An in silico analysis of cytochrome c from phanerochaete chrysosporium: Its amino acid sequence and characterization of gene structural elements

In Silico Biology

Volumn 8, Issue 1, 2008, Pages 1-13

  Bumpus, John A ^a   Trax, Mark ^a,b   Reisdorph, Ashley ^a   Boyd, Cindi ^c   Gilbert, Damien ^a,c   Techau, Sara ^b   Ventullo, Roy M ^b  

^a UNIVERSITY OF NORTHERN IOWA   (United States)

^b WARTBURG COLLEGE   (United States)

^c Hawkeye Community College   (United States)

Author keywords

Amino acid sequence; Biodegradation; Cytochrome c; Fungi; Gene; Lignin; Lignin peroxidases; Phanerochaete chrysosporium; White rot fungi

Indexed keywords

ALANYLVALANYLASPARAGINE; ALANYTYROSINE; CYTOCHROME C; CYTOCHROME P450; DIPEPTIDE; HEMOPROTEIN; LIGNIN PEROXIDASE; METHIONYLPROPYLTYROSYLALANYLPROLINE; PENTAPEPTIDE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER ANALYSIS; COMPUTER MODEL; DNA SEQUENCE; EUKARYOTE; FUNGUS; GENOME; INTRON; NONHUMAN; PHANEROCHAETE; PREDICTION; SCHIZOSACCHAROMYCES POMBE; SEQUENCE HOMOLOGY; STOP CODON;

AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CYTOCHROMES C; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENOME, FUNGAL; INTRONS; MOLECULAR SEQUENCE DATA; PHANEROCHAETE; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 42549103614     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (34)

