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Frendorf PO, Heyde SAH, Nørholm MHH. Mutations upstream from sdaC and malT in Escherichia coli uncover a complex interplay between the cAMP receptor protein and different sigma factors. J Bacteriol 2024; 206:e0035523. [PMID: 38197669 PMCID: PMC10882989 DOI: 10.1128/jb.00355-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
In Escherichia coli, one of the best understood microorganisms, much can still be learned about the basic interactions between transcription factors and promoters. When a cAMP-deficient cya mutant is supplied with maltose as the main carbon source, mutations develop upstream from the two genes malT and sdaC. Here, we explore the regulation of the two promoters, using fluorescence-based genetic reporters in combination with both spontaneously evolved and systematically engineered cis-acting mutations. We show that in the cya mutant, regulation of malT and sdaC evolves toward cAMP-independence and increased expression in the stationary phase. Furthermore, we show that the location of the cAMP receptor protein (Crp) binding site upstream of malT is important for alternative sigma factor usage. This provides new insights into the architecture of bacterial promoters and the global interplay between Crp and sigma factors in different growth phases.IMPORTANCEThis work provides new general insights into (1) the architecture of bacterial promoters, (2) the importance of the location of Class I Crp-dependent promoters, and (3) the global interplay between Crp and sigma factors in different growth phases.
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Affiliation(s)
- Pernille Ott Frendorf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Sophia A. H. Heyde
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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2
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Chen Y, Lin YCD, Luo Y, Cai X, Qiu P, Cui S, Wang Z, Huang HY, Huang HD. Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis. Brief Bioinform 2023; 24:7145906. [PMID: 37114659 DOI: 10.1093/bib/bbad138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023] Open
Abstract
Cyclic AMP receptor proteins (CRPs) are important transcription regulators in many species. The prediction of CRP-binding sites was mainly based on position-weighted matrixes (PWMs). Traditional prediction methods only considered known binding motifs, and their ability to discover inflexible binding patterns was limited. Thus, a novel CRP-binding site prediction model called CRPBSFinder was developed in this research, which combined the hidden Markov model, knowledge-based PWMs and structure-based binding affinity matrixes. We trained this model using validated CRP-binding data from Escherichia coli and evaluated it with computational and experimental methods. The result shows that the model not only can provide higher prediction performance than a classic method but also quantitatively indicates the binding affinity of transcription factor binding sites by prediction scores. The prediction result included not only the most knowns regulated genes but also 1089 novel CRP-regulated genes. The major regulatory roles of CRPs were divided into four classes: carbohydrate metabolism, organic acid metabolism, nitrogen compound metabolism and cellular transport. Several novel functions were also discovered, including heterocycle metabolic and response to stimulus. Based on the functional similarity of homologous CRPs, we applied the model to 35 other species. The prediction tool and the prediction results are online and are available at: https://awi.cuhk.edu.cn/∼CRPBSFinder.
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Affiliation(s)
- Yigang Chen
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yang-Chi-Dung Lin
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yijun Luo
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Xiaoxuan Cai
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Peng Qiu
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Shidong Cui
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Zhe Wang
- School of Humanities and Social Science, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Hsi-Yuan Huang
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Hsien-Da Huang
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
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Park H, McGill SL, Arnold AD, Carlson RP. Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor. Cell Mol Life Sci 2020; 77:395-413. [PMID: 31768608 PMCID: PMC7015805 DOI: 10.1007/s00018-019-03377-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
Abstract
Microorganisms acquire energy and nutrients from dynamic environments, where substrates vary in both type and abundance. The regulatory system responsible for prioritizing preferred substrates is known as carbon catabolite repression (CCR). Two broad classes of CCR have been documented in the literature. The best described CCR strategy, referred to here as classic CCR (cCCR), has been experimentally and theoretically studied using model organisms such as Escherichia coli. cCCR phenotypes are often used to generalize universal strategies for fitness, sometimes incorrectly. For instance, extremely competitive microorganisms, such as Pseudomonads, which arguably have broader global distributions than E. coli, have achieved their success using metabolic strategies that are nearly opposite of cCCR. These organisms utilize a CCR strategy termed 'reverse CCR' (rCCR), because the order of preferred substrates is nearly reverse that of cCCR. rCCR phenotypes prefer organic acids over glucose, may or may not select preferred substrates to optimize growth rates, and do not allocate intracellular resources in a manner that produces an overflow metabolism. cCCR and rCCR have traditionally been interpreted from the perspective of monocultures, even though most microorganisms live in consortia. Here, we review the basic tenets of the two CCR strategies and consider these phenotypes from the perspective of resource acquisition in consortia, a scenario that surely influenced the evolution of cCCR and rCCR. For instance, cCCR and rCCR metabolism are near mirror images of each other; when considered from a consortium basis, the complementary properties of the two strategies can mitigate direct competition for energy and nutrients and instead establish cooperative division of labor.
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Affiliation(s)
- Heejoon Park
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
| | - S Lee McGill
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
| | - Adrienne D Arnold
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, USA.
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, USA.
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Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PLoS One 2018; 13:e0197272. [PMID: 29771928 PMCID: PMC5957442 DOI: 10.1371/journal.pone.0197272] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70 are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation.
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Affiliation(s)
- Haythem Latif
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Stephen Federowicz
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Ali Ebrahim
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Janna Tarasova
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Richard Szubin
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Jose Utrilla
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Karsten Zengler
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bernhard O. Palsson
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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5
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Schulte J, Baumgart M, Bott M. Identification of the cAMP phosphodiesterase CpdA as novel key player in cAMP-dependent regulation in Corynebacterium glutamicum. Mol Microbiol 2016; 103:534-552. [PMID: 27862445 DOI: 10.1111/mmi.13574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2016] [Indexed: 02/03/2023]
Abstract
The second messenger cyclic AMP (cAMP) plays an important role in the metabolism of Corynebacterium glutamicum, as the global transcriptional regulator GlxR requires complex formation with cAMP to become active. Whereas a membrane-bound adenylate cyclase, CyaB, was shown to be involved in cAMP synthesis, enzymes catalyzing cAMP degradation have not been described yet. In this study we identified a class II cAMP phosphodiesterase named CpdA (Cg2761), homologs of which are present in many Actinobacteria. The purified enzyme has a Kmapp value of 2.5 ± 0.3 mM for cAMP and a Vmaxapp of 33.6 ± 4.3 µmol min-1 mg-1 . A ΔcpdA mutant showed a twofold increased cAMP level on glucose and reduced growth rates on all carbon sources tested. A transcriptome comparison revealed 247 genes with a more than twofold altered mRNA level in the ΔcpdA mutant, 82 of which are known GlxR targets. Expression of cpdA was positively regulated by GlxR, thereby creating a negative feedback loop allowing to counteract high cAMP levels. The results show that CpdA plays a key role in the control of the cellular cAMP concentration and GlxR activity and is crucial for optimal metabolism and growth of C. glutamicum.
