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Journal articles on the topic "Regulator Genes"
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Chaturongakul, Soraya, Sarita Raengpradub, M. Elizabeth Palmer, Teresa M. Bergholz, Renato H. Orsi, Yuewei Hu, Juliane Ollinger, Martin Wiedmann, and Kathryn J. Boor. "Transcriptomic and Phenotypic Analyses Identify Coregulated, Overlapping Regulons among PrfA, CtsR, HrcA, and the Alternative Sigma Factors σB, σC, σH, and σLinListeria monocytogenes." Applied and Environmental Microbiology 77, no. 1 (October 29, 2010): 187–200. http://dx.doi.org/10.1128/aem.00952-10.
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ABSTRACTA set of sevenListeria monocytogenes10403S mutant strains, each bearing an in-frame null mutation in a gene encoding a key regulatory protein, was used to characterize transcriptional networks inL. monocytogenes; the seven regulatory proteins addressed include all fourL. monocytogenesalternative sigma factors (σB, σC, σH, and σL), the virulence gene regulator PrfA, and the heat shock-related negative regulators CtsR and HrcA. Whole-genome microarray analyses, used to identify regulons for each of these 7 transcriptional regulators, showed considerable overlap among regulons. Among 188 genes controlled by more than one regulator, 176 were coregulated by σB, including 92 genes regulated by both σBand σH(with 18 of these genes coregulated by σB, σH, and at least one additional regulator) and 31 genes regulated by both σBand σL(with 10 of these genes coregulated by σB, σL, and at least one additional regulator). Comparative phenotypic characterization measuring acid resistance, heat resistance, intracellular growth in J774 cells, invasion into Caco-2 epithelial cells, and virulence in the guinea pig model indicated contributions of (i) σBto acid resistance, (ii) CtsR to heat resistance, and (iii) PrfA, σB, and CtsR to virulence-associated characteristics. Loss of the remaining transcriptional regulators (i.e.,sigH,sigL, orsigC) resulted in limited phenotypic consequences associated with stress survival and virulence. Identification of overlaps among the regulons provides strong evidence supporting the existence of complex regulatory networks that appear to provide the cell with regulatory redundancies, along with the ability to fine-tune gene expression in response to rapidly changing environmental conditions.
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Munson, George P., and June R. Scott. "Binding Site Recognition by Rns, a Virulence Regulator in the AraC Family." Journal of Bacteriology 181, no. 7 (April 1, 1999): 2110–17. http://dx.doi.org/10.1128/jb.181.7.2110-2117.1999.
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ABSTRACT The expression of CS1 pili by enterotoxigenic strains ofEscherichia coli is regulated at the transcriptional level and requires the virulence regulator Rns, a member of the AraC family of regulatory proteins. Rns binds at two separate sites upstream of Pcoo (the promoter of CS1 pilin genes), which were identified in vitro with an MBP::Rns fusion protein in gel mobility and DNase I footprinting assays. At each site, Rns recognizes asymmetric nucleotide sequences in two regions of the major groove and binds along one face of the DNA helix. Both binding sites are required for activation of Pcoo in vivo, because mutagenesis of either site significantly reduced the level of expression from this promoter. Thus, Rns regulates the expression of CS1 pilin genes directly, not via a regulatory cascade. Analysis of Rns-nucleotide interactions at each site suggests that binding sites for Rns and related virulence regulators are not easily identified because they do not bind palindromic or repeated sequences. A strategy to identify asymmetric binding sites is presented and applied to locate potential binding sites upstream of other genes that Rns can activate, including those encoding the CS2 and CFA/I pili of enterotoxigenic E. coli and the global regulator virB of Shigella flexneri.
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Meibom, Karin L., Anna-Lena Forslund, Kerstin Kuoppa, Khaled Alkhuder, Iharilalao Dubail, Marion Dupuis, Åke Forsberg, and Alain Charbit. "Hfq, a Novel Pleiotropic Regulator of Virulence-Associated Genes in Francisella tularensis." Infection and Immunity 77, no. 5 (February 17, 2009): 1866–80. http://dx.doi.org/10.1128/iai.01496-08.
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ABSTRACT Francisella tularensis is a highly infectious pathogen that infects animals and humans, causing tularemia. The ability to replicate within macrophages is central for virulence and relies on expression of genes located in the Francisella pathogenicity island (FPI), as well as expression of other genes. Regulation of FPI-encoded virulence gene expression in F. tularensis involves at least four regulatory proteins and is not fully understood. Here we studied the RNA-binding protein Hfq in F. tularensis and particularly the role that it plays as a global regulator of gene expression in stress tolerance and pathogenesis. We demonstrate that Hfq promotes resistance to several cellular stresses (including osmotic and membrane stresses). Furthermore, we show that Hfq is important for the ability of the F. tularensis vaccine strain LVS to induce disease and persist in organs of infected mice. We also demonstrate that Hfq is important for stress tolerance and full virulence in a virulent clinical isolate of F. tularensis, FSC200. Finally, microarray analyses revealed that Hfq regulates expression of numerous genes, including genes located in the FPI. Strikingly, Hfq negatively regulates only one of two divergently expressed putative operons in the FPI, in contrast to the other known regulators, which regulate the entire FPI. Hfq thus appears to be a new pleiotropic regulator of virulence in F. tularensis, acting mostly as a repressor, in contrast to the other regulators identified so far. Moreover, the results obtained suggest a novel regulatory mechanism for a subset of FPI genes.
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Luong, Thanh T., Paul M. Dunman, Ellen Murphy, Steven J. Projan, and Chia Y. Lee. "Transcription Profiling of the mgrA Regulon in Staphylococcus aureus." Journal of Bacteriology 188, no. 5 (March 1, 2006): 1899–910. http://dx.doi.org/10.1128/jb.188.5.1899-1910.2006.
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ABSTRACT MgrA has been shown to affect multiple Staphylococcus aureus genes involved in virulence and antibiotic resistance. To comprehensively identify the target genes regulated by mgrA, we employed a microarray method to analyze the transcription profiles of S. aureus Newman, its isogeneic mgrA mutant, and an MgrA-overproducing derivative. We compared genes that were differentially expressed at exponential or early stationary growth phases. Our results showed that MgrA affected an impressive number of genes, 175 of which were positively regulated and 180 of which were negatively regulated in an mgrA-specific manner. The target genes included all functional categories. The microarray results were validated by real-time reverse transcription-PCR quantitation of a set of selected genes from different functional categories. Our data also indicate that mgrA regulates virulence factors in a fashion analogous to that of the accessory gene regulatory locus (agr). Accordingly, exoproteins are upregulated and surface proteins are downregulated by the regulator, suggesting that mgrA may function in concert with agr. The fact that a large number of genes are regulated by mgrA implies that MgrA is a major global regulator in S. aureus.
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Altman, Efrat, and Gil Segal. "The Response Regulator CpxR Directly Regulates Expression of Several Legionella pneumophila icm/dot Components as Well as New Translocated Substrates." Journal of Bacteriology 190, no. 6 (January 11, 2008): 1985–96. http://dx.doi.org/10.1128/jb.01493-07.
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ABSTRACT Legionella pneumophila has been shown to utilize the icm/dot type IV secretion system for pathogenesis. This system was shown to be composed of icm/dot complex components and accessory proteins, as well as a large number of translocated substrates. Bioinformatic analysis of the regulatory regions of all the genes revealed that several icm/dot genes, as well as two genes encoding icm/dot translocated substrates, contain the conserved CpxR regulatory element, a regulator that has been shown previously to control the expression of the icmR gene. An experimental analysis, which included a comparison of gene expression in a L. pneumophila wild-type strain and gene expression in a cpxR deletion mutant, construction of mutants with mutations in the CpxR conserved regulatory elements, controlled expression studies, and mobility shift assays, demonstrated the direct relationship between the CpxR regulator and the expression of the genes. Furthermore, genomic analysis identified nine additional genes that contain a putative CpxR regulatory element; five of these genes (two legA genes and three ceg genes) were suggested previously to be putative icm/dot translocated substrates. The three ceg genes identified, which were shown previously to contain a putative PmrA regulatory element, were found here to be regulated by both CpxR and PmrA. The other six genes (two legA genes and four new genes products were found to be regulated by CpxR. Moreover, using the CyaA translocation assay, these nine gene products were found to be translocated into host cells in an Icm/Dot-dependent manner. Our results establish that the CpxR regulator is a fundamental regulator of the icm/dot type IV secretion system in L. pneumophila.
