Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes

Biochemistry. 2012 Feb 7;51(5):1009-19. doi: 10.1021/bi2014739. Epub 2012 Jan 27.

Abstract

5-Hydroxymethylcytosine (5-hmC) is an enzymatic oxidative product of 5-methylcytosine (5-mC). The Ten Eleven Translocation (TET) family of enzymes catalyze the conversion of 5-mC to 5-hmC. Phage-encoded glucosyltransferases are known to glucosylate 5-hmC, which can be utilized to detect and analyze the 5-hmC as an epigenetic mark in the mammalian epigenome. Here we have performed a detailed biochemical characterization and steady-state kinetic parameter analysis of T4 phage β-glucosyltransferase (β-GT). Recombinant β-GT glucosylates 5-hmC DNA in a nonprocessive manner, and binding to either 5-hmC DNA or uridine diphosphoglucose (UDP-glucose) substrates is random, with both binary complexes being catalytically competent. Product inhibition studies with β-GT demonstrated that UDP is a competitive inhibitor with respect to UDP-glucose and a mixed inhibitor with respect to 5-hmC DNA. Similarly, the glucosylated-5-hmC (5-ghmC) DNA is a competitive inhibitor with respect to 5-hmC DNA and mixed inhibitor with respect to UDP-glucose. 5-hmC DNA binds ~10 fold stronger to the β-GT enzyme when compared to its glucosylated product. The numbers of 5-hmC on target sequences influenced the turnover numbers for recombinant β-GT. Furthermore, we have utilized recombinant β-GT to estimate global 5-hmC content in a variety of genomic DNAs. Most of the genomic DNAs derived from vertebrate tissue and cell lines contained 5-hmC. DNA from mouse, human, and bovine brains displayed 0.5-0.9% of the total nucleotides as 5-hmC, which was higher compared to the levels found in other tissues. A comparison between cancer and healthy tissue genomes suggested a lower percentage of 5-hmC in cancer, which may reflect the global hypomethylation of 5-mC observed during oncogenesis.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • Animals
  • Arabidopsis Proteins / chemistry
  • Arabidopsis Proteins / genetics
  • Bacteriophage T4 / enzymology
  • Cattle
  • Cytosine / analogs & derivatives*
  • Cytosine / chemistry
  • Deoxyribonucleases, Type II Site-Specific / chemistry
  • Deoxyribonucleases, Type II Site-Specific / genetics
  • Escherichia coli / enzymology
  • Escherichia coli / virology
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Female
  • Genome, Plant / genetics
  • Genome, Viral / genetics
  • Glucosyltransferases / antagonists & inhibitors
  • Glucosyltransferases / chemistry*
  • Glucosyltransferases / genetics
  • HCT116 Cells
  • HEK293 Cells
  • Humans
  • Male
  • Mice
  • NIH 3T3 Cells
  • Rats
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Substrate Specificity / genetics

Substances

  • Arabidopsis Proteins
  • Escherichia coli Proteins
  • Recombinant Proteins
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • Glucosyltransferases
  • sucrose synthase
  • DNA beta-glucosyltransferase
  • endodeoxyribonuclease MfeI
  • Deoxyribonucleases, Type II Site-Specific