DNA repair nucleases

Marti, Thomas; Fleck, Oliver

doi:10.1007/s00018-003-3223-4

Cited by 86 publications

(51 citation statements)

References 187 publications

(259 reference statements)

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“…DNA repair and recombination require a variety of specific deoxyribonucleases (1,2). RNA metabolism also requires various ribonucleases (RNases) 2 for a broad range of processes (3,4). In mRNA turnover, mRNA decay is an important determinant of gene expression and is mediated by several RNases with endonuclease and exonuclease activity.…”

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confidence: 99%

“…: 81-6-6850-5434; Fax: 81-6-6850-5442; E-mail: rmasui@bio.sci.osaka-u.ac.jp. 2 The abbreviations used are: RNase, ribonuclease; cd-ttRecJ, core domain of ttRecJ; dsDNA, double-stranded DNA; OB-fold, oligonucleotide/oligosaccharide-binding-fold; pAp, 3Ј-phosphoadenosine 5Ј-phosphate; ssDNA, single-stranded DNA; ssRNA, single-stranded RNA; ttRecJ, T. thermophilus RecJ.…”

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Role of RecJ-like Protein with 5′-3′ Exonuclease Activity in Oligo(deoxy)nucleotide Degradation

Wakamatsu

Kim

Uemura

et al. 2011

Journal of Biological Chemistry

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RecJ-like proteins belonging to the DHH family have been proposed to function as oligoribonucleases and 3-phosphoadenosine 5-phosphate (pAp) phosphatases in bacteria and archaea, which do not have Orn (oligoribonuclease) and CysQ (pAp phosphatase) homologs. In this study, we analyzed the biochemical and physiological characterization of the RecJ-like protein TTHA0118 from Thermus thermophilus HB8. TTHA0118 had high enzymatic activity as an oligodeoxyribonucleotide-and oligoribonucleotide-specific exonuclease and as pAp phosphatase. The polarity of degradation was 5 to 3, in contrast to previous reports about Bacillus subtilis NrnA, a RecJ-like protein. TTHA0118 preferentially hydrolyzed short oligodeoxyribonucleotides and oligoribonucleotides, whereas the RecJ exonuclease from T. thermophilus HB8 showed no such length dependence on oligodeoxyribonucleotide substrates. An insertion mutation of the ttha0118 gene led to growth reduction in minimum essential medium. Added 5-mononucleotides, nucleosides, and cysteine increased growth of the ttha0118 mutant in minimum essential medium. The RecJ-like protein Mpn140 from Mycoplasma pneumoniae M129, which cannot synthesize nucleic acid precursors de novo, showed similar biochemical features to TTHA0118. Furthermore, B. subtilis NrnA also hydrolyzed oligo(deoxy)ribonucleotides in a 5-3 direction. These results suggested that these RecJ-like proteins act in recycling short oligonucleotides to mononucleotides and in controlling pAp concentrations in vivo.Nucleases are essential for nucleic acid metabolism and cell viability. DNA repair and recombination require a variety of specific deoxyribonucleases (1, 2). RNA metabolism also requires various ribonucleases (RNases) 2 for a broad range of processes (3, 4). In mRNA turnover, mRNA decay is an important determinant of gene expression and is mediated by several RNases with endonuclease and exonuclease activity. Nucleases belonging to different superfamilies have been identified with endonuclease and exonuclease activities (5-8).In addition, genome sequences have revealed numerous ORFs annotated as putative nucleases.One of the phosphoesterase families is the DHH superfamily (9), which includes phosphodiesterase and exopolyphosphatase (10 -12). RecJ is a DNA exonuclease in the DHH protein superfamily, with DHH motifs I-IV and an associated DHHA1 motif (9), as described in the Pfam database (13). The RecJ protein is a Mg 2ϩ -or Mn 2ϩ -dependent single-stranded DNA (ssDNA)-specific 5Ј-3Ј exonuclease/deoxyribophosphodiesterase and plays a role in homologous recombination, mismatch repair, and base excision repair (14 -19). Although the ORFs annotated as RecJ-related proteins also have DHH and DHHA1 motifs, each RecJ-related protein has to be investigated for nuclease activity similar to RecJ protein. According to the SYSTERS database (20), proteins with DHH and DHHA1 motifs can be further divided into three main families. Representatives of each family are RecJ (N_155469 in SYSTERS), putative poly(A) polymerase (O_142140), and ex...