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Kendall, Sharon L., Farahnaz Movahedzadeh, Andreas Wietzorrek, and Neil G. Stoker. "Microarray Analysis of Bacterial Gene Expression: Towards the Regulome." Comparative and Functional Genomics 3, no. 4 (2002): 352–54. http://dx.doi.org/10.1002/cfg.193.
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Microarray technology allows co-regulated genes to be identified. In order to identify genes that are controlled by specific regulators, gene expression can be compared in mutant and wild-type bacteria. However, there are a number of pitfalls with this approach; in particular, the regulator may not be active under the conditions in which the wild-type strain is cultured. Once co-regulated genes have been identified, proteinbinding motifs can be identified. By combining these data with a map of promoters, or operons (the operome), the regulatory networks in the cell (the regulome) can start to be built up.
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Veyrier, Frédéric, Battouli Saïd-Salim, and Marcel A. Behr. "Evolution of the Mycobacterial SigK Regulon." Journal of Bacteriology 190, no. 6 (January 18, 2008): 1891–99. http://dx.doi.org/10.1128/jb.01452-07.
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ABSTRACT Previous studies have established that members of the Mycobacterium tuberculosis complex exhibit variable production of the antigenic proteins MPT70 and MPT83 due to mutations in their positive regulator, SigK (sigma factor K), and their negative regulator, RskA (regulator of sigma K). To further understand this highly specific SigK-controlled regulon, we have undertaken evolutionary studies to determine the presence of homologues of SigK-regulated genes in other organisms and to predict its transcriptional network. Evolutionary analysis indicates that the positive and negative regulators are conserved across many organisms, but that the genes under their control are variable. Moreover, the addition, loss, and movement of various genes in the mpt70/83 locus suggest that these genes are unlikely to be cotranscribed. To test predictions from sequence analysis, we have used promoter luciferase fusions and Northern blots to show that the majority of genes in this locus have their own promoters, of which a subset are SigK regulated (mpt83, dipZ, mpt70, and Rv0449c). Next, we have shown that the intracellular inducibility of mpt70 and mpt83 is a conserved property, shared between M. tuberculosis and Mycobacterium marinum. In addition, we have shown that SigK and RskA from an environmental mycobacterium isolate (M. gilvum PYR-GCK) complemented the regulatory activity of M. tuberculosis ΔsigK rskA. Together, our data indicate that the regulatory system SigK/RskA is conserved across the Mycobacterium genus, whereas the regulon under its control varies considerably across species.
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Pérez-Morales, Deyanira, Jessica Nava-Galeana, Roberto Rosales-Reyes, Paige Teehan, Helen Yakhnin, Erika I. Melchy-Pérez, Yvonne Rosenstein, Miguel A. De la Cruz, Paul Babitzke, and Víctor H. Bustamante. "An incoherent feedforward loop formed by SirA/BarA, HilE and HilD is involved in controlling the growth cost of virulence factor expression by Salmonella Typhimurium." PLOS Pathogens 17, no. 5 (May 28, 2021): e1009630. http://dx.doi.org/10.1371/journal.ppat.1009630.
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An intricate regulatory network controls the expression of Salmonella virulence genes. The transcriptional regulator HilD plays a central role in this network by controlling the expression of tens of genes mainly required for intestinal colonization. Accordingly, the expression/activity of HilD is highly regulated by multiple factors, such as the SirA/BarA two-component system and the Hcp-like protein HilE. SirA/BarA positively regulates translation of hilD mRNA through a regulatory cascade involving the small RNAs CsrB and CsrC, and the RNA-binding protein CsrA, whereas HilE inhibits HilD activity by protein-protein interaction. In this study, we show that SirA/BarA also positively regulates translation of hilE mRNA through the same mentioned regulatory cascade. Thus, our results reveal a paradoxical regulation exerted by SirA/BarA-Csr on HilD, which involves simultaneous opposite effects, direct positive control and indirect negative control through HilE. This kind of regulation is called an incoherent type-1 feedforward loop (I1-FFL), which is a motif present in certain regulatory networks and represents a complex biological problem to decipher. Interestingly, our results, together with those from a previous study, indicate that HilE, the repressor component of the I1-FFL reported here (I1-FFLSirA/BarA-HilE-HilD), is required to reduce the growth cost imposed by the expression of the genes regulated by HilD. Moreover, we and others found that HilE is necessary for successful intestinal colonization by Salmonella. Thus, these findings support that I1-FFLSirA/BarA-HilE-HilD cooperates to control the precise amount and activity of HilD, for an appropriate balance between the growth cost and the virulence benefit generated by the expression of the genes induced by this regulator. I1-FFLSirA/BarA-HilE-HilD represents a complex regulatory I1-FFL that involves multiple regulators acting at distinct levels of gene expression, as well as showing different connections to the rest of the regulatory network governing Salmonella virulence.
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Zhang, Weibin, Junhua Ma, Chengyuan Zang, Yingying Song, and Peipei Liu. "The Fur Transcription Regulator and Fur-Regulated Genes inClostridium botulinumA ATCC 3502." Journal of Biomedicine and Biotechnology 2011 (2011): 1–6. http://dx.doi.org/10.1155/2011/934756.
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Clostridium botulinumis a spore-forming bacterium that can produce a very powerful neurotoxin that causes botulism. In this study, we have investigated the Fur transcription regulators inClostridium botulinumand Fur-regulated genes inClostridium botulinumA ATCC 3502. We found that gene loss may be the main cause leading to the different numbers of Fur transcription regulators in differentClostridium botulinumstrains. Meanwhile, 46 operons were found to be regulated by the Fur transcription regulator inClostridium botulinumA ATCC 3502, involved in several functional classifications, including iron acquisition, iron utilization, iron transport, and transcription regulator. Under an iron-restricted medium, we experimentally found that a Fur transcription regulator (CBO1372) and two operons (DedA, CBO2610–CBO2614 and ABC transporter, CBO0845–CBO0847) are shown to be differentially expressed inClostridium botulinumA ATCC 3502. This study has provided-us novel insights into the diversity of Fur transcription regulators in differentClostridium botulinumstrains and diversity of Fur-targeted genes, as well as a better understanding of the dynamic changes in iron restriction occurring in response to this stress.
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Gu, Dan, Huan Liu, Zhen Yang, Yuanxing Zhang, and Qiyao Wang. "Chromatin Immunoprecipitation Sequencing Technology Reveals Global Regulatory Roles of Low-Cell-Density Quorum-Sensing Regulator AphA in the Pathogen Vibrio alginolyticus." Journal of Bacteriology 198, no. 21 (August 22, 2016): 2985–99. http://dx.doi.org/10.1128/jb.00520-16.
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ABSTRACTQuorum sensing (QS) is an important regulatory system in virulence expression and environmental adaptation in bacteria. The master QS regulators (MQSR) LuxR and AphA reciprocally control QS gene expression in vibrios. However, the molecular basis for the regulatory functions of AphA remains undefined. In this study, we characterized its regulatory roles inVibrio alginolyticus, an important zoonotic pathogen causing diseases in marine animals as well as in humans. AphA is involved in the motility ability, biofilm formation, andin vivosurvival ofV. alginolyticus. Specifically, AphA is expressed at low-cell-density growth phases. In addition, AphA negatively regulates the expression of the main virulence factor, alkaline serine protease (Asp), through LuxR. Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) detected 49 enriched loci harboring AphA-binding peaks across theV. alginolyticusgenome. An AphA-specific binding motif was identified and further confirmed by electrophoretic mobility shift assay (EMSA) and mutagenesis analysis. A quantitative real-time PCR (qRT-PCR) assay further validated the regulation of AphA on these genes. AphA binds directly to theaphApromoter and negatively regulates its own expression. Moreover, AphA directly regulates genes encoding adenylate cyclase, anti-σD, FabR, and the small RNA CsrB, revealing versatile regulatory roles of AphA in its physiology and virulence. Furthermore, our data indicated that AphA modulates motility through the coordinated function of LuxR and CsrB. Collectively, the findings of this work contribute to better understanding of the regulatory roles of AphA in QS and non-QS genes.IMPORTANCEIn this work, we determined that AphA, the master regulator of QS at low cell density, plays essential roles in expression of genes associated with physiology and virulence inV. alginolyticus, a Gram-negative pathogen for humans and marine animals. We further uncovered that 49 genes could be directly regulated by AphA and a 19-bp consensus binding sequence was identified. Among the 49 genes, the QS and other non-QS-associated genes were identified to be regulated by AphA. Besides, the small RNA CsrB was negatively regulated by AphA, and AphA regulate motility abilities through both CsrB and LuxR. Taken together, the findings of this study improve our understanding of the complex regulation network of AphA and QS.
