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Ma K, Chinelo OR, Gu M, Kong F, Jiang Y, Wang H, Xue T. Role of ArcA in the regulation of antibiotic sensitivity in avian pathogenic Escherichia coli. Poult Sci 2024; 103:103686. [PMID: 38574461 PMCID: PMC11004985 DOI: 10.1016/j.psj.2024.103686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is one of the common extraintestinal infectious disease pathogens in chickens, geese, and other birds, inducing serious impediments to the development of the poultry industry. Hence, investigating how bacteria regulate themselves amidst different challenging conditions is immense essential in prevention and treatment for bacterial pathogen infections. The ArcA regulatory factor has been reported to regulate oxygen availability in strains, but its role in regulation of antibiotics resistance in APEC is unclear. This study delved into understanding how ArcA regulates antibiotic resistance in APEC. An E. coli APEC40 arcA knockout strain was constructed, and the regulatory mechanism of arcA on APEC antibiotic susceptibility was identified by drug sensitivity test, colony counting assay, real-time quantitative PCR, β-galactosidase assays and electrophoretic mobility shift assay (EMSA). The results showed that ArcA directly binds to the promoter region of the outer membrane protein OmpC/OmpW and regulates bacterial susceptibility to kanamycin and penicillin G. At the same time, the double knockout of ompW and ompW/arcA resulted in an increase in resistance to kanamycin compared to the deletion of the arcA gene. This outcome provided experimental proof suggesting that the outer membrane protein OmpW could serve as a crucial pathway for the ingress of kanamycin into cells. These results confirmed the important regulatory role of ArcA transcription factors under APEC antibiotic stress.
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Affiliation(s)
- Kai Ma
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Okoro Ruth Chinelo
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Mantian Gu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Fanwenqing Kong
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ying Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hui Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China.
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2
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Wölflingseder M, Fengler VH, Standhartinger V, Wagner GE, Reidl J. The regulatory network comprising ArcAB-RpoS-RssB influences motility in Vibrio cholerae. Mol Microbiol 2024. [PMID: 38323722 DOI: 10.1111/mmi.15235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 02/08/2024]
Abstract
The diarrheal disease cholera is caused by the versatile and responsive bacterium Vibrio cholerae, which is capable of adapting to environmental changes. Among others, the alternative sigma factor RpoS activates response pathways, including regulation of motility- and chemotaxis-related genes under nutrient-poor conditions in V. cholerae. Although RpoS has been well characterised, links between RpoS and other regulatory networks remain unclear. In this study, we identified the ArcAB two-component system to control rpoS transcription and RpoS protein stability in V. cholerae. In a manner similar to that seen in Escherichia coli, the ArcB kinase not only activates the response regulator ArcA but also RssB, the anti-sigma factor of RpoS. Our results demonstrated that, in V. cholerae, RssB is phosphorylated by ArcB, which subsequently activates RpoS proteolysis. Furthermore, ArcA acts as a repressor of rpoS transcription. Additionally, we determined that the cysteine residue at position 180 of ArcB is crucial for signal recognition and activity. Thus, our findings provide evidence linking RpoS response to the anoxic redox control system ArcAB in V. cholerae.
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Affiliation(s)
- Martina Wölflingseder
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Vera H Fengler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Verena Standhartinger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Gabriel E Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Joachim Reidl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
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3
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Jiang F, Yang Y, Mao Z, Cai W, Li G. ArcA positively regulates the expression of virulence genes and contributes to virulence of porcine Shiga toxin-producing enterotoxigenic Escherichia coli. Microbiol Spectr 2023; 11:e0152523. [PMID: 37916813 PMCID: PMC10714933 DOI: 10.1128/spectrum.01525-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Enterotoxigenic Escherichia coli (ETEC) cause severe diarrhea in humans and animals, leading to death and huge economic loss worldwide. Thus, elucidation of ETEC's pathogenic mechanisms will provide powerful data for the discovery of drugs serving as prevention or therapeutics against ETEC-caused diarrheal diseases. Here, we report that ArcA plays an essential role in the pathogenicity and virulence regulation in ETEC by positively regulating the expression of several key virulence factors including F18 fimbriae, heat-labile and heat-stable toxins, Shiga toxin 2e, and hemolysin, under microaerobic conditions and in vivo. Moreover, we found that positive regulation of several virulence genes by ArcA requires a global repressor H-NS (histone-like nucleoid structuring), implying that ArcA may exert positive effects by antagonizing H-NS. Collectively, our data established a key role for ArcA in the pathogenicity of porcine ETEC and ETEC strains isolated from human infections. Moreover, our work reveals another layer of regulation in relation to oxygen control of virulence factors in ETEC.
