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Lipopolysaccharide of the Yersinia pseudotuberculosis Complex. Biomolecules 2021; 11:biom11101410. [PMID: 34680043 PMCID: PMC8533242 DOI: 10.3390/biom11101410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
Lipopolysaccharide (LPS), localized in the outer leaflet of the outer membrane, serves as the major surface component of the Gram-negative bacterial cell envelope responsible for the activation of the host's innate immune system. Variations of the LPS structure utilized by Gram-negative bacteria promote survival by providing resistance to components of the innate immune system and preventing recognition by TLR4. This review summarizes studies of the biosynthesis of Yersinia pseudotuberculosis complex LPSs, and the roles of their structural components in molecular mechanisms of yersiniae pathogenesis and immunogenesis.
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Steinum TM, Turgay E, Yardımcı RE, Småge SB, Karataş S. Tenacibaculum maritimum CRISPR loci analysis and evaluation of isolate spoligotyping. J Appl Microbiol 2021; 131:1848-1857. [PMID: 33905598 DOI: 10.1111/jam.15116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 11/27/2022]
Abstract
AIMS We performed in silico analysis of CRISPRcas loci from Tenacibaculum maritimum, evaluated spoligotyping as a subtyping method and genotyped uncharacterized Turkish isolates from European sea bass by multilocus sequence typing (MLST). METHODS AND RESULTS Spoligotyping was performed with primers designed to allow amplification and sequencing of whole CRISPR-arrays from 23 T. maritimum isolates. Twenty-three completed/draft genomes were also downloaded from the NCBI database and analysed. MLST of Turkish isolates was achieved with a well-established 7-gene scheme. Tenacibaculum maritimum genomes carry a structurally complete but partially defective class II CRISPRcas locus due to known amino acid substitutions in encoded Cas9 proteins. Our spacer identification suggests that the host range of bacteriophage P2559Y and Vibrio phage nt-1 include T. maritimum and that the most recurrent infection recorded by isolates has been with Tenacibaculum phage PTm5. Thirty-eight isolates with this CRISPRcas locus belonged to 25 spoligotypes and to 24 sequence types by MLST, respectively. According to MLST, T. maritimum isolates from Turkey are most related to previously defined sequence types ST3, ST40 and ST41 isolates from Spain, Malta and France. CONCLUSIONS The evaluated spoligotyping offers discriminatory power comparable to MLST. SIGNIFICANCE AND IMPACT OF THE STUDY Spoligotyping has potential as a quick, easy and cheap tool for subtyping of T. maritimum isolates.
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Affiliation(s)
- T M Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - E Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | - R E Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | | | - S Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
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Genomic analysis and immune response in a murine mastitis model of vB_EcoM-UFV13, a potential biocontrol agent for use in dairy cows. Sci Rep 2018; 8:6845. [PMID: 29717158 PMCID: PMC5931544 DOI: 10.1038/s41598-018-24896-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/11/2018] [Indexed: 02/02/2023] Open
Abstract
Bovine mastitis remains the main cause of economic losses for dairy farmers. Mammary pathogenic Escherichia coli (MPEC) is related to an acute mastitis and its treatment is still based on the use of antibiotics. In the era of antimicrobial resistance (AMR), bacterial viruses (bacteriophages) present as an efficient treatment or prophylactic option. However, this makes it essential that its genetic structure, stability and interaction with the host immune system be thoroughly characterized. The present study analyzed a novel, broad host-range anti-mastitis agent, the T4virus vB_EcoM-UFV13 in genomic terms, and its activity against a MPEC strain in an experimental E. coli-induced mastitis mouse model. 4,975 Single Nucleotide Polymorphisms (SNPs) were assigned between vB_EcoM-UFV13 and E. coli phage T4 genomes with high impact on coding sequences (CDS) (37.60%) for virion proteins. Phylogenetic trees and genome analysis supported a recent infection mix between vB_EcoM-UFV13 and Shigella phage Shfl2. After a viral stability evaluation (e.g pH and temperature), intramammary administration (MOI 10) resulted in a 10-fold reduction in bacterial load. Furthermore, pro-inflammatory cytokines, such as IL-6 and TNF-α, were observed after viral treatment. This work brings the whole characterization and immune response to vB_EcoM-UFV13, a biocontrol candidate for bovine mastitis.