1. Ballance, D. J. (1986). Sequences important for gene expression in filamentous fungi. Yeast 2, 229-236.
2. Ballance, D. J. (1991). Transformation systems for filamentous fungi and an overview of fungal gene structure. In: Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi, Leong, S. A. and Berka, R. M. (eds.), Marcel Dekker, Inc. New York, N.Y., pp. 1-30.
3. Banci, L., Bertini, I., Rosato, A. and Varani, G. (1999). Mitochondrial cytochromes c: A comparative analysis. J. Biol. Inorg. Chem. 4, 824-837.
4. Barr, D. and Aust, S. D. (1994). Mechanisms white rot fungi use to degrade pollutants. Environ. Sci. Technol. 28, 79A-87A.
5. Bumpus, J. A. (1998). Perspectives on the use of White Rot Fungi in Bioremediation Technologies. In: Bioremediation: Principles and Practices Volume II, Irvine, R. L. and Sikdar, S. K. (eds.), Technomic Publishing Co., Inc., Lancaster, PA., pp. 67-109.
6. Bumpus, J. A. (2004). Biodegradation of Azo Dyes by Fungi. In: Fungal Biotechnology in Agricultural, Food and Environmental Application, 2nd edition, Arora, D. K., Bridge, P. D., Bhatnagar, D. and Bigelow, D. (eds.), Marcel Dekker, Inc., New York, N.Y., pp. 457-469.
7. Bumpus, J. A. and Aust, S. D. (1987). Biodegradation of Environmental Pollutants by the White Rot Fungus Phanerochaete chrysosporium: Involvement of the Lignin Degrading System. BioEssays 6, 166-170.
8. Bumpus, J. A., Tien, M., Wright, D. and Aust, S. D. (1985). Oxidation of persistent enviromental pollutants by a white rot fungus. Science 228 1434-1436.
9. Dickerson, R. E. (1971). The structure of cytochrome c and the rates of molecular evolution. J. Mol. Evol. 1, 26-45.
10. Dickerson, R. E., Takano, T., Eisenberg, D., Kallai, O. B., Samson, L., Cooper, A. and Margoliash, E. (1971). Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 A resolution. J. Biol. Chem. 246, 1511-1535.
11. Dickerson. R. E. (1973). The structure-and history of an ancient protein. In: Organic Chemistry of Life: Readings from Scientific American, Calvin, M. and Pryor, W. A. (eds.), W. H. Freeman, San Francisco, CA, pp. 189-202.
12. Doddapaneni, H., Chakraborty, R. and Yadav, J. S. (2005). Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive-gene clustering. BMC Genomics 6, 92-116.
13. Felsenstein, J. (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166.
14. Germann, U., Müller, G., Hunziker, P. E. and Lerch, K. (1988). Characterization of two allelic forms of Neurospora crassa laccase. Amino- and carboxyl-terminal processing of a precursor. J. Biol. Chem. 263, 885-896.
15. Guindon, S. and Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704.
16. Guindon, S., Lethiec, F., Duroux, P. and Gascuel, O. (2005). PHYML Online-a web server for fast maximum likelihood-based, phylogenetic inference. Nucleic Acids Res. 33, W557-W559.
17. Harvey, P. J. and Thurston, C. F. (2001). The biochemistry of ligninolytic fungi. In: Fungi in Bioremediation, Gadd, G. M. (ed.), Cambridge University Press, Cambridge, UK, pp. 27-51.
18. Hatton, A. R., Subramaniam, V. and Lopez, A. J. (1998). Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions. Mol. Cell 2, 787-796
19. Holzbaur, E. L. F., Andrawis, A. and Tien, M. (1991). Molecular biology of lignin peroxidases from Phanerochaete chrysosporium. In: Molecular.Industrial Mycology: Systems and Applications for Filamentous Fungi, Leong, S. A. and Berka, R. M. (eds.), Marcel Dekker, New York: N. Y., pp. 197-223.
20. Jones, D. T. Taylor, W. R. and Thornton, J. M.(1992). The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
21. Kirk, T. K. and Farrell, R. L. (1987). Enzymatic "combustion": The microbial degradation of lignin. Altnu. Rev. Microbiol. 41, 465-505.
22. Leonowicz, A., Matuszewska, A., Luterek, J., Ziegenhagen, D., Wojtaś-Wasilewska, M., Cho, N-S., Hoftichter, M. and Rogalski, J. (1999). Biodegradation of lignin by white rot fungi. Fungal Genet. Biol. 27, 175-185.
23. Martinez, D., Larrondo, L. F., Putnam, N., Gelpke, M. D., Huang, K., Chapman, J., Helfenbein, K. G., Ramaiya, P., Detter, J. C., Larimer F., Coutinho, P. M., Henrissat, B., Berka, R., Cullen, D. and Rokhsa, D. (2004). Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. NA. Biotechnol. 22, 695-700.
24. Mount, S. M. (2000). Genomic sequence, splicing, and gene annotation. Am. J. Hum. Genet. 67, 788-792.
25. Mills, G. (1991). Cytochrome c: Gene structure, homology and ancestral relationships. J. Theor. Biol. 152, 177-190.
26. Padgett, R. A., Grabowski, P. J., Konarska, M. M., Seiler, S. and Sharp, P. A. (1986). Splicing of messenger RNA precursors. Annu. Rev. Biochem. 55, 1119-1150.
27. Quiles-Rosillo, M. D., Ruiz-Vázques, R. M., Torres-Martínez, S. and Garre, V. (2003). Cloning, characterization and heterologous expression of the Blakeslea trispora gene encoding orotidine-5′-monophosphate decarboxylase. FEMS Microbiol. Lett. 222 229-236.
28. Reddy, C. A. and D'Souza, I M. (1994). Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysospotium. FEMS Microbiol. Rev. 13, 137-152.
29. Sipiczki, M. (2000). Where does fission yeast sit on the tree of life? Genome Biology 1, reviews101.1-1011.4.
30. Sun, Y.-L., Zhao, Y., Hong, X. and Zhai, Z.-H. (1999). Cytochrome c release and caspase activation during menadione-induced apoptosis in plants. FEBS Lett. 462, 317-321.
31. Voet, D. and Voet, J. G. (1995). Biochemistry, 2nd edition. John Wiley and Sons, Inc., New York, p. 947.
32. Yadav, J. S., Soellner, M. B., Loper, J. C. and Mishra, R K. (2003). Tandem cytochrome P-450 monooxygenase genes and splice variants in the white rot fungus Phanerochaete chrysosporium: Cloning, sequence analysis, and regulation of differential expression. Fungal Genet. Biol. 38, 10-21.
33. Wood, V. et al. (2002). The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880.
34. Zhang, Z and Gerstein, M. (2003). The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse. Gene 312, 61-72.