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https://www.readbyqxmd.com/read/27789741/the-bacterial-enhancer-dependent-rna-polymerase
#1
REVIEW
Nan Zhang, Vidya C Darbari, Robert Glyde, Xiaodong Zhang, Martin Buck
Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the RNA polymerase down into a state unable to melt out promoter DNA for transcription initiation. Promoter DNA opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bEBPs) that remodel the sigma54 factor within the closed promoter complexes...
November 1, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27193545/transcription-regulation-and-membrane-stress-management-in-enterobacterial-pathogens
#2
REVIEW
Nan Zhang, Goran Jovanovic, Christopher McDonald, Oscar Ces, Xiaodong Zhang, Martin Buck
Transcription regulation in a temporal and conditional manner underpins the lifecycle of enterobacterial pathogens. Upon exposure to a wide array of environmental cues, these pathogens modulate their gene expression via the RNA polymerase and associated sigma factors. Different sigma factors, either involved in general 'house-keeping' or specific responses, guide the RNA polymerase to their cognate promoter DNAs. The major alternative sigma54 factor when activated helps pathogens manage stresses and proliferate in their ecological niches...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/26283774/regulation-of-nitrite-stress-response-in-desulfovibrio-vulgaris-hildenborough-a-model-sulfate-reducing-bacterium
#3
Lara Rajeev, Amy Chen, Alexey E Kazakov, Eric G Luning, Grant M Zane, Pavel S Novichkov, Judy D Wall, Aindrila Mukhopadhyay
UNLABELLED: Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon...
November 2015: Journal of Bacteriology
https://www.readbyqxmd.com/read/26010401/a-perspective-on-the-enhancer-dependent-bacterial-rna-polymerase
#4
REVIEW
Nan Zhang, Martin Buck
Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the sigma54 factor, functions for regulated gene expression. We consider what gaps exist in our understanding of its genetic, biochemical and biophysical functioning and how they might be addressed.
2015: Biomolecules
https://www.readbyqxmd.com/read/25079303/dna-affinity-purified-chip-dap-chip-method-to-determine-gene-targets-for-bacterial-two-component-regulatory-systems
#5
Lara Rajeev, Eric G Luning, Aindrila Mukhopadhyay
In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of limited use in exploring bacterial two component regulatory systems with uncharacterized activation conditions. Such systems regulate transcription only when activated in the presence of unique signals. Since these signals are often unknown, the in vitro microarray based method described in this video article can be used to determine gene targets and binding sites for response regulators...
2014: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/24007446/use-of-a-promiscuous-constitutively-active-bacterial-enhancer-binding-protein-to-define-the-%C3%AF-%C3%A2-%C2%B5%C3%A2-rpon-regulon-of-salmonella-typhimurium-lt2
#6
David J Samuels, Jonathan G Frye, Steffen Porwollik, Michael McClelland, Jan Mrázek, Timothy R Hoover, Anna C Karls
BACKGROUND: Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ⁵⁴ regulon in a bacterium is that the σ⁵⁴ RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a σ⁵⁴-dependent promoter. Many bacteria possess multiple bEBPs, which are activated by diverse environmental stimuli. In this work, we assess the ability of a promiscuous, constitutively-active bEBP-the AAA+ ATPase domain of DctD from Sinorhizobium meliloti-to activate transcription from all σ⁵⁴-dependent promoters for the characterization of the σ⁵⁴ regulon of Salmonella Typhimurium LT2...
2013: BMC Genomics
https://www.readbyqxmd.com/read/21378190/regulation-of-type-vi-secretion-gene-clusters-by-sigma54-and-cognate-enhancer-binding-proteins
#7
Christophe S Bernard, Yannick R Brunet, Marthe Gavioli, Roland Lloubès, Eric Cascales
Type VI secretion systems (T6SS) are bacteriophage-derived macromolecular machines responsible for the release of at least two proteins in the milieu, which are thought to form an extracellular appendage. Although several T6SS have been shown to be involved in the virulence of animal and plant pathogens, clusters encoding these machines are found in the genomes of most species of gram-negative bacteria, including soil, marine, and environmental isolates. T6SS have been associated with several phenotypes, ranging from virulence to biofilm formation or stress sensing...
May 2011: Journal of Bacteriology
https://www.readbyqxmd.com/read/20533077/improvement-of-an-e-coli-bioreporter-for-monitoring-trace-amounts-of-phenol-by-deletion-of-the-inducible-sigma54-dependent-promoter
#8
Zixin Peng, Yongliang Yan, Yuquan Xu, Masahiro Takeo, Haiying Yu, Zhonglin Zhao, Yuhua Zhan, Wei Zhang, Min Lin, Ming Chen
An Escherichia coli bioreporter harboring the phenol-inducible mphK promoter (P(mphK)) from Acinetobacter calcoaceticus PHEA-2 fused to a beta-galactosidase gene (lacZ) and the regulator gene (mopR) of A. calcoaceticus NCIB8250 was constructed to detect phenol. P(mphK) containing three inverted repeats (IR1, IR2 and IR3) upstream of mphK was activated by the regulator MopR in the presence of phenol. Deletion analysis of P(mphK) revealed that IR2 and IR3 were essential for promoter activity, while IR1 was involved in transcriptional repression...
