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de Palma TH, Powers C, McPartland MJ, Mark Welch J, Ramsey M. Essential genes for Haemophilus parainfluenzae survival and biofilm growth. mSystems 2024; 9:e0067424. [PMID: 39166876 DOI: 10.1128/msystems.00674-24] [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: 05/13/2024] [Accepted: 07/21/2024] [Indexed: 08/23/2024] Open
Abstract
Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.
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Affiliation(s)
- Thais H de Palma
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Chris Powers
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Morgan J McPartland
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Jessica Mark Welch
- Department of Microbiology, ADA Forsyth Institute, Cambridge, Massachusetts, USA
| | - Matthew Ramsey
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
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2
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de Palma TH, Powers C, McPartland MJ, Welch JM, Ramsey M. Essential genes for Haemophilus parainfluenzae survival and biofilm growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587483. [PMID: 38585970 PMCID: PMC10996682 DOI: 10.1101/2024.03.31.587483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Haemophilus parainfluenzae ( Hp ) is a Gram-negative, pleomorphic rod, highly prevalent and abundant as a commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the tongue dorsum, keratinized gingiva, and the supragingival plaque biofilm. As a member of the HACEK group, Hp is also known to cause infective endocarditis. Additionally, case reports have identified Hp as the causative agent of meningitis, septic arthritis, chronic osteomyelitis, septicemia, and a variety of other infectious diseases. Little is known about how Hp interacts with its neighbors in the healthy biofilm nor about its mechanisms of pathogenesis as an extraoral opportunistic pathogen. To address these unknowns, we identified the essential genomes of two Hp strains and the conditionally essential genes for their growth in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain ( Hp 392) and a commensal oral isolate EL1 ( Hp EL1), we show that the essential genome of Hp 392 and Hp EL1 is composed of 395 and 384 genes, respectively. The core essential genome, consisting of 341 essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains of Hp . Additionally, RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic biofilm survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo oral habitat. Further, the creation of this library presents a valuable tool for further investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.
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Haidar-Ahmad N, Manigat FO, Silué N, Pontier SM, Campbell-Valois FX. A Tale about Shigella: Evolution, Plasmid, and Virulence. Microorganisms 2023; 11:1709. [PMID: 37512882 PMCID: PMC10383432 DOI: 10.3390/microorganisms11071709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Shigella spp. cause hundreds of millions of intestinal infections each year. They target the mucosa of the human colon and are an important model of intracellular bacterial pathogenesis. Shigella is a pathovar of Escherichia coli that is characterized by the presence of a large invasion plasmid, pINV, which encodes the characteristic type III secretion system and icsA used for cytosol invasion and cell-to-cell spread, respectively. First, we review recent advances in the genetic aspects of Shigella, shedding light on its evolutionary history within the E. coli lineage and its relationship to the acquisition of pINV. We then discuss recent insights into the processes that allow for the maintenance of pINV. Finally, we describe the role of the transcription activators VirF, VirB, and MxiE in the major virulence gene regulatory cascades that control the expression of the type III secretion system and icsA. This provides an opportunity to examine the interplay between these pINV-encoded transcriptional activators and numerous chromosome-encoded factors that modulate their activity. Finally, we discuss novel chromosomal genes icaR, icaT, and yccE that are regulated by MxiE. This review emphasizes the notion that Shigella and E. coli have walked the fine line between commensalism and pathogenesis for much of their history.
