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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

Multiple sequence alignment of the RecT/Redβ superfamily of proteins. Proteins are denoted with their gene names, species abbreviation and gi numbers. The coloring reflects the amino acid conservation at 85% consensus. The consensus abbreviations and coloring scheme are as follows: h: hydrophobic residues (L,I,Y,F,M,W,A,C,V), l: aliphatic (L,I,A,V) and a: aromatic (F,Y,W,H) residues shaded yellow; o: alcohol (S,T), colored blue, c: charged (K,E,R,D,H) residues, +: basic (K/R/H) residues, -: acidic (D,E) residues, and p: polar (S,T,E,C,D,R,K,H,N,Q) residues colored purple; s: small (S,A,C,G,D,N,P,V,T) and u:tiny (G,A,S) residues, colored green; b: big (L,I,F,M,W,Y,E,R,K,Q) residues shaded gray. Secondary structure assignments are as follows: H: Helix, E: Extended (Strand). Species abbreviations are as follows: Bh: Bacillus halodurans, Borhercp: Borrelia hermsii circular plasmid, BPA118: Bacteriophage A118, BPbIL309: Bacteriophage bIL309, BPphi31_1: Bacteriophage phi31.1, BPPVL: Bacteriophage PVL, BPR1T: Bacteriophage R1T, Bs: Bacillus subtilis, ec: Escherichia coli, lambda: Bacteriophage λ, Li: Listeria innocua, Lp: Legionella pneumophila, Ml: Mesorhizobium loti, Salent: Salmonella enterica subsp. enterica serovar Typhi, SaN315: Staphylococcus aureus N315 subsp. aureus N315,Sd: Shigella dysenteriae, SPP1: Bacteriophage SPP1, StLT2: Salmonella typhimurium LT2, Strpy: Streptococcus pyogenes, Uu: Ureaplasma urealyticum, Xf; Xylella fastidiosa
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Figure 1: Multiple sequence alignment of the RecT/Redβ superfamily of proteins. Proteins are denoted with their gene names, species abbreviation and gi numbers. The coloring reflects the amino acid conservation at 85% consensus. The consensus abbreviations and coloring scheme are as follows: h: hydrophobic residues (L,I,Y,F,M,W,A,C,V), l: aliphatic (L,I,A,V) and a: aromatic (F,Y,W,H) residues shaded yellow; o: alcohol (S,T), colored blue, c: charged (K,E,R,D,H) residues, +: basic (K/R/H) residues, -: acidic (D,E) residues, and p: polar (S,T,E,C,D,R,K,H,N,Q) residues colored purple; s: small (S,A,C,G,D,N,P,V,T) and u:tiny (G,A,S) residues, colored green; b: big (L,I,F,M,W,Y,E,R,K,Q) residues shaded gray. Secondary structure assignments are as follows: H: Helix, E: Extended (Strand). Species abbreviations are as follows: Bh: Bacillus halodurans, Borhercp: Borrelia hermsii circular plasmid, BPA118: Bacteriophage A118, BPbIL309: Bacteriophage bIL309, BPphi31_1: Bacteriophage phi31.1, BPPVL: Bacteriophage PVL, BPR1T: Bacteriophage R1T, Bs: Bacillus subtilis, ec: Escherichia coli, lambda: Bacteriophage λ, Li: Listeria innocua, Lp: Legionella pneumophila, Ml: Mesorhizobium loti, Salent: Salmonella enterica subsp. enterica serovar Typhi, SaN315: Staphylococcus aureus N315 subsp. aureus N315,Sd: Shigella dysenteriae, SPP1: Bacteriophage SPP1, StLT2: Salmonella typhimurium LT2, Strpy: Streptococcus pyogenes, Uu: Ureaplasma urealyticum, Xf; Xylella fastidiosa

Mentions: Several lines of evidence, including genetic analyses, and similarities in biochemistry and quaternary structures, suggest that the E. coli RecT and phage λ Redβ proteins are functionally equivalent as mediators of single-strand exchange in DNA recombination [10,12]. However, no sequence similarity has been detected between these proteins leaving their actual evolutionary relationships unresolved. In order to gain a better understanding of their functions and origins, we undertook a detailed sequence analysis of these two proteins using iterative sequence profile searches with the PSI-BLAST program with a inclusion threshold of .01 iterated until convergence. Such searches, with Redβ proteins from different lambdoid bacteriophages as queries, retrieved not only other obvious Redβ homologs, but also the RecT protein family. For example, searches initiated with the Redβ homolog, PF161 protein (Genbank gi: 9836834 amino acids 1 to 188) from Borrelia hermsii[18], detected the E. coli RecT protein in the 5th iteration with significant expectation (e) values (3 × 10-3). Subsequent iterations retrieved several more RecT-related proteins from diverse sources. Further, transitive searches with the proteins detected in the above searches resulted in the identification of more divergent homologs, such as a protein termed the 'enterohemolysin associated protein' (EHAP1) from E. coli[19] and its orthologs in Salmonella (Fig. 1). An examination of the pairwise alignments generated by these searches showed that all these proteins shared a characteristic set of residues, including two highly conserved aromatic residues at the N- and C-termini, respectively, and two consecutive acidic residues near the C-terminus. These observations strongly suggested that RecT and Redβ, along with several other proteins, could be unified into a single protein superfamily with a core conserved domain of approximately 200 amino acid residues.


