Biochemical characterization of an ATP-dependent DNA ligase from the hyperthermophilic crenarchaeon Sulfolobus shibatae

Lai, Xiaoqin; Shao, Hongbing; Hao, Fushun; Huang, Li

doi:10.1007/s00792-002-0284-5

Cited by 35 publications

(38 citation statements)

References 31 publications

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“…1a). Previous analysis suggests that enzymes from Crenarchaea are homologues of Eukaryotic DNA ligase I, whilst the versions from Euryarchaea are more similar to ATP-dependent enzymes from some Viruses (Lai et al 2002). Interestingly, motif V of DNA ligases from the Thermoplasmatales, which includes FaLig, are more similar to DNA ligases from Crenarchaeota compared to those from Euryarchaeota (Fig.…”

Section: Identification Of An Atp-dependent Dna Ligase Within the Genmentioning

confidence: 89%

“…In terms of archaea that grow at neutral pH, the optimal activity of their DNA ligases has been detected to be pH 7-8.5 (Jeon and Ishikawa 2003;Keppetipola and Shuman 2005;Rolland et al 2004;Sriskanda et al 2000). For DNA ligase from S. shibatae, which is able to grow at pH 2-4, optimal nickjoining was detected at pH 6-7 (Lai et al 2002). From these results it is tempting to speculate that those organisms that can grow in acidic environments have DNA ligases with pH optima that are more acidic.…”

Section: Biochemical Characterization Of Nick-joining By Faligmentioning

confidence: 94%

“…Generally, the putative DNA ligases of Archaea are of fairly uniform size and their primary structures are extensively conserved. Despite this overall similarity, DNA ligases from Crenarchaeota and Euryarchaeota differ in the sequence of motif V as well as in the spacing between some motifs (Lai et al 2002) (also see Fig. 1b).…”

Section: Introductionmentioning

confidence: 98%

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Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “Ferroplasma acidarmanus” Fer1

et al. 2006

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Section: Identification Of An Atp-dependent Dna Ligase Within the Genmentioning

confidence: 89%

Section: Biochemical Characterization Of Nick-joining By Faligmentioning

confidence: 94%

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Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “Ferroplasma acidarmanus” Fer1

et al. 2006

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“…6, lane 2). Consequently, nucleotides known to interfere with DNA repair and replication processes such as ATP (replication clamp assembly, DNA helicase activation and charging of archaeal and mammalian DNA ligases by adenylation) (22,32,36), ADP (a possible alternative for ATP in [hyper]thermophiles) (27), AMP (the energy-deficient counterpart to ATP and/or ADP which may inhibit their action), and NAD (charging of bacterial DNA ligases by adenylation) (32,49) were assayed for their effect on BER with or without dNTPs added. When [␣-32 P]dCTP was used as the labeling nucleotide, a direct comparison of the short-patch and long-patch BER modes can be made from the amount of repair intermediates formed.…”

Section: Excision Of Uracil From Dna By T Acidophilum Cell Extractmentioning

confidence: 99%

Uracil-DNA Glycosylase of Thermoplasma acidophilumDirects Long-Patch Base Excision Repair, Which Is Promoted by Deoxynucleoside Triphosphates and ATP/ADP, into Short-Patch Repair

et al. 2011

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Hydrolytic deamination of cytosine to uracil in DNA is increased in organisms adapted to high temperatures. Hitherto, the uracil base excision repair (BER) pathway has only been described in two archaeons, the crenarchaeon Pyrobaculum aerophilum and the euryarchaeon Archaeoglobus fulgidus, which are hyperthermophiles and use single-nucleotide replacement. In the former the apurinic/apyrimidinic (AP) site intermediate is removed by the sequential action of a 5-acting AP endonuclease and a 5-deoxyribose phosphate lyase, whereas in the latter the AP site is primarily removed by a 3-acting AP lyase, followed by a 3-phosphodiesterase. We describe here uracil BER by a cell extract of the thermoacidophilic euryarchaeon Thermoplasma acidophilum, which prefers a similar short-patch repair mode as A. fulgidus. Importantly, T. acidophilum cell extract also efficiently executes ATP/ADP-stimulated long-patch BER in the presence of deoxynucleoside triphosphates, with a repair track of ϳ15 nucleotides. Supplementation of recombinant uracil-DNA glycosylase (rTaUDG; ORF Ta0477) increased the formation of short-patch at the expense of long-patch repair intermediates, and additional supplementation of recombinant DNA ligase (rTalig; Ta1148) greatly enhanced repair product formation. TaUDG seems to recruit AP-incising and -excising functions to prepare for rapid singlenucleotide insertion and ligation, thus excluding slower and energy-costly long-patch BER.In all cells, deamination of cytosine to uracil is only surpassed by depurination as the most common hydrolytic DNAdamaging event (38). While the apurinic/apyrimidinic (AP) site is primarily a cytotoxic lesion inhibiting replication or transcription, deaminated cytosines result in G ⅐ C to A ⅐ T transition mutations if they are not repaired before DNA synthesis. In addition, some dUTP escapes hydrolysis by dUTPase causing a certain amount of uracil introduced into DNA opposite adenine during replication (5, 32).Uracil is excised from DNA by a specific monofunctional uracil-DNA glycosylase (UDG) enzyme in virtually all organisms, including those living at the highest temperatures (22,33,47). After such enzyme-catalyzed, as well as spontaneous, base removal, a single nucleotide is reinserted by the sequential action of a 5Ј-acting AP endonuclease, 5Ј-deoxyribose phosphate (5Ј-dRP) lyase, DNA polymerase, and DNA ligase (22, 32), which constitute the short-patch mode of the base excision repair (BER) pathway. In eukaryotes, like mammals, the 5Ј-dRP lyase activity (35, 41) is a function of DNA polymerase ␤ (41, 62). BER is quantitatively the most important repair mechanism for the removal of spontaneously generated base modifications in DNA and is thus necessary to secure genomic integrity (38). The 5Ј-AP site remnant following strand incision blocks ligation, and when it is chemically modified in such a way that efficient removal by the 5Ј-dRP lyase is obstructed, polymerization will continue past one nucleotide and the downstream DNA strand is displaced. This long-patch mode of BER ...