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Affiliation(s)
- Nathaline Haidar-Ahmad
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - France Ourida Manigat
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Navoun Silué
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Stéphanie M Pontier
- Centre de Recherche Santé Environnementale et Biodiversité de l'Outaouais (SEBO), CEGEP de l'Outaouais, Gatineau, QC J8Y 6M4, Canada
| | - François-Xavier Campbell-Valois
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Centre for Infection, Immunity and Inflammation, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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Li Y, Ma B, Hua K, Gong H, He R, Luo R, Bi D, Zhou R, Langford PR, Jin H. PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes. Microbiol Spectr 2023; 11:e0387122. [PMID: 36602356 PMCID: PMC9927313 DOI: 10.1128/spectrum.03871-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
Identification of microbial functional association networks allows interpretation of biological phenomena and a greater understanding of the molecular basis of pathogenicity and also underpins the formulation of control measures. Here, we describe PPNet, a tool that uses genome information and analysis of phylogenetic profiles with binary similarity and distance measures to derive large-scale bacterial gene association networks of a single species. As an exemplar, we have derived a functional association network in the pig pathogen Streptococcus suis using 81 binary similarity and dissimilarity measures which demonstrates excellent performance based on the area under the receiver operating characteristic (AUROC), the area under the precision-recall (AUPR), and a derived overall scoring method. Selected network associations were validated experimentally by using bacterial two-hybrid experiments. We conclude that PPNet, a publicly available (https://github.com/liyangjie/PPNet), can be used to construct microbial association networks from easily acquired genome-scale data. IMPORTANCE This study developed PPNet, the first tool that can be used to infer large-scale bacterial functional association networks of a single species. PPNet includes a method for assigning the uniqueness of a bacterial strain using the average nucleotide identity and the average nucleotide coverage. PPNet collected 81 binary similarity and distance measures for phylogenetic profiling and then evaluated and divided them into four groups. PPNet can effectively capture gene networks that are functionally related to phenotype from publicly prokaryotic genomes, as well as provide valuable results for downstream analysis and experiment testing.
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Affiliation(s)
- Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Bin Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Kexin Hua
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huimin Gong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rongrong He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dingren Bi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Paul R. Langford
- Section of Paediatric Infectious Disease, Imperial College London, St Mary’s Campus, London, United Kingdom
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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5
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Bajunaid W, Haidar-Ahmad N, Kottarampatel AH, Ourida Manigat F, Silué N, F. Tchagang C, Tomaro K, Campbell-Valois FX. The T3SS of Shigella: Expression, Structure, Function, and Role in Vacuole Escape. Microorganisms 2020; 8:microorganisms8121933. [PMID: 33291504 PMCID: PMC7762205 DOI: 10.3390/microorganisms8121933] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022] Open
Abstract
Shigella spp. are one of the leading causes of infectious diarrheal diseases. They are Escherichia coli pathovars that are characterized by the harboring of a large plasmid that encodes most virulence genes, including a type III secretion system (T3SS). The archetypal element of the T3SS is the injectisome, a syringe-like nanomachine composed of approximately 20 proteins, spanning both bacterial membranes and the cell wall, and topped with a needle. Upon contact of the tip of the needle with the plasma membrane, the injectisome secretes its protein substrates into host cells. Some of these substrates act as translocators or effectors whose functions are key to the invasion of the cytosol and the cell-to-cell spread characterizing the lifestyle of Shigella spp. Here, we review the structure, assembly, function, and methods to measure the activity of the injectisome with a focus on Shigella, but complemented with data from other T3SS if required. We also present the regulatory cascade that controls the expression of T3SS genes in Shigella. Finally, we describe the function of translocators and effectors during cell-to-cell spread, particularly during escape from the vacuole, a key element of Shigella’s pathogenesis that has yet to reveal all of its secrets.
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Affiliation(s)
- Waad Bajunaid
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nathaline Haidar-Ahmad
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Anwer Hasil Kottarampatel
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - France Ourida Manigat
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Navoun Silué
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caetanie F. Tchagang
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kyle Tomaro
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - François-Xavier Campbell-Valois
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Correspondence:
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Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet 2020; 21:699-714. [PMID: 32665585 PMCID: PMC7990032 DOI: 10.1038/s41576-020-0254-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
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Affiliation(s)
- Citlalli Mejía-Almonte
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | | | - Joseph T Wade
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jacques van Helden
- Aix-Marseille University, INSERM UMR S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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Cervantes-Rivera R, Tronnet S, Puhar A. Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination. BMC Genomics 2020; 21:285. [PMID: 32252626 PMCID: PMC7132871 DOI: 10.1186/s12864-020-6565-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
Background Shigella is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans. Shigella invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strain S. flexneri serotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches. Results We have sequenced, assembled, annotated and manually curated the full genome of S. flexneri 5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new hybrid strategy to prepare gapless, highly accurate genome sequences, which also cover AT-rich tracks or repetitive sequences that are transcribed. Furthermore, we have performed genome-wide analysis of transcriptional start sites (TSS) and determined the length of 5′ untranslated regions (5′-UTRs) at typical culture conditions for the inoculum of in vitro infection experiments. We identified 6723 primary TSS (pTSS) and 7328 secondary TSS (sTSS). The S. flexneri 5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (http://regulondb.ccg.unam.mx) and RSAT (http://embnet.ccg.unam.mx/rsat/) databases to use their analysis tools in the S. flexneri 5a M90T genome. Conclusions We provide the first complete genome for S. flexneri serotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employing S. flexneri M90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation of S. flexneri 5a M90T. Further, we present a new hybrid strategy to prepare gapless, highly accurate genome sequences. Unlike currently used hybrid strategies combining long- and short-read DNA sequencing technologies to maximize accuracy, our workflow using long-read DNA sequencing and short-read RNA sequencing provides the added value of using non-redundant technologies, which yield distinct, exploitable datasets.
