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Han ML, Alsaadi Y, Zhao J, Zhu Y, Lu J, Jiang X, Ma W, Patil NA, Dunstan RA, Le Brun AP, Wickremasinghe H, Hu X, Wu Y, Yu HH, Wang J, Barlow CK, Bergen PJ, Shen HH, Lithgow T, Creek DJ, Velkov T, Li J. Arginine catabolism is essential to polymyxin dependence in Acinetobacter baumannii. Cell Rep 2024; 43:114410. [PMID: 38923457 DOI: 10.1016/j.celrep.2024.114410] [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: 11/03/2023] [Revised: 02/03/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Polymyxins are often the only effective antibiotics against the "Critical" pathogen Acinetobacter baumannii. Worryingly, highly polymyxin-resistant A. baumannii displaying dependence on polymyxins has emerged in the clinic, leading to diagnosis and treatment failures. Here, we report that arginine metabolism is essential for polymyxin-dependent A. baumannii. Specifically, the arginine degradation pathway was significantly altered in polymyxin-dependent strains compared to wild-type strains, with critical metabolites (e.g., L-arginine and L-glutamate) severely depleted and expression of the astABCDE operon significantly increased. Supplementation of arginine increased bacterial metabolic activity and suppressed polymyxin dependence. Deletion of astA, the first gene in the arginine degradation pathway, decreased phosphatidylglycerol and increased phosphatidylethanolamine levels in the outer membrane, thereby reducing the interaction with polymyxins. This study elucidates the molecular mechanism by which arginine metabolism impacts polymyxin dependence in A. baumannii, underscoring its critical role in improving diagnosis and treatment of life-threatening infections caused by "undetectable" polymyxin-dependent A. baumannii.
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Affiliation(s)
- Mei-Ling Han
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia.
| | - Yasser Alsaadi
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Jinxin Zhao
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Yan Zhu
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Jing Lu
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Xukai Jiang
- National Glycoengineering Research Centre, Shandong University, Qingdao 266237, China
| | - Wendong Ma
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Nitin A Patil
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Rhys A Dunstan
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Hasini Wickremasinghe
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Xiaohan Hu
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Yimin Wu
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Heidi H Yu
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Jiping Wang
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Christopher K Barlow
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Phillip J Bergen
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Hsin-Hui Shen
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Trevor Lithgow
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
| | - Darren J Creek
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Tony Velkov
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jian Li
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia.
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2
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Barnes AJ, Bennett EF, Vezina B, Hudson AW, Hernandez GE, Nutter NA, Bray AS, Nagpal R, Wyres KL, Zafar MA. Ethanolamine metabolism through two genetically distinct loci enables Klebsiella pneumoniae to bypass nutritional competition in the gut. PLoS Pathog 2024; 20:e1012189. [PMID: 38713723 PMCID: PMC11101070 DOI: 10.1371/journal.ppat.1012189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 05/17/2024] [Accepted: 04/10/2024] [Indexed: 05/09/2024] Open
Abstract
Successful microbial colonization of the gastrointestinal (GI) tract hinges on an organism's ability to overcome the intense competition for nutrients in the gut between the host and the resident gut microbiome. Enteric pathogens can exploit ethanolamine (EA) in the gut to bypass nutrient competition. However, Klebsiella pneumoniae (K. pneumoniae) is an asymptomatic gut colonizer and, unlike well-studied enteric pathogens, harbors two genetically distinct ethanolamine utilization (eut) loci. Our investigation uncovered unique roles for each eut locus depending on EA utilization as a carbon or nitrogen source. Murine gut colonization studies demonstrated the necessity of both eut loci in the presence of intact gut microbiota for robust GI colonization by K. pneumoniae. Additionally, while some Escherichia coli gut isolates could metabolize EA, other commensals were incapable, suggesting that EA metabolism likely provides K. pneumoniae a selective advantage in gut colonization. Molecular and bioinformatic analyses unveiled the conservation of two eut loci among K. pneumoniae and a subset of the related taxa in the K. pneumoniae species complex, with the NtrC-RpoN regulatory cascade playing a pivotal role in regulation. These findings identify EA metabolism as a critical driver of K. pneumoniae niche establishment in the gut and propose microbial metabolism as a potential therapeutic avenue to combat K. pneumoniae infections.
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Affiliation(s)
- Andrew J. Barnes
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Emma F. Bennett
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andrew W. Hudson
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Giovanna E. Hernandez
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Noah A. Nutter
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Andrew S. Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ravinder Nagpal
- Department of Health, Nutrition, and Food Science, Florida State University, Tallahassee, Florida, United States of America
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - M. Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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3
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Dahiya M, Jovel J, Monaghan T, Wong K, Elhenawy W, Chui L, McAlister F, Kao D. In Silico Analysis of Changes in Predicted Metabolic Capabilities of Intestinal Microbiota after Fecal Microbial Transplantation for Treatment of Recurrent Clostridioides difficile Infection. Microorganisms 2023; 11:microorganisms11041078. [PMID: 37110500 PMCID: PMC10143790 DOI: 10.3390/microorganisms11041078] [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: 02/15/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
IMPORTANCE Although highly effective in treating recurrent Clostridioides difficile infection (RCDI), the mechanisms of action of fecal microbial transplantation (FMT) are not fully understood. AIM The aim of this study was to explore microbially derived products or pathways that could contribute to the therapeutic efficacy of FMT. METHODS Stool shotgun metagenomic sequencing data from 18 FMT-treated RCDI patients at 4 points in time were used for the taxonomic and functional profiling of their gut microbiome. The abundance of the KEGG orthology (KO) groups was subjected to univariate linear mixed models to assess the significance of the observed differences between 0 (pre-FMT), 1, 4, and 12 weeks after FMT. RESULTS Of the 59,987 KO groups identified by shotgun metagenomic sequencing, 27 demonstrated a statistically significant change after FMT. These KO groups are involved in many cellular processes, including iron homeostasis, glycerol metabolism, and arginine regulation, all of which have been implicated to play important roles in bacterial growth and virulence in addition to modulating the intestinal microbial composition. CONCLUSION Our findings suggest potential changes in key KO groups post-FMT, which may contribute to FMT efficacy beyond the restored microbial composition/diversity and metabolism of bile acids and short-chain fatty acids. Future larger studies that include a fecal metabolomics analysis combined with animal model validation work are required to further elucidate the molecular mechanisms.
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Affiliation(s)
- Monica Dahiya
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Juan Jovel
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Tanya Monaghan
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Karen Wong
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Wael Elhenawy
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Linda Chui
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB T6G 2R3, Canada
| | - Finlay McAlister
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Dina Kao
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
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4
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Adams JD, Sander KB, Criddle CS, Arkin AP, Clark DS. Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products. Microb Cell Fact 2023; 22:69. [PMID: 37046248 PMCID: PMC10091555 DOI: 10.1186/s12934-023-02064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achieved either through mechanical disruption or reagent-based methods, which introduce issues of energy demand, material needs, high costs, and scaling problems. Osmolysis, a cell lysis method that relies on hypoosmotic downshock upon resuspension of cells in distilled water, has been applied for bioseparation of intracellular products from extreme halophiles and mammalian cells. However, most industrial bacterial strains are non-halotolerant and relatively resistant to hypoosmotic cell lysis. RESULTS To overcome this limitation, we developed two strategies to increase the susceptibility of non-halotolerant hosts to osmolysis using Cupriavidus necator, a strain often used in electromicrobial production, as a prototypical strain. In one strategy, C. necator was evolved to increase its halotolerance from 1.5% to 3.25% (w/v) NaCl through adaptive laboratory evolution, and genes potentially responsible for this phenotypic change were identified by whole genome sequencing. The evolved halotolerant strain experienced an osmolytic efficiency of 47% in distilled water following growth in 3% (w/v) NaCl. In a second strategy, the cells were made susceptible to osmolysis by knocking out the large-conductance mechanosensitive channel (mscL) gene in C. necator. When these strategies were combined by knocking out the mscL gene from the evolved halotolerant strain, greater than 90% osmolytic efficiency was observed upon osmotic downshock. A modified version of this strategy was applied to E. coli BL21 by deleting the mscL and mscS (small-conductance mechanosensitive channel) genes. When grown in medium with 4% NaCl and subsequently resuspended in distilled water, this engineered strain experienced 75% cell lysis, although decreases in cell growth rate due to higher salt concentrations were observed. CONCLUSIONS Our strategy is shown to be a simple and effective way to lyse cells for the purification of intracellular biomacromolecules and may be applicable in many bacteria used for bioproduction.