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Affiliation(s)
- Julia Schulte
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, 52425, Germany
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6
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Yang S, Xu H, Wang J, Liu C, Lu H, Liu M, Zhao Y, Tian B, Wang L, Hua Y. Cyclic AMP Receptor Protein Acts as a Transcription Regulator in Response to Stresses in Deinococcus radiodurans. PLoS One 2016; 11:e0155010. [PMID: 27182600 PMCID: PMC4868304 DOI: 10.1371/journal.pone.0155010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/22/2016] [Indexed: 11/24/2022] Open
Abstract
The cyclic AMP receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. Here, we identify four homologs of the CRP family in Deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and DNA-damaging reagents. Transcriptional levels of CRP were increased under hydrogen peroxide (H2O2) treatment during the stationary growth phase, indicating that CRPs function in response to oxidative stress. By constructing all CRP single knockout mutants, we found that the dr0997 mutant showed the lowest tolerance toward H2O2, ultraviolet radiation, ionizing radiation, and mitomycin C, while the phenotypes of the dr2362, dr0834, and dr1646 mutants showed slight or no significant differences from those of the wild-type strain. Taking advantage of the conservation of the CRP-binding site in many bacteria, we found that transcription of 18 genes, including genes encoding chromosome-partitioning protein (dr0998), Lon proteases (dr0349 and dr1974), NADH-quinone oxidoreductase (dr1506), thiosulfate sulfurtransferase (dr2531), the DNA repair protein UvsE (dr1819), PprA (dra0346), and RecN (dr1447), are directly regulated by DR0997. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses showed that certain genes involved in anti-oxidative responses, DNA repair, and various cellular pathways are transcriptionally attenuated in the dr0997 mutant. Interestingly, DR0997 also regulate the transcriptional levels of all CRP genes in this bacterium. These data suggest that DR0997 contributes to the extreme stress resistance of D. radiodurans via its regulatory role in multiple cellular pathways, such as anti-oxidation and DNA repair pathways.
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Affiliation(s)
- Su Yang
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Hong Xu
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Jiali Wang
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Chengzhi Liu
- Laboratory of Microbiology and Genomics, Zhejiang Institute of Microbiology, Hangzhou, China
| | - Huizhi Lu
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Mengjia Liu
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Ye Zhao
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Bing Tian
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Liangyan Wang
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
- * E-mail: (YH); (LW)
| | - Yuejin Hua
- Key Laboratory of Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
- * E-mail: (YH); (LW)
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7
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Molecular Mechanisms of Transcription Initiation at gal Promoters and their Multi-Level Regulation by GalR, CRP and DNA Loop. Biomolecules 2015; 5:2782-807. [PMID: 26501343 PMCID: PMC4693257 DOI: 10.3390/biom5042782] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/25/2015] [Indexed: 11/16/2022] Open
Abstract
Studying the regulation of transcription of the gal operon that encodes the amphibolic pathway of d-galactose metabolism in Escherichia coli discerned a plethora of principles that operate in prokaryotic gene regulatory processes. In this chapter, we have reviewed some of the more recent findings in gal that continues to reveal unexpected but important mechanistic details. Since the operon is transcribed from two overlapping promoters, P1 and P2, regulated by common regulatory factors, each genetic or biochemical experiment allowed simultaneous discernment of two promoters. Recent studies range from genetic, biochemical through biophysical experiments providing explanations at physiological, mechanistic and single molecule levels. The salient observations highlighted here are: the axiom of determining transcription start points, discovery of a new promoter element different from the known ones that influences promoter strength, occurrence of an intrinsic DNA sequence element that overrides the transcription elongation pause created by a DNA-bound protein roadblock, first observation of a DNA loop and determination its trajectory, and piggybacking proteins and delivering to their DNA target.
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8
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Murayama S, Ishikawa S, Chumsakul O, Ogasawara N, Oshima T. The Role of α-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells. PLoS One 2015; 10:e0131588. [PMID: 26154296 PMCID: PMC4495994 DOI: 10.1371/journal.pone.0131588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 06/02/2015] [Indexed: 11/22/2022] Open
Abstract
The amino acid sequence of the RNA polymerase (RNAP) α-subunit is well conserved throughout the Eubacteria. Its C-terminal domain (α-CTD) is important for the transcriptional regulation of specific promoters in both Escherichia coli and Bacillus subtilis, through interactions with transcription factors and/or a DNA element called the "UP element". However, there is only limited information regarding the α-CTD regulated genes in B. subtilis and the importance of this subunit in the transcriptional regulation of B. subtilis. Here, we established strains and the growth conditions in which the α-subunit of RNAP was replaced with a C-terminally truncated version. Transcriptomic and ChAP-chip analyses revealed that α-CTD deficiency reduced the transcription and RNAP binding of genes related to the utilization of secondary carbon sources, transition state responses, and ribosome synthesis. In E. coli, it is known that α-CTD also contributes to the expression of genes related to the utilization of secondary carbon sources and ribosome synthesis. Our results suggest that the biological importance of α-CTD is conserved in B. subtilis and E. coli, but that its specific roles have diversified between these two bacteria.
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Affiliation(s)
- Satohiko Murayama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Shu Ishikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Onuma Chumsakul
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
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9
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The transport and mediation mechanisms of the common sugars in Escherichia coli. Biotechnol Adv 2014; 32:905-19. [DOI: 10.1016/j.biotechadv.2014.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/23/2014] [Accepted: 04/18/2014] [Indexed: 11/17/2022]
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10
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Abstract
Glucose confers acid resistance on exponentially growing bacteria by repressing formation of the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex and consequently activating acid resistance genes. Therefore, in a glucose-rich growth environment, bacteria are capable of resisting acidic stresses due to low levels of cAMP-CRP. Here we reveal a second mechanism for glucose-conferred acid resistance. We show that glucose induces acid resistance in exponentially growing bacteria through pyruvate, the glycolysis product. Pyruvate and/or the downstream metabolites induce expression of the small noncoding RNA (sncRNA) Spot42, and the sncRNA, in turn, activates expression of the master regulator of acid resistance, RpoS. In contrast to glucose, pyruvate has little effect on levels of the cAMP-CRP complex and does not require the complex for its effects on acid resistance. Another important difference between glucose and pyruvate is that pyruvate can be produced by bacteria. This means that bacteria have the potential to protect themselves from acidic stresses by controlling glucose-derived generation of pyruvate, pyruvate-acetate efflux, or reversion from acetate to pyruvate. We tested this possibility by shutting down pyruvate-acetate efflux and found that the resulting accumulation of pyruvate elevated acid resistance. Many sugars can be broken into glucose, and the subsequent glycolysis generates pyruvate. Therefore, pyruvate-associated acid resistance is not confined to glucose-grown bacteria but is functional in bacteria grown on various sugars.
