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Pokorzynski ND, Groisman EA. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiol Mol Biol Rev 2023; 87:e0019822. [PMID: 37358444 PMCID: PMC10521370 DOI: 10.1128/mmbr.00198-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.
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Affiliation(s)
- Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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2
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Chang CP, Lagitnay RBJS, Li TR, Lai WT, Derilo RC, Chuang DY. Unleashing the Influence of cAMP Receptor Protein: The Master Switch of Bacteriocin Export in Pectobacterium carotovorum subsp. carotovorum. Int J Mol Sci 2023; 24:ijms24119752. [PMID: 37298703 DOI: 10.3390/ijms24119752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Pectobacterium carotovorum subsp. carotovorum (Pcc) is a Gram-negative phytopathogenic bacterium that produces carocin, a low-molecular-weight bacteriocin that can kill related strains in response to factors in the environment such as UV exposure or nutritional deficiency. The function of the catabolite activator protein (CAP), also known as the cyclic AMP receptor protein (CRP), as a regulator of carocin synthesis was examined. The crp gene was knocked out as part of the investigation, and the outcomes were assessed both in vivo and in vitro. Analysis of the DNA sequence upstream of the translation initiation site of carocin S3 revealed two putative binding sites for CRP that were confirmed using a biotinylated probe pull-down experiment. This study revealed that the deletion of crp inhibited genes involved in extracellular bacteriocin export via the flagellar type III secretion system and impacted the production of many low-molecular-weight bacteriocins. The biotinylated probe pull-down test demonstrated that when UV induction was missing, CRP preferentially attached to one of the two CAP sites while binding to both when UV induction was present. In conclusion, our research aimed to simulate the signal transduction system that controls the expression of the carocin gene in response to UV induction.
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Affiliation(s)
- Chung-Pei Chang
- Department of Anesthesiology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
| | - Ruchi Briam James Sersenia Lagitnay
- College of Arts and Sciences, Bayombong Campus, Nueva Vizcaya State University, Bayombong 3700, Philippines
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Tzu-Rong Li
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Wei-Ting Lai
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Reymund Calanga Derilo
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
- College of Teacher Education, Bambang Campus, Nueva Vizcaya State University, Bambang 3702, Philippines
| | - Duen-Yau Chuang
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
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3
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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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4
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Wu J, Chen D, Wu J, Chu X, Yang Y, Fang L, Zhang W. Comparative Transcriptome Analysis Demonstrates the Positive Effect of the Cyclic AMP Receptor Protein Crp on Daptomycin Biosynthesis in Streptomyces roseosporus. Front Bioeng Biotechnol 2021; 9:618029. [PMID: 34150723 PMCID: PMC8212052 DOI: 10.3389/fbioe.2021.618029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/23/2021] [Indexed: 11/21/2022] Open
Abstract
Daptomycin, which is produced by Streptomyces roseosporus, has been characterized as a novel cyclic lipopeptide antibiotic that is effective against Gram-positive bacteria. The biosynthesis of daptomycin is regulated by various factors. In the present study, we demonstrated that the cyclic AMP receptor protein (Crp) plays an important role in producing daptomycin in the S. roseosporus industrial strain. We found that daptomycin production from the crp deletion strain decreased drastically, whereas production from the crp overexpression strain increased by 22.1%. Transcriptome and qPCR analyses showed that some genes related to the daptomycin biosynthetic gene cluster (dpt) and the pleiotropic regulator (adpA) were significantly upregulated. RNA-seq also shows Crp to be a multifunctional regulator that modulates primary metabolism and enhances precursor flux to secondary metabolite biosynthesis. These results provide guidance for the development and improvement of potential natural products.
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Affiliation(s)
- Jiequn Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Danqing Chen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Jinrong Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Yongmei Yang
- Hangzhou Zhongmei Huadong Pharmaceutical Co., Ltd., Hangzhou, China
| | - Lina Fang
- Hangzhou Zhongmei Huadong Pharmaceutical Co., Ltd., Hangzhou, China
| | - Wei Zhang
- Hangzhou Zhongmei Huadong Pharmaceutical Co., Ltd., Hangzhou, China
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5
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Anzai T, Imamura S, Ishihama A, Shimada T. Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility. Microb Genom 2020; 6. [PMID: 32975502 PMCID: PMC7660256 DOI: 10.1099/mgen.0.000442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The transcription factor PdhR has been recognized as the master regulator of the pyruvate catabolism pathway in Escherichia coli, including both NAD-linked oxidative decarboxylation of pyruvate to acetyl-CoA by PDHc (pyruvate dehydrogenase complex) and respiratory electron transport of NADH to oxygen by Ndh-CyoABCD enzymes. To identify the whole set of regulatory targets under the control of pyruvate-sensing PdhR, we performed genomic SELEX (gSELEX) screening in vitro. A total of 35 PdhR-binding sites were identified along the E. coli K-12 genome, including previously identified targets. Possible involvement of PdhR in regulation of the newly identified target genes was analysed in detail by gel shift assay, RT-qPCR and Northern blot analysis. The results indicated the participation of PdhR in positive regulation of fatty acid degradation genes and negative regulation of cell mobility genes. In fact, GC analysis indicated an increase in free fatty acids in the mutant lacking PdhR. We propose that PdhR is a bifunctional global regulator for control of a total of 16–23 targets, including not only the genes involved in central carbon metabolism but also some genes for the surrounding pyruvate-sensing cellular pathways such as fatty acid degradation and flagella formation. The activity of PdhR is controlled by pyruvate, the key node between a wide variety of metabolic pathways, including generation of metabolic energy and cell building blocks.
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Affiliation(s)
- Takumi Anzai
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Akira Ishihama
- Micro-Nanotechnology Research Center, Hosei University, Koganei, Tokyo, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
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6
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Integrating CRISPR-Enabled Trackable Genome Engineering and Transcriptomic Analysis of Global Regulators for Antibiotic Resistance Selection and Identification in Escherichia coli. mSystems 2020; 5:5/2/e00232-20. [PMID: 32317390 PMCID: PMC7174635 DOI: 10.1128/msystems.00232-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growing threat of antimicrobial resistance poses a serious threat to public health care and motivates efforts to understand the means by which resistance acquisition occurs and how this can be combatted. To address these challenges, we expedited the identification of novel mutations that enable complex phenotypic changes that result in improved tolerance to antibiotics by integrating CREATE and transcriptomic analysis of global regulators. The results give us a better understanding of the mechanisms of resistance to tetracycline antibiotics and aminoglycoside antibiotics and also indicate that the method may be used for quickly identifying resistance-related mutations. It is important to expedite our understanding of antibiotic resistance to address the increasing numbers of fatalities and environmental pollution due to the emergence of antibiotic resistance and multidrug-resistant strains. Here, we combined the CRISPR-enabled trackable genome engineering (CREATE) technology and transcriptomic analysis to investigate antibiotic tolerance in Escherichia coli. We developed rationally designed site saturation mutagenesis libraries targeting 23 global regulators to identify fitness-conferring mutations in response to diverse antibiotic stresses. We identified seven novel mutations that confer resistance to the ribosome-targeting antibiotics doxycycline, thiamphenicol, and gentamicin in E. coli. To the best of our knowledge, these mutations that we identified have not been reported previously during treatment with the indicated antibiotics. Transcriptome sequencing-based transcriptome analysis was further employed to evaluate the genome-wide changes in gene expression in E. coli for SoxR G121P and cAMP receptor protein (CRP) V140W reconstructions, and improved fitness in response to doxycycline and gentamicin was seen. In the case of doxycycline, we speculated that SoxR G121P significantly increased the expression of genes involved in carbohydrate metabolism and energy metabolism to promote cell growth for improved adaptation. In the CRP V140W mutant with improved gentamicin tolerance, the expression of several amino acid biosynthesis genes and fatty acid degradation genes was significantly changed, and these changes probably altered the cellular energy state to improve adaptation. These findings have important significance for understanding such nonspecific mechanisms of antibiotic resistance and developing new antibacterial drugs. IMPORTANCE The growing threat of antimicrobial resistance poses a serious threat to public health care and motivates efforts to understand the means by which resistance acquisition occurs and how this can be combatted. To address these challenges, we expedited the identification of novel mutations that enable complex phenotypic changes that result in improved tolerance to antibiotics by integrating CREATE and transcriptomic analysis of global regulators. The results give us a better understanding of the mechanisms of resistance to tetracycline antibiotics and aminoglycoside antibiotics and also indicate that the method may be used for quickly identifying resistance-related mutations.
