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Singh S, Gola C, Singh B, Agrawal V, Chaba R. D-galactonate metabolism in enteric bacteria: a molecular and physiological perspective. Curr Opin Microbiol 2024; 81:102524. [PMID: 39137493 DOI: 10.1016/j.mib.2024.102524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024]
Abstract
D-galactonate, a widely prevalent sugar acid, was first reported as a nutrient source for enteric bacteria in the 1970s. Since then, decades of research enabled a description of the modified Entner-Doudoroff pathway involved in its degradation and reported the structural and biochemical features of its metabolic enzymes, primarily in Escherichia coli K-12. However, only in the last few years, the D-galactonate transporter has been characterized, and the regulation of the dgo operon, encoding the structural genes for the transporter and enzymes of D-galactonate metabolism, has been detailed. Notably, in recent years, multiple evolutionary studies have identified the dgo operon as a dominant target for adaptation of E. coli in the mammalian gut. Despite considerable research on dgo operon, numerous fundamental questions remain to be addressed. The emerging relevance of the dgo operon in host-bacterial interactions further necessitates the study of D-galactonate metabolism in other enterobacterial strains.
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Affiliation(s)
- Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Chetna Gola
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Vishal Agrawal
- Amity School of Biological Sciences, Amity University Punjab, Mohali, SAS Nagar, Punjab 140306, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India.
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2
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Zhang L, Fu Y, Xu Q, Chen X, Xie Y, Zhang B, Lin X. Quantitative proteomics reveals the complex regulatory networks of LTTR-type regulators in pleiotropic functions of Aeromonas hydrophila. Int J Biol Macromol 2024; 270:132315. [PMID: 38740149 DOI: 10.1016/j.ijbiomac.2024.132315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
LysR-type transcriptional regulators (LTTRs) are ubiquitously distributed and abundant transcriptional regulators in prokaryotes, playing pivotal roles in diverse physiological processes. Nonetheless, despite their prevalence, the intricate functionalities and physiological implications of this protein family remain incompletely elucidated. In this study, we employed a comprehensive approach to deepen our understanding of LTTRs by generating a collection of 20 LTTR gene-deletion strains in Aeromonas hydrophila, accounting for 42.6 % of the predicted total LTTR repertoire, and subjected them to meticulous assessment of their physiological phenotypes. Leveraging quantitative proteomics, we conducted a comparative analysis of protein expression variations between six representative mutants and the wild-type strain. Subsequent bioinformatics analysis unveiled the involvement of these LTTRs in modulating a wide array of biological processes, notably including two-component regulatory systems (TCSs) and intracellular central metabolism. Moreover, employing subsequent microbiological methodologies, we experimentally verified the direct involvement of at least six LTTRs in the regulation of galactose metabolism. Importantly, through ELISA and competitive ELISA assays, we demonstrated the competitive binding capabilities of these LTTRs with the promoter of the α-galactosidase gene AHA_1897 and identified that four LTTRs (XapR, YidZ, YeeY, and AHA_1805) do not engage in competitive binding with other LTTRs. Overall, our comprehensive findings not only provide fundamental insights into the regulatory mechanisms governing crucial physiological functions of bacteria through LTTR family proteins but also uncover an intricate and interactive regulatory network mediated by LTTRs.
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Affiliation(s)
- Lishan Zhang
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuying Fu
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou, Fujian Province 350007, China
| | - Qiaozhen Xu
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Chen
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuyue Xie
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binghui Zhang
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou 350003, China
| | - Xiangmin Lin
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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3
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Ye H, Borusak S, Eberl C, Krasenbrink J, Weiss AS, Chen SC, Hanson BT, Hausmann B, Herbold CW, Pristner M, Zwirzitz B, Warth B, Pjevac P, Schleheck D, Stecher B, Loy A. Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut. Nat Commun 2023; 14:5533. [PMID: 37723166 PMCID: PMC10507020 DOI: 10.1038/s41467-023-41008-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/21/2023] [Indexed: 09/20/2023] Open
Abstract
Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.