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11
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Shimamoto N. Nanobiology of RNA polymerase: biological consequence of inhomogeneity in reactant. Chem Rev 2013; 113:8400-22. [PMID: 24074222 DOI: 10.1021/cr400006b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nobuo Shimamoto
- Faculty of Life Sciences, Kyoto Sangyo University , Kamigamo-Motoyama, Kita-Ku, Kyoto, 603-8555 Japan
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12
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Sun Y, Bernardy EE, Hammer BK, Miyashiro T. Competence and natural transformation in vibrios. Mol Microbiol 2013; 89:583-95. [PMID: 23803158 DOI: 10.1111/mmi.12307] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2013] [Indexed: 01/01/2023]
Abstract
Natural transformation is a major mechanism of horizontal gene transfer in bacteria. By incorporating exogenous DNA elements into chromosomes, bacteria are able to acquire new traits that can enhance their fitness in different environments. Within the past decade, numerous studies have revealed that natural transformation is prevalent among members of the Vibrionaceae, including the pathogen Vibrio cholerae. Four environmental factors: (i) nutrient limitation, (ii) availability of extracellular nucleosides, (iii) high cell density and (iv) the presence of chitin, promote genetic competence and natural transformation in Vibrio cholerae by co-ordinating expression of the regulators CRP, CytR, HapR and TfoX respectively. Studies of other Vibrionaceae members highlight the general importance of natural transformation within this bacterial family.
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Affiliation(s)
- Yan Sun
- Department of Biochemistry and Molecular Biology Eberly College of Science The Pennsylvania State University 219 Wartik Lab University Park, PA 16802, USA
| | - Eryn E Bernardy
- School of Biology Georgia Institute of Technology 310 Ferst Drive, Atlanta, GA 30332-0230
| | - Brian K Hammer
- School of Biology Georgia Institute of Technology 310 Ferst Drive, Atlanta, GA 30332-0230
| | - Tim Miyashiro
- Department of Biochemistry and Molecular Biology Eberly College of Science The Pennsylvania State University 219 Wartik Lab University Park, PA 16802, USA
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Wilksch JJ, Yang J, Clements A, Gabbe JL, Short KR, Cao H, Cavaliere R, James CE, Whitchurch CB, Schembri MA, Chuah MLC, Liang ZX, Wijburg OL, Jenney AW, Lithgow T, Strugnell RA. MrkH, a novel c-di-GMP-dependent transcriptional activator, controls Klebsiella pneumoniae biofilm formation by regulating type 3 fimbriae expression. PLoS Pathog 2011; 7:e1002204. [PMID: 21901098 PMCID: PMC3161979 DOI: 10.1371/journal.ppat.1002204] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 06/24/2011] [Indexed: 12/17/2022] Open
Abstract
Klebsiella pneumoniae causes significant morbidity and mortality worldwide, particularly amongst hospitalized individuals. The principle mechanism for pathogenesis in hospital environments involves the formation of biofilms, primarily on implanted medical devices. In this study, we constructed a transposon mutant library in a clinical isolate, K. pneumoniae AJ218, to identify the genes and pathways implicated in biofilm formation. Three mutants severely defective in biofilm formation contained insertions within the mrkABCDF genes encoding the main structural subunit and assembly machinery for type 3 fimbriae. Two other mutants carried insertions within the yfiN and mrkJ genes, which encode GGDEF domain- and EAL domain-containing c-di-GMP turnover enzymes, respectively. The remaining two isolates contained insertions that inactivated the mrkH and mrkI genes, which encode for novel proteins with a c-di-GMP-binding PilZ domain and a LuxR-type transcriptional regulator, respectively. Biochemical and functional assays indicated that the effects of these factors on biofilm formation accompany concomitant changes in type 3 fimbriae expression. We mapped the transcriptional start site of mrkA, demonstrated that MrkH directly activates transcription of the mrkA promoter and showed that MrkH binds strongly to the mrkA regulatory region only in the presence of c-di-GMP. Furthermore, a point mutation in the putative c-di-GMP-binding domain of MrkH completely abolished its function as a transcriptional activator. In vivo analysis of the yfiN and mrkJ genes strongly indicated their c-di-GMP-specific function as diguanylate cyclase and phosphodiesterase, respectively. In addition, in vitro assays showed that purified MrkJ protein has strong c-di-GMP phosphodiesterase activity. These results demonstrate for the first time that c-di-GMP can function as an effector to stimulate the activity of a transcriptional activator, and explain how type 3 fimbriae expression is coordinated with other gene expression programs in K. pneumoniae to promote biofilm formation to implanted medical devices. Biofilms are surface-associated communities of microorganisms. Biofilm-associated bacteria are protected from host defenses and antibiotics and are the cause of many infections. Klebsiella pneumoniae is primarily a hospital-acquired bacterial pathogen that causes pneumonia, urinary tract infections and septicemia. Its success is related to its ability to form biofilms on medical devices, such as catheters. In K. pneumoniae, biofilm formation is mediated by type 3 fimbriae – hair-like, protein appendages extending out from the cell surface that adhere to surfaces. This study investigated how K. pneumoniae regulates the expression of these fimbriae. We identified a protein, MrkH, which behaves as a “biofilm switch” that turns on the expression of genes responsible for producing type 3 fimbriae. MrkH works by binding to regulatory regions of DNA nearby to these genes and initiates their expression. Importantly, MrkH binds to DNA strongly only when the protein is stimulated by a small molecule, c-di-GMP. Furthermore, we identified bacterial enzymes that either produce or break down c-di-GMP to control its concentration within the cell, and thus modulate MrkH activity. Understanding the molecular basis for these processes may lead to the development of therapeutic compounds, possibly for incorporation into medical device materials to inhibit biofilm formation and pathogenesis.
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Affiliation(s)
- Jonathan J Wilksch
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia.
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14
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Rojo F. Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 2010; 34:658-84. [PMID: 20412307 DOI: 10.1111/j.1574-6976.2010.00218.x] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Metabolically versatile free-living bacteria have global regulation systems that allow cells to selectively assimilate a preferred compound among a mixture of several potential carbon sources. This process is known as carbon catabolite repression (CCR). CCR optimizes metabolism, improving the ability of bacteria to compete in their natural habitats. This review summarizes the regulatory mechanisms responsible for CCR in the bacteria of the genus Pseudomonas, which can live in many different habitats. Although the information available is still limited, the molecular mechanisms responsible for CCR in Pseudomonas are clearly different from those of Enterobacteriaceae or Firmicutes. An understanding of the molecular mechanisms underlying CCR is important to know how metabolism is regulated and how bacteria degrade compounds in the environment. This is particularly relevant for compounds that are degraded slowly and accumulate, creating environmental problems. CCR has a major impact on the genes involved in the transport and metabolism of nonpreferred carbon sources, but also affects the expression of virulence factors in several bacterial species, genes that are frequently directed to allow the bacterium to gain access to new sources of nutrients. Finally, CCR has implications in the optimization of biotechnological processes such as biotransformations or bioremediation strategies.