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Affiliation(s)
- Fengwei Jiang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Yan Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhao Mao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wentong Cai
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ganwu Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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4
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Li Y, Yan J, Li J, Xue X, Wang Y, Cao B. A novel quorum sensing regulator LuxT contributes to the virulence of Vibrio cholerae. Virulence 2023; 14:2274640. [PMID: 37908129 PMCID: PMC10621291 DOI: 10.1080/21505594.2023.2274640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Vibrio cholerae is a waterborne bacterium that primarily infects the human intestine and causes cholera fatality. Quorum sensing (QS) negatively regulates the expression of V. cholerae virulence gene. However, the primary associated mechanisms remain undetermined. This investigation identified a new QS regulator from the TetR family, LuxT, which increases V. cholerae virulence by directly inhibiting hapR expression. HapR is a master QS regulator that suppresses virulence cascade expression. The expression of luxT increased 4.8-fold in the small intestine of infant mice than in Luria-Bertani broth. ΔluxT mutant strain revealed a substantial defect in the colonizing ability of the small intestines. At low cell densities, the expression level of hapR was upregulated by luxT deletion, suggesting that LuxT can suppress hapR transcription. The electrophoretic mobility shift analysis revealed that LuxT directly binds to the hapR promoter region. Furthermore, luxT expression was upregulated by the two-component system ArcB/ArcA, which responses to changes in oxygen levels in response to the host's small intestine's anaerobic signals. In conclusion, this research reveals a novel cell density-mediated virulence regulation pathway and contributes to understanding the complex association between V. cholerae virulence and QS signals. This evidence furnishes new insights for future studies on cholerae's pathogenic mechanisms.
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Affiliation(s)
- Yuehua Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, China
| | - Junxiang Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, China
| | - Jinghao Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, China
| | - Xinke Xue
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, China
| | - Ying Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, China
| | - Boyang Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, China
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5
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Yan J, Yang B, Xue X, Li J, Li Y, Li A, Ding P, Cao B. Transcriptome Analysis Reveals the Effect of PdhR in Plesiomonas shigelloides. Int J Mol Sci 2023; 24:14473. [PMID: 37833920 PMCID: PMC10572922 DOI: 10.3390/ijms241914473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The pyruvate dehydrogenase complex regulator (PdhR) was originally identified as a repressor of the pdhR-aceEF-lpd operon, which encodes the pyruvate dehydrogenase complex (PDHc) and PdhR itself. According to previous reports, PdhR plays a regulatory role in the physiological and metabolic pathways of bacteria. At present, the function of PdhR in Plesiomonas shigelloides is still poorly understood. In this study, RNA sequencing (RNA-Seq) of the wild-type strain and the ΔpdhR mutant strains was performed for comparison to identify the PdhR-controlled pathways, revealing that PdhR regulates ~7.38% of the P. shigelloides transcriptome. We found that the deletion of pdhR resulted in the downregulation of practically all polar and lateral flagella genes in P. shigelloides; meanwhile, motility assay and transmission electron microscopy (TEM) confirmed that the ΔpdhR mutant was non-motile and lacked flagella. Moreover, the results of RNA-seq and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) showed that PdhR positively regulated the expression of the T3SS cluster, and the ΔpdhR mutant significantly reduced the ability of P. shigelloides to infect Caco-2 cells compared with the WT. Consistent with previous research, pyruvate-sensing PdhR directly binds to its promoter and inhibits pdhR-aceEF-lpd operon expression. In addition, we identified two additional downstream genes, metR and nuoA, that are directly negatively regulated by PdhR. Furthermore, we also demonstrated that ArcA was identified as being located upstream of pdhR and lpdA and directly negatively regulating their expression. Overall, we revealed the function and regulatory pathway of PdhR, which will allow for a more in-depth investigation into P. shigelloides pathogenicity as well as the complex regulatory network.
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Affiliation(s)
- Junxiang Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Xinke Xue
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Jinghao Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Yuehua Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Ang Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
- College of Pharmacy Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Peng Ding
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Boyang Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
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6
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Tristano J, Danforth DR, Wargo MJ, Mintz KP. Regulation of adhesin synthesis in Aggregatibacter actinomycetemcomitans. Mol Oral Microbiol 2023; 38:237-250. [PMID: 36871155 PMCID: PMC10175207 DOI: 10.1111/omi.12410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Aggregatibacter actinomycetemcomitans is a gram-negative bacterium associated with periodontal disease and a variety of disseminated extra-oral infections. Tissue colonization is mediated by fimbriae and non-fimbriae adhesins resulting in the formation of a sessile bacterial community or biofilm, which confers enhanced resistance to antibiotics and mechanical removal. The environmental changes experienced by A. actinomycetemcomitans during infection are detected and processed by undefined signaling pathways that alter gene expression. In this study, we have characterized the promoter region of the extracellular matrix protein adhesin A (EmaA), which is an important surface adhesin in biofilm biogenesis and disease initiation using a series of deletion constructs consisting of the emaA intergenic region and a promotor-less lacZ sequence. Two regions of the promoter sequence were found to regulate gene transcription and in silico analysis indicated the presence of multiple transcriptional regulatory binding sequences. Analysis of four regulatory elements, CpxR, ArcA, OxyR, and DeoR, was undertaken in this study. Inactivation of arcA, the regulator moiety of the ArcAB two-component signaling pathway involved in redox homeostasis, resulted in a decrease in EmaA synthesis and biofilm formation. Analysis of the promoter sequences of other adhesins identified binding sequences for the same regulatory proteins, which suggests that these proteins are involved in the coordinate regulation of adhesins required for colonization and pathogenesis.