Dissertations / Theses on the topic "Regulator Genes"
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Cleavinger, Peter Jay. "Role of the long terminal repeat in transcriptional regulation of rous sarcoma virus gene expression." free to MU campus, to others for purchase, 1996. http://wwwlib.umi.com/cr/mo/fullcit?p9841207.
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Chen, Di. "Regulatory pathways controlling larval development in caenorhabditis elegans." Free to MU Campus, others may purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3144405.
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Blackwell, Gemma. "Regulation of flagellin glycosylation genes in Campylobacter jejuni : influence of NssR, the nitrosative stress response regulator." Thesis, University of Birmingham, 2010. http://etheses.bham.ac.uk//id/eprint/639/.
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Campylobacter jejuni is one of the leading causes of food borne illness worldwide; the main cause of infection is the consumption of undercooked, contaminated poultry. Motility, mediated by single polar flagella, is necessary for Campylobacter virulence. The flagellin proteins are extensively glycosylated in C. jejuni with pseudaminic acid and related derivatives; glycosylation is required for flagella filament formation. The flagellin glycosylation locus in C. jejuni NCTC11168 comprises 50 genes, 50% are potentially involved in glycan biosynthesis and others are hypothetical; the regulatory mechanism(s) of flagellin glycosylation remain unclear. The response to nitric oxide stress in C. jejuni is regulated by NssR, which also regulates a small number of genes in the flagellin glycosylation locus; an nssR mutant has defective motility. This work aims to elucidate the mechanisms by which NssR regulates these genes and investigate the consequences of nssR mutation. Transcriptional organisation of the affected genes was deduced and chromatin immunoprecipitation (ChIP) used to map NssR binding to six potential locations in the region. Methods to measure bacterial motility were assessed and used to document the defective motility of the nssR mutant, which was found to be due to truncated, sometimes asymmetric, flagella. Finally, mass spectrometry was used to examine flagellin glycosylation in all strains.
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Messenger, Sarah Louise. "Aerobic activity of FNR : the anaerobic transcription regulator of Escherichia coli." Thesis, University of Sheffield, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391167.
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Smeds, Johanna. "Role of the CDKN2A and related cell cycle regulatory genes in melanoma and other human cancers /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-105-5/.
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Cordeiro, André Miguel Henriques. "The rice Phytochrome-Interacting Factor 14 – a regulator of cold, jasmonic acid and light related genes." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica António Xavier, 2017. http://hdl.handle.net/10362/77055.
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"Rice (Oryza sativa L.) is the staple food for more than half of the world population, and it is very sensitive to adverse environmental conditions. It is also very important for Portugal, which is the biggest rice consumer in Europe with a consumption of 14.8 kg/capita/year. Nowadays, due to climate changes and competition with other crops, the arable land for rice is decreasing. To overcome this and feed the growing world population, keeping the prices affordable, it is estimated that rice yield needs to grow 1.0–1.2% annually beyond 2020. Therefore, it is urgent to develop rice with higher grain yield and more resistant to adverse environmental conditions.(...)"N/A
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Kanth, Anna. "Studies on global regulators involved in virulence gene expression in Staphylococcus aureus /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-494-1/.
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Christensen, Kimberly Laura. "The developmental regulator SIX1 plays multiple roles in breast cancer initiation and progression /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2007.
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Thesis (Ph.D. in Biophysics & Genetics, Program in Molecular Biology) -- University of Colorado Denver, 2007.Typescript. Includes bibliographical references (leaves 115-132). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;
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Goymer, Patrick. "The role of the WspR response regulator in the adaptive evolution of experimental populations of Pseudomonas fluorescens SBW25." Thesis, University of Oxford, 2002. http://ora.ox.ac.uk/objects/uuid:52629a69-2863-4d90-8193-641ed91c286b.
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The role of ecological opportunity in adaptive radiation has been demonstrated by the diversification of the bacterium Pseudomonas fluorescens SBW25 in a spatially structured microcosm. This provides an ideal system for studying the genetics of adaptation and asking questions about the genes that matter in evolution. Previous studies have identified the genes that are necessary for the evolved, biofilm-forming, niche-specialist genotype, the wrinkly spreader (WS). These genes are organised in two operons: the wss operon that encodes the genes for cellulose biosynthesis, and the wsp operon that encodes a chemosensory pathway. The terminal gene in the wsp operon, wspR, encodes a novel response regulator thought to regulate the activity of the wss operon. This gene forms the basis of this study, which assesses the role of regulatory genes in adaptive evolution. The structure-function relationship of WspR is established through the phenotypic analysis of overexpressed wspR random point mutants. On this basis a model of WspR activity is proposed which is tested by molecular genetic analysis. The role of phosphorylation is demonstrated by site-directed mutagenesis, and domain liberation is used to study the interaction of WspR with the other components of the signalling pathway. As the overexpression of certain wspR mutant alleles mimics the evolutionary transition from ancestor to niche-specialist, the fitness effects of such overexpression are measured. It is found that some, but not all, wspR alleles do indeed cause adaptation. It is also found that a phenotypically-plastic genotype, with enhanced fitness, can be created by artificial manipulation, but does not occur naturally; this demonstrates the existence of a constraint on evolution. Sequence analysis of independently-isolated WS genotypes shows no evidence of wspR sequence variation, despite its capacity to enhance fitness. A further proteomic and phenotypic characterisation shows variation between ancestral and WS genotypes, and also between different WS genotypes. This demonstrates that there are different mutational routes to the same adaptation.
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Chen, Hsiuyi V. "Systematic Dissection of Roles for Chromatin Regulators in Dynamics of Transcriptional Response to Stress in Yeast: A Dissertation." eScholarship@UMMS, 2015. http://escholarship.umassmed.edu/gsbs_diss/808.
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The following work demonstrates that chromatin regulators play far more pronounced roles in dynamic gene expression than they do in steady-state. Histone modifications have been associated with transcription activity. However, previous analyses of gene expression in mutants affecting histone modifications show limited alteration. I systematically dissected the effects of 83 histone mutants and 119 gene deletion mutants on gene induction/repression in response to diamide stress in yeast. Importantly, I observed far more changes in gene induction/repression than changes in steady-state gene expression. The extensive dynamic gene expression profile of histone mutants and gene deletion mutants also allowed me to identify specific interactions between histone modifications and chromatin modifiers. Furthermore, by combining these functional results with genome-wide mapping of several histone modifications in the same time course, I was able to investigate the correspondence between histone modification occurrence and function. One such observation was the role of Set1-dependent H3K4 methylation in the repression of ribosomal protein genes (RPGs) during multiple stresses. I found that proper repression of RPGs in stress required the presence, but not the specific sequence, of an intron, an element which is almost unique to this gene class in Saccharomyces cerevisiae. This repression may be related to Set1’s role in antisense RNA-mediated gene silencing. Finally, I found a potential role for Set1 in producing or maintaining uncapped mRNAs in cells through a mechanism that does not involved nuclear exoribonucleases. Thus, deletion of Set1 in xrn1Δ suppresses the accumulation of uncapped transcripts observed in xrn1Δ. These findings reveal that Set1, along with other chromatin regulators, plays important roles in dynamic gene expression through diverse mechanisms and thus provides a coherent means of responding to environmental cues.
Books on the topic "Regulator Genes"
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Lundblad, James Robert. Transcriptional regulation of rat proopiomelanocortin gene expression. [New Yoork]: [Columbia University], 1993.
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NATO/CEC, Advanced Research Workshop on "Post-Transcriptional Control of Gene Expression" (1990 Goslar Germany). Post-transcriptional control of gene expression. Berlin: Springer-Verlag, 1990.
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1936-, Granner Daryl K., Rosenfeld Michael G, Chang Shing, and Cetus-UCLA Symposium on "Transcriptional Control Mechanisms" (1986 : Keystone, Colo.), eds. Transcriptional control mechanisms: Proceedings of a Cetus-UCLA symposium held in Keystone, Colorado, April 6-13, 1986. New York: A.R. Liss, 1987.
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L, McKnight Steven, and Yamamoto Keith R, eds. Transcriptional regulation. Plainview, N.Y: Cold Spring Harbor Laboratory Press, 1992.
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Barrett, Lucy W. Untranslated gene regions and other non-coding elements: Regulation of eukaryotic gene expression. Basel: Springer, 2013.
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Sansom, Roger. Ingenious genes: How gene regulation networks evolve to control development. Cambridge, Mass: MIT Press, 2011.
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Marc, Feldmann, and McMichael Andrew J, eds. Regulation of immune gene expression. Clifton, N.J: Humana Press, 1986.
