Sequence Analysis and Structural Characterization

Authors: Sudeshna Sengupta T S Chandra

Publish Date: 2010/09/06

Volume: 171, Issue: 2, Pages: 123-131

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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 glyceraldehyde3phosphate dehydrogenase GPD through reverse transcriptase polymerase chain reaction RT–PCR and 5′3′ rapid amplification of cDNA ends RACEPCR This nucleotide sequence had a high similarity of 88 with GPD sequence of Ashbya gossypii The putative GPD peptide of 331aa 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 3558 kDa with an estimated pI of 57 A neighborjoining 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 Kluyveromycesmarxianus GPD PDB 2I5P as template indicated high structural similarityWe would like to acknowledge Dept of Biotechnology DBT Govt of India for supporting this project We thank Prof Peter Philippsen Biozentrum Basel for hosting Sudeshna under the ISJRP funding and to carry out RACEPCR in his laboratory We would like to thank Mr Ravishankar and Dr N Manoj for helping us with the bioinformatics analysis

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