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7
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Pokharel P, Habouria H, Bessaiah H, Dozois CM. Serine Protease Autotransporters of the Enterobacteriaceae (SPATEs): Out and About and Chopping It Up. Microorganisms 2019; 7:E594. [PMID: 31766493 PMCID: PMC6956023 DOI: 10.3390/microorganisms7120594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Autotransporters are secreted proteins with multiple functions produced by a variety of Gram-negative bacteria. In Enterobacteriaceae, a subgroup of these autotransporters are the SPATEs (serine protease autotransporters of Enterobacteriaceae). SPATEs play a crucial role in survival and virulence of pathogens such as Escherichia coli and Shigella spp. and contribute to intestinal and extra-intestinal infections. These high molecular weight proteases are transported to the external milieu by the type Va secretion system and function as proteases with diverse substrate specificities and biological functions including adherence and cytotoxicity. Herein, we provide an overview of SPATEs and discuss recent findings on the biological roles of these secreted proteins, including proteolysis of substrates, adherence to cells, modulation of the immune response, and virulence in host models. In closing, we highlight recent insights into the regulation of expression of SPATEs that could be exploited to understand fundamental SPATE biology.
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Affiliation(s)
- Pravil Pokharel
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Hajer Habouria
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Hicham Bessaiah
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
- Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
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8
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Mettert EL, Kiley PJ. Reassessing the Structure and Function Relationship of the O 2 Sensing Transcription Factor FNR. Antioxid Redox Signal 2018; 29:1830-1840. [PMID: 28990402 PMCID: PMC6217745 DOI: 10.1089/ars.2017.7365] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE The Escherichia coli regulatory protein fumarate nitrate reduction (FNR) mediates a global transcriptional response upon O2 deprivation. Spanning nearly 40 years of research investigations, our understanding of how FNR senses and responds to O2 has considerably progressed despite a lack of structural information for most of that period. This knowledge has established the paradigm for how facultative anaerobic bacteria sense changes in O2 tension. Recent Advances: Recently, the X-ray crystal structure of Aliivibrio fischeri FNR with its [4Fe-4S] cluster cofactor was solved and has provided valuable new insight into FNR structure and function. These findings have alluded to the conformational changes that may occur to alter FNR activity in response to O2. CRITICAL ISSUES Here, we review the major features of this structure in context of previously acquired data. In doing so, we discuss additional mechanistic aspects of FNR function that warrant further investigation. FUTURE DIRECTIONS To complement the [4Fe-4S]-FNR structure, the structures of apo-FNR and FNR bound to DNA or RNA polymerase are needed. Together, these structures would elevate our understanding of how ligation of its [4Fe-4S] cluster allows FNR to regulate transcription according to the level of environmental O2.
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Affiliation(s)
- Erin L Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison , Madison, Wisconsin
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison , Madison, Wisconsin
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9
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Einav T, Duque J, Phillips R. Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants. PLoS One 2018; 13:e0204275. [PMID: 30256816 PMCID: PMC6157895 DOI: 10.1371/journal.pone.0204275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/05/2018] [Indexed: 12/27/2022] Open
Abstract
Allosteric transcription factors undergo binding events at inducer binding sites as well as at distinct DNA binding domains, and it is difficult to disentangle the structural and functional consequences of these two classes of interactions. We compare the ability of two statistical mechanical models—the Monod-Wyman-Changeux (MWC) and the Koshland-Némethy-Filmer (KNF) models of protein conformational change—to characterize the multi-step activation mechanism of the broadly acting cyclic-AMP receptor protein (CRP). We first consider the allosteric transition resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. We use these models to examine a beautiful recent experiment that created a single-chain version of the CRP homodimer, creating six mutants using all possible combinations of the wild type, D53H, and S62F subunits. We demonstrate that the MWC model can explain the behavior of all six mutants using a small, self-consistent set of parameters whose complexity scales with the number of subunits, providing a significant benefit over previous models. In comparison, the KNF model not only leads to a poorer characterization of the available data but also fails to generate parameter values in line with the available structural knowledge of CRP. In addition, we discuss how the conceptual framework developed here for CRP enables us to not merely analyze data retrospectively, but has the predictive power to determine how combinations of mutations will interact, how double mutants will behave, and how each construct would regulate gene expression.
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Affiliation(s)
- Tal Einav
- Department of Physics, California Institute of Technology, Pasadena, CA, United States of America
| | - Julia Duque
- Department of Physics and the London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, CA, United States of America
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, United States of America
- * E-mail:
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10
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Tsai MJ, Wang JR, Yang CD, Kao KC, Huang WL, Huang HY, Tseng CP, Huang HD, Ho SY. PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli. Sci Rep 2018; 8:951. [PMID: 29343727 PMCID: PMC5772556 DOI: 10.1038/s41598-017-18648-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/13/2017] [Indexed: 02/04/2023] Open
Abstract
Cyclic AMP receptor protein (CRP), a global regulator in Escherichia coli, regulates more than 180 genes via two roles: activation and repression. Few methods are available for predicting the regulatory roles from the binding sites of transcription factors. This work proposes an accurate method PredCRP to derive an optimised model (named PredCRP-model) and a set of four interpretable rules (named PredCRP-ruleset) for predicting and analysing the regulatory roles of CRP from sequences of CRP-binding sites. A dataset consisting of 169 CRP-binding sites with regulatory roles strongly supported by evidence was compiled. The PredCRP-model, using 12 informative features of CRP-binding sites, and cooperating with a support vector machine achieved a training and test accuracy of 0.98 and 0.93, respectively. PredCRP-ruleset has two activation rules and two repression rules derived using the 12 features and the decision tree method C4.5. This work further screened and identified 23 previously unobserved regulatory interactions in Escherichia coli. Using quantitative PCR for validation, PredCRP-model and PredCRP-ruleset achieved a test accuracy of 0.96 (=22/23) and 0.91 (=21/23), respectively. The proposed method is suitable for designing predictors for regulatory roles of all global regulators in Escherichia coli. PredCRP can be accessed at https://github.com/NctuICLab/PredCRP.
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Affiliation(s)
- Ming-Ju Tsai
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Jyun-Rong Wang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chi-Dung Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Kuo-Ching Kao
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen-Lin Huang
- Department and Institute of Industrial Engineering and Management, Minghsin University of Science and Technology, Hsinchu, Taiwan
| | - Hsi-Yuan Huang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ching-Ping Tseng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
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11
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Jers C, Ravikumar V, Lezyk M, Sultan A, Sjöling Å, Wai SN, Mijakovic I. The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators. Front Cell Infect Microbiol 2018; 7:537. [PMID: 29376036 PMCID: PMC5768985 DOI: 10.3389/fcimb.2017.00537] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/26/2017] [Indexed: 01/16/2023] Open
Abstract
Protein lysine acetylation is recognized as an important reversible post translational modification in all domains of life. While its primary roles appear to reside in metabolic processes, lysine acetylation has also been implicated in regulating pathogenesis in bacteria. Several global lysine acetylome analyses have been carried out in various bacteria, but thus far there have been no reports of lysine acetylation taking place in the important human pathogen Vibrio cholerae. In this study, we analyzed the lysine acetylproteome of the human pathogen V. cholerae V52. By applying a combination of immuno-enrichment of acetylated peptides and high resolution mass spectrometry, we identified 3,402 acetylation sites on 1,240 proteins. Of the acetylated proteins, more than half were acetylated on two or more sites. As reported for other bacteria, we observed that many of the acetylated proteins were involved in metabolic and cellular processes and there was an over-representation of acetylated proteins involved in protein synthesis. Of interest, we demonstrated that many global transcription factors such as CRP, H-NS, IHF, Lrp and RpoN as well as transcription factors AphB, TcpP, and PhoB involved in direct regulation of virulence in V. cholerae were acetylated. In conclusion, this is the first global protein lysine acetylome analysis of V. cholerae and should constitute a valuable resource for in-depth studies of the impact of lysine acetylation in pathogenesis and other cellular processes.