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Affiliation(s)
- Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
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15
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Xu M, Su Z. Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes. BMC Genomics 2009; 10:23. [PMID: 19146659 PMCID: PMC2633013 DOI: 10.1186/1471-2164-10-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Accepted: 01/15/2009] [Indexed: 11/30/2022] Open
Abstract
Background Cyclic AMP receptor protein (CRP), also known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. Results We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. Conclusion The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The loss of CRPs in these species leads to the rapid loss of their binding sites in the genomes.
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Affiliation(s)
- Minli Xu
- Department of Bioinformatics and Genomics, Bioinformatics Research Center, the University of North Carolina at Charlotte, Charlotte, NC 28233, USA.
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16
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Görke B, Stülke J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 2008; 6:613-24. [PMID: 18628769 DOI: 10.1038/nrmicro1932] [Citation(s) in RCA: 1089] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Most bacteria can selectively use substrates from a mixture of different carbon sources. The presence of preferred carbon sources prevents the expression, and often also the activity, of catabolic systems that enable the use of secondary substrates. This regulation, called carbon catabolite repression (CCR), can be achieved by different regulatory mechanisms, including transcription activation and repression and control of translation by an RNA-binding protein, in different bacteria. Moreover, CCR regulates the expression of virulence factors in many pathogenic bacteria. In this Review, we discuss the most recent findings on the different mechanisms that have evolved to allow bacteria to use carbon sources in a hierarchical manner.
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Affiliation(s)
- Boris Görke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr 8, D-37077 Göttingen, Germany
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17
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Laishram RS, Gowrishankar J. Environmental regulation operating at the promoter clearance step of bacterial transcription. Genes Dev 2008; 21:1258-72. [PMID: 17504942 PMCID: PMC1865496 DOI: 10.1101/gad.1520507] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In vivo transcription of the Escherichia coli argO gene, which encodes an arginine (Arg) exporter, requires the LysR-family regulator protein ArgP (previously called IciA) and is induced in the presence of Arg or its naturally occurring antimetabolite analog canavanine. Lysine (Lys) addition, on the other hand, phenocopies an argP mutation to result in the shutoff of argO expression. We now report that the ArgP dimer by itself is able to bind the argO promoter-operator region to form a binary complex, but that the formation of a ternary complex with RNA polymerase is greatly stimulated only in presence of a coeffector. Both Arg and Lys were proficient as coeffectors for ArgP-mediated recruitment of RNA polymerase to, and open complex formation at, the argO promoter, although only Arg (but not Lys) was competent to activate transcription. The two coeffectors competed for binding to ArgP, and the ternary complex that had been assembled on the argO template in the presence of Lys could be chased into a transcriptionally active state upon Arg addition. Our results support a novel mechanism of argO regulation in which Lys-bound ArgP reversibly restrains RNA polymerase at the promoter, at a step (following open complex formation) that precedes, and is common to, both abortive and productive transcription. This represents, therefore, the first example of an environmental signal regulating the final step of promoter clearance by RNA polymerase in bacterial transcription. We propose that, in E. coli cells, the ternary complex remains assembled and poised at the argO promoter at all times to respond, positively or negatively, to instantaneous changes in the ratio of intracellular Arg to Lys concentrations.
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Affiliation(s)
- Rakesh S. Laishram
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500076, India
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500076, India
- Corresponding author.E-MAIL ; FAX 91-40-27155610
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18
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Shinkai A, Kira S, Nakagawa N, Kashihara A, Kuramitsu S, Yokoyama S. Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J Bacteriol 2007; 189:3891-901. [PMID: 17369302 PMCID: PMC1913326 DOI: 10.1128/jb.01739-06] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The extremely thermophilic bacterium Thermus thermophilus HB8, which belongs to the phylum Deinococcus-Thermus, has an open reading frame encoding a protein belonging to the cyclic AMP (cAMP) receptor protein (CRP) family present in many bacteria. The protein named T. thermophilus CRP is highly homologous to the CRP family proteins from the phyla Firmicutes, Actinobacteria, and Cyanobacteria, and it forms a homodimer and interacts with cAMP. CRP mRNA and intracellular cAMP were detected in this strain, which did not drastically fluctuate during cultivation in a rich medium. The expression of several genes was altered upon disruption of the T. thermophilus CRP gene. We found six CRP-cAMP-dependent promoters in in vitro transcription assays involving DNA fragments containing the upstream regions of the genes exhibiting decreased expression in the CRP disruptant, indicating that the CRP is a transcriptional activator. The consensus T. thermophilus CRP-binding site predicted upon nucleotide sequence alignment is 5'-(C/T)NNG(G/T)(G/T)C(A/C)N(A/T)NNTCACAN(G/C)(G/C)-3'. This sequence is unique compared with the known consensus binding sequences of CRP family proteins. A putative -10 hexamer sequence resides at 18 to 19 bp downstream of the predicted T. thermophilus CRP-binding site. The CRP-regulated genes found in this study comprise clustered regularly interspaced short palindromic repeat (CRISPR)-associated (cas) ones, and the genes of a putative transcriptional regulator, a protein containing the exonuclease III-like domain of DNA polymerase, a GCN5-related acetyltransferase homolog, and T. thermophilus-specific proteins of unknown function. These results suggest a role for cAMP signal transduction in T. thermophilus and imply the T. thermophilus CRP is a cAMP-responsive regulator.
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Affiliation(s)
- Akeo Shinkai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
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19
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Abstract
In transcription initiation, all RNA polymerase molecules bound to a promoter have been conventionally supposed to proceed into elongation of transcript. However, for Escherichia coli RNA polymerase, evidence has been accumulated for a view that only its fraction can proceed into elongation and the rest is retained at a promoter in non-productive form: a pathway branching in transcription initiation. Proteins such as GreA and GreB affect these fractions at several promoters in vitro. To reveal the ubiquitous existence of the branched mechanism in E. coli, we searched for candidate genes whose transcription decreased by disruption of greA and greB using a DNA array. Among the arbitrarily selected 11 genes from over 100, the atpC, cspA and rpsA passed the test by Northern blotting. The Gre factors activated transcription initiation from their promoters in vitro, and the results demonstrated that the branched mechanism is exploited in vivo regulation. Consistently, decrease in the level of the GreA in an anaerobic stationary condition accompanied a decrease in the levels of transcripts of these genes.
