A distinctive single‐stranded DNA‐binding protein from the Archaeon <i>Sulfolobus solfataricus</i>

Haseltine, Cynthia A.; Kowalczykowski, Stephen C.

doi:10.1046/j.1365-2958.2002.02807.x

Cited by 55 publications

(67 citation statements)

References 56 publications

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“…In contrast, members of the archaea harbor different forms of singlestranded DNA (ssDNA) binding proteins that are more similar to their eukaryotic counterpart at the amino acid sequence level (9,(11)(12)(13)(14). The archaeal RPA proteins are either single polypeptides (9,11,12,25) or heterocomplexes of more than one protein (5,14).In the mesophilic archaeon Methanosarcina acetivorans we demonstrated the presence of three functional RPA proteins (22), which are also conserved in its relatives Methanosarcina mazei and Methanosarcina barkeri. Two of the RPA proteins were of similar architecture, in that both proteins (M. acetivorans RPA2 [MacRPA2] and MacRPA3) have two OB folds within the N-terminal half and a zinc finger domain in the C-terminal half (22).…”

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confidence: 91%

Methanosarcina acetivorans Flap Endonuclease 1 Activity Is Inhibited by a Cognate Single-Stranded-DNA-Binding Protein

Lin¹,

Guzman²,

McKinney³

et al. 2006

J Bacteriol

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The oligonucleotide/oligosaccharide-binding (OB) fold is central to the architecture of single-stranded-DNA-binding proteins, which are polypeptides essential for diverse cellular processes, including DNA replication, repair, and recombination. In archaea, single-stranded DNA-binding proteins composed of multiple OB folds and a zinc finger domain, in a single polypeptide, have been described. The OB folds of these proteins were more similar to their eukaryotic counterparts than to their bacterial ones. Thus, the archaeal protein is called replication protein A (RPA), as in eukaryotes. Unlike most organisms, Methanosarcina acetivorans harbors multiple functional RPA proteins, and it was our interest to determine whether the different proteins play different roles in DNA transactions. Of particular interest was lagging-strand DNA synthesis, where recently RPA has been shown to regulate the size of the 5 region cleaved during Okazaki fragment processing. We report here that M. acetivorans RPA1 (MacRPA1), a protein composed of four OB folds in a single polypeptide, inhibits cleavage of a long flap (20 nucleotides) by M. acetivorans flap endonuclease 1 (MacFEN1). To gain a further insight into the requirement of the different regions of MacRPA1 on its inhibition of MacFEN1 endonuclease activity, N-terminal and C-terminal truncated derivatives of the protein were made and were biochemically and biophysically analyzed. Our results suggested that MacRPA1 derivatives with at least three OB folds maintained the properties required for inhibition of MacFEN1 endonuclease activity. Despite these interesting observations, further biochemical and genetic analyses are required to gain a deeper understanding of the physiological implications of our findings.Single-stranded-DNA-binding proteins (SSB) in the bacterial lineage and replication protein A (RPA) in the archaeal/ eukaryotic sister lineages are proteins required for diverse DNA transactions, including replication, repair, and recombination (16,26). Central to the structure of SSB and RPA proteins is the so-called oligonucleotide/oligosaccharide-binding (OB) fold, a small motif usually ranging from 70 to 150 amino acids (18). Structurally, OB folds consist of a pair of three antiparallel ␤-sheets, although in many cases, the first ␤-sheet is shared by the two groups (18). Between the third and fourth strands is usually an ␣-helix. The large variation in length of the OB folds is primarily due to the length of the variable loops found in their conserved secondary structural elements (24) (Fig. 1A).The bacterial SSB, in general, is composed of a single OB fold, although in solution the protein oligomerizes into a homotetramer (16). Recently, a new form of bacterial SSB that harbors two OB folds in a single polypeptide was isolated from Deinococcus radiodurans. This protein forms a homodimer to mimic the homotetrameric bacterial SSB (2). The eukaryotic RPA, on the other hand, is composed of three different proteins (RPA70, RPA32, and RPA14) that form a heterotrimeric complex...

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confidence: 91%

Methanosarcina acetivorans Flap Endonuclease 1 Activity Is Inhibited by a Cognate Single-Stranded-DNA-Binding Protein

Lin¹,

Guzman²,

McKinney³

et al. 2006

J Bacteriol

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“…Although many hypothetical RPA proteins have been identified in the numerous genomes analyzed, there is no quaternary structure that is common to all. In the crenarchaea, the RPA from Sulfolobus solfataricus is encoded by a single gene and exists as a monomer or a homotetramer (Haseltine & Kowalczykowski, 2002;Kerr, et al, 2001;Kerr, et al, 2003;Wadsworth & White, 2001). The different quaternary structures confer distinct binding capabilities (Rolfsmeier & Haseltine, 2010).…”

Section: Multiplicity Of Homologsmentioning

confidence: 99%

“…The different quaternary structures confer distinct binding capabilities (Rolfsmeier & Haseltine, 2010). Despite the similarity to bacterial SSB, and the ability of the gene to complement the lethality of an E. coli ssb mutation, the DNA-binding domain of this protein more closely resembles those of eukaryotic RPA1 (Haseltine & Kowalczykowski, 2002;Kerr, et al, 2003). Although the genomes of two related crenarchaea, P. aerophilum and A. pernix, have been reported to contain no obvious RPA or SSB homolog (Luo, et al, 2007), a previous study found a Sulfolobus-like SSB in A. pernix (Haseltine & Kowalczykowski, 2002).…”

