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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.


RF1-RF2 gene conversion in the evolution of Chloroflexi.(a). ‘7 aa-motif’ shared between RF1 and RF2 in three members of Chloroflexi. We aligned the RF1 and RF2 sequences of 9 species—six members of Bacteroidetes (Prevotella nigrescens, Psychroflexus torquis, Microscilla marina, Riemerella anatipestifer, Gillisia limnaea, and Emticicia oligotrophica), and three members of Chloroflexi (Roseiflexus castenholzii, Roseiflexus sp., and Herpetosiphon aurantiacus). We here present a portion of the RF1 and RF2 sequences corresponding to amino acid (aa) residues 237–268 in P. nigrescens 12aa_motif-type RF1 (GenBank accession no. EGQ17478.1). The RF1 and RF2 sequences of Roseiflexus spp. and H. aurantiacus are shaded in green. (b). ∆lnL profiles from the sliding window (SW) analyses of three ‘6-pair’ alignments. The details of the alignments were described in the main text. Note that neither 4 aa-motif nor 7 aa-motif was remained in 6-pair alignments. The broken line indicates the estimate of the 0.99th quantile (∆lnLs = −0.1) of the  distribution obtained from the parametric bootstrap analysis. The details of this plot are same as described in the legend of Fig. 3B.
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f7: RF1-RF2 gene conversion in the evolution of Chloroflexi.(a). ‘7 aa-motif’ shared between RF1 and RF2 in three members of Chloroflexi. We aligned the RF1 and RF2 sequences of 9 species—six members of Bacteroidetes (Prevotella nigrescens, Psychroflexus torquis, Microscilla marina, Riemerella anatipestifer, Gillisia limnaea, and Emticicia oligotrophica), and three members of Chloroflexi (Roseiflexus castenholzii, Roseiflexus sp., and Herpetosiphon aurantiacus). We here present a portion of the RF1 and RF2 sequences corresponding to amino acid (aa) residues 237–268 in P. nigrescens 12aa_motif-type RF1 (GenBank accession no. EGQ17478.1). The RF1 and RF2 sequences of Roseiflexus spp. and H. aurantiacus are shaded in green. (b). ∆lnL profiles from the sliding window (SW) analyses of three ‘6-pair’ alignments. The details of the alignments were described in the main text. Note that neither 4 aa-motif nor 7 aa-motif was remained in 6-pair alignments. The broken line indicates the estimate of the 0.99th quantile (∆lnLs = −0.1) of the distribution obtained from the parametric bootstrap analysis. The details of this plot are same as described in the legend of Fig. 3B.

Mentions: The same procedures described above identified an additional case of the putative RF1-RF2 gene conversion in the evolution of the phylum Chloroflexi. We found a unique ‘7 aa-motif,’ which is shared between RF1 and RF2 of three members of Chloroflexi, Roseiflexus castenholzii, Roseiflexus sp., and Herpetosiphon aurantiacus. The position of 7 aa-motif is seemingly homologous to those of 4 aa- and 12 aa-motifs, but the three motifs are clearly distinct from each other (Fig. 7A). Thus, we conclude that 7 aa-motif and 12 aa-motif were emerged separately in the RF evolution. To assess whether 7 aa-motif was shared between RF paralogues via gene conversion, we analyzed three 6-pair alignments (230 aa positions), which contain a pair of the RF1 and RF2 sequences with 7 aa-motif of R. castenholzii, Roseiflexus sp. or H. aurantiacus, and five pairs of the 4aa_motif-type RFs of P. torquis, M. marina, Ri. anatipestifer, G. limnaea, and E. oligotrophica belonging to Bacteroidetes. As shown in Fig. 7B, the SW analyses, coupled with the corresponding parametric bootstrap test, detected the signal of gene conversion in windows 11–15 (alignment positions 101–190). The boundary estimation based on a 6-pair alignment containing a pair of 7aa_motif-type RF1 and RF2 of R. castenholzii nominated alignment positions 108–207 as the putative GC-region. Intriguingly, the putative GC-region occupies almost entire domain 3, as the gene conversion identified in Bacteroidia (see above). The details of the SW analyses and boundary estimation described in this section were same as those assessing the RF1-RF2 gene conversion in Bacteroidia (see above).


