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Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.

Tamarit D, Ellegaard KM, Wikander J, Olofsson T, Vásquez A, Andersson SG - Genome Biol Evol (2015)

Bottom Line: A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution.We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication.The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.

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Related in: MedlinePlus

Overview of the location and presence profile of genes coding for secreted proteins. The upper line represents the segment of the Fhon2 genome surrounding the origin of replication (green bar) and the location of the genes coding for secreted proteins (red bars). Tick marks represent the distance in kb. For each gene, its presence/absence profile is shown. Yellow boxes represent genes for secreted proteins that are present in L. kunkeei but in no other lactobacilli for which complete genome data are present, gray boxes represent genes with orthologs in other lactobacilli and white boxes represent genes putatively falsely predicted to be secreted. The tree topology and the microclusters (letters A–D) are as in figure 1b.
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evv079-F5: Overview of the location and presence profile of genes coding for secreted proteins. The upper line represents the segment of the Fhon2 genome surrounding the origin of replication (green bar) and the location of the genes coding for secreted proteins (red bars). Tick marks represent the distance in kb. For each gene, its presence/absence profile is shown. Yellow boxes represent genes for secreted proteins that are present in L. kunkeei but in no other lactobacilli for which complete genome data are present, gray boxes represent genes with orthologs in other lactobacilli and white boxes represent genes putatively falsely predicted to be secreted. The tree topology and the microclusters (letters A–D) are as in figure 1b.

Mentions: Previous studies have shown that the addition of lipopolysaccharides from Pseudomonas aeruginosa to cell cultures of Fhon2 resulted in the production and secretion of 24 extracellular proteins (Butler et al. 2013). The hypothesis was that these proteins are involved in the defense of their niche (the honey crop) against other microbes, and that their secretion is triggered by surface molecules of bacteria such as Pseudomonas that are commonly present in flowers. Remarkably, 19 of these genes are located within a region of 300 kb on either side of the origin of replication (fig. 5). Of the five genes located more distantly from ori, two were coding for ribosomal proteins and one for lactate dehydrogenase. The latter three are the only proteins in the whole set that did not contain a signal peptide, and are thus likely to represent false positives. The 19 genes located in the segment flanking ori were generally well conserved, and as many as 14 were identified in all strains of L. kunkeei. Consistent with their identification in the secreted pool of proteins, all 19 proteins contain a signal peptide (supplementary table S6, Supplementary Material online). Eight of these secreted proteins have homologs in one or more of the closest relatives to L. kunkeei, indicative of vertical inheritance. These include genes for a serine peptidase, a transpeptidase involved in the crosslinking of the Brauns peptide to the peptidoglycan and endopeptidases putatively involved in the hydrolysis of the peptide stem of the peptidoglycan. The identification of secreted proteins involved in the modification of the peptidoglycan is consistent with the hypothesis that these proteins change the surface structure of L. kunkeei and/or of other bacteria.Fig. 5.—


Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.

Tamarit D, Ellegaard KM, Wikander J, Olofsson T, Vásquez A, Andersson SG - Genome Biol Evol (2015)

Overview of the location and presence profile of genes coding for secreted proteins. The upper line represents the segment of the Fhon2 genome surrounding the origin of replication (green bar) and the location of the genes coding for secreted proteins (red bars). Tick marks represent the distance in kb. For each gene, its presence/absence profile is shown. Yellow boxes represent genes for secreted proteins that are present in L. kunkeei but in no other lactobacilli for which complete genome data are present, gray boxes represent genes with orthologs in other lactobacilli and white boxes represent genes putatively falsely predicted to be secreted. The tree topology and the microclusters (letters A–D) are as in figure 1b.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4494060&req=5

evv079-F5: Overview of the location and presence profile of genes coding for secreted proteins. The upper line represents the segment of the Fhon2 genome surrounding the origin of replication (green bar) and the location of the genes coding for secreted proteins (red bars). Tick marks represent the distance in kb. For each gene, its presence/absence profile is shown. Yellow boxes represent genes for secreted proteins that are present in L. kunkeei but in no other lactobacilli for which complete genome data are present, gray boxes represent genes with orthologs in other lactobacilli and white boxes represent genes putatively falsely predicted to be secreted. The tree topology and the microclusters (letters A–D) are as in figure 1b.
Mentions: Previous studies have shown that the addition of lipopolysaccharides from Pseudomonas aeruginosa to cell cultures of Fhon2 resulted in the production and secretion of 24 extracellular proteins (Butler et al. 2013). The hypothesis was that these proteins are involved in the defense of their niche (the honey crop) against other microbes, and that their secretion is triggered by surface molecules of bacteria such as Pseudomonas that are commonly present in flowers. Remarkably, 19 of these genes are located within a region of 300 kb on either side of the origin of replication (fig. 5). Of the five genes located more distantly from ori, two were coding for ribosomal proteins and one for lactate dehydrogenase. The latter three are the only proteins in the whole set that did not contain a signal peptide, and are thus likely to represent false positives. The 19 genes located in the segment flanking ori were generally well conserved, and as many as 14 were identified in all strains of L. kunkeei. Consistent with their identification in the secreted pool of proteins, all 19 proteins contain a signal peptide (supplementary table S6, Supplementary Material online). Eight of these secreted proteins have homologs in one or more of the closest relatives to L. kunkeei, indicative of vertical inheritance. These include genes for a serine peptidase, a transpeptidase involved in the crosslinking of the Brauns peptide to the peptidoglycan and endopeptidases putatively involved in the hydrolysis of the peptide stem of the peptidoglycan. The identification of secreted proteins involved in the modification of the peptidoglycan is consistent with the hypothesis that these proteins change the surface structure of L. kunkeei and/or of other bacteria.Fig. 5.—

Bottom Line: A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution.We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication.The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.

Show MeSH
Related in: MedlinePlus