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1935-, Zakut Haim, ed. Cholinesterase genes: Multileveled regulation. Basel: Karger, 1990.
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1954-, Gann Alexander, ed. Genes & signals. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory Press, 2002.
Find full textBook chapters on the topic "Regulator Genes"
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Bagchi, Rushita A., and Michael P. Czubryt. "Scleraxis: A New Regulator of Extracellular Matrix Formation." In Genes and Cardiovascular Function, 57–65. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-1-4419-7207-1_6.
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Barry, M., S. T. Wasilenko, T. L. Stewart, and J. M. Taylor. "Apoptosis Regulator Genes Encoded by Poxviruses." In Viruses and Apoptosis, 19–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-74264-7_2.
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Wang, Lingfei, and Tom Michoel. "Detection of Regulator Genes and eQTLs in Gene Networks." In Systems Biology in Animal Production and Health, Vol. 1, 1–23. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-43335-6_1.
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Boycheva, Irina, Ralitsa Georgieva, Lubomir Stoilov, and Vasilissa Manova. "Effects of light and UV-C radiation on the transcriptional activity of COP1 and HY5 gene homologues in barley." In Mutation breeding, genetic diversity and crop adaptation to climate change, 478–86. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0049.
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Abstract Photomorphogenic regulators COP1 (Constitutive Photomorphogenic 1) and HY5 (Elongated Hypocotyl 5) play a key role in plant development by guiding the transition from dark to light growth. In Arabidopsis they are also implicated in the transcriptional control of photolyase genes. Here we characterize the transcript abundance of COP1 and HY5 gene homologues in barley in relation to light-grown conditions and UV-damage response. Etiolated and green 6-day-old seedlings were UV-C irradiated and exposed to light or kept in darkness. The abundance of barley COP1 and HY5 transcripts was assessed by real-time RT-PCR. In etiolated leaves we found several-fold lower levels of COP1 transcripts which reached the levels of the green ones after 1 h of light exposure. Barley HY5 transcripts were very low in the dark-grown seedlings and after 1 h of illumination they increased drastically to levels significantly exceeding those measured in the green leaves. Both genes were upregulated by light in the irradiated plants as well, but to a lesser extent compared with their controls, probably due to the presence of non-repaired DNA damage in the etiolated leaves soon after irradiation. The enhanced transcription of barley COP1 under light is unexpected in view of the well-known function of COP1 as a negative regulator of plant photomorphogenesis but conforms to the positive role reported for AtCOP1 in UV-B signalling. HY5 is recognized as a stimulator of light-inducible genes and our data support such a role for the barley HY5 homologue as well. Our study shows that, in barley seedlings, the regulation of COP1 and HY5 gene expression is achieved through light-positive transcriptional modulation, suggesting that both genes contribute to the de-etiolation phase in barley. According to our knowledge, this is the first quantitation of the COP1 and HY5 mRNAs in barley that also regards the UV-damage response of this crop.
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Yasukawa, Hideo, Ichiko Kinjyo, and Akihiko Yoshimura. "Negative Regulator of Cytokine Signaling (SOCS) Genes in Inflammation." In Developments in Cardiovascular Medicine, 27–38. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4419-9264-2_3.
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Ntambi, James M. "Stearoyl-CoA Desaturase-1 Is a Biological Regulator of Energy Homeostasis." In Stearoyl-CoA Desaturase Genes in Lipid Metabolism, 27–35. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7969-7_3.
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Riviere, Y., M. N. Robertson, and F. Buseyne. "Cytotoxic T Lymphocytes in Human Immunodeficiency Virus Infection: Regulator Genes." In Current Topics in Microbiology and Immunology, 65–74. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/978-3-642-78530-6_4.
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Cui, Jun, Ning Jiang, Jun Meng, and Yushi Luan. "Genome-Wide Analysis of Response Regulator Genes in Solanum lycopersicum." In Bioinformatics Research and Applications, 379–84. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-59575-7_38.
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Monsalve, María, Ignacio Prieto, Andreza Fabro de Bem, and Yolanda Olmos. "Methodological Approach for the Evaluation of FOXO as a Positive Regulator of Antioxidant Genes." In FOXO Transcription Factors, 61–76. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8900-3_6.
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Safran, Marilyn, Naomi Rosen, Michal Twik, Ruth BarShir, Tsippi Iny Stein, Dvir Dahary, Simon Fishilevich, and Doron Lancet. "The GeneCards Suite." In Practical Guide to Life Science Databases, 27–56. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-5812-9_2.
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AbstractThe GeneCards® database of human genes was launched in 1997 and has expanded since then to encompass gene-centric, disease-centric, and pathway-centric entities and relationships within the GeneCards Suite, effectively navigating the universe of human biological data—genes, proteins, cells, regulatory elements, biological pathways, and diseases—and the connections among them. The knowledgebase amalgamates information from >150 selected sources related to genes, proteins, ncRNAs, regulatory elements, chemical compounds, drugs, splice variants, SNPs, signaling molecules, differentiation protocols, biological pathways, stem cells, genetic tests, clinical trials, diseases, publications, and more and empowers the suite’s Next Generation Sequencing (NGS), gene set, shared descriptors, and batch query analysis tools.
Conference papers on the topic "Regulator Genes"
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CALIFANO, ANDREA. "MOLECULAR INTERACTION NETWORK BASED DISCOVERY OF MASTER REGULATOR GENES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2008. http://dx.doi.org/10.1142/9789812836939_0044.
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Teixeira, Lívia, Izabela Conceição, Paulo Caramelli, Marcelo Luizon, and Karina Gomes. "ALZHEIMER’S DISEASE AND TYPE 2 DIABETES MELLITUS: COMMON MIRNAS, GENES AND REGULATORY BIOLOGICAL PATHWAYS." In XIII Meeting of Researchers on Alzheimer's Disease and Related Disorders. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1980-5764.rpda066.
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Background: The increased incidence of Type 2 Diabetes Mellitus (T2DM) in the 21st century, along with the higher risk of developing Alzheimer’s disease (AD) in diabetic patients have stimulated the search for pathways that link glycemic disorders to neurodegeneration. MicroRNAs (miRNAs) are non-coding RNAs that play key roles in regulating gene expression. Objective: To identify miRNAs, genes and their regulatory pathways in common in AD and T2DM. Methods: Literature search was carried out to find miRNAs commonly expressed in AD and T2DM. MiRTarBase database was used to provide experimentally validated information on the interactions between miRNAs and their target genes. The functional enrichment of molecular pathways differentially regulated by these miRNAs was performed using EnrichR with Reactome gene set annotation. Results: We found six circulating miRNAs commonly expressed in both diseases (hsa-mir-21; hsamir-103a-1; hsa-mir-103a-2; hsa-mir-107; hsa-mir-146a and hsa-mir-144), which regulate 129 target genes. The common pathways between AD and T2DM were related to inflammatory mediators, cell death and axon formation signalling with p-adjust <10-5. Conclusion: Our study provides evidence that AD and T2DM share common pathophysiological mechanisms and regulators miRNAs, and suggests miRNAs as potential markers related to both diseases.
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Nathaniel, S., K. Arendes, H. Q. Xiang, R. Mitra, and D. E. Gottlieb. "Downregulation of Regulator Genes as Embryonic Stem (ES) Cells Differentiate into Neurons." In Minority Trainee Research Forum, 2004. TheScientificWorld Ltd, 2004. http://dx.doi.org/10.1100/tsw.2004.168.
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CHOY, WENG-KEONG, VLADIMIR B. BAJIC, MOK-WEI HENG, MERLIN VERONIKA, and SANJAY SWARUP. "REGULATORY NETWORKS OF GENES AFFECTED BY MORA, A GLOBAL REGULATOR CONTAINING GGDEF AND EAL DOMAINS IN PSEUDOMONAS AERUGINOSA." In Proceedings of the 3rd Annual RECOMB Workshop. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2008. http://dx.doi.org/10.1142/9781848162525_0022.
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Hoey, David A., and Christopher R. Jacobs. "Oscillatory Fluid Flow Affects the Osteogenic Differentiation of Human Bone Marrow Stromal Cells in a Primary Cilium Dependent Manner." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53435.
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Osteoporosis is a debilitating bone disease which occurs in part when bone marrow stromal cells (BMSCs) fail to produce sufficient numbers of osteoblasts to counteract bone resorption by osteoclasts. The majority of research to date has described chemically induced differentiation of BMSCs but a key regulator of stromal cell differentiation is physical loading. BMSCs experience both hydrostatic pressure and fluid flow within the marrow cavity and such modes of loading have been shown to significantly alter gene expression in vitro [1,2]. In particular, the effect of oscillatory fluid flow (OFF) induced shear stress results in the upregulation of osteogenic genes in preosteoblastic cells; however the effect of this mode of loading is not well characterized in human MSCs (hMSCs) [3].
