activation by agonists, i.e., increases in inositol trisphosphate and diacylglycerol levels caused by activation of a polyphosphoinositide-specific phospholipase C and decrease in cyclic AMP concentration caused by inhibition of adenylate cyclase.Both actions of platelet-activating agents apparently involve G-proteins as transducing elements. Generally, the function of a G-protein in signal transduction can be measured either by its ability to regulate the activity of the effector molecule (phospholipase C or adenylate cyclase) or the binding affinity of an agonist to its specific receptor or by the abitlity of the G-protein to bind and hydrolyze GTP or one of its analogs in response to agonist-activated receptors. Some platelet-activating agonists (e.g. thrombin) can cause both adenylate cyclase inhibition and phospholipase C activation, whereas others induce either inhibition of adenylate cyclase (e.g. α2-adrenoceptor agonists) or activation of phospholipase C (e.g. stable endoperoxide analogs) . It is not yet known whether the simultaneous activation of two signal transduction systems is due to activation of two separate G-proteins by one receptor, to two distinct receptors activating each a distinct G-protein or to activation of two effector molecules by one G-protein.For some of the G-proteins, rather specific compounds are available causing inactivation of their function. In comparison to Gs, the stimulatory G-protein of the adenylate cyclase system, the adenylate cyclase inhibitory Gi-protein is rather specifically inactivated by ADP-ribosylation of its a-subunit by pertussis toxin, “unfortunately” not acting in intact platelets, and by SH-group reactive agents such as N-ethylmaleimide and diamide, apparently also affecting the Giα-subunit. Both of these treatments completely block α2-adrenoceptor-induced GTPase stimulation and adenylate cyclase inhibition and also thrombin-induced inhibition of adenylate cyclase. In order to know whether the G-protein coupling receptors to phospholipase C is similar to or different from the Gi-protein, high affinity GTPase stimulation by agents known to activate phospholipase C was evaluated in platelet membranes. The data obtained indicated that GTPase stimulation by agents causing both adenylate cyclase inhibition and phospholipase C activation is reduced, but only partially, by the above mentioned Gi-inactivating agents, while stimulation of GTPase by agents stimulating only phospholipase C is not affected by these treatments. These data suggested that the G-protein regulating phospholipase C activity in platelet membranes is different from the Gi-protein and may also not be a substrate for pertussis toxin. Measuring thrombin stimulation of inositol phosphate and diacylglycerol formation in saponin-permeabilized platelets, apparently contradictory data were reported after pertussis toxin treatment, being without effect or causing even an increase in thrombin stimulation of inositol phosphate formation (Lapetina: BBA 884, 219, 1986) or being inhibitory to thrombin stimulation of diacylglycerol formation (Brass et al.: JBC 261, 16838, 1986). These data indicate that the nature of the phospholipase C-related G-protein(s) is not yet defined and that their elucidation requires more specific tools as well as purification and reconstitution experiments. Preliminary data suggest that some antibiotics may serve as useful tools to characterize the phospho-lipase-related G-proteins. The possible role of G-protein phosphorylation by intracellular signal molecule-activated protein kinases in attenuation of signal transduction in platelets will be discussed.

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Lapetina, Eduardo G. "THE ROLE OF INOSITIDES, PHOSPHOLIPASE C AND G-PROTEINS IN RECEPTOR TRANSDUCTION." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644775.