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Affiliation(s)
- Huimin Ye
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Sabrina Borusak
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Claudia Eberl
- Max-von-Pettenkofer Institute, Ludwig Maximilian University Munich, Munich, Germany
| | - Julia Krasenbrink
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna S Weiss
- Max-von-Pettenkofer Institute, Ludwig Maximilian University Munich, Munich, Germany
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Buck T Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o Waitaha, University of Canterbury, Christchurch, New Zealand
| | - Manuel Pristner
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria
| | - Benjamin Zwirzitz
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria
- Exposome Austria, Research Infrastructure and National EIRENE Hub, Vienna, Austria
| | - Petra Pjevac
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - David Schleheck
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, Ludwig Maximilian University Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Ludwig Maximilian University Munich, Munich, Germany
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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4
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Zhu Q, Bai X, Li Q, Zhang M, Hu G, Pan K, Liu H, Ke Z, Hong Q, Qiu J. PcaR, a GntR/FadR Family Transcriptional Repressor Controls the Transcription of Phenazine-1-Carboxylic Acid 1,2-Dioxygenase Gene Cluster in Sphingomonas histidinilytica DS-9. Appl Environ Microbiol 2023; 89:e0212122. [PMID: 37191535 PMCID: PMC10304782 DOI: 10.1128/aem.02121-22] [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: 12/16/2022] [Accepted: 04/29/2023] [Indexed: 05/17/2023] Open
Abstract
In our previous study, the phenazine-1-carboxylic acid (PCA) 1,2-dioxygenase gene cluster (pcaA1A2A3A4 cluster) in Sphingomonas histidinilytica DS-9 was identified to be responsible for the conversion of PCA to 1,2-dihydroxyphenazine (Ren Y, Zhang M, Gao S, Zhu Q, et al. 2022. Appl Environ Microbiol 88:e00543-22). However, the regulatory mechanism of the pcaA1A2A3A4 cluster has not been elucidated yet. In this study, the pcaA1A2A3A4 cluster was found to be transcribed as two divergent operons: pcaA3-ORF5205 (named A3-5205 operon) and pcaA1A2-ORF5208-pcaA4-ORF5210 (named A1-5210 operon). The promoter regions of the two operons were overlapped. PcaR acts as a transcriptional repressor of the pcaA1A2A3A4 cluster, and it belongs to GntR/FadR family transcriptional regulator. Gene disruption of pcaR can shorten the lag phase of PCA degradation. The results of electrophoretic mobility shift assay and DNase I footprinting showed that PcaR binds to a 25-bp motif in the ORF5205-pcaA1 intergenic promoter region to regulate the expression of two operons. The 25-bp motif covers the -10 region of the promoter of A3-5205 operon and the -35 region and -10 region of the promoter of A1-5210 operon. The TNGT/ANCNA box within the motif was essential for PcaR binding to the two promoters. PCA acted as an effector of PcaR, preventing it from binding to the promoter region and repressing the transcription of the pcaA1A2A3A4 cluster. In addition, PcaR represses its own transcription, and this repression can be relieved by PCA. This study reveals the regulatory mechanism of PCA degradation in strain DS-9, and the identification of PcaR increases the variety of regulatory model of the GntR/FadR-type regulator. IMPORTANCE Sphingomonas histidinilytica DS-9 is a phenazine-1-carboxylic acid (PCA)-degrading strain. The 1,2-dioxygenase gene cluster (pcaA1A2A3A4 cluster, encoding dioxygenase PcaA1A2, reductase PcaA3, and ferredoxin PcaA4) is responsible for the initial degradation step of PCA and widely distributed in Sphingomonads, but its regulatory mechanism has not been investigated yet. In this study, a GntR/FadR-type transcriptional regulator PcaR repressing the transcription of pcaA1A2A3A4 cluster and pcaR gene was identified and characterized. The binding site of PcaR in ORF5205-pcaA1 intergenic promoter region contains a TNGT/ANCNA box, which is important for the binding. These findings enhance our understanding of the molecular mechanism of PCA degradation.
