A versatile endonuclease IV from Thermus thermophilus has uracil-excising and 3′–5′ exonuclease activity

Back, Jinwook; Chung, Ji Hyung; Park, Jong Hwa; Han, Ye

doi:10.1016/j.bbrc.2006.05.187

Cited by 5 publications

(18 citation statements)

References 31 publications

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“…Specifically, a range of fragments was observed, the majority of which had lengths smaller than, or equal to, 18 nt. This Mg 2+ -dependent activity of the mycoplasmal Nfo proteins probably results from these proteins' inherent 39A59 exonucleolytic activity, which has previously also been attributed to other Nfo proteins (Back et al, 2006;Kerins et al, 2003;Liu et al, 2007). As expected, this activity was independent of the presence of an abasic site in the DNA substrate; substrate Ds was degraded with a similar efficiency by the Nfo proteins as was substrate Ds-AP (Fig.…”

Section: Endonucleolytic and Exonucleolytic Activities Of The Nfo Prosupporting

confidence: 70%

“…The Nfo Eco counterparts of the targeted amino acid residues were found to interact with no, one or two of the three divalent cations (Zn 1 , Zn 2 and Zn 3 ) that were identified previously in Nfo Eco 's active site (Garcin et al, 2008;Hosfield et al, 1999 In addition to the damage-specific endoncleolytic activities of Nfo Mpn and Nfo Mge , we also found these proteins to possess non-specific 39A59 exonucleolytic activity. Such activity has previously also been attributed to other Nfo proteins (Back et al, 2006;Kerins et al, 2003;Liu et al, 2007). It is interesting to note, however, that while the AP cleavage activity of Nfo Eco had already been identified in 1977 (Ljungquist, 1977), the exonucleolytic activity of this enzyme was only reported in 2003 (Kerins et al, 2003).…”

Section: Discussionmentioning

confidence: 86%

“…3(a), the AP site cleavage activity of both H 10 -Nfo Mpn (lanes 2-7) and H 10 -Nfo Mge (lanes 8-13) is not influenced significantly by concentrations of EDTA up to 10 mM. In contrast, the Nfo protein from Thermus thermophilus (Nfo Tth ) was reported to be inactive at an EDTA concentration of 10 mM (Back et al, 2006). At relatively low concentrations of EDTA (up to 1 mM), additional DNA fragments are produced that are one or two nucleotides smaller than both the uncleaved and cleaved substrate.…”

Section: Divalent Cation Requirements Of the Nfo Proteinsmentioning

confidence: 99%

“…Another activity that has been attributed to the Nfo Eco protein is 39A59 exonuclease activity (Kerins et al, 2003). Nfo homologues from other bacterial species were also reported to have this activity (Back et al, 2006;Kerins et al, 2003;Liu et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Uncoupling of the apyrimidinic/apurinic endonucleolytic and 3′→5′ exonucleolytic activities of the Nfo protein of Mycoplasma pneumoniae through mutation of specific amino acid residues

et al. 2014

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The DNA recombination and repair machineries of Mycoplasma pneumoniae and Mycoplasma genitalium were predicted to consist of a set of~11 proteins. The function of one of these proteins was inferred from its homology with proteins belonging to the Endo IV enzyme family. The members of this family function in the repair of apyrimidinic/apurinic (AP) sites in DNA. As such activity may be crucial in the mycoplasmal life cycle, we set out to study the Endo IV-like proteins encoded by M. pneumoniae and M. genitalium. Both proteins, termed Nfo Mpn and Nfo Mge , respectively, were assessed for their ability to interact with damaged and undamaged DNA. In the absence of divalent cations, both proteins exhibited specific cleavage of AP sites. Surprisingly, the proteins also recognized and cleaved cholesteryl-bound deoxyribose moieties in DNA, showing that these Nfo proteins may also function in repair of large DNA adducts. In the presence of Mg 2+ , Nfo Mpn and Nfo Mge also showed 39A59 exonucleolytic activity. By introduction of 13 single point mutations at highly conserved positions within Nfo Mpn , two major types of mutants could be distinguished: (i) mutants that showed no, or limited, AP cleavage activity in the presence of EDTA, but displayed significant levels of AP cleavage activity in the presence of Mg 2+ ; these mutants displayed no, or very low, exonucleolytic activity; and (ii) mutants that only demonstrated marginal levels of AP site cleavage activity in the presence of Mg 2+ and did not show exonucleolytic activity. Together, these results indicated that the AP endonucleolytic activity of the Nfo Mpn protein can be uncoupled from its 39A59 exonucleolytic activity.