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It is now widely recognized that the activation of phospholipase C by specific agonists leads to the formation of two second messengers: (1) inositol trisphosphate, which releases Ca2+ from the endoplasmic reticulum to the cytosol and (2) 1,2- diacylglycerol, which stimulates protein kinase C. In the past few years, GTP-binding proteins have been associated with the regulation of phospholipase C. However, the identity of the GTP-binding protein involved and the type of association with phospholipase C is not yet known. It is now recognized that there are two types of phospholipase C enzymes: (a) a soluble enzyme that has been characterized in several tissues and does not preferentially hydrolyze polyphospholinositides and (b) membrane-bound enzymes that are coupled to the receptors, specifically hydrolyzing polyphosphoinositides and activated by membrane guanine nucleotide-binding proteins. Recent reports have tried to assess the involvement of GTP-binding proteins in the agonist-induced stimulation of phospholipase C, and various related aspects have been reported. These are concerned with: (a) detection of various GTP-binding proteins in platelets, (b) the effects of known inhibitors of GTP-binding proteins such as GDPgS or pertussis toxin on the agonist-induced stimulation of phospholipase C, (c) the direct effects of stimulators of GTP-binding proteins such as GTP, GTP-analogs and fluoride on phospholipase C activity, (d) the possible association of GTP-binding proteins to cytosolic phospholipase C that would then lead to degradation of the membrane-bound inositides and (e) cytosolic phospholipase C response to the activation of cell surface receptors. The emerging information has had contradictory conclusions. (1) Pretreatment of saponin-permeabilized platelets with pertussis toxin has been shown to enhance and to inhibit the thrombin-induced activation of phospholipase C. Therefore, it is not clear if a G protein that is affected by pertussis toxin in a manner similar to Gi or Go plays a central role in activation of phospholipase C. (2) Studies on the effect of GDPβ;S are also conflicting indicating that there may be GTP-independent and/or -dependent pathways for the activation of phosphoinositide hydrolysis. (3) A cytosolic phospholipase C is activated by GTP, and it has been advanced that this activity might trigger the hydrolysis of membrane-bound inositides. A cytosolic GTP-binding protein might be involved in this action, and it is speculated that an α-subunit might be released to the cytoplasm by a receptor-coupled mechanism to activate phospholipase C. However, no direct evidence exists to support this conclusion. Moreover, the exact contribution of phospholipase C from the membranes or the cytosol to inositide hydrolysis in response to cellular agonists and the relationship of those activites to membrane-bound or soluble GTP-binding proteins are unknown. Our results indicate that the stimulation of phospholipase C in platelets by GDPβS and thrombin are affected differently by GDPβS. GDPgSinhibits the formation of inositol phosphates produced by GTPγS but not that induced by thrombin. Thrombin, therefore, can directly stimulate phospholipase C without the involvement of a “stimulatory” GTP-binding protein, such as Gs, for the agonist stimulation of adenylate cyclase. However, an “inhibitory” GTP-binding protein might have some influence on thrombin-stimulated phospholipase C, since in the presence of GDPγS thrombin produces a more profound stimulation of phospholipase C.This “inhibitory” GTP-binding protein might be ADP-ribosylated by pertussis toxin because pertussis toxin can also enhance thrombin action on phospholipase C activity. Therefore, phospholipase C that responds to thrombin could be different from the one that responds to GTPγS. Cytosolic phospholipase C can be activated by GTP or GTP analogs, and the one that responds to thrombin should be coupled to the receptors present in the plasma membrane. The initial action of thrombin is to directly activate the plasma membrane-bound phospholipase C and the mechanism of this activation is probably related to the proteolytic action of thrombin or the activation of platelet proteases by thrombin. In agreement with this, trypsin can also directly activate platelet phospholipase C and, subsequently, GTPyS produces further activation of phospholipase C. If these two mechanisms are operative in platelets, the inhibition of cytosolic phospholipase C by GDPβS would allow a larger fraction of inositides for degradation of the thrombin-stimulated phospholipase C, as our results show.

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Yan, Changhui, and Wen Cheng. "Graph methods for protein-nucleotide interactions." In BCB '14: ACM-BCB '14. New York, NY, USA: ACM, 2014. http://dx.doi.org/10.1145/2649387.2660802.

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McCauley, Micah, Philip R. Hardwidge, L. J. Maher III, and Mark C. Williams. "DNA binding proteins that alter nucleic acid flexibility." In NanoScience + Engineering, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2007. http://dx.doi.org/10.1117/12.736306.

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Reports on the topic "Nucleoid Proteins"

1

Richards, John H., John N. Abelson, Leroy E. Hood, Melvin I. Simon, and Judith L. Campbell. Biopolymers: Protein and Nucleic Acids. Fort Belvoir, VA: Defense Technical Information Center, September 1987. http://dx.doi.org/10.21236/ada185837.

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Epel, Bernard L., Roger N. Beachy, A. Katz, G. Kotlinzky, M. Erlanger, A. Yahalom, M. Erlanger, and J. Szecsi. Isolation and Characterization of Plasmodesmata Components by Association with Tobacco Mosaic Virus Movement Proteins Fused with the Green Fluorescent Protein from Aequorea victoria. United States Department of Agriculture, September 1999. http://dx.doi.org/10.32747/1999.7573996.bard.