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Affiliation(s)
- Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden.,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Sophie Tronnet
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden.,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden. .,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden. .,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden.
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9
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Ondari EM, Klemm EJ, Msefula CL, El Ghany MA, Heath JN, Pickard DJ, Barquist L, Dougan G, Kingsley RA, MacLennan CA. Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313. Wellcome Open Res 2019; 4:74. [PMID: 31231691 PMCID: PMC6560496 DOI: 10.12688/wellcomeopenres.15059.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2019] [Indexed: 11/20/2022] Open
Abstract
Background:
Salmonella Typhimurium ST313 exhibits signatures of adaptation to invasive human infection, including higher resistance to humoral immune responses than gastrointestinal isolates. Full resistance to antibody-mediated complement killing (serum resistance) among nontyphoidal
Salmonellae is uncommon, but selection of highly resistant strains could compromise vaccine-induced antibody immunity. Here, we address the hypothesis that serum resistance is due to a distinct genotype or transcriptome response in
S. Typhimurium ST313. Methods: Six
S. Typhimurium ST313 bloodstream isolates, three of which were antibody resistant, were studied. Genomic content (single nucleotide polymorphisms and larger chromosomal modifications) of the strains was determined by Illumina and PACBIO sequencing, and functionally characterized using RNA-seq, transposon directed insertion site sequencing (TraDIS), targeted gene deletion and transfer of selected point mutations in an attempt to identify features associated with serum resistance.
Results: Sequence polymorphisms in genes from strains with atypical serum susceptibility when transferred from strains that were highly resistant or susceptible to a strain that exhibited intermediate susceptibility did not significantly alter serum killing phenotype. No large chromosomal modifications typified serum resistance or susceptibility. Genes required for resistance to serum identified by TraDIS and RNA-seq included those involved in exopolysaccharide synthesis, iron scavenging and metabolism. Most of the down-regulated genes were associated with membrane proteins. Resistant and susceptible strains had distinct transcriptional responses to serum, particularly related to genes responsible for polysaccharide biosynthesis. There was higher upregulation of
wca locus genes, involved in the biosynthesis of colanic acid exopolysaccharide, in susceptible strains and increased expression of
fepE, a regulator of very long-chain lipopolysaccharide in resistant strains. Conclusion: Clinical isolates of
S. Typhimurium ST313 exhibit distinct antibody susceptibility phenotypes that may be associated with changes in gene expression on exposure to serum.
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Affiliation(s)
- Edna M Ondari
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Novartis Vaccines Institute for Global Health, Siena, Italy.,Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Chisomo L Msefula
- Wellcome Trust Sanger Institute, Hinxton, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Institute, Blantyre, Malawi.,Department of Microbiology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Moataz Abd El Ghany
- Wellcome Trust Sanger Institute, Hinxton, UK.,The Westmead Institute for Medical Research and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead, Australia.,King Abdullah University of Science and Technology , Thuwal, Saudi Arabia
| | - Jennifer N Heath
- Institute of Immunology and Immuotherapy, University of Birmingham, Birmingham, UK
| | | | - Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, UK.,Helmholtz Institute for RNA-based Infection Research , Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Medicine, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, UK
| | | | - Calman A MacLennan
- Institute of Immunology and Immuotherapy, University of Birmingham, Birmingham, UK.,Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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González-Flores YE, de Dios R, Reyes-Ramírez F, Santero E. The response of Sphingopyxis granuli strain TFA to the hostile anoxic condition. Sci Rep 2019; 9:6297. [PMID: 31000749 PMCID: PMC6472365 DOI: 10.1038/s41598-019-42768-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/05/2019] [Indexed: 01/02/2023] Open
Abstract
Sphingomonads comprises a group of interesting aerobic bacteria because of their ubiquity and metabolic capability of degrading many recalcitrant contaminants. The tetralin-degrader Sphingopyxis granuli strain TFA has been recently reported as able to anaerobically grow using nitrate as the alternative electron acceptor and so far is the only bacterium with this ability within the sphingomonads group. To understand how strain TFA thrives under anoxic conditions, a differential transcriptomic analysis while growing under aerobic or anoxic conditions was performed. This analysis has been validated and complemented with transcription kinetics of representative genes of different functional categories. Results show an extensive change of the expression pattern of this strain in the different conditions. Consistently, the most induced operon in anoxia codes for proteases, presumably required for extensive changes in the protein profile. Besides genes that respond to lack of oxygen in other bacteria, there are a number of genes that respond to stress or to damage of macromolecules, including genes of the SOS DNA-damage response, which suggest that anoxic conditions represent a hostile environment for this bacterium. Interestingly, growth under anoxic conditions also resulted in repression of all flagellar and type IV pilin genes, which suggested that this strain shaves its appendages off while growing in anaerobiosis.
