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Chen Z, Guan D, Wang Z, Li X, Dong S, Huang J, Zhou W. Microbiota in cancer: molecular mechanisms and therapeutic interventions. MedComm (Beijing) 2023; 4:e417. [PMID: 37937304 PMCID: PMC10626288 DOI: 10.1002/mco2.417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023] Open
Abstract
The diverse bacterial populations within the symbiotic microbiota play a pivotal role in both health and disease. Microbiota modulates critical aspects of tumor biology including cell proliferation, invasion, and metastasis. This regulation occurs through mechanisms like enhancing genomic damage, hindering gene repair, activating aberrant cell signaling pathways, influencing tumor cell metabolism, promoting revascularization, and remodeling the tumor immune microenvironment. These microbiota-mediated effects significantly impact overall survival and the recurrence of tumors after surgery by affecting the efficacy of chemoradiotherapy. Moreover, leveraging the microbiota for the development of biovectors, probiotics, prebiotics, and synbiotics, in addition to utilizing antibiotics, dietary adjustments, defensins, oncolytic virotherapy, and fecal microbiota transplantation, offers promising alternatives for cancer treatment. Nonetheless, due to the extensive and diverse nature of the microbiota, along with tumor heterogeneity, the molecular mechanisms underlying the role of microbiota in cancer remain a subject of intense debate. In this context, we refocus on various cancers, delving into the molecular signaling pathways associated with the microbiota and its derivatives, the reshaping of the tumor microenvironmental matrix, and the impact on tolerance to tumor treatments such as chemotherapy and radiotherapy. This exploration aims to shed light on novel perspectives and potential applications in the field.
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Affiliation(s)
- Zhou Chen
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Defeng Guan
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Zhengfeng Wang
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Xin Li
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
| | - Shi Dong
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
| | - Junjun Huang
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Wence Zhou
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
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2
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Verster KI, Cinege G, Lipinszki Z, Magyar LB, Kurucz É, Tarnopol RL, Ábrahám E, Darula Z, Karageorgi M, Tamsil JA, Akalu SM, Andó I, Whiteman NK. Evolution of insect innate immunity through domestication of bacterial toxins. Proc Natl Acad Sci U S A 2023; 120:e2218334120. [PMID: 37036995 PMCID: PMC10120054 DOI: 10.1073/pnas.2218334120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/01/2023] [Indexed: 04/12/2023] Open
Abstract
Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B (cdtB) and apoptosis-inducing protein of 56 kDa (aip56), were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular (cdtB) or fused copies (cdtB::aip56) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo's serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.
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Affiliation(s)
- Kirsten I. Verster
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Gyöngyi Cinege
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Lilla B. Magyar
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
- Doctoral School of Biology, University of Szeged, Szeged6720, Hungary
| | - Éva Kurucz
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Rebecca L. Tarnopol
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
| | - Edit Ábrahám
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Zsuzsanna Darula
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, Szeged6728, Hungary
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | | | - Josephine A. Tamsil
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Saron M. Akalu
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - István Andó
- Innate Immunity Group, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged6726, Hungary
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA94720
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3
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Feiss M, Young R, Ramsey J, Adhya S, Georgopoulos C, Hendrix RW, Hatfull GF, Gilcrease EB, Casjens SR. Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology. Microbiol Mol Biol Rev 2022; 86:e0012421. [PMID: 36165780 PMCID: PMC9799177 DOI: 10.1128/mmbr.00124-21] [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] [Indexed: 01/01/2023] Open
Abstract
Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.
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Affiliation(s)
- Michael Feiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ryland Young
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Jolene Ramsey
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, The National Cancer Institute, Bethesda, Maryland, USA
| | - Costa Georgopoulos
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Roger W. Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eddie B. Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Sherwood R. Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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4
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Fang Y, Yan C, Zhao Q, Xu J, Liu Z, Gao J, Zhu H, Dai Z, Wang D, Tang D. The roles of microbial products in the development of colorectal cancer: a review. Bioengineered 2021; 12:720-735. [PMID: 33618627 PMCID: PMC8806273 DOI: 10.1080/21655979.2021.1889109] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A large number of microbes exist in the gut and they have the ability to process and utilize ingested food. It has been reported that their products are involved in colorectal cancer development. The molecular mechanisms which underlie the relationship between gut microbial products and CRC are still not fully understood. The role of some microbial products in CRC is particularly controversial. Elucidating the effects of gut microbiota products on CRC and their possible mechanisms is vital for CRC prevention and treatment. In this review, recent studies are examined in order to describe the contribution metabolites and toxicants which are produced by gut microbes make to CRC, primarily focusing on the involved molecular mechanisms.Abbreviations: CRC: colorectal cancer; SCFAs: short chain fatty acids; HDAC: histone deacetylase; TCA cycle: tricarboxylic acid cycle; CoA: cytosolic acyl coenzyme A; SCAD: short chain acyl CoA dehydrogenase; HDAC: histone deacetylase; MiR-92a: microRNA-92a; KLF4: kruppel-like factor; PTEN: phosphatase and tensin homolog; PI3K: phosphoinositide 3-kinase; PIP2: phosphatidylinositol 4, 5-biphosphate; PIP3: phosphatidylinositol-3,4,5-triphosphate; Akt1: protein kinase B subtype α; ERK1/2: extracellular signal-regulated kinases 1/2; EMT: epithelial-to-mesenchymal transition; NEDD9: neural precursor cell expressed developmentally down-regulated9; CAS: Crk-associated substrate; JNK: c-Jun N-terminal kinase; PRMT1: protein arginine methyltransferase 1; UDCA: ursodeoxycholic acid; BA: bile acids; CA: cholic acid; CDCA: chenodeoxycholic acid; DCA: deoxycholic acid; LCA: lithocholic acid; CSCs: cancer stem cells; MHC: major histocompatibility; NF-κB: NF-kappaB; GPR: G protein-coupled receptors; ROS: reactive oxygen species; RNS: reactive nitrogen substances; BER: base excision repair; DNA: deoxyribonucleic acid; EGFR: epidermal growth factor receptor; MAPK: mitogen activated protein kinase; ERKs: extracellular signal regulated kinases; AKT: protein kinase B; PA: phosphatidic acid; TMAO: trimethylamine n-oxide; TMA: trimethylamine; FMO3: flavin-containing monooxygenase 3; H2S: Hydrogen sulfide; SRB: sulfate-reducing bacteria; IBDs: inflammatory bowel diseases; NSAID: non-steroidal anti-inflammatory drugs; BFT: fragile bacteroides toxin; ETBF: enterotoxigenic fragile bacteroides; E-cadherin: extracellular domain of intercellular adhesive protein; CEC: colonic epithelial cells; SMOX: spermine oxidase; SMO: smoothened; Stat3: signal transducer and activator of transcription 3; Th17: T helper cell 17; IL17: interleukin 17; AA: amino acid; TCF: transcription factor; CDT: cytolethal distending toxin; PD-L1: programmed cell death 1 ligand 1.