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Section: Endonucleolytic and Exonucleolytic Activities Of The Nfo Prosupporting

confidence: 70%

Section: Discussionmentioning

confidence: 86%

Section: Divalent Cation Requirements Of the Nfo Proteinsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Uncoupling of the apyrimidinic/apurinic endonucleolytic and 3′→5′ exonucleolytic activities of the Nfo protein of Mycoplasma pneumoniae through mutation of specific amino acid residues

et al. 2014

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“…Human Ape1 reportedly has strong AP endonuclease activity, but Ape2 exhibits relatively weak activity. The main catalytic property distinguishing Nfo from XthA is the lack of 3′ exonuclease activity as described in the recent review article (5) and also in the textbook (14), although a report in the year 2003 showed that Nfo and its homolog from the hyperthermophilic eubacteria, Thermotoga maritime and Thermus thermophilus , have the exonuclease activity (15,16). The physiological function of the AP endonuclease-associated 3′-exonuclease activity is not fully understood.…”

Section: Introductionmentioning

confidence: 99%

Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus

Kiyonari

Tahara

Shirai

et al. 2009

Nucleic Acids Research

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Apurinic/apyrimidinic (AP) sites are the most frequently found mutagenic lesions in DNA, and they arise mainly from spontaneous base loss or modified base removal by damage-specific DNA glycosylases. AP sites are cleaved by AP endonucleases, and the resultant gaps in the DNA are repaired by DNA polymerase/DNA ligase reactions. We identified the gene product that is responsible for the AP endonuclease activity in the hyperthermophilic euryarchaeon, Pyrococcus furiosus. Furthermore, we detected the physical interaction between P. furiosus AP endonuclease (PfuAPE) and proliferating cell nuclear antigen (PCNA; PfuPCNA) by a pull-down assay and a surface plasmon resonance analysis. Interestingly, the associated 3′–5′ exonuclease activity, but not the AP endonuclease activity, of PfuAPE was stimulated by PfuPCNA. Immunoprecipitation experiments using the P. furiosus cell extracts supported the interaction between PfuAPE and PfuPCNA in the cells. This is the first report describing the physical and functional interactions between an archaeal AP endonuclease and PCNA. We also detected the ternary complex of PfuPCNA, PfuAPE and Pfu uracil-DNA glycosylase. This complex probably functions to enhance the repair of uracil-containing DNA in P. furiosus cells.

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The mechanisms underlying antigenic variation and maintenance of genomic integrity in Mycoplasma pneumoniae and Mycoplasma genitalium

et al. 2020

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Mycoplasma pneumoniae and Mycoplasma genitalium are important causative agents of infections in humans. Like all other mycoplasmas, these species possess genomes that are significantly smaller than that of other prokaryotes. Moreover, both organisms possess an exceptionally compact set of DNA recombination and repair-associated genes. These genes, however, are sufficient to generate antigenic variation by means of homologous recombination between specific repetitive genomic elements. At the same time, these mycoplasmas have likely evolved strategies to maintain the stability and integrity of their 'minimal' genomes. Previous studies have indicated that there are considerable differences between mycoplasmas and other bacteria in the composition of their DNA recombination and repair machinery. However, the complete repertoire of activities executed by the putative recombination and repair enzymes encoded by Mycoplasma species is not yet fully understood. In this paper, we review the current knowledge on the proteins that likely form part of the DNA repair and recombination pathways of two of the most clinically relevant Mycoplasma species, M. pneumoniae and M. genitalium. The characterization of these proteins will help to define the minimal enzymatic requirements for creating bacterial genetic diversity (antigenic variation) on the one hand, while maintaining genomic integrity on the other.

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A versatile endonuclease IV from Thermus thermophilus has uracil-excising and 3′–5′ exonuclease activity

Cited by 5 publications

References 31 publications

Uncoupling of the apyrimidinic/apurinic endonucleolytic and 3′→5′ exonucleolytic activities of the Nfo protein of Mycoplasma pneumoniae through mutation of specific amino acid residues

Uncoupling of the apyrimidinic/apurinic endonucleolytic and 3′→5′ exonucleolytic activities of the Nfo protein of Mycoplasma pneumoniae through mutation of specific amino acid residues

Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus

The mechanisms underlying antigenic variation and maintenance of genomic integrity in Mycoplasma pneumoniae and Mycoplasma genitalium

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