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Affiliation(s)
- Jeremy David Adams
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Kyle B Sander
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
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5
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Yang HW, Lee JH, Zhao Y. RpoN Regulon in Erwinia amylovora Revealed by Transcriptional Profiling and In Silico Binding Site Analysis. PHYTOPATHOLOGY 2023; 113:183-193. [PMID: 35994732 DOI: 10.1094/phyto-07-22-0255-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Erwinia amylovora causes a devastating fire blight disease in apples and pears. One of the main virulence determinants in E. amylovora is the hypersensitive response (HR) and pathogenicity (hrp)-type III secretion system (T3SS), which is activated by the RpoN-HrpL sigma factor cascade. However, the RpoN regulon in E. amylovora has not been investigated. In this study, we determined the RpoN regulon in E. amylovora by combining RNA-seq transcriptomic analysis with in silico binding site analysis. RNA-seq revealed that 262 genes, approximately 7.5% genes in the genome of E. amylovora, were differentially transcribed in the rpoN mutant as compared with the wild type. Specifically, genes associated with virulence, motility, nitrogen assimilation, the PspF system, stress response, and arginine biosynthesis are positively regulated by RpoN, whereas genes associated with biosynthesis of amino acids and sorbitol transport are negatively regulated by RpoN. In silico binding site analysis identified 46 potential target genes with a putative RpoN binding site, and the upstream sequences of six, three, and three genes also contain putative GlnG, PspF, and YfhA binding sites, respectively. Overall, RpoN directly regulates genes associated with virulence, nitrogen assimilation, the PspF system, motility and the YfhA/YfhK two-component regulatory system.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Jae-Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
- Department of Plant Pathology, WSU-IAREC, Prosser, WA 99350, U.S.A
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6
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Li H, Xie R, Xu X, Liao X, Guo J, Fang Y, Fang Z, Huang J. Static Magnetic Field Inhibits Growth of Escherichia coli Colonies via Restriction of Carbon Source Utilization. Cells 2022; 11:cells11050827. [PMID: 35269449 PMCID: PMC8909705 DOI: 10.3390/cells11050827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Magnetobiological effects on growth and virulence have been widely reported in Escherichia coli (E. coli). However, published results are quite varied and sometimes conflicting because the underlying mechanism remains unknown. Here, we reported that the application of 250 mT static magnetic field (SMF) significantly reduces the diameter of E. coli colony-forming units (CFUs) but has no impact on the number of CFUs. Transcriptomic analysis revealed that the inhibitory effect of SMF is attributed to differentially expressed genes (DEGs) primarily involved in carbon source utilization. Consistently, the addition of glycolate or glyoxylate to the culture media successfully restores the bacterial phenotype in SMF, and knockout mutants lacking glycolate oxidase are no longer sensitive to SMF. These results suggest that SMF treatment results in a decrease in glycolate oxidase activity. In addition, metabolomic assay showed that long-chain fatty acids (LCFA) accumulate while phosphatidylglycerol and middle-chain fatty acids decrease in the SMF-treated bacteria, suggesting that SMF inhibits LCFA degradation. Based on the published evidence together with ours derived from this study, we propose a model showing that free radicals generated by LCFA degradation are the primary target of SMF action, which triggers the bacterial oxidative stress response and ultimately leads to growth inhibition.
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Affiliation(s)
- Haodong Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Runnan Xie
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xiang Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xingru Liao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Jiaxin Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Yanwen Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Zhicai Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
- Correspondence:
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7
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Zou H, Shen Y, Li C, Li Q. Two Phenotypes of Klebsiella pneumoniae ST147 Outbreak from Neonatal Sepsis with a Slight Increase in Virulence. Infect Drug Resist 2022; 15:1-12. [PMID: 35023933 PMCID: PMC8748007 DOI: 10.2147/idr.s343292] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/09/2021] [Indexed: 01/26/2023] Open
Abstract
Purpose Severe infection has been the leading causes of neonatal death, especially the emergency of multidrug-resistant bacteria such as carbapenem-resistant Enterobacteriaceae. This study aimed to investigate the outbreak of carbapenem-resistant Klebsiella pneumoniae (CR-KP) in neonatal wards and to explore the possible pathogenesis of Klebsiella pneumoniae. Materials and Methods CR-KP were collected from neonatal ward of Chongqing Health Center for Women and Children between 2017 and 2019. Broth microdilution method was used to evaluate the antimicrobial activities in vitro, at the same time, the virulence of the strain was evaluated by in vitro and in vivo experiments. At last, prokaryotic chain specific transcriptome sequencing was conducted to explore the possible pathogenesis of CR-KP. Results In this study, a total of 14 carbapenem-resistant-Klebsiella pneumoniae (CR-KP) strains were isolated from Chongqing Health Center for Women and Children, among which all CR-KP isolates were identified as NDM-1-producers. Molecular epidemiological studies revealed ST147 being the most common sequence type (ST). Moreover, we first found two phenotypes of K. pneumoniae with different virulence from the same specimen. Type I, which was a white and sticky colony had a slight increase in virulence with higher biofilm formation, serum resistance and virulence than Type II with gray colony. Compared with the Type II, 10 pathways were obviously changed in Type I especially amino acid metabolism, such as arginine and proline metabolism. Conclusion Our findings revealed a new potential threat of NDM-1-positive CR-KP with higher virulence in neonatal ICU ward. We found two phenotypes of K. pneumoniae with different virulent, which may be due to the difference expression of arginine and proline metabolism.
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Affiliation(s)
- Hua Zou
- Department of Laboratory Medicine, Chongqing Health Center for Women and Children, Chongqing, 400016, People's Republic of China
| | - Yan Shen
- Department of Laboratory Medicine, Chongqing Health Center for Women and Children, Chongqing, 400016, People's Republic of China
| | - Chunli Li
- Department of Laboratory Medicine, Chongqing Health Center for Women and Children, Chongqing, 400016, People's Republic of China
| | - Qiuhong Li
- Department of Laboratory Medicine, Chongqing Health Center for Women and Children, Chongqing, 400016, People's Republic of China
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Reprogramming microbial populations using a programmed lysis system to improve chemical production. Nat Commun 2021; 12:6886. [PMID: 34824227 PMCID: PMC8617184 DOI: 10.1038/s41467-021-27226-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.
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9
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Prieto A, Bernabeu M, Sánchez-Herrero JF, Pérez-Bosque A, Miró L, Bäuerl C, Collado C, Hüttener M, Juárez A. Modulation of AggR levels reveals features of virulence regulation in enteroaggregative E. coli. Commun Biol 2021; 4:1295. [PMID: 34785760 PMCID: PMC8595720 DOI: 10.1038/s42003-021-02820-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) strains are one of the diarrheagenic pathotypes. EAEC strains harbor a virulence plasmid (pAA2) that encodes, among other virulence determinants, the aggR gene. The expression of the AggR protein leads to the expression of several virulence determinants in both plasmids and chromosomes. In this work, we describe a novel mechanism that influences AggR expression. Because of the absence of a Rho-independent terminator in the 3'UTR, aggR transcripts extend far beyond the aggR ORF. These transcripts are prone to PNPase-mediated degradation. Structural alterations in the 3'UTR result in increased aggR transcript stability, leading to increased AggR levels. We therefore investigated the effect of increased AggR levels on EAEC virulence. Upon finding the previously described AggR-dependent virulence factors, we detected novel AggR-regulated genes that may play relevant roles in EAEC virulence. Mutants exhibiting high AggR levels because of structural alterations in the aggR 3'UTR show increased mobility and increased pAA2 conjugation frequency. Furthermore, among the genes exhibiting increased fold change values, we could identify those of metabolic pathways that promote increased degradation of arginine, fatty acids and gamma-aminobutyric acid (GABA), respectively. In this paper, we discuss how the AggR-dependent increase in specific metabolic pathways activity may contribute to EAEC virulence.
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Affiliation(s)
- Alejandro Prieto
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Manuel Bernabeu
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | | | - Anna Pérez-Bosque
- Department of Biochemistry and Physiology, Universitat de Barcelona, Barcelona, Spain
- Institut de Nutrició i Seguretat Alimentària, Universitat de Barcelona, Barcelona, Spain
| | - Lluïsa Miró
- Department of Biochemistry and Physiology, Universitat de Barcelona, Barcelona, Spain
- Institut de Nutrició i Seguretat Alimentària, Universitat de Barcelona, Barcelona, Spain
| | - Christine Bäuerl
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Carmen Collado
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Mário Hüttener
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain.
| | - Antonio Juárez
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain.
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain.
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10
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Lin J, Luo X, Gänzle MG, Luo L. Characterization of the two nonidentical ArgR regulators of Tetragenococcus halophilus and their regulatory effects on arginine metabolism. Appl Microbiol Biotechnol 2020; 104:8775-8787. [PMID: 32880693 DOI: 10.1007/s00253-020-10868-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022]
Abstract
The halophilic lactic acid bacterium Tetragenococcus halophilus has been widely used in high-salinity fermentation processes of food. Previous studies have indicated that the catabolism of arginine may contribute to the osmotic stress adaptation of T. halophilus. Unusually, in the chromosome of T. halophilus, preceding the arginine deiminase (ADI) operon, locate two co-transcribed genes, both encoding an ArgR regulator; similar structure was rarely found and the roles of the regulators have not been demonstrated. In the current study, regulatory roles of these two nonidentical ArgR regulators on the arginine metabolism of T. halophilus were investigated. The results show that these two regulators play different roles in arginine metabolism, ArgR1 acts as a negative regulator of the ADI pathway by binding to the promoter sequences and repressing the transcription of genes, and the addition of arginine or hyper-osmotic stress conditions can abolish the ArgR1 repression, whereas ArgR2 negatively regulates the genes involved in arginine biosynthesis. Our study found that despite the commonly known roles of the ArgR regulators as the activator of arginine catabolism and the repressor of arginine biosynthesis, which are found in most studied bacteria possessed one ArgR regulator, the two nonidentical ArgR regulators of T. halophilus both act as repressors, and the repression by which is regulated when sensing changes of environments. By revealing the regulation of arginine metabolism, the current study provides molecular insights and potential tools for future applications of halophiles in biotechnology. KEY POINTS: • The expression of the ADI pathway of T. halophilus is regulated by carbon sources and osmotic stress. • The arginine metabolism process of T. halophilus is fine-tuned by the two ArgR regulators. • The ADI pathway may contribute to the osmotic stress adaptation by generating more energy and accumulating citrulline which acts as compatible solute.