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Affiliation(s)
- Motoki Susa
- Structural Biology Center, National Institute of Genetics, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
| | - Tomoko Kubori
- Structural Biology Center, National Institute of Genetics, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
| | - Nobuo Shimamoto
- Structural Biology Center, National Institute of Genetics, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced StudiesMishima, Shizuoka 411-8540, Japan
- *For correspondence. E-mail ; Tel. (+81) 55 981 6843; Fax (+81) 55 981 6844
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20
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Durante-Rodríguez G, Zamarro MT, García JL, Díaz E, Carmona M. Oxygen-dependent regulation of the central pathway for the anaerobic catabolism of aromatic compounds in Azoarcus sp. strain CIB. J Bacteriol 2006; 188:2343-54. [PMID: 16547020 PMCID: PMC1428410 DOI: 10.1128/jb.188.7.2343-2354.2006] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 01/11/2006] [Indexed: 11/20/2022] Open
Abstract
The role of oxygen in the transcriptional regulation of the PN promoter that controls the bzd operon involved in the anaerobic catabolism of benzoate in the denitrifying Azoarcus sp. strain CIB has been investigated. In vivo experiments using PN::lacZ translational fusions, in both Azoarcus sp. strain CIB and Escherichia coli cells, have shown an oxygen-dependent repression effect on the transcription of the bzd catabolic genes. E. coli Fnr was required for the anaerobic induction of the PN promoter, and the oxygen-dependent repression of the bzd genes could be bypassed by the expression of a constitutively active Fnr* protein. In vitro experiments revealed that Fnr binds to the PN promoter at a consensus sequence centered at position -41.5 from the transcription start site overlapping the -35 box, suggesting that PN belongs to the class II Fnr-dependent promoters. Fnr interacts with RNA polymerase (RNAP) and is strictly required for transcription initiation after formation of the RNAP-PN complex. An fnr ortholog, the acpR gene, was identified in the genome of Azoarcus sp. strain CIB. The Azoarcus sp. strain CIB acpR mutant was unable to grow anaerobically on aromatic compounds and it did not drive the expression of the PN::lacZ fusion, suggesting that AcpR is the cognate transcriptional activator of the PN promoter. Since the lack of AcpR in Azoarcus sp. strain CIB did not affect growth on nonaromatic carbon sources, AcpR can be considered a transcriptional regulator of the Fnr/Crp superfamily that has evolved to specifically control the central pathway for the anaerobic catabolism of aromatic compounds in Azoarcus.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Dept. de Microbiología Molecular, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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21
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Liu M, Garges S, Adhya S. lacP1 promoter with an extended -10 motif. Pleiotropic effects of cyclic AMP protein at different steps of transcription initiation. J Biol Chem 2004; 279:54552-7. [PMID: 15385551 DOI: 10.1074/jbc.m408609200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyclic AMP receptor protein (CRP), which activates transcription from the wild-type lacP1 promoter and most of its mutants, represses productive RNA synthesis from a lacP1 promoter variant that contains an extended -10 element, although CRP enhances RNA polymerase binding as well as open complex formation in both promoters. Moreover, abortive RNA synthesis, which is already higher in the extended -10 variant compared with the parent promoter, was further enhanced by CRP. These results, together with the observed decrease in productive RNA synthesis, indicate that CRP, while facilitating the earlier steps of initiation, inhibits transcription from the extended -10 lacP1 by hindering promoter clearance. We propose that CRP decreases energetic barriers to RNA polymerase binding, isomerization, and abortive RNA synthesis but stabilizes the abortive RNA initiating complex, which results in increasing the activation energy of the transition state before the elongation complex. The results demonstrate for the first time that a DNA-binding regulatory protein acts as an activator or a repressor in different steps of the transcription initiation pathway because of the energetic differences of the intermediate complex in the same promoter.
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Affiliation(s)
- Mofang Liu
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892-4264, USA
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22
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Shimamoto N. Assay for Movements of RNA Polymerase along DNA. Methods Enzymol 2003; 371:50-70. [PMID: 14712691 DOI: 10.1016/s0076-6879(03)71004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Nobuo Shimamoto
- National Institute of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, 411-8540 Japan
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23
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Abstract
Promoter escape is the last stage of transcription initiation when RNA polymerase, having initiated de novo phosphodiester bond synthesis, must begin to relinquish its hold on promoter DNA and advance to downstream regions (DSRs) of the template. In vitro, this process is marked by the release of high levels of abortive transcripts at most promoters, reflecting the high instability of initial transcribing complexes (ITCs) and indicative of the existence of barriers to the escape process. The high abortive initiation level is the result of the existence of unproductive ITCs that carry out repeated initiation and abortive release without escaping the promoter. The formation of unproductive ITCs is a widespread phenomenon, but it occurs to different extent on different promoters. Quantitative analysis of promoter mutations suggests that the extent and pattern of abortive initiation and promoter escape is determined by the sequence of promoter elements, both in the promoter recognition region (PRR) and the initial transcribed sequence (ITS). A general correlation has been found that the stronger the promoter DNA-polymerase interaction, the poorer the ability of RNA polymerase to escape the promoter. In gene regulation, promoter escape can be the rate-limiting step for transcription initiation. An increasing number of regulatory proteins are known to exert their control at this step. Examples are discussed with an emphasis on the diverse mechanisms involved. At the molecular level, the X-ray crystal structures of RNA polymerase and its various transcription complexes provide the framework for understanding the functional data on abortive initiation and promoter escape. Based on structural and biochemical evidence, a mechanism for abortive initiation and promoter escape is described.
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Affiliation(s)
- Lilian M Hsu
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA.
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24
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Yang J, Camakaris H, Pittard J. Molecular analysis of tyrosine-and phenylalanine-mediated repression of the tyrB promoter by the TyrR protein of Escherichia coli. Mol Microbiol 2002; 45:1407-19. [PMID: 12207706 DOI: 10.1046/j.1365-2958.2002.03108.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mechanism of repression of the tyrB promoter by TyrR protein has been studied in vivo and in vitro. In tyrR+ strains, transcription of tyrB is repressed by either tyrosine or phenylalanine. Both of the TyrR binding sites (strong and weak TyrR boxes) lie downstream of the tyrB transcription start site and are required for tyrosine- or phenylalanine-mediated repression. Our results establish that the binding of the TyrR protein to the weak box, induced by cofactor tyrosine or phenylalanine, is critical for repression to occur. Neither the binding of the TyrR protein dimer formed in the presence of phenylalanine, nor the binding of the hexamer formed in the presence of tyrosine, blocks the binding of RNA polymerase to the promoter. Instead, open complex formation is inhibited in the presence of tyrosine whereas a step(s) following open complex formation is inhibited in the presence of phenylalanine. Moving the TyrR boxes 3 bp or more further away from the promoter affects tyrosine-mediated repression without affecting phenylalanine-mediated repression which remains unaltered until 6 bp are inserted between the TyrR boxes and the promoter. Analysis of deletion and insertion mutants fails to reveal any face of the helix specificity for either tyrosine- or phenylalanine-mediated repression.