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Affiliation(s)
- Yongkun Fang
- Department of Clinical Medical College, Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Cheng Yan
- Department of Clinical Medical College, Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Qi Zhao
- Department of Clinical Medical College, Yangzhou University, Yangzhou, P.R. China
| | - Jiaming Xu
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Zhuangzhuang Liu
- Department of Clinical Medical College, Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Jin Gao
- Department of Clinical Medical College, Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Hanjian Zhu
- Department of Clinical Medical College, Yangzhou University, Yangzhou, P.R. China
| | - Zhujiang Dai
- Department of Clinical Medical College, Yangzhou University, Yangzhou, P.R. China
| | - Daorong Wang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
- CONTACT Dong TangDepartment of General Surgery, Institute of General Surgery, Northern Jiangsu People’s Hospital, Clinical Medical College, Yangzhou University, Yangzhou225001, China
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5
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Hinenoya A, Awasthi SP, Yasuda N, Nagano K, Hassan J, Takehira K, Hatanaka N, Saito S, Watabe T, Yoshizawa M, Inoue H, Yamasaki S. Detection, isolation and molecular characterization of Escherichia albertii in wild birds in West Japan. Jpn J Infect Dis 2021; 75:156-163. [PMID: 34470969 DOI: 10.7883/yoken.jjid.2021.355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Escherichia albertii is an emerging zoonotic foodborne pathogen. Several outbreaks of E. albertii have occurred particularly in Japan. Although birds have been considered as one of the most important reservoirs of this bacterium, information regarding the prevalence in birds is still scanty. We performed a survey of E. albertii in wild birds in Japan, and examined characteristics of the isolates. E. albertii specific gene was detected in 5 cloacal swabs out of 156 birds by PCR. Four E. albertii were isolated from a swallow with 2 different E. albertii strains and 2 pigeons in a flock by XRM-MacConkey agar. These isolates were assigned to biogroup 3, shown no resistance to any antimicrobials tested, and classified into 2 EAO-genotypes (EAOg2 and EAOg33) and untypable. Similar to clinical E. albertii strains, these isolates carried virulence genes including eae (n=4), paa (n=4), Eccdt-I (n=2) and stx2f (n=1) in addition to Eacdt. Interestingly, stx2f genes in a strain were located on an inducible bacteriophage, which can confer the ability to produce Stx2f to E. coli. In conclusion, Japanese wild birds carried E. albertii at the similar levels to the reported prevalence in birds. These isolates may have a potential to cause gastroenteritis in humans.
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Affiliation(s)
- Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Japan.,School of Life and Environmental Sciences, Osaka Prefecture University, Japan.,Asian Health Science Research Institute, Osaka Prefecture University, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Japan
| | - Sharda Prasad Awasthi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Japan.,Asian Health Science Research Institute, Osaka Prefecture University, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Japan
| | - Noritomo Yasuda
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Japan
| | - Keigo Nagano
- School of Life and Environmental Sciences, Osaka Prefecture University, Japan
| | - Jayedul Hassan
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Japan
| | - Keiji Takehira
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Japan
| | - Noritoshi Hatanaka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Japan.,School of Life and Environmental Sciences, Osaka Prefecture University, Japan.,Asian Health Science Research Institute, Osaka Prefecture University, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Japan
| | | | | | | | | | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Japan.,School of Life and Environmental Sciences, Osaka Prefecture University, Japan.,Asian Health Science Research Institute, Osaka Prefecture University, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Japan
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6
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Cytolethal distending toxin: from genotoxin to a potential biomarker and anti-tumor target. World J Microbiol Biotechnol 2021; 37:150. [PMID: 34379213 DOI: 10.1007/s11274-021-03117-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/31/2021] [Indexed: 10/20/2022]
Abstract
Cytolethal Distending Toxin (CDT) belongs to the AB toxin family and is produced by a plethora of Gram-negative bacteria. Eight human-affecting enteropathogens harbor CDT that causes irritable bowel syndrome (IBS), dysentery, chancroid, and periodontitis worldwide. They have a novel molecular mode of action as they interfere in the eukaryotic cell-cycle progression leading to G2/M arrest and apoptosis. CDT, the first bacterial genotoxin described, is encoded in a single operon possessing three proteins, CdtA, CdtB, and CdtC. CdtA and CdtC are needed for the binding of the CDT toxin complex to the cholesterol-rich lipid domains of the host cell while the CdtB is the active moiety. Sequence and 3D structural-based analysis of CdtB showed similarities with nucleases and phosphatases, it was hypothesized that CdtB exercises a biochemical function identical to both these enzymes. CDT is secreted through the outer membrane vesicles from the producing bacteria. It is internalized in the target cells via clathrin-dependent endocytosis and translocated to the host cell nucleus through the Golgi complex and ER. This study discusses the virulence role of CDT, causing pathogenicity by acting as a tri-perditious complex in the CDT-producing species with an emphasis on its potential role as a biomarker and an anti-tumor agent.
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7
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Smyshlyaev G, Bateman A, Barabas O. Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. Mol Syst Biol 2021; 17:e9880. [PMID: 34018328 PMCID: PMC8138268 DOI: 10.15252/msb.20209880] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence‐based classification system that dissects the characteristics of MGE‐borne YRs. We revealed that MGE‐related YRs evolved from non‐mobile YRs by acquisition of a regulatory arm‐binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination.
