- Article -
| In Silico Biology 8, 0001 (2007); ©2007, Bioinformation Systems e.V. |
An in silico analysis of cytochrome c from Phanerochaete chrysosporium: its amino acid sequence and characterization of gene structural elements
John A. Bumpus1*, Mark Trax1,2, Ashley Reisdorph1, Cindi Boyd3, Damien Gilbert1,3, Sara Techau2 and Roy M. Ventullo2
1 Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, Iowa 50614, USA
2 Department of Biology, Wartburg College, Waverly, Iowa 50677, USA
3 Mathematics and Science Department, Hawkeye Community College, Waterloo, Iowa 50704, USA
* Corresponding authors
Email: john.bumpus@uni.edu
Edited by E. Wingender; received May 08, 2007; revised September 30, 2007; accepted November 11, 2007; published December 15, 2007
Abstract
An in silico approach was used to investigate cytochrome c and the cytochrome c gene of Phanerochaete chrysosporium. The cytochrome c gene contains four introns. Omission of the introns reveals a DNA sequence coding for a complete predicted amino acid sequence for P. chrysosporium cytochrome c consistent with those of other cytochromes c. Fungal cytochromes c often have a short N-terminal peptide preceding a Gly that is the N-terminal amino acid in many cytochromes c. Thus a microexon codes for an N-terminal pentapeptide (MetProTyrAlaPro) in P. chrysosporium that is identical to the N-terminal pentapeptide of Schizosaccharomyces pombe, a well studied yeast, the genome of which bears more similarity to higher eukaryotes than to other fungi. The fourth intron, when omitted, reveals the presence of another microexon resulting in a sequence for the C-terminal portion of the protein and the stop codon. Interestingly, two interpretations for the sequence of this intron leads to predictions that the C-terminal sequence ends with either AlaValAsn or AlaTyr. Selected aspects of the molecular architecture of cytochrome c and regulatory control elements of the P. chrysosporium cytochrome c gene were analyzed and compared to those present in other fungi and to those present in genes for lignin peroxidases and cytochromes P-450, two important families of hemeproteins produced by this fungus.
Keywords: Phanerochaete chrysosporium, white rot fungi, fungi, cytochrome c, amino acid sequence, gene, lignin, lignin peroxidases, biodegradation