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Craig, Amanda J., Seungyeul Yoo, Verónica Miguela, Delia D'Avola, Pedro Molina-Sánchez, Josep Llovet, Amaia Lujambio, Jun Zhu, and Augusto Villanueva. "Abstract 4393: Integrative molecular analysis of gene expression and methylation reveals 116 putative key regulator genes of human hepatocarcinogenesis." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-4393.
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Chiu, Ching-Chi, Hsiao-Fang Li, Yin-Ju Chen, and Ann-Joy Chen. "Abstract 3067: Differential proteomic profilingidentifies HNSCCinvasion genes: GANAB is negative regulator in HNSCC invasion." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-3067.
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"Expression of IPD3, a transcriptional regulator of AM symbiosis, affects immunity and flowering time in non-host Arabidopsis." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-13.
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Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants. The ability to host AM has since been lost from diverse plant species. Genes in the Common Symbiosis Pathway that are essential to establish AM hosting were lost from Brassicaceae along with the trait itself, including Interacting Protein of DMI3 (IPD3), a key transcription factor connecting upstream signaling of AM fungal presence to the downstream gene-regulatory network for AM functions. We generated transgenic Arabidopsis plants expressing the DNA-binding domain of IPD3 and used phenotypic and transcriptome analysis to characterize the effect of IPD3 expression in Arabidopsis in the presence and absence of AM fungus Rhizophagus irregularis. We compared these results to the AM-host model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 expression to Arabidopsis significantly altered transcription related to growth and defense, and delayed flowering time. Our comparative transcriptomic results indicate that some genetic connections for IPD3 remain conserved in Arabidopsis despite the long evolutionary time since its loss.
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Ahmad, Salma, Hanan Nazar, Nouralhuda Alatieh, Maryam Al-Mansoob, Zainab Farooq, Muna Yusuf, and Allal Ouhtit. "Validation of Novel Transcriptional Targets that Underpin CD44-promoted breast cancer cell invasion." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2021. http://dx.doi.org/10.29117/quarfe.2021.0153.
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Introduction: Breast cancer (BC) is the most common cancer worldwide, and metastasis is its worst aspect and the first cause of death. Metastasis is a multistep process, where an invasion is a recurring event. The process of BC cell invasion involves three major factors, including cell adhesion molecules (CAM), proteinases and Growth factors.CD44, a family of CAM proteins and the hyaluronic acid (HA) cell surface receptor, acts as cell differentiation, cell migration/invasion and apoptosis regulator. Rationale: We have previously established a tetracycline (Tet)-OFF-regulated expression system, both in vitro and in vivo (Hill et al, 2006). As a complementary approach, the highly metastatic MDA-MB-231 BC cells expressing high levels of endogenous CD44s (the standard form of CD44), was cultured in the presence and absence of 50 µg/ml of HA. RNA samples were isolated from both cell experimental models, and microarray analysis (12K CHIP from Affymetrix) was applied. More than 200 CD44s transcriptional target genes were identified and were sub-divided into groups of genes based on their function: cell motility, cytoskeletal organization, ability to degrade ECM, and cell survival. Hypothesis: Among these 200 identified genes, we selected seven genes (ICAP-1, KYNU, AHR, SIRT1, SRSF8, PRAD1, and SOD2) and hypothesized that based on evidence from literature, these genes are potential novel targets of CD44-downstream signaling mediating BC cell invasion. Specific Aims: Pursuant to this goal, we proposed the following objectives: 1- Structural validation of ICAP-1, KYNU, AHR, SIRT1, SRSF8, PRAD1 and SOD2 as novel transcriptional targets of CD44/HA-downstream signaling at both RNA and Protein level using reverse transcription polymerase chain reaction (RT-PCR) and Western Blot respectively. 2-Functional validation of ICAP-1, KYNU, AHR, SIRT1, SRSF8, PRAD1and SOD2 as novel transcriptional targets that underpin CD44-promoted BC cell migration using wound healing assay after the transfection with siRNA. Innovation/Consclusion: This study validated seven transcriptional targets of CD44/HA-downstream signaling promoting BC cell invasion. Ongoing experiments aim to dissect the signaling pathways that link CD44 activation by HA to the transcription of these seven genes.
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Wilson, Mary E., Lina M. González, Warren C. Ruder, and Philip R. LeDuc. "Engineering Magnetic Nanomaterial Production in Magnetotactic Bacteria Through Gene Regulation." In ASME 2012 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/sbc2012-80446.
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Magnetotactic bacteria endogenously synthesize intracellular magnetic nanoparticles (magnetosomes); however, little is known regarding the genetic regulatory networks that control magnetosome production. In this paper, we explore the genetic response of Magnetospirillum magneticum strain AMB-1 to an applied electromagnetic field as a means to identify genes activated by magnetic stimulation. The expression of magnetosome island, flagellar and cytoskeletal genes was found to be differentially altered by magnetic stimulation at short and long times points. These results indicate previously uncharacterized endogenous gene network modules that could be exploited to engineer magnetic bacteria as magnetic nanomaterial producing-machines through gene regulation.
Reports on the topic "Regulator Genes"
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Prusky, Dov, Nancy P. Keller, and Amir Sherman. global regulation of mycotoxin accumulation during pathogenicity of Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600012.bard.
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Background to the topic- Penicilliumas a postharvest pathogen and producer of the mycotoxin PAT. Penicilliumspp. are destructive phytopathogens, capable of causing decay in many deciduous fruits, during postharvest handling and storage; and the resulting losses can amount to 10% of the stored produce and the accumulation of large amounts of the mycotoxinpatulin. The overall goal of this proposal is to identify critical host and pathogen factors that modulate P. expansummycotoxin genes and pathways which are required for PAT production and virulence. Our preliminary results indicated that gluconic acid are strongly affecting patulin accumulation during colonization. P. expansumacidifies apple fruit tissue during colonization in part through secretion of gluconic acid (GLA). Several publications suggested that GLA accumulation is an essential factor in P. expansumpathogenicity. Furthermore, down regulation of GOX2 significantly reduced PAT accumulation and pathogenicity. PAT is a polyketide and its biosynthesis pathway includes a 15-gene cluster. LaeA is a global regulator of mycotoxin synthesis. It is now known that patulin synthesis might be subjected to LaeA and sometimes by environmental sensing global regulatory factors including the carbon catabolite repressor CreA as well as the pH regulator factor PacC and nitrogen regulator AreA. The mechanisms by which LaeA regulates patulin synthesis was not fully known and was part of our work. Furthermore, the regulatory system that controls gene expression in accordance with ambient pH was also included in our work. PacC protein is in an inactive conformation and is unable to bind to the promoter sites of the target genes; however, under alkaline growth conditions activated PacC acts as both an activator of alkaline-expressed genes and a repressor of acid-expressed genes. The aims of the project- This project aims to provide new insights on the roles of LaeA and PacC and their signaling pathways that lead to GLA and PAT biosynthesis and pathogenicity on the host. Specifically, our specific aims were: i) To elucidate the mechanism of pH-controlled regulation of GLA and PAT, and their contribution to pathogenesis of P. expansum. We are interested to understanding how pH and/or GLA impact/s under PacC regulation affect PAT production and pathogenesis. ii) To characterize the role of LaeA, the global regulator of mycotoxin production, and its effect on PAT and PacC activity. iii) To identify the signaling pathways leading to GLA and PAT synthesis. Using state- of-the-art RNAseq technologies, we will interrogate the transcriptomes of laeAand pacCmutants, to identify the common signaling pathways regulating synthesis of both GLA and PAT. Major conclusions, solutions, achievements- In our first Aim our results demonstrated that ammonia secreted at the leading edge of the fungal colony induced transcript activation of the global pH modulator PacC and PAT accumulation in the presence of GLA. We assessed these parameters by: (i) direct exogenous treatment of P. expansumgrowing on solid medium; (ii) direct exogenous treatment on colonized apple tissue; (iii) growth under self-ammonia production conditions with limited carbon; and (iv) analysis of the transcriptional response to ammonia of the PAT biosynthesis cluster. Ammonia induced PAT accumulation concurrently with the transcript activation of pacCand PAT biosynthesis cluster genes, indicating the regulatory effect of ammonia on pacCtranscript expression under acidic conditions. Transcriptomic analysis of pH regulated processes showed that important genes and BARD Report - Project 4773 Page 2 of 10 functionalities of P. expansumwere controlled by environmental pH. The differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Concerning the second and third Aims, we demonstrated that LaeA regulates several secondary metabolite genes, including the PAT gene cluster and concomitant PAT synthesis invitro. Virulence studies of ΔlaeAmutants of two geographically distant P. expansumisolates (Pe-21 from Israel and Pe-T01 from China) showed differential reduction in disease severity in freshly harvested fruit ranging from no reduction for Ch-Pe-T01 strains in immature fruit to 15–25% reduction for both strains in mature fruit, with the ΔlaeAstrains of Is-Pe-21 always showing a greater loss in virulence. Results suggest the importance of LaeA regulation of PAT and other secondary metabolites on pathogenicity. Our work also characterized for the first time the role of sucrose, a key nutritional factor present in apple fruit, as a negative regulator of laeAexpression and consequent PAT production in vitro. This is the first report of sugar regulation of laeAexpression, suggesting that its expression may be subject to catabolite repression by CreA. Some, but not all of the 54 secondary metabolite backbone genes in the P. expansumgenome, including the PAT polyketide backbone gene, were found to be regulated by LaeA. Together, these findings enable for the first time a straight analysis of a host factor that potentially activates laeAand subsequent PAT synthesis.