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Affiliation(s)
- Georgy Smyshlyaev
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Orsolya Barabas
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
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8
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Rodríguez-Rubio L, Haarmann N, Schwidder M, Muniesa M, Schmidt H. Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity. Pathogens 2021; 10:404. [PMID: 33805526 PMCID: PMC8065619 DOI: 10.3390/pathogens10040404] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded in the genome of lambdoid bacteriophages, which spend the most time of their life cycle integrated as prophages in specific sites of the bacterial chromosome. Upon spontaneous induction or induction by chemical or physical stimuli, the stx genes are co-transcribed together with the late phase genes of the prophages. After being assembled in the cytoplasm, and after host cell lysis, mature bacteriophage particles are released into the environment, together with Stx. As members of the group of lambdoid phages, Stx phages share many genetic features with the archetypical temperate phage Lambda, but are heterogeneous in their DNA sequences due to frequent recombination events. In addition to Stx phages, the genome of pathogenic STEC bacteria may contain numerous prophages, which are either cryptic or functional. These prophages may carry foreign genes, some of them related to virulence, besides those necessary for the phage life cycle. Since the production of one or more Stx is considered the major pathogenicity factor of STEC, we aim to highlight the new insights on the contribution of Stx phages and other STEC phages to pathogenicity.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Nadja Haarmann
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maike Schwidder
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
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9
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Liu X, Tang K, Zhang D, Li Y, Liu Z, Yao J, Wood TK, Wang X. Symbiosis of a P2‐family phage and deep‐sea
Shewanella putrefaciens. Environ Microbiol 2019; 21:4212-4232. [DOI: 10.1111/1462-2920.14781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Dali Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention Guangdong Provincial Institute of Public Health Guangzhou 511430 China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Thomas K. Wood
- Department of Chemical Engineering Pennsylvania State University University Park PA 16802‐4400 USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
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10
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Druzhinin VG, Matskova LV, Fucic A. Induction and modulation of genotoxicity by the bacteriome in mammals. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 776:70-77. [PMID: 29807578 DOI: 10.1016/j.mrrev.2018.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 02/07/2023]
Abstract
The living environment is a multilevel physical and chemical xenobiotic complex with potentially mutagenic effects and health risks. In addition to inorganic exposures, all terrestrial and aquatic living forms interact with microbiota as selectively established communities of bacteria, viruses and fungi. Along these lines, the human organism should then be considered a "meta-organism" with complex dynamics of interaction between the environment and microbiome. Bacterial communities within the microbiome, bacteriome, by its mass, symbiotic or competitive position and composition are in a fragile balance with the host organisms and have a crucial impact on their homeostasis. Bacteriome taxonomic composition is modulated by age, sex and host genetic profile and may be changed by adverse environmental exposures and life style factors such as diet or drug intake. A changed and/or misbalanced bacteriome has genotoxic potential with significant impact on the pathogenesis of acute, chronic and neoplastic diseases in the host organism. Bacteria may produce genotoxins, express a variety of pathways in which they generate free radicals or affect DNA repair causing genome damage, cell cycle arrest and apoptosis, modulate immune response and launch carcinogenesis in the host organism. Future investigations should focus on the interplay between exposure to xenobiotics and bacteriome composition, immunomodulation caused by misbalanced bacteriome, impact of the environment on bacteriome composition in children and its lifelong effect on health risks.
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Affiliation(s)
- V G Druzhinin
- Department of Genetics, Kemerovo State University, Kemerovo. Russia; Federal Research Center of Coal and Coal Chemistry of Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia
| | - L V Matskova
- Department of Microbiology and Tumor Biology, Karolinska Institute, Stockholm. Sweden
| | - A Fucic
- Institute for Medical Research and Occupational Health, Zagreb, Croatia.
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11
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Abstract
We report the whole-genome sequence of a new Escherichia coli temperate phage, Ayreon, comprising a linear double-stranded DNA (dsDNA) genome of 44,708 bp.
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12
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Javadi M, Oloomi M, Bouzari S. In Silico Signature Prediction Modeling in Cytolethal Distending Toxin-Producing Escherichia coli Strains. Genomics Inform 2017. [PMID: 28638312 PMCID: PMC5478710 DOI: 10.5808/gi.2017.15.2.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, cytolethal distending toxin (CDT) producer isolates genome were compared with genome of pathogenic and commensal Escherichia coli strains. Conserved genomic signatures among different types of CDT producer E. coli strains were assessed. It was shown that they could be used as biomarkers for research purposes and clinical diagnosis by polymerase chain reaction, or in vaccine development. cdt genes and several other genetic biomarkers were identified as signature sequences in CDT producer strains. The identified signatures include several individual phage proteins (holins, nucleases, and terminases, and transferases) and multiple members of different protein families (the lambda family, phage-integrase family, phage-tail tape protein family, putative membrane proteins, regulatory proteins, restriction-modification system proteins, tail fiber-assembly proteins, base plate-assembly proteins, and other prophage tail-related proteins). In this study, a sporadic phylogenic pattern was demonstrated in the CDT-producing strains. In conclusion, conserved signature proteins in a wide range of pathogenic bacterial strains can potentially be used in modern vaccine-design strategies.
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Affiliation(s)
- Maryam Javadi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran
| | - Mana Oloomi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran
| | - Saeid Bouzari
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran
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Scuron MD, Boesze-Battaglia K, Dlakić M, Shenker BJ. The Cytolethal Distending Toxin Contributes to Microbial Virulence and Disease Pathogenesis by Acting As a Tri-Perditious Toxin. Front Cell Infect Microbiol 2016; 6:168. [PMID: 27995094 PMCID: PMC5136569 DOI: 10.3389/fcimb.2016.00168] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022] Open
Abstract
This review summarizes the current status and recent advances in our understanding of the role that the cytolethal distending toxin (Cdt) plays as a virulence factor in promoting disease by toxin-producing pathogens. A major focus of this review is on the relationship between structure and function of the individual subunits that comprise the AB2 Cdt holotoxin. In particular, we concentrate on the molecular mechanisms that characterize this toxin and which account for the ability of Cdt to intoxicate multiple cell types by utilizing a ubiquitous binding partner on the cell membrane. Furthermore, we propose a paradigm shift for the molecular mode of action by which the active Cdt subunit, CdtB, is able to block a key signaling cascade and thereby lead to outcomes based upon programming and the role of the phosphatidylinositol 3-kinase (PI-3K) in a variety of cells. Based upon the collective Cdt literature, we now propose that Cdt is a unique and potent virulence factor capable of acting as a tri-perditious toxin that impairs host defenses by: (1) disrupting epithelial barriers; (2) suppressing acquired immunity; (3) promoting pro-inflammatory responses. Thus, Cdt plays a key role in facilitating the early stages of infection and the later stages of disease progression by contributing to persistence and impairing host elimination.
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Affiliation(s)
- Monika D Scuron
- Department of Pathology, School of Dental Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Kathleen Boesze-Battaglia
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Mensur Dlakić
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
| | - Bruce J Shenker
- Department of Pathology, School of Dental Medicine, University of Pennsylvania Philadelphia, PA, USA
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Taieb F, Petit C, Nougayrède JP, Oswald E. The Enterobacterial Genotoxins: Cytolethal Distending Toxin and Colibactin. EcoSal Plus 2016; 7. [PMID: 27419387 DOI: 10.1128/ecosalplus.esp-0008-2016] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 06/06/2023]
Abstract
While the DNA damage induced by ionizing radiation and by many chemical compounds and drugs is well characterized, the genotoxic insults inflicted by bacteria are only scarcely documented. However, accumulating evidence indicates that we are exposed to bacterial genotoxins. The prototypes of such bacterial genotoxins are the Cytolethal Distending Toxins (CDTs) produced by Escherichia coli and Salmonella enterica serovar Typhi. CDTs display the DNase structure fold and activity, and induce DNA strand breaks in the intoxicated host cell nuclei. E. coli and certain other Enterobacteriaceae species synthesize another genotoxin, colibactin. Colibactin is a secondary metabolite, a hybrid polyketide/nonribosomal peptide compound synthesized by a complex biosynthetic machinery. In this review, we summarize the current knowledge on CDT and colibactin produced by E. coli and/or Salmonella Typhi. We describe their prevalence, genetic determinants, modes of action, and impact in infectious diseases or gut colonization, and discuss the possible involvement of these genotoxigenic bacteria in cancer.