Section: Multiplicity Of Homologsmentioning

confidence: 99%

“…Despite the similarity to bacterial SSB, and the ability of the gene to complement the lethality of an E. coli ssb mutation, the DNA-binding domain of this protein more closely resembles those of eukaryotic RPA1 (Haseltine & Kowalczykowski, 2002;Kerr, et al, 2003). Although the genomes of two related crenarchaea, P. aerophilum and A. pernix, have been reported to contain no obvious RPA or SSB homolog (Luo, et al, 2007), a previous study found a Sulfolobus-like SSB in A. pernix (Haseltine & Kowalczykowski, 2002). Given the recent identification of a novel SSB in D. radiodurans, and the fundamental role that ssDNA binding proteins play in replication and repair, it is likely that a protein carrying out these essential functions will be found in all organisms.…”

Section: Multiplicity Of Homologsmentioning

confidence: 99%

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Role of RPA Proteins in Radiation Repair and Recovery

Gygli¹,

Lockhart²,

DeVeaux³

2011

Selected Topics in DNA Repair

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“…The SsoRPA contains a single OB fold, and while it has been reported to oligomerize to form a homotetramer (6), a different report found that the protein exists as monomers (23). In the Euryarchaeota, RPAs display an unusual diversity and distribution.…”

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confidence: 99%

Engineering of Functional Replication Protein A Homologs Based on Insights into the Evolution of Oligonucleotide/ Oligosaccharide-Binding Folds

Lin¹,

Lin²,

Sriratana³

et al. 2008

J Bacteriol

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The bacterial single-stranded DNA (ssDNA)-binding protein (SSB) and the archaeal/eukaryotic replication protein A (RPA) play multiple and essential roles in almost every aspect of nucleic acid metabolism, including DNA replication, repair, and recombination (14, 25). The SSBs and RPAs across the three domains of life share a common and conserved module called the oligonucleotide/oligosaccharide-binding fold (OB fold) (16). Structurally, the common OB folds consist of fivestranded ␤-sheets coiled to form a closed ␤-barrel structure usually capped by an alpha-helix (13, 16). Most of the bacterial SSBs have a single OB fold per polypeptide that oligomerizes in solution to form a homotetramer (14). However, in Deinococcus radiodurans and Thermus aquaticus, SSB polypeptides that contain two OB folds have been reported, and as expected, the functional form of the protein is a homodimer that mimics the homotetrameric bacterial SSB (2). In eukaryotes, RPA is a heterotrimeric complex composed of RPA70, RPA32, and RPA14 proteins of approximately 70, 32, and 14 kDa, respectively. Each subunit harbors at least one OB fold, and the largest subunit RPA70 contains a zinc finger motif at the C-terminal region (25). The OB folds in archaeal RPAs show high sequence and structural similarity to eukaryotic RPAs (7, 10). However, the number and organization of OB folds in the RPAs of archaea differ from those of their eukaryotic counterparts. In the Crenarchaeota, the Sulfolobus solfataricus RPA (SsoRPA) is the only well-characterized protein.The SsoRPA contains a single OB fold, and while it has been reported to oligomerize to form a homotetramer (6), a different report found that the protein exists as monomers (23). In the Euryarchaeota, RPAs display an unusual diversity and distribution. Single-subunit RPAs containing multiple OB folds and a putative zinc finger motif have been characterized for Methanocaldococcus jannaschii (7) and Methanothermobacter thermautotrophicus (9). The M. jannaschii RPA (MjaRPA) and M. thermautotrophicus RPA (MthRPA) contain four and five OB folds, respectively, with each protein harboring a putative Zn finger motif at the C-terminal region. The RPA in Pyrococcus furiosus exists as a stable heterotrimer consisting of three subunits, RPA41, RPA32, and RPA14. Each of the P. furiosus RPA subunits contains an OB fold, and in addition, RPA41 contains a zinc finger-like motif (12). The presence of three functional RPAs in the mesophilic archaeon Methanosarcina acetivorans has been demonstrated. Unlike the multiple RPAs found in P. furiosus, each M. acetivorans RPA (MacRPA) can act as a distinct SSB (19).Modular rearrangements have been a well-known mechanism of protein evolution (24). Domains are basic evolutionary

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A distinctive single‐stranded DNA‐binding protein from the Archaeon Sulfolobus solfataricus

Cited by 55 publications

References 56 publications

Methanosarcina acetivorans Flap Endonuclease 1 Activity Is Inhibited by a Cognate Single-Stranded-DNA-Binding Protein

Methanosarcina acetivorans Flap Endonuclease 1 Activity Is Inhibited by a Cognate Single-Stranded-DNA-Binding Protein

Role of RPA Proteins in Radiation Repair and Recovery

Engineering of Functional Replication Protein A Homologs Based on Insights into the Evolution of Oligonucleotide/ Oligosaccharide-Binding Folds

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