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Jaishankar J, Keshav A, Jayaram B, Chavan S, Srivastava P. Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194843. [PMID: 35840055 DOI: 10.1016/j.bbagrm.2022.194843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Divergent promoters are often responsible for controlling gene expression of related genes of the same pathway or for coordinating regulation at different time points. There are relatively few reports on characterization of divergent promoters in bacteria. In the present study, microarray profiling was carried out to analyze gene expression during growth of Gordonia sp. IITR100, which led to the identification of 35 % of adjacent gene candidates that are divergently transcribed. We focus here on the in-depth characterization of one such pair of genes. Two divergent promoters, PmaiA and Phyd, drive the expression of genes encoding maleate cis-trans isomerase (maiA) and hydantoinase (hyd), respectively. Our findings reveal asymmetric promoter activity with higher activity in the reverse orientation (Phyd) as compared to the forward orientation (PmaiA). Minimal promoter region for each orientation was identified by deletion mapping. Deletion of a 5'-untranslated region of each gene resulted in an increase in promoter activity. A putative binding site for CRP (Catabolite Repressor Protein) transcription regulator was also identified in the 80 bp common regulatory region between the -35 hexamers of the two promoters. The results of this study suggest that CRP-mediated repression of PmaiA occurs only in the cells grown in glucose. Phyd, on the other hand, is not repressed by CRP. However, deletion of the CRP binding site located between -95 to -110 upstream to the transcription start site of the maiA gene resulted in increased activity of PmaiA and decreased activity of Phyd. A single CRP binding site, therefore, affects the two promoters differently.
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Affiliation(s)
- Jananee Jaishankar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Aditi Keshav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Bijjiga Jayaram
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Sourabh Chavan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India.
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Abstract
DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB), and III (dnaQ/mutD); Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG), and X (exoX); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.
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Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keleş S, Landick R, Kiley PJ. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet 2013; 9:e1003565. [PMID: 23818864 PMCID: PMC3688515 DOI: 10.1371/journal.pgen.1003565] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/29/2013] [Indexed: 01/05/2023] Open
Abstract
FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors that influence its function on a genome-wide scale are poorly understood. Here, we report a functional genomic analysis of FNR action. We find that FNR occupancy at many target sites is strongly influenced by nucleoid-associated proteins (NAPs) that restrict access to many FNR binding sites. At a genome-wide level, only a subset of predicted FNR binding sites were bound under anaerobic fermentative conditions and many appeared to be masked by the NAPs H-NS, IHF and Fis. Similar assays in cells lacking H-NS and its paralog StpA showed increased FNR occupancy at sites bound by H-NS in WT strains, indicating that large regions of the genome are not readily accessible for FNR binding. Genome accessibility may also explain our finding that genome-wide FNR occupancy did not correlate with the match to consensus at binding sites, suggesting that significant variation in ChIP signal was attributable to cross-linking or immunoprecipitation efficiency rather than differences in binding affinities for FNR sites. Correlation of FNR ChIP-seq peaks with transcriptomic data showed that less than half of the FNR-regulated operons could be attributed to direct FNR binding. Conversely, FNR bound some promoters without regulating expression presumably requiring changes in activity of condition-specific transcription factors. Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-fluctuating environment of the mammalian gut. Regulation of gene expression by transcription factors (TFs) is key to adaptation to environmental changes. Our comprehensive, genome-scale analysis of a prototypical global TF, the anaerobic regulator FNR from Escherichia coli, leads to several novel and unanticipated insights into the influences on FNR binding genome-wide and the complex structure of bacterial regulons. We found that binding of NAPs restricts FNR binding at a subset of sites, suggesting that the bacterial genome is not freely accessible for FNR binding. Our finding that less than half of the predicted FNR binding sites were occupied in vivo further challenges the utility of using bioinformatic searches alone to predict regulon structure, reinforcing the need for experimental determination of TF binding. By correlating the occupancy data with transcriptomic data, we confirm that FNR serves as a global signal of anaerobiosis but expression of some operons in the FNR regulon require other regulators sensitive to alternative environmental stimuli. Thus, FNR binding and regulation appear to depend on both the nucleoprotein structure of the chromosome and on combinatorial binding of FNR with other regulators. Both of these phenomena are typical of TF binding in eukaryotes; our results establish that they are also features of bacterial TF binding.