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Affiliation(s)
- Frederic Taieb
- Institut de Recherche en Santé Digestive (IRSD), INRA UMR1416, INSERM U1220, Université de Toulouse, CHU Purpan, Toulouse, FRANCE
| | - Claude Petit
- Institut de Recherche en Santé Digestive (IRSD), INRA UMR1416, INSERM U1220, Université de Toulouse, CHU Purpan, Toulouse, FRANCE
| | - Jean-Philippe Nougayrède
- Institut de Recherche en Santé Digestive (IRSD), INRA UMR1416, INSERM U1220, Université de Toulouse, CHU Purpan, Toulouse, FRANCE
| | - Eric Oswald
- Institut de Recherche en Santé Digestive (IRSD), INRA UMR1416, INSERM U1220, Université de Toulouse, CHU Purpan, Toulouse, FRANCE
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15
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Diverse Bacteriophage Roles in an Aphid-Bacterial Defensive Mutualism. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [DOI: 10.1007/978-3-319-28068-4_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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16
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Oloomi M, Javadi M, Bouzari S. Presence of pathogenicity island related and plasmid encoded virulence genes in cytolethal distending toxin producing Escherichia coli isolates from diarrheal cases. Int J Appl Basic Med Res 2015; 5:181-6. [PMID: 26539367 PMCID: PMC4606577 DOI: 10.4103/2229-516x.165366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Context: Mobile genetic elements such as plasmids, bacteriophages, insertion elements, and genomic islands play a critical role in virulence of bacterial pathogens. These elements transfer horizontally and could play an important role in the evolution and virulence of many pathogens. A broad spectrum of gram-negative bacterial species has been shown to produce a cytolethal distending toxin (CDT). On the other hand, Shiga toxin producing Escherichia coli are the one carry virulence genes such as stx 1 and stx 2 (Shiga toxin) and these genes can be acquired by horizontal gene transfer. Aim: The aim of this study was to investigate the presence of other virulence associated genes among CDT producing E. coli strains. Materials and Methods: Thirty CDT positive strains isolated from patients with diarrhea were characterized. Thereafter, the association with virulent genetic elements in known pathogenicity islands (PAIs) was assessed by polymerase chain reaction. Results: In this study, it was shown that the most CDT producing E. coli isolates express Shiga toxin. Moreover, the presence of prophages framing cdt genes (like P2 phage) was also identified in each cdt-type genomic group. Flanked regions of cdt-I, cdt-IV, and cdt-V-type was similar to plasmid sequences while cdt-II and cdt-III-type regions similarity with hypothetical protein (orf3) was observed. Conclusion: The occurrence of each cdt-type groups with specific virulence genes and PAI genetic elements is indicative of horizontal gene transfer by these mobile genetic elements, which could lead to diversity among the isolates.
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Affiliation(s)
- Mana Oloomi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran
| | - Maryam Javadi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran
| | - Saeid Bouzari
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran
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Bacterial Genotoxins: Merging the DNA Damage Response into Infection Biology. Biomolecules 2015; 5:1762-82. [PMID: 26270677 PMCID: PMC4598774 DOI: 10.3390/biom5031762] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 02/07/2023] Open
Abstract
Bacterial genotoxins are unique among bacterial toxins as their molecular target is DNA. The consequence of intoxication or infection is induction of DNA breaks that, if not properly repaired, results in irreversible cell cycle arrest (senescence) or death of the target cells. At present, only three bacterial genotoxins have been identified. Two are protein toxins: the cytolethal distending toxin (CDT) family produced by a number of Gram-negative bacteria and the typhoid toxin produced by Salmonella enterica serovar Typhi. The third member, colibactin, is a peptide-polyketide genotoxin, produced by strains belonging to the phylogenetic group B2 of Escherichia coli. This review will present the cellular effects of acute and chronic intoxication or infection with the genotoxins-producing bacteria. The carcinogenic properties and the role of these effectors in the context of the host-microbe interaction will be discussed. We will further highlight the open questions that remain to be solved regarding the biology of this unusual family of bacterial toxins.
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Abstract
Some of the most potent toxins produced by plants and bacteria are members of a large family known as the AB toxins. AB toxins are generally characterized by a heterogenous complex consisting of two protein chains arranged in various monomeric or polymeric configurations. The newest class within this superfamily is the cytolethal distending toxin (Cdt). The Cdt is represented by a subfamily of toxins produced by a group of taxonomically distinct Gram negative bacteria. Members of this subfamily have a related AB-type chain or subunit configuration and properties distinctive to the AB paradigm. In this review, the unique structural and cytotoxic properties of the Cdt subfamily, target cell specificities, intoxication pathway, modes of action, and relationship to the AB toxin superfamily are compared and contrasted.
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Martínez-Castillo A, Muniesa M. Implications of free Shiga toxin-converting bacteriophages occurring outside bacteria for the evolution and the detection of Shiga toxin-producing Escherichia coli. Front Cell Infect Microbiol 2014; 4:46. [PMID: 24795866 PMCID: PMC3997033 DOI: 10.3389/fcimb.2014.00046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/27/2014] [Indexed: 11/13/2022] Open
Abstract
In this review we highlight recent work that has increased our understanding of the distribution of Shiga toxin-converting phages that can be detected as free phage particles, independently of Shiga toxin-producing bacteria (STEC). Stx phages are a quite diverse group of temperate phages that can be found in their prophage state inserted within the STEC chromosome, but can also be found as phages released from the cell after activation of their lytic cycle. They have been detected in extraintestinal environments such as water polluted with feces from humans or animals, food samples or even in stool samples of healthy individuals. The high persistence of phages to several inactivation conditions makes them suitable candidates for the successful mobilization of stx genes, possibly resulting in the genes reaching a new bacterial genomic background by means of transduction, where ultimately they may be expressed, leading to Stx production. Besides the obvious fact that Stx phages circulating between bacteria can be, and probably are, involved in the emergence of new STEC strains, we review here other possible ways in which free Stx phages could interfere with the detection of STEC in a given sample by current laboratory methods and how to avoid such interference.