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Mikoulinskaia GV, Chernyshov SV, Shavrina MS, Molochkov NV, Lysanskaya VY, Zimin AA. Two novel thermally resistant endolysins encoded by pseudo T-even bacteriophages RB43 and RB49. J Gen Virol 2018; 99:402-415. [DOI: 10.1099/jgv.0.001014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Galina V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry RAS, Pushchino, Moscow region 142290, Russia
| | - Sergei V. Chernyshov
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry RAS, Pushchino, Moscow region 142290, Russia
| | - Maria S. Shavrina
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry RAS, Pushchino, Moscow region 142290, Russia
| | - Nikolai V. Molochkov
- Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow region 142290, Russia
| | - Valentina Ya. Lysanskaya
- Skryabin’s Institute of Biochemistry and Physiology of Micro-organisms RAS, Pushchino, Moscow region 142290, Russia
| | - Andrei A. Zimin
- Skryabin’s Institute of Biochemistry and Physiology of Micro-organisms RAS, Pushchino, Moscow region 142290, Russia
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Abstract
Tailed bacteriophages with genomes larger than 200 kbp are classified as Jumbo phages, and are rarely isolated by conventional methods. These phages are designated “jumbo” owing to their most notable features of a large phage virion and large genome size. However, in addition to these, jumbo phages also exhibit several novel characteristics that have not been observed for phages with smaller genomes, which differentiate jumbo phages in terms of genome organization, virion structure, progeny propagation, and evolution. In this review, we summarize available reports on jumbo phages and discuss the differences between jumbo phages and small-genome phages. We also discuss data suggesting that jumbo phages might have evolved from phages with smaller genomes by acquiring additional functional genes, and that these additional genes reduce the dependence of the jumbo phages on the host bacteria.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
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Lal TM, Sano M, Hatai K, Ransangan J. Complete genome sequence of a giant Vibrio phage ValKK3 infecting Vibrio alginolyticus. GENOMICS DATA 2016; 8:37-8. [PMID: 27114905 PMCID: PMC4832046 DOI: 10.1016/j.gdata.2016.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/08/2016] [Indexed: 11/11/2022]
Abstract
This paper describes the complete sequence of a giant lytic marine myophage, Vibrio phage ValKK3 that is specific to Vibrio alginolyticus ATCC® 17749™. Vibrio phage ValKK3 was subjected to whole genome sequencing on MiSeq sequencing platform and annotated using Blast2Go. The complete sequence of ValKK3 genome was deposited in DBBJ/EMBL/GenBank under accession number KP671755.
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Affiliation(s)
- Tamrin M Lal
- Microbiology and Fish Disease Laboratory, Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Motohiko Sano
- Laboratory of Fish Pathology, Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Room 223, Building No. 2 2F, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan
| | - Kishio Hatai
- Microbiology and Fish Disease Laboratory, Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Julian Ransangan
- Microbiology and Fish Disease Laboratory, Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
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Abstract
Bacteriophage play many varied roles in microbial ecology and evolution. This chapter collates a vast body of knowledge and expertise on Yersinia pestis phages, including the history of their isolation and classical methods for their isolation and identification. The genomic diversity of Y. pestis phage and bacteriophage islands in the Y. pestis genome are also discussed because all phage research represents a branch of genetics. In addition, our knowledge of the receptors that are recognized by Y. pestis phage, advances in phage therapy for Y. pestis infections, the application of phage in the detection of Y. pestis, and clustered regularly interspaced short palindromic repeats (CRISPRs) sequences of Y. pestis from prophage DNA are all reviewed here.
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Puxty RJ, Perez-Sepulveda B, Rihtman B, Evans DJ, Millard AD, Scanlan DJ. Spontaneous Deletion of an "ORFanage" Region Facilitates Host Adaptation in a "Photosynthetic" Cyanophage. PLoS One 2015; 10:e0132642. [PMID: 26177354 PMCID: PMC4503421 DOI: 10.1371/journal.pone.0132642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/16/2015] [Indexed: 01/29/2023] Open
Abstract
Viruses have been suggested to be the largest source of genetic diversity on Earth. Genome sequencing and metagenomic surveys reveal that novel genes with unknown functions are abundant in viral genomes. Yet few observations exist for the processes and frequency by which these genes are gained and lost. The surface waters of marine environments are dominated by marine picocyanobacteria and their co-existing viruses (cyanophages). Recent genome sequencing of cyanophages has revealed a vast array of genes that have been acquired from their cyanobacterial hosts. Here, we re-sequenced the cyanophage S-PM2 genome after 10 years of near continuous passage through its marine Synechococcus host. During this time a spontaneous mutant (S-PM2d) lacking 13% of the S-PM2 ORFs became dominant in the cyanophage population. These ORFs are found at one loci and are not homologous to any proteins in any other sequenced organism (ORFans). We demonstrate a fitness cost to S-PM2WT associated with possession of these ORFs under standard laboratory growth. Metagenomic surveys reveal these ORFs are present in various aquatic environments, are likely of cyanophage origin and appear to be enriched in environments from the extremes of salinity (freshwater and hypersaline). We posit that these ORFs contribute to the flexible gene content of cyanophages and offer a distinct fitness advantage in freshwater and hypersaline environments.
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Affiliation(s)
- Richard J. Puxty
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Blanca Perez-Sepulveda
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - David J. Evans
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Andrew D. Millard
- Warwick Medical School, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
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