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Prusky, Dov, and Jeffrey Rollins. Modulation of pathogenicity of postharvest pathogens by environmental pH. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7587237.bard.
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Until recently, environmental pH was not considered a factor in determining pathogen compatibility. Our hypothesis was that the environmental pH at the infection site, which is dynamically controlled by activities of both the host and the pathogen, regulates the expression of genes necessary for disease development in Colletotrichum gloeosporioides and Sclerotinia sclerotiorum. This form of regulation ensures that genes are expressed at optimal conditions for their encoded activities.Pectate lyase encoded by pelB, has been demonstrated to play a key role in virulence of C. gloeosporioides in avocado fruit. Polyglacturonase synergism with oxalic acid production is considered to be an essential pathogenicity determinant in the interactions of S. sclerotiorum with its numerous hosts. A common regulatory feature of these virulence and pathogenicity factors is their dependence upon environmental pH conditions within the host niche to create optimal conditions for expression and secretion. In this proposal we have examined, 1) the mechanisms employed by these fungi to establish a suitable pH environment, 2) the molecular levels at which genes and gene products are regulated in response to environmental pH, and 3) the molecular basis and functional importance of pH-responsive gene regulation during pathogenicity. The specific objectives of the proposal were: 1. Characterize the mechanism of local pH modulation and the effect of ambient pH on the expression and secretion of virulence factors. 2. Provide evidence that a conserved molecular pathway for pH-responsive gene expression exists in C. gloeosporioides by cloning a pacC gene homologue. 3. Determine the role of pacC in pathogenicity by gene disruption and activating mutations. Major conclusions 1. We determined the importance of nitrogen source and external pH in the secretion of the virulence factor pectate lyase with respect to the ambient pH transcriptional regulator pacC. It was concluded that nitrogen source availability and ambient pH are two independent signals for the transcriptional regulation of genes required for the disease process of C. gloeosporioides and possibly of other pathogens. 2. We also determined that availability of ammonia regulate independently the alkalinization process and pelB expression, pecate lyase secretion and virulence of C. gloeosporioides. 3. Gene disruption of pacC reduced virulence of C. gloeosporioides however did not reduced fully pelB expression. It was concluded that pelB expression is regulated by several factors including pH, nitrogen and carbon sources. 4. Gene disruption of pacC reduced virulence of S. slcerotiourum Creation of a dominant activating
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Tucker, Mark L., Shimon Meir, Amnon Lers, Sonia Philosoph-Hadas, and Cai-Zhong Jiang. Elucidation of signaling pathways that regulate ethylene-induced leaf and flower abscission of agriculturally important plants. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597929.bard.
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The Problem: Abscission is a highly regulated process, occurring as a natural terminal stage of development, in which various organs are separated from the parent plant. In most plant species, the process is initiated by a decrease in active auxin in the abscission zone (AZ) and an increase in ethylene, and may be accelerated by postharvest or environmental stresses. Another potential key regulator in abscission is IDA (Inflorescence Deficient in Abscission), which was identified as an essential peptide signal for floral organ abscission in Arabidopsis. However, information is still lacking regarding the molecular mechanisms integrating all these regulators. In our previous BARD funded research we made substantial progress towards understanding these molecular events in tomato, and the study is still in progress. We established a powerful platform for analysis of genes for regulatory proteins expressed in AZ. We identified changes in gene expression for several transcription factors (TFs) directly linked to ethylene and auxin signaling and several additional regulatory proteins not so obviously linked to these hormones. Moreover, we demonstrated using a virus-induced gene silencing (VIGS) assay that several play a functional role in the onset of abscission. Based on these results we have selected 14 genes for further analysis in stably transformed tomato plants. All 14 genes were suppressed by RNA interference (RNAi) using a constitutive promoter, and 5 of them were also suppressed using an abscission-specific promoter. Transformations are currently at different stages of progress including some lines that already display an abscission phenotype. Objectives: We propose here to (1) complete the functional analysis of the stably transformed tomato plants with T2 lines and perform transcriptome analysis using custom abscission-specific microarrays; (2) conduct an indepth analysis of the role of IDA signaling in tomato leaf and flower abscission; (3) perform transcriptome and proteome analyses to extend the earlier gene expression studies to identify transcripts and proteins that are highly specific to the separation layer (i.e., target cells for cell separation) prior to the onset of abscission; (4) extend and compliment the work in tomato using a winnowed set of genes in soybean. Methodology: Next Generation Sequencing (NGS) of mRNA will be used to further increase the list of abscission-associated genes, and for preparation of a custom tomato abscission microarray to test altered gene expression in transgenic plants. Tandem mass spectrometry (LC-MS/MS) of protein extracts from leaf petiole, flower pedicel and their AZ tissues will be used to identify the proteome of the AZ before and during abscission. AZ-specific gene promoters will be used in stably transformed tomato plants to reduce non-target phenotypes. The bean pod mottle virus (BPMV) plasmid vectors will be used for VIGS analysis in soybean. Expected Contribution: Our study will provide new insights into the regulation of ethylene-induced abscission by further revealing the role of key regulators in the process. This will permit development of novel techniques for manipulating leaf and flower abscission, thereby improving the postharvest performance of agriculturally important crops.
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Eshed, Yuval, and Sarah Hake. Exploring General and Specific Regulators of Phase Transitions for Crop Improvement. United States Department of Agriculture, November 2012. http://dx.doi.org/10.32747/2012.7699851.bard.
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The transition of plants from a juvenile to adult growth phase entails a wide range of changes in growth habit, physiological competence and composition. Strikingly, most of these changes are coordinated by the expression of a single regulator, micro RNA 156 (miR156) that coordinately regulates a family of SBP genes containing a miR156 recognition site in the coding region or in their 3’ UTR. In the framework of this research, we have taken a broad taxonomic approach to examine the role of miR156 and other genetic regulators in phase change transition and its implication to plant development and crop improvement. We set to: Determine the common and unique factors that are altered upon juvenile to adult phase transition. Determine the functions of select miR156 target genes in tomato and maize, and identify those targets that mediate phase transition. Characterize the role of miR172 and its targets in tomato phase change. Determine the relationships between the various molecular circuits directing phase change. Determine the effects of regulated manipulation of phase change genes on plant architecture and if applicable, productivity. In the course of the study, a new technology for gene expression was introduced – next generation sequencing (NGS). Hence some of the original experiments that were planned with other platforms of RNA profiling, primarily Affymetrix arrays, were substituted with the new technology. Yet, not all were fully completed. Moreover, once the initial stage was completed, each group chose to focus its efforts on specific components of the phase change program. The Israeli group focused on the roles of the DELAYED SYMPODIAL TERMINATION and FALSIFLORA factors in tomato age dependent programs whereas the US group characterized in detail the role of miR156 (also termed Cg) in other grasses and in maize, its interplay with the many genes encoding miR172.
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Horwitz, Benjamin A., and Barbara Gillian Turgeon. Fungal Iron Acquisition, Oxidative Stress and Virulence in the Cochliobolus-maize Interaction. United States Department of Agriculture, March 2012. http://dx.doi.org/10.32747/2012.7709885.bard.