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Affiliation(s)
- Yolanda Elisabet González-Flores
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Rubén de Dios
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Francisca Reyes-Ramírez
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain.
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
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11
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Abstract
ABSTRACT
Shigella
is a genus of Gram-negative enteropathogens that have long been, and continue to be, an important public health concern worldwide. Over the past several decades,
Shigella
spp. have also served as model pathogens in the study of bacterial pathogenesis, and
Shigella flexneri
has become one of the best-studied pathogens on a molecular, cellular, and tissue level. In the arms race between
Shigella
and the host immune system,
Shigella
has developed highly sophisticated mechanisms to subvert host cell processes in order to promote infection, escape immune detection, and prevent bacterial clearance. Here, we give an overview of
Shigella
pathogenesis while highlighting innovative techniques and methods whose application has significantly advanced our understanding of
Shigella
pathogenesis in recent years.
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12
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Silué N, Marcantonio E, Campbell-Valois FX. RNA-Seq analysis of the T3SA regulon in Shigella flexneri reveals two new chromosomal genes upregulated in the on-state. Methods 2019; 176:71-81. [PMID: 30905752 DOI: 10.1016/j.ymeth.2019.03.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/11/2019] [Accepted: 03/20/2019] [Indexed: 02/06/2023] Open
Abstract
Shigella spp. are enterobacteria that invade human colonic mucosal cells using their Type Three Secretion Apparatus (T3SA). Shigella spp. possess a large plasmid that encodes most of its virulence factors and has been the focus of seminal work that defined the T3SA regulon. Thus, a global assessment of the transcriptional response regulated by the T3SA has been lacking. Herein we used RNA-Seq to identify genes that are differentially expressed when the T3SA is active (on-state) versus inactive (off-state). The quality of the RNA-Seq dataset was validated by its correlation with a prior microarray study. Using novel insights about the expression of non-coding regions, bioinformatic tools and experimentations, we demonstrated the existence of six operons and evidence that ipaH2.5 is a pseudogene. In addition, 86 chromosomal genes were downregulated in the on-state including several non-coding transcripts corresponding to short antisense RNA embedded in the 16S and 23S RNA genes, and 40 coding transcripts, whose cognate proteins were highly connected at the genetic and biochemical levels. Finally, we identified two novel chromosomal genes dubbed gem1 and gem3, which were upregulated in the on-state similarly to genes belonging to the T3SA regulon. The latter findings were validated on biological triplicates by droplet digital PCR. To our knowledge gem1 and gem3 are the first chromosomal members of the T3SA regulon that have no homologs on the plasmid. Our approach provides a path to optimizing RNA-Seq studies in case of bacterial models that had previously been the subject of medium to large scale studies.
