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Zhilenkov, E. L.; Popova, V. M.; Попов, Д. В.; Zavalsky, L Yu; Svetoch, E. A.; Stern, N. J.; Seal, BS

doi:10.1186/1743-422x-3-50

Cited by 16 publications

(9 citation statements)

References 31 publications

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“…The major structural component of the flagellum, the FlaB flagelin, is less than 70% similar to the core encoded flagelin, suggesting that variable extracellular structures are determined by the presence of this ICE. This probably influences surface attachment [81] or phage recognition [82] . In addition, a 12 ORFs locus encoding type IV adhesion pili, promoting bacterial attachment to, and colonization of a wide variety of surfaces [83] is exclusively present within the ICE.2 type elements.…”

Section: Resultsmentioning

confidence: 99%

Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus

et al. 2013

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Background Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome.Principal FindingsComparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions.SignificanceFor many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.

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Section: Resultsmentioning

confidence: 99%

Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus

et al. 2013

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“…Chi phage serves as the prime example of a group of closely related Chi-like phages (Moreno Switt et al, 2013;Grose and Casjens, 2014;Hendrix et al, 2015), most of which infect Salmonella enterica serovars, but some of which are reported to be specific for Enterobacter cancerogenous (Kazaks et al, 2012) or Providencia stuartii (Onmus-Leone et al, 2013). Diverse flagellotropic phages have been identified to infect a range of bacterial species including Aeromonas-phage PM3 (Merino et al, 1990), Agrobacterium-phages 7-7-1, GS2 and GS6 (Bradley et al, 1984;Kropinski et al, 2012), Asticcacaulis and Caulobacterphages ϕAcS2, ϕAcM4, ϕCp34, ϕCb13 and ϕCbK and ϕ6 (Jollick and Wright, 1974;Fukuda et al, 1976;Pate et al, 1979;Guerrero-Ferreira et al, 2011), Bacillus-phages AR9, 3NT, PBS1, SP3 and PBP1 (Lovett, 1972;Shea and Seaman, 1984;Vieira et al, 1989), Campylobacter-phage F431 (Baldvinsson et al, 2014) Proteus-phage PV22 (Zhilenkov et al, 2006) and Pseudomonas-phage ϕCTX (Geiben-Lynn et al, 2001). Interestingly, for ϕCb13 and ϕCbK, targeting the flagellum of their host is performed by a flexible filament emanating from its capsid rather than the distal tail complex observed in Chi phage for example (Guerrero-Ferreira et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi‐like protein tail fibre

Dunstan

Pickard

Dougan

et al. 2019

Molecular Microbiology

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Summary The discovery of a Salmonella‐targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi‐like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi‐like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.

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“…3C). The flagellum has been suggested to be the target for recognition by phages in A. macleodii (23), and flagellum-specific phages may interact with their host by attachment to flagella followed by DNA injection (30). Our analysis suggests that recombination with divergent alleles may allow A. macleodii to escape from phage infection.…”

Section: Resultsmentioning

confidence: 75%

Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation

Sun

Luo

2018

Appl Environ Microbiol

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Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to ∼50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in , exopolysaccharide production in, hydrocarbon degradation in , and cold adaptation in Intriguingly, the outlier loci feature polysaccharide catabolism in but not in, consistent with their primary habitat preferences in macroalga and beach sands respectively. Likewise, analysis of showed that photosynthesis related genes listed in the outlier loci are only found in high-light adapted ecotype but not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages. Acquisition of new metabolic genes has been known as an important mechanism driving bacterial evolution and adaptation in the ocean, but acquisition of novel alleles of existing genes and its potential ecological role has not been examined. Guided by population genetic theories, our genomic analysis showed that divergent allele acquisition is prevalent in phylogenetically diverse marine bacterial lineages and that the affected loci often encode metabolic functions that underlies the known ecological roles of the lineages under study.

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Cited by 16 publications

References 31 publications

Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus

Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi‐like protein tail fibre

Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation

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