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Role of RecJ-like Protein with 5′-3′ Exonuclease Activity in Oligo(deoxy)nucleotide Degradation

Wakamatsu

Kim

Uemura

et al. 2011

Journal of Biological Chemistry

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“…These enzymes process DNA 3Ј ends by removing nucleotides one at a time to remodel 3Ј termini for subsequent molecular events in cells (1,2). TREX1 is the most active 3Ј-deoxyribonuclease purified from mammalian cells (3,4).…”

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Cooperative DNA Binding and Communication across the Dimer Interface in the TREX2 3′ → 5′-Exonuclease

Perrino

Silva

Harvey

et al. 2008

Journal of Biological Chemistry

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The activity of human TREX2-catalyzed 3 3 5-deoxyribonuclease has been analyzed in steady-state and single turnover kinetic assays and in equilibrium DNA binding studies. These kinetic data provide evidence for cooperative DNA binding within TREX2 and for coordinated catalysis between the TREX2 active sites supporting a model for communication between the protomers of a TREX2 dimer. Mobile loops positioned adjacent to the active sites provide the major DNA binding contribution and facilitate subsequent binding into the active sites. Mutations of three arginine residues on these loops cause decreased TREX2 activities by up to 60-fold. Steady-state kinetic assays of these arginine to alanine TREX2 variants result in increased K m values for DNA substrate with no effect on k cat values indicating contributions exclusively to DNA binding by all three of the loop arginines. TREX2 heterodimers were prepared to determine whether exonuclease activity in one protomer is communicated to the opposing protomer. Evidence for communication across the dimer interface is provided by the 7-fold lower catalytic activity measured in the TREX2 WT/H188A heterodimer compared with the TREX2 WT homodimer, contrasting the 2-fold lower activity measured in the TREX2 WT/R163A,R165A,R167A heterodimer. The measured activity in TREX2WT/H188A heterodimer indicates that defective catalysis in one protomer reduces activity in the opposing protomer. A DNA binding analysis of TREX2 and the heterodimers indicates a cooperative binding effect within the TREX2 protomer. Finally, single turnover kinetic assays identify DNA binding as the rate-limiting step in TREX2 catalysis.The 3Ј 3 5Ј-deoxyribonucleases play fundamental roles in a variety of DNA metabolic pathways. These enzymes process DNA 3Ј ends by removing nucleotides one at a time to remodel 3Ј termini for subsequent molecular events in cells (1, 2). TREX1 is the most active 3Ј-deoxyribonuclease purified from mammalian cells (3, 4). TREX2 has not been purified from cells, but recombinant TREX1 and TREX2 generated in Escherichia coli confirm the robust nature of these deoxyribonucleases with TREX1 exhibiting about a 10-fold greater activity than TREX2(5-7). The high catalytic efficiencies measured for TREX1 and TREX2 can be attributed in part to the nature of the active sites. The TREX gene sequences and Mg 2ϩ ion dependence suggested that these deoxyribonucleases might be members of the DnaQ-like exonuclease family that utilize a two Mg 2ϩ ion-dependent mechanism for catalysis (8 -12). The DnaQ-like family contains both deoxyribo-and riboexonucleases and has been divided into two subfamilies characterized by the presence of four conserved carboxylate residues and a histidine (DEDD-h) or a tyrosine (DEDD-y) positioned in the active site (13). The TREX enzymes prefer excision of deoxynucleotide polymers over ribonucleotide polymers by about 1000-fold (5) 2 with specificity for unmodified 3Ј termini (14, 15). The four carboxylate residue side chains in the DnaQ-like enzymes coordinate two divalen...

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“…We did not find any evidence that the sole HC1 protein is able to cleave 5' of UV or cisplatin damage (not shown). As the XPF protein has an endonuclease catalytic activity but performs its activity only as heterodimers with ERCC1 (Marti and Fleck, 2004), it is possible that HC1 helps the XPF protein in 5' incisions. Based on our in vivo and in vitro data, we propose that HC1 protein may sense a DNA lesion before recruiting an endonuclease that cuts the DNA 5' from the damage.…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of HC1: a novel human DNA repair gene

Lopes

Falconi²,

Góes³

et al. 2009

Genet. Mol. Res.

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AbStRACt. Nucleotide excision repair (NER) acts on a broad spectrum of large lesions, while base excision repair removes individual modified bases. Although both processes have been well studied in human cells, novel genes involved in these DNA repair pathways have been described. Using a heterologous complementation approach, we identified a fetal human cDNA that complemented two Escherichia coli mutants that are defective in 3-methyl adenine glycosylase and in three endonucleases, all of which are enzymes with important roles in base excision repair. The central cDNA open reading frame complemented NER mutant strains and promoted an increase in survival rate of bacteria exposed to UV light. The corresponding protein was able to restore nucleotide-excision-repair activity when added to a cell extract from Chinese hamster ovary cells deficient in the ERCC1 protein, an enzyme known to promote incision at the 5' end of the lesion during NER. In contrast, that protein was not able to complement XPG Chinese hamster ovary cells deficient in the 3' incision step of NER. These data indicate a new human repair gene, which we named HC1; it is involved in the recognition of two kinds of DNA lesions and it contributes to the 5' DNA incision step in NER.

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DNA repair nucleases

Cited by 86 publications

References 187 publications

Role of RecJ-like Protein with 5′-3′ Exonuclease Activity in Oligo(deoxy)nucleotide Degradation

Role of RecJ-like Protein with 5′-3′ Exonuclease Activity in Oligo(deoxy)nucleotide Degradation

Cooperative DNA Binding and Communication across the Dimer Interface in the TREX2 3′ → 5′-Exonuclease

Isolation and characterization of HC1: a novel human DNA repair gene

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