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Affiliation(s)
- Navoun Silué
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Endrei Marcantonio
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - F-X Campbell-Valois
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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13
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Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, Dordel J, Campbell JI, Lan NPH, Mayho M, Langridge GC, Hadfield J, Chau NVV, Thwaites GE, Parkhill J, Thomson NR, Holt KE, Baker S. Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microb Genom 2019; 5. [PMID: 30720421 PMCID: PMC6421349 DOI: 10.1099/mgen.0.000246] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The increasing incidence and emergence of multi-drug resistant (MDR) Acinetobacter baumannii has become a major global health concern. Colistin is a historic antimicrobial that has become commonly used as a treatment for MDR A. baumannii infections. The increase in colistin usage has been mirrored by an increase in colistin resistance. We aimed to identify the mechanisms associated with colistin resistance in A. baumannii using multiple high-throughput-sequencing technologies, including transposon-directed insertion site sequencing (TraDIS), RNA sequencing (RNAseq) and whole-genome sequencing (WGS) to investigate the genotypic changes of colistin resistance in A. baumannii. Using TraDIS, we found that genes involved in drug efflux (adeIJK), and phospholipid (mlaC, mlaF and mlaD) and lipooligosaccharide synthesis (lpxC and lpsO) were required for survival in sub-inhibitory concentrations of colistin. Transcriptomic (RNAseq) analysis revealed that expression of genes encoding efflux proteins (adeI, adeC, emrB, mexB and macAB) was enhanced in in vitro generated colistin-resistant strains. WGS of these organisms identified disruptions in genes involved in lipid A (lpxC) and phospholipid synthesis (mlaA), and in the baeS/R two-component system (TCS). We additionally found that mutations in the pmrB TCS genes were the primary colistin-resistance-associated mechanisms in three Vietnamese clinical colistin-resistant A. baumannii strains. Our results outline the entire range of mechanisms employed in A. baumannii for resistance against colistin, including drug extrusion and the loss of lipid A moieties by gene disruption or modification.
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Affiliation(s)
- Christine J Boinett
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Amy K Cain
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,4Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Jane Hawkey
- 5Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia.,6Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia.,7Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Nhu Tran Do Hoang
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhu Nguyen Thi Khanh
- 8School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Duy Pham Thanh
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Janina Dordel
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,9Department of Biology, Drexel University, Philadelphia 19104, PA, USA
| | - James I Campbell
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Nguyen Phu Huong Lan
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,10Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Matthew Mayho
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Gemma C Langridge
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,11Norwich Medical School, University of East Anglia, Norwich, UK
| | - James Hadfield
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - Guy E Thwaites
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Julian Parkhill
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nicholas R Thomson
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,12Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Kathryn E Holt
- 5Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia.,6Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Baker
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,13Medicine, The University of Cambridge, Cambridge, UK.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
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14
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out multiple functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters with small/redox-active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial reprogramming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances: Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high-resolution structural data. Although this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
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15
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Dorman MJ, Dorman CJ. Regulatory Hierarchies Controlling Virulence Gene Expression in Shigella flexneri and Vibrio cholerae. Front Microbiol 2018; 9:2686. [PMID: 30473684 PMCID: PMC6237886 DOI: 10.3389/fmicb.2018.02686] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/22/2018] [Indexed: 12/13/2022] Open
Abstract
Gram-negative enteropathogenic bacteria use a variety of strategies to cause disease in the human host and gene regulation in some form is typically a part of the strategy. This article will compare the toxin-based infection strategy used by the non-invasive pathogen Vibrio cholerae, the etiological agent in human cholera, with the invasive approach used by Shigella flexneri, the cause of bacillary dysentery. Despite the differences in the mechanisms by which the two pathogens cause disease, they use environmentally-responsive regulatory hierarchies to control the expression of genes that have some features, and even some components, in common. The involvement of AraC-like transcription factors, the integration host factor, the Factor for inversion stimulation, small regulatory RNAs, the RNA chaperone Hfq, horizontal gene transfer, variable DNA topology and the need to overcome the pervasive silencing of transcription by H-NS of horizontally acquired genes are all shared features. A comparison of the regulatory hierarchies in these two pathogens illustrates some striking cross-species similarities and differences among mechanisms coordinating virulence gene expression. S. flexneri, with its low infectious dose, appears to use a strategy that is centered on the individual bacterial cell, whereas V. cholerae, with a community-based, quorum-dependent approach and an infectious dose that is several orders of magnitude higher, seems to rely more on the actions of a bacterial collective.