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Affiliation(s)
- Carsten Jers
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Vaishnavi Ravikumar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mateusz Lezyk
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Abida Sultan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sun N Wai
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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12
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Gayán E, Cambré A, Michiels CW, Aertsen A. RpoS-independent evolution reveals the importance of attenuated cAMP/CRP regulation in high hydrostatic pressure resistance acquisition in E. coli. Sci Rep 2017; 7:8600. [PMID: 28819154 PMCID: PMC5561100 DOI: 10.1038/s41598-017-08958-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 07/20/2017] [Indexed: 11/09/2022] Open
Abstract
High hydrostatic pressure (HHP) processing is an attractive non-thermal alternative to food pasteurization. Nevertheless, the large inter- and intra-species variations in HHP resistance among foodborne pathogens and the ease by which they can acquire extreme resistance are an issue of increasing concern. Since RpoS activity has been considered as a central determinant in the HHP resistance of E. coli and its pathovars, this study probed for the potential of an E. coli MG1655 ΔrpoS mutant to acquire HHP resistance by directed evolution. Despite the higher initial HHP sensitivity of the ΔrpoS mutant compared to the wild-type strain, evolved lineages of the former readily managed to restore or even succeed wild-type levels of resistance. A number of these ΔrpoS derivatives were affected in cAMP/CRP regulation, and this could be causally related to their HHP resistance. Subsequent inspection revealed that some of previously isolated HHP-resistant mutants derived from the wild-type strain also incurred a causal decrease in cAMP/CRP regulation. cAMP/CRP attenuated HHP-resistant mutants also exhibited higher resistance to fosfomycin, a preferred treatment for STEC infections. As such, this study reveals attenuation of cAMP/CRP regulation as a relevant and RpoS-independent evolutionary route towards HHP resistance in E. coli that coincides with fosfomycin resistance.
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Affiliation(s)
- Elisa Gayán
- KU Leuven, Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Leuven, Belgium
| | - Alexander Cambré
- KU Leuven, Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Leuven, Belgium
| | - Chris W Michiels
- KU Leuven, Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Leuven, Belgium.
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13
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Basak S, Sahoo NG, Pavanasam AK. Genome mining, in silico validation and phase selection of a novel aldo-keto reductase from Candida glabrata for biotransformation. Bioengineered 2017. [PMID: 28644714 PMCID: PMC5972913 DOI: 10.1080/21655979.2017.1342911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Previously, we published cloning, overexpression, characterization and subsequent exploitation of a carbonyl reductase (cr) gene, belonging to general family aldo-keto reductase from Candida glabrata CBS138 to convert keto ester (COBE) to a chiral alcohol (ethyl-4-chloro-3-hydroxybutanoate or CHBE). Exploiting global transcription factor CRP, rDNA and transporter engineering, we have improved batch production of CHBE by trinomial bioengineering. Herein, we present the exploration of cr gene in Candida glabrata CBS138 through genome mining approach, in silico validation of its activity and selection of its biocatalytic phase. For exploration of the gene under investigation, 3 template genes were chosen namely Saccharomyces cerevisae YDR541c, YGL157w and YOL151w. The CR showed significant homology match, overlapping of substrate binding site and NADPH binding site with the template proteins. The binding affinity of COBE toward CR (-4.6 Kcal/ mol) was found higher than that of the template proteins (-3.5 to -4.5 Kcal/ mol). Biphasic biocatalysis with cofactor regeneration improved product titer 4∼5 times better than monophasic biotransformation. Currently we are working on DNA Shuffling as a next level of strain engineering and we demonstrate this approach herein as a future strategy of biochemical engineering.
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Affiliation(s)
- Souvik Basak
- a Dr. B.C. Roy College of Pharmacy & Allied Health Sciences , Durgapur , WB , India
| | - Nanda Gopal Sahoo
- b Nanoscience and Nanotechnology Centre, Department of Chemistry , Kumaun University , Nainital , Uttarakhand , India
| | - Angayar K Pavanasam
- c International College of Engineering and Management (University of Central Lancashire, UK Affiliation) , Muscat , Oman
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14
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Turner K, Joel S, Feliciano J, Feltus A, Pasini P, Wynn D, Dau P, Dikici E, Deo SK, Daunert S. Transcriptional regulatory proteins as biosensing tools. Chem Commun (Camb) 2017; 53:6820-6823. [PMID: 28492634 PMCID: PMC6648647 DOI: 10.1039/c6cc09512g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed sensing systems employing different classes of transcriptional regulatory proteins genetically and chemically modified to incorporate a fluorescent reporter molecule for detection of arsenic, hydroxylated polychlorinated biphenyls (OH-PCBs), and cyclic AMP (cAMP). These are the first examples of optical sensing systems based on transcriptional regulatory proteins.
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Affiliation(s)
- Kendrick Turner
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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15
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Sim DW, Choi JW, Kim JH, Ryu KS, Kim M, Yu HW, Jo KS, Kim EH, Seo MD, Jeon YH, Lee BJ, Kim YP, Won HS. C-terminal dimerization of apo-cyclic AMP receptor protein validated in solution. FEBS Lett 2017; 591:1064-1070. [PMID: 28245055 DOI: 10.1002/1873-3468.12613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/28/2017] [Accepted: 02/23/2017] [Indexed: 11/07/2022]
Abstract
Although cyclic AMP receptor protein (CRP) has long served as a typical example of effector-mediated protein allostery, mechanistic details into its regulation have been controversial due to discrepancy between the known crystal structure and NMR structure of apo-CRP. Here, we report that the recombinant protein corresponding to its C-terminal DNA-binding domain (CDD) forms a dimer. This result, together with structural information obtained in the present NMR study, is consistent with the previous crystal structure and validates its relevance also in solution. Therefore, our findings suggest that dissociation of the CDD may be critically involved in cAMP-induced allosteric activation of CRP.
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Affiliation(s)
- Dae-Won Sim
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, Korea
| | - Jae Wan Choi
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, Korea
| | - Ji-Hun Kim
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, Korea
| | - Kyoung-Seok Ryu
- Protein Structure Group, Korea Basic Science Institute, Ochang, Chungbuk, Korea
| | - Myeongkyu Kim
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, Korea
| | - Hee-Wan Yu
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, Korea
| | - Ku-Sung Jo
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, Korea
| | - Eun-Hee Kim
- Protein Structure Group, Korea Basic Science Institute, Ochang, Chungbuk, Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi, Korea
- Research Institute of Pharmaceutical Science and Technology, College of Pharmacy, Ajou University, Suwon, Gyeonggi, Korea
| | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong, Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Young Pil Kim
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, Gyeonggi, Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, Korea
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16
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Good JAD, Andersson C, Hansen S, Wall J, Krishnan KS, Begum A, Grundström C, Niemiec MS, Vaitkevicius K, Chorell E, Wittung-Stafshede P, Sauer UH, Sauer-Eriksson AE, Almqvist F, Johansson J. Attenuating Listeria monocytogenes Virulence by Targeting the Regulatory Protein PrfA. Cell Chem Biol 2016; 23:404-14. [PMID: 26991105 PMCID: PMC4802734 DOI: 10.1016/j.chembiol.2016.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 01/27/2016] [Accepted: 02/19/2016] [Indexed: 01/28/2023]
Abstract
The transcriptional activator PrfA, a member of the Crp/Fnr family, controls the expression of some key virulence factors necessary for infection by the human bacterial pathogen Listeria monocytogenes. Phenotypic screening identified ring-fused 2-pyridone molecules that at low micromolar concentrations attenuate L. monocytogenes cellular uptake by reducing the expression of virulence genes. These inhibitors bind the transcriptional regulator PrfA and decrease its affinity for the consensus DNA-binding site. Structural characterization of this interaction revealed that one of the ring-fused 2-pyridones, compound 1, binds at two separate sites on the protein: one within a hydrophobic pocket or tunnel, located between the C- and N-terminal domains of PrfA, and the second in the vicinity of the DNA-binding helix-turn-helix motif. At both sites the compound interacts with residues important for PrfA activation and helix-turn-helix formation. Ring-fused 2-pyridones represent a new class of chemical probes for studying virulence in L. monocytogenes. Inhibitors of L. monocytogenes infectivity reduce virulence gene expression Binding of inhibitor to the PrfA regulator reduces affinity for its DNA motif First crystal structure of a Crp family regulator with an inhibitor Provides rationale for screening with Crp family transcriptional regulators
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Affiliation(s)
- James A D Good
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - Christopher Andersson
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Sabine Hansen
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Jessica Wall
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - K Syam Krishnan
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - Afshan Begum
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - Christin Grundström
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | | | - Karolis Vaitkevicius
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | | | - Uwe H Sauer
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - A Elisabeth Sauer-Eriksson
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden.