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Affiliation(s)
- Kevin S. Myers
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Huihuang Yan
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Irene M. Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dongjun Chung
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kun Liang
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Frances Tran
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (RL); (PJK)
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (RL); (PJK)
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Downregulation of the Escherichia coli guaB promoter by upstream-bound cyclic AMP receptor protein. J Bacteriol 2009; 191:6094-104. [PMID: 19633076 DOI: 10.1128/jb.00672-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli guaB promoter (P(guaB)) is responsible for directing transcription of the guaB and guaA genes, which specify the biosynthesis of the nucleotide GMP. P(guaB) is subject to growth rate-dependent control (GRDC) and possesses an UP element that is required for this regulation. In addition, P(guaB) contains a discriminator, three binding sites for the nucleoid-associated protein FIS, and putative binding sites for the regulatory proteins DnaA, PurR, and cyclic AMP receptor protein (CRP). Here we show that the CRP-cyclic AMP (cAMP) complex binds to a site located over 100 bp upstream of the guaB transcription start site, where it serves to downregulate P(guaB). The CRP-mediated repression of P(guaB) activity increases in media that support lower growth rates. Inactivation of the crp or cyaA gene or ablation/translocation of the CRP site relieves repression by CRP and results in a loss of GRDC of P(guaB). Thus, GRDC of P(guaB) involves a progressive increase in CRP-mediated repression of the promoter as the growth rate decreases. Our results also suggest that the CRP-cAMP complex does not direct GRDC at P(guaB) and that at least one other regulatory factor is required for conferring GRDC on this promoter. However, PurR and DnaA are not required for this regulatory mechanism.
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Husnain SI, Thomas MS. Downregulation of the Escherichia coli guaB promoter by FIS. MICROBIOLOGY-SGM 2008; 154:1729-1738. [PMID: 18524927 PMCID: PMC2885671 DOI: 10.1099/mic.0.2008/016774-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Escherichia coli guaB promoter (PguaB) regulates transcription of two genes, guaB and guaA, that are required for the synthesis of guanosine 5′-monophosphate (GMP), a precursor for the synthesis of guanine nucleoside triphosphates. Transcription from PguaB increases as a function of increasing cellular growth rate, and this is referred to as growth rate-dependent control (GRDC). Here we investigated the role of the factor for inversion stimulation (FIS) in the regulation of this promoter. The results showed that there are three binding sites for FIS centred near positions −11, +8 and +29 relative to the guaB transcription start site. Binding of FIS to these sites results in repression of PguaB in vitro but not in vivo. Deletion of the fis gene results in increased PguaB activity in vivo, but GRDC of PguaB is maintained.
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Affiliation(s)
- Seyyed I Husnain
- F Floor, School of Medicine and Biomedical Sciences, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Mark S Thomas
- F Floor, School of Medicine and Biomedical Sciences, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
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The UP element is necessary but not sufficient for growth rate-dependent control of the Escherichia coli guaB promoter. J Bacteriol 2008; 190:2450-7. [PMID: 18203835 DOI: 10.1128/jb.01732-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli guaB promoter (P(guaB)) regulates the transcription of two genes, guaB and guaA, that are required for de novo synthesis of GMP, a precursor for the synthesis of guanine nucleoside triphosphates. The activity of P(guaB) is subject to growth rate-dependent control (GRDC). Here we show that the A+T-rich sequence located between positions -59 and -38 relative to the guaB transcription start site stimulates transcription from P(guaB) approximately 8- to 10-fold and, in common with other UP elements, requires the C-terminal domain of the RNA polymerase alpha subunit for activity. Like the rrnB P1 UP element, the P(guaB) UP element contains two independently acting subsites located at positions -59 to -47 and -46 to -38 and can stimulate transcription when placed upstream of the lacP1 promoter. We reveal a novel role for the P(guaB) UP element by demonstrating that it is required for GRDC. The involvement of the UP element in GRDC also requires the participation of sequences located at least 100 bp upstream of the guaB transcription start site. These sequences are required for down-regulation of P(guaB) activity at lower growth rates.