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Affiliation(s)
- Qian Zhu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Xuekun Bai
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Qian Li
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Mingliang Zhang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Gang Hu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Kaihua Pan
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Hongfei Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zhijian Ke
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, Zhejiang, People’s Republic of China
| | - Qing Hong
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Jiguo Qiu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
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5
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Batarni S, Nayak N, Chang A, Li F, Hareendranath S, Zhou L, Xu H, Stroud R, Eriksen J, Edwards RH. Substrate recognition and proton coupling by a bacterial member of solute carrier family 17. J Biol Chem 2023; 299:104646. [PMID: 36965620 PMCID: PMC10149257 DOI: 10.1016/j.jbc.2023.104646] [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: 09/09/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 03/27/2023] Open
Abstract
The solute carrier 17 family transports diverse organic anions using two distinct modes of coupling to a source of energy. Transporters that package glutamate and nucleotide into secretory vesicles for regulated release by exocytosis are driven by membrane potential but subject to allosteric regulation by H+ and Cl-. Other solute carrier 17 members including the lysosomal sialic acid exporter couple the flux of organic anion to cotransport of H+. To begin to understand how similar proteins can perform such different functions, we have studied Escherichia coli DgoT, a H+/galactonate cotransporter. A recent structure of DgoT showed many residues contacting D-galactonate, and we now find that they do not tolerate even conservative substitutions. In contrast, the closely related lysosomal H+/sialic acid cotransporter Sialin tolerates similar mutations, consistent with its recognition of diverse substrates with relatively low affinity. We also find that despite coupling to H+, DgoT transports more rapidly but with lower apparent affinity at high pH. Indeed, membrane potential can drive uptake, indicating electrogenic transport and suggesting a H+:galactonate stoichiometry >1. Located in a polar pocket of the N-terminal helical bundle, Asp46 and Glu133 are each required for net flux by DgoT, but the E133Q mutant exhibits robust exchange activity and rescues exchange by D46N, suggesting that these two residues operate in series to translocate protons. E133Q also shifts the pH sensitivity of exchange by DgoT, supporting a central role for the highly conserved TM4 glutamate in H+ coupling by DgoT.
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Affiliation(s)
- Samir Batarni
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California
| | - Nanda Nayak
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California
| | - Audrey Chang
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California
| | - Fei Li
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California
| | - Surabhi Hareendranath
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California
| | - Lexi Zhou
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California
| | - Hongfei Xu
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California
| | - Robert Stroud
- Department of Biochemistry & Biophysics, UCSF School of Medicine, San Francisco, California
| | - Jacob Eriksen
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California.
| | - Robert H Edwards
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, California.
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Gomes MZR, de Lima EM, Martins Aires CA, Pereira PS, Yim J, Silva FH, Rodrigues CAS, Oliveira TRTE, da Silva PP, Eller CM, de Souza CMR, Rybak MJ, Albano RM, de Miranda AB, Machado E, Catanho M. Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes. Sci Rep 2023; 13:6238. [PMID: 37069157 PMCID: PMC10110528 DOI: 10.1038/s41598-023-31901-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients' comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.
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Affiliation(s)
- Marisa Zenaide Ribeiro Gomes
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
- Hospital Federal Servidores do Estado, Ministry of Health, Rio de Janeiro, Brazil.
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
- Hospital Infection Control Committee, Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Caio Augusto Martins Aires
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
- Departamento de Ciência da Saúde, Universidade Federal Rural do Semi-Árido (UFERSA), Mossoró, Rio Grande do Norte, Brazil
| | - Polyana Silva Pereira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Juwon Yim
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Fernando Henrique Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Priscila Pinho da Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Cristiane Monteiro Eller
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Claudio Marcos Rocha de Souza
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Michael J Rybak
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, IBRAG, Universidade do Estado do Rio de Janeiro,, Rio de Janeiro, Brazil
| | - Antonio Basílio de Miranda
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Edson Machado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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7
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Li F, Eriksen J, Finer-Moore J, Stroud RM, Edwards RH. Diversity of function and mechanism in a family of organic anion transporters. Curr Opin Struct Biol 2022; 75:102399. [PMID: 35660266 PMCID: PMC9884543 DOI: 10.1016/j.sbi.2022.102399] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 02/01/2023]
Abstract
Originally identified as transporters for inorganic phosphate, solute carrier 17 (SLC17) family proteins subserve diverse physiological roles. The vesicular glutamate transporters (VGLUTs) package the principal excitatory neurotransmitter glutamate into synaptic vesicles (SVs). In contrast, the closely related sialic acid transporter sialin mediates the flux of sialic acid in the opposite direction, from lysosomes to the cytoplasm. The two proteins couple in different ways to the H+ electrochemical gradient driving force, and high-resolution structures of the Escherichia coli homolog d-galactonate transporter (DgoT) and more recently rat VGLUT2 now begin to suggest the mechanisms involved as well as the basis for substrate specificity.
