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Hao H, Ren N, Han J, Foley SL, Iqbal Z, Cheng G, Kuang X, Liu J, Liu Z, Dai M, Wang Y, Yuan Z. Virulence and Genomic Feature of Multidrug Resistant Campylobacter jejuni Isolated from Broiler Chicken. Front Microbiol 2016; 7:1605. [PMID: 27790202 PMCID: PMC5064177 DOI: 10.3389/fmicb.2016.01605] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022] Open
Abstract
The aim of this study was to reveal the molecular mechanism involved in multidrug resistance and virulence of Campylobacter jejuni isolated from broiler chickens. The virulence of six multidrug resistant C. jejuni was determined by in vitro and in vivo methods. The de novo whole genome sequencing technology and molecular biology methods were used to analyze the genomic features associated with the multidrug resistance and virulence of a selected isolate (C. jejuni 1655). The comparative genomic analyses revealed a large number of single nucleotide polymorphisms, deletions, rearrangements, and inversions in C. jejuni 1655 compared to reference C. jejuni genomes. The co-emergence of Thr-86-Ile mutation in gyrA gene, A2075G mutation in 23S rRNA gene, tetO, aphA and aadE genes and pTet plasmid in C. jejuni 1655 contributed its multidrug resistance to fluoroquinolones, macrolides, tetracycline, and aminoglycosides. The combination of multiple virulence genes may work together to confer the relative higher virulence in C. jejuni 1655. The co-existence of mobile gene elements (e.g., pTet) and CRISPR-Cas system in C. jejuni 1655 may play an important role in the gene transfer and immune defense. The present study provides basic information of phenotypic and genomic features of C. jejuni 1655, a strain recently isolated from a chicken displaying multidrug resistance and relatively high level of virulence.
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Affiliation(s)
- Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug ResiduesWuhan, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry ProductsWuhan, China; Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Huazhong Agricultural UniversityWuhan, China
| | - Ni Ren
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry ProductsWuhan, China; Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Huazhong Agricultural UniversityWuhan, China
| | - Jing Han
- Division of Microbiology, FDA, National Center for Toxicological Research Jefferson, AR, USA
| | - Steven L Foley
- Division of Microbiology, FDA, National Center for Toxicological Research Jefferson, AR, USA
| | - Zahid Iqbal
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products Wuhan, China
| | - Guyue Cheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues Wuhan, China
| | - Xiuhua Kuang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products Wuhan, China
| | - Jie Liu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products Wuhan, China
| | - Zhenli Liu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products Wuhan, China
| | - Menghong Dai
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products Wuhan, China
| | - Yulian Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues Wuhan, China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug ResiduesWuhan, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry ProductsWuhan, China; Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Huazhong Agricultural UniversityWuhan, China
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52
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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53
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Bertelli C, Cissé OH, Rusconi B, Kebbi-Beghdadi C, Croxatto A, Goesmann A, Collyn F, Greub G. CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium. Genome Biol Evol 2016; 8:2376-86. [PMID: 27516530 PMCID: PMC5010888 DOI: 10.1093/gbe/evw138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,285 bp megaplasmid. For the first time within the Chlamydiales order, we describe the presence of a clustered regularly interspaced short palindromic repeats (CRISPR) system, the immune system of bacteria, located on the chromosome. It is composed of a small CRISPR locus comprising eight repeats and associated cas-cse genes of the subtype I-E. A CRISPR locus is also present within Chlamydia sp. Diamant, another Pr. naegleriophila strain, suggesting that the CRISPR system was acquired by a common ancestor of Pr. naegleriophila, after its divergence from Pr. amoebophila. Both nucleotide bias and comparative genomics approaches identified probable horizontal gene acquisitions within two and four genomic islands in Pr. naegleriophila KNic and Diamant genomes, respectively. The plasmid encodes an F-type conjugative system highly similar to 1) that found in the Pam100G genomic island of Pr. amoebophila UWE25 chromosome, as well as on the plasmid of Rubidus massiliensis and 2) to the three genes remaining in the chromosome of Parachlamydia acanthamoebae strains. Therefore, this conjugative system was likely acquired on an ancestral plasmid before the divergence of Parachlamydiaceae Overall, this new complete Pr. naegleriophila genome sequence enables further investigation of the dynamic processes shaping the genomes of the family Parachlamydiaceae and the genus Protochlamydia.