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Affiliation(s)
- Jake Tristano
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - David R Danforth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Matthew J Wargo
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Keith P Mintz
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
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7
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Arrieta-Ortiz ML, Pan M, Kaur A, Pepper-Tunick E, Srinivas V, Dash A, Immanuel SRC, Brooks AN, Shepherd TR, Baliga NS. Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli. mSystems 2023; 8:e0090422. [PMID: 36537814 DOI: 10.1128/msystems.00904-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (TetR) Escherichia coli undergoes global transcriptional and metabolic remodeling, including downregulation of tricarboxylic acid cycle and disruption of redox homeostasis, to support consumption of the proton motive force for tetracycline efflux. Using a pooled genome-wide library of single-gene deletion strains, at least 308 genes, including four transcriptional regulators identified by our network analysis, were confirmed as essential for restoring the fitness of TetR E. coli during treatment with tetracycline. Targeted knockout of ArcA, identified by network analysis as a master regulator of this new compensatory physiological state, significantly compromised fitness of TetR E. coli during tetracycline treatment. A drug, sertraline, which generated a similar metabolome profile as the arcA knockout strain, also resensitized TetR E. coli to tetracycline. We discovered that the potentiating effect of sertraline was eliminated upon knocking out arcA, demonstrating that the mechanism of potential synergy was through action of sertraline on the tetracycline-induced ArcA network in the TetR strain. Our findings demonstrate that therapies that target mechanistic drivers of compensatory physiological states could resensitize AMR pathogens to lost antibiotics. IMPORTANCE Antimicrobial resistance (AMR) is projected to be the cause of >10 million deaths annually by 2050. While efforts to find new potent antibiotics are effective, they are expensive and outpaced by the rate at which new resistant strains emerge. There is desperate need for a rational approach to accelerate the discovery of drugs and drug combinations that effectively clear AMR pathogens and even prevent the emergence of new resistant strains. Using tetracycline-resistant (TetR) Escherichia coli, we demonstrate that gaining resistance is accompanied by loss of fitness, which is restored by compensatory physiological changes. We demonstrate that transcriptional regulators of the compensatory physiologic state are promising drug targets because their disruption increases the susceptibility of TetR E. coli to tetracycline. Thus, we describe a generalizable systems biology approach to identify new vulnerabilities within AMR strains to rationally accelerate the discovery of therapeutics that extend the life span of existing antibiotics.
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8
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Huang LH, Li XJ, Wang YT, Jia SR, Xin B, Zhong C. Enhancing bacterial cellulose production with hypoxia-inducible factors. Appl Microbiol Biotechnol 2022; 106:7099-7112. [PMID: 36184690 DOI: 10.1007/s00253-022-12192-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 12/01/2022]
Abstract
Komagataeibacter xylinus is an aerobic strain that produces bacterial cellulose (BC). Oxygen levels play a critical role in regulating BC synthesis in K. xylinus, and an increase in oxygen tension generally means a decrease in BC production. Fumarate nitrate reduction protein (FNR) and aerobic respiration control protein A (ArcA) are hypoxia-inducible factors, which can signal whether oxygen is present in the environment. In this study, FNR and ArcA were used to enhance the efficiency of oxygen signaling in K. xylinus, and globally regulate the transcription of the genome to cope with hypoxic conditions, with the goal of improving growth and BC production. FNR and ArcA were individually overexpressed in K. xylinus, and the engineered strains were cultivated under different oxygen tensions to explore how their overexpression affects cellular metabolism and regulation. Although FNR overexpression did not improve BC production, ArcA overexpression increased BC production by 24.0% and 37.5% as compared to the control under oxygen tensions of 15% and 40%, respectively. Transcriptome analysis showed that FNR and ArcA overexpression changed the way K. xylinus coped with oxygen tension changes, and that both FNR and ArcA overexpression enhanced the BC synthesis pathway. The results of this study provide a new perspective on the effect of oxygen signaling on growth and BC production in K. xylinus and suggest a promising strategy for enhancing BC production through metabolic engineering. KEY POINTS: • K. xylinus BC production increased after overexpression of ArcA • The young's modulus is enhanced by the ArcA overexpression • ArcA and FNR overexpression changed how cells coped with changes in oxygen tension.
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Affiliation(s)
- Long-Hui Huang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Xue-Jing Li
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Yi-Tong Wang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Shi-Ru Jia
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Bo Xin
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China.
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China.