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Affiliation(s)
- Fei Li
- Department of Biochemistry & Biophysics, UCSF School of Medicine, CA, USA,Departments of Neurology and Physiology, UCSF School of Medicine, CA, USA
| | - Jacob Eriksen
- Departments of Neurology and Physiology, UCSF School of Medicine, CA, USA
| | - Janet Finer-Moore
- Department of Biochemistry & Biophysics, UCSF School of Medicine, CA, USA
| | - Robert M. Stroud
- Department of Biochemistry & Biophysics, UCSF School of Medicine, CA, USA
| | - Robert H. Edwards
- Departments of Neurology and Physiology, UCSF School of Medicine, CA, USA
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8
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Cohen H, Hoede C, Scharte F, Coluzzi C, Cohen E, Shomer I, Mallet L, Holbert S, Serre RF, Schiex T, Virlogeux-Payant I, Grassl GA, Hensel M, Chiapello H, Gal-Mor O. Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium. PLoS Pathog 2022; 18:e1010425. [PMID: 35381053 PMCID: PMC9012535 DOI: 10.1371/journal.ppat.1010425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/15/2022] [Accepted: 03/09/2022] [Indexed: 12/21/2022] Open
Abstract
Although Salmonella Typhimurium (STM) and Salmonella Paratyphi A (SPA) belong to the same phylogenetic species, share large portions of their genome and express many common virulence factors, they differ vastly in their host specificity, the immune response they elicit, and the clinical manifestations they cause. In this work, we compared their intracellular transcriptomic architecture and cellular phenotypes during human epithelial cell infection. While transcription induction of many metal transport systems, purines, biotin, PhoPQ and SPI-2 regulons was similar in both intracellular SPA and STM, we identified 234 differentially expressed genes that showed distinct expression patterns in intracellular SPA vs. STM. Surprisingly, clear expression differences were found in SPI-1, motility and chemotaxis, and carbon (mainly citrate, galactonate and ethanolamine) utilization pathways, indicating that these pathways are regulated differently during their intracellular phase. Concurring, on the cellular level, we show that while the majority of STM are non-motile and reside within Salmonella-Containing Vacuoles (SCV), a significant proportion of intracellular SPA cells are motile and compartmentalized in the cytosol. Moreover, we found that the elevated expression of SPI-1 and motility genes by intracellular SPA results in increased invasiveness of SPA, following exit from host cells. These findings demonstrate unexpected flagellum-dependent intracellular motility of a typhoidal Salmonella serovar and intriguing differences in intracellular localization between typhoidal and non-typhoidal salmonellae. We propose that these differences facilitate new cycles of host cell infection by SPA and may contribute to the ability of SPA to disseminate beyond the intestinal lamina propria of the human host during enteric fever. Salmonella enterica is a ubiquitous, facultative intracellular animal and human pathogen. Although non-typhoidal Salmonella (NTS) and typhoidal Salmonella serovars belong to the same phylogenetic species and share many virulence factors, the disease they cause in humans is very different. While the underlying mechanisms for these differences are not fully understood, one possible reason expected to contribute to their different pathogenicity is a distinct expression pattern of genes involved in host-pathogen interactions. Here, we compared the global gene expression and intracellular phenotypes, during human epithelial cell infection of S. Paratyphi A (SPA) and S. Typhimurium (STM), as prototypical serovars of typhoidal and NTS, respectively. Interestingly, we identified different expression patterns in key virulence and metabolic pathways, cytosolic motility and increased reinvasion of SPA, following exit from infected cells. We hypothesize that these differences contribute to the invasive and systemic disease developed following SPA infection in humans.