September 2010: Biotechnology Letters
https://www.readbyqxmd.com/read/20167112/multiple-controls-affect-arsenite-oxidase-gene-expression-in-herminiimonas-arsenicoxydans
#9
Sandrine Koechler, Jessica Cleiss-Arnold, Caroline Proux, Odile Sismeiro, Marie-Agnès Dillies, Florence Goulhen-Chollet, Florence Hommais, Didier Lièvremont, Florence Arsène-Ploetze, Jean-Yves Coppée, Philippe N Bertin
BACKGROUND: Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism...
2010: BMC Microbiology
https://www.readbyqxmd.com/read/20053297/global-transcriptional-analysis-of-nitrogen-fixation-and-ammonium-repression-in-root-associated-pseudomonas-stutzeri-a1501
#10
Yongliang Yan, Shuzhen Ping, Junping Peng, Yunlei Han, Liang Li, Jian Yang, Yuetan Dou, Yan Li, Huili Fan, Ying Fan, Danhua Li, Yuhua Zhan, Ming Chen, Wei Lu, Wei Zhang, Qi Cheng, Qi Jin, Min Lin
BACKGROUND: Biological nitrogen fixation is highly controlled at the transcriptional level by regulatory networks that respond to the availability of fixed nitrogen. In many diazotrophs, addition of excess ammonium in the growth medium results in immediate repression of nif gene transcription. Although the regulatory cascades that control the transcription of the nif genes in proteobacteria have been well investigated, there are limited data on the kinetics of ammonium-dependent repression of nitrogen fixation...
2010: BMC Genomics
https://www.readbyqxmd.com/read/19969540/promoter-and-regulon-analysis-of-nitrogen-assimilation-factor-sigma54-reveal-alternative-strategy-for-e-coli-mg1655-flagellar-biosynthesis
#11
Kai Zhao, Mingzhu Liu, Richard R Burgess
Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarrays representing the entire Escherichia coli genome and promoter validation approaches, we identify 40 in vivo targets of sigma(54), the nitrogen assimilation sigma factor, and estimate that there are 70 sigma(54) promoters in total...
March 2010: Nucleic Acids Research
https://www.readbyqxmd.com/read/19955233/essential-roles-of-three-enhancer-sites-in-sigma54-dependent-transcription-by-the-nitric-oxide-sensing-regulatory-protein-norr
#12
Nicholas P Tucker, Tamaswati Ghosh, Matthew Bush, Xiaodong Zhang, Ray Dixon
The bacterial activator protein NorR binds to enhancer-like elements, upstream of the promoter site, and activates sigma(54)-dependent transcription of genes that encode nitric oxide detoxifying enzymes (NorVW), in response to NO stress. Unique to the norVW promoter in Escherichia coli is the presence of three enhancer sites associated with a binding site for sigma(54)-RNA polymerase. Here we show that all three sites are required for NorR-dependent catalysis of open complex formation by sigma(54)-RNAP holoenzyme (Esigma(54))...
March 2010: Nucleic Acids Research
https://www.readbyqxmd.com/read/19942662/sigma54-mediated-control-of-the-mannose-phosphotransferase-sytem-in-lactobacillus-plantarum-impacts-on-carbohydrate-metabolism
#13
Marc J A Stevens, Douwe Molenaar, Anne de Jong, Willem M De Vos, Michiel Kleerebezem
Sigma factors direct specific binding of the bacterial RNA polymerase to the promoter. Here we present the elucidation of the sigma(54 ) regulon in Lactobacillus plantarum. A sequence-based regulon prediction of sigma(54)-dependent promoters revealed an operon encoding a mannose phosphotransferase system (PTS) as the best candidate for sigma(54)-mediated control. A sigma (54) (rpoN) mutant derivative did not grow on mannose, confirming this prediction. Additional mutational analyses established the presence of one functional mannose PTS in L...
March 2010: Microbiology
https://www.readbyqxmd.com/read/19915033/identification-of-the-geobacter-metallireducens-bamvw-two-component-system-involved-in-transcriptional-regulation-of-aromatic-degradation
#14
Javier F Juárez, María Teresa Zamarro, María J L Barragán, Blas Blázquez, Matthias Boll, Kevin Kuntze, José Luis García, Eduardo Díaz, Manuel Carmona
Regulation of aromatic degradation in obligate anaerobes was studied in the Fe(III)-respiring model organism Geobacter metallireducens GS-15. A two-component system and a sigma54-dependent promoter were identified that are both involved in the regulation of the gene coding for benzoate-coenzyme A ligase, catalyzing the initial step of benzoate degradation.