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9
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Zhou Y, Pu Q, Chen J, Hao G, Gao R, Ali A, Hsiao A, Stock AM, Goulian M, Zhu J. Thiol-based functional mimicry of phosphorylation of the two-component system response regulator ArcA promotes pathogenesis in enteric pathogens. Cell Rep 2021; 37:110147. [PMID: 34936880 PMCID: PMC8728512 DOI: 10.1016/j.celrep.2021.110147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
Pathogenic bacteria can rapidly respond to stresses such as reactive oxygen species (ROS) using reversible redox-sensitive oxidation of cysteine thiol (-SH) groups in regulators. Here, we use proteomics to profile reversible ROS-induced thiol oxidation in Vibrio cholerae, the etiologic agent of cholera, and identify two modified cysteines in ArcA, a regulator of global carbon oxidation that is phosphorylated and activated under low oxygen. ROS abolishes ArcA phosphorylation but induces the formation of an intramolecular disulfide bond that promotes ArcA-ArcA interactions and sustains activity. ArcA cysteines are oxidized in cholera patient stools, and ArcA thiol oxidation drives in vitro ROS resistance, colonization of ROS-rich guts, and environmental survival. In other pathogens, such as Salmonella enterica, oxidation of conserved cysteines of ArcA orthologs also promotes ROS resistance, suggesting a common role for ROS-induced ArcA thiol oxidation in modulating ArcA activity, allowing for a balance of expression of stress- and pathogenesis-related genetic programs.
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Affiliation(s)
- Yitian Zhou
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qinqin Pu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiandong Chen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guijuan Hao
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Afsar Ali
- Department of Environmental and Global Health, College of Public Health and Health Professions and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Ansel Hsiao
- Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Zhu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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10
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Yan J, Li Y, Guo X, Wang X, Liu F, Li A, Cao B. The effect of ArcA on the growth, motility, biofilm formation, and virulence of Plesiomonas shigelloides. BMC Microbiol 2021; 21:266. [PMID: 34607564 DOI: 10.1186/s12866-021-02322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The anoxic redox control binary system plays an important role in the response to oxygen as a signal in the environment. In particular, phosphorylated ArcA, as a global transcription factor, binds to the promoter regions of its target genes to regulate the expression of aerobic and anaerobic metabolism genes. However, the function of ArcA in Plesiomonas shigelloides is unknown. RESULTS In the present study, P. shigelloides was used as the research object. The differences in growth, motility, biofilm formation, and virulence between the WT strain and the ΔarcA isogenic deletion mutant strain were compared. The data showed that the absence of arcA not only caused growth retardation of P. shigelloides in the log phase, but also greatly reduced the glucose utilization in M9 medium before the stationary phase. The motility of the ΔarcA mutant strain was either greatly reduced when grown in swim agar, or basically lost when grown in swarm agar. The electrophoretic mobility shift assay results showed that ArcA bound to the promoter regions of the flaK, rpoN, and cheV genes, indicating that ArcA directly regulates the expression of these three motility-related genes in P. shigelloides. Meanwhile, the ability of the ΔarcA strain to infect Caco-2 cells was reduced by 40%; on the contrary, its biofilm formation was enhanced. Furthermore, the complementation of the WT arcA gene from pBAD33-arcA+ was constructed and all of the above features of the pBAD33-arcA+ complemented strain were restored to the WT level. CONCLUSIONS We showed the effect of ArcA on the growth, motility, biofilm formation, and virulence of Plesiomonas shigelloides, and demonstrated that ArcA functions as a positive regulator controls the motility of P. shigelloides by directly regulating the expression of flaK, rpoN and cheV genes.
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11
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Xie P, Wang J, Liang H, Gao H. Shewanella oneidensis arcA Mutation Impairs Aerobic Growth Mainly by Compromising Translation. Life (Basel) 2021; 11:life11090926. [PMID: 34575075 PMCID: PMC8470723 DOI: 10.3390/life11090926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 12/27/2022] Open
Abstract
Arc (anoxic redox control), one of the most intensely investigated two-component regulatory systems in γ-proteobacteria, plays a major role in mediating the metabolic transition from aerobiosis to anaerobiosis. In Shewanella oneidensis, a research model for respiratory versatility, Arc is crucial for aerobic growth. However, how this occurs remains largely unknown. In this study, we demonstrated that the loss of the response regulator ArcA distorts the correlation between transcription and translation by inhibiting the ribosome biosynthesis. This effect largely underlies the growth defect because it concurs with the effect of chloramphenicol, which impairs translation. Reduced transcription of ArcA-dependent ribosomal protein S1 appears to have a significant impact on ribosome assembly. We further show that the lowered translation efficiency is not accountable for the envelope defect, another major defect resulting from the ArcA loss. Overall, our results suggest that although the arcA mutation impairs growth through multi-fold complex impacts in physiology, the reduced translation efficacy appears to be a major cause for the phenotype, demonstrating that Arc is a primary system that coordinates proteomic resources with metabolism in S. oneidensis.