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Affiliation(s)
- Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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16
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Horn N, Bhunia AK. Food-Associated Stress Primes Foodborne Pathogens for the Gastrointestinal Phase of Infection. Front Microbiol 2018; 9:1962. [PMID: 30190712 PMCID: PMC6115488 DOI: 10.3389/fmicb.2018.01962] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022] Open
Abstract
The incidence of foodborne outbreaks and product recalls is on the rise. The ability of the pathogen to adapt and survive under stressful environments of food processing and the host gastrointestinal tract may contribute to increasing foodborne illnesses. In the host, multiple factors such as bacteriolytic enzymes, acidic pH, bile, resident microflora, antimicrobial peptides, and innate and adaptive immune responses are essential in eliminating pathogens. Likewise, food processing and preservation techniques are employed to eliminate or reduce human pathogens load in food. However, sub-lethal processing or preservation treatments may evoke bacterial coping mechanisms that alter gene expression, specifically and broadly, resulting in resistance to the bactericidal insults. Furthermore, environmentally cued changes in gene expression can lead to changes in bacterial adhesion, colonization, invasion, and toxin production that contribute to pathogen virulence. The shared microenvironment between the food preservation techniques and the host gastrointestinal tract drives microbes to adapt to the stressful environment, resulting in enhanced virulence and infectivity during a foodborne illness episode.
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Affiliation(s)
- Nathan Horn
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
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17
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Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR. Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Sci Rep 2018; 8:9868. [PMID: 29959380 PMCID: PMC6026146 DOI: 10.1038/s41598-018-28199-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/08/2018] [Indexed: 11/09/2022] Open
Abstract
Colistin remains one of the few antibiotics effective against multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is rapidly increasing. Characterized mechanisms of colR in K. pneumoniae are largely due to chromosomal mutations in two-component regulators, although a plasmid-mediated colR mechanism has recently been uncovered. However, the effects of intrinsic colistin resistance are yet to be characterized on a whole-genome level. Here, we used a genomics-based approach to understand the mechanisms of adaptive colR acquisition in K. pneumoniae. In controlled directed-evolution experiments we observed two distinct paths to colistin resistance acquisition. Whole genome sequencing identified mutations in two colistin resistance genes: in the known colR regulator phoQ which became fixed in the population and resulted in a single amino acid change, and unstable minority variants in the recently described two-component sensor crrB. Through RNAseq and microscopy, we reveal the broad range of effects that colistin exposure has on the cell. This study is the first to use genomics to identify a population of minority variants with mutations in a colR gene in K. pneumoniae.
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Affiliation(s)
- Amy K Cain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Würzburg, D-97080, Germany
| | - Janina Dordel
- Department of Biology, Drexel University, Philadelphia, 19104, PA, USA
| | - Maria Fookes
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - David Goulding
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ryan R Wick
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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18
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out a wide range of functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters towards small/redox active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial re-programming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances. Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high resolution structural data. Though this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- School of Chemistry , University of East Anglia , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry , University plain , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
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19
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Arena ET, Tinevez JY, Nigro G, Sansonetti PJ, Marteyn BS. The infectious hypoxia: occurrence and causes during Shigella infection. Microbes Infect 2016; 19:157-165. [PMID: 27884799 DOI: 10.1016/j.micinf.2016.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 12/19/2022]
Abstract
Hypoxia is defined as a tissue oxygenation status below physiological needs. During Shigella infection, an infectious hypoxia is induced within foci of infection. In this review, we discuss how Shigella physiology and virulence are modulated and how the main recruited immune cells, the neutrophils, adapt to this environment.
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Affiliation(s)
- Ellen T Arena
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Citech, Imagopole, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Giulia Nigro
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Philippe J Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Collège de France, 11 Place Marcellin Berthelot, F-75231, Paris Cedex 05, France
| | - Benoit S Marteyn
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Gustave Roussy Cancer Campus, Laboratoire de Thérapie Cellulaire, 114 Rue Edouard Vaillant, 94800 Villejuif, France.
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20
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Faherty CS, Wu T, Morris CR, Grassel CL, Rasko DA, Harper JM, Shea-Donohue T, Fasano A, Barry EM. The synthesis of OspD3 (ShET2) in Shigella flexneri is independent of OspC1. Gut Microbes 2016; 7:486-502. [PMID: 27657187 PMCID: PMC5103656 DOI: 10.1080/19490976.2016.1239682] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shigella flexneri is a Gram-negative pathogen that invades the colonic epithelium and causes millions of cases of watery diarrhea or bacillary dysentery predominately in children under the age of 5 years in developing countries. The effector Shigella enterotoxin 2 (ShET2), or OspD3, is encoded by the sen or ospD3 gene on the virulence plasmid. Previous literature has suggested that ospD3 is in an operon downstream of the ospC1 gene, and expression of both genes is controlled by a promoter upstream of ospC1. Since the intergenic region is 328 bases in length and contains several putative promoter regions, we hypothesized the genes are independently expressed. Here we provide data that ospD3 and ospC1 are not co-transcribed and that OspC1 is not required for OspD3/ShET2 function. Most importantly, we identified strong promoter activity in the intergenic region and demonstrate that OspD3/ShET2 can be expressed and secreted independently of OspC1. This work increases our understanding of the synthesis of a unique virulence factor and provides further insights into Shigella pathogenesis.