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Our project focused on genes for high affinity iron acquisition in Cochliobolus heterostrophus, a necrotrophic pathogen of maize, and their intertwined relationship to oxidative stress status and virulence of the fungus on the host. An intriguing question was why mutants lacking the nonribosomal peptide synthetase (NRPS) gene (NPS6) responsible for synthesis of the extracellular siderophore, coprogen, are sensitive to oxidative stress. Our overall objective was to understand the mechanistic connection between iron stress and oxidative stress as related to virulence of a plant pathogen to its host. The first objective was to examine the interface where small molecule peptide and reactive oxygen species (ROS) mechanisms overlap. The second objective was to determine if the molecular explanation for common function is common signal transduction pathways. These pathways, built around sensor kinases, response regulators, and transcription factors may link sequestering of iron, production of antioxidants, resistance to oxidative stress, and virulence. We tested these hypotheses by genetic manipulation of the pathogen, virulence assays on the host plant, and by following the expression of key fungal genes. An addition to the original program, made in the first year, was to develop, for fungi, a genetically encoded indicator of redox state based on the commercially available Gfp-based probe pHyper, designed for animal cell biology. We implemented several tools including a genetically encoded indicator of redox state, a procedure to grow iron-depleted plants, and constructed a number of new mutants in regulatory genes. Lack of the major Fe acquisition pathways results in an almost completely avirulent phenotype, showing how critical Fe acquisition is for the pathogen to cause disease. Mutants in conserved signaling pathways have normal ability to regulate NPS6 in response to Fe levels, as do mutants in Lae1 and Vel1, two master regulators of gene expression. Vel1 mutants are sensitive to oxidative stress, and the reason may be underexpression of a catalase gene. In nps6 mutants, CAT3 is also underexpressed, perhaps explaining the sensitivity to oxidative stress. We constructed a deletion mutant for the Fe sensor-regulator SreA and found that it is required for down regulation of NPS6 under Fe-replete conditions. Lack of SreA, though, did not make the fungus over-sensitive to ROS, though the mutant had a slow growth rate. This suggests that overproduction of siderophore under Fe-replete conditions is not very damaging. On the other hand, increasing Fe levels protected nps6 mutants from inhibition by ROS, implying that Fe-catalyzed Fenton reactions are not the main factor in its sensitivity to ROS. We have made some progress in understanding why siderophore mutants are sensitive to oxidative stress, and in doing so, defined some novel regulatory relationships. Catalase genes, which are not directly related to siderophore biosynthesis, are underexpressed in nps6 mutants, suggesting that the siderophore product (with or without bound Fe) may act as a signal. Siderophores, therefore, could be a target for intervention in the field, either by supplying an incorrect signal or blocking a signal normally provided during infection. We already know that nps6 mutants cause smaller lesions and have difficulty establishing invasive growth in the host. Lae1 and Vel1 are the first factors shown to regulate both super virulence conferred by T-toxin, and basic pathogenicity, due to unknown factors. The mutants are also altered in oxidative stress responses, key to success in the infection court, asexual and sexual development, essential for fungal dissemination in the field, aerial hyphal growth, and pigment biosynthesis, essential for survival in the field. Mutants in genes encoding NADPH oxidase (Nox) are compromised in development and virulence. Indeed the triple mutant, which should lack all Nox activity, was nearly avirulent. Again, gene expression experiments provided us with initial evidence that superoxide produced by the fungus may be most important as a signal. Blocking oxidant production by the pathogen may be a way to protect the plant host, in interactions with necrotrophs such as C. heterostrophus which seem to thrive in an oxidant environment.
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Barkan, Alice, and Zach Adam. The Role of Proteases in Regulating Gene Expression and Assembly Processes in the Chloroplast. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7695852.bard.
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Chloroplasts house many biochemical processes that are essential for plant viability. Foremost, among these is photosynthesis, which requires the protein-rich thylakoid membrane system. The activation of chloroplast genes encoding thylakoid membrane proteins and the targeting and assembly of these proteins together with their nuclear-encoded partners are essential for the elaboration of the thylakoid membrane. Several nuclear-encoded proteins that regulate chloroplast gene expression and that mediate the targeting of proteins to the thylakoid membrane have been identified in recent years, and many more remain to be discovered. The abundance of such proteins is critical and is likely to be determined to a significant extent by their stability, which in turn, is influenced by chloroplast protease activities. The primary goal of this project was to link specific proteases to specific substrates, and in particular, to specific regulatory and assembly proteins. We proposed a two-pronged approach, involving genetic analysis of the consequences of the mutational loss of chloroplast proteases, and biochemical analysis of the degradation pathways of specific proteins that have been shown to control chloroplast gene expression. Our initial bioinformatic analysis of chloroplast proteases allowed us to identify the set of pro teases that is targeted to the chloroplast. We used that information to recover three Arabidopsis mutants with T - DNA insertions in specific chloroplast protease genes. We carried out the first analysis of the stability of a regulator of chloroplast gene expression (CRS2), and found that the protein is much less stable than are typical components of the photosynthetic apparatus. Genetic reagents and analytical methods were developed that have set the stage for a rapid advancement of our understanding of chloroplast proteolysis. The results obtained may be useful for manipulating the expression of transgenes in the chloroplast and for engineering plants whose photosynthetic activity is optimized under harsh environmental conditions.
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Ohad, Nir, and Robert Fischer. Regulation of plant development by polycomb group proteins. United States Department of Agriculture, January 2008. http://dx.doi.org/10.32747/2008.7695858.bard.
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Our genetic and molecular studies have indicated that FIE a WD-repeat Polycomb group (PcG) protein takes part in multi-component protein complexes. We have shown that FIE PcG protein represses inappropriate programs of development during the reproductive and vegetative phases of the Arabidopsis life cycle. Moreover, we have shown that FIE represses the expression of key regulatory genes that promote flowering (AG and LFY), embryogenesis (LEC1), and shoot formation (KNAT1). These results suggest that the FIE PcG protein participates in the formation of distinct PcG complexes that repress inappropriate gene expression at different stages of plant development. PcG complexes modulate chromatin compactness by modifying histones and thereby regulate gene expression and imprinting. The main goals of our original project were to elucidate the biological functions of PcG proteins, and to understand the molecular mechanisms used by FIE PcG complexes to repress the expression of its gene targets. Our results show that the PcG complex acts within the central cell of the female gametophyte to maintain silencing of MEA paternal allele. Further more we uncovered a novel example of self-imprinting mechanism by the PgG complex. Based on results obtained in the cures of our research program we extended our proposed goals and elucidated the role of DME in regulating plant gene imprinting. We discovered that in addition to MEA,DME also imprints two other genes, FWA and FIS2. Activation of FWA and FIS2 coincides with a reduction in 5-methylcytosine in their respective promoters. Since endosperm is a terminally differentiated tissue, the methylation status in the FWA and FIS2 promoters does not need to be reestablished in the following generation. We proposed a “One-Way Control” model to highlight differences between plant and animal genomic imprinting. Thus we conclude that DEMETER is a master regulator of plant gene imprinting. Future studies of DME function will elucidate its role in processes and disease where DNA methylation has a key regulatory role both in plants and animals. Such information will provide valuable insight into developing novel strategies to control and improve agricultural traits and overcome particular human diseases.
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Friedman, Haya, Julia Vrebalov, and James Giovannoni. Elucidating the ripening signaling pathway in banana for improved fruit quality, shelf-life and food security. United States Department of Agriculture, October 2014. http://dx.doi.org/10.32747/2014.7594401.bard.