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12
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Sun H, Song Y, Chen F, Zhou C, Liu P, Fan Y, Zheng Y, Wan X, Feng L. An ArcA-Modulated Small RNA in Pathogenic Escherichia coli K1. Front Microbiol 2020; 11:574833. [PMID: 33329434 PMCID: PMC7719688 DOI: 10.3389/fmicb.2020.574833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/23/2020] [Indexed: 02/05/2023] Open
Abstract
Escherichia coli K1 is the leading cause of meningitis in newborns. Understanding the molecular basis of E. coli K1 pathogenicity will help develop treatment of meningitis and prevent neurological sequelae. E. coli K1 replicates in host blood and forms a high level of bacteremia to cause meningitis in human. However, the mechanisms that E. coli K1 employs to sense niche signals for survival in host blood are poorly understood. We identified one intergenic region in E. coli K1 genome that encodes a novel small RNA, sRNA-17. The expression of sRNA-17 was downregulated by ArcA in microaerophilic blood. The ΔsRNA-17 strain grew better in blood than did the wild-type strain and enhanced invasion frequency in human brain microvascular endothelial cells. Transcriptome analyses revealed that sRNA-17 regulates tens of differentially expressed genes. These data indicate that ArcA downregulates the sRNA-17 expression to benefit bacterial survival in blood and penetration of the blood–brain barrier. Our findings reveal a signaling mechanism in E. coli K1 for host adaptation.
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Affiliation(s)
- Hao Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
| | - Yajun Song
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
| | - Fang Chen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Changhong Zhou
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Peng Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Yu Fan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Yangyang Zheng
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
| | - Xuehua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Lu Feng
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
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13
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Cabezas CE, Laulié AM, Briones AC, Pardo-Esté C, Lorca DE, Cofré AA, Morales EH, Mora AY, Krüger GI, Bueno SM, Hidalgo AA, Saavedra CP. Activation of regulator ArcA in the presence of hypochlorite in Salmonella enterica serovar Typhimurium. Biochimie 2020; 180:178-185. [PMID: 33188860 DOI: 10.1016/j.biochi.2020.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/24/2023]
Abstract
Oxidative stress is the main mechanism behind efficient disinfectants, causing damage in bacterial macromolecules. Importantly, bacteria activate resistance mechanisms in response to damage generated by oxidative stress. Strategies allowing pathogens to survive oxidative stress are highly conserved among microorganisms. Many of these strategies entail genomic responses triggered by signals transduced through Two Component Systems (TCS). Recently, we demonstrated that the TCS ArcAB (specifically ArcA) participates in bacterial responses to hypochlorite, regulating the uptake of this toxic compound and being involved in resistance and survival inside neutrophils, where hypochlorous acid abounds. Here, we demonstrated that ArcA is required in the response to oxidative stress generated by hypochlorite, independent of its cognate sensor ArcB or the Asp54 of ArcA, the only phosphorylable residue in ArcA, which is required to function as a gene regulator. Our results suggest that ArcA could have additional functions to respond to oxidative stress, independent of its regulatory activity, which might require interaction with other unknown relevant proteins.
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Affiliation(s)
- Carolina E Cabezas
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Arlette M Laulié
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alan C Briones
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Diego E Lorca
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Agustin A Cofré
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | | | - Aracely Y Mora
- Laboratorio de patogénesis molecular y antimicrobianos y Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Gabriel I Krüger
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Susan M Bueno
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandr A Hidalgo
- Laboratorio de patogénesis molecular y antimicrobianos y Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
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14
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Nochino N, Toya Y, Shimizu H. Transcription Factor ArcA is a Flux Sensor for the Oxygen Consumption Rate in Escherichia coli. Biotechnol J 2020; 15:e1900353. [PMID: 32383263 DOI: 10.1002/biot.201900353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/30/2020] [Indexed: 12/24/2022]
Abstract
Oxygen supply is one of the major factors determining the metabolic state in microorganisms, and it affects the productivity of various compounds during bioproduction. In Escherichia coli (E. coli), the expression levels of numerous metabolic genes are regulated by transcription factors in response to changes in environmental oxygen conditions. Even at a same dissolved oxygen concentration, the amount of available oxygen changes depending on the oxygen transfer coefficient. However, it is not known whether E. coli is able to sense differences in the oxygen consumption rate. Therefore, the present study, is focused on the role of the transcription factor ArcA in the oxygen response of E. coli and investigated the relationship between ArcA activity and the oxygen consumption rate. To evaluate the activity of ArcA, a sensor plasmid expressing fluorescent protein under the control of the icd promoter, which is regulated by ArcA, is designed. E. coli containing the sensor plasmid is grown in continuous cultures with different oxygen supplies under different dilution rates. Although there is no correlation between ArcA activity and dissolved oxygen concentration, a strong negative correlation between ArcA activity and the specific oxygen consumption rate (R2 > 0.93) is observed.