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ousmane H Cissé
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Brigida Rusconi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Antony Croxatto
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Germany
| | - François Collyn
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
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54
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Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 2016; 353:aad5147. [PMID: 27493190 DOI: 10.1126/science.aad5147] [Citation(s) in RCA: 402] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adaptive immunity had been long thought of as an exclusive feature of animals. However, the discovery of the CRISPR-Cas defense system, present in almost half of prokaryotic genomes, proves otherwise. Because of the everlasting parasite-host arms race, CRISPR-Cas has rapidly evolved through horizontal transfer of complete loci or individual modules, resulting in extreme structural and functional diversity. CRISPR-Cas systems are divided into two distinct classes that each consist of three types and multiple subtypes. We discuss recent advances in CRISPR-Cas research that reveal elaborate molecular mechanisms and provide for a plausible scenario of CRISPR-Cas evolution. We also briefly describe the latest developments of a wide range of CRISPR-based applications.
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Affiliation(s)
- Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Bernd Zetsche
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands.
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55
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Castillo D, Christiansen RH, Dalsgaard I, Madsen L, Espejo R, Middelboe M. Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum. PLoS One 2016; 11:e0152515. [PMID: 27071075 PMCID: PMC4829187 DOI: 10.1371/journal.pone.0152515] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/15/2016] [Indexed: 11/18/2022] Open
Abstract
Flavobacterium psychrophilum is a fish pathogen in salmonid aquaculture worldwide that causes cold water disease (CWD) and rainbow trout fry syndrome (RTFS). Comparative genome analyses of 11 F. psychrophilum isolates representing temporally and geographically distant populations were used to describe the F. psychrophilum pan-genome and to examine virulence factors, prophages, CRISPR arrays, and genomic islands present in the genomes. Analysis of the genomic DNA sequences were complemented with selected phenotypic characteristics of the strains. The pan genome analysis showed that F. psychrophilum could hold at least 3373 genes, while the core genome contained 1743 genes. On average, 67 new genes were detected for every new genome added to the analysis, indicating that F. psychrophilum possesses an open pan genome. The putative virulence factors were equally distributed among isolates, independent of geographic location, year of isolation and source of isolates. Only one prophage-related sequence was found which corresponded to the previously described prophage 6H, and appeared in 5 out of 11 isolates. CRISPR array analysis revealed two different loci with dissimilar spacer content, which only matched one sequence in the database, the temperate bacteriophage 6H. Genomic Islands (GIs) were identified in F. psychrophilum isolates 950106-1/1 and CSF 259–93, associated with toxins and antibiotic resistance. Finally, phenotypic characterization revealed a high degree of similarity among the strains with respect to biofilm formation and secretion of extracellular enzymes. Global scale dispersion of virulence factors in the genomes and the abilities for biofilm formation, hemolytic activity and secretion of extracellular enzymes among the strains suggested that F. psychrophilum isolates have a similar mode of action on adhesion, colonization and destruction of fish tissues across large spatial and temporal scales of occurrence. Overall, the genomic characterization and phenotypic properties may provide new insights to the mechanisms of pathogenicity in F. psychrophilum.
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Affiliation(s)
- Daniel Castillo
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Rói Hammershaimb Christiansen
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Inger Dalsgaard
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Lone Madsen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Romilio Espejo
- Centro Nacional de Genómica y Bioinformática and Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Macul, Santiago, Chile
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
- * E-mail:
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56
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Scalfaro C, Iacobino A, Grande L, Morabito S, Franciosa G. Effects of Megaplasmid Loss on Growth of Neurotoxigenic Clostridium butyricum Strains and Botulinum Neurotoxin Type E Expression. Front Microbiol 2016; 7:217. [PMID: 26941734 PMCID: PMC4766289 DOI: 10.3389/fmicb.2016.00217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/10/2016] [Indexed: 11/13/2022] Open
Abstract
Clostridium butyricum strains that atypically produce the botulinum neurotoxin type E (BoNT/E) possess a megaplasmid of unknown functions in their genome. In this study, we cured two botulinum neurotoxigenic C. butyricum type E strains of their megaplasmids, and compared the obtained megaplasmid-cured strains to their respective wild-type parental strains. Our results showed that the megaplasmids do not confer beta-lactam resistance on the neurotoxigenic C. butyricum type E strains, although they carry several putative beta-lactamase genes. Instead, we found that the megaplasmids are essential for growth of the neurotoxigenic C. butyricum type E strains at the relatively low temperature of 15°C, and are also relevant for growth of strains under limiting pH and salinity conditions, as well as under favorable environmental conditions. Moreover, the presence of the megaplasmids was associated with increased transcript levels of the gene encoding BoNT/E in the C. butyricum type E strains, indicating that the megaplasmids likely contain transcriptional regulators. However, the levels of BoNT/E in the supernatants of the cured and uncured strains were similar after 24 and 48 h culture, suggesting that expression of BoNT/E in the C. butyricum type E strains is not ultimately controlled by the megaplasmids. Together, our results reveal that the C. butyricum type E megaplasmids exert pleiotropic effects on the growth of their microbial hosts under optimal and limiting environmental conditions, and also highlight the possibility of original regulatory mechanisms controlling the expression of BoNT/E.
