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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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Gene order structures of the segment coding for giant extracellular proteins. Each arrow represents a gene inferred to code for a giant protein, with colors representing distinct protein orthologs. Red lines are shown for tBLASTx hits with more than 50% identity over more than 100 amino acids. White spaces represent either absence of BLAST hits or hits below the established thresholds. Shown at the top is the consensus order of genes and their average lengths. The tree topology and the microclusters (letters A–D) are as in figure 1b.
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evv079-F6: Gene order structures of the segment coding for giant extracellular proteins. Each arrow represents a gene inferred to code for a giant protein, with colors representing distinct protein orthologs. Red lines are shown for tBLASTx hits with more than 50% identity over more than 100 amino acids. White spaces represent either absence of BLAST hits or hits below the established thresholds. Shown at the top is the consensus order of genes and their average lengths. The tree topology and the microclusters (letters A–D) are as in figure 1b.

Mentions: The most remarkable of these putative outer surface and/or secreted proteins of unknown functions belong to a family of proteins that are huge in size, ranging from 3,000 to 9,000 amino acids, and solely present in the L. kunkeei species complex. The genes are organized in an array of 4–5 genes and cover a total of 100 kb located about 250 kb downstream of the origin of replication (fig. 6). This region displays atypically high GC-content values and deviating GC-skew values compared with the neighboring segments (fig. 3 and supplementary fig. S3, Supplementary Material online), indicative of acquisition by horizontal gene transfer or strong compositional selection. The encoded proteins showed no similarity to sequences in the Uniprot or NR databases (BLASTp, E < 1e-05), and contained no recognizable domains according to the SCOP superfamily classification system. Only the signal peptide at the N-terminal segment, plus a conserved sequence of 60 residues at the C-terminus of unknown function could be detected in all proteins. Psi-BLAST hits were obtained against matrix-binding proteins such as the large EbhA from Staphylococcus aureus. Additionally, homology-based structural analysis also detected regions of similarity to EbhA, as well as to streptococcal adhesins, immunoglobulin/albumin-binding domain-like, and catenin alpha-1 (supplementary table S7, Supplementary Material online), suggesting a role in attachment.Fig. 6.—


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)

Gene order structures of the segment coding for giant extracellular proteins. Each arrow represents a gene inferred to code for a giant protein, with colors representing distinct protein orthologs. Red lines are shown for tBLASTx hits with more than 50% identity over more than 100 amino acids. White spaces represent either absence of BLAST hits or hits below the established thresholds. Shown at the top is the consensus order of genes and their average lengths. The tree topology and the microclusters (letters A–D) are as in figure 1b.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494060&req=5

evv079-F6: Gene order structures of the segment coding for giant extracellular proteins. Each arrow represents a gene inferred to code for a giant protein, with colors representing distinct protein orthologs. Red lines are shown for tBLASTx hits with more than 50% identity over more than 100 amino acids. White spaces represent either absence of BLAST hits or hits below the established thresholds. Shown at the top is the consensus order of genes and their average lengths. The tree topology and the microclusters (letters A–D) are as in figure 1b.
Mentions: The most remarkable of these putative outer surface and/or secreted proteins of unknown functions belong to a family of proteins that are huge in size, ranging from 3,000 to 9,000 amino acids, and solely present in the L. kunkeei species complex. The genes are organized in an array of 4–5 genes and cover a total of 100 kb located about 250 kb downstream of the origin of replication (fig. 6). This region displays atypically high GC-content values and deviating GC-skew values compared with the neighboring segments (fig. 3 and supplementary fig. S3, Supplementary Material online), indicative of acquisition by horizontal gene transfer or strong compositional selection. The encoded proteins showed no similarity to sequences in the Uniprot or NR databases (BLASTp, E < 1e-05), and contained no recognizable domains according to the SCOP superfamily classification system. Only the signal peptide at the N-terminal segment, plus a conserved sequence of 60 residues at the C-terminus of unknown function could be detected in all proteins. Psi-BLAST hits were obtained against matrix-binding proteins such as the large EbhA from Staphylococcus aureus. Additionally, homology-based structural analysis also detected regions of similarity to EbhA, as well as to streptococcal adhesins, immunoglobulin/albumin-binding domain-like, and catenin alpha-1 (supplementary table S7, Supplementary Material online), suggesting a role in attachment.Fig. 6.—

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