Natural replacement of vertically inherited <i>lux‐rib</i> genes of <i>Photobacterium aquimaris</i> by horizontally acquired homologues

Urbanczyk, Henryk; Furukawa, Takashi; Yamamoto, Yuki; Dunlap, Paul V.

doi:10.1111/j.1758-2229.2012.00355.x

Cited by 16 publications

(11 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Studies of origin and evolutionary history of the luminous genes offer a unique insight into processes shaping the evolution and diversity of Vibrionaceae. The lux operon evolution was proposed to involve recruitment of regulatory genes, duplication of some genes, loss of some luminous genes from the lux operon, as well as horizontal transfer of complete and functional lux operon [1,5,20,21]. Studies of the lux genes evolutionary history rely on the accurate taxonomic classification of luminous Vibrio isolates and understanding of evolutionary relationship between luminous species in the family.…”

Section: Introductionmentioning

confidence: 99%

Description of a novel marine bacterium, Vibrio hyugaensis sp. nov., based on genomic and phenotypic characterization

Urbanczyk¹,

Ogura²,

Hayashi³

et al. 2015

Systematic and Applied Microbiology

Self Cite

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 99%

Description of a novel marine bacterium, Vibrio hyugaensis sp. nov., based on genomic and phenotypic characterization

Urbanczyk¹,

Ogura²,

Hayashi³

et al. 2015

Systematic and Applied Microbiology

Self Cite

View full text Add to dashboard Cite

“…HGT can occur by uptake of environmental DNA, conjugative plasmids and bacteriophage infection. In the Photobacterium genus, studies on HGT are limited to the lux-rib operon, and a chitinase A and deoxyribodipyrimidine photolyase genes (Urbanczyk et al, 2008, 2012; Hunt et al, 2008b; Lauro et al, 2014) Here, we searched for evidence of genomic exchange by identifying prophages, transposases, CRISPR-Cas systems, genomic islands and secondary metabolite biosynthetic gene clusters.…”

Section: Resultsmentioning

confidence: 99%

“…The lux genes were identified by homology search to previously described genes (Ast and Dunlap, 2004; Urbanczyk et al, 2008, 2012) using protein sequence BLAST tools of CLC Main Workbench with identity/query coverage cutoff of 50/50. Identified lux operons were then blasted against whole genome sequences of the studied Photobacterium strains using MultiGeneBLAST (Medema et al, 2013).…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

Machado

Gram

2017

Front. Microbiol.

View full text Add to dashboard Cite

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

show abstract

“…To what degree will the adaptive pathways of the modified organism recapitulate the organism’s evolutionary history and thus allow researchers to address the role of chance and necessity at the molecular level? The key to resolving these prior questions is, at least in part, to assess the degree to which our system tracks or differs from experimental systems that replace genomic components with homologs obtained from other extant organisms (Acevedo-Rocha et al 2013; Agashe et al 2013; Andersson and Hughes 2009; Pena et al 2010; Urbanczyk et al 2012). …”

Section: Introductionmentioning

confidence: 99%

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Kacar

Sanyal

et al. 2017

J Mol Evol

View full text Add to dashboard Cite

The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. While the ancient homolog was not lethal to the cell, it did cause a twofold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2000 generations in the laboratory and examined the adaptive response via fitness assays, whole genome sequencing, proteomics, and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by upregulation of protein production. Our results suggest that an ancient–modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-017-9781-0) contains supplementary material, which is available to authorized users.

show abstract

Natural replacement of vertically inherited lux‐rib genes of Photobacterium aquimaris by horizontally acquired homologues

Cited by 16 publications

References 26 publications

Description of a novel marine bacterium, Vibrio hyugaensis sp. nov., based on genomic and phenotypic characterization

Description of a novel marine bacterium, Vibrio hyugaensis sp. nov., based on genomic and phenotypic characterization

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

Contact Info

Product

Resources

About