Sequence analysis and structural characterization of a glyceraldehyde-3-phosphate dehydrogenase gene from the phytopathogenic fungus Eremothecium ashbyi

Mycopathologia. 2011 Feb;171(2):123-31. doi: 10.1007/s11046-010-9357-7. Epub 2010 Sep 6.

Abstract

Eremothecium ashbyi is a phytopathogenic fungus infesting cotton, soybeans and several other plants. This highly flavinogenic fungus has been phylogenetically characterized, but the genetic aspects of its central metabolic and riboflavin biosynthetic pathways are unknown. An ORF of 996 bp was obtained from E. ashbyi by using degenerate primers for glyceraldehyde-3-phosphate dehydrogenase (GPD) through reverse transcriptase polymerase chain reaction (RT-PCR) and 5'-3' rapid amplification of cDNA ends (RACE-PCR). This nucleotide sequence had a high similarity of 88% with GPD sequence of Ashbya gossypii. The putative GPD peptide of 331-aa had a high similarity of 85% with the GPD sequence from other ascomycetes. The ORF had an unusually strong codon bias with 5 amino acids showing strict preference of a single codon. The theoretical molecular weight for the putative peptide was 35.58 kDa with an estimated pI of 5.7. A neighbor-joining tree showed that the putative peptide from E. ashbyi displayed the highest similarity to GPD of A. gossypii. The gene sequence is available at the GenBank, accession number EU717696. Homology modeling done with Kluyveromyces marxianus GPD (PDB: 2I5P) as template indicated high structural similarity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Cloning, Molecular
  • Cluster Analysis
  • DNA, Fungal / chemistry
  • DNA, Fungal / genetics
  • Eremothecium / enzymology*
  • Glyceraldehyde-3-Phosphate Dehydrogenases / chemistry*
  • Glyceraldehyde-3-Phosphate Dehydrogenases / genetics*
  • Isoelectric Point
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Weight
  • Phylogeny
  • Protein Structure, Secondary
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid

Substances

  • DNA, Fungal
  • Glyceraldehyde-3-Phosphate Dehydrogenases

Associated data

  • GENBANK/EU717696