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Affiliation(s)
- Ji Yang
- Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010, Australia
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25
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Susa M, Sen R, Shimamoto N. Generality of the branched pathway in transcription initiation by Escherichia coli RNA polymerase. J Biol Chem 2002; 277:15407-12. [PMID: 11854291 DOI: 10.1074/jbc.m112481200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription initiation has been assumed to be a multi-step sequential process, although additional steps could exist. Initiation from the T7A1 promoter, in particular, apparently behaves in vitro in a manner that can be fully explained by the sequential pathway. However, initiation from the lambda P(R)AL promoter has been shown to follow a branched pathway from which a part of the enzyme-promoter complex is arrested at the promoter raising the question as to which mechanism is general. We found that a moribund complex, characteristic of the arrested branch, is formed at the T7A1 promoter, especially in low salt condition indicating that the initiation mechanism for this promoter is also branched. The results of DNA footprinting suggested that holoenzyme in the moribund complex is dislocated on DNA from the position of productive complex. However, only a small fraction of the binary complex becomes arrested at this promoter, and the interconversion between subspecies of binary complex is apparently more reversible than at the lambda P(R)AL promoter, which explains why the reaction pathway appears to be sequential. These findings suggest a generality of the branched pathway mechanism, which would resolve contradictory observations that have been reported for various promoters.
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Affiliation(s)
- Motoki Susa
- Structural Biology Center, National Institute of Genetics and Department of Genetics, The Graduate University for Advanced Studies, 1111 Yata, Mishima, Japan, 411-8540
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26
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Pemberton IK, Muskhelishvili G, Travers AA, Buckle M. FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter. J Mol Biol 2002; 318:651-63. [PMID: 12054813 DOI: 10.1016/s0022-2836(02)00142-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have applied laser UV photo-footprinting to characterise kinetically complexes involving the activator protein FIS, RNA polymerase and the tyrT promoter of Escherichia coli. FIS photo-footprints strongly to three binding sites upstream of the core promoter. The polymerase photo-footprints in the near-consensus -35 hexamer on the non-template strand of DNA in a fashion similar to that of stable complexes involving the lacUV5 promoter. The kinetics of the interactions of polymerase alone with the tyrT promoter differ from those observed previously at the lacUV5 promoter. In the absence of FIS, we observe an upstream polymerase-induced signal at -122 within FIS site III that occurs subsequent to changes in the core promoter region and is strongly dependent on negative supercoiling. These observations support the proposal that the upstream region of the promoter is wrapped around the polymerase. We propose that the wrapped DNA allows the polymerase to overcome, at least in part, the barrier to DNA untwisting imparted by the G+C-rich discriminator. We further suggest that FIS plays a similar role and may facilitate polymerase escape.
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Affiliation(s)
- Iain K Pemberton
- Enzymologie et Cinétique Structurale, UMR 8532 du CNRS, LBPA, Ecole Normale Supérieure de Cachan, 94235 Cachan, France
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27
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Chan CL, Gross CA. The anti-initial transcribed sequence, a portable sequence that impedes promoter escape, requires sigma70 for function. J Biol Chem 2001; 276:38201-9. [PMID: 11481327 DOI: 10.1074/jbc.m104764200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The anti-sequence, a portable element extending from +1 to +15 of the transcript, is sufficient to prevent promoter escape from a variety of strong final sigma70 promoters. We show here that this sequence does not function with even the strongest final sigma32 promoter. Moreover, a particular class of substitutions in final sigma70 that disrupt interaction between Region 2.2 of final sigma70 and a coiled-coiled motif in the beta'-subunit of RNA polymerase antagonizes the function of the anti-element. This same group of mutants prevents lambdaQ-mediated anti-termination at the lambdaP(R') promoter. At this promoter, interaction of final sigma70 with the non-template strand of the initial transcribed sequence (ITS) is required to promote the pause prerequisite for anti-termination. These mutants prevent pausing because they are defective in this recognition event. By analogy, we suggest that interaction of final sigma70 with the non-template strand of the anti-ITS is required for function of this portable element, thus explaining why neither final sigma32 nor the Region 2.2 final sigma70 mutants mediate anti-function. Support for the analogy with the lambdaP(R') promoter comes from preliminary experiments suggesting that the anti-ITS, like the lambdaP(R') ITS, is bipartite.
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Affiliation(s)
- C L Chan
- Department of Stomatology, University of California, San Francisco, 94143, USA
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28
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Abstract
The cyclic AMP receptor protein (CRP) of Escherichia coli is a dimer made up of identical subunits. Each CRP subunit contains a cyclic nucleotide binding pocket and the CRP dimer exhibits negative cooperativity in binding cAMP. In solutions containing cAMP, CRP undergoes sequential conformation changes from the inactive apo-form through the active CRP:(cAMP)(1) complex to the less active CRP:(cAMP)(2) complex depending on the cAMP concentration. Apo-CRP binds DNA with low affinity and no apparent sequence specificity. The CRP:(cAMP)(1) complex exhibits high affinity, sequence-specific DNA binding and interacts with RNA polymerase, whether free in solution or complexed with DNA. The results of genetic, biochemical and biophysical studies have helped to uncover many of the details of cAMP-mediated allosteric control over CRP conformation and activity as a transcription factor. These studies indicate that cAMP binding produces only small, but significant, changes in CRP structure; changes that include subunit realignment and concerted motion of the secondary structure elements within the C-terminal DNA binding domain of each subunit. These adjustments promote CRP surface-patch interaction with RNA polymerase and protrusion of the F-helix to promote CRP site-specific interaction with DNA. Interactions between CRP and RNA polymerase at CRP-dependent promoters produce active ternary transcription complexes.
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Affiliation(s)
- J G Harman
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
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29
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Sen R, Nagai H, Shimamoto N. Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated by elongation factor GreA and GreB. Genes Cells 2001; 6:389-401. [PMID: 11380617 DOI: 10.1046/j.1365-2443.2001.00436.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The initiation arrest at a modified lambdaPR promoter is caused by irreversible divergence of the reaction pathway into productive and arrested branches. Escherichia coli GreA and GreB induce cleavage of the nascent transcript and relieve arrest in elongation. They also reduce abortive synthesis at several promoters and relieve initiation arrest. Their mechanism of action during initiation, and its relationship to the branched initiation pathway are unknown. RESULTS The Gre factors mitigated initiation arrest only when they were added to the binary complex of the holoenzyme bound to the lambdaPR promoter, prior to RNA synthesis. They exerted little effect when they were added to ternary initiation complexes. They accelerated the exchange of the binary complex with its free components by 6-9-fold. When they are present, a high concentration of the initiating nucleotide increased yield of the full-length transcript, whereas a low concentration did not. CONCLUSIONS All the results presented above can be explained by a model where the productive and arrested pathways diverge at the binary complex stage. The Gre factors relieve the initiation arrest by introducing reversibility between subspecies of the binary complex that are precursors of the two pathways. RNA cleavage is unlikely to cause relief of initiation arrest.
