<i>An Introduction to Old Irish</i>. R. P. M. Lehmann , W. P. Lehmann

Meyer, Robert T.

doi:10.2307/2855007

Cited by 19 publications

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“…Both SSB proteins formed dimer complexes containing two SSB tetramers on longer oligonucleotides. Some models for the binding of E. coli SSB feature pairs of tetramers associating in "octamers" in the presence of DNA (1,3,16). The nature of interactions between SSB tetramers in such higher order complexes are not well understood.…”

Section: Discussionmentioning

confidence: 99%

“…Single-stranded DNA-binding proteins (SSB) 1 comprise a group of proteins which bind preferentially and with high affinity to single-stranded DNA. SSB proteins are present in prokaryotic and eukaryotic cells and are assumed to be essential for DNA metabolism in all organisms.…”

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confidence: 99%

“…One of the best characterized prokaryotic SSBs, Escherichia coli SSB, is a stable homotetramer of subunits containing 177 amino acids (18.8 kDa). Both biochemical and genetic data indicate that E. coli SSB is involved in DNA replication, repair, and recombination (1). Depending on the ionic conditions this protein binds to DNA in multiple modes with an apparent binding site size varying from 35 to 56 or 65 nucleotides (2,3).…”

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Effects of Xenopus laevis Mitochondrial Single-stranded DNA-binding Protein on Primer-Template Binding and 3′→5′ Exonuclease Activity of DNA Polymerase γ

Mikhailov

Bogenhagen

1996

Journal of Biological Chemistry

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Mitochondrial DNA (mtDNA) is replicated by DNA polymerase ␥ by a strand displacement mechanism involving mitochondrial single-stranded DNA-binding protein (mtSSB). mtSSB stimulates the overall rate of DNA synthesis on singly-primed M13 DNA mainly by stimulating the processivity of DNA synthesis rather than by stimulating primer recognition. We used electrophoretic mobility shift methods to study the effects of mtSSB on primer-template recognition by DNA pol ␥. Preliminary experiments showed that single mtSSB tetramers bind tightly to oligo(dT) single strands containing 32 to 48 residues. An oligonucleotide primer-template was designed with an 18-mer primer annealed to the 3-portion of a 71-mer template containing 40 dT residues at its 5-end as a binding site for mtSSB. DNA pol ␥ bound to this primer-template either in the absence or presence of mtSSB in complexes that remained intact and enzymatically active following native gel electrophoresis. Association of mtSSB with the 5-dT 40 -tail in the 18:71-mer primer-template reduced the binding of DNA polymerase ␥ and the efficiency of primer extension. Binding of mtSSB to single-stranded DNA was also observed to block the action of the 335 exonuclease of DNA polymerase ␥. The size of fragments protected from 335 exonuclease trimming increases with increasing ionic strength in a manner consistent with the known salt dependence of the binding site size of Escherichia coli SSB.Single-stranded DNA-binding proteins (SSB) 1 comprise a group of proteins which bind preferentially and with high affinity to single-stranded DNA. SSB proteins are present in prokaryotic and eukaryotic cells and are assumed to be essential for DNA metabolism in all organisms. One of the best characterized prokaryotic SSBs, Escherichia coli SSB, is a stable homotetramer of subunits containing 177 amino acids (18.8 kDa). Both biochemical and genetic data indicate that E. coli SSB is involved in DNA replication, repair, and recombination (1). Depending on the ionic conditions this protein binds to DNA in multiple modes with an apparent binding site size varying from 35 to 56 or 65 nucleotides (2, 3). Eukaryotes contain two different families of nuclear and mitochondrial SSB proteins. Heterotrimeric nuclear SSBs (RPA) (subunits of about 70, 32, and 14 kDa) have been found in all eukaryotic cells examined. These proteins are essential for replication, are involved in recombination and repair, and interact specifically with other proteins involved in DNA metabolism although they have little sequence homology with prokaryotic SSBs (4).Mitochondrial SSBs have been isolated from Xenopus laevis oocytes (5), rat liver (6, 7), yeast (8), and Drosophila (9). Two Xenopus mtSSBs have been described. One of these, mtSSB-1 has been fully sequenced (10) and is represented in a fulllength cDNA clone (11). The second, mtSSB-2, has not been cloned and has been only partially sequenced. The first 80 residues of mtSSB-2 reveal 91% identity to mtSSB-1, which contains 129 amino acids (14.6 kDa). Both Xenopus (12) and ...

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Effects of Xenopus laevis Mitochondrial Single-stranded DNA-binding Protein on Primer-Template Binding and 3′→5′ Exonuclease Activity of DNA Polymerase γ

Mikhailov

Bogenhagen

1996

Journal of Biological Chemistry

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“…However, whereas the molecular size and oligomeric state of these proteins vary dramatically between the members of the functional family, it has recently been proposed that portions of their DNA‐binding domains show some resemblance to the oligomer‐binding (OB) fold [7]. The SSB from E. coli ( Eco SSB) consists of 177 amino acids (excluding the N‐terminal methionine) and forms a very stable homotetramer [8–11]. Crystallisation studies by us [12]and others [13–16]were complicated by the fact that of the four polypeptide chains, at least two have to be truncated at their carboxy termini to obtain X‐ray‐grade crystals ([12–14]; Pasutto et al, in preparation).…”

