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Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52.

Iyer LM, Koonin EV, Aravind L - BMC Genomics (2002)

Bottom Line: There are three evolutionarily distinct superfamilies of SSAPs, namely the RecT/Redbeta, ERF, and RAD52, that have different sequence conservation patterns and predicted folds.All these SSAPs appear to be primarily of bacteriophage origin and have been acquired by numerous phylogenetically distant cellular genomes.They generally occur in predicted operons encoding one or more of a set of conserved DNA recombination proteins that appear to be the principal functional partners of the SSAPs.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. lakshmin@ncbi.nlm.nih.gov

ABSTRACT

Background: The DNA single-strand annealing proteins (SSAPs), such as RecT, Redbeta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood.

Results: Using sensitive computational sequence analysis, we show that the RecT and Redbeta proteins, along with several other bacterial proteins, form a distinct superfamily. The ERF and Rad52 families show no direct evolutionary relationship to these proteins and define novel superfamilies of their own. We identify several previously unknown members of each of these superfamilies and also report, for the first time, bacterial and viral homologs of Rad52. Additionally, we predict the presence of aberrant HhH modules in RAD52 that are likely to be involved in DNA-binding. Using the contextual information obtained from the analysis of gene neighborhoods, we provide evidence of the interaction of the bacterial members of each of these SSAP superfamilies with a similar set of DNA repair/recombination protein. These include different nucleases or Holliday junction resolvases, the ABC ATPase SbcC and the single-strand-binding protein. We also present evidence of independent assembly of some of the predicted operons encoding SSAPs and in situ displacement of functionally similar genes.

Conclusions: There are three evolutionarily distinct superfamilies of SSAPs, namely the RecT/Redbeta, ERF, and RAD52, that have different sequence conservation patterns and predicted folds. All these SSAPs appear to be primarily of bacteriophage origin and have been acquired by numerous phylogenetically distant cellular genomes. They generally occur in predicted operons encoding one or more of a set of conserved DNA recombination proteins that appear to be the principal functional partners of the SSAPs.

No MeSH data available.


Related in: MedlinePlus

Maximum likelihood tree for the ERF superfamily of proteins. The designations, gene names and species abbreviations are as in Fig. 2A. The internal branches with RELL bootstrap support >70% are indicated by blue circles. The gene neighborhoods of the ERF proteins are shown whenever they contained gene coding for proteins with potential functional relevance. Gene abbreviations are as in Fig. 1B
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Figure 4: Maximum likelihood tree for the ERF superfamily of proteins. The designations, gene names and species abbreviations are as in Fig. 2A. The internal branches with RELL bootstrap support >70% are indicated by blue circles. The gene neighborhoods of the ERF proteins are shown whenever they contained gene coding for proteins with potential functional relevance. Gene abbreviations are as in Fig. 1B

Mentions: ERF homologs are encoded by the genomes of several temperate phages of Gram-positive bacteria and γ-proteobacteria; additionally, we detected members of this superfamily in Listeria and in all the circular plasmids and one linear plasmid of Borrelia burgdorferi (Fig. 4). Thus, like the RecT/Redβ superfamily, the ERF family is likely to have emerged in the temperate phages, and was disseminated to the Borrelia circular plasmids and some bacterial genomes via prophages.


Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52.

Iyer LM, Koonin EV, Aravind L - BMC Genomics (2002)

Maximum likelihood tree for the ERF superfamily of proteins. The designations, gene names and species abbreviations are as in Fig. 2A. The internal branches with RELL bootstrap support >70% are indicated by blue circles. The gene neighborhoods of the ERF proteins are shown whenever they contained gene coding for proteins with potential functional relevance. Gene abbreviations are as in Fig. 1B
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC101383&req=5

Figure 4: Maximum likelihood tree for the ERF superfamily of proteins. The designations, gene names and species abbreviations are as in Fig. 2A. The internal branches with RELL bootstrap support >70% are indicated by blue circles. The gene neighborhoods of the ERF proteins are shown whenever they contained gene coding for proteins with potential functional relevance. Gene abbreviations are as in Fig. 1B
Mentions: ERF homologs are encoded by the genomes of several temperate phages of Gram-positive bacteria and γ-proteobacteria; additionally, we detected members of this superfamily in Listeria and in all the circular plasmids and one linear plasmid of Borrelia burgdorferi (Fig. 4). Thus, like the RecT/Redβ superfamily, the ERF family is likely to have emerged in the temperate phages, and was disseminated to the Borrelia circular plasmids and some bacterial genomes via prophages.

Bottom Line: There are three evolutionarily distinct superfamilies of SSAPs, namely the RecT/Redbeta, ERF, and RAD52, that have different sequence conservation patterns and predicted folds.All these SSAPs appear to be primarily of bacteriophage origin and have been acquired by numerous phylogenetically distant cellular genomes.They generally occur in predicted operons encoding one or more of a set of conserved DNA recombination proteins that appear to be the principal functional partners of the SSAPs.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. lakshmin@ncbi.nlm.nih.gov

ABSTRACT

Background: The DNA single-strand annealing proteins (SSAPs), such as RecT, Redbeta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood.

Results: Using sensitive computational sequence analysis, we show that the RecT and Redbeta proteins, along with several other bacterial proteins, form a distinct superfamily. The ERF and Rad52 families show no direct evolutionary relationship to these proteins and define novel superfamilies of their own. We identify several previously unknown members of each of these superfamilies and also report, for the first time, bacterial and viral homologs of Rad52. Additionally, we predict the presence of aberrant HhH modules in RAD52 that are likely to be involved in DNA-binding. Using the contextual information obtained from the analysis of gene neighborhoods, we provide evidence of the interaction of the bacterial members of each of these SSAP superfamilies with a similar set of DNA repair/recombination protein. These include different nucleases or Holliday junction resolvases, the ABC ATPase SbcC and the single-strand-binding protein. We also present evidence of independent assembly of some of the predicted operons encoding SSAPs and in situ displacement of functionally similar genes.

Conclusions: There are three evolutionarily distinct superfamilies of SSAPs, namely the RecT/Redbeta, ERF, and RAD52, that have different sequence conservation patterns and predicted folds. All these SSAPs appear to be primarily of bacteriophage origin and have been acquired by numerous phylogenetically distant cellular genomes. They generally occur in predicted operons encoding one or more of a set of conserved DNA recombination proteins that appear to be the principal functional partners of the SSAPs.

No MeSH data available.


Related in: MedlinePlus