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

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

Multiple sequence alignment of the RecT/Redβ superfamily of proteins. Proteins are denoted with their gene names, species abbreviation and gi numbers. The coloring reflects the amino acid conservation at 85% consensus. The consensus abbreviations and coloring scheme are as follows: h: hydrophobic residues (L,I,Y,F,M,W,A,C,V), l: aliphatic (L,I,A,V) and a: aromatic (F,Y,W,H) residues shaded yellow; o: alcohol (S,T), colored blue, c: charged (K,E,R,D,H) residues, +: basic (K/R/H) residues, -: acidic (D,E) residues, and p: polar (S,T,E,C,D,R,K,H,N,Q) residues colored purple; s: small (S,A,C,G,D,N,P,V,T) and u:tiny (G,A,S) residues, colored green; b: big (L,I,F,M,W,Y,E,R,K,Q) residues shaded gray. Secondary structure assignments are as follows: H: Helix, E: Extended (Strand). Species abbreviations are as follows: Bh: Bacillus halodurans, Borhercp: Borrelia hermsii circular plasmid, BPA118: Bacteriophage A118, BPbIL309: Bacteriophage bIL309, BPphi31_1: Bacteriophage phi31.1, BPPVL: Bacteriophage PVL, BPR1T: Bacteriophage R1T, Bs: Bacillus subtilis, ec: Escherichia coli, lambda: Bacteriophage λ, Li: Listeria innocua, Lp: Legionella pneumophila, Ml: Mesorhizobium loti, Salent: Salmonella enterica subsp. enterica serovar Typhi, SaN315: Staphylococcus aureus N315 subsp. aureus N315,Sd: Shigella dysenteriae, SPP1: Bacteriophage SPP1, StLT2: Salmonella typhimurium LT2, Strpy: Streptococcus pyogenes, Uu: Ureaplasma urealyticum, Xf; Xylella fastidiosa
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Figure 1: Multiple sequence alignment of the RecT/Redβ superfamily of proteins. Proteins are denoted with their gene names, species abbreviation and gi numbers. The coloring reflects the amino acid conservation at 85% consensus. The consensus abbreviations and coloring scheme are as follows: h: hydrophobic residues (L,I,Y,F,M,W,A,C,V), l: aliphatic (L,I,A,V) and a: aromatic (F,Y,W,H) residues shaded yellow; o: alcohol (S,T), colored blue, c: charged (K,E,R,D,H) residues, +: basic (K/R/H) residues, -: acidic (D,E) residues, and p: polar (S,T,E,C,D,R,K,H,N,Q) residues colored purple; s: small (S,A,C,G,D,N,P,V,T) and u:tiny (G,A,S) residues, colored green; b: big (L,I,F,M,W,Y,E,R,K,Q) residues shaded gray. Secondary structure assignments are as follows: H: Helix, E: Extended (Strand). Species abbreviations are as follows: Bh: Bacillus halodurans, Borhercp: Borrelia hermsii circular plasmid, BPA118: Bacteriophage A118, BPbIL309: Bacteriophage bIL309, BPphi31_1: Bacteriophage phi31.1, BPPVL: Bacteriophage PVL, BPR1T: Bacteriophage R1T, Bs: Bacillus subtilis, ec: Escherichia coli, lambda: Bacteriophage λ, Li: Listeria innocua, Lp: Legionella pneumophila, Ml: Mesorhizobium loti, Salent: Salmonella enterica subsp. enterica serovar Typhi, SaN315: Staphylococcus aureus N315 subsp. aureus N315,Sd: Shigella dysenteriae, SPP1: Bacteriophage SPP1, StLT2: Salmonella typhimurium LT2, Strpy: Streptococcus pyogenes, Uu: Ureaplasma urealyticum, Xf; Xylella fastidiosa
Mentions: Several lines of evidence, including genetic analyses, and similarities in biochemistry and quaternary structures, suggest that the E. coli RecT and phage λ Redβ proteins are functionally equivalent as mediators of single-strand exchange in DNA recombination [10,12]. However, no sequence similarity has been detected between these proteins leaving their actual evolutionary relationships unresolved. In order to gain a better understanding of their functions and origins, we undertook a detailed sequence analysis of these two proteins using iterative sequence profile searches with the PSI-BLAST program with a inclusion threshold of .01 iterated until convergence. Such searches, with Redβ proteins from different lambdoid bacteriophages as queries, retrieved not only other obvious Redβ homologs, but also the RecT protein family. For example, searches initiated with the Redβ homolog, PF161 protein (Genbank gi: 9836834 amino acids 1 to 188) from Borrelia hermsii[18], detected the E. coli RecT protein in the 5th iteration with significant expectation (e) values (3 × 10-3). Subsequent iterations retrieved several more RecT-related proteins from diverse sources. Further, transitive searches with the proteins detected in the above searches resulted in the identification of more divergent homologs, such as a protein termed the 'enterohemolysin associated protein' (EHAP1) from E. coli[19] and its orthologs in Salmonella (Fig. 1). An examination of the pairwise alignments generated by these searches showed that all these proteins shared a characteristic set of residues, including two highly conserved aromatic residues at the N- and C-termini, respectively, and two consecutive acidic residues near the C-terminus. These observations strongly suggested that RecT and Redβ, along with several other proteins, could be unified into a single protein superfamily with a core conserved domain of approximately 200 amino acid residues.

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