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Affiliation(s)
- R Sen
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka-411, Japan
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30
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Sen R, Nagai H, Shimamoto N. Polymerase arrest at the lambdaP(R) promoter during transcription initiation. J Biol Chem 2000; 275:10899-904. [PMID: 10753887 DOI: 10.1074/jbc.275.15.10899] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During transcription initiation by Escherichia coli RNA polymerase, a fraction of the homogeneous enzyme population has been kinetically shown to form two types of nonproductive complexes at some promoters: moribund complexes, which produce only abortive transcripts, and fully inactive ternary complexes (Kubori, T., and Shimamoto, N. (1996) J. Mol. Biol. 256, 449-457). Here we report biochemical isolation of the complexes arrested at the lambdaP(R) promoter and an analysis of their structure by DNA and protein footprintings. We found that the isolated promoter-arrested complexes retain a stoichiometric amount of sigma(70) subunit. Exonuclease III footprints of the arrested complexes are backtracked compared with that of the binary complex, and KMnO(4) footprinting reveals a decrease in the melting of DNA in the promoter region. Protein footprints of the retained sigma(70) have shown a more exposed conformation in region 3, compared with binary complexes. This feature is similar to that of the complexes arrested in inactive state during transcription elongation, indicating the existence of a common inactivating mechanism during transcription initiation and elongation. The possible involvement of the promoter arrest in transcriptional regulation is discussed.
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Affiliation(s)
- R Sen
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540, USA
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31
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Gulati A, Mahadevan S. Mechanism of catabolite repression in the bgl operon of Escherichia coli: involvement of the anti-terminator BglG, CRP-cAMP and EIIAGlc in mediating glucose effect downstream of transcription initiation. Genes Cells 2000; 5:239-50. [PMID: 10792463 DOI: 10.1046/j.1365-2443.2000.00322.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Expression of the bgl operon of Escherichia coli, involved in the regulated uptake and utilization of aromatic beta-glucosides, is extremely sensitive to the presence of glucose in the growth medium. We have analysed the mechanism by which glucose exerts its inhibitory effect on bgl expression. RESULTS Our studies show that initiation of transcription from the bgl promoter is only marginally sensitive to glucose. Instead, glucose exerts a more significant inhibition on the elongation of transcription beyond the rho-independent terminator present within the leader sequence. Transcriptional analyses using plasmids that carry mutations in bglG or within the terminator, suggest that the target for glucose-mediated repression is the anti-terminator protein, BglG. Introduction of multiple copies of bglG or the presence of mutations that inhibit its phosphorylation by Enzyme IIBgl (BglF), result in loss of glucose repression. Studies using crp, cya and crr strains show that both CRP-cAMP and the Enzyme IIAGlc (EIIAGlc) are involved in the regulation. Although transcription initiation is normal in a crp, cya double mutant, no detectable transcription is seen downstream of the terminator, which is restored by a mutation within the terminator. Transcription past the terminator is also partly restored by the addition of exogenous cAMP to glucose-grown cultures of a crp+ strain. Glucose repression is lost in the crr mutant strain. CONCLUSIONS The results summarized above indicate that glucose repression in the bgl operon is mediated at the level of transcription anti-termination, and glucose affects the activity of BglG by altering its phosphorylation by BglF. The CRP-cAMP complex is also involved in this regulation. The results using the crr mutant suggest a negative role for EIIAGlc in the catabolite repression of the bgl genes.
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Affiliation(s)
- A Gulati
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
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Schreiber V, Richet E. Self-association of the Escherichia coli transcription activator MalT in the presence of maltotriose and ATP. J Biol Chem 1999; 274:33220-6. [PMID: 10559195 DOI: 10.1074/jbc.274.47.33220] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MalT, the transcriptional activator of the Escherichia coli maltose regulon, binds the MalT-dependent promoters and activates transcription initiation only in the presence of maltotriose and ATP (or adenylyl imidodiphosphate (AMP-PNP)). Cooperative binding of MalT to the array of cognate sites present in the MalT-dependent promoters suggests that promoter binding involves MalT oligomerization. Gel filtration and sedimentation experiments were used to analyze the quaternary structure of MalT in solution in the absence or presence of maltotriose and/or AMP-PNP, ATP, or ADP. The protein is monomeric in the absence of ligands and in the presence of ADP. In the presence of maltotriose, AMP-PNP, or ATP only, the protein self-associates, but a large fraction of the protein remains monomeric. In the presence of both maltotriose and AMP-PNP (ATP or ADP), the protein is essentially oligomeric, with the difference being that the oligomerization is less favored in the presence of ADP + maltotriose than in the presence of AMP-PNP + maltotriose. We present evidence that the association pathway comprises the following steps: monomers --> dimers --> (MalT)(n) --> aggregates, where 3 </= n </= 6. From these data, we conclude that the role of maltotriose and ATP as positive effectors is to induce the multimerization of MalT, and hence its cooperative binding to the mal promoters.
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Affiliation(s)
- V Schreiber
- Unité de Génétique Moléculaire, URA CNRS 1773, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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Abstract
Transcription activation by Escherichia coli catabolite activator protein (CAP) at each of two classes of simple CAP-dependent promoters is understood in structural and mechanistic detail. At class I CAP-dependent promoters, CAP activates transcription from a DNA site located upstream of the DNA site for RNA polymerase holoenzyme (RNAP); at these promoters, transcription activation involves protein-protein interactions between CAP and the RNAP alpha subunit C-terminal domain that facilitate binding of RNAP to promoter DNA to form the RNAP-promoter closed complex. At class II CAP-dependent promoters, CAP activates transcription from a DNA site that overlaps the DNA site for RNAP; at these promoters, transcription activation involves both: (i) protein-protein interactions between CAP and RNAP alpha subunit C-terminal domain that facilitate binding of RNAP to promoter DNA to form the RNAP-promoter closed complex; and (ii) protein-protein interactions between CAP and RNAP alpha subunit N-terminal domain that facilitates isomerization of the RNAP-promoter closed complex to the RNAP-promoter open complex. Straightforward combination of the mechanisms for transcription activation at class I and class II CAP-dependent promoters permits synergistic transcription activation by multiple molecules of CAP, or by CAP and other activators. Interference with determinants of CAP or RNAP involved in transcription activation at class I and class II CAP-dependent promoters permits "anti-activation" by negative regulators. Basic features of transcription activation at class I and class II CAP-dependent promoters appear to be generalizable to other activators.