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Affiliation(s)
| | - Maite Muniesa
- Department of Microbiology, Faculty of Biology, University of BarcelonaBarcelona, Spain
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Evolution of a self-inducible cytolethal distending toxin type V-encoding bacteriophage from Escherichia coli O157:H7 to Shigella sonnei. J Virol 2013; 87:13665-75. [PMID: 24109226 DOI: 10.1128/jvi.02860-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some cdt genes are located within the genome of inducible or cryptic bacteriophages, but there is little information about the mechanisms of cdt transfer because of the reduced number of inducible Cdt phages described. In this study, a new self-inducible Myoviridae Cdt phage (ΦAA91) was isolated from a nonclinical O157:H7 Shiga toxin-producing Escherichia coli strain and was used to lysogenize a cdt-negative strain of Shigella sonnei. We found that the phage induced from S. sonnei (ΦAA91-ss) was not identical to the original phage. ΦAA91-ss was used to infect a collection of 57 bacterial strains, was infectious in 59.6% of the strains, and was able to lysogenize 22.8% of them. The complete sequence of ΦAA91-ss showed a 33,628-bp genome with characteristics of a P2-like phage with the cdt operon located near the cosR site. We found an IS21 element composed of two open reading frames inserted within the cox gene of the phage, causing gene truncation. Truncation of cox does not affect lytic induction but could contribute to phage recombination and generation of lysogens. The IS21 element was not present in the ΦAA91 phage from E. coli, but it was incorporated into the phage genome after its transduction in Shigella. This study shows empirically the evolution of temperate bacteriophages carrying virulence genes after infecting a new host and the generation of a phage population with better lysogenic abilities that would ultimately lead to the emergence of new pathogenic strains.
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21
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Sequence variability of P2-like prophage genomes carrying the cytolethal distending toxin V operon in Escherichia coli O157. Appl Environ Microbiol 2013; 79:4958-64. [PMID: 23770900 DOI: 10.1128/aem.01134-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytolethal distending toxins (CDT) are potent cytotoxins of several Gram-negative pathogenic bacteria, including Escherichia coli, in which five types (CDT-I to CDT-V) have been identified so far. CDT-V is frequently associated with Shiga-toxigenic E. coli (STEC), enterohemorrhagic E. coli (EHEC) O157 strains, and strains not fitting any established pathotypes. In this study, we were the first to sequence and annotate a 31.2-kb-long, noninducible P2-like prophage carrying the cdt-V operon from an stx- and eae-negative E. coli O157:H43 strain of bovine origin. The cdt-V operon is integrated in the place of the tin and old phage immunity genes (termed the TO region) of the prophage, and the prophage itself is integrated into the bacterial chromosome between the housekeeping genes cpxP and fieF. The presence of P2-like genes (n = 20) was investigated in a further five CDT-V-positive bovine E. coli O157 strains of various serotypes, three EHEC O157:NM strains, four strains expressing other variants of CDT, and eight CDT-negative strains. All but one CDT-V-positive atypical O157 strain uniformly carried all the investigated genomic regions of P2-like phages, while the EHEC O157 strains missed three regions and the CDT-V-negative strains carried only a few P2-like sequences. Our results suggest that P2-like phages play a role in the dissemination of cdt-V between E. coli O157 strains and that after integration into the bacterial chromosome, they adapted to the respective hosts and became temperate.
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22
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Kwon HJ, Seong WJ, Kim JH. Molecular prophage typing of avian pathogenic Escherichia coli. Vet Microbiol 2013; 162:785-792. [DOI: 10.1016/j.vetmic.2012.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 10/03/2012] [Accepted: 10/06/2012] [Indexed: 11/28/2022]
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23
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Roberts GA, Stephanou AS, Kanwar N, Dawson A, Cooper LP, Chen K, Nutley M, Cooper A, Blakely GW, Dryden DTF. Exploring the DNA mimicry of the Ocr protein of phage T7. Nucleic Acids Res 2012; 40:8129-43. [PMID: 22684506 PMCID: PMC3439906 DOI: 10.1093/nar/gks516] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 11/30/2022] Open
Abstract
DNA mimic proteins have evolved to control DNA-binding proteins by competing with the target DNA for binding to the protein. The Ocr protein of bacteriophage T7 is the most studied DNA mimic and functions to block the DNA-binding groove of Type I DNA restriction/modification enzymes. This binding prevents the enzyme from cleaving invading phage DNA. Each 116 amino acid monomer of the Ocr dimer has an unusual amino acid composition with 34 negatively charged side chains but only 6 positively charged side chains. Extensive mutagenesis of the charges of Ocr revealed a regression of Ocr activity from wild-type activity to partial activity then to variants inactive in antirestriction but deleterious for cell viability and lastly to totally inactive variants with no deleterious effect on cell viability. Throughout the mutagenesis the Ocr mutant proteins retained their folding. Our results show that the extreme bias in charged amino acids is not necessary for antirestriction activity but that less charged variants can affect cell viability by leading to restriction proficient but modification deficient cell phenotypes.
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Affiliation(s)
- Gareth A. Roberts
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Augoustinos S. Stephanou
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Nisha Kanwar
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Angela Dawson
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Laurie P. Cooper
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Kai Chen
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Margaret Nutley
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Alan Cooper
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Garry W. Blakely
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - David T. F. Dryden
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
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Allué-Guardia A, Jofre J, Muniesa M. Stability and infectivity of cytolethal distending toxin type V gene-carrying bacteriophages in a water mesocosm and under different inactivation conditions. Appl Environ Microbiol 2012; 78:5818-23. [PMID: 22685154 PMCID: PMC3406162 DOI: 10.1128/aem.00997-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/01/2012] [Indexed: 11/20/2022] Open
Abstract
Two cytolethal distending toxin (Cdt) type V-encoding bacteriophages (Φ62 and Φ125) were induced spontaneously from their wild-type Escherichia coli strains and from the lysogens generated in Shigella sonnei. The stability of Cdt phages was determined at various temperatures and pH values after 1 month of storage by means of infectivity tests using a plaque blot assay and analysis of phage genomes using real-time quantitative PCR (qPCR): both were highly stable. We assessed the inactivation of Cdt phages by thermal treatment, chlorination, UV radiation, and in a mesocosm in both summer and winter. The results for the two Cdt phages showed similar trends and were also similar to the phage SOM23 used for reference, but they showed a much higher persistence than Cdt-producing E. coli. Cdt phages showed maximal inactivation after 1 h at 70°C, 30 min of UV radiation, and 30 min of contact with a 10-ppm chlorine treatment. Inactivation in a mesocosm was higher in summer than in winter, probably because of solar radiation. The treatments reduced the number of infectious phages but did not have a significant effect on the Cdt phage particles detected by qPCR. Cdt phages were quantified by qPCR in 73% of river samples, and these results suggest that Cdt phages are a genetic vehicle and the natural reservoir for cdt in the environment.