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Affiliation(s)
- Jieting Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Xiaotong Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Lixin Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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11
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Qu C, Chen L, Fu H, Wang J. Engineering Thermoanaerobacterium aotearoense SCUT27 with argR knockout for enhanced ethanol production from lignocellulosic hydrolysates. BIORESOURCE TECHNOLOGY 2020; 310:123435. [PMID: 32361198 DOI: 10.1016/j.biortech.2020.123435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Although Thermoanaerobacterium aotearoense SCUT27 (SCUT27) could co-utilize glucose and xylose, the presence of glucose still repressed xylose catabolism. Arginine repressors (ArgRs) were involved in several key metabolic pathways and might be the global regulator. In SCUT27, three genes (V518_0585; V518_1870; V518_1864) were annotated as argR and only the deficiency of argR1864 could greatly improve the co-utilization of glucose and xylose, due to the enhanced activity of xylose isomerase, xylulokinase and the higher energy level. The metabolic flux of SCUT27/ΔargR1864 indicated that new carbon distribution had been re-established and the ethanol yield had increased by 82.95%, strains growth and acetate yield improved by ~35.91% without detectable lactate for the poor activity of lactate dehydrogenase. The improved concentration of ATP and NAD(H) in SCUT27/ΔargR1864 provided more energy to respond the stress, which enabled the mutant the better cell viability to utilize lignocellulosic hydrolysates for enhanced ethanol formation.
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Affiliation(s)
- Chunyun Qu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Lili Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; The State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China.
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12
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Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
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13
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Geraskina NV, Sycheva EV, Samsonov VV, Eremina NS, Hook CD, Serebrianyi VA, Stoynova NV. Engineering Escherichia coli for autoinducible production of L-valine: An example of an artificial positive feedback loop in amino acid biosynthesis. PLoS One 2019; 14:e0215777. [PMID: 31022249 PMCID: PMC6483228 DOI: 10.1371/journal.pone.0215777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
Artificial metabolically regulated inducible expression systems are often used for the production of essential compounds. In most cases, the application of such systems enables regulating the expression of an entire group of genes in response to any internal signal such as an aerobic/anaerobic switch, a transition to stationary phase, or the exhausting of essential compounds. In this work, we demonstrate an example of another type of artificial autoinducible module, denoted a positive feedback module. This positive feedback module generates an inducer molecule that in turn enhances its own synthesis, promoting an activation signal. Due to the use of acetolactate, an intermediate of the L-valine biosynthetic pathway, as a specific inducer molecule, we realized a positive feedback loop in the biosynthetic pathway of branched chain amino acids. Such positive feedback was demonstrated to improve the production of a target compound.
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Affiliation(s)
| | - Elena V. Sycheva
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
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14
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Zhu K, Li G, Wei R, Mao Y, Zhao Y, He A, Bai Z, Deng Y. Systematic analysis of the effects of different nitrogen source and ICDH knockout on glycolate synthesis in Escherichia coli. J Biol Eng 2019; 13:30. [PMID: 30988698 PMCID: PMC6449901 DOI: 10.1186/s13036-019-0159-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/26/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Glycolate is an important α-hydroxy carboxylic acid widely used in industrial and consumer applications. The production of glycolate from glucose in Escherichia coli is generally carried out by glycolysis and glyoxylate shunt pathways, followed by reduction to glycolate. Glycolate accumulation was significantly affected by nitrogen sources and isocitrate dehydrogenase (ICDH), which influenced carbon flux distribution between the tricarboxylic acid (TCA) cycle and the glyoxylate shunt, however, the mechanism was unclear. RESULTS Herein, we used RNA-Seq to explore the effects of nitrogen sources and ICDH knockout on glycolate production. The Mgly534 strain and the Mgly624 strain (with the ICDH deletion in Mgly534), displaying different phenotypes on organic nitrogen sources, were also adopted for the exploration. Though the growth of Mgly534 was improved on organic nitrogen sources, glycolate production decreased and acetate accumulated, while Mgly624 achieved a balance between cell growth and glycolate production, reaching 0.81 g glycolate/OD (2.6-fold higher than Mgly534). To further study Mgly624, the significant changed genes related to N-regulation, oxidative stress response and iron transport were analyzed. Glutamate and serine were found to increase the biomass and productivity respectively. Meanwhile, overexpressing the arginine transport gene argT accelerated the cell growth rate and increased the biomass. Further, the presence of Fe2+ also speeded up the cells growth and compensated for the lack of reducing equivalents. CONCLUSION Our studies identified that ICDH knockout strain was more suitable for glycolate production. RNA-Seq provided a better understanding of the ICDH knockout on cellular physiology and glycolate production.
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Affiliation(s)
- Kangjia Zhu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Ren Wei
- Institute of Biochemistry, Leipzig University, Johannisallee 23, D-04103 Leipzig, Germany
| | - Yin Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Aiyong He
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 China
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15
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Azarian B, Azimi A, Sepehri M, Samimi Fam V, Rezaie F, Talebkhan Y, Khalaj V, Davami F. Proteomics investigation of molecular mechanisms affected by EnBase culture system in anti-VEGF fab fragment producing E. coli BL21 (DE3). Prep Biochem Biotechnol 2019; 49:48-57. [PMID: 30735089 DOI: 10.1080/10826068.2018.1508037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aggregation of recombinant proteins, a major problem in E. coli expression system, is improved by using EnBase culture system based on slow release of glucose. In the present study, to understand the intracellular mechanisms involved in increased solubility of the target recombinant protein through EnBase system, the effect of this system was investigated on E. coli cells proteome profile. The proteome profile of E. coli cells cultured in EnBase and conventional batch mode was analyzed by two-dimensional gel electrophoresis. The proteins with significant expressional changes were identified through MALDI-TOF/TOF mass spectrometry. In EnBase system, the expressions of carbon metabolism-related proteins, sugar transport system-related proteins, and amino acids metabolism-related proteins were significantly altered. Furthermore, the expression of Thioredoxin 1 as the facilitator of protein folding was up-regulated in EnBase system that could be related to the increased solubility of recombinant protein. The proteomics analysis of E. coli cells cultured in EnBase system revealed that Thioredoxin 1 can be a potential candidate for future studies aiming at increased anti-VEGF fab fragment solubility. Studying proteomics is a valuable tool for revealing the target proteins that play the central role in EnBase culture system for increasing the solubility.
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Affiliation(s)
- Bahareh Azarian
- a Protein Chemistry Unit, Biotechnology Research Centre , Pasteur Institute of Iran , Tehran , Iran
| | - Amin Azimi
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,c Department of Biotechnology , College of Science, University of Tehran , Tehran , Iran
| | - Mahboubeh Sepehri
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,d Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences & Technology , Pharmaceutical sciences Branch, Islamic Azad University , Tehran , Iran
| | - Vahideh Samimi Fam
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,e Department of Microbiology , Islamic Azad University Rasht Branch , Rasht , Guilan , Iran
| | - Faegheh Rezaie
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Yeganeh Talebkhan
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Vahid Khalaj
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Fatemeh Davami
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
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16
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Gravina F, Sanchuki HS, Rodrigues TE, Gerhardt ECM, Pedrosa FO, Souza EM, Valdameri G, de Souza GA, Huergo LF. Proteome analysis of an Escherichia coli ptsN-null strain under different nitrogen regimes. J Proteomics 2017; 174:28-35. [PMID: 29274402 DOI: 10.1016/j.jprot.2017.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/29/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022]
Abstract
The carbohydrate-uptake phosphorelay PTS system plays a key role in metabolic regulation in Bacteria controlling the utilization of secondary carbon sources. Some bacteria, such as Escherichia coli, encode a paralogous system named PTSNtr (nitrogen related PTS). PTSNtr is composed of EINtr (ptsP), NPr (ptsO), and EIIANtr (ptsN). These proteins act as a phosphorelay system from phosphoenolpyruvate to EINtr, NPr and them to EIIANtr. PTSNtr is not involved in carbohydrate uptake and it may be dedicated to performing regulatory functions. The phosphorylation state of EINtr is regulated by allosteric binding of glutamine and 2-oxoglutarate, metabolites whose intracellular levels reflect the nitrogen status. Although PTSNtr is designated as having nitrogen-sensory properties, no major effect of this system on nitrogen regulation has been described in E. coli. Here we show that an E. coli ptsN deletion mutant has impaired growth in minimal medium. Proteome analysis of the ∆ptsN strain under different nitrogen regimes revealed no involvement in regulation of the canonical nitrogen regulatory (Ntr) system. The proteomic data support the conclusion that ptsN is required to balance the activities of the sigma factors RpoS and RpoD in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed. SIGNIFICANCE The nitrogen related PTSNtr phosphorelay system has been hypothesized to participate in the control of nitrogen metabolism. Here we used a proteomics approach to show that an Escherichia coli ptsN null strain, which misses the final module of PTSNtr phosphorelay, has no significant effects on nitrogen metabolism under different nitrogen regimes. We noted that ptsN is required for fitness under minimal medium and for the proper balance between RpoS and sigma 70 activities in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed.
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Affiliation(s)
- Fernanda Gravina
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Heloisa S Sanchuki
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Thiago E Rodrigues
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | | | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Gláucio Valdameri
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Departamento de Análises Clínicas, UFPR, Curitiba, PR, Brazil
| | - Gustavo A de Souza
- Oslo University Hospital, The Proteomics Core Facility, Rikshospitalet, Oslo, Norway; Instituto do Cérebro, UFRN, Natal, RN, Brazil
| | - Luciano F Huergo
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Setor Litoral, UFPR, Matinhos, PR, Brazil.
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Levy L, Anavy L, Solomon O, Cohen R, Brunwasser-Meirom M, Ohayon S, Atar O, Goldberg S, Yakhini Z, Amit R. A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ 54 Promoters. Cell Rep 2017; 21:845-858. [DOI: 10.1016/j.celrep.2017.09.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/30/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022] Open
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Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. J Bacteriol 2017; 199:JB.00755-16. [PMID: 28115545 DOI: 10.1128/jb.00755-16] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/12/2017] [Indexed: 01/31/2023] Open
Abstract
The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS.IMPORTANCE The sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.