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Affiliation(s)
- Helit Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Claire Hoede
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
| | - Felix Scharte
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Charles Coluzzi
- INRAE, Université Paris-Saclay, MaIAGE, Jouy-en-Josas, France
| | - Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Inna Shomer
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ludovic Mallet
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
| | | | | | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, Toulouse, France
| | | | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hanover, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs–Center of Cellular Nanoanalytics Osnabrück, Universität Osnabrück, Osnabrück, Germany
- * E-mail: (MH); (HC); (OG-M)
| | - Hélène Chiapello
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
- INRAE, Université Paris-Saclay, MaIAGE, Jouy-en-Josas, France
- * E-mail: (MH); (HC); (OG-M)
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail: (MH); (HC); (OG-M)
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9
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Zheng H, Shu W, Fu X, Wang J, Yang Y, Xu J, Song H, Ma Y. A pyruvate-centered metabolic regulation mechanism for the enhanced expression of exogenous genes in Escherichia coli. Int J Biol Macromol 2022; 203:58-66. [DOI: 10.1016/j.ijbiomac.2022.01.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/11/2022] [Accepted: 01/22/2022] [Indexed: 11/29/2022]
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10
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Aguirre-Sanchez JR, Ibarra-Rodriguez JR, Vega-Lopez IF, Martínez-Urtaza J, Chaidez-Quiroz C. Genomic signatures of adaptation to natural settings in non-typhoidal Salmonella enterica Serovars Saintpaul, Thompson and Weltevreden. INFECTION GENETICS AND EVOLUTION 2021; 90:104771. [PMID: 33592318 DOI: 10.1016/j.meegid.2021.104771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
Salmonella enterica is a pathogenic bacterium responsible for intestinal illness and systemic diseases such as typhoid and paratyphoid fevers. Among clinical manifestation classification, non-typhoidal Salmonella is mainly known as foodborne pathogen associated with the consumption of fecal contaminated food and water. Even though Salmonella hosts include humans and warm-blooded animals, it has been found in non-host environments as river water where the bacteria use different strategies to fitness the environment persisting and establishment. Now with the availability of WGS and bioinformatics tools, we can explore bacterial genomes with higher resolution to increase our understanding of specific genetic signatures among environmental and clinical isolates, being the goal of this work. Pangenome construction allowed the detection of specific environmental and clinical gene clusters related to metabolism and secretion systems as the main signature respectively. Specifically, D-galactonate degradation pathway was observed mainly in environmental genomes while T3SS and flagellum genes were detected for all clinical but not for all environmental isolates. Gene duplication and pseudogenes accumulation were detected as the main adaptation strategy for environmental isolates; thus, isolation source may play an important role in genome plasticity, conferring a selective advantage to survive and persist for environmental Salmonella isolates. Intact prophage sequences with cargo genes were observable for both isolation sources playing an important role in virulence contribution.
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Affiliation(s)
| | | | - I F Vega-Lopez
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | - J Martínez-Urtaza
- Departement of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - C Chaidez-Quiroz
- Centro de Investigación en Alimentación y Desarrollo, Culiacán, Mexico.
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11
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Lin Z, Sun Y, Liu Y, Tong S, Shang Z, Cai Y, Lin W. Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket. Front Microbiol 2020; 11:590330. [PMID: 33224125 PMCID: PMC7674646 DOI: 10.3389/fmicb.2020.590330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022] Open
Abstract
The transcription repressor of D-galactonate metabolism, DgoR, from Escherichia coli belongs to the FadR family of the GntR superfamily. In the presence of D-galactonate, DgoR binds to two inverted repeats overlapping the dgo cis-acting promoter repressing the expression of genes involved in D-galactonate metabolism. To further understand the structural and molecular details of ligand and effector interactions between D-galactonate and this FadR family member, herein we solved the crystal structure of C-terminal domain of DgoR (DgoR_C), which revealed a unique divalent metal-containing substrate binding pocket. The metal ion is required for D-galactonate binding, as evidenced by the dramatically decreased affinity between D-galactonate and DgoR in the presence of EDTA, which can be reverted by the addition of Zn2+, Mg2+, and Ca2+. The key amino acid residues involved in the interactions between D-galactonate and DgoR were revealed by molecular docking studies and further validated with biochemical studies by site-directed mutagenesis. It was found that changes to alanine in residues R102, W181, T191, and R224 resulted in significantly decreased binding affinities for D-galactonate, as determined by EMSA and MST assays. These results suggest that the molecular modifications induced by a D-galactonate and a metal binding in the DgoR are required for DNA binding activity and consequently, transcriptional inhibition.