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The coordination and regulation of growth and development in multicellular organisms is dependent, in part, on the controlled short and long-distance transport of signaling molecule: In plants, symplastic communication is provided by trans-wall co-axial membranous tunnels termed plasmodesmata (Pd). Plant viruses spread cell-to-cell by altering Pd. This movement scenario necessitates a targeting mechanism that delivers the virus to a Pd and a transport mechanism to move the virion or viral nucleic acid through the Pd channel. The identity of host proteins with which MP interacts, the mechanism of the targeting of the MP to the Pd and biochemical information on how Pd are alter are questions which have been dealt with during this BARD project. The research objectives of the two labs were to continue their biochemical, cellular and molecular studies of Pd composition and function by employing infectious modified clones of TMV in which MP is fused with GFP. We examined Pd composition, and studied the intra- and intercellular targeting mechanism of MP during the infection cycle. Most of the goals we set for ourselves were met. The Israeli PI and collaborators (Oparka et al., 1999) demonstrated that Pd permeability is under developmental control, that Pd in sink tissues indiscriminately traffic proteins of sizes of up to 50 kDa and that during the sink to source transition there is a substantial decrease in Pd permeability. It was shown that companion cells in source phloem tissue export proteins which traffic in phloem and which unload in sink tissue and move cell to cell. The TAU group employing MP:GFP as a fluorescence probe for optimized the procedure for Pd isolation. At least two proteins kinases found to be associated with Pd isolated from source leaves of N. benthamiana, one being a calcium dependent protein kinase. A number of proteins were microsequenced and identified. Polyclonal antibodies were generated against proteins in a purified Pd fraction. A T-7 phage display library was created and used to "biopan" for Pd genes using these antibodies. Selected isolates are being sequenced. The TAU group also examined whether the subcellular targeting of MP:GFP was dependent on processes that occurred only in the presence of the virus or whether targeting was a property indigenous to MP. Mutant non-functional movement proteins were also employed to study partial reactions. Subcellular targeting and movement were shown to be properties indigenous to MP and that these processes do not require other viral elements. The data also suggest post-translational modification of MP is required before the MP can move cell to cell. The USA group monitored the development of the infection and local movement of TMV in N. benthamiana, using viral constructs expressing GFP either fused to the MP of TMV or expressing GFP as a free protein. The fusion protein and/or the free GFP were expressed from either the movement protein subgenomic promoter or from the subgenomic promoter of the coat protein. Observations supported the hypothesis that expression from the cp sgp is regulated differently than expression from the mp sgp (Szecsi et al., 1999). Using immunocytochemistry and electron microscopy, it was determined that paired wall-appressed bodies behind the leading edge of the fluorescent ring induced by TMV-(mp)-MP:GFP contain MP:GFP and the viral replicase. These data suggest that viral spread may be a consequence of the replication process. Observation point out that expression of proteins from the mp sgp is temporary regulated, and degradation of the proteins occurs rapidly or more slowly, depending on protein stability. It is suggested that the MP contains an external degradation signal that contributes to rapid degradation of the protein even if expressed from the constitutive cp sgp. Experiments conducted to determine whether the degradation of GFP and MP:GFP was regulated at the protein or RNA level, indicated that regulation was at the protein level. RNA accumulation in infected protoplast was not always in correlation with protein accumulation, indicating that other mechanisms together with RNA production determine the final intensity and stability of the fluorescent proteins.

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Gafni, Yedidya, and Vitaly Citovsky. Molecular interactions of TYLCV capsid protein during assembly of viral particles. United States Department of Agriculture, April 2007. http://dx.doi.org/10.32747/2007.7587233.bard.

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Tomato yellow leaf curl geminivirus (TYLCV) is a major pathogen of cultivated tomato, causing up to 100% crop loss in many parts of the world. The present proposal, a continuation of a BARD-funded project, expanded our understanding of the molecular mechanisms by which CP molecules, as well as its pre-coat partner V2, interact with each other (CP), with the viral genome, and with cellular proteins during assembly and movement of the infectious virions. Specifically, two major objectives were proposed: I. To study in detail the molecular interactions between CP molecules and between CP and ssDNA leading to assembly of infectious TYLCV virions. II. To study the roles of host cell factors in TYLCV assembly. Our research toward these goals has produced the following major achievements: • Characterization of the CP nuclear shuttling interactor, karyopherin alpha 1, its pattern of expression and the putative involvement of auxin in regulation of its expression. (#1 in our list of publication, Mizrachy, Dabush et al. 2004). • Identify a single amino acid in the capsid protein’s sequence that is critical for normal virus life-cycle. (#2 in our list of publications, Yaakov, Levy et al. in preparation). • Development of monoclonal antibodies with high specificity to the capsid protein of TYLCV. (#3 in our list of publications, Solmensky, Zrachya et al. in press). • Generation of Tomato plants resistant to TYLCV by expressing transgene coding for siRNA targeted at the TYLCV CP. (#4 in our list of publications, Zrachya, Kumar et al. in press). •These research findings provided significant insights into (i) the molecular interactions of TYLCV capsid protein with the host cell nuclear shuttling receptor, and (ii) the mechanism by which TYLCV V2 is involved in the silencing of PTGS and contributes to the virus pathogenicity effect. Furthermore, the obtained knowledge helped us to develop specific strategies to attenuate TYLCV infection, for example, by blocking viral entry into and/or exit out of the host cell nucleus via siRNA as we showed in our publication recently (# 4 in our list of publications). Finally, in addition to the study of TYLCV nuclear import and export, our research contributed to our understanding of general mechanisms for nucleocytoplasmic shuttling of proteins and nucleic acids in plant cells. Also integration for stable transformation of ssDNA mediated by our model pathogen Agrobacterium tumefaciens led to identification of plant specific proteins involved.