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Complementation of Arginine Auxotrophy for Genetic Transformation of Coxiella burnetii by Use of a Defined Axenic Medium. Appl Environ Microbiol 2016; 82:3042-51. [PMID: 26969695 DOI: 10.1128/aem.00261-16] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/08/2016] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Host cell-free (axenic) culture of Coxiella burnetii in acidified citrate cysteine medium-2 (ACCM-2) has provided important opportunities for investigating the biology of this naturally obligate intracellular pathogen and enabled the development of tools for genetic manipulation. However, ACCM-2 has complex nutrient sources that preclude a detailed study of nutritional factors required for C. burnetii growth. Metabolic reconstruction of C. burnetii predicts that the bacterium cannot synthesize all amino acids and therefore must sequester some from the host. To examine C. burnetii amino acid auxotrophies, we developed a nutritionally defined medium with known amino acid concentrations, termed ACCM-D. Compared to ACCM-2, ACCM-D supported longer logarithmic growth, a more gradual transition to stationary phase, and approximately 5- to 10-fold greater overall replication. Small-cell-variant morphological forms generated in ACCM-D also showed increased viability relative to that generated in ACCM-2. Lack of growth in amino acid-deficient formulations of ACCM-D revealed C. burnetii auxotrophy for 11 amino acids, including arginine. Heterologous expression of Legionella pneumophila argGH in C. burnetii permitted growth in ACCM-D missing arginine and supplemented with citrulline, thereby providing a nonantibiotic means of selection of C. burnetii genetic transformants. Consistent with bioinformatic predictions, the elimination of glucose did not impair C. burnetii replication. Together, these results highlight the advantages of a nutritionally defined medium in investigations of C. burnetii metabolism and the development of genetic tools. IMPORTANCE Host cell-free growth and genetic manipulation of Coxiella burnetii have revolutionized research of this intracellular bacterial pathogen. Nonetheless, undefined components of growth medium have made studies of C. burnetii physiology difficult and have precluded the development of selectable markers for genetic transformation based on nutritional deficiencies. Here, we describe a medium, containing only amino acids as the sole source of carbon and energy, which supports robust growth and improved viability of C. burnetii Growth studies confirmed that C. burnetii cannot replicate in medium lacking arginine. However, genetic transformation of the bacterium with constructs containing the last two genes in the L. pneumophila arginine biosynthesis pathway (argGH) allowed growth on defined medium missing arginine but supplemented with the arginine precursor citrulline. Our results advance the field by facilitating studies of C. burnetii metabolism and allowing non-antibiotic-based selection of C. burnetii genetic transformants, an important achievement considering that selectable makers based on antibiotic resistance are limited.
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Brunwasser-Meirom M, Pollak Y, Goldberg S, Levy L, Atar O, Amit R. Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression. Nat Commun 2016; 7:10407. [PMID: 26832446 PMCID: PMC4740811 DOI: 10.1038/ncomms10407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 12/02/2015] [Indexed: 01/20/2023] Open
Abstract
We explore a model for 'quenching-like' repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model's predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10-11 bp insertions or deletions (INDELs) and sensitive to 5-6 bp INDELs. We test this prediction on 61 σ(54)-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers' sequences to the DNA's helical repeat.
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Affiliation(s)
- Michal Brunwasser-Meirom
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Yaroslav Pollak
- Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Lior Levy
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Orna Atar
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
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Abstract
Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.
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Abstract
This review considers the pathways for the degradation of amino acids and a few related compounds (agmatine, putrescine, ornithine, and aminobutyrate), along with their functions and regulation. Nitrogen limitation and an acidic environment are two physiological cues that regulate expression of several amino acid catabolic genes. The review considers Escherichia coli, Salmonella enterica serovar Typhimurium, and Klebsiella species. The latter is included because the pathways in Klebsiella species have often been thoroughly characterized and also because of interesting differences in pathway regulation. These organisms can essentially degrade all the protein amino acids, except for the three branched-chain amino acids. E. coli, Salmonella enterica serovar Typhimurium, and Klebsiella aerogenes can assimilate nitrogen from D- and L-alanine, arginine, asparagine, aspartate, glutamate, glutamine, glycine, proline, and D- and L-serine. There are species differences in the utilization of agmatine, citrulline, cysteine, histidine, the aromatic amino acids, and polyamines (putrescine and spermidine). Regardless of the pathway of glutamate synthesis, nitrogen source catabolism must generate ammonia for glutamine synthesis. Loss of glutamate synthase (glutamineoxoglutarate amidotransferase, or GOGAT) prevents utilization of many organic nitrogen sources. Mutations that create or increase a requirement for ammonia also prevent utilization of most organic nitrogen sources.
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Peng Q, Wang G, Liu G, Zhang J, Song F. Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis. Front Microbiol 2015; 6:407. [PMID: 26029175 PMCID: PMC4428206 DOI: 10.3389/fmicb.2015.00407] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022] Open
Abstract
Sigma(54) (σ(54)) regulates nitrogen and carbon utilization in bacteria. Promoters that are σ(54)-dependent are highly conserved and contain short sequences located at the -24 and -12 positions upstream of the transcription initiation site. σ(54) requires regulatory proteins known as bacterial enhancer-binding proteins (bEBPs) to activate gene transcription. We show that σ(54) regulates the capacity to grow on various nitrogen sources using a Bacillus thuringiensis HD73 mutant lacking the sigL gene encoding σ(54) (ΔsigL). A 2-fold-change cutoff and a false discovery rate cutoff of P < 0.05 were used to analyze the DNA microarray data, which revealed 255 genes that were downregulated and 121 that were upregulated in the ΔsigL mutant relative to the wild-type HD73 strain. The σ(54) regulon (stationary phase) was characterized by DNA microarray, bioinformatics, and functional assay; 16 operons containing 47 genes were identified whose promoter regions contain the conserved -12/-24 element and whose transcriptional activities were abolished or reduced in the ΔsigL mutant. Eight σ(54)-dependent transcriptional bEBPs were found in the Bt HD73 genome, and they regulated nine σ(54)-dependent promoters. The metabolic pathways activated by σ(54) in this process have yet to be identified in Bacillus thuringiensis; nonetheless, the present analysis of the σ(54) regulon provides a better understanding of the physiological roles of σ factors in bacteria.
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Affiliation(s)
- Qi Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Guannan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Guiming Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
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Shimizu K. Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 155:1-54. [PMID: 25712586 DOI: 10.1007/10_2015_320] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Living organisms have sophisticated but well-organized regulation system. It is important to understand the metabolic regulation mechanisms in relation to growth environment for the efficient design of cell factories for biofuels and biochemicals production. Here, an overview is given for carbon catabolite regulation, nitrogen regulation, ion, sulfur, and phosphate regulations, stringent response under nutrient starvation as well as oxidative stress regulation, redox state regulation, acid-shock, heat- and cold-shock regulations, solvent stress regulation, osmoregulation, and biofilm formation, and quorum sensing focusing on Escherichia coli metabolism and others. The coordinated regulation mechanisms are of particular interest in getting insight into the principle which governs the cell metabolism. The metabolism is controlled by both enzyme-level regulation and transcriptional regulation via transcription factors such as cAMP-Crp, Cra, Csr, Fis, P(II)(GlnB), NtrBC, CysB, PhoR/B, SoxR/S, Fur, MarR, ArcA/B, Fnr, NarX/L, RpoS, and (p)ppGpp for stringent response, where the timescales for enzyme-level and gene-level regulations are different. Moreover, multiple regulations are coordinated by the intracellular metabolites, where fructose 1,6-bisphosphate (FBP), phosphoenolpyruvate (PEP), and acetyl-CoA (AcCoA) play important roles for enzyme-level regulation as well as transcriptional control, while α-ketoacids such as α-ketoglutaric acid (αKG), pyruvate (PYR), and oxaloacetate (OAA) play important roles for the coordinated regulation between carbon source uptake rate and other nutrient uptake rate such as nitrogen or sulfur uptake rate by modulation of cAMP via Cya.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan. .,Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
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25
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Lal PB, Schneider BL, Vu K, Reitzer L. The redundant aminotransferases in lysine and arginine synthesis and the extent of aminotransferase redundancy in Escherichia coli. Mol Microbiol 2014; 94:843-56. [PMID: 25243376 DOI: 10.1111/mmi.12801] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2014] [Indexed: 11/30/2022]
Abstract
Aminotransferases can be redundant or promiscuous, but the extent and significance of these properties is not known in any organism, even in Escherichia coli. To determine the extent of redundancy, it was first necessary to identify the redundant aminotransferases in arginine and lysine synthesis, and then complement all aminotransferase-deficient mutants with genes for all aminotransferases. The enzymes with N-acetylornithine aminotransferase (ACOAT) activity in arginine synthesis were ArgD, AstC, GabT and PuuE; the major anaerobic ACOAT was ArgD. The major enzymes with N-succinyl-l,l-diaminopimelate aminotransferase (SDAP-AT) activity in lysine synthesis were ArgD, AstC, and SerC. Seven other aminotransferases, when overproduced, complemented the defect in a triple mutant. Lysine availability did not regulate synthesis of the major SDAP-ATs. Complementation analysis of mutants lacking aminotransferases showed that the SDAP-ATs and alanine aminotransferases were exceptionally redundant, and it is proposed that this redundancy may ensure peptidoglycan synthesis. An overview of all aminotransferase reactions indicates that redundancy and broad specificity are common properties of aminotransferases.