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden.
| | - Jörgen Johansson
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden.
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17
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Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria. Proc Natl Acad Sci U S A 2016; 113:14733-14738. [PMID: 27930316 DOI: 10.1073/pnas.1614028114] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Infection by the human bacterial pathogen Listeria monocytogenes is mainly controlled by the positive regulatory factor A (PrfA), a member of the Crp/Fnr family of transcriptional activators. Published data suggest that PrfA requires the binding of a cofactor for full activity, and it was recently proposed that glutathione (GSH) could fulfill this function. Here we report the crystal structures of PrfA in complex with GSH and in complex with GSH and its cognate DNA, the hly operator PrfA box motif. These structures reveal the structural basis for a GSH-mediated allosteric mode of activation of PrfA in the cytosol of the host cell. The crystal structure of PrfAWT in complex only with DNA confirms that PrfAWT can adopt a DNA binding-compatible structure without binding the GSH activator molecule. By binding to PrfA in the cytosol of the host cell, GSH induces the correct fold of the HTH motifs, thus priming the PrfA protein for DNA interaction.
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18
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Zhang Z, Saier MH. Transposon-mediated activation of the Escherichia coli glpFK operon is inhibited by specific DNA-binding proteins: Implications for stress-induced transposition events. Mutat Res 2016; 793-794:22-31. [PMID: 27810619 DOI: 10.1016/j.mrfmmm.2016.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/18/2016] [Accepted: 10/22/2016] [Indexed: 11/16/2022]
Abstract
Escherichia coli cells deleted for the cyclic AMP (cAMP) receptor protein (Crp) gene (Δcrp) cannot utilize glycerol because cAMP-Crp is a required activator of the glycerol utilization operon, glpFK. We have previously shown that a transposon, Insertion Sequence 5 (IS5), can insert into the upstream regulatory region of the operon to activate the glpFK promoter and enable glycerol utilization. GlpR, which represses glpFK transcription, binds to the glpFK upstream region near the site of IS5 insertion and inhibits insertion. By adding cAMP to the culture medium in ΔcyaA cells, we here show that the cAMP-Crp complex, which also binds to the glpFK upstream regulatory region, inhibits IS5 hopping into the activating site. Control experiments showed that the frequencies of mutations in response to cAMP were independent of parental cell growth rate and the selection procedure. These findings led to the prediction that glpFK-activating IS5 insertions can also occur in wild-type (Crp+) cells under conditions that limit cAMP production. Accordingly, we found that IS5 insertion into the activating site in wild-type cells is elevated in the presence of glycerol and a non-metabolizable sugar analogue that lowers cytoplasmic cAMP concentrations. The resultant IS5 insertion mutants arising in this minimal medium become dominant constituents of the population after prolonged periods of growth. The results show that DNA binding transcription factors can reversibly mask a favored transposon target site, rendering a hot spot for insertion less favored. Such mechanisms could have evolved by natural selection to overcome environmental adversity.
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Affiliation(s)
- Zhongge Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States.
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19
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Chen S, Thompson KM, Francis MS. Environmental Regulation of Yersinia Pathophysiology. Front Cell Infect Microbiol 2016; 6:25. [PMID: 26973818 PMCID: PMC4773443 DOI: 10.3389/fcimb.2016.00025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/15/2016] [Indexed: 12/26/2022] Open
Abstract
Hallmarks of Yersinia pathogenesis include the ability to form biofilms on surfaces, the ability to establish close contact with eukaryotic target cells and the ability to hijack eukaryotic cell signaling and take over control of strategic cellular processes. Many of these virulence traits are already well-described. However, of equal importance is knowledge of both confined and global regulatory networks that collaborate together to dictate spatial and temporal control of virulence gene expression. This review has the purpose to incorporate historical observations with new discoveries to provide molecular insight into how some of these regulatory mechanisms respond rapidly to environmental flux to govern tight control of virulence gene expression by pathogenic Yersinia.
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Affiliation(s)
- Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, China
| | - Karl M Thompson
- Department of Microbiology, College of Medicine, Howard University Washington, DC, USA
| | - Matthew S Francis
- Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden; Department of Molecular Biology, Umeå UniversityUmeå, Sweden
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20
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Augimeri RV, Strap JL. The Phytohormone Ethylene Enhances Cellulose Production, Regulates CRP/FNRKx Transcription and Causes Differential Gene Expression within the Bacterial Cellulose Synthesis Operon of Komagataeibacter (Gluconacetobacter) xylinus ATCC 53582. Front Microbiol 2015; 6:1459. [PMID: 26733991 PMCID: PMC4686702 DOI: 10.3389/fmicb.2015.01459] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/04/2015] [Indexed: 01/22/2023] Open
Abstract
Komagataeibacter (formerly Gluconacetobacter) xylinus ATCC 53582 is a plant-associated model organism for bacterial cellulose (BC) biosynthesis. This bacterium inhabits the carposphere where it interacts with fruit through the bi-directional transfer of phytohormones. The majority of research regarding K. xylinus has been focused on identifying and characterizing structural and regulatory factors that control BC biosynthesis, but its ecophysiology has been generally overlooked. Ethylene is a phytohormone that regulates plant development in a variety of ways, but is most commonly known for its positive role on fruit ripening. In this study, we utilized ethephon (2-chloroethylphosphonic acid) to produce in situ ethylene to investigate the effects of this phytohormone on BC production and the expression of genes known to be involved in K. xylinus BC biosynthesis (bcsA, bcsB, bcsC, bcsD, cmcAx, ccpAx and bglAx). Using pellicle assays and reverse transcription quantitative polymerase chain reaction (RT-qPCR), we demonstrate that ethephon-derived ethylene enhances BC directly in K. xylinus by up-regulating the expression of bcsA and bcsB, and indirectly though the up-regulation of cmcAx, ccpAx, and bglAx. We confirm that IAA directly decreases BC biosynthesis by showing that IAA down-regulates bcsA expression. Similarly, we confirm that ABA indirectly influences BC biosynthesis by showing it does not affect the expression of bcs operon genes. In addition, we are the first to report the ethylene and indole-3-acetic acid (IAA) induced differential expression of genes within the bacterial cellulose synthesis (bcs) operon. Using bioinformatics we have identified a novel phytohormone-regulated CRP/FNRKx transcription factor and provide evidence that it influences BC biosynthesis in K. xylinus. Lastly, utilizing current and previous data, we propose a model for the phytohormone-mediated fruit-bacteria interactions that K. xylinus experiences in nature.
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Affiliation(s)
| | - Janice L. Strap
- Molecular Microbial Biochemistry Laboratory, Faculty of Science, University of Ontario Institute of Technology, OshawaON, Canada
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21
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Crystal structure of cyclic nucleotide-binding-like protein from Brucella abortus. Biochem Biophys Res Commun 2015; 468:647-52. [PMID: 26549229 DOI: 10.1016/j.bbrc.2015.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
The cyclic nucleotide-binding (CNB)-like protein (CNB-L) from Brucella abortus shares sequence homology with CNB domain-containing proteins. We determined the crystal structure of CNB-L at 2.0 Å resolution in the absence of its C-terminal helix and nucleotide. The 3D structure of CNB-L is in a two-fold symmetric form. Each protomer shows high structure similarity to that of cGMP-binding domain-containing proteins, and likely mimics their nucleotide-free conformation. A key residue, Glu17, mediates the dimerization and prevents binding of cNMP to the canonical ligand-pocket. The structurally observed dimer of CNB-L is stable in solution, and thus is likely to be biologically relevant.
