IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

Bertelli, Claire; Laird, Matthew R.; Williams, Kelly P.; Lau, Britney Y.; Hoad, Gemma; Winsor, Geoffrey L.; Brinkman, Fiona S. L.

doi:10.1093/nar/gkx343

Cited by 1,134 publications

(936 citation statements)

References 32 publications

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“…Accordingly, a conjugative transposon carrying four antibiotics resistance genes (tetracycline inactivation enzyme, chloramphenicol O-acetyltransferase and two β-lactamase) was identified in Myroides odoratimimus This tree is part of the tree shown in Fig. 1, where (Bertelli et al, 2017). We predicted that both conjugative transfer genes (traN, traJ and traM) and site-specific recombinase genes (SSR) were repeatedly acquired in nonmarine lineages ( Fig.…”

Section: Gains and Losses Of Genomic Traits To Facilitate Hostassociamentioning

confidence: 92%

Repeated evolutionary transitions of flavobacteria from marine to non‐marine habitats

Zhang

Yoshizawa

Sun

et al. 2019

Environmental Microbiology

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Summary The taxonomy of marine and non‐marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean‐to‐land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non‐marine adaptive genes. This included various Na+‐dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non‐marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K+ scavenging ATPase was repeatedly gained whereas the corresponding low‐affinity transporter repeatedly lost upon transitions, reflecting K+ ions are less available to non‐marine bacteria. Strikingly, the central metabolism Na+‐translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H+‐translocating counterpart was repeatedly gained in non‐marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non‐marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non‐marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.

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Section: Gains and Losses Of Genomic Traits To Facilitate Hostassociamentioning

confidence: 92%

Repeated evolutionary transitions of flavobacteria from marine to non‐marine habitats

Zhang

Yoshizawa

Sun

et al. 2019

Environmental Microbiology

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“…Certain genomic features within the genomes were also identified. Genomic islands were 627 identified using IslandViewer (Bertelli et al, 2017). Regions that may represent genomic islands 628 were also identified using the Mean Shift Genomic Island Predictor (MSGIP; de Brito et al, 629 2016).…”

Section: Conclusion 517mentioning

confidence: 99%

Distinctive Gene and Protein Characteristics of Extremely PiezophilicColwellia

Peoples

Kyaw

Ugalde

et al. 2020

Preprint

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Background 24The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low 25 concentrations of organic matter. While these conditions likely select for distinct genomic 26 characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are 27 relatively unexplored. In this study, we compared the genomes of seven strains within the genus 28Colwellia, including some of the most piezophilic microbes known, to identify genomic features 29 that enable life in the deep sea. 30 31 Results 32 Significant differences were found to exist between piezophilic and non-piezophilic strains of 33 Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic 34 abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell 35 wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, 36 and membrane fluidity adjustment vary between the strains, with operons for a nuo 37 dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive 38 members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A 39 number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-40 alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD + 41 homeostasis, and archaeal methyltransferase for tRNA modification. Many of these piezophile-42 specific genes are in variable regions of the genome near genomic islands, transposases, and 43 toxin-antitoxin systems. 44 45 Conclusions 46We identified a number of adaptations that may facilitate deep-sea radiation in members of the 47 genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and 48 hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins 49 as a result of high pressure. Variations in genes associated with the membrane, including those 50 involved in unsaturated fatty acid production and respiration, indicate that membrane-based 51 adaptations are critical for coping with high pressure. The presence of many piezophile-specific 52 genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by 53 horizontal gene transfer through transposases or other mobile elements. Some of these genes are 54 amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea 55 microorganisms.

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“…Strain sequence type was determined using the MLST2 server (Larsen et al, 2012), and plasmids were typed using the pMLST 2.0 server (Carattoli et al, 2014). Pathogenicity islands were detected using IslandViewer 4 (Bertelli et al, 2017) and VRprofile 2 .…”

Section: Ater I a L S A N D M E Th O Ds G En O M E A N A Lys I Smentioning

confidence: 99%

Identification and characterization of OmpT‐like proteases in uropathogenic Escherichia coli clinical isolates

et al. 2019

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Bacterial colonization of the urogenital tract is limited by innate defenses, including the production of antimicrobial peptides (AMPs). Uropathogenic Escherichia coli (UPEC) resist AMP‐killing to cause a range of urinary tract infections (UTIs) including asymptomatic bacteriuria, cystitis, pyelonephritis, and sepsis. UPEC strains have high genomic diversity and encode numerous virulence factors that differentiate them from non‐UTI‐causing strains, including ompT. As OmpT homologs cleave and inactivate AMPs, we hypothesized that UPEC strains from patients with symptomatic UTIs have high OmpT protease activity. Therefore, we measured OmpT activity in 58 clinical E. coli isolates. While heterogeneous OmpT activities were observed, OmpT activity was significantly greater in UPEC strains isolated from patients with symptomatic infections. Unexpectedly, UPEC strains exhibiting the greatest protease activities harbored an additional ompT‐like gene called arlC (ompTp). The presence of two OmpT‐like proteases in some UPEC isolates led us to compare the substrate specificities of OmpT‐like proteases found in E. coli. While all three cleaved AMPs, cleavage efficiency varied on the basis of AMP size and secondary structure. Our findings suggest the presence of ArlC and OmpT in the same UPEC isolate may confer a fitness advantage by expanding the range of target substrates.

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IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

Cited by 1,134 publications

References 32 publications

Repeated evolutionary transitions of flavobacteria from marine to non‐marine habitats

Repeated evolutionary transitions of flavobacteria from marine to non‐marine habitats

Distinctive Gene and Protein Characteristics of Extremely PiezophilicColwellia

Identification and characterization of OmpT‐like proteases in uropathogenic Escherichia coli clinical isolates

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