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Multiple conversion between the genes encoding bacterial class-I release factors.

Ishikawa SA, Kamikawa R, Inagaki Y - Sci Rep (2015)

Bottom Line: In both cases, RF1-RF2 gene conversion was predicted to occur in the region encoding nearly entire domain 3, of which functions are common between RF paralogues.Nevertheless, the 'direction' of gene conversion appeared to be opposite from one another-from RF2 gene to RF1 gene in one case, while from RF1 gene to RF2 gene in the other.The two cases of RF1-RF2 gene conversion prompt us to propose two novel aspects in the evolution of bacterial class-I release factors: (i) domain 3 is interchangeable between RF paralogues, and (ii) RF1-RF2 gene conversion have occurred frequently in bacterial genome evolution.

View Article: PubMed Central - PubMed

Affiliation: 1] Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan [2] Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.

ABSTRACT
Bacteria require two class-I release factors, RF1 and RF2, that recognize stop codons and promote peptide release from the ribosome. RF1 and RF2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. This scenario expects that the two RF gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. However, we here report two independent cases of conversion between RF1 and RF2 genes (RF1-RF2 gene conversion), which were severely examined by procedures incorporating the maximum-likelihood phylogenetic method. In both cases, RF1-RF2 gene conversion was predicted to occur in the region encoding nearly entire domain 3, of which functions are common between RF paralogues. Nevertheless, the 'direction' of gene conversion appeared to be opposite from one another-from RF2 gene to RF1 gene in one case, while from RF1 gene to RF2 gene in the other. The two cases of RF1-RF2 gene conversion prompt us to propose two novel aspects in the evolution of bacterial class-I release factors: (i) domain 3 is interchangeable between RF paralogues, and (ii) RF1-RF2 gene conversion have occurred frequently in bacterial genome evolution.

No MeSH data available.


‘12 aa-motif’ and ‘4 aa-motif’ in RF paralogues of 99 members of Bacteroidetes.(a) RF1 amino acid (aa) alignment that corresponds to aa residues 237–268 in Prevotella nigrescens RF1 (GenBank accession no. EGQ17478.1). (b) RF2 aa alignment that corresponds to aa residues 245–276 in P. nigrescens RF2 (GenBank accession no. EGQ14454.1).
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f1: ‘12 aa-motif’ and ‘4 aa-motif’ in RF paralogues of 99 members of Bacteroidetes.(a) RF1 amino acid (aa) alignment that corresponds to aa residues 237–268 in Prevotella nigrescens RF1 (GenBank accession no. EGQ17478.1). (b) RF2 aa alignment that corresponds to aa residues 245–276 in P. nigrescens RF2 (GenBank accession no. EGQ14454.1).

Mentions: RF1 and RF2 were most likely separated from each other at a very early stage of bacterial evolution12. Nevertheless, we noticed that a characteristic sequence motif ‘shared’ between RF1 and RF2 in a member of the class Bacteroidia, Bacteroides thetaiotaomicron8. The aa sequence alignment presented in Baranov et al. (2006)8 displayed that B. thetaiotaomicron RF1 and RF2 ‘shared’ a motif of 12 aa residues in the homologous position, which were absent from any other RF sequences in the particular alignment (see Fig. 1 in the original article). As independent acquisition of the homologous motif in RF1 and RF2 is highly unlikely, there are two scenarios for the motif ‘shared’ exclusively between B. thetaiotaomicron RF1 and RF2. The first scenario assumes that the motif predates the separation of RF1 and RF2, followed by (potentially massive) parallel losses of the motif in both RF1 and RF2 of extant bacteria, except B. thetaiotaomicron (and its relatives; see below). Alternatively, either RF1 or RF2 may have acquired the motif in the common ancestor of a taxonomic unit including B. thetaiotaomicron, followed by a conversion of the RF gene fragment encoding a portion encompassing the motif into the paralogous gene, of which product lacked the motif.