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Affiliation(s)
- Piyush Behari Lal
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA
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26
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Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus. Extremophiles 2014; 18:995-1008. [DOI: 10.1007/s00792-014-0669-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
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Miller DP, Frederick JR, Sarkar J, Marconi RT. The Treponema denticola AtcR LytTR domain-containing response regulator interacts with three architecturally distinct promoter elements: implications for understanding the molecular signaling mechanisms that drive the progression of periodontal disease. Mol Oral Microbiol 2014; 29:219-32. [PMID: 24890414 DOI: 10.1111/omi.12059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2014] [Indexed: 12/27/2022]
Abstract
Treponema denticola is an oral spirochete and periopathogen that transitions from low abundance in healthy subgingival crevices to high abundance in periodontal pockets. The T. denticola response regulator AtcR harbors the relatively rare, LytTR DNA-binding domain. LytTR domain containing response regulators control critical transcriptional responses required for environmental adaptation. Using a multi-step bioinformatics approach, 26 strong lytTR recognition motifs were identified in the genome of T. denticola strain 35405. Electrophoretic mobility shift assays demonstrated that AtcR binds to these recognition motifs. High specificity-high affinity complexes formed with phosphorylated AtcR. The LytTR recognition sequences were found to exist in three distinct promoter architectures designated as LytTR1, LytTR2 and LytTR3 promoters. LytTR1 and LytTR2 promoters harbor σ(54) binding sites. The functional diversity of the proteins encoded by the putative AtcR regulon suggests that AtcR sits at the top of a regulatory cascade that plays a central role in facilitating T. denticola's ability to adapt to changing environmental conditions and thrive in periodontal pockets.
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Affiliation(s)
- D P Miller
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, USA
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Brown DR, Barton G, Pan Z, Buck M, Wigneshweraraj S. Nitrogen stress response and stringent response are coupled in Escherichia coli. Nat Commun 2014; 5:4115. [PMID: 24947454 PMCID: PMC4066584 DOI: 10.1038/ncomms5115] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/13/2014] [Indexed: 01/10/2023] Open
Abstract
Assimilation of nitrogen is an essential process in bacteria. The nitrogen regulation stress response is an adaptive mechanism used by nitrogen-starved Escherichia coli to scavenge for alternative nitrogen sources and requires the global transcriptional regulator NtrC. In addition, nitrogen-starved E. coli cells synthesize a signal molecule, guanosine tetraphosphate (ppGpp), which serves as an effector molecule of many processes including transcription to initiate global physiological changes, collectively termed the stringent response. The regulatory mechanisms leading to elevated ppGpp levels during nutritional stresses remain elusive. Here, we show that transcription of relA, a key gene responsible for the synthesis of ppGpp, is activated by NtrC during nitrogen starvation. The results reveal that NtrC couples these two major bacterial stress responses to manage conditions of nitrogen limitation, and provide novel mechanistic insights into how a specific nutritional stress leads to elevating ppGpp levels in bacteria.
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Affiliation(s)
- Daniel R. Brown
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Geraint Barton
- Centre for Systems Biology and Bioinformatics, Division of Biosciences, Imperial College London, London SW7 2AZ, UK
| | - Zhensheng Pan
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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Lévi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Monot M, Jagla B, Coppée JY, Dupuy B, Norel F. Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella. PLoS One 2014; 9:e96918. [PMID: 24810289 PMCID: PMC4014581 DOI: 10.1371/journal.pone.0096918] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/13/2014] [Indexed: 12/31/2022] Open
Abstract
The RpoS/σS sigma subunit of RNA polymerase (RNAP) controls a global adaptive response that allows many Gram-negative bacteria to survive starvation and various stresses. σS also contributes to biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). In this study, we used directional RNA-sequencing and complementary assays to explore the σS-dependent transcriptome of S. Typhimurium during late stationary phase in rich medium. This study confirms the large regulatory scope of σS and provides insights into the physiological functions of σS in Salmonella. Extensive regulation by σS of genes involved in metabolism and membrane composition, and down-regulation of the respiratory chain functions, were important features of the σS effects on gene transcription that might confer fitness advantages to bacterial cells and/or populations under starving conditions. As an example, we show that arginine catabolism confers a competitive fitness advantage in stationary phase. This study also provides a firm basis for future studies to address molecular mechanisms of indirect regulation of gene expression by σS. Importantly, the σS-controlled downstream network includes small RNAs that might endow σS with post-transcriptional regulatory functions. Of these, four (RyhB-1/RyhB-2, SdsR, SraL) were known to be controlled by σS and deletion of the sdsR locus had a competitive fitness cost in stationary phase. The σS-dependent control of seven additional sRNAs was confirmed in Northern experiments. These findings will inspire future studies to investigate molecular mechanisms and the physiological impact of post-transcriptional regulation by σS.
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Affiliation(s)
- Corinne Lévi-Meyrueis
- Institut Pasteur, Unité de Génétique Moléculaire, Département de Microbiologie, Paris, France
- CNRS, ERL3526, Paris, France
- Université Paris Sud XI, Orsay, France
| | - Véronique Monteil
- Institut Pasteur, Unité de Génétique Moléculaire, Département de Microbiologie, Paris, France
- CNRS, ERL3526, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Marie-Agnès Dillies
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Marc Monot
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, Paris, France
| | - Bernd Jagla
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Bruno Dupuy
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, Paris, France
| | - Françoise Norel
- Institut Pasteur, Unité de Génétique Moléculaire, Département de Microbiologie, Paris, France
- CNRS, ERL3526, Paris, France
- * E-mail:
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Abstract
Beyond fuelling cellular activities with building blocks and energy, metabolism also integrates environmental conditions into intracellular signals. The underlying regulatory network is complex and multifaceted: it ranges from slow interactions, such as changing gene expression, to rapid ones, such as the modulation of protein activity via post-translational modification or the allosteric binding of small molecules. In this Review, we outline the coordination of common metabolic tasks, including nutrient uptake, central metabolism, the generation of energy, the supply of amino acids and protein synthesis. Increasingly, a set of key metabolites is recognized to control individual regulatory circuits, which carry out specific functions of information input and regulatory output. Such a modular view of microbial metabolism facilitates an intuitive understanding of the molecular mechanisms that underlie cellular decision making.
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Li Z, Nimtz M, Rinas U. The metabolic potential of Escherichia coli BL21 in defined and rich medium. Microb Cell Fact 2014; 13:45. [PMID: 24656150 PMCID: PMC4021462 DOI: 10.1186/1475-2859-13-45] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The proteome reflects the available cellular machinery to deal with nutrients and environmental challenges. The most common E. coli strain BL21 growing in different, commonly employed media was evaluated using a detailed quantitative proteome analysis. RESULTS The presence of preformed biomass precursor molecules in rich media such as Luria Bertani supported rapid growth concomitant to acetate formation and apparently unbalanced abundances of central metabolic pathway enzymes, e.g. high levels of lower glycolytic pathway enzymes as well as pyruvate dehydrogenase, and low levels of TCA cycle and high levels of the acetate forming enzymes Pta and AckA. The proteome of cells growing exponentially in glucose-supplemented mineral salt medium was dominated by enzymes of amino acid synthesis pathways, contained more balanced abundances of central metabolic pathway enzymes, and a lower portion of ribosomal and other translational proteins. Entry into stationary phase led to a reconstruction of the bacterial proteome by increasing e.g. the portion of proteins required for scavenging rare nutrients and general cell protection. This proteomic reconstruction during entry into stationary phase was more noticeable in cells growing in rich medium as they have a greater reservoir of recyclable proteins from the translational machinery. CONCLUSIONS The proteomic comparison of cells growing exponentially in different media reflected the antagonistic and competitive regulation of central metabolic pathways through the global transcriptional regulators Cra, Crp, and ArcA. For example, the proteome of cells growing exponentially in rich medium was consistent with a dominating role of phosphorylated ArcA most likely a result from limitations in reoxidizing reduced quinones in the respiratory chain under these growth conditions. The proteomic alterations of exponentially growing cells into stationary phase cells were consistent with stringent-like and stationary phase responses and a dominating control through DksA-ppGpp and RpoS.
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Affiliation(s)
| | | | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany.
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Zhang YT, Jiang F, Tian ZX, Huo YX, Sun YC, Wang YP. CRP-cyclic AMP dependent inhibition of the xylene-responsive σ(54)-promoter Pu in Escherichia coli. PLoS One 2014; 9:e86727. [PMID: 24466213 PMCID: PMC3900584 DOI: 10.1371/journal.pone.0086727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2013] [Indexed: 11/18/2022] Open
Abstract
The expression of σ(54)-dependent Pseudomonas putida Pu promoter is activated by XylR activator when cells are exposed to a variety of aromatic inducers. In this study, the transcriptional activation of the P. putida Pu promoter was recreated in the heterologous host Escherichia coli. Here we show that the cAMP receptor protein (CRP), a well-known carbon utilization regulator, had an inhibitory effect on the expression of Pu promoter in a cAMP-dependent manner. The inhibitory effect was not activator specific. In vivo KMnO4 and DMS footprinting analysis indicated that CRP-cAMP poised the RNA polymerase at Pu promoter, inhibiting the isomerization step of the transcription initiation even in the presence of an activator. Therefore, the presence of PTS-sugar, which eliminates cAMP, could activate the poised RNA polymerase at Pu promoter to transcribe. Moreover, the activation region 1 (AR1) of CRP, which interacts directly with the αCTD (C-terminal domain of α-subunit) of RNA polymerase, was found essential for the CRP-mediated inhibition at Pu promoter. A model for the above observations is discussed.