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25
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Martínez-Castillo A, Allué-Guardia A, Dahbi G, Blanco J, Creuzburg K, Schmidt H, Muniesa M. Type III effector genes and other virulence factors of Shiga toxin-encoding Escherichia coli isolated from wastewater. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:147-155. [PMID: 23757242 DOI: 10.1111/j.1758-2229.2011.00317.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pathogenic Shiga toxin-producing Escherichia coli (STEC) strains share the genes encoding Shiga toxins (stx) and many other virulence factors. The classification and evolutionary studies of pathogenic E. coli based on their virulence genes have been conducted with E. coli isolated from human and animal infections or outbreaks. In this study, we used 103 STEC strains isolated from faecally polluted water environments to analyse 23 virulence genes (stx1 , cdt, hlyA, saa, eae, three type III effector genes encoded within the locus of enterocyte effacement (LEE) and 15 non-LEE-encoded type III effector genes). Despite the presence of several stx2 variants, our isolates demonstrated low prevalence of the virulence genes (only 46.6% of the strains were positive for virulence determinants). Among these, the largest repertoire was found in a few O157:H7 isolates (most from cattle wastewater and one from sewage), while other serotypes showed fewer virulence determinants. The occurrence of most virulence genes seemed to be independent from one another. This was clear for hlyA (the most prevalent), cdt and cif (the least prevalent). Other effector genes, could be found or not in combination with others, suggesting that they can be mobilized independently. Our data suggest that E. coli strains can evolve separately by independently acquiring mobile genetic elements.
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Affiliation(s)
- Alexandre Martínez-Castillo
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain. Laboratorio de Referencia de E. coli (LREC), Department of Microbiology and Parasitology, Faculty of Veterinary Science, University of Santiago de Compostela, 27002 Lugo, Spain. Institute of Food Science and Biotechnology, Department of Food Microbiology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany
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Molecular characterizations of cytolethal distending toxin produced by Providencia alcalifaciens strains isolated from patients with diarrhea. Infect Immun 2012; 80:1323-32. [PMID: 22252871 DOI: 10.1128/iai.05831-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytolethal distending toxins (CDTs), which block eukaryotic cell proliferation by acting as inhibitory cyclomodulins, are produced by diverse groups of Gram-negative bacteria. Active CDT is composed of three polypeptides--CdtA, CdtB, and CdtC--encoded by the genes cdtA, cdtB, and cdtC, respectively. We developed a PCR-restriction fragment length polymorphism assay for the detection and differentiation of five alleles of cdtB (Cdt-I through Cdt-V) in Escherichia coli and used the assay to investigate the prevalence and characteristic of CDT-producing E. coli in children with diarrhea (A. Hinenoya et al., Microbiol. Immunol. 53:206-215, 2009). In these assays, two untypable cdtB genes were detected and the organisms harboring the cdtB gene were identified as Providencia alcalifaciens (strains AH-31 and AS-1). Nucleotide sequence analysis of the cdt gene cluster revealed that the cdtA, cdtB, and cdtC genes of P. alcalifaciens are of 750, 810, and 549 bp, respectively. To understand the possible horizontal transfer of the cdt genes among closely related species, the presence of cdt genes was screened in various Providencia spp. by colony hybridization assay, and the cdt gene cluster was found in only limited strains of P. alcalifaciens. Genome walking revealed that the cdt gene cluster of P. alcalifaciens is located adjacent to a putative transposase gene, suggesting the locus might be horizontally transferable. Interestingly, the CDT of P. alcalifaciens (PaCDT) showed some homology with the CDT of Shigella boydii. Whereas filter-sterilized lysates of strains AH-31 and AS-1 showed distention of CHO but not of HeLa cells, E. coli CDT-I exhibited distention of both cells. This activity of PaCDT was confirmed by generating recombinant PaCDT protein, which could also be neutralized by rabbit anti-PaCdtB antibody. Furthermore, recombinant PaCDT was found to induce G(2)/M cell cycle arrest and phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks. To our knowledge, this is the first report showing that certain clinical P. alcalifaciens strains could produce variants of the CDTs compared.
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Abstract
The role of bacteriophages as natural vectors for some of the most potent bacterial toxins is well recognized and includes classical type I membrane-acting superantigens, type II pore-forming lysins, and type III exotoxins, such as diphtheria and botulinum toxins. Among Gram-negative pathogens, a novel class of bacterial virulence factors called effector proteins (EPs) are phage encoded among pathovars of Escherichia coli, Shigella spp., and Salmonella enterica. This chapter gives an overview of the different types of virulence factors encoded within phage genomes based on their role in bacterial pathogenesis. It also discusses phage-pathogenicity island interactions uncovered from studies of phage-encoded EPs. A detailed examination of the filamentous phage CTXφ that encodes cholera toxin is given as the sole example to date of a single-stranded DNA phage that encodes a bacterial toxin.
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28
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Bacteriophage-encoding cytolethal distending toxin type V gene induced from nonclinical Escherichia coli isolates. Infect Immun 2011; 79:3262-72. [PMID: 21646456 DOI: 10.1128/iai.05071-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytolethal distending toxin (Cdt) is produced by a variety of pathogenic bacteria, including pathogenic serotypes of Shiga toxin-producing Escherichia coli (STEC). The Cdt family comprises five variants (Cdt-I to Cdt-V) encoded by three genes located within the chromosome or plasmids or, in the case of Cdt-I, within bacteriophages. In this study, we evaluated the occurrence of the cdt gene in a collection of 140 environmental STEC isolates. cdt was detected in 12.1% of strains, of which five strains carried inducible bacteriophages containing the Cdt-V variant. Two Cdt-V phages of the Siphoviridae morphology lysogenized Shigella sonnei, generating two lysogens: a single Cdt phage lysogen and a double lysogen, containing a Cdt phage and an Stx phage, both from the wild-type strain. The rates of induction of Cdt phages were evaluated by quantitative PCR, and spontaneous induction of Cdt-V phage was observed, whereas induction of Stx phage in the double lysogen was mitomycin C dependent. The Cdt distending effect was observed in HeLa cells inoculated with the supernatant of the Cdt-V phage lysogen. A ClaI fragment containing the cdt-V gene of one phage was cloned, and sequencing confirmed the presence of Cdt-V, as well as a fragment downstream from the cdt homolog to gpA, encoding a replication protein of bacteriophage P2. Evaluation of Cdt-V phages in nonclinical water samples showed densities of 10(2) to 10(9) gene copies in 100 ml, suggesting the high prevalence of Cdt phages in nonclinical environments.