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Affiliation(s)
- Zhaozhu Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Sun
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu Liu
- Department of Chemistry, Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Shujuan Tong
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanheng Cai
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY, United States
| | - Wei Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
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12
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Arya G, Pal M, Sharma M, Singh B, Singh S, Agrawal V, Chaba R. Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli. Mol Microbiol 2020; 115:591-609. [PMID: 33068046 DOI: 10.1111/mmi.14625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023]
Abstract
Several GntR/FadR transcriptional regulators govern sugar acid metabolism in bacteria. Although effectors have been identified for a few sugar acid regulators, the mode of effector binding is unknown. Even in the overall FadR subfamily, there are limited details on effector-regulator interactions. Here, we identified the effector-binding cavity in Escherichia coli DgoR, a FadR subfamily transcriptional repressor of D-galactonate metabolism that employs D-galactonate as its effector. Using a genetic screen, we isolated several dgoR superrepressor alleles. Blind docking suggested eight amino acids corresponding to these alleles to form a part of the effector-binding cavity. In vivo and in vitro assays showed that these mutations compromise the inducibility of DgoR without affecting its oligomeric status or affinity for target DNA. Taking Bacillus subtilis GntR as a representative, we demonstrated that the effector-binding cavity is similar among FadR subfamily sugar acid regulators. Finally, a comparison of sugar acid regulators with other FadR members suggested conserved features of effector-regulator recognition within the FadR subfamily. Sugar acid metabolism is widely implicated in bacterial colonization and virulence. The present study sets the basis to investigate the influence of natural genetic variations in FadR subfamily regulators on their sensitivity to sugar acids and ultimately on host-bacterial interactions.
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Affiliation(s)
- Garima Arya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Mohinder Pal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Vishal Agrawal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
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13
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Burin R, Shah DH. Global transcriptional profiling of tyramine and d-glucuronic acid catabolism in Salmonella. Int J Med Microbiol 2020; 310:151452. [PMID: 33091748 DOI: 10.1016/j.ijmm.2020.151452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Salmonella has evolved various metabolic pathways to scavenge energy from the metabolic byproducts of the host gut microbiota, however, the precise metabolic byproducts and pathways utilized by Salmonella remain elusive. Previously we reported that Salmonella can proliferate by deriving energy from two metabolites that naturally occur in the host as gut microbial metabolic byproducts, namely, tyramine (TYR, an aromatic amine) and d-glucuronic acid (DGA, a hexuronic acid). Salmonella Pathogenicity Island 13 (SPI-13) plays a critical role in the ability of Salmonella to derive energy from TYR and DGA, however the catabolic pathways of these two micronutrients in Salmonella are poorly defined. The objective of this study was to identify the specific genetic components and construct the regulatory circuits for the TYR and DGA catabolic pathways in Salmonella. To accomplish this, we employed TYR and DGA-induced global transcriptional profiling and gene functional network analysis approaches. We report that TYR induced differential expression of 319 genes (172 up-regulated and 157 down-regulated) when Salmonella was grown in the presence of TYR as a sole energy source. These included the genes originally predicted to be involved in the classical TYR catabolic pathway. TYR also induced expression of majority of genes involved in the acetaldehyde degradation pathway and aided identification of a few new genes that are likely involved in alternative pathway for TYR catabolism. In contrast, DGA induced differential expression of 71 genes (58 up-regulated and 13 down-regulated) when Salmonella was grown in the presence of DGA as a sole energy source. These included the genes originally predicted to be involved in the classical pathway and a few new genes likely involved in the alternative pathway for DGA catabolism. Interestingly, DGA also induced expression of SPI-2 T3SS, suggesting that DGA may also influence nutritional virulence of Salmonella. In summary, this is the first report describing the global transcriptional profiling of TYR and DGA catabolic pathways of Salmonella. This study will contribute to the better understanding of the role of TYR and DGA in metabolic adaptation and virulence of Salmonella.
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Affiliation(s)
- Raquel Burin
- Department of Veterinary Microbiology and Pathology, United States
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, United States; Paul Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, 99164-7040, United States.
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