Full textAbstract:
Background : Banana being a monocot and having distinct peel and pulp tissues is unique among the fleshy fruits and hence can provide a more comprehensive understanding of fruit ripening. Our previous research which translated ripening discoveries from tomato, led to the identification of six banana fruit-associated MADS-box genes, and we confirmed the positive role of MaMADS1/2 in banana ripening. The overall goal was to further elucidate the banana ripening signaling pathway as mediated by MADS-boxtranscriptional regulators. Specific objectives were: 1) characterize transcriptional profiles and quality of MaMADS1/2 repressed fruit; 2) reveal the role of additional MaMADSgenes in ripening; 3) develop a model of fruit MaMADS-box mode of action; and 4) isolate new components of the banana ripening signaling pathway. Major conclusion: The functions of the banana MaMADS1-5 have been examined by complimenting the rinor the TAGL1-suppressed lines of tomato. Only MaMADS5 exhibited partial complementation of TAGL1-suppressed and rinlines, suggesting that while similar genes play corresponding roles in ripening, evolutionary divergence makes heterologous complementation studies challenging. Nevertheless, the partial complementation of tomato TAGL1-surpessed and rinlines with MaMADS5 suggests this gene is likely an important ripening regulator in banana, worthy of further study. RNA-seqtranscriptome analysis during ripening was performed on WT and MaMADS2-suppressed lines revealing additional candidate genes contributing to ripening control mechanisms. In summary, we discovered 39 MaMADS-box genes in addition to homologues of CNR, NOR and HB-1 expressed in banana fruits, and which were shown in tomato to play necessary roles in ripening. For most of these genes the expression in peel and pulp was similar. However, a number of key genes were differentially expressed between these tissues indicating that the regulatory components which are active in peel and pulp include both common and tissue-specific regulatory systems, a distinction as compared to the more uniform tomato fruit pericarp. Because plant hormones are well documented to affect fruit ripening, the expressions of genes within the auxin, gibberellin, abscisic acid, jasmonic acid, salicylic and ethylene signal transduction and synthesis pathways were targeted in our transcriptome analysis. Genes’ expression associated with these pathways generally declined during normal ripening in both peel and pulp, excluding cytokinin and ethylene, and this decline was delayed in MaMADS2-suppressed banana lines. Hence, we suggest that normal MaMADS2 activity promotes the observed downward expression within these non-ethylene pathways (especially in the pulp), thus enabling ripening progression. In contrast, the expressions of ACSand ACOof the ethylene biosynthesis pathway increase in peel and pulp during ripening and are delayed/inhibited in the transgenic bananas, explaining the reduced ethylene production of MaMADS2-suppressed lines. Inferred by the different genes’ expression in peel and pulp of the gibberellins, salicylic acid and cytokinins pathways, it is suggested that hormonal regulation in these tissues is diverse. These results provide important insights into possible avenues of ripening control in the diverse fruit tissues of banana which was not previously revealed in other ripening systems. As such, our transcriptome analysis of WT and ripening delayed banana mutants provides a starting point for further characterization of ripening. In this study we also developed novel evidence that the cytoskeleton may have a positive role in ripening as components of this pathway were down-regulated by MaMADS2 suppression. The mode of cytoskeleton involvement in fruit ripening remains unclear but presents a novel new frontier in ripening investigations. In summary, this project yielded functional understanding of the role and mode of action of MaMADS2 during ripening, pointing to both induction of ethylene and suppression of non-ethylene hormonal singling pathways. Furthermore, our data suggest important roles for cytoskeleton components and MaMADS5 in the overall banana ripening control network. Implications: The project revealed new molecular components/genes involved in banana ripening and refines our understanding of ripening responses in the peel and pulp tissues of this important species. This information is novel as compared to that derived from the more uniform carpel tissues of other highly studied ripening systems including tomato and grape. The work provides specific target genes for potential modification through genetic engineering or for exploration of useful genetic diversity in traditional breeding. The results from the project might point toward improved methods or new treatments to improve banana fruit storage and quality.
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Newton, Ronald, Joseph Riov, and John Cairney. Isolation and Functional Analysis of Drought-Induced Genes in Pinus. United States Department of Agriculture, September 1993. http://dx.doi.org/10.32747/1993.7568752.bard.
Full textAbstract:
Drought is a common factor limiting timber production in the U.S. and Israel. Loblolly (Pinus taeda) and alleppo pine (Pinus halepensis) seedling survival is reduced when out planted, and growth and reproduction are often hindered by periodic droughts during later stages of tree development. Molecular and gene responses to drought stress have not been characterized. The objectives were to characterize drought-induced gene clones from these pines, to determine the effects of a growth regulator on drought tolerance, ABA levels, and drought-induced gene expression in alleppo pine, and to develop procedures for loblolly pine transformation. Nearly 20 cDNA clones influenced by gradual, prolonged drought stress have been isolated. Many of these have been shown to be induced by drought stress, whereas several others are down-regulated. These are the first drought-induced genes isolated from a pine species. Two genomic clones (lp5-1 and lp3-1) have been sequenced and characterized, and each has been found to be associated with a gene family. Clone lp5 appears to code for a cell wall protein, and clone lp3 codes for a nuclear protein. The former may be associated with changing the elastic properties of the cell wall, while the latter may be involved in signal transduction and/or protection from desiccation in the nucleus. Clone lp3 is similar to a drought-induced gene from tomato and is regulated by ABA. Several DNA sequences that are specific to induction during growth-retardation in alleppo pine by uniconazole have been identified. The active DNA species is now being identified. Promoters from genomic clones, lp3 and lp5, have been sequenced. Both are functional when fused with the gus reporter gene and transferred to other plant tissues as well as responding to a simulated drought stress. Through exodeletion analysis, it has been established that the promoter ABRE element of lp3 responds to ABA and that drought-induction of lp3 expression may also involve ABA. Stable tobacco transformants carrying either the lp5 or the lp3 promoter fused to a reporter gus gene have been obtained. The lp5lgus fusion was expressed at several stages of tobacco development and differentiation including the reproductive stage. There was no difference in phenotype between the transformants and the wild type. Embryogenesis procedures were developed for slash pine, but attempts to couple this process with gene transfer and plantlet transformation were not successful. Transformation of pine using Agrobacterium appears tractable, but molecular data supporting stable integration of the Agrobacterium-transferred gene are still inconclusive.
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Coplin, David, Isaac Barash, and Shulamit Manulis. Role of Proteins Secreted by the Hrp-Pathways of Erwinia stewartii and E. herbicola pv. gypsophilae in Eliciting Water-Soaking Symptoms and Initiating Galls. United States Department of Agriculture, June 2001. http://dx.doi.org/10.32747/2001.7580675.bard.
Full textAbstract:
Many bacterial pathogens of plants can inject pathogenicity proteins into host cells using a specialized type III secretion system encoded by hrpgenes. This system deliver effector proteins, into plant cells that function in both susceptible and resistant interactions. We have found that the virulence of Erwinia stewartii(Es; syn. Pantoea stewartii) and Erwinia herbicola pv. gypsophilae (Ehg, syn. Pantoea agglomerans), which cause Stewart's wilt of corn and galls on Gypsophila, respectively, depends on hrpgenes. The major objectives of this project were: To increase expression of hrpgenes in order to identify secreted proteins; to identify genes for proteins secreted by the type-III systems and determine if they are required for pathogenicity; and to determine if the secreted proteins can function within eukaryotic cells. We found that transcription of the hrp and effector genes in Es and Ehg is controlled by at least four genes that constitute a regulatory cascade. Environmental and/or physiological signaling appears to be mediated by the HrpX/HrpY two component system, with HrpX functioning as a sensor-kinase and HrpY as a response regulator. HrpYupregulateshrpS, which encodes a transcriptional enhancer. HrpS then activates hrpL, which encodes an alternate sigma factor that recognizes "hrp boxes". All of the regulatory genes are essential for pathogenicity, except HrpX, which appears only to be required for induction of the HR in tobacco by Es. In elucidating this regulatory pathway in both species, we made a number of significant new discoveries. HrpX is unusual for a sensor-kinase because it is cytoplasmic and contains PAS domains, which may sense the redox state of the bacterium. In Es, a novel methyl-accepting protein may function upstream of hrpY and repress hrp gene expression in planta. The esaIR quorum sensing system in Es represses hrp gene expression in Es in response to cell-density. We have discovered six new type III effector proteins in these species, one of which (DspE in Ehg and WtsE in Es) is common to both pathogens. In addition, Es wtsG, which is a homolog of an avrPpiB from P. syringae pv. pisi, and an Ehg ORF, which is a homolog of P. syringae pv. phaseolicola AvrPphD, were both demonstrated to encode virulence proteins. Two plasmidborne, Ehg Hop proteins, HsvG and PthG, are required for infection of gypsophilia, but interestingly, PthG also acts as an Avr elicitor in beets. Using a calmodulin-dependent adenylate cyclase (cyaA) reporter gene, we were successful in demonstrating that an HsvG-CyaA fusion protein can be transferred into human HeLa cells by the type-III system of enteropathogenic E. coli. This is a highly significant accomplishment because it is the first direct demonstration that an effector protein from a plant pathogenic bacterium is capable of being translocated into a eukaryotic cell by a type-III secretion system. Ehg is considered a limiting factor in Gypsophila production in Israel and Stewart’s Wilt is a serious disease in the Eastern and North Central USA, especially on sweet corn in epidemic years. We believe that our basic research on the characterization of type III virulence effectors should enable future identification of their receptors in plant cells. This may lead to novel approaches for genetically engineering resistant plants by modifying their receptors or inactivating effectors and thus blocking the induction of the susceptible response. Alternatively, hrp gene regulation might also provide a target for plant produced compounds that interfere with recognition of the host by the pathogen. Such strategies would be broadly applicable to a wide range of serious bacterial diseases on many crops throughout the USA and Israel.