Multiple conversion between the genes encoding bacterial class-I release factors.

Ishikawa SA, Kamikawa R, Inagaki Y - Sci Rep (2015)

‘12 aa-motif’ and ‘4 aa-motif’ in RF paralogues of 99 members of Bacteroidetes.(a) RF1 amino acid (aa) alignment that corresponds to aa residues 237–268 in Prevotella nigrescens RF1 (GenBank accession no. EGQ17478.1). (b) RF2 aa alignment that corresponds to aa residues 245–276 in P. nigrescens RF2 (GenBank accession no. EGQ14454.1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4530459&req=5

f1: ‘12 aa-motif’ and ‘4 aa-motif’ in RF paralogues of 99 members of Bacteroidetes.(a) RF1 amino acid (aa) alignment that corresponds to aa residues 237–268 in Prevotella nigrescens RF1 (GenBank accession no. EGQ17478.1). (b) RF2 aa alignment that corresponds to aa residues 245–276 in P. nigrescens RF2 (GenBank accession no. EGQ14454.1).
Mentions: RF1 and RF2 were most likely separated from each other at a very early stage of bacterial evolution12. Nevertheless, we noticed that a characteristic sequence motif ‘shared’ between RF1 and RF2 in a member of the class Bacteroidia, Bacteroides thetaiotaomicron8. The aa sequence alignment presented in Baranov et al. (2006)8 displayed that B. thetaiotaomicron RF1 and RF2 ‘shared’ a motif of 12 aa residues in the homologous position, which were absent from any other RF sequences in the particular alignment (see Fig. 1 in the original article). As independent acquisition of the homologous motif in RF1 and RF2 is highly unlikely, there are two scenarios for the motif ‘shared’ exclusively between B. thetaiotaomicron RF1 and RF2. The first scenario assumes that the motif predates the separation of RF1 and RF2, followed by (potentially massive) parallel losses of the motif in both RF1 and RF2 of extant bacteria, except B. thetaiotaomicron (and its relatives; see below). Alternatively, either RF1 or RF2 may have acquired the motif in the common ancestor of a taxonomic unit including B. thetaiotaomicron, followed by a conversion of the RF gene fragment encoding a portion encompassing the motif into the paralogous gene, of which product lacked the motif.

Bottom Line: In both cases, RF1-RF2 gene conversion was predicted to occur in the region encoding nearly entire domain 3, of which functions are common between RF paralogues.Nevertheless, the 'direction' of gene conversion appeared to be opposite from one another-from RF2 gene to RF1 gene in one case, while from RF1 gene to RF2 gene in the other.The two cases of RF1-RF2 gene conversion prompt us to propose two novel aspects in the evolution of bacterial class-I release factors: (i) domain 3 is interchangeable between RF paralogues, and (ii) RF1-RF2 gene conversion have occurred frequently in bacterial genome evolution.

View Article: PubMed Central - PubMed

Affiliation: 1] Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan [2] Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.

ABSTRACT
Bacteria require two class-I release factors, RF1 and RF2, that recognize stop codons and promote peptide release from the ribosome. RF1 and RF2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. This scenario expects that the two RF gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. However, we here report two independent cases of conversion between RF1 and RF2 genes (RF1-RF2 gene conversion), which were severely examined by procedures incorporating the maximum-likelihood phylogenetic method. In both cases, RF1-RF2 gene conversion was predicted to occur in the region encoding nearly entire domain 3, of which functions are common between RF paralogues. Nevertheless, the 'direction' of gene conversion appeared to be opposite from one another-from RF2 gene to RF1 gene in one case, while from RF1 gene to RF2 gene in the other. The two cases of RF1-RF2 gene conversion prompt us to propose two novel aspects in the evolution of bacterial class-I release factors: (i) domain 3 is interchangeable between RF paralogues, and (ii) RF1-RF2 gene conversion have occurred frequently in bacterial genome evolution.

No MeSH data available.