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Affiliation(s)
- Yuan-Tao Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Feng Jiang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhe-Xian Tian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yi-Xin Huo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yi-Cheng Sun
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- * E-mail:
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Abstract
RpoS (σ(38)) is required for cell survival under stress conditions, but it can inhibit growth if produced inappropriately and, consequently, its production and activity are elaborately regulated. Crl, a transcriptional activator that does not bind DNA, enhances RpoS activity by stimulating the interaction between RpoS and the core polymerase. The crl gene has two overlapping promoters, a housekeeping, RpoD- (σ(70)) dependent promoter, and an RpoN (σ(54)) promoter that is strongly up-regulated under nitrogen limitation. However, transcription from the RpoN promoter prevents transcription from the RpoD promoter, and the RpoN-dependent transcript lacks a ribosome-binding site. Thus, activation of the RpoN promoter produces a long noncoding RNA that silences crl gene expression simply by being made. This elegant and economical mechanism, which allows a near-instantaneous reduction in Crl synthesis without the need for transacting regulatory factors, restrains the activity of RpoS to allow faster growth under nitrogen-limiting conditions.
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Samuels DJ, Frye JG, Porwollik S, McClelland M, Mrázek J, Hoover TR, Karls AC. Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ⁵⁴ (RpoN) regulon of Salmonella Typhimurium LT2. BMC Genomics 2013; 14:602. [PMID: 24007446 PMCID: PMC3844500 DOI: 10.1186/1471-2164-14-602] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022] Open
Abstract
Background Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ54 regulon in a bacterium is that the σ54 RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a σ54-dependent promoter. Many bacteria possess multiple bEBPs, which are activated by diverse environmental stimuli. In this work, we assess the ability of a promiscuous, constitutively-active bEBP—the AAA+ ATPase domain of DctD from Sinorhizobium meliloti—to activate transcription from all σ54-dependent promoters for the characterization of the σ54 regulon of Salmonella Typhimurium LT2. Results The AAA+ ATPase domain of DctD was able to drive transcription from nearly all previously characterized or predicted σ54-dependent promoters in Salmonella under a single condition. These promoters are controlled by a variety of native activators and, under the condition tested, are not transcribed in the absence of the DctD AAA+ ATPase domain. We also identified a novel σ54-dependent promoter upstream of STM2939, a homolog of the cas1 component of a CRISPR system. ChIP-chip analysis revealed at least 70 σ54 binding sites in the chromosome, of which 58% are located within coding sequences. Promoter-lacZ fusions with selected intragenic σ54 binding sites suggest that many of these sites are capable of functioning as σ54-dependent promoters. Conclusion Since the DctD AAA+ ATPase domain proved effective in activating transcription from the diverse σ54-dependent promoters of the S. Typhimurium LT2 σ54 regulon under a single growth condition, this approach is likely to be valuable for examining σ54 regulons in other bacterial species. The S. Typhimurium σ54 regulon included a high number of intragenic σ54 binding sites/promoters, suggesting that σ54 may have multiple regulatory roles beyond the initiation of transcription at the start of an operon.
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Affiliation(s)
- David J Samuels
- Department of Microbiology, University of Georgia, 30602, Athens, GA, USA.
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35
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Schneider BL, Hernandez VJ, Reitzer L. Putrescine catabolism is a metabolic response to several stresses in Escherichia coli. Mol Microbiol 2013; 88:537-50. [PMID: 23531166 DOI: 10.1111/mmi.12207] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2013] [Indexed: 12/12/2022]
Abstract
Genes whose products degrade arginine and ornithine, precursors of putrescine synthesis, are activated by either regulators of the nitrogen-regulated (Ntr) response or σ(S) -RNA polymerase. To determine if dual control regulates a complete putrescine catabolic pathway, we examined expression of patA and patD, which specify the first two enzymes of one putrescine catabolic pathway. Assays of PatA (putrescine transaminase) activity and β-galactosidase from cells with patA-lacZ transcriptional and translational fusions indicate dual control of patA transcription and putrescine-stimulated patA translation. Similar assays for PatD indicate that patD transcription required σ(S) -RNA polymerase, and Nac, an Ntr regulator, enhanced the σ(S) -dependent transcription. Since Nac activation via σ(S) -RNA polymerase is without precedent, transcription with purified components was examined and the results confirmed this conclusion. This result indicates that the Ntr regulon can intrude into the σ(S) regulon. Strains lacking both polyamine catabolic pathways have defective responses to oxidative stress, high temperature and a sublethal concentration of an antibiotic. These defects and the σ(S) -dependent expression indicate that polyamine catabolism is a core metabolic response to stress.
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Affiliation(s)
- Barbara L Schneider
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
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36
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Newman J, Seabrook S, Surjadi R, Williams CC, Lucent D, Wilding M, Scott C, Peat TS. Determination of the structure of the catabolic N-succinylornithine transaminase (AstC) from Escherichia coli. PLoS One 2013; 8:e58298. [PMID: 23484010 PMCID: PMC3590144 DOI: 10.1371/journal.pone.0058298] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/01/2013] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli possesses two acyl ornithine aminotransferases, one catabolic (AstC) and the other anabolic (ArgD), that participate in L-arginine metabolism. Although only 58% identical, the enzymes have been shown to be functionally interchangeable. Here we have purified AstC and have obtained X-ray crystal structures of apo and holo-AstC and of the enzyme complexed with its physiological substrate, succinylornithine. We compare the structures obtained in this study with those of ArgD from Salmonella typhimurium obtained elsewhere, finding several notable differences. Docking studies were used to explore the docking modes of several substrates (ornithine, succinylornithine and acetylornithine) and the co-substrate glutamate/α-ketogluterate. The docking studies support our observations that AstC has a strong preference for acylated ornithine species over ornithine itself, and suggest that the increase in specificity associated with acylation is caused by steric and desolvation effects rather than specific interactions between the substrate and enzyme.
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Affiliation(s)
- Janet Newman
- CSIRO Materials, Science and Engineering, Parkville, Australia
| | - Shane Seabrook
- CSIRO Materials, Science and Engineering, Parkville, Australia
| | - Regina Surjadi
- CSIRO Materials, Science and Engineering, Parkville, Australia
| | | | - Del Lucent
- CSIRO Materials, Science and Engineering, Parkville, Australia
| | | | - Colin Scott
- CSIRO Ecosystem Sciences, Canberra, Australia
| | - Thomas S. Peat
- CSIRO Materials, Science and Engineering, Parkville, Australia
- * E-mail:
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37
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Al Mamun AAM, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM. Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 2012; 338:1344-8. [PMID: 23224554 PMCID: PMC3782309 DOI: 10.1126/science.1226683] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mechanisms of DNA repair and mutagenesis are defined on the basis of relatively few proteins acting on DNA, yet the identities and functions of all proteins required are unknown. Here, we identify the network that underlies mutagenic repair of DNA breaks in stressed Escherichia coli and define functions for much of it. Using a comprehensive screen, we identified a network of ≥93 genes that function in mutation. Most operate upstream of activation of three required stress responses (RpoS, RpoE, and SOS, key network hubs), apparently sensing stress. The results reveal how a network integrates mutagenic repair into the biology of the cell, show specific pathways of environmental sensing, demonstrate the centrality of stress responses, and imply that these responses are attractive as potential drug targets for blocking the evolution of pathogens.
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Affiliation(s)
- Abu Amar M. Al Mamun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Mary-Jane Lombardo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Chandan Shee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Andreas M. Lisewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Caleb Gonzalez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Dongxu Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Ralf B. Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Claude Saint-Ruf
- U1001 INSERM, Université Paris, Descartes, Sorbonne Paris cité, site Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
| | - Janet L. Gibson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Ryan L. Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. J. Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
| | - Susan M. Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030–3411, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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Seo JH, Hong JSJ, Kim D, Cho BK, Huang TW, Tsai SF, Palsson BO, Charusanti P. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics 2012. [PMID: 23194155 PMCID: PMC3536570 DOI: 10.1186/1471-2164-13-679] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background The increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide. The development of next-generation sequencing technologies now permits rapid sequencing of many K. pneumoniae isolates, but sequence information alone does not provide important structural and operational information for its genome. Results Here we take a systems biology approach to annotate the K. pneumoniae MGH 78578 genome at the structural and operational levels. Through the acquisition and simultaneous analysis of multiple sample-matched –omics data sets from two growth conditions, we detected 2677, 1227, and 1066 binding sites for RNA polymerase, RpoD, and RpoS, respectively, 3660 RNA polymerase-guided transcript segments, and 3585 transcription start sites throughout the genome. Moreover, analysis of the transcription start site data identified 83 probable leaderless mRNAs, while analysis of unannotated transcripts suggested the presence of 119 putative open reading frames, 15 small RNAs, and 185 antisense transcripts that are not currently annotated. Conclusions These findings highlight the strengths of systems biology approaches to the refinement of sequence-based annotations, and to provide new insight into fundamental genome-level biology for this important human pathogen.
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Affiliation(s)
- Joo-Hyun Seo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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Abstract
Putrescine as the sole carbon source requires a novel catabolic pathway with glutamylated intermediates. Nitrogen limitation does not induce genes of this glutamylated putrescine (GP) pathway but instead induces genes for a putrescine catabolic pathway that starts with a transaminase-dependent deamination. We determined pathway utilization with putrescine as the sole nitrogen source by examining mutants with defects in both pathways. Blocks in both the GP and transaminase pathways were required to prevent growth with putrescine as the sole nitrogen source. Genetic and biochemical analyses showed redundant enzymes for γ-aminobutyraldehyde dehydrogenase (PatD/YdcW and PuuC), γ-aminobutyrate transaminase (GabT and PuuE), and succinic semialdehyde dehydrogenase (GabD and PuuC). PuuC is a nonspecific aldehyde dehydrogenase that oxidizes all the aldehydes in putrescine catabolism. A puuP mutant failed to use putrescine as the nitrogen source, which implies one major transporter for putrescine as the sole nitrogen source. Analysis of regulation of the GP pathway shows induction by putrescine and not by a product of putrescine catabolism and shows that putrescine accumulates in puuA, puuB, and puuC mutants but not in any other mutant. We conclude that two independent sets of enzymes can completely degrade putrescine to succinate and that their relative importance depends on the environment.