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Affiliation(s)
- Concetta Scalfaro
- Unit of Foodborne Zoonoses, Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità Rome, Italy
| | - Angelo Iacobino
- Unit of Foodborne Zoonoses, Department of Food Safety and Veterinary Public Health, Istituto Superiore di SanitàRome, Italy; Unit of Systemic Bacterial Infections, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di SanitàRome, Italy
| | - Laura Grande
- Unit of Foodborne Zoonoses, Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità Rome, Italy
| | - Stefano Morabito
- Unit of Foodborne Zoonoses, Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità Rome, Italy
| | - Giovanna Franciosa
- Unit of Foodborne Zoonoses, Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità Rome, Italy
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57
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van Belkum A, Soriaga LB, LaFave MC, Akella S, Veyrieras JB, Barbu EM, Shortridge D, Blanc B, Hannum G, Zambardi G, Miller K, Enright MC, Mugnier N, Brami D, Schicklin S, Felderman M, Schwartz AS, Richardson TH, Peterson TC, Hubby B, Cady KC. Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa. mBio 2015; 6:e01796-15. [PMID: 26604259 PMCID: PMC4669384 DOI: 10.1128/mbio.01796-15] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates. IMPORTANCE P. aeruginosa is both an antibiotic-refractory pathogen and an important model system for type I CRISPR-Cas bacterial immune systems. By combining the genome sequences of 672 newly and previously sequenced genomes, we were able to provide a global view of the phylogenetic distribution, conservation, and potential targets of these systems. This analysis identified a new and putatively mobile P. aeruginosa CRISPR-Cas subtype, characterized the diverse distribution of known CRISPR-inhibiting genes, and provided a potential new use for CRISPR spacer libraries in accessory genome analysis. Our data demonstrated the importance of CRISPR-Cas systems in modulating the accessory genomes of globally distributed strains while also providing substantial data for subsequent genomic and experimental studies in multiple fields. Understanding why certain genotypes of P. aeruginosa are clinically prevalent and adept at horizontally acquiring virulence and antibiotic resistance elements is of major clinical and economic importance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Mark C Enright
- Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Daniel Brami
- Synthetic Genomics, Inc., La Jolla, California, USA
| | | | | | | | | | | | - Bolyn Hubby
- Synthetic Genomics, Inc., La Jolla, California, USA
| | - Kyle C Cady
- Synthetic Genomics, Inc., La Jolla, California, USA
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58
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An updated evolutionary classification of CRISPR-Cas systems. NATURE REVIEWS. MICROBIOLOGY 2015. [PMID: 26411297 DOI: 10.1038/nrmicro3569.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
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59
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Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJM, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 2015; 13:722-36. [PMID: 26411297 DOI: 10.1038/nrmicro3569] [Citation(s) in RCA: 1565] [Impact Index Per Article: 173.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Omer S Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Fabrizio Costa
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Shiraz A Shah
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Sita J Saunders
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27606, USA
| | - Stan J J Brouns
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703HB Wageningen, Netherlands
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Philippe Horvath
- DuPont Nutrition and Health, BP10, Dangé-Saint-Romain 86220, France
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Francisco J M Mojica
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante. 03080-Alicante, Spain
| | - Rebecca M Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, Georgia 30602, USA
| | - Michael P Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, Georgia 30602, USA
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, M5S 3E5, Canada
| | - Roger A Garrett
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703HB Wageningen, Netherlands
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany.,BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, Germany
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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60
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Gasparini R, Panatto D, Bragazzi NL, Lai PL, Bechini A, Levi M, Durando P, Amicizia D. How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines. J Immunol Res 2015; 2015:189153. [PMID: 26351643 PMCID: PMC4553322 DOI: 10.1155/2015/189153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/09/2015] [Indexed: 01/17/2023] Open
Abstract
In the last decades, tremendous advancement in dissecting the mechanisms of pathogenicity of Neisseria meningitidis at a molecular level has been achieved, exploiting converging approaches of different disciplines, ranging from pathology to microbiology, immunology, and omics sciences (such as genomics and proteomics). Here, we review the molecular biology of the infectious agent and, in particular, its interactions with the immune system, focusing on both the innate and the adaptive responses. Meningococci exploit different mechanisms and complex machineries in order to subvert the immune system and to avoid being killed. Capsular polysaccharide and lipooligosaccharide glycan composition, in particular, play a major role in circumventing immune response. The understanding of these mechanisms has opened new horizons in the field of vaccinology. Nowadays different licensed meningococcal vaccines are available and used: conjugate meningococcal C vaccines, tetravalent conjugate vaccines, an affordable conjugate vaccine against the N. menigitidis serogroup A, and universal vaccines based on multiple antigens each one with a different and peculiar function against meningococcal group B strains.