Section: Introductionmentioning

confidence: 99%

A common core for binding single‐stranded DNA: structural comparison of the single‐stranded DNA‐binding proteins (SSB) from E. coli and human mitochondria

Webster¹,

Genschel

Curth

et al. 1997

FEBS Letters

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The crystal structure of the DNA‐binding domain of E. coli SSB (EcoSSB) has been determined to a resolution of 2.5 Å. This is the first reported structure of a prokaryotic SSB. The structure of the DNA‐binding domain of the E. coli protein is compared to that of the human mitochondrial SSB (HsmtSSB). In spite of the relatively low sequence identity between them, the two proteins display a high degree of structural similarity. EcoSSB crystallises with two dimers in the asymmetric unit, unlike HsmtSSB which contains only a dimer. This is probably a consequence of the different polypeptide chain lengths in the EcoSSB heterotetramer. Crucial differences in the dimer‐dimer interface of EcoSSB may account for the inability of EcoSSB and HsmtSSB to form cross‐species heterotetramers, in contrast to many bacterial SSBs.

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“…Thus, we believe that recp can interact with a stretch of DNA between 5-10 nucleotides. Based on the detailed studies of the interactions of E. coli single-stranded-binding protein with single-stranded DNA, such binding is likely to be dependent on ionic conditions, pH and protein concentration (Bujalowski and Lohman, 1986;Meyer and Lane, 1990). The E. coli RecA protein is known to protect between three and five nucleotides of DNA when binding as a monomer (see Roca and Cox, 1990, for review).…”

Section: Discussionmentioning

confidence: 99%

ATP‐independent DNA renaturation catalyzed by a protein from Ustilago maydis

Cole

Kmiec

1994

European Journal of Biochemistry

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A protein that catalyzes the renaturation of complementary strands of DNA has been purified from mitotic cells of the lower eukaryote Ustilago muydis. The most highly purified fraction contains a polypeptide with a molecular mass of 20 kDa as determined by SDSE'AGE and glycerol gradient sedimentation. DNA reannealing is enhanced by the presence of a divalent cation but does not require ATP nor any other nucleotide triphosphate. Reassociation proceeds with fast kinetics as more than 60% of the DNA is reannealed within 4 min at a 30 : 1 nucleotide/protein monomer ratio, results which suggest that the protein acts in a stoichiometric fashion. Amino acid analysis revealed that the protein contained an elevated level of basic residues and low levels of tryptophan and tyrosine. The protein binds to an oligonucleotide of ten residues but not to one having only five. As judged by agarose gel assays, the protein does not catalyze strand-transfer reactions but does promote the annealing of a 58-residue polynucleotide onto single-stranded circles and gapped linear duplexes. These latter reactions are dependent on the presence of DNA sequence similarity between the pairing partners.The renaturation of nucleic acid strands is a fundamental step in the cellular process of recombination. Prokaryotic enzymes such as the RecA protein of Escherichia coli (see Radding, 1988 for review) and p protein of ; 1 phage (Kmiec and Holloman, 1981) have been shown to catalyze fundamental pairing reactions central to homologous recombination pathways. Eukaryotic organisms also harbor enzymes that promote homologous pairing of DNA molecules. DNA annealing proteins have been isolated from HeLa cells (Hsieh and Camerini-Otero, 1989), Drosophila embryos (Eisen and Camerini-Otero, 1988;McCarthy et al., 1988), yeast (Kolodner et al., 1987;Sugino et al., 1988;Halbrook and McEntee, 1989) and human cells (Fishel et al., 1988). Some of these enzymes have been referred to as 'recombinases' or 'strand transferases' . In all of these cases, however, enzyme activity is not dependent on ATP, a significant difference from RecA-promoted reactions. In addition, the eukaryotic enzymes will not act on duplex DNA unless a region that is complementary to the pairing partner is at least partially single-stranded.There is, however, a notable exception to the ATP-independent annealing proteins of eukaryotes : the recl protein of Ustilago muydis Holloman, 1982, 1986). This 70-kDa protein possesses a DNA-dependent ATPase activity that functions during DNA annealing and strand-transfer reactions. ATP-dependent renaturation occurs through firstorder kinetics and the ATPase activity exhibits positive cooperativity. During the routine purification and characterization of the recl protein, we noticed an activity that catalyzed DNA reannealing in an ATP-independent fashion. This activity co-purified with reca protein through several columns,Correspondence to E. B. Kmiec, Department of Pharmacology, Jefferson Cancer Institute, Thomas Jefferson University, 233 S. 10th Street...

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An Introduction to Old Irish. R. P. M. Lehmann , W. P. Lehmann

Cited by 19 publications

References 0 publications

Effects of Xenopus laevis Mitochondrial Single-stranded DNA-binding Protein on Primer-Template Binding and 3′→5′ Exonuclease Activity of DNA Polymerase γ

Effects of Xenopus laevis Mitochondrial Single-stranded DNA-binding Protein on Primer-Template Binding and 3′→5′ Exonuclease Activity of DNA Polymerase γ

A common core for binding single‐stranded DNA: structural comparison of the single‐stranded DNA‐binding proteins (SSB) from E. coli and human mitochondria

ATP‐independent DNA renaturation catalyzed by a protein from Ustilago maydis

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