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Pérez-Redondo R, Rodríguez-García A, Botas A, Santamarta I, Martín JF, Liras P. ArgR of Streptomyces coelicolor is a versatile regulator. PLoS One 2012; 7:e32697. [PMID: 22403700 PMCID: PMC3293853 DOI: 10.1371/journal.pone.0032697] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/29/2012] [Indexed: 11/19/2022] Open
Abstract
ArgR is the regulator of arginine biosynthesis genes in Streptomyces species. Transcriptomic comparison by microarrays has been made between Streptomyces coelicolor M145 and its mutant S. coelicolor ΔargR under control, unsupplemented conditions, and in the presence of arginine. Expression of 459 genes was different in transcriptomic assays, but only 27 genes were affected by arginine supplementation. Arginine and pyrimidine biosynthesis genes were derepressed by the lack of ArgR, while no strong effect on expression resulted on arginine supplementation. Several nitrogen metabolism genes expression as glnK, glnA and glnII, were downregulated in S. coelicolor ΔargR. In addition, downregulation of genes for the yellow type I polyketide CPK antibiotic and for the antibiotic regulatory genes afsS and scbR was observed. The transcriptomic data were validated by either reverse transcription-PCR, expression of the gene-promoter coupled to the luciferase gene, proteomic or by electrophoresis mobility shift assay (EMSA) using pure Strep-tagged ArgR. Two ARG-boxes in the arginine operon genes suggest that these genes are more tightly controlled. Other genes, including genes encoding regulatory proteins, possess a DNA sequence formed by a single ARG-box which responds to ArgR, as validated by EMSA.
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Affiliation(s)
- Rosario Pérez-Redondo
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain
- Instituto de Biotecnología, Parque Científico de León, León, Spain
| | - Antonio Rodríguez-García
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain
- Instituto de Biotecnología, Parque Científico de León, León, Spain
| | - Alma Botas
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain
- Instituto de Biotecnología, Parque Científico de León, León, Spain
| | - Irene Santamarta
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain
- Instituto de Biotecnología, Parque Científico de León, León, Spain
| | - Juan F. Martín
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain
- Instituto de Biotecnología, Parque Científico de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain
- Instituto de Biotecnología, Parque Científico de León, León, Spain
- * E-mail:
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Abstract
One of the greatest challenges facing synthetic biology is to develop a technology that allows gene regulatory circuits in microbes to integrate multiple inputs or stimuli using a small DNA sequence "foot-print", and which will generate precise and reproducible outcomes. Achieving this goal is hindered by the routine utilization of the commonplace σ(70) promoters in gene-regulatory circuits. These promoters typically are not capable of integrating binding of more than two or three transcription factors in natural examples, which has limited the field to developing integrated circuits made of two-input biological "logic" gates. In natural examples the regulatory elements, which integrate multiple inputs are called enhancers. These regulatory elements are ubiquitous in all organisms in the tree of life, and interestingly metazoan and bacterial enhancers are significantly more similar in terms of both Transcription Factor binding site arrangement and biological function than previously thought. These similarities imply that there may be underlying enhancer design principles or grammar rules by which one can engineer novel gene regulatory circuits. However, at present our current understanding of enhancer structure-function relationship in all organisms is limited, thus preventing us from using these objects routinely in synthetic biology application. In order to alleviate this problem, in this book chapter, I will review our current view of bacterial enhancers, allowing us to first highlight the potential of enhancers to be a game-changing tool in synthetic biology application, and subsequently to draw a road-map for developing the necessary quantitative understanding to reach this goal.
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Affiliation(s)
- Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel,
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Cho BK, Federowicz S, Park YS, Zengler K, Palsson BØ. Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol 2011; 8:65-71. [PMID: 22082910 DOI: 10.1038/nchembio.710] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 08/27/2011] [Indexed: 11/09/2022]
Abstract
Although metabolic networks have been reconstructed on a genome scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here we reconstruct such an integrated network for amino acid metabolism in Escherichia coli. Analysis of ChIP-chip and gene expression data for the transcription factors ArgR, Lrp and TrpR showed that 19 out of 20 amino acid biosynthetic pathways are either directly or indirectly controlled by these regulators. Classifying the regulated genes into three functional categories of transport, biosynthesis and metabolism leads to the elucidation of regulatory motifs that constitute the integrated network's basic building blocks. The regulatory logic of these motifs was determined on the basis of relationships between transcription factor binding and changes in the amount of transcript in response to exogenous amino acids. Remarkably, the resulting logic shows how amino acids are differentiated as signaling and nutrient molecules, revealing the overarching regulatory principles of the amino acid stimulon.
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Affiliation(s)
- Byung-Kwan Cho
- Department of Bioengineering, University of California at San Diego, La Jolla, California, USA.
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Amit R, Garcia HG, Phillips R, Fraser SE. Building enhancers from the ground up: a synthetic biology approach. Cell 2011; 146:105-18. [PMID: 21729783 DOI: 10.1016/j.cell.2011.06.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 01/25/2011] [Accepted: 06/14/2011] [Indexed: 11/25/2022]
Abstract
A challenge of the synthetic biology approach is to use our understanding of a system to recreate a biological function with specific properties. We have applied this framework to bacterial enhancers, combining a driver, transcription factor binding sites, and a poised polymerase to create synthetic modular enhancers. Our findings suggest that enhancer-based transcriptional control depends critically and quantitatively on DNA looping, leading to complex regulatory effects when the enhancer cassettes contain additional transcription factor binding sites for TetR, a bacterial transcription factor. We show through a systematic interplay of experiment and thermodynamic modeling that the level of gene expression can be modulated to convert a variable inducer concentration input into discrete or step-like output expression levels. Finally, using a different DNA-binding protein (TraR), we show that the regulatory output is not a particular feature of the specific DNA-binding protein used for the enhancer but a general property of synthetic bacterial enhancers.
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Affiliation(s)
- Roee Amit
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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44
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Ouyang Z, Deka RK, Norgard MV. BosR (BB0647) controls the RpoN-RpoS regulatory pathway and virulence expression in Borrelia burgdorferi by a novel DNA-binding mechanism. PLoS Pathog 2011; 7:e1001272. [PMID: 21347346 PMCID: PMC3037356 DOI: 10.1371/journal.ppat.1001272] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 01/06/2011] [Indexed: 11/29/2022] Open
Abstract
In Borrelia burgdorferi (Bb), the Lyme disease spirochete, the alternative σ factor σ54 (RpoN) directly activates transcription of another alternative σ factor, σS (RpoS) which, in turn, controls the expression of virulence-associated membrane lipoproteins. As is customary in σ54-dependent gene control, a putative NtrC-like enhancer-binding protein, Rrp2, is required to activate the RpoN-RpoS pathway. However, recently it was found that rpoS transcription in Bb also requires another regulator, BosR, which was previously designated as a Fur or PerR homolog. Given this unexpected requirement for a second activator to promote σ54-dependent gene transcription, and the fact that regulatory mechanisms among similar species of pathogenic bacteria can be strain-specific, we sought to confirm the regulatory role of BosR in a second virulent strain (strain 297) of Bb. Indeed, BosR displayed the same influence over lipoprotein expression and mammalian infectivity for strain Bb 297 that were previously noted for Bb strain B31. We subsequently found that recombinant BosR (rBosR) bound to the rpoS gene at three distinct sites, and that binding occurred despite the absence of consensus Fur or Per boxes. This led to the identification of a novel direct repeat sequence (TAAATTAAAT) critical for rBosR binding in vitro. Mutations in the repeat sequence markedly inhibited or abolished rBosR binding. Taken together, our studies provide new mechanistic insights into how BosR likely acts directly on rpoS as a positive transcriptional activator. Additional novelty is engendered by the facts that, although BosR is a Fur or PerR homolog and it contains zinc (like Fur and PerR), it has other unique features that clearly set it apart from these other regulators. Our findings also have broader implications regarding a previously unappreciated layer of control that can be involved in σ54–dependent gene regulation in bacteria. Lyme disease, caused by the bacterium Borrelia burgdorferi (Bb), remains the most common arthropod-borne illness in the United States. A critical strategy for Bb to maintain its presence in nature is adaptation to its diverse tick and mammalian (mouse) hosts. To accomplish this, Bb encodes a potential gene regulator, BB0647 (BosR). Herein, we confirmed that BosR is essential for Bb to establish mammalian infection. We then found that purified recombinant BosR bound to the promoter DNA (regulatory region) of rpoS, suggesting that BosR directly controls the expression of the rpoS gene. This study has revealed a new mechanism of bacterial gene control. The discovery that BosR governs Bb's virulence may lead to new strategies to interrupt the bacterium's complex life cycle.
