Novel DNA ligase with broad nucleotide cofactor specificity from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii: influence of ancestral DNA ligase on cofactor utilization.
DNA ligases are divided into two groups according to their cofactor requirement to form ligase-adenylate, ATP-dependent DNA ligases and NAD(+)-dependent DNA ligases. The conventional view that archaeal DNA ligases only utilize ATP has recently been disputed with discoveries of dual-specificity DNA ligases (ATP/ADP or ATP/NAD(+)) from the orders Desulfurococcales and Thermococcales. Here, we studied DNA ligase encoded by the hyperthermophilic crenarchaeon Sulfophobococcus zilligii. The ligase exhibited multiple cofactor specificity utilizing ADP and GTP in addition to ATP. The unusual cofactor specificity was confirmed via a DNA ligase nick-closing activity assay using a fluorescein/biotin-labelled oligonucleotide and a radiolabelled oligonucleotide. The exploitation of GTP as a catalytic energy source has not to date been reported in any known DNA ligase. This phenomenon may provide evolutionary evidence of the nucleotide cofactor utilization by DNA ligases. To bolster this hypothesis, we summarize and evaluate previous assertions. We contend that DNA ligase evolution likely started from crenarchaeotal DNA ligases and diverged to eukaryal DNA ligases and euryarchaeotal DNA ligases. Subsequently, the NAD(+)-utilizing property of some euryarchaeotal DNA ligases may have successfully differentiated to bacterial NAD(+)-dependent DNA ligases.
Sun
Younguk
Y
Department of Genetic Engineering, Sungkyunkwan University, 300 Chunchun-dong, Jangan-gu, Suwon 440-746, Korea.
Seo
Moo Seok
MS
Kim
Jae Hyun
JH
Kim
Yun Jae
YJ
Kim
Gun A
GA
Lee
Jong Il
JI
Lee
Jung-Hyun
JH
Kwon
Suk-Tae
ST
D000244:Adenosine Diphosphate / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D003067:Coenzymes / Q000494:pharmacology*; D004247:DNA / Q000378:metabolism; D053904:DNA Breaks, Single-Stranded; D011088:DNA Ligases / Q000235:genetics* / Q000378:metabolism*; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D019620:Desulfurococcaceae / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D006160:Guanosine Triphosphate / Q000378:metabolism; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000494:pharmacology*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D003067:Coenzymes; D019641:DNA, Archaeal; D009711:Nucleotides; D000244:Adenosine Diphosphate; D006160:Guanosine Triphosphate; D000255:Adenosine Triphosphate; D004247:DNA; D011088:DNA Ligases