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Avni, Adi, and Gitta L. Coaker. Proteomic investigation of a tomato receptor like protein recognizing fungal pathogens. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600030.bard.

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Maximizing food production with minimal negative effects on the environment remains a long-term challenge for sustainable food production. Microbial pathogens cause devastating diseases, minimizing crop losses by controlling plant diseases can contribute significantly to this goal. All plants possess an innate immune system that is activated after recognition of microbial-derived molecules. The fungal protein Eix induces defense responses in tomato and tobacco. Plants recognize Eix through a leucine-rich-repeat receptor- like-protein (LRR-RLP) termed LeEix. Despite the knowledge obtained from studies on tomato, relatively little is known about signaling initiated by RLP-type immune receptors. The focus of this grant proposal is to generate a foundational understanding of how the tomato xylanase receptor LeEix2 signals to confer defense responses. LeEix2 recognition results in pattern triggered immunity (PTI). The grant has two main aims: (1) Isolate the LeEix2 protein complex in an active and resting state; (2) Examine the biological function of the identified proteins in relation to LeEix2 signaling upon perception of the xylanase elicitor Eix. We used two separate approaches to isolate receptor interacting proteins. Transgenic tomato plants expressing LeEix2 fused to the GFP tag were used to identify complex components at a resting and activated state. LeEix2 complexes were purified by mass spectrometry and associated proteins identified by mass spectrometry. We identified novel proteins that interact with LeEix receptor by proteomics analysis. We identified two dynamin related proteins (DRPs), a coiled coil – nucleotide binding site leucine rich repeat (SlNRC4a) protein. In the second approach we used the split ubiquitin yeast two hybrid (Y2H) screen system to identified receptor-like protein kinase At5g24010-like (SlRLK-like) (Solyc01g094920.2.1) as an interactor of LeEIX2. We examined the role of SlNRC4a in plant immunity. Co-immunoprecipitation demonstrates that SlNRC4a is able to associate with different PRRs. Physiological assays with specific elicitors revealed that SlNRC4a generally alters PRR-mediated responses. SlNRC4a overexpression enhances defense responses while silencing SlNRC4 reduces plant immunity. We propose that SlNRC4a acts as a non-canonical positive regulator of immunity mediated by diverse PRRs. Thus, SlNRC4a could link both intracellular and extracellular immune perception. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 inVHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune . The interaction of LeEIX2 with SlRLK-like was verified using co- immunoprecipitation and a bimolecular fluorescence complementation assay. The defence responses induced by EIX were markedly reduced when SlRLK-like was over-expressed, and mutation of slrlk-likeusing CRISPR/Cas9 increased EIX- induced ethylene production and SlACSgene expression in tomato. Co-expression of SlRLK-like with different RLPs and RLKs led to their degradation, apparently through an endoplasmic reticulum-associated degradation process. We provided new knowledge and expertise relevant to expression of specific be exploited to enhance immunity in crops enabling the development of novel environmentally friendly disease control strategies.

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Silver, Pamela A. Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, April 2005. http://dx.doi.org/10.21236/ada435620.

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Silver, Pamela A. Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2004. http://dx.doi.org/10.21236/ada426138.

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Silver, Pamela A. Genome-Wide Nucleic Acid/Protein Interactions in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2003. http://dx.doi.org/10.21236/ada416691.

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Berman, Helen M., and Janet Thornton. PROTEIN NUCLEIC ACID INTERACTIONS GRANT # DE-FG02-96ER62166 FINAL REPORT. Office of Scientific and Technical Information (OSTI), February 2005. http://dx.doi.org/10.2172/836885.

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9

Trewhella, J., E. M. Bradbury, G. Gupta, B. Imai, R. Martinez, and C. Unkefer. Development of experimental techniques to study protein and nucleic acid structures. Office of Scientific and Technical Information (OSTI), April 1996. http://dx.doi.org/10.2172/212551.

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Whalen, Janey D. Peptide-Mediated Transduction of Proteins and Nucleic Acids to Prevent and Treat Experimental Prostate Cancer. Fort Belvoir, VA: Defense Technical Information Center, April 2005. http://dx.doi.org/10.21236/ada611051.

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