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Affiliation(s)
- Zhiming Ouyang
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ranjit K. Deka
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael V. Norgard
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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45
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Fulde M, Willenborg J, de Greeff A, Benga L, Smith HE, Valentin-Weigand P, Goethe R. ArgR is an essential local transcriptional regulator of the arcABC operon in Streptococcus suis and is crucial for biological fitness in an acidic environment. MICROBIOLOGY-SGM 2010; 157:572-582. [PMID: 20947575 DOI: 10.1099/mic.0.043067-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptococcus suis is one of the most important pathogens in pigs and can also cause severe infections in humans. Despite its clinical relevance, very little is known about the factors that contribute to its virulence. Recently, we identified a new putative virulence factor in S. suis, the arginine deiminase system (ADS), an arginine catabolic enzyme system encoded by the arcABC operon, which enables S. suis to survive in an acidic environment. In this study, we focused on ArgR, an ADS-associated regulator belonging to the ArgR/AhrC arginine repressor family. Using an argR knockout strain we were able to show that ArgR is essential for arcABC operon expression and necessary for the biological fitness of S. suis. By cDNA expression microarray analyses and quantitative real-time RT-PCR we found that the arcABC operon is the only gene cluster regulated by ArgR, which is in contrast to the situation in many other bacteria. Reporter gene analysis with gfp under the control of the arcABC promoter demonstrated that ArgR is able to activate the arcABC promoter. Electrophoretic mobility shift assays with fragments of the arcABC promoter and recombinant ArgR, and chromatin immunoprecipitation with antibodies directed against ArgR, revealed that ArgR interacts with the arcABC promoter in vitro and in vivo by binding to a region from -147 to -72 bp upstream of the transcriptional start point. Overall, our results show that in S. suis, ArgR is an essential, system-specific transcriptional regulator of the ADS that interacts directly with the arcABC promoter in vivo.
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Affiliation(s)
- Marcus Fulde
- Institut für Mikrobiologie, Zentrum für Infektionsmedizin, Stiftung Tierärztliche Hochschule Hannover, 30173 Hannover, Germany
| | - Joerg Willenborg
- Institut für Mikrobiologie, Zentrum für Infektionsmedizin, Stiftung Tierärztliche Hochschule Hannover, 30173 Hannover, Germany
| | - Astrid de Greeff
- Animal Sciences Group (ASG), Wageningen UR, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Laurentiu Benga
- Institut für Mikrobiologie, Zentrum für Infektionsmedizin, Stiftung Tierärztliche Hochschule Hannover, 30173 Hannover, Germany
| | - Hilde E Smith
- Animal Sciences Group (ASG), Wageningen UR, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Peter Valentin-Weigand
- Institut für Mikrobiologie, Zentrum für Infektionsmedizin, Stiftung Tierärztliche Hochschule Hannover, 30173 Hannover, Germany
| | - Ralph Goethe
- Institut für Mikrobiologie, Zentrum für Infektionsmedizin, Stiftung Tierärztliche Hochschule Hannover, 30173 Hannover, Germany
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Abstract
Legionella pneumophila is an intracellular pathogen that infects protozoa in aquatic environments and when inhaled by susceptible human hosts replicates in alveolar macrophages and can result in the often fatal pneumonia called Legionnaires' disease. The ability of L. pneumophila to replicate within host cells requires the establishment of a specialized compartment that evades normal phagolysosome fusion called the Legionella-containing vacuole (LCV). Elucidation of the biochemical composition of the LCV and the identification of the regulatory signals sensed during intracellular replication are inherently challenging. L-Arginine is a critical nutrient in the metabolism of both prokaryotic and eukaryotic organisms. We showed that the L. pneumophila arginine repressor homolog, ArgR, is required for maximal intracellular growth in the unicellular host Acanthamoeba castellanii. In this study, we present evidence that the concentration of L-arginine in the LCV is sensed by ArgR to produce an intracellular transcriptional response. We characterized the L. pneumophila ArgR regulon by global gene expression analysis, identified genes highly affected by ArgR, showed that ArgR repression is dependent upon the presence of L-arginine, and demonstrated that ArgR-regulated genes are derepressed during intracellular growth. Additional targets of ArgR that may account for the argR mutant's intracellular multiplication defect are discussed. These results suggest that L-arginine availability functions as a regulatory signal during Legionella intracellular growth.
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47
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Lee SY, Kim YH, Min J. The effect of ArgR-DNA binding affinity on ornithine production in Corynebacterium glutamicum. Curr Microbiol 2009; 59:483-8. [PMID: 19688381 DOI: 10.1007/s00284-009-9467-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 05/07/2009] [Accepted: 07/17/2009] [Indexed: 11/26/2022]
Abstract
pEMBTL-SY1, which can over produce the ArgR protein in Corynebacterium glutamicum, was constructed. The DNA-binding affinity of ArgR was analyzed using a Chromatin Immunoprecipitation (ChIP) assay. The level of ArgR protein expression in the plasmid-carrying C. glutamicum (pEMBTL-SY1) was higher than that in the wild-type strain. On the other hand, there was no increase in the DNA-binding affinity of ArgR on the upstream of argB and the level of ornithine production. The DNA-binding affinity of ArgR on the arg operon and the level of ornithine production in the presence of three metabolites, ornithine, arginine, and proline, were examined as feedback controlling effectors in the arginine biosynthesis pathway in C. glutamicum. The ChIP assay showed that the supplemented metabolites altered the ArgR-binding affinity on the upstream of argB, which is consistent with the change in ornithine production. This suggests that the regulation of ornithine biosynthesis by the transcriptional regulator, ArgR, depends on the DNA-binding affinity of the arg operon, which is regulated by the feedback controlling effectors, rather than on the level of ArgR protein expression.
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Affiliation(s)
- Soo Youn Lee
- Division of Chemical Engineering, Chonbuk National University, Jeonju, South Korea
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Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z. A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol 2008; 4:e1000044. [PMID: 18369434 PMCID: PMC2266799 DOI: 10.1371/journal.pcbi.1000044] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 02/28/2008] [Indexed: 02/07/2023] Open
Abstract
While Escherichia coli has one of the most comprehensive datasets of experimentally verified transcriptional regulatory interactions of any organism, it is still far from complete. This presents a problem when trying to combine gene expression and regulatory interactions to model transcriptional regulatory networks. Using the available regulatory interactions to predict new interactions may lead to better coverage and more accurate models. Here, we develop SEREND (SEmi-supervised REgulatory Network Discoverer), a semi-supervised learning method that uses a curated database of verified transcriptional factor-gene interactions, DNA sequence binding motifs, and a compendium of gene expression data in order to make thousands of new predictions about transcription factor-gene interactions, including whether the transcription factor activates or represses the gene. Using genome-wide binding datasets for several transcription factors, we demonstrate that our semi-supervised classification strategy improves the prediction of targets for a given transcription factor. To further demonstrate the utility of our inferred interactions, we generated a new microarray gene expression dataset for the aerobic to anaerobic shift response in E. coli. We used our inferred interactions with the verified interactions to reconstruct a dynamic regulatory network for this response. The network reconstructed when using our inferred interactions was better able to correctly identify known regulators and suggested additional activators and repressors as having important roles during the aerobic-anaerobic shift interface.
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Affiliation(s)
- Jason Ernst
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Qasim K. Beg
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Krin A. Kay
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gábor Balázsi
- Department of Systems Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Zoltán N. Oltvai
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ziv Bar-Joseph
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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Han Y, Qiu J, Guo Z, Gao H, Song Y, Zhou D, Yang R. Comparative transcriptomics in Yersinia pestis: a global view of environmental modulation of gene expression. BMC Microbiol 2007; 7:96. [PMID: 17963531 PMCID: PMC2231364 DOI: 10.1186/1471-2180-7-96] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Accepted: 10/29/2007] [Indexed: 12/22/2022] Open
Abstract
Background Environmental modulation of gene expression in Yersinia pestis is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions in vitro. Results To provide us with a comprehensive view of environmental modulation of global gene expression in Y. pestis, we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of Y. pestis were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). Conclusion The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in Y. pestis, it also serves as a basis for integrating increasing volumes of microarray data using existing methods.
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Affiliation(s)
- Yanping Han
- State Key laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 20, Dongdajie, Fengtai, Beijing 100071, China.
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50
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Caldara M, Minh PNL, Bostoen S, Massant J, Charlier D. ArgR-dependent repression of arginine and histidine transport genes in Escherichia coli K-12. J Mol Biol 2007; 373:251-67. [PMID: 17850814 DOI: 10.1016/j.jmb.2007.08.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 07/31/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022]
Abstract
In Escherichia coli L-arginine is taken up by three periplasmic binding protein-dependent transport systems that are encoded by two genetic loci: the artPIQM-artJ and argT-hisJQMP gene clusters. The transcription of the artJ, artPIQM and hisJQMP genes and operons is repressed by liganded ArgR, whereas argT, encoding the LAO (lysine, arginine, ornithine) periplasmic binding protein, is insensitive to the repressor. Here we characterize the repressible Esigma70 P artJ, P artP and P hisJ promoters and demonstrate that the cognate operators consist of two 18 bp ARG boxes separated by 3 bp. Determination of the energy landscape of the ArgR-operator contacts by missing contact probing and mutant studies indicated that each box of a pair contributes to complex formation in vitro and to the repressibility in vivo, but to a different extent. The organization of the ARG boxes and promoter elements in the control regions of the uptake genes is distinct from that of the arginine biosynthetic genes. The hisJQMP operon is the first member of the E. coli ArgR regulon, directly repressed by liganded ArgR, where none of the core promoter elements overlaps the ARG boxes. Single round in vitro transcription assays and DNase I footprinting experiments indicate that liganded ArgR inhibits P artJ and P artP promoter activity by steric exclusion of the RNA polymerase. In contrast, ArgR-mediated repression of P hisJ by inhibition of RNA polymerase binding appears to occur through topological changes of the promoter region.
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Affiliation(s)
- Marina Caldara
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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