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Affiliation(s)
- S Busby
- School of Biosciences, The University of Birmingham, Birmingham, B15 2TT, UK
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Olekhnovich IN, Dahl JL, Kadner RJ. Separate contributions of UhpA and CAP to activation of transcription of the uhpT promoter of Escherichia coli. J Mol Biol 1999; 292:973-86. [PMID: 10512697 DOI: 10.1006/jmbi.1999.3127] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Activation of promoters by multiple transcription factors might occur through favorable contacts of the activators with themselves or RNA polymerase, or by changes in DNA geometry that enhance formation of the transcription complex. Transcription of the Escherichia coli uhpT gene, encoding the organophosphate transporter, requires the response regulator UhpA and is stimulated by the global regulator protein CAP. CAP binds to the uhpT promoter at a single site, centered at -103.5 bp relative to the start of transcription, and UhpA binds to multiple sites between positions -80 and -32. Overexpression of UhpA did not reduce the degree of CAP stimulation of uhpT-lacZ expression, showing that CAP action is more complex than enhancement of the binding of UhpA. Footprinting experiments demonstrated that UhpA and CAP modestly stimulated each other's binding to the uhpT promoter, but did not affect the positioning of the binding sites. An in vitro transcription system was used to examine the contribution of each transcription factor at the uhpT promoter. Action of UhpA and CAP proteins was not affected by template supercoiling. Kinetic analyses of productive and abortive initiation showed that CAP acted both to stabilize by fivefold the open promoter complexes formed in the presence of UhpA and to enhance by twofold the rate of their formation. These results indicate that open complex formation requires UhpA and that CAP stabilizes the open complex.
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Affiliation(s)
- I N Olekhnovich
- Department of Microbiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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Tagami H, Aiba H. An inactive open complex mediated by an UP element at Escherichia coli promoters. Proc Natl Acad Sci U S A 1999; 96:7202-7. [PMID: 10377392 PMCID: PMC22052 DOI: 10.1073/pnas.96.13.7202] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A specific interaction between the alpha subunit of RNA polymerase and an A+T-rich upstream sequence (UP element) stimulates transcription at some promoters in Escherichia coli. We found that RNA polymerase formed a heparin-resistant nonproductive initiation complex at the malT promoter which has an A+T-rich upstream sequence that begins 9 bp upstream of the -35 region. Substitution of other sequences for the A+T-rich sequence eliminated both the formation of heparin-resistant complexes and alpha binding to the malT promoter. A 5-bp deletion between the A+T-rich sequence and the -35 region increased promoter activity. The UP element derived from the rrnB P1 promoter stimulated transcription of the malT core promoter when placed 4 bp upstream from the malT -35 region, but insertion of an additional 4 bp between the rrnB P1 UP element and the -35 element eliminated transcription activity without eliminating heparin-resistant complex formation. Similar UP element effects were observed in hybrids with the lac core promoter, even though the region around the transcription start site was melted in both productive and nonproductive complexes. We conclude that UP elements can mediate the formation of both productive and nonproductive open complexes, depending on their location with respect to the core promoter.
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Affiliation(s)
- H Tagami
- Department of Molecular Biology, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
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He Y, Gaal T, Karls R, Donohue TJ, Gourse RL, Roberts GP. Transcription activation by CooA, the CO-sensing factor from Rhodospirillum rubrum. The interaction between CooA and the C-terminal domain of the alpha subunit of RNA polymerase. J Biol Chem 1999; 274:10840-5. [PMID: 10196160 DOI: 10.1074/jbc.274.16.10840] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CooA, a member of the cAMP receptor protein (CRP) family, is a CO-sensing transcription activator from Rhodospirillum rubrum that binds specific DNA sequences in response to CO. The location of the CooA-binding sites relative to the start sites of transcription suggested that the CooA-dependent promoters are analogous to class II CRP-dependent promoters. In this study, we developed an in vivo CooA reporter system in Escherichia coli and an in vitro transcription assay using RNA polymerases (RNAP) from E. coli and from Rhodobacter sphaeroides to study the transcription properties of CooA and the protein-protein interaction between CooA and RNAP. The ability of CooA to activate CO-dependent transcription in vivo in heterologous backgrounds suggested that CooA is sufficient to direct RNAP to initiate transcription and that no other factors are required. This hypothesis was confirmed in vitro with purified CooA and purified RNAP. Use of a mutant form of E. coli RNAP with alpha subunits lacking their C-terminal domain (alpha-CTD) dramatically decreased CooA-dependent transcription of the CooA-regulated R. rubrum promoter PcooF in vitro, which indicates that alpha-CTD plays an important role in this activation. DNase I footprinting analysis showed that CooA facilitates binding of wild-type RNAP, but not alpha-CTD-truncated RNAP, to PcooF. This facilitated binding provides evidence for a direct contact between CooA and alpha-CTD of RNAP during activation of transcription. Mapping the CooA-contact site in alpha-CTD suggests that CooA is similar but not identical to CRP in terms of its contact sites to the alpha-CTD at class II promoters.
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Affiliation(s)
- Y He
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
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Seoh HK, Tai PC. Catabolic repression of secB expression is positively controlled by cyclic AMP (cAMP) receptor protein-cAMP complexes at the transcriptional level. J Bacteriol 1999; 181:1892-9. [PMID: 10074084 PMCID: PMC93590 DOI: 10.1128/jb.181.6.1892-1899.1999] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SecB, a protein export-specific chaperone, enhances the export of a subset of proteins across cytoplasmic membranes of Escherichia coli. Previous studies showed that the synthesis of SecB is repressed by the presence of glucose in the medium. The derepression of SecB requires the products of both the cya and crp genes, indicating that secB expression is under the control of catabolic repression. In this study, two secB-specific promoters were identified. In addition, 5' transcription initiation sites from these two promoters were determined by means of secB-lacZ fusions and primer extension. The distal P1 promoter appeared to be independent of carbon sources, whereas the proximal P2 promoter was shown to be subject to control by the cyclic AMP (cAMP) receptor protein (CRP)-cAMP complexes. Gel-mobility shift studies showed that this regulation results from direct interaction between the secB P2 promoter region and the CRP-cAMP complex. Moreover, the CRP binding site on the secB gene was determined by DNase I footprinting and further substantiated by mutational analysis. The identified secB CRP binding region is centered at the -61.5 region of the secB gene and differed from the putative binding sites predicted by computer analysis.
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Affiliation(s)
- H K Seoh
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
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