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Jinadasa RN, Bloom SE, Weiss RS, Duhamel GE. Cytolethal distending toxin: a conserved bacterial genotoxin that blocks cell cycle progression, leading to apoptosis of a broad range of mammalian cell lineages. MICROBIOLOGY-SGM 2011; 157:1851-1875. [PMID: 21565933 DOI: 10.1099/mic.0.049536-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytolethal distending toxin (CDT) is a heterotrimeric AB-type genotoxin produced by several clinically important Gram-negative mucocutaneous bacterial pathogens. Irrespective of the bacterial species of origin, CDT causes characteristic and irreversible cell cycle arrest and apoptosis in a broad range of cultured mammalian cell lineages. The active subunit CdtB has structural homology with the phosphodiesterase family of enzymes including mammalian DNase I, and alone is necessary and sufficient to account for cellular toxicity. Indeed, mammalian cells treated with CDT initiate a DNA damage response similar to that elicited by ionizing radiation-induced DNA double strand breaks resulting in cell cycle arrest and apoptosis. The mechanism of CDT-induced apoptosis remains incompletely understood, but appears to involve both p53-dependent and -independent pathways. While epithelial, endothelial and fibroblast cell lines respond to CDT by undergoing arrest of cell cycle progression resulting in nuclear and cytoplasmic distension that precedes apoptotic cell death, cells of haematopoietic origin display rapid apoptosis following a brief period of cell cycle arrest. In this review, the ecology of pathogens producing CDT, the molecular biology of bacterial CDT and the molecular mechanisms of CDT-induced cytotoxicity are critically appraised. Understanding the contribution of a broadly conserved bacterial genotoxin that blocks progression of the mammalian cell cycle, ultimately causing cell death, should assist with elucidating disease mechanisms for these important pathogens.
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Affiliation(s)
- Rasika N Jinadasa
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Stephen E Bloom
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Gerald E Duhamel
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
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Oliver KM, Degnan PH, Burke GR, Moran NA. Facultative symbionts in aphids and the horizontal transfer of ecologically important traits. ANNUAL REVIEW OF ENTOMOLOGY 2010; 55:247-66. [PMID: 19728837 DOI: 10.1146/annurev-ento-112408-085305] [Citation(s) in RCA: 578] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aphids engage in symbiotic associations with a diverse assemblage of heritable bacteria. In addition to their obligate nutrient-provisioning symbiont, Buchnera aphidicola, aphids may also carry one or more facultative symbionts. Unlike obligate symbionts, facultative symbionts are not generally required for survival or reproduction and can invade novel hosts, based on both phylogenetic analyses and transfection experiments. Facultative symbionts are mutualistic in the context of various ecological interactions. Experiments on pea aphids (Acyrthosiphon pisum) have demonstrated that facultative symbionts protect against entomopathogenic fungi and parasitoid wasps, ameliorate the detrimental effects of heat, and influence host plant suitability. The protective symbiont, Hamiltonella defensa, has a dynamic genome, exhibiting evidence of recombination, phage-mediated gene uptake, and horizontal gene transfer and containing virulence and toxin-encoding genes. Although transmitted maternally with high fidelity, facultative symbionts occasionally move horizontally within and between species, resulting in the instantaneous acquisition of ecologically important traits, such as parasitoid defense.
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Affiliation(s)
- Kerry M Oliver
- Department of Entomology, University of Georgia, Athens, GA 30602, USA.
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Sun Q, Kuty GF, Arockiasamy A, Xu M, Young R, Sacchettini JC. Regulation of a muralytic enzyme by dynamic membrane topology. Nat Struct Mol Biol 2009; 16:1192-4. [PMID: 19881499 PMCID: PMC3075974 DOI: 10.1038/nsmb.1681] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 08/26/2009] [Indexed: 11/09/2022]
Abstract
R(21), the lysozyme of coliphage 21, has an N-terminal signal-anchor-release (SAR) domain that directs its secretion in a membrane-tethered, inactive form and then its release and activation in the periplasm. Both genetic and crystallographic studies show that the SAR domain, once extracted from the bilayer, refolds into the body of the enzyme and effects muralytic activation by repositioning one residue of the canonical lysozyme catalytic triad.
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Affiliation(s)
- Qingan Sun
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128
| | - Gabriel F. Kuty
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128
| | - Arulandu Arockiasamy
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Min Xu
- Department of Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128
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Samba-Louaka A, Taieb F, Nougayrède JP, Oswald E. Cif type III effector protein: a smart hijacker of the host cell cycle. Future Microbiol 2009; 4:867-77. [PMID: 19722840 DOI: 10.2217/fmb.09.60] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During coevolution with their hosts, bacteria have developed functions that allow them to interfere with the mechanisms controlling the proliferation of eukaryotic cells. Cycle inhibiting factor (Cif) is one of these cyclomodulins, the family of bacterial effectors that interfere with the host cell cycle. Acquired early during evolution by bacteria isolated from vertebrates and invertebrates, Cif is an effector protein of type III secretion machineries. Cif blocks the host cell cycle in G1 and G2 by inducing the accumulation of the cyclin-dependent kinase inhibitors p21(waf1/cip1) and p27(kip1). The x-ray crystal structure of Cif reveals it to be a divergent member of a superfamily of enzymes including cysteine proteases and acetyltransferases. This review summarizes and discusses what we know about Cif, from the bacterial gene to the host target.
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Søreide K. Bacterial genotoxins, gene methylation, and RNA interference: pointing to colorectal cancer as an infectious disease? Scand J Gastroenterol 2009; 43:1529-33. [PMID: 18654935 DOI: 10.1080/00365520802272134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kjetil Søreide
- Department of Surgery, Stavanger University Hospital, Stavanger, Norway.
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Hinenoya A, Naigita A, Ninomiya K, Asakura M, Shima K, Seto K, Tsukamoto T, Ramamurthy T, Faruque SM, Yamasaki S. Prevalence and characteristics of cytolethal distending toxin-producing Escherichia coli from children with diarrhea in Japan. Microbiol Immunol 2009; 53:206-15. [DOI: 10.1111/j.1348-0421.2009.00116.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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de Mello Varani A, Souza RC, Nakaya HI, de Lima WC, Paula de Almeida LG, Kitajima EW, Chen J, Civerolo E, Vasconcelos ATR, Van Sluys MA. Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PLoS One 2008; 3:e4059. [PMID: 19116666 PMCID: PMC2605562 DOI: 10.1371/journal.pone.0004059] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 11/07/2008] [Indexed: 11/19/2022] Open
Abstract
Xylella fastidiosa is a Gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced X. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. To better evaluate the recent evolution of the X. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and Temecula1), and in two candidate molecules (Ann1 and Dixon) were assessed. Based on comparative best bidirectional hit analyses, the majority (51%) of the predicted genes in the X. fastidiosa prophage-like regions are related to structural phage genes belonging to the Siphoviridae family. Electron micrograph reveals the existence of putative viral particles with similar morphology to lambda phages in the bacterial cell in planta. Moreover, analysis of microarray data indicates that 9a5c strain cultivated under stress conditions presents enhanced expression of phage anti-repressor genes, suggesting switches from lysogenic to lytic cycle of phages under stress-induced situations. Furthermore, virulence-associated proteins and toxins are found within these prophage-like elements, thus suggesting an important role in host adaptation. Finally, clustering analyses of phage integrase genes based on multiple alignment patterns reveal they group in five lineages, all possessing a tyrosine recombinase catalytic domain, and phylogenetically close to other integrases found in phages that are genetic mosaics and able to perform generalized and specialized transduction. Integration sites and tRNA association is also evidenced. In summary, we present comparative and experimental evidence supporting the association and contribution of phage activity on the differentiation of Xylella genomes.