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Affiliation(s)
- Naoya Nochino
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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15
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Pardo-Esté C, Castro-Severyn J, Krüger GI, Cabezas CE, Briones AC, Aguirre C, Morales N, Baquedano MS, Sulbaran YN, Hidalgo AA, Meneses C, Poblete-Castro I, Castro-Nallar E, Valvano MA, Saavedra CP. The Transcription Factor ArcA Modulates Salmonella's Metabolism in Response to Neutrophil Hypochlorous Acid-Mediated Stress. Front Microbiol 2019; 10:2754. [PMID: 31866961 PMCID: PMC6906141 DOI: 10.3389/fmicb.2019.02754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 01/03/2023] Open
Abstract
Salmonella Typhimurium, a bacterial pathogen with high metabolic plasticity, can adapt to different environmental conditions; these traits enhance its virulence by enabling bacterial survival. Neutrophils play important roles in the innate immune response, including the production of microbicidal reactive oxygen species (ROS). In addition, the myeloperoxidase in neutrophils catalyzes the formation of hypochlorous acid (HOCl), a highly toxic molecule that reacts with essential biomolecules, causing oxidative damage including lipid peroxidation and protein carbonylation. The bacterial response regulator ArcA regulates adaptive responses to oxygen levels and influences the survival of Salmonella inside phagocytic cells. Here, we demonstrate by whole transcriptomic analyses that ArcA regulates genes related to various metabolic pathways, enabling bacterial survival during HOCl-stress in vitro. Also, inside neutrophils, ArcA controls the transcription of several metabolic pathways by downregulating the expression of genes related to fatty acid degradation, lysine degradation, and arginine, proline, pyruvate, and propanoate metabolism. ArcA also upregulates genes encoding components of the oxidative pathway. These results underscore the importance of ArcA in ATP generation inside the neutrophil phagosome and its participation in bacterial metabolic adaptations during HOCl stress.
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Affiliation(s)
- Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Gabriel I Krüger
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carolina Elizabeth Cabezas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alan Cristóbal Briones
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Camila Aguirre
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Naiyulin Morales
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Maria Soledad Baquedano
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Yoelvis Noe Sulbaran
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alejandro A Hidalgo
- Laboratorio de Patogenesis Bacteriana, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Ignacio Poblete-Castro
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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16
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Lu J, Peng Y, Wan S, Frost LS, Raivio T, Glover JNM. Cooperative Function of TraJ and ArcA in Regulating the F Plasmid tra Operon. J Bacteriol 2019; 201:e00448-18. [PMID: 30322855 DOI: 10.1128/JB.00448-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
The F plasmid tra operon encodes most of the proteins required for bacterial conjugation. TraJ and ArcA are known activators of the tra operon promoter PY, which is subject to H-NS-mediated silencing. Donor ability and promoter activity assays indicated that PY is inactivated by silencers and requires both TraJ and ArcA for activation to support efficient F conjugation. The observed low-level, ArcA-independent F conjugation is caused by tra expression from upstream alternative promoters. Electrophoretic mobility shift assays showed that TraJ alone weakly binds to PY regulatory DNA; however, TraJ binding is significantly enhanced by ArcA binding to the same DNA, indicating cooperativity of the two proteins. Analysis of binding affinities between ArcA and various DNA fragments in the PY regulatory region defined a 22-bp tandem repeat sequence (from -76 to -55 of PY) sufficient for optimal ArcA binding, which is immediately upstream of the predicted TraJ-binding site (from -54 to -34). Deletion analysis of the PY promoter in strains deficient in TraJ, ArcA, and/or H-NS determined that sequences upstream of -103 are required by silencers including H-NS for PY silencing, whereas sequences downstream of -77 are targeted by TraJ and ArcA for activation. TraJ and ArcA appear not only to counteract PY silencers but also to directly activate PY in a cooperative manner. Our data reveal the cooperativity of TraJ and ArcA during PY activation and provide insights into the regulatory circuit controlling F-family plasmid-mediated bacterial conjugation.IMPORTANCE Conjugation is a major mechanism for dissemination of antibiotic resistance and virulence among bacterial populations. The tra operon in the F family of conjugative plasmids encodes most of the proteins involved in bacterial conjugation. This work reveals that activation of tra operon transcription requires two proteins, TraJ and ArcA, to bind cooperatively to adjacent sites immediately upstream of the major tra promoter PY The interaction of TraJ and ArcA with the tra operon not only relieves PY from silencers but also directly activates it. These findings provide insights into the regulatory circuit of the F-family plasmid-mediated bacterial conjugation.