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Oshchepkova-Nedosekina EA, Likhoshvai VA. A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesis. Theor Biol Med Model 2007; 4:11. [PMID: 17326829 PMCID: PMC1808444 DOI: 10.1186/1742-4682-4-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Accepted: 02/27/2007] [Indexed: 12/01/2022] Open
Abstract
Background Development of the mathematical models that adequately describe biochemical reactions and molecular-genetic mechanisms is one of the most important tasks in modern bioinformatics. Because the enzyme adenylosuccinate synthetase (AdSS) has long been extensively studied, a wealth of kinetic data has been accumulated. Results We describe a mathematical model for the reaction catalyzed by AdSS. The model's parameters were fitted to experimental data obtained from published literature. The advantage of our model is that it includes relationships between the reaction rate, the concentrations of three substrates (GTP, IMP and ASP), the effects of five inhibitors (GMP, GDP, AMP, ASUC and SUCC), and the influence of Mg2+ ions. Conclusion Our model describes the reaction catalyzed by AdSS as a fully random process. The model structure implies that each of the inhibitors included in it is only competitive to one of the substrates. The model was tested for adequacy using experimental data published elsewhere. The values obtained for the parameters are as follows: Vmax = 1.35·10-3 mM/min, KmGTP = 0.023 mM, KmIMP = 0.02 mM, KmASP = 0.3 mM, KiGMP = 0.024 mM, KiGDP = 8·10-3 mM, KiAMP = 0.01 mM, KiASUC = 7.5·10-3 mM, KiSUCC = 8 mM, KmMg = 0.08 mM.
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Rathsam C, Eaton RE, Simpson CL, Browne GV, Valova VA, Harty DWS, Jacques NA. Two-dimensional fluorescence difference gel electrophoretic analysis of Streptococcus mutans biofilms. J Proteome Res 2006; 4:2161-73. [PMID: 16335963 DOI: 10.1021/pr0502471] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compared with traditional two-dimensional (2D) proteome analysis of Streptococcus mutans grown as a biofilm from a planktonic culture at steady state (Rathsam et al., Microbiol. 2005, 151, 1823-1837), the use of 2D fluorescence difference gel electrophoresis (DIGE) led to a 3-fold increase in the number of identified protein spots that were significantly altered in their level of expression (P < 0.050). Of the 73 identified proteins, only nine were up-regulated in biofilm grown cells. The results supported the previously surmised hypothesis that general metabolic functions were down-regulated in response to a reduction in growth rate in mature S. mutans biofilms. Up-regulation of competence proteins without any concomitant increase in stress-responsive proteins was confirmed, while the levels of glucosyltransferase C (GtfC), involved in glucan formation, O-acetylserine sulfhyrylase (cysteine synthetase A; CsyK), implicated in the formation of [Fe-S] clusters, and a hypothetical protein encoded by the open reading frame, SMu0188, were also up-regulated.
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Affiliation(s)
- Catherine Rathsam
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, Westmead, New South Wales, Australia
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El-Robh MS, Busby SJW. The Escherichia coli cAMP receptor protein bound at a single target can activate transcription initiation at divergent promoters: a systematic study that exploits new promoter probe plasmids. Biochem J 2002; 368:835-43. [PMID: 12350222 PMCID: PMC1223047 DOI: 10.1042/bj20021003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2002] [Revised: 08/13/2002] [Accepted: 09/26/2002] [Indexed: 11/17/2022]
Abstract
We report the first detailed quantitative study of divergent promoters dependent on the Escherichia coli cAMP receptor protein (CRP), a factor known to activate transcription initiation at target promoters by making direct interactions with the RNA polymerase holoenzyme. In this work, we show that CRP bound at a single target site is able to activate transcription at two divergently organized promoters. Experiments using promoter probe plasmids, designed to study divergent promoters in vivo and in vitro, show that the divergent promoters function independently. Further in vitro experiments show that two holo RNA polymerase molecules cannot be accommodated simultaneously at the divergent promoters.
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Affiliation(s)
- Mohamed Samir El-Robh
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Smulski DR, Huang LL, McCluskey MP, Reeve MJ, Vollmer AC, Van Dyk TK, LaRossa RA. Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12. J Bacteriol 2001; 183:3353-64. [PMID: 11344143 PMCID: PMC99633 DOI: 10.1128/jb.183.11.3353-3364.2001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acivicin, a modified amino acid natural product, is a glutamine analog. Thus, it might interfere with metabolism by hindering glutamine transport, formation, or usage in processes such as transamidation and translation. This molecule prevented the growth of Escherichia coli in minimal medium unless the medium was supplemented with a purine or histidine, suggesting that the HisHF enzyme, a glutamine amidotransferase, was the target of acivicin action. This enzyme, purified from E. coli, was inhibited by low concentrations of acivicin. Acivicin inhibition was overcome by the presence of three distinct genetic regions when harbored on multicopy plasmids. Comprehensive transcript profiling using DNA microarrays indicated that histidine biosynthesis was the predominant process blocked by acivicin. The response to acivicin, however, was quite complex, suggesting that acivicin inhibition resonated through more than a single cellular process.
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Affiliation(s)
- D R Smulski
- Biochemical Science and Engineering, Central Research and Development, DuPont Company, Wilmington, DE 19880-0173, USA
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