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“…The biochemical characterization of DNA ligase from the euryarchaeon Methanobacterium thermautotrophicum revealed that its sealing reaction depended on ATP and that NAD ϩ could not substitute for ATP (20). Utilization of ATP but not NAD ϩ was also reported for the DNA ligase encoded by the crenarchaeon Sulfolobus shibatae (9). Given that all known archaeal proteomes contain a single homolog of the M. thermautotrophicum ligase enzyme and none contain an obvious homolog of bacterial NAD ϩ -dependent ligase, it was presumed that the archaeal ligases would rely exclusively on ATP as their nucleotide substrate.…”

mentioning

confidence: 97%

Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii

Keppetipola

Shuman

2005

J Bacteriol

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Archaea encode a DNA ligase composed of a C-terminal catalytic domain typical of ATP-dependent ligases plus an N-terminal domain similar to that found in eukaryotic cellular and poxvirus DNA ligases. All archaeal DNA ligases characterized to date have ATP-dependent adenylyltransferase and nick-joining activities. However, recent reports of dual-specificity ATP/NAD ؉ ligases in two Thermococcus species and Pyrococcus abyssi and an ATP/ADP ligase in Aeropyrum pernix raise the prospect that certain archaeal enzymes might exemplify an undifferentiated ancestral stage in the evolution of ligase substrate specificity. Here we analyze the biochemical properties of Pyrococcus horikoshii DNA ligase. P. horikoshii ligase catalyzes autoadenylylation and nick sealing in the presence of a divalent cation and ATP; it is unable to utilize NAD ؉ or ADP to promote ligation in lieu of ATP. P. horikoshii ligase is thermophilic in vitro, with optimal adenylyltransferase activity at 90°C and nick-joining activity at 70 to 90°C. P. horikoshii ligase resembles the ligases of Methanobacterium thermautotrophicum and Sulfolobus shibatae in its strict specificity for ATP.DNA ligases are essential components of the DNA replication, repair, and recombination machinery in all domains of the phylogenetic tree: eucarya, archaea, and bacteria. Ligases seal 3Ј OH and 5Ј PO 4 ends via three nucleotidyl transfer reactions (10). First, a lysine nucleophile on the enzyme attacks the ␣-phosphorus of ATP or NAD ϩ , which results in the formation of a covalent ligase-adenylate intermediate and the release of pyrophosphate or nicotinamide mononucleotide. Second, attack by the 5Ј PO 4 on ligase-adenylate results in expulsion of the active-site lysine and formation of an activated DNA-adenylate intermediate. Third, ligase catalyzes the attack of a 3Ј OH on the DNA-adenylate, resulting in the release of AMP and formation of a phosphodiester.DNA ligases are grouped into two families, depending on their requirement for ATP or NAD ϩ in the ligase adenylylation reaction. Whereas NAD ϩ -dependent ligases are found only in bacteria and eukaryotic viruses, ATP-dependent DNA ligases are found in bacteria (and bacteriophages), eucarya (and eukaryotic viruses), and archaea (8,10,21,27). A core ligase module composed of nucleotidyltransferase and OB-fold domains is shared by all known DNA ligases (3,15,16,24). The adenylate-binding pocket is located within the nucleotidyltransferase domain and is composed of five conserved peptide motifs (19). The substrate specificity of NAD ϩ -dependent ligase is dictated by a unique domain that binds the nicotinamide mononucleotide component of the nucleotide substrate (3, 23); the specificity of ATP-dependent ligases is determined, at least in part, by a distinctive motif within the OB-fold domain that coordinates the beta and gamma phosphates of the nucleotide (5,19,22).The archaea are unicellular anucleate organisms with distinctive biosynthetic capacities and an ability to thrive under extreme environmental conditions. The dom...

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Biochemical characterization of an ATP-dependent DNA ligase from the hyperthermophilic crenarchaeon Sulfolobus shibatae

Cited by 35 publications

References 31 publications

Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “Ferroplasma acidarmanus” Fer1

Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “Ferroplasma acidarmanus” Fer1

Uracil-DNA Glycosylase of Thermoplasma acidophilumDirects Long-Patch Base Excision Repair, Which Is Promoted by Deoxynucleoside Triphosphates and ATP/ADP, into Short-Patch Repair

Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii

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