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Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments.

Moreno-Letelier A, Olmedo G, Eguiarte LE, Martinez-Castilla L, Souza V - Int J Evol Biol (2011)

Bottom Line: Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed.The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer.Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ecologia Evolutiva, Instituto de Ecologia, Universidad Nacional Autónoma de México, Apdo. Postal 70-275, Ciudad Universitaria, 04510 México D. F., Mexico.

ABSTRACT
The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.

No MeSH data available.


Maximum likelihood phylogeny of Firmicutes based on the concatenated amino acid sequence of 14 housekeeping genes and dated with a penalized likelihood method. The branch colors indicate the type of operon present in each taxon. Tag colors refer to the type of habitat. Clade I corresponds to aerobic Firmicutes and clade II includes CCB and marine Bacillus. Clade I had a fixed age of 2300 my and clades III and IV had a fixed minimum age of 35 my. Bootstrap values above 70% are denoted with an asterisk. Clades with branch lengths of 0 were collapsed (D. hafniense DCB-2-D. hafniense Y51 and G. thermodenitrificans NG80-2-G.sp. G11MC16).
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fig3: Maximum likelihood phylogeny of Firmicutes based on the concatenated amino acid sequence of 14 housekeeping genes and dated with a penalized likelihood method. The branch colors indicate the type of operon present in each taxon. Tag colors refer to the type of habitat. Clade I corresponds to aerobic Firmicutes and clade II includes CCB and marine Bacillus. Clade I had a fixed age of 2300 my and clades III and IV had a fixed minimum age of 35 my. Bootstrap values above 70% are denoted with an asterisk. Clades with branch lengths of 0 were collapsed (D. hafniense DCB-2-D. hafniense Y51 and G. thermodenitrificans NG80-2-G.sp. G11MC16).

Mentions: The phylogenetic reconstruction of the concatenated PstC, PstA, and PstB protein sequences showed two distinct and highly supported clades (Figure 2) that bear no relation to either the type of habitat or the phylogenetic relationships obtained with the amino acid sequences from housekeeping genes (Figure 3). Reconstructions made with each sequence independently, yielded the same basic topology, with minor differences in branch length (data not shown), so the phylogenetic signal was present in all three genes. We named one of the clades “cereus-like”, which consists of the pstSCABU operon structure (operon architecture A, in Figure 1), and it includes all members of the B. cereus group, most of Bacillus and Staphylococcus, Exiguobacterium, an anaerobic soil firmicute Desulfitobacterium hafniense, and most noteworthy, several Cyanobacteria and Archaea (Figure 2). None of the members of that clade have the duplication of gene pstB, and only two taxa (Desulfitobacterium and Oceanobacillus) lack the gene phoU in the operon (for the operon structure of all taxa in the dataset see Table S1 of Supplementary Material).


Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments.

Moreno-Letelier A, Olmedo G, Eguiarte LE, Martinez-Castilla L, Souza V - Int J Evol Biol (2011)

Maximum likelihood phylogeny of Firmicutes based on the concatenated amino acid sequence of 14 housekeeping genes and dated with a penalized likelihood method. The branch colors indicate the type of operon present in each taxon. Tag colors refer to the type of habitat. Clade I corresponds to aerobic Firmicutes and clade II includes CCB and marine Bacillus. Clade I had a fixed age of 2300 my and clades III and IV had a fixed minimum age of 35 my. Bootstrap values above 70% are denoted with an asterisk. Clades with branch lengths of 0 were collapsed (D. hafniense DCB-2-D. hafniense Y51 and G. thermodenitrificans NG80-2-G.sp. G11MC16).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3065170&req=5

fig3: Maximum likelihood phylogeny of Firmicutes based on the concatenated amino acid sequence of 14 housekeeping genes and dated with a penalized likelihood method. The branch colors indicate the type of operon present in each taxon. Tag colors refer to the type of habitat. Clade I corresponds to aerobic Firmicutes and clade II includes CCB and marine Bacillus. Clade I had a fixed age of 2300 my and clades III and IV had a fixed minimum age of 35 my. Bootstrap values above 70% are denoted with an asterisk. Clades with branch lengths of 0 were collapsed (D. hafniense DCB-2-D. hafniense Y51 and G. thermodenitrificans NG80-2-G.sp. G11MC16).
Mentions: The phylogenetic reconstruction of the concatenated PstC, PstA, and PstB protein sequences showed two distinct and highly supported clades (Figure 2) that bear no relation to either the type of habitat or the phylogenetic relationships obtained with the amino acid sequences from housekeeping genes (Figure 3). Reconstructions made with each sequence independently, yielded the same basic topology, with minor differences in branch length (data not shown), so the phylogenetic signal was present in all three genes. We named one of the clades “cereus-like”, which consists of the pstSCABU operon structure (operon architecture A, in Figure 1), and it includes all members of the B. cereus group, most of Bacillus and Staphylococcus, Exiguobacterium, an anaerobic soil firmicute Desulfitobacterium hafniense, and most noteworthy, several Cyanobacteria and Archaea (Figure 2). None of the members of that clade have the duplication of gene pstB, and only two taxa (Desulfitobacterium and Oceanobacillus) lack the gene phoU in the operon (for the operon structure of all taxa in the dataset see Table S1 of Supplementary Material).

Bottom Line: Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed.The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer.Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ecologia Evolutiva, Instituto de Ecologia, Universidad Nacional Autónoma de México, Apdo. Postal 70-275, Ciudad Universitaria, 04510 México D. F., Mexico.

ABSTRACT
The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.

No MeSH data available.