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17
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Egoburo DE, Diaz Peña R, Alvarez DS, Godoy MS, Mezzina MP, Pettinari MJ. Microbial Cell Factories à la Carte: Elimination of Global Regulators Cra and ArcA Generates Metabolic Backgrounds Suitable for the Synthesis of Bioproducts in Escherichia coli. Appl Environ Microbiol 2018; 84:e01337-18. [PMID: 30030227 DOI: 10.1128/AEM.01337-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
Manipulation of global regulators is one of the strategies used for the construction of bacterial strains suitable for the synthesis of bioproducts. However, the pleiotropic effects of these regulators can vary under different conditions and are often strain dependent. This study analyzed the effects of ArcA, CreC, Cra, and Rob using single deletion mutants of the well-characterized and completely sequenced Escherichia coli strain BW25113. Comparison of the effects of each regulator on the synthesis of major extracellular metabolites, tolerance to several compounds, and synthesis of native and nonnative bioproducts under different growth conditions allowed the discrimination of the particular phenotypes that can be attributed to the individual mutants and singled out Cra and ArcA as the regulators with the most important effects on bacterial metabolism. These data were used to identify the most suitable backgrounds for the synthesis of the reduced bioproducts succinate and 1,3-propanediol (1,3-PDO). The Δcra mutant was further modified to enhance succinate synthesis by the addition of enzymes that increase NADH and CO2 availability, achieving an 80% increase compared to the parental strain. Production of 1,3-PDO in the ΔarcA mutant was optimized by overexpression of PhaP, which increased more than twice the amount of the diol compared to the wild type in a semidefined medium using glycerol, resulting in 24 g · liter-1 of 1,3-PDO after 48 h, with a volumetric productivity of 0.5 g · liter-1 h-1 IMPORTANCE Although the effects of many global regulators, especially ArcA and Cra, have been studied in Escherichia coli, the metabolic changes caused by the absence of global regulators have been observed to differ between strains. This scenario complicates the identification of the individual effects of the regulators, which is essential for the design of metabolic engineering strategies. The genome of Escherichia coli BW25113 has been completely sequenced and does not contain additional mutations that could mask or interfere with the effects of the global regulator mutations. The uniform genetic background of the Keio collection mutants enabled the characterization of the physiological consequences of altered carbon and redox fluxes caused by each global regulator deletion, eliminating possible strain-dependent results. As a proof of concept, Δcra and ΔarcA mutants were subjected to further manipulations to obtain large amounts of succinate and 1,3-PDO, demonstrating that the metabolic backgrounds of the mutants were suitable for the synthesis of bioproducts.
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18
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Fernández PA, Velásquez F, Garcias-Papayani H, Amaya FA, Ortega J, Gómez S, Santiviago CA, Álvarez SA. Fnr and ArcA Regulate Lipid A Hydroxylation in Salmonella Enteritidis by Controlling lpxO Expression in Response to Oxygen Availability. Front Microbiol 2018; 9:1220. [PMID: 29937757 PMCID: PMC6002686 DOI: 10.3389/fmicb.2018.01220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/18/2018] [Indexed: 12/22/2022] Open
Abstract
Lipid A is the bioactive component of lipopolysaccharide, and presents a dynamic structure that undergoes modifications in response to environmental signals. Many of these structural modifications influence Salmonella virulence. This is the case of lipid A hydroxylation, a modification catalyzed by the dioxygenase LpxO. Although it has been established that oxygen is required for lipid A hydroxylation acting as substrate of LpxO in Salmonella, an additional regulatory role for oxygen in lpxO expression has not been described. The existence of this regulation could be relevant considering that Salmonella faces low oxygen tension during infection. This condition leads to an adaptive response by changing the expression of numerous genes, and transcription factors Fnr and ArcA are major regulators of this process. In this work, we describe for the first time that lipid A hydroxylation and lpxO expression are modulated by oxygen availability in Salmonella enterica serovar Enteritidis (S. Enteritidis). Biochemical and genetic analyses indicate that this process is regulated by Fnr and ArcA controlling the expression of lpxO. In addition, according to our results, this regulation occurs by direct binding of both transcription factors to specific elements present in the lpxO promoter region. Altogether, our observations revealed a novel role for oxygen acting as an environment signal controlling lipid A hydroxylation in S. Enteritidis.