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Affiliation(s)
- R. Gasparini
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Panatto
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - N. L. Bragazzi
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - P. L. Lai
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - A. Bechini
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - M. Levi
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - P. Durando
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Amicizia
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
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61
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Tu Z, Yang W, Yan S, Guo X, Li XJ. CRISPR/Cas9: a powerful genetic engineering tool for establishing large animal models of neurodegenerative diseases. Mol Neurodegener 2015; 10:35. [PMID: 26238861 PMCID: PMC4524001 DOI: 10.1186/s13024-015-0031-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/24/2015] [Indexed: 02/07/2023] Open
Abstract
Animal models are extremely valuable to help us understand the pathogenesis of neurodegenerative disorders and to find treatments for them. Since large animals are more like humans than rodents, they make good models to identify the important pathological events that may be seen in humans but not in small animals; large animals are also very important for validating effective treatments or confirming therapeutic targets. Due to the lack of embryonic stem cell lines from large animals, it has been difficult to use traditional gene targeting technology to establish large animal models of neurodegenerative diseases. Recently, CRISPR/Cas9 was used successfully to genetically modify genomes in various species. Here we discuss the use of CRISPR/Cas9 technology to establish large animal models that can more faithfully mimic human neurodegenerative diseases.
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Affiliation(s)
- Zhuchi Tu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weili Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sen Yan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiangyu Guo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiao-Jiang Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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62
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Fiebig A, Loof TG, Babbar A, Itzek A, Koehorst JJ, Schaap PJ, Nitsche-Schmitz DP. Comparative genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice. Int J Med Microbiol 2015; 305:532-43. [PMID: 26129624 DOI: 10.1016/j.ijmm.2015.06.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 06/15/2015] [Accepted: 06/19/2015] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pyogenes serotype M1 is a frequent cause of severe infections in humans. Some M1 isolates are pathogenic in mice and used in studies on infection pathogenesis. We observed marked differences in murine infections caused by M1 strain SF370, 5448, 5448AP or AP1 which prompted us to sequence the whole genome of isolates 5448 and AP1 for comparative analysis. Strain 5448 is known to acquire inactivating mutations in the CovRS two-component system during mouse infection, producing hypervirulent progeny such as 5448AP. Isolates AP1 and 5448AP, more than 5448, caused disseminating infections that became systemic and lethal. SF370 was not pathogenic. Phages caused gross genetic differences and increased the gene content of AP1 by 8% as compared to 5448 and SF370. Each of six examined M1 genomes contained two CRISPR-Cas systems. Phage insertion destroyed a type II CRISPR-Cas system in AP1 and other strains of serotypes M1, M3, M6 and M24, but not in M1 strains 5448, SF370, MGAS5005, A20 or M1 476. A resulting impaired defence against invading genetic elements could have led to the wealth of phages in AP1. AP1 lacks genetic features of the MGAS5005-like clonal complex including the streptodornase that drives selection for hypervirulent clones with inactivated CovRS system. Still, inactivating mutations in covS were a common genetic feature of AP1 and the MGAS5005-like isolate 5448AP. Abolished expression of the cysteine proteinase SpeB, due to CovRS inactivation could be a common cause for hypervirulence of the two isolates. Moreover, an additional protein H-coding gene and a mutation in the regulator gene rofA distinguished AP1 form other M1 isolates. In conclusion, hypervirulence of S. pyogenes M1 in mice is not limited to the MGAS5005-like genotype.
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Affiliation(s)
- Anne Fiebig
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Torsten G Loof
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anshu Babbar
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Itzek
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research Centre, Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research Centre, Wageningen, the Netherlands
| | - D Patric Nitsche-Schmitz
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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63
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Abstract
ABSTRACT
Horizontal gene transfer drives the evolution of bacterial genomes, including the adaptation to changing environmental conditions. Exogenous DNA can enter a bacterial cell through transformation (free DNA or plasmids) or through the transfer of mobile genetic elements by conjugation (plasmids) and transduction (bacteriophages). Favorable genes can be acquired, but undesirable traits can also be inadvertently acquired through these processes. Bacteria have systems, such as clustered regularly interspaced short palindromic repeat CRISPR–associated genes (CRISPR-Cas), that can cleave foreign nucleic acid molecules. In this review, we discuss recent advances in understanding CRISPR-Cas system activity against mobile genetic element transfer through transformation and conjugation. We also highlight how CRISPR-Cas systems influence bacterial evolution and how CRISPR-Cas components affect plasmid replication.