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

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

RF1-RF2 gene conversion in the evolution of Chloroflexi.(a). ‘7 aa-motif’ shared between RF1 and RF2 in three members of Chloroflexi. We aligned the RF1 and RF2 sequences of 9 species—six members of Bacteroidetes (Prevotella nigrescens, Psychroflexus torquis, Microscilla marina, Riemerella anatipestifer, Gillisia limnaea, and Emticicia oligotrophica), and three members of Chloroflexi (Roseiflexus castenholzii, Roseiflexus sp., and Herpetosiphon aurantiacus). We here present a portion of the RF1 and RF2 sequences corresponding to amino acid (aa) residues 237–268 in P. nigrescens 12aa_motif-type RF1 (GenBank accession no. EGQ17478.1). The RF1 and RF2 sequences of Roseiflexus spp. and H. aurantiacus are shaded in green. (b). ∆lnL profiles from the sliding window (SW) analyses of three ‘6-pair’ alignments. The details of the alignments were described in the main text. Note that neither 4 aa-motif nor 7 aa-motif was remained in 6-pair alignments. The broken line indicates the estimate of the 0.99th quantile (∆lnLs = −0.1) of the  distribution obtained from the parametric bootstrap analysis. The details of this plot are same as described in the legend of Fig. 3B.
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Related In: Results  -  Collection

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f7: RF1-RF2 gene conversion in the evolution of Chloroflexi.(a). ‘7 aa-motif’ shared between RF1 and RF2 in three members of Chloroflexi. We aligned the RF1 and RF2 sequences of 9 species—six members of Bacteroidetes (Prevotella nigrescens, Psychroflexus torquis, Microscilla marina, Riemerella anatipestifer, Gillisia limnaea, and Emticicia oligotrophica), and three members of Chloroflexi (Roseiflexus castenholzii, Roseiflexus sp., and Herpetosiphon aurantiacus). We here present a portion of the RF1 and RF2 sequences corresponding to amino acid (aa) residues 237–268 in P. nigrescens 12aa_motif-type RF1 (GenBank accession no. EGQ17478.1). The RF1 and RF2 sequences of Roseiflexus spp. and H. aurantiacus are shaded in green. (b). ∆lnL profiles from the sliding window (SW) analyses of three ‘6-pair’ alignments. The details of the alignments were described in the main text. Note that neither 4 aa-motif nor 7 aa-motif was remained in 6-pair alignments. The broken line indicates the estimate of the 0.99th quantile (∆lnLs = −0.1) of the distribution obtained from the parametric bootstrap analysis. The details of this plot are same as described in the legend of Fig. 3B.
Mentions: The same procedures described above identified an additional case of the putative RF1-RF2 gene conversion in the evolution of the phylum Chloroflexi. We found a unique ‘7 aa-motif,’ which is shared between RF1 and RF2 of three members of Chloroflexi, Roseiflexus castenholzii, Roseiflexus sp., and Herpetosiphon aurantiacus. The position of 7 aa-motif is seemingly homologous to those of 4 aa- and 12 aa-motifs, but the three motifs are clearly distinct from each other (Fig. 7A). Thus, we conclude that 7 aa-motif and 12 aa-motif were emerged separately in the RF evolution. To assess whether 7 aa-motif was shared between RF paralogues via gene conversion, we analyzed three 6-pair alignments (230 aa positions), which contain a pair of the RF1 and RF2 sequences with 7 aa-motif of R. castenholzii, Roseiflexus sp. or H. aurantiacus, and five pairs of the 4aa_motif-type RFs of P. torquis, M. marina, Ri. anatipestifer, G. limnaea, and E. oligotrophica belonging to Bacteroidetes. As shown in Fig. 7B, the SW analyses, coupled with the corresponding parametric bootstrap test, detected the signal of gene conversion in windows 11–15 (alignment positions 101–190). The boundary estimation based on a 6-pair alignment containing a pair of 7aa_motif-type RF1 and RF2 of R. castenholzii nominated alignment positions 108–207 as the putative GC-region. Intriguingly, the putative GC-region occupies almost entire domain 3, as the gene conversion identified in Bacteroidia (see above). The details of the SW analyses and boundary estimation described in this section were same as those assessing the RF1-RF2 gene conversion in Bacteroidia (see above).

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.