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Affiliation(s)
- Paulina A Fernández
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Felipe Velásquez
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Héctor Garcias-Papayani
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Fernando A Amaya
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Jaime Ortega
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Sebastián Gómez
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Sergio A Álvarez
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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19
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Matsuoka Y, Kurata H. Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations. Biotechnol Biofuels 2017; 10:183. [PMID: 28725263 PMCID: PMC5512849 DOI: 10.1186/s13068-017-0867-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Microbial production of biofuels and biochemicals from renewable feedstocks has received considerable recent attention from environmental protection and energy production perspectives. Many biofuels and biochemicals are produced by fermentation under oxygen-limited conditions following initiation of aerobic cultivation to enhance the cell growth rate. Thus, it is of significant interest to investigate the effect of dissolved oxygen concentration on redox regulation in Escherichia coli, a particularly popular cellular factory due to its high growth rate and well-characterized physiology. For this, the systems biology approach such as modeling is powerful for the analysis of the metabolism and for the design of microbial cellular factories. RESULTS Here, we developed a kinetic model that describes the dynamics of fermentation by taking into account transcription factors such as ArcA/B and Fnr, respiratory chain reactions and fermentative pathways, and catabolite regulation. The hallmark of the kinetic model is its ability to predict the dynamics of metabolism at different dissolved oxygen levels and facilitate the rational design of cultivation methods. The kinetic model was verified based on the experimental data for a wild-type E. coli strain. The model reasonably predicted the metabolic characteristics and molecular mechanisms of fnr and arcA gene-knockout mutants. Moreover, an aerobic-microaerobic dual-phase cultivation method for lactate production in a pfl-knockout mutant exhibited promising yield and productivity. CONCLUSIONS It is quite important to understand metabolic regulation mechanisms from both scientific and engineering points of view. In particular, redox regulation in response to oxygen limitation is critically important in the practical production of biofuel and biochemical compounds. The developed model can thus be used as a platform for designing microbial factories to produce a variety of biofuels and biochemicals.
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Affiliation(s)
- Yu Matsuoka
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502 Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502 Japan
- Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502 Japan
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Silva-Valenzuela CA, Velásquez F, Peñailillo J, Garcias-Papayani H, Fernández P, Tobar P, Contreras I, Santiviago CA, Álvarez SA. O-antigen chain-length distribution in Salmonella enterica serovar Enteritidis is regulated by oxygen availability. Biochem Biophys Res Commun 2016; 477:563-567. [PMID: 27343553 DOI: 10.1016/j.bbrc.2016.06.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
Lipopolysaccharide (LPS) consists of three covalently linked domains: the lipid A, the core region and the O antigen (OAg), consisting of repeats of an oligosaccharide. Salmonella enterica serovar Enteritidis (S. Enteritidis) produces a LPS with two OAg preferred chain lengths: a long (L)-OAg controlled by WzzSE and a very long (VL)-OAg controlled by WzzfepE. In this work, we show that OAg produced by S. Enteritidis grown in E minimal medium also presented two preferred chain-lengths. However, a simultaneous and opposing change in the production of L-OAg and VL-OAg was observed in response to oxygen availability. Biochemical and genetics analyses indicate that this process is regulated by transcriptional factors Fnr and ArcA by means of controlling the transcription of genes encoding WzzSE and WzzfepE in response to oxygen availability. Thus, our results revealed a sophisticated regulatory mechanism involved in the adaptation of S. Enteritidis to one of the main environmental cues faced by this pathogen during infection.
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Affiliation(s)
- Cecilia A Silva-Valenzuela
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile; Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Felipe Velásquez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Johany Peñailillo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Héctor Garcias-Papayani
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Paulina Fernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Pía Tobar
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Inés Contreras
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Sergio A Álvarez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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Leuze MR, Karpinets TV, Syed MH, Beliaev AS, Uberbacher EC. Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA. Gene Regul Syst Bio 2012; 6:93-107. [PMID: 22701314 PMCID: PMC3370831 DOI: 10.4137/grsb.s9357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of which are palindromic, are known as regulatory elements or transcription factor binding sites (TFBS). Some TFs are global regulators that can modulate the expression of hundreds of genes. In this study we examine global regulator half-sites, where a half-site, which we shall call a binding motif (BM), is one half of a palindromic TFBS. We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full TFBS quality or location.
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Affiliation(s)
- Michael R. Leuze
- Computer Science and Mathematics Division, Oak Ridge National
Laboratory, Oak Ridge, TN, USA
| | - Tatiana V. Karpinets
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN,
USA
- Department of Plant Sciences, University of Tennessee, Knoxville,
TN, USA
| | - Mustafa H. Syed
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN,
USA
| | - Alexander S. Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory,
Richland, WA, USA
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Wong SMS, Akerley BJ. Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis. Front Cell Infect Microbiol 2012; 2:23. [PMID: 22919615 PMCID: PMC3417392 DOI: 10.3389/fcimb.2012.00023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/15/2012] [Indexed: 12/28/2022] Open
Abstract
Haemophilus influenzae is a Gram-negative bacterium that has no identified natural niche outside of the human host. It primarily colonizes the nasopharyngeal mucosa in an asymptomatic mode, but has the ability to disseminate to other anatomical sites to cause otitis media, upper, and lower respiratory tract infections, septicemia, and meningitis. To persist in diverse environments the bacterium must exploit and utilize the nutrients and other resources available in these sites for optimal growth/survival. Recent evidence suggests that regulatory factors that direct such adaptations also control virulence determinants required to resist and evade immune clearance mechanisms. In this review, we describe the recent application of whole-genome approaches that together provide insight into distinct survival mechanisms of H. influenzae in the context of different sites of pathogenesis.
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Affiliation(s)
- Sandy M S Wong
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School Worcester, MA, USA
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