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22
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cAMP receptor protein (CRP)-mediated resistance/tolerance in bacteria: mechanism and utilization in biotechnology. Appl Microbiol Biotechnol 2015; 99:4533-43. [DOI: 10.1007/s00253-015-6587-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/31/2015] [Accepted: 04/03/2015] [Indexed: 02/05/2023]
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23
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Expression of different bacterial cytotoxins is controlled by two global transcription factors, CRP and Fis, that co-operate in a shared-recruitment mechanism. Biochem J 2015; 466:323-35. [DOI: 10.1042/bj20141315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Expression of related autotransporter toxin genes in pathogenic Escherichia coli and Shigella sonnei require the CRP and Fis global regulators. At promoters controlling toxin production, CRP is suboptimally positioned and Fis compensates for this impediment by facilitating RNA polymerase recruitment.
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24
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Townsend PD, Jungwirth B, Pojer F, Bußmann M, Money VA, Cole ST, Pühler A, Tauch A, Bott M, Cann MJ, Pohl E. The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors. PLoS One 2014; 9:e113265. [PMID: 25469635 PMCID: PMC4254451 DOI: 10.1371/journal.pone.0113265] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/16/2014] [Indexed: 12/01/2022] Open
Abstract
The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in bacterial metabolic regulatory networks. In C. glutamicum, which is widely used for the industrial production of amino acids and serves as a non-pathogenic model organism for members of the Corynebacteriales including Mycobacterium tuberculosis, the GlxR homodimer controls the transcription of a large number of genes involved in carbon metabolism. GlxR therefore represents a key target for understanding the regulation and coordination of C. glutamicum metabolism. Here we investigate cylic AMP and DNA binding of GlxR from C. glutamicum and describe the crystal structures of apo GlxR determined at a resolution of 2.5 Å, and two crystal forms of holo GlxR at resolutions of 2.38 and 1.82 Å, respectively. The detailed structural analysis and comparison of GlxR with CRP reveals that the protein undergoes a distinctive conformational change upon cyclic AMP binding leading to a dimer structure more compatible to DNA-binding. As the two binding sites in the GlxR homodimer are structurally identical dynamic changes upon binding of the first ligand are responsible for the allosteric behavior. The results presented here show how dynamic and structural changes in GlxR lead to optimization of orientation and distance of its two DNA-binding helices for optimal DNA recognition.
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Affiliation(s)
- Philip D. Townsend
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Britta Jungwirth
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Florence Pojer
- Global Health Institute, Protein Crystallography Core Facility, Ecole Poytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Bußmann
- Institute of Bio- and Geosciences, IBG-1:Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Victoria A. Money
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Stewart T. Cole
- Global Health Institute, Protein Crystallography Core Facility, Ecole Poytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andreas Tauch
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1:Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin J. Cann
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Ehmke Pohl
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- * E-mail:
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25
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Seok SH, Im H, Won HS, Seo MD, Lee YS, Yoon HJ, Cha MJ, Park JY, Lee BJ. Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers. ACTA ACUST UNITED AC 2014; 70:1726-42. [PMID: 24914983 DOI: 10.1107/s139900471400724x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/01/2014] [Indexed: 11/10/2022]
Abstract
The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP-CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors. The cAMP-induced conformational transition, including dynamic fluctuations, can be driven by the fundamental folding forces that cause water-soluble globular proteins to construct an optimized hydrophobic core, including secondary-structure formation. The observed conformational asymmetries underlie a negative cooperativity in the sequential binding of cyclic nucleotides and a stepwise manner of binding with discrimination between the effector molecules. Additionally, the finding that cGMP, which is specifically recognized in a syn conformation, induces an inhibitory conformational change, rather than a null effect, on CRP supports the intriguing possibility that cGMP signalling could be widely utilized in prokaryotes, including in aggressive inhibition of CRP-like proteins.
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Affiliation(s)
- Seung-Hyeon Seok
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Min-Duk Seo
- College of Pharmacy, Ajou University, Suwon, Kyeonggi 443-749, Republic of Korea
| | - Yoo-Sup Lee
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Min-Jeong Cha
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jin-Young Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
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Huang J, Wu T, Guo Z, Lou T, Yu S, Gong W, Ji C. Crystallization and preliminary X-ray diffraction analysis of D53H mutant Escherichia coli cAMP receptor protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1436-9. [PMID: 24316848 DOI: 10.1107/s174430911303145x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022]
Abstract
The Escherichia coli cyclic AMP receptor protein (CRP) is a prokaryotic global transcription activator protein that controls the expression of many different genes. Wild-type CRP can bind to special DNA sequences in the presence of cAMP. The substitution of Asp53 by His results in the CRP* phenotype, which does not require exogenous cAMP. In the present study, the D53H CRP mutant was overexpressed, purified and crystallized. cAMP-free D53H CRP crystals were obtained and diffracted to a resolution of 2.9 Å. Based on the systematic absences of the crystals, the space group is likely to be P2(1)2(1)2(1), with unit-cell parameters a = 76.66, b = 152.14, c = 176.11 Å. The asymmetric unit was confirmed to contain four protein dimers, with a Matthews coefficient of 2.71 Å(3) Da(-1) and a solvent content of 54.68%.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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Rodgers TL, Townsend PD, Burnell D, Jones ML, Richards SA, McLeish TCB, Pohl E, Wilson MR, Cann MJ. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors. PLoS Biol 2013; 11:e1001651. [PMID: 24058293 PMCID: PMC3769225 DOI: 10.1371/journal.pbio.1001651] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 07/31/2013] [Indexed: 12/11/2022] Open
Abstract
Allostery in bacterial transcription factors arises from changes in global low-frequency protein dynamics. Amino acids that regulate low-frequency dynamics are identified and seen to be evolutionarily conserved. Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein “design space” that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to occupy a dynamic space that fine-tunes biological activity and thus establishes the means to engineer allosteric mechanisms driven by low-frequency dynamics. Allostery is a process by which a molecule binding to one site of a protein alters the activity of the protein at another site. Allostery is typically thought to occur through a change in protein structure, but there is now clear evidence that the dynamic properties of a protein can also regulate allostery without a change in overall conformation. Here we examine two members of a large family of bacterial transcription factors and provide a mechanism to describe the allosteric binding of their activating ligands. We demonstrate, in these systems, that allostery arises as a natural consequence of changes in global low-frequency protein fluctuations on ligand binding. We further demonstrate that the higher dimensional parameter space that describes all potential variant transcription factors can be reduced to a two-dimensional free energy landscape that determines the key molecular parameters that predominantly regulate allostery. We additionally show that the amino acids we determine as contributing sensitively to allosteric control tend to be conserved in diverse bacteria; thus we identify a link between residues that contribute to low-frequency fluctuations and evolutionary selection pressures.
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Affiliation(s)
- Thomas L. Rodgers
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Philip D. Townsend
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - David Burnell
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Matthew L. Jones
- Department of Physics, Durham University, Durham, United Kingdom
| | - Shane A. Richards
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - Tom C. B. McLeish
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
- Department of Physics, Durham University, Durham, United Kingdom
| | - Ehmke Pohl
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - Mark R. Wilson
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Martin J. Cann
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
- * E-mail:
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28
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Aykaç Fas B, Tutar Y, Haliloğlu T. Dynamic fluctuations provide the basis of a conformational switch mechanism in apo cyclic AMP receptor protein. PLoS Comput Biol 2013; 9:e1003141. [PMID: 23874183 PMCID: PMC3715548 DOI: 10.1371/journal.pcbi.1003141] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 05/31/2013] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli cyclic AMP Receptor Protein (CRP) undergoes conformational changes with cAMP binding and allosterically promotes CRP to bind specifically to the DNA. In that, the structural and dynamic properties of apo CRP prior to cAMP binding are of interest for the comprehension of the activation mechanism. Here, the dynamics of apo CRP monomer/dimer and holo CRP dimer were studied by Molecular Dynamics (MD) simulations and Gaussian Network Model (GNM). The interplay of the inter-domain hinge with the cAMP and DNA binding domains are pre-disposed in the apo state as a conformational switch in the CRP's allosteric communication mechanism. The hinge at L134-D138 displaying intra- and inter-subunit coupled fluctuations with the cAMP and DNA binding domains leads to the emergence of stronger coupled fluctuations between the two domains and describes an on state. The flexible regions at K52-E58, P154/D155 and I175 maintain the dynamic coupling of the two domains. With a shift in the inter-domain hinge position towards the N terminus, nevertheless, the latter correlations between the domains loosen and become disordered; L134-D138 dynamically interacts only with the cAMP and DNA binding domains of its own subunit, and an off state is assumed. We present a mechanistic view on how the structural dynamic units are hierarchically built for the allosteric functional mechanism; from apo CRP monomer to apo-to-holo CRP dimers.