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Affiliation(s)
- Christina S. Faherty
- Department of Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland,Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts,CONTACT Christina S. Faherty Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, 114 16th Street (114-3503), Charlestown, MA, 02129
| | - Tao Wu
- Department of Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
| | - Carolyn R. Morris
- Department of Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland,Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Christen L. Grassel
- Department of Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
| | - David A. Rasko
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Jill M. Harper
- Department of Medicine, Mucosal Biology Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Terez Shea-Donohue
- Department of Medicine, Mucosal Biology Research Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Alessio Fasano
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Eileen M. Barry
- Department of Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
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21
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Standish AJ, Teh MY, Tran ENH, Doyle MT, Baker PJ, Morona R. Unprecedented Abundance of Protein Tyrosine Phosphorylation Modulates Shigella flexneri Virulence. J Mol Biol 2016; 428:4197-4208. [PMID: 27380737 DOI: 10.1016/j.jmb.2016.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/06/2016] [Accepted: 06/23/2016] [Indexed: 01/09/2023]
Abstract
Evidence is accumulating that protein tyrosine phosphorylation plays a crucial role in the ability of important human bacterial pathogens to cause disease. While most works have concentrated on its role in the regulation of a major bacterial virulence factor, the polysaccharide capsule, recent studies have suggested a much broader role for this post-translational modification. This prompted us to investigate protein tyrosine phosphorylation in the human pathogen Shigella flexneri. We first completed a tyrosine phosphoproteome, identifying 905 unique tyrosine phosphorylation sites on at least 573 proteins (approximately 15% of all proteins). This is the most tyrosine-phosphorylated sites and proteins in a single bacterium identified to date, substantially more than the level seen in eukaryotic cells. Most had not previously been identified and included proteins encoded by the virulence plasmid, which is essential for S. flexneri to invade cells and cause disease. In order to investigate the function of these phosphorylation sites in important virulence factors, phosphomimetic and ablative mutations were constructed in the type 3 secretion system ATPase Spa47 and the master virulence regulator VirB. This revealed that tyrosine residues phosphorylated in our study are critical for Spa47 and VirB activity, and tyrosine phosphorylation likely regulates their functional activity and subsequently the virulence of this major human pathogen. This study suggests that tyrosine phosphorylation plays a critical role in regulating a wide variety of virulence factors in the human pathogen S. flexneri and serves as a base for future studies defining its complete role.
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Affiliation(s)
- Alistair James Standish
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Min Yan Teh
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth Ngoc Hoa Tran
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew Thomas Doyle
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul J Baker
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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Wallace N, Zani A, Abrams E, Sun Y. The Impact of Oxygen on Bacterial Enteric Pathogens. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:179-204. [PMID: 27261784 DOI: 10.1016/bs.aambs.2016.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacterial enteric pathogens are responsible for a tremendous amount of foodborne illnesses every year through the consumption of contaminated food products. During their transit from contaminated food sources to the host gastrointestinal tract, these pathogens are exposed and must adapt to fluctuating oxygen levels to successfully colonize the host and cause diseases. However, the majority of enteric infection research has been conducted under aerobic conditions. To raise awareness of the importance in understanding the impact of oxygen, or lack of oxygen, on enteric pathogenesis, we describe in this review the metabolic and physiological responses of nine bacterial enteric pathogens exposed to environments with different oxygen levels. We further discuss the effects of oxygen levels on virulence regulation to establish potential connections between metabolic adaptations and bacterial pathogenesis. While not providing an exhaustive list of all bacterial pathogens, we highlight key differences and similarities among nine facultative anaerobic and microaerobic pathogens in this review to argue for a more in-depth understanding of the diverse impact oxygen levels have on enteric pathogenesis.
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Affiliation(s)
- N Wallace
- University of Dayton, Dayton, OH, United States
| | - A Zani
- University of Dayton, Dayton, OH, United States
| | - E Abrams
- University of Dayton, Dayton, OH, United States
| | - Y Sun
- University of Dayton, Dayton, OH, United States
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