January 2010: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/19854901/structure-and-regulation-of-the-gab-gene-cluster-involved-in-the-gamma-aminobutyric-acid-shunt-are-controlled-by-a-sigma54-factor-in-bacillus-thuringiensis
#15
Li Zhu, Qi Peng, Fuping Song, Yanan Jiang, Changpo Sun, Jie Zhang, Dafang Huang
The structure and regulation of the gab gene cluster, involved in gamma-aminobutyric acid (GABA) shunt, were studied by characterizing gabT and gabD genes cloned from Bacillus thuringiensis. Deletions of the gabT and gabD genes in B. thuringiensis strain HD-73 did not affect the growth of mutant strains in rich culture media, but the growth of a gabT deletion mutant strain was reduced in basic media (containing 0.2% GABA). Genome analysis indicates that the structure of the gab gene cluster in B. thuringiensis HD-73 is different from that in Escherichia coli and Bacillus subtilis but is common in strains of the Bacillus cereus group...
January 2010: Journal of Bacteriology
https://www.readbyqxmd.com/read/19840105/nifa-is-required-for-maximal-expression-of-denitrification-genes-in-bradyrhizobium-japonicum
#16
Emilio Bueno, Socorro Mesa, Cristina Sanchez, Eulogio J Bedmar, María J Delgado
In Bradyrhizobium japonicum the napEDABC, nirK, norCBQD and nosRZDYFLX genes, which encode reductases for nitrate, nitrite, nitric oxide and nitrous oxide, respectively, are required for denitrification. Microaerobic induction of these genes depends on fixLJ and fixK2, whose products form the FixLJ-FixK2 regulatory cascade. In B. japonicum, a second oxygen-responsive regulatory cascade mediated by the nitrogen fixation regulatory protein, NifA, has been described. In this study, we show that disruption of nifA caused a growth defect in B...
February 2010: Environmental Microbiology
https://www.readbyqxmd.com/read/19763344/scaling-relationship-in-the-gene-content-of-transcriptional-machinery-in-bacteria
#17
REVIEW
Ernesto Pérez-Rueda, Sarath Chandra Janga, Agustino Martínez-Antonio
The metabolic, defensive, communicative and pathogenic capabilities of eubacteria depend on their repertoire of genes and ability to regulate the expression of them. Sigma and transcription factors have fundamental roles in controlling these processes. Here, we show that sigma, transcription factors (TFs) and the number of protein coding genes occur in different magnitudes across 291 non-redundant eubacterial genomes. We suggest that these differences can be explained based on the fact that the universe of TFs, in contrast to sigma factors, exhibits a greater flexibility for transcriptional regulation, due to their ability to sense diverse stimuli through a variety of ligand-binding domains by discriminating over longer regions on DNA, through their diverse DNA-binding domains, and by their combinatorial role with other sigmas and TFs...
December 2009: Molecular BioSystems
https://www.readbyqxmd.com/read/19699748/receiver-domains-control-the-active-state-stoichiometry-of-aquifex-aeolicus-sigma54-activator-ntrc4-as-revealed-by-electrospray-ionization-mass-spectrometry
#18
Joseph D Batchelor, Harry J Sterling, Eunmi Hong, Evan R Williams, David E Wemmer
A common challenge with studies of proteins in vitro is determining which constructs and conditions are most physiologically relevant. sigma(54) activators are proteins that undergo regulated assembly to form an active ATPase ring that enables transcription by sigma(54)-polymerase. Previous studies of AAA(+) ATPase domains from sigma(54) activators have shown that some are heptamers, while others are hexamers. Because active oligomers assemble from off-state dimers, it was thought that even-numbered oligomers should dominate, and that heptamer formation would occur when individual domains of the activators, rather than the intact proteins, were studied...
October 30, 2009: Journal of Molecular Biology
https://www.readbyqxmd.com/read/19692583/the-role-of-the-conserved-phenylalanine-in-the-sigma54-interacting-gaftga-motif-of-bacterial-enhancer-binding-proteins
#19
Nan Zhang, Nicolas Joly, Patricia C Burrows, Milija Jovanovic, Siva R Wigneshweraraj, Martin Buck
sigma(54)-dependent transcription requires activation by bacterial enhancer binding proteins (bEBPs). bEBPs are members of the AAA+ (ATPases associated with various cellular activities) protein family and typically form hexameric structures that are crucial for their ATPase activity. The precise mechanism by which the energy derived from ATP hydrolysis is coupled to biological output has several unknowns. Here we use Escherichia coli PspF, a model bEBP involved in the transcription of stress response genes (psp operon), to study determinants of its contact features with the closed promoter complex...
October 2009: Nucleic Acids Research
https://www.readbyqxmd.com/read/19474350/construction-and-functional-analyses-of-a-comprehensive-sigma54-site-directed-mutant-library-using-alanine-cysteine-mutagenesis
#20
Yan Xiao, Siva R Wigneshweraraj, Robert Weinzierl, Yi-Ping Wang, Martin Buck
The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction and open complex formation. To systematically define sigma(54) residues that contribute to each of these functions and to generate a resource for site specific protein labeling, a complete mutant library of sigma(54) was constructed by alanine-cysteine scanning mutagenesis...
July 2009: Nucleic Acids Research
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