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Affiliation(s)
- Burcu Aykaç Fas
- Department of Chemical Engineering and Polymer Research Center, Boğaziçi University, Bebek, İstanbul, Turkey
| | - Yusuf Tutar
- Department of Chemistry, Department of Biochemistry and CUTFAM Research Center, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Türkan Haliloğlu
- Department of Chemical Engineering and Polymer Research Center, Boğaziçi University, Bebek, İstanbul, Turkey
- * E-mail:
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29
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Inactivation of cyclic Di-GMP binding protein TDE0214 affects the motility, biofilm formation, and virulence of Treponema denticola. J Bacteriol 2013; 195:3897-905. [PMID: 23794624 DOI: 10.1128/jb.00610-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
As a ubiquitous second messenger, cyclic dimeric GMP (c-di-GMP) has been studied in numerous bacteria. The oral spirochete Treponema denticola, a periodontal pathogen associated with human periodontitis, has a complex c-di-GMP signaling network. However, its function remains unexplored. In this report, a PilZ-like c-di-GMP binding protein (TDE0214) was studied to investigate the role of c-di-GMP in the spirochete. TDE0214 harbors a PilZ domain with two signature motifs: RXXXR and DXSXXG. Biochemical studies showed that TDE0214 binds c-di-GMP in a specific manner, with a dissociation constant (Kd) value of 1.73 μM, which is in the low range compared to those of other reported c-di-GMP binding proteins. To reveal the role of c-di-GMP in T. denticola, a TDE0214 deletion mutant (TdΔ214) was constructed and analyzed in detail. First, swim plate and single-cell tracking analyses showed that TdΔ214 had abnormal swimming behaviors: the mutant was less motile and reversed more frequently than the wild type. Second, we found that biofilm formation of TdΔ214 was substantially repressed (∼6.0-fold reduction). Finally, in vivo studies using a mouse skin abscess model revealed that the invasiveness and ability to induce skin abscesses and host humoral immune responses were significantly attenuated in TdΔ214, indicative of the impact that TDE0214 has on the virulence of T. denticola. Collectively, the results reported here indicate that TDE0214 plays important roles in motility, biofilm formation, and virulence of the spirochete. This report also paves a way to further unveil the roles of the c-di-GMP signaling network in the biology and pathogenicity of T. denticola.
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Chen B, Liang W, Wu R, Liang P, Kan B. Phenotype microarray screening of carbon sources used by Vibrio cholerae identifies genes regulated by the cAMP receptor protein. Can J Microbiol 2013; 59:472-8. [PMID: 23826956 DOI: 10.1139/cjm-2013-0084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The cyclic AMP receptor protein (CRP) regulates genes involved in carbon source metabolism, iron uptake, and virulence in bacteria. Identifying the carbon sources utilized by bacteria that are regulated by CRP will help elucidate the CRP regulation cascade and associated responses to environmental stimuli. CRP-dependent regulation of carbon source metabolism in Vibrio cholerae is not thoroughly understood. To identify the candidate carbon sources utilized by V. cholerae that are affected by CRP, we used high-throughput screening to compare the metabolic differences between wild-type and CRP mutant strains of V. cholerae O1 El Tor. Phenotype microarray was used for primary screening of the wild-type and mutant strains, followed by minimal media growth assays and quantitative RT-PCR to validate the candidate carbon sources. In total, 24 carbon sources were subject to CRP regulation, 11 of which have not been previously reported in bacteria. The genes known to be involved in the metabolism of 4 of the carbon sources identified were verified by quantitative RT-PCR. In addition, gel shift experiments showed that CRP bound directly to VCA0053 and VC0391 promoters. Overall, this comprehensive analysis of CRP-mediated catabolite control in V. cholerae has identified new candidate carbon sources for in-depth experimental studies.
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Affiliation(s)
- Baoli Chen
- National Institute for Communicable Disease Control and Prevention and State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China
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31
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Gancedo JM. Biological roles of cAMP: variations on a theme in the different kingdoms of life. Biol Rev Camb Philos Soc 2013; 88:645-68. [PMID: 23356492 DOI: 10.1111/brv.12020] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 12/18/2022]
Abstract
Cyclic AMP (cAMP) plays a key regulatory role in most types of cells; however, the pathways controlled by cAMP may present important differences between organisms and between tissues within a specific organism. Changes in cAMP levels are caused by multiple triggers, most affecting adenylyl cyclases, the enzymes that synthesize cAMP. Adenylyl cyclases form a large and diverse family including soluble forms and others with one or more transmembrane domains. Regulatory mechanisms for the soluble adenylyl cyclases involve either interaction with diverse proteins, as happens in Escherichia coli or yeasts, or with calcium or bicarbonate ions, as occurs in mammalian cells. The transmembrane cyclases can be regulated by a variety of proteins, among which the α subunit and the βγ complex from G proteins coupled to membrane receptors are prominent. cAMP levels also are controlled by the activity of phosphodiesterases, enzymes that hydrolyze cAMP. Phosphodiesterases can be regulated by cAMP, cGMP or calcium-calmodulin or by phosphorylation by different protein kinases. Regulation through cAMP depends on its binding to diverse proteins, its proximal targets, this in turn causing changes in a variety of distal targets. Specifically, binding of cAMP to regulatory subunits of cAMP-dependent protein kinases (PKAs) affects the activity of substrates of PKA, binding to exchange proteins directly activated by cAMP (Epac) regulates small GTPases, binding to transcription factors such as the cAMP receptor protein (CRP) or the virulence factor regulator (Vfr) modifies the rate of transcription of certain genes, while cAMP binding to ion channels modulates their activity directly. Further studies on cAMP signalling will have important implications, not only for advancing fundamental knowledge but also for identifying targets for the development of new therapeutic agents.
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Affiliation(s)
- Juana M Gancedo
- Department of Metabolism and Cell Signalling, Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Madrid 28029, Spain.
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32
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LOMOZIK L, GASOWSKA A, BASINSKI K, BREGIER-JARZEBOWSKA R, JASTRZAB R. Potentiometric and spectral studies of complex formation in the Cu(II), 3′,5′-cyclic adenosine monophosphate, and tetramine systems. J COORD CHEM 2013. [DOI: 10.1080/00958972.2012.754019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- L. LOMOZIK
- a Faculty of Chemistry, Adam Mickiewicz University , Poznan , Poland
- b Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences , Bydgoszcz , Poland
| | - A. GASOWSKA
- a Faculty of Chemistry, Adam Mickiewicz University , Poznan , Poland
| | - K. BASINSKI
- a Faculty of Chemistry, Adam Mickiewicz University , Poznan , Poland
| | | | - R. JASTRZAB
- a Faculty of Chemistry, Adam Mickiewicz University , Poznan , Poland
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33
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Peuker S, Cukkemane A, Held M, Noé F, Kaupp UB, Seifert R. Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys J 2013; 104:63-74. [PMID: 23332059 DOI: 10.1016/j.bpj.2012.11.3816] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 11/14/2012] [Accepted: 11/27/2012] [Indexed: 12/17/2022] Open
Abstract
Many receptors and ion channels are activated by ligands. One key question concerns the binding mechanism. Does the ligand induce conformational changes in the protein via the induced-fit mechanism? Or does the protein preexist as an ensemble of conformers and the ligand selects the most complementary one, via the conformational selection mechanism? Here, we study ligand binding of a tetrameric cyclic nucleotide-gated channel from Mesorhizobium loti and of its monomeric binding domain (CNBD) using rapid mixing, mutagenesis, and structure-based computational biology. Association rate constants of ∼10(7) M(-1) s(-1) are compatible with diffusion-limited binding. Ligand binding to the full-length CNG channel and the isolated CNBD differ, revealing allosteric control of the CNBD by the effector domain. Finally, mutagenesis of allosteric residues affects only the dissociation rate constant, suggesting that binding follows the induced-fit mechanism. This study illustrates the strength of combining mutational, kinetic, and computational approaches to unravel important mechanistic features of ligand binding.
