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Multiple genome comparison within a bacterial species reveals a unit of evolution spanning two adjacent genes in a tandem paralog cluster.

Tsuru T, Kobayashi I - Mol. Biol. Evol. (2008)

Bottom Line: A highly conserved nucleotide sequence found within every lpl ORF is likely to provide a site for homologous recombination.This result has strong impact on our understanding of gene evolution because most gene lineages underwent tandem duplication and then diversified.This work also illustrates the use of multiple genome sequences for high-resolution evolutionary analysis within the same species.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.

ABSTRACT
It has been assumed that an open reading frame (ORF) represents a unit of gene evolution as well as a unit of gene expression and function. In the present work, we report a case in which a unit comprising the 3' region of an ORF linked to a downstream intergenic region that is in turn linked to the 5' region of a downstream ORF has been conserved, and has served as the unit of gene evolution. The genes are tandem paralogous genes from the bacterium Staphylococcus aureus, for which more than ten entire genomes have been sequenced. We compared these multiple genome sequences at a locus for the lpl (lipoprotein-like) cluster (encoding lipoprotein homologs presumably related to their host interaction) in the genomic island termed nuSaalpha. A highly conserved nucleotide sequence found within every lpl ORF is likely to provide a site for homologous recombination. Comparison of phylogenies of the 5'-variable region and the 3'-variable region within the same ORF revealed significant incongruence. In contrast, pairs of the 3'-variable region of an ORF and the 5'-variable region of the next downstream ORF gave more congruent phylogenies, with distinct groups of conserved pairs. The intergenic region seemed to have coevolved with the flanking variable regions. Multiple recombination events at the central conserved region appear to have caused various types of rearrangements among strains, shuffling the two variable regions in one ORF, but maintaining a conserved unit comprising the 3'-variable region, the intergenic region, and the 5'-variable region spanning adjacent ORFs. This result has strong impact on our understanding of gene evolution because most gene lineages underwent tandem duplication and then diversified. This work also illustrates the use of multiple genome sequences for high-resolution evolutionary analysis within the same species.

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The lpl homologs in Staphylococcus aureus genome and their phylogenetic tree. (A) Location of four lpl loci, Locus 0 through Locus III, on the genome of strain N315. Note that the lpl homologs are found in the corresponding loci in all the sequenced S. aureus strains. (B) A nucleotide NJ phylogenetic tree for the lpl ORFs and their homologs in two other Staphylococcus species. The uncondensed version of this tree is presented in supplementary figure S1A (Supplementary Material online).
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fig1: The lpl homologs in Staphylococcus aureus genome and their phylogenetic tree. (A) Location of four lpl loci, Locus 0 through Locus III, on the genome of strain N315. Note that the lpl homologs are found in the corresponding loci in all the sequenced S. aureus strains. (B) A nucleotide NJ phylogenetic tree for the lpl ORFs and their homologs in two other Staphylococcus species. The uncondensed version of this tree is presented in supplementary figure S1A (Supplementary Material online).

Mentions: An initial multiple sequence alignment of the nucleotide sequences for all the lpl ORFs was constructed using ClustalW with the default parameters. Then a Neighbor-Joining (NJ) phylogeny for the alignment was constructed using MEGA 4.0 (Tamura et al. 2007; http://www.megasoftware.net/) with pairwise deletion mode for gaps and with a maximum composite likelihood model for substitutions (fig. 1B and supplementary fig. S1A [Supplementary Material online]).


Multiple genome comparison within a bacterial species reveals a unit of evolution spanning two adjacent genes in a tandem paralog cluster.

Tsuru T, Kobayashi I - Mol. Biol. Evol. (2008)

The lpl homologs in Staphylococcus aureus genome and their phylogenetic tree. (A) Location of four lpl loci, Locus 0 through Locus III, on the genome of strain N315. Note that the lpl homologs are found in the corresponding loci in all the sequenced S. aureus strains. (B) A nucleotide NJ phylogenetic tree for the lpl ORFs and their homologs in two other Staphylococcus species. The uncondensed version of this tree is presented in supplementary figure S1A (Supplementary Material online).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2568036&req=5

fig1: The lpl homologs in Staphylococcus aureus genome and their phylogenetic tree. (A) Location of four lpl loci, Locus 0 through Locus III, on the genome of strain N315. Note that the lpl homologs are found in the corresponding loci in all the sequenced S. aureus strains. (B) A nucleotide NJ phylogenetic tree for the lpl ORFs and their homologs in two other Staphylococcus species. The uncondensed version of this tree is presented in supplementary figure S1A (Supplementary Material online).
Mentions: An initial multiple sequence alignment of the nucleotide sequences for all the lpl ORFs was constructed using ClustalW with the default parameters. Then a Neighbor-Joining (NJ) phylogeny for the alignment was constructed using MEGA 4.0 (Tamura et al. 2007; http://www.megasoftware.net/) with pairwise deletion mode for gaps and with a maximum composite likelihood model for substitutions (fig. 1B and supplementary fig. S1A [Supplementary Material online]).

Bottom Line: A highly conserved nucleotide sequence found within every lpl ORF is likely to provide a site for homologous recombination.This result has strong impact on our understanding of gene evolution because most gene lineages underwent tandem duplication and then diversified.This work also illustrates the use of multiple genome sequences for high-resolution evolutionary analysis within the same species.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.

ABSTRACT
It has been assumed that an open reading frame (ORF) represents a unit of gene evolution as well as a unit of gene expression and function. In the present work, we report a case in which a unit comprising the 3' region of an ORF linked to a downstream intergenic region that is in turn linked to the 5' region of a downstream ORF has been conserved, and has served as the unit of gene evolution. The genes are tandem paralogous genes from the bacterium Staphylococcus aureus, for which more than ten entire genomes have been sequenced. We compared these multiple genome sequences at a locus for the lpl (lipoprotein-like) cluster (encoding lipoprotein homologs presumably related to their host interaction) in the genomic island termed nuSaalpha. A highly conserved nucleotide sequence found within every lpl ORF is likely to provide a site for homologous recombination. Comparison of phylogenies of the 5'-variable region and the 3'-variable region within the same ORF revealed significant incongruence. In contrast, pairs of the 3'-variable region of an ORF and the 5'-variable region of the next downstream ORF gave more congruent phylogenies, with distinct groups of conserved pairs. The intergenic region seemed to have coevolved with the flanking variable regions. Multiple recombination events at the central conserved region appear to have caused various types of rearrangements among strains, shuffling the two variable regions in one ORF, but maintaining a conserved unit comprising the 3'-variable region, the intergenic region, and the 5'-variable region spanning adjacent ORFs. This result has strong impact on our understanding of gene evolution because most gene lineages underwent tandem duplication and then diversified. This work also illustrates the use of multiple genome sequences for high-resolution evolutionary analysis within the same species.

Show MeSH
Related in: MedlinePlus