Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease

Gyles, Carlton

doi:10.1177/0300985813511131

Cited by 171 publications

(122 citation statements)

References 138 publications

(330 reference statements)

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“…Horizontal transfer often involves plasmids, and horizontally transferred genes in bacteria are often related to virulence or antibiotic resistance, but this process can also occur in eukaryotes and transferred genes can be incorporated into the genome (61,121). Genes that have recently undergone horizontal transfer often have unusual GC content and codon usage compared with their host genome, and researchers have used this unusual codon usage to develop algorithms to identify putative horizontally transferred genes (49).…”

Section: Codon Usage In Horizontally Transferred Genesmentioning

confidence: 99%

Roles for Synonymous Codon Usage in Protein Biogenesis

Chaney¹,

Clark

2015

Annu. Rev. Biophys.

267

255

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Owing to the degeneracy of the genetic code, a protein sequence can be encoded by many different synonymous mRNA coding sequences. Synonymous codon usage was once thought to be functionally neutral, but evidence now indicates it is shaped by evolutionary selection and affects other aspects of protein biogenesis beyond specifying the amino acid sequence of the protein. Synonymous rare codons, once thought to have only negative impacts on the speed and accuracy of translation, are now known to play an important role in diverse functions, including regulation of cotranslational folding, covalent modifications, secretion, and expression level. Mutations altering synonymous codon usage are linked to human diseases. However, much remains unknown about the molecular mechanisms connecting synonymous codon usage to efficient protein biogenesis and proper cell physiology. Here we review recent literature on the functional effects of codon usage, including bioinformatics approaches aimed at identifying general roles for synonymous codon usage.

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Section: Codon Usage In Horizontally Transferred Genesmentioning

confidence: 99%

Roles for Synonymous Codon Usage in Protein Biogenesis

Chaney¹,

Clark

2015

Annu. Rev. Biophys.

267

255

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“…" Bacterial species can also evolve through the acquisition of foreign DNA through horizontal gene transfer events. The acquisition of foreign DNA can have a dramatic impact on the ecology of bacterial strains and species (46). We used Blast searches against the nonredundant protein database to identify candidate horizontally acquired genes in the core and accessory genomes of L. iners and L. crispatus.…”

Section: Fig 6 Scatterplot Of Nucleotide Diversity (X Axis) Versus Dnmentioning

confidence: 99%

Genomic Comparisons of Lactobacillus crispatus and Lactobacillus iners Reveal Potential Ecological Drivers of Community Composition in the Vagina

Mendes‐Soares

Forney

2016

Appl Environ Microbiol

119

115

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Lactobacillus crispatus and Lactobacillus iners are common inhabitants of the healthy human vagina. These two species are closely related and are thought to perform similar ecological functions in the vaginal environment. Temporal data on the vaginal microbiome have shown that nontransient instances of cooccurrence are uncommon, while transitions from an L. iners-dominated community to one dominated by L. crispatus, and vice versa, occur often. This suggests that there is substantial overlap in the fundamental niches of these species. Given this apparent niche overlap, it is unclear how they have been maintained as common inhabitants of the human vagina. In this study, we characterized and compared the genomes of L. iners and L. crispatus to gain insight into possible mechanisms driving the maintenance of this species diversity. Our results highlight differences in the genomes of these two species that may facilitate the partitioning of their shared niche space. Many of the identified differences may impact the protective benefits provided to the host by these two species. IMPORTANCEThe microbial communities that inhabit the human vagina play a critical role in the maintenance of vaginal health through the production of lactic acid and lowering the environmental pH. This precludes the growth of nonindigenous organisms and protects against infectious disease. The two most common types of vaginal communities are dominated by either Lactobacillus iners or Lactobacillus crispatus, while some communities alternate between the two over time. We combined ecological theory with state-of-the-art genome analyses to characterize how these two species might partition their shared niche space in the vagina. We show that the genomes of L. iners and L. crispatus differ in many respects, several of which may drive differences in their competitive abilities in the vagina. Our results provide insight into factors that drive the complicated temporal dynamics of the vaginal microbiome and demonstrate how closely related microbial species partition shared fundamental niche space. The microbial communities that inhabit the vaginas of healthy reproductive age women commonly contain high proportions of Lactobacillus species (1). Studies have shown that these communities can be divided into five different types, four of which are dominated by either Lactobacillus iners, Lactobacillus crispatus, Lactobacillus gasseri, or Lactobacillus jensenii (2). These four species are closely related and are thought to perform similar ecological functions in the vaginal environment (namely, the production of lactic acid) (3, 4). Instances of cooccurrence among these species are rare, and temporal data have demonstrated that shifts in the dominant Lactobacillus are common (5), suggesting that the species compete for shared niche space in the vagina. Ecological theory predicts that multiple species cannot occupy the same niche indefinitely, as one will eventually outcompete the others (6). Therefore, it is unclear how the four Lactobacillus spec...

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“…In given areas of our planet, plants and animals coevolve. Though well-known vertical and more recently proved horizontal gene transfers (Gyles and Boerlin, 2014;Keeling and Palmer, 2008), these communities build more complex and functional ecosystems thanks to perpetual interchanges. The functionality of living organisms is DNA depending.…”

Section: Is Soil Involved In the Process Of Natural Evolution?mentioning

confidence: 99%

Humusica 2, article 18: Techno humus systems and global change – Greenhouse effect, soil and agriculture

Zanella

Ponge

Hager

et al. 2018

Applied Soil Ecology

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A B S T R A C TThe article is structured in six sections. A first portion is dedicated to the state of the art concerning climatic change and agriculture. Internet available IPCC maps and cartographic documents made by scientific Centres of research were used for illustrating forecasted climatic changes. In Sections 2 and 3, bibliographic evidences were collected for supporting a vegetation and soil co-evolution theory. Humus, soil and vegetation systems are presented at planet level in many synthetic maps. In Sections 4, 5 and 6 the authors discussed the human influence on the soil evolution during the Anthropocene. It appears that humans detected and used the Mull humus systems all over planet Earth for crop production and pasture. Human pressure impoverished these humus systems, which tend to evolve toward Amphi or Moder systems, losing their natural biostructure and carbon content.

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Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease

Cited by 171 publications

References 138 publications

Roles for Synonymous Codon Usage in Protein Biogenesis

Roles for Synonymous Codon Usage in Protein Biogenesis

Genomic Comparisons of Lactobacillus crispatus and Lactobacillus iners Reveal Potential Ecological Drivers of Community Composition in the Vagina

Humusica 2, article 18: Techno humus systems and global change – Greenhouse effect, soil and agriculture

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