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Affiliation(s)
- Sebastian Peuker
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, Bonn, Germany
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34
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Error-prone PCR of global transcription factor cyclic AMP receptor protein for enhanced organic solvent (toluene) tolerance. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Rinaldo S, Castiglione N, Giardina G, Caruso M, Arcovito A, Longa SD, D'Angelo P, Cutruzzolà F. Unusual heme binding properties of the dissimilative nitrate respiration regulator, a bacterial nitric oxide sensor. Antioxid Redox Signal 2012; 17:1178-89. [PMID: 22424265 DOI: 10.1089/ars.2011.4226] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AIMS In the opportunistic pathogen Pseudomonas aeruginosa, nitric oxide (NO) triggers the respiration of nitrate (denitrification), thus allowing survival in chronic infection sites as a microaerobic-anaerobic biofilm. The NO-dependent induction of denitrification is mediated by the dissimilative nitrate respiration regulator (DNR), a transcription factor forming a stable complex with heme, which is required to sense the physiological messenger (i.e., NO). The molecular details of NO sensing in DNR and, more in general, in this class of sensors are largely unknown, and a study aimed at integrating microbiology and biochemistry is needed. RESULTS Here we present a comprehensive study, including in vivo results and spectroscopy, kinetics, and protein engineering, that demonstrates the direct involvement of a histidine residue in heme iron coordination. Moreover, a peculiar phenomenon of ligand switching around heme iron, which hampers the identification of the second heme axial ligand, is also suggested. These results indicate that DNR is characterized by a remarkable flexibility in solution, as observed for other cAMP receptor protein/fumarate and nitrate reductase regulators (CRP-FNR) to which DNR belongs. INNOVATION The present work represents one of the few studies focused on the biochemistry of NO sensing by bacterial transcriptional regulators. The data presented demonstrate that structural plasticity of DNR is crucial for the sensing activity and confers to the protein unusual heme binding properties. CONCLUSIONS Protein flexibility and dynamics is a key structural feature essential to explain the evolutionary success and adaptability of CRP-FNR, and may represent a common strategy employed by heme-based redox sensors, which presents features deeply different from those of canonical hemeproteins.
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Affiliation(s)
- Serena Rinaldo
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
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36
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Gushchin IY, Gordeliy VI, Grudinin S. A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating. J Mol Model 2012; 18:4053-60. [PMID: 22476580 DOI: 10.1007/s00894-012-1404-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 03/07/2012] [Indexed: 11/30/2022]
Abstract
Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cation channels. Despite the availability of CNBD crystal structures of bacterial cyclic nucleotide-gated (CNG) and mammalian hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels in presence and absence of the cNMP, the full understanding of CNBD conformational changes during activation is lacking. Here, we describe a novel CNBD dimerization interface found in crystal structures of bacterial CNG channel MlotiK1 and mammalian cAMP-activated guanine nucleotide-exchange factor Epac2. Molecular dynamics simulations show that the found interface is stable on the studied timescale of 100 ns, in contrast to the dimerization interface, reported previously. Comparisons with cN-bound structures of CNBD show that the dimerization is incompatible with cAMP binding. Thus, the cAMP-dependent monomerization of CNBD may be an alternative mechanism of the cAMP sensing. Based on these findings, we propose a model of the bacterial CNG channel modulation by cAMP.
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Affiliation(s)
- Ivan Y Gushchin
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Joseph Fourier - Grenoble 1, Grenoble, France
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37
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Tutar Y. Neglected role of cAMP receptor protein monomer. Mol Biol Rep 2011; 39:4261-5. [PMID: 21779799 DOI: 10.1007/s11033-011-1212-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 07/14/2011] [Indexed: 11/28/2022]
Abstract
Lac operon transcription activation through CRP dimer depends on cAMP second messenger. The formation of CRP homodimers is mediated by protein-protein interactions between the monomers. Cyclic AMP ligand binding brings CRP dimer to an active state via conformational changes. Molecular modeling studies in our lab showed the importance of monomer in transcription activation through its pre-existing conformational state. Until now CRP experiments were carried out at protein concentrations higher than that of CRP dimer dissociation value making all CRP monomers dimer and ignore the importance of CRP monomer in allosteric activation. Labeling CRP monomers with fluorophores exterminate using excess protein concentration and allow monitoring CRP monomer behavior. CRP monomer exchange accelerates in the presence of non specific DNA whereas the exchange is inhibited in the presence of specific DNA and cAMP ligand. Degree of subunit exchange depends on the stability of CRP dimer. Cyclic AMP forms a single molecule from two monomers and addition of specific DNA further stabilizes CRP dimer and decreases monomer exchange. On the other hand, addition of non specific DNA increases CRP monomer exchange and may explain the mechanism of CRP monomer removal and dissociation of CRP dimer:cAMP:DNA complex. The exchange behavior of CRP in the presence of different factors implies importance of monomer in transcription complex association and dissociation.
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Affiliation(s)
- Yusuf Tutar
- Department of Biochemistry, Faculty of Medicine, Cumhuriyet University, 58140, Sivas, Turkey.
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38
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Shimada T, Fujita N, Yamamoto K, Ishihama A. Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS One 2011; 6:e20081. [PMID: 21673794 PMCID: PMC3105977 DOI: 10.1371/journal.pone.0020081] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 04/18/2011] [Indexed: 12/17/2022] Open
Abstract
CRP (cAMP receptor protein), the global regulator of genes for carbon source utilization in the absence of glucose, is the best-studied prokaryotic transcription factor. A total of 195 target promoters on the Escherichia coli genome have been proposed to be under the control of cAMP-bound CRP. Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites. Based on their location on the E. coli genome, we predict a total of at least 183 novel regulation target operons, altogether with the 195 hitherto known targets, reaching to the minimum of 378 promoters as the regulation targets of cAMP-CRP. All the promoters selected from the newly identified targets and examined by using the lacZ reporter assay were found to be under the control of CRP, indicating that the Genomic SELEX screening allowed to identify the CRP targets with high accuracy. Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration. One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons.
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Affiliation(s)
- Tomohiro Shimada
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
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39
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Rossiter AE, Browning DF, Leyton DL, Johnson MD, Godfrey RE, Wardius CA, Desvaux M, Cunningham AF, Ruiz-Perez F, Nataro JP, Busby SJW, Henderson IR. Transcription of the plasmid-encoded toxin gene from enteroaggregative Escherichia coli is regulated by a novel co-activation mechanism involving CRP and Fis. Mol Microbiol 2011; 81:179-91. [PMID: 21542864 DOI: 10.1111/j.1365-2958.2011.07685.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enteroaggregative Escherichia coli (EAEC) is a major cause of diarrhoea in developing countries. EAEC 042 is the prototypical strain. EAEC 042 secretes the functionally well-characterized Pet autotransporter toxin that contributes to virulence through its cytotoxic effects on intestinal epithelial cells. Following a global transposon mutagenesis screen of EAEC 042, the transcription factors, CRP and Fis, were identified as essential for transcription of the pet gene. Using both in vivo and in vitro techniques, we show that the pet promoter is co-dependent on CRP and Fis. We present a novel co-activation mechanism whereby CRP is placed at a non-optimal position for transcription initiation, creating dependence on Fis for full activation of pet. This study complements previous findings that establish Fis as a key virulence regulator in EAEC 042.
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Affiliation(s)
- Amanda E Rossiter
- School of Immunity and Infection School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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40
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Kalodimos CG. NMR reveals novel mechanisms of protein activity regulation. Protein Sci 2011; 20:773-82. [PMID: 21404360 DOI: 10.1002/pro.614] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/16/2011] [Accepted: 02/21/2011] [Indexed: 11/06/2022]
Abstract
NMR spectroscopy is one of the most powerful tools for the characterization of biomolecular systems. A unique aspect of NMR is its capacity to provide an integrated insight into both the structure and intrinsic dynamics of biomolecules. In addition, NMR can provide site-resolved information about the conformation entropy of binding, as well as about energetically excited conformational states. Recent advances have enabled the application of NMR for the characterization of supramolecular systems. A summary of mechanisms underpinning protein activity regulation revealed by the application of NMR spectroscopy in a number of biological systems studied in the lab is provided.
