Genomic and systems evolution in Vibrionaceae species

Gu, Jianying; Neary, Jennifer L.; Cai, Hong-Hong; Moshfeghian, Audrey; Rodriguez, Stephen A.; Lilburn, Timothy; Wang, Yufeng

doi:10.1186/1471-2164-10-s1-s11

Cited by 18 publications

(20 citation statements)

References 56 publications

(47 reference statements)

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“…In contrast to these examples of conservation, populations of V. cholerae and V. vulnificus maintain much more genomic diversity due, in part, to the genes captured within a super-integron locus (Chen et al, 2003;Chun et al, 2009;Boucher et al, 2011). Similarly, V. harveyi uses extensive gene duplication and fixation to diversify its genome (Gu et al, 2009). However, the most striking example of extensive evolution with a Vibrio species is the remarkably high genomic diversity reported for V. splendidus strains; even environmentally co-occurring isolates have up to 1-Mb difference in gene content from one to another (Thompson et al, 2005;Le Roux et al, 2009).…”

Section: Discussionmentioning

confidence: 98%

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A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

et al. 2016

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Newly hatched Euprymna scolopes squid obtain their specific light-organ symbionts from an array of Vibrio (Allivibrio) fischeri strains present in their environment. Two genetically distinct populations of this squid species have been identified, one in Kaneohe Bay (KB), and another in Maunaloa Bay (MB), Oahu. We asked whether symbionts isolated from squid in each of these populations outcompete isolates from the other population in mixed-infection experiments. No relationship was found between a strain's host source (KB or MB) and its ability to competitively colonize KB or MB juveniles in a mixed inoculum. Instead, two colonization behaviors were identified among the 11 KB and MB strains tested: a 'dominant' outcome, in which one strain outcompetes the other for colonization, and a 'sharing' outcome, in which two strains co-colonize the squid. A genome-level comparison of these and other V. fischeri strains suggested that the core genomic structure of this species is both syntenous and highly conserved over time and geographical distance. We also identified~250 Kb of sequence, encoding 194 dispersed orfs, that was specific to those strains that expressed the dominant colonization behavior. Taken together, the results indicate a link between the genome content of V. fischeri strains and their colonization behavior when initiating a light-organ symbiosis.

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Section: Discussionmentioning

confidence: 98%

“…(Gu et al, 2009). However, around 200 genes, found in 41 loci comprising two or more adjacent orfs, are present only in the genomes of D-type strains.…”

Section: Discussionmentioning

confidence: 99%

A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

et al. 2016

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“…Analysis by BLAST revealed that sequences homologous to VC1372 are found only in a few Vibrio species, dominated by strains of V. cholerae. A previous study has also noted that VC1372 is unique to V. cholerae among members of the genus Vibrio (72).…”

Section: Discussionmentioning

confidence: 99%

Bile Acids and Bicarbonate Inversely Regulate Intracellular Cyclic di-GMP in Vibrio cholerae

Koestler

Waters

2014

Infect Immun

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Vibrio cholerae is a Gram-negative bacterium that persists in aquatic reservoirs and causes the diarrheal disease cholera upon entry into a human host. V. cholerae employs the second messenger molecule 3=,5=-cyclic diguanylic acid (c-di-GMP) to transition between these two distinct lifestyles. c-di-GMP is synthesized by diguanylate cyclase (DGC) enzymes and hydrolyzed by phosphodiesterase (PDE) enzymes. Bacteria typically encode many different DGCs and PDEs within their genomes. Presumably, each enzyme senses and responds to cognate environmental cues by alteration of enzymatic activity. c-di-GMP represses the expression of virulence factors in V. cholerae, and it is predicted that the intracellular concentration of c-di-GMP is low during infection. Contrary to this model, we found that bile acids, a prevalent constituent of the human proximal small intestine, increase intracellular c-di-GMP in V. cholerae. We identified four c-di-GMP turnover enzymes that contribute to increased intracellular c-di-GMP in the presence of bile acids, and deletion of these enzymes eliminates the bile induction of c-di-GMP and biofilm formation. Furthermore, this bile-mediated increase in c-di-GMP is quenched by bicarbonate, the intestinal pH buffer secreted by intestinal epithelial cells. Our results lead us to propose that V. cholerae senses distinct microenvironments within the small intestine using bile and bicarbonate as chemical cues and responds by modulating the intracellular concentration of c-di-GMP.

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“…Gene duplication and lateral gene transfer (LGT) are believed to be major evolutionary forces driving the genome evolution in bacteria [7-9]. Gene duplication is of paramount importance for functional innovation.…”

Section: Introductionmentioning

confidence: 99%

Genome plasticity and systems evolution in Streptomyces

Zhou

et al. 2012

BMC Bioinformatics

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BackgroundStreptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.ResultsWe present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.ConclusionsOur results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.

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Genomic and systems evolution in Vibrionaceae species

Cited by 18 publications

References 56 publications

A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

Bile Acids and Bicarbonate Inversely Regulate Intracellular Cyclic di-GMP in Vibrio cholerae

Genome plasticity and systems evolution in Streptomyces

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