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Affiliation(s)
- Alessandro de Mello Varani
- Genome and Transposable Elements Laboratory (GaTE Lab), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Rangel Celso Souza
- Laboratório de Bioinformática (LABINFO), Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Helder I. Nakaya
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Wanessa Cristina de Lima
- Genome and Transposable Elements Laboratory (GaTE Lab), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Luiz Gonzaga Paula de Almeida
- Laboratório de Bioinformática (LABINFO), Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Elliot Watanabe Kitajima
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Jianchi Chen
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Edwin Civerolo
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Ana Tereza Ribeiro Vasconcelos
- Laboratório de Bioinformática (LABINFO), Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Marie-Anne Van Sluys
- Genome and Transposable Elements Laboratory (GaTE Lab), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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Cytolethal distending toxin type I and type IV genes are framed with lambdoid prophage genes in extraintestinal pathogenic Escherichia coli. Infect Immun 2008; 77:492-500. [PMID: 18981247 DOI: 10.1128/iai.00962-08] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five types of cytolethal distending toxin (CDT-I to CDT-V) have been identified in Escherichia coli. In the present study we cloned and sequenced the cdt-IV operon and flanking region from a porcine extraintestinal pathogenic E. coli (ExPEC) strain belonging to serogroup O75. We confirmed that similar to other CDTs, CDT-IV induced phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks, and blocked the HeLa cell cycle at the G(2)-M transition. The cdt-IV genes were framed by lambdoid prophage genes. We cloned and sequenced the cdt-I operon and flanking regions from a human ExPEC O18:K1:H7 strain and observed that cdt-I genes were also flanked by lambdoid prophage genes. PCR studies indicated that a gene coding for a putative protease was always associated with the cdtC-IV gene but was not associated with cdtC genes in strains producing CDT-I, CDT-III, and CDT-V. Our results suggest that the cdt-I and cdt-IV genes might have been acquired from a common ancestor by phage transduction and evolved in their bacterial hosts. The lysogenic bacteriophages have the potential to carry nonessential "cargo" genes or "morons" and therefore play a crucial role in the generation of genetic diversity within ExPEC.
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Abstract
The lysogenic bacteriophage APSE infects "Candidatus Hamiltonella defensa," a facultative endosymbiont of aphids and other sap-feeding insects. This endosymbiont has established a beneficial association with aphids, increasing survivorship following attack by parasitoid wasps. Although APSE and "Ca. Hamiltonella defensa" are effectively maternally transmitted between aphid generations, they can also be horizontally transferred among insect hosts, which results in genetically distinct "Ca. Hamiltonella defensa" strains infecting the same aphid species and sporadic distributions of both APSE and "Ca. Hamiltonella defensa" among hosts. Aphids infected only with "Ca. Hamiltonella defensa" have significantly less protection than those infected with both "Ca. Hamiltonella defensa" and APSE. This protection has been proposed to be connected to eukaryote-targeted toxins previously discovered in the genomes of two characterized APSE strains. In this study, we have sequenced partial genomes from seven additional APSE strains to address the evolution and extent of toxin variation in this phage. The APSE lysis region has been a hot spot for nonhomologous recombination of novel virulence cassettes. We identified four new toxins from three protein families, Shiga-like toxin, cytolethal distending toxin, and YD-repeat toxins. These recombination events have also resulted in reassortment of the downstream lysozyme and holin genes. Analysis of the conserved APSE genes flanking the variable toxin cassettes reveals a close phylogenetic association with phage sequences from two other facultative endosymbionts of insects. Thus, phage may act as a conduit for ongoing gene exchange among heritable endosymbionts.
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Ge Z, Schauer DB, Fox JG. In vivo virulence properties of bacterial cytolethal-distending toxin. Cell Microbiol 2008; 10:1599-607. [PMID: 18489725 DOI: 10.1111/j.1462-5822.2008.01173.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple pathogenic Gram-negative bacteria produce cytolethal-distending toxins (CDTs). CDT is typically composed of three subunits: the catalytic subunit CdtB has DNase I-like activity, whereas CdtA and CdtC are binding proteins for delivering CdtB into target cells. Translocation of CdtB to the nucleus induces genotoxic effects on host DNA, triggering DNA repair cascades that lead to cell cycle arrest and eventual cell death. Several lines of evidence indicate that this toxin contributes to the pathogenicity of CDT-producing bacteria in vivo. Helicobacter hepaticus and Campylobacter jejuni CDTs are essential for persistent infection of the gastrointestinal tract and increase the severity of mucosal inflammation or liver disease in susceptible mouse strains. Haemophilus ducreyi CDT may contribute to the pathogenesis of chancroid in rabbits. Recently, H. hepaticus CDT has been shown to play a crucial role in promoting the progression of infectious hepatitis to pre-malignant, dysplastic lesions via activation of a pro-inflammatory NF-kappaB pathway and increased proliferation of hepatocytes, providing the first evidence that CDT has carcinogenic potential in vivo. Thus, both in vitro and in vivo data indicate that CDT is a bacterial virulence factor.
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Affiliation(s)
- Zhongming Ge
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Regulation of expression and secretion of NleH, a new non-locus of enterocyte effacement-encoded effector in Citrobacter rodentium. J Bacteriol 2008; 190:2388-99. [PMID: 18223087 DOI: 10.1128/jb.01602-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Together with enterohemorrhagic Escherichia coli and enteropathogenic Escherichia coli, Citrobacter rodentium is a member of the attaching-and-effacing (A/E) family of bacterial pathogens. A/E pathogens use a type III secretion system (T3SS) to translocate an assortment of effector proteins, encoded both within and outside the locus of enterocyte effacement (LEE), into the colonized host cell, leading to the formation of A/E lesions and disease. Here we report the identification and characterization of a new non-LEE encoded effector, NleH, in C. rodentium. NleH is conserved among A/E pathogens and shares identity with OspG, a type III secreted effector protein in Shigella flexneri. Downstream of nleH, genes encoding homologues of the non-LEE-encoded effectors EspJ and NleG/NleI are found. NleH secretion and translocation into Caco-2 cells requires a functional T3SS and signals located at its amino-terminal domain. Transcription of nleH is not significantly reduced in mutants lacking the LEE-encoded regulators Ler and GrlA; however, NleH protein levels are highly reduced in these strains, as well as in escN and cesT mutants. Inactivation of Lon, but not of ClpP, protease restores NleH levels even in the absence of CesT. Our results indicate that the efficient engagement of NleH in active secretion is needed for its stability, thus establishing a posttranslational regulatory mechanism that coregulates NleH levels with the expression of LEE-encoded proteins. A C. rodentium nleH mutant shows a moderate defect during the colonization of C57BL/6 mice at early stages of infection.
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