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Affiliation(s)
- Charalampos G Kalodimos
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
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Drepper T, Krauss U, Meyer zu Berstenhorst S, Pietruszka J, Jaeger KE. Lights on and action! Controlling microbial gene expression by light. Appl Microbiol Biotechnol 2011; 90:23-40. [PMID: 21336931 DOI: 10.1007/s00253-011-3141-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/05/2011] [Accepted: 01/05/2011] [Indexed: 01/10/2023]
Abstract
Light-mediated control of gene expression and thus of any protein function and metabolic process in living microbes is a rapidly developing field of research in the areas of functional genomics, systems biology, and biotechnology. The unique physical properties of the environmental factor light allow for an independent photocontrol of various microbial processes in a noninvasive and spatiotemporal fashion. This mini review describes recently developed strategies to generate photo-sensitive expression systems in bacteria and yeast. Naturally occurring and artificial photoswitches consisting of light-sensitive input domains derived from different photoreceptors and regulatory output domains are presented and individual properties of light-controlled expression systems are discussed.
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Affiliation(s)
- Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.
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Tao W, Gao Z, Gao Z, Zhou J, Huang Z, Dong Y, Yu S. The 1.6Å resolution structure of activated D138L mutant of catabolite gene activator protein with two cAMP bound in each monomer. Int J Biol Macromol 2011; 48:459-65. [PMID: 21255606 DOI: 10.1016/j.ijbiomac.2011.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 12/27/2010] [Accepted: 01/10/2011] [Indexed: 11/17/2022]
Abstract
The X-ray crystal structure of the cAMP-liganded D138L mutant of Escherichia coli catabolite gene activator protein (CAP) was determined at a resolution of 1.66Å. This high resolution crystal structure reveals four cAMP binding sites in the homodimer. Two anti conformations of cAMPs (anti-cAMP) locate between the β-barrel and the C-helix of each subunit; two syn conformations of cAMPs (syn-cAMP) bind on the surface of the C-terminal domain. With two syn-cAMP molecules bound, the D138L CAP is highly symmetrical with both subunits assuming a "closed" conformation. These differences make the hinge region of the mutant more flexible. Protease susceptibility measurements indicate that D138L is more susceptible to proteases than that of wild type (WT) CAP. The results of protein dynamic experiments (H/D exchange measurements) indicate that the structure of D138L mutant is more dynamic than that of WT CAP, which may impact the recognition of specific DNA sequences.
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Affiliation(s)
- Wenbing Tao
- Department of Chemistry and Institutes of Biomedical Science, Fudan University, Shanghai 200433, China
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Tzeng SR, Kalodimos CG. Dynamic activation of an allosteric regulatory protein. Nature 2009; 462:368-72. [PMID: 19924217 DOI: 10.1038/nature08560] [Citation(s) in RCA: 305] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 10/07/2009] [Indexed: 11/09/2022]
Abstract
Allosteric regulation is used as a very efficient mechanism to control protein activity in most biological processes, including signal transduction, metabolism, catalysis and gene regulation. Allosteric proteins can exist in several conformational states with distinct binding or enzymatic activity. Effectors are considered to function in a purely structural manner by selectively stabilizing a specific conformational state, thereby regulating protein activity. Here we show that allosteric proteins can be regulated predominantly by changes in their structural dynamics. We have used NMR spectroscopy and isothermal titration calorimetry to characterize cyclic AMP (cAMP) binding to the catabolite activator protein (CAP), a transcriptional activator that has been a prototype for understanding effector-mediated allosteric control of protein activity. cAMP switches CAP from the 'off' state (inactive), which binds DNA weakly and non-specifically, to the 'on' state (active), which binds DNA strongly and specifically. In contrast, cAMP binding to a single CAP mutant, CAP-S62F, fails to elicit the active conformation; yet, cAMP binding to CAP-S62F strongly activates the protein for DNA binding. NMR and thermodynamic analyses show that despite the fact that CAP-S62F-cAMP(2) adopts the inactive conformation, its strong binding to DNA is driven by a large conformational entropy originating in enhanced protein motions induced by DNA binding. The results provide strong evidence that changes in protein motions may activate allosteric proteins that are otherwise structurally inactive.
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Affiliation(s)
- Shiou-Ru Tzeng
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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CbpA: a polarly localized novel cyclic AMP-binding protein in Pseudomonas aeruginosa. J Bacteriol 2009; 191:7193-205. [PMID: 19801409 DOI: 10.1128/jb.00970-09] [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
In Pseudomonas aeruginosa, cyclic AMP (cAMP) signaling regulates the transcription of hundreds of genes encoding diverse virulence factors, including the type II secretion system (T2SS) and type III secretion system (T3SS) and their associated toxins, type IV pili (TFP), and flagella. Vfr, a cAMP-dependent transcriptional regulator that is homologous to the Escherichia coli catabolite repressor protein, is thought to be the major cAMP-binding protein that regulates these important virulence determinants. Using a bioinformatic approach, we have identified a gene (PA4704) encoding an additional putative cAMP-binding protein in P. aeruginosa PAO1, which we herein refer to as CbpA, for cAMP-binding protein A. Structural modeling predicts that CbpA is composed of a C-terminal cAMP-binding (CAP) domain and an N-terminal degenerate CAP domain and is structurally similar to eukaryotic protein kinase A regulatory subunits. We show that CbpA binds to cAMP-conjugated agarose via its C-terminal CAP domain. Using in vitro trypsin protection assays, we demonstrate that CbpA undergoes a conformational change upon cAMP binding. Reporter gene assays and electrophoresis mobility shift assays defined the cbpA promoter and a Vfr-binding site that are necessary for Vfr-dependent transcription. Although CbpA is highly regulated by Vfr, deletion of cbpA did not affect known Vfr-dependent functions, including the T2SS, the T3SS, flagellum- or TFP-dependent motility, virulence in a mouse model of acute pneumonia, or protein expression profiles. Unexpectedly, CbpA-green fluorescent protein was found to be localized to the flagellated old cell pole in a cAMP-dependent manner. These results suggest that polar localization of CbpA may be important for its function.
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Reddy MCM, Palaninathan SK, Bruning JB, Thurman C, Smith D, Sacchettini JC. Structural insights into the mechanism of the allosteric transitions of Mycobacterium tuberculosis cAMP receptor protein. J Biol Chem 2009; 284:36581-36591. [PMID: 19740754 DOI: 10.1074/jbc.m109.041343] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cAMP receptor protein (CRP) from Mycobacterium tuberculosis is a cAMP-responsive global transcriptional regulator, responsible for the regulation of a multitude of diverse proteins. We have determined the crystal structures of the CRP.cAMP and CRP.N(6)-cAMP derivative-bound forms of the enzyme to 2.2- and 2.3 A-resolution, respectively, to investigate cAMP-mediated conformational and structural changes. The allosteric switch from the open, inactive conformation to the closed, active conformation begins with a number of changes in the ligand-binding cavity upon cAMP binding. These subtle structural changes and numerous non-bonding interactions between cAMP, the N-domain residues, and the C-domain helices demonstrate that the N-domain hairpin loop acts as a structural mediator of the allosteric switch. Based on the CRP.N(6)-cAMP crystal structure, binding of N(6)-cAMP with a bulkier methylphenylethyl extension from the N6 atom stabilizes the cAMP-binding domain, N-domain hairpin, and C-terminal domain in a similar manner as that of the CRP.cAMP structure, maintaining structural integrity within the subunits. However, the bulkier N6 extension of N(6)-cAMP (in R conformation) is accommodated only in subunit A with minor changes, whereas in subunit B, the N6 extension is in the S conformation hindering the hinge region of the central helix. As a result, the entire N-domain and the C-domain of subunit B integrated by the cAMP portion of this ligand, together tilt away ( approximately 7 degrees tilt) from central helix C, positioning the helix-turn-helix motif in an unfavorable position for the DNA substrate, asymmetrically. Together, these crystal structures demonstrate the mechanism of action of the cAMP molecule and its role in integrating the active CRP structure.
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Affiliation(s)
- Manchi C M Reddy
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Satheesh K Palaninathan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - John B Bruning
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Cory Thurman
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Danielle Smith
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843.
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