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64
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Alegría Á, Delgado S, Guadamuro L, Flórez AB, Felis GE, Torriani S, Mayo B. The genome of Bifidobacterium pseudocatenulatum IPLA 36007, a human intestinal strain with isoflavone-activation activity. Gut Pathog 2014; 6:31. [PMID: 25097668 PMCID: PMC4121622 DOI: 10.1186/1757-4749-6-31] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 07/16/2014] [Indexed: 12/31/2022] Open
Abstract
Background Bifidobacterium species, including Bifidobacterium pseudocatenulatum, are among the dominant microbial populations of the human gastrointestinal tract. They are also major components of many commercial probiotic products. Resident and transient bifidobacteria are thought to have several beneficial health effects. However, our knowledge of how these bacteria interact and communicate with host cells remains poor. This knowledge is essential for scientific support of their purported health benefits and their rational inclusion in functional foods. Results This work describes the draft genome sequence of Bifidobacterium pseudocatenulatum IPLA 36007, a strain isolated as dominant from the feces of a healthy human. Besides several properties of probiosis, IPLA 36007 exhibited the capability of releasing aglycones from soy isoflavone glycosides. The genome contains 1,851 predicted genes, including 54 genes for tRNAs and fie copies of unique 16S, 23S and 5S rRNA genes. As key attributes of the IPLA 36007 genome we can mention the presence of a lysogenic phage, a cluster encoding type IV fimbriae, and a locus encoding a clustered, regularly interspaced, short, palindromic repeat (CRISPR)-Cas system. Four open reading frames (orfs) encoding β-glucosidases belonging to the glycosyl hydrolase family 3, which may act on isoflavone glycosides, were encountered. Additionally, one gene was found to code for a glycosyl hydrolase of family 1 that might also have β-glucosidase activity. Conclusion The availability of the B. pseudocatenulatum IPLA 36007 genome should allow the enzyme system involved in the release of soy isoflavone aglycones from isoflavone glycosides, and the molecular mechanisms underlying the strain’s probiotic properties, to be more easily understood.
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Affiliation(s)
- Ángel Alegría
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300 Villaviciosa, Asturias, Spain
| | - Susana Delgado
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300 Villaviciosa, Asturias, Spain
| | - Lucía Guadamuro
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300 Villaviciosa, Asturias, Spain
| | - Ana Belén Flórez
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300 Villaviciosa, Asturias, Spain
| | - Giovanna E Felis
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie, 15, 37134 Verona, Italy
| | - Sandra Torriani
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie, 15, 37134 Verona, Italy
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300 Villaviciosa, Asturias, Spain
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65
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Mosier AC, Li Z, Thomas BC, Hettich RL, Pan C, Banfield JF. Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME JOURNAL 2014; 9:180-94. [PMID: 25050524 DOI: 10.1038/ismej.2014.113] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/01/2014] [Accepted: 06/03/2014] [Indexed: 01/08/2023]
Abstract
Microbial communities that underpin global biogeochemical cycles will likely be influenced by elevated temperature associated with environmental change. Here, we test an approach to measure how elevated temperature impacts the physiology of individual microbial groups in a community context, using a model microbial-based ecosystem. The study is the first application of tandem mass tag (TMT)-based proteomics to a microbial community. We accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 °C. Elevated temperature led to upregulation of proteins involved in amino-acid metabolism at the level of individual organisms and the entire community. Proteins from related organisms differed in their relative abundance and functional responses to temperature. Elevated temperature repressed carbon fixation proteins from two Leptospirillum genotypes, whereas carbon fixation proteins were significantly upregulated at higher temperature by a third member of this genus. Leptospirillum group III bacteria may have been subject to viral stress at elevated temperature, which could lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, these findings highlight the utility of proteomics-enabled community-based physiology studies, and provide a methodological framework for possible extension to additional mixed culture and environmental sample analyses.
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Affiliation(s)
- Annika C Mosier
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Zhou Li
- 1] Oak Ridge National Laboratory, Oak Ridge, TN, USA [2] Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Knoxville, TN, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | - Chongle Pan
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jillian F Banfield
- 1] Department of Earth and Planetary Science, University of California, Berkeley, CA, USA [2] Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
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