Comprehensive genome-wide analysis reveals different classes of enigmatic old yellow enzyme in fungi

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Nizam, Shadab ^a   Verma, Sandhya ^a   Borah, Nilam Nayan ^a   Gazara, Rajesh Kumar ^a   Verma, Praveen Kumar ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE DEHYDROGENASE;

AMINO ACID SEQUENCE; ARTICLE; ASCOMYCETES; BIOSYNTHESIS; CELL LINEAGE; CLASSIFICATION; ENZYMOLOGY; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; OXIDATIVE STRESS; PHYLOGENY; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ASCOMYCOTA; CELL LINEAGE; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENETIC VARIATION; NADPH DEHYDROGENASE; OXIDATIVE STRESS; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 84893824032     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep04013     Document Type: Article

References (42)

1. Warburg, O. &Christian, W. Ein zweites sauerstoffubertragendes Ferment und sein Absorptionspektrum. Naturwissenschaften 20, 688 (1932)
2. Warburg, O. &Christian, W.U ber das gelbe oxydationsferment. Biochem. Z. 263, 228-229 (1933)
3. Saito, K., Thiele, D. J., Davio, M., Lockridge, O. &Massey, V. The cloning and expression of a gene encoding old yellow enzyme from Saccharomyces carlsbergensis. J. Biol. Chem. 266, 20720-20724 (1991) (Pubitemid 21908522)
4. Stott, K., Saito, K., Thiele, D. J. &Massey, V. Old Yellow Enzyme- the discovery of multiple isozymes and a family of related proteins. J. Biol. Chem. 268, 6097-6106 (1993) (Pubitemid 23099294)
5. Massey, V. &Schopfer, L. M. Reactivity of old yellow enzyme with alpha-NADPH and other pyridine nucleotide derivatives. J. Biol. Chem. 261, 1215-22 (1986) (Pubitemid 16103929)
6. French, C. E. &Bruce, N. C. Purification and characterization of morphinone reductase from Pseudomonas putida M10. Biochem. J. 301, 97-103 (1994) (Pubitemid 24214687)
7. French, C. E. &Bruce, N. C. Bacterial morphinone reductase is related to Old- Yellow Enzyme. Biochem. J. 312, 671-678 (1995) (Pubitemid 26005972)
8. Blehert, D. S., Fox, B. G. &Chambliss, G. H. Cloning and sequence analysis of two Pseudomonas flavoprotein xenobiotic reductases. J. Bacteriol. 181, 6254-6263 (1999) (Pubitemid 29512932)
9. White, G. F., Snape, J. R. &Nicklin, S. Biodegradation of glycerol trinitrate and pentaerythritol tetranitrate by Agrobacterium radiobacter. Appl. Environ. Microbiol. 62, 637-642 (1996) (Pubitemid 26047429)
10. French, C. E., Nicklin, S.&Bruce, N. C. Sequence and properties of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2. J. Bacteriol. 178, 6623-6627 (1996) (Pubitemid 26374732)
11. Nivinskas, H. et al. Reduction of aliphatic nitroesters and N-nitramines by Enterobactercloacae PB2 pentaerythritol tetranitrate reductase. FEBS J. 275, 6192-6203 (2008)
12. Miura, K. et al. Molecular cloning of the nemA gene encoding the Nethylmaleimide reductase from Escherichia coli. Biol. Pharm. Bull. 20, 110-112 (1997) (Pubitemid 27065820)
13. Schaller, F. &Weiler, E. W. Molecular cloning and characterization of 12- oxophytodienoate reductase, an enzyme of the octadecanoid signaling pathway from Arabidopsis thaliana. J. Biol. Chem. 272, 28066-28072 (1997) (Pubitemid 27473615)
14. Strassner, J., Furholz, A.,Macheroux, P., Amrhein, N. &Schaller, A. A homolog of Old Yellow Enzyme in tomato - spectral properties and substrate specificity of the recombinant protein. J. Biol. Chem. 274, 35067-35073 (1999) (Pubitemid 129509559)
15. Niino, Y. S., Chakraborty, S., Brown, B. J. &Massey, V. A new old yellow enzyme of Saccharomyces cerevisiae. J. Biol. Chem. 270, 1983-1991 (1995)
16. Miranda,M. et al. Nucleotide sequence and chromosomal localization of the gene encoding the Old Yellow Enzyme from Kluyveromyces lactis. Yeast 11, 459-465 (1995)
17. Komduur, J. A., Leao, A. N.,Monastyrska, I., Veenhuis, M. &Kiel, J. A. Old yellow enzyme confers resistance of Hansenula polymorpha towards allyl alcohol. Curr. Genet. 41, 401-406 (2002) (Pubitemid 36075983)
18. Uchida, K. et al. Acrolein is a product of lipid peroxidation reaction. J. Biol. Chem. 273, 16058-16066 (1998)
19. Trotter, E. W., Collinson, E. J., Dawes, I. W. &Grant, C. M. Old yellow enzymes protect against acrolein toxicity in the yeast Saccharomyces cerevisiae. App. l Environ. Microbiol. 72, 4885-4892 (2006) (Pubitemid 44078817)
20. Kubata, B. K. et al. A key role for old yellow enzyme in the metabolism of drugs by Trypanosoma cruzi. J. Exp. Med. 196, 1241-1251 (2002) (Pubitemid 35304189)
21. Cheng, J. Z., Coyle, C. M., Panaccione, D. G. &OConnor, S. E. A role for old yellow enzyme in ergot alkaloid biosynthesis. J. Am. Chem. Soc. 132, 1776-1777 (2010)
22. Coyle, C. M., Cheng, J. Z., OConnor, S. E. &Panaccione, D. G. An old yellow enzyme gene controls the branch point between Aspergillus fumigatus and Claviceps purpurea ergot alkaloid pathways. Appl Environ Microbiol. 76, 3898-3903 (2010)
23. Brown, B. J., Deng, Z., Karplus, P. A. &Massey, V. On the active site of Old Yellow Enzyme. Role of histidine 191 and asparagine 194. J. Biol. Chem. 273, 32753-32762 (1998) (Pubitemid 28557661)
24. Kohli, R. M. &Massey, V. The oxidative half-reaction of old yellow enzyme. The role of tyrosine 196. J. Biol. Chem. 273, 32763-32770 (1998) (Pubitemid 28557662)
25. Fox, K. M. &Karplus, P. A. Old yellow enzyme at 2A? resolution: overall structure, ligand binding, and comparison with related flavoproteins. Structure 2, 1089-1105 (1994)
26. Kitzing, K. et al. The 1.3A? crystal structure of the flavoprotein YqjM reveals a novel class of old yellow enzymes. J. Biol. Chem. 280, 27904-27913 (2005) (Pubitemid 41076908)
27. Griese, J. J., Jakob, R. P., Schwarzinger, S. &Dobbek, H. Xenobiotic reductase A in the degradation of quinoline by Pseudomonas putida 86: physiological function, structure and mechanism of 8-hydroxycoumarin reduction. J. Mol. Biol. 361, 140-152 (2006) (Pubitemid 44041458)
28. Opperman, D. J., Piater, L. A. &Heerden, E. V. A novel chromate reductase from Thermus scotoductus SA-01 related to old yellow enzyme. J. Bacteriol. 190, 3076-3082 (2008) (Pubitemid 351508208)
29. Goffeau, A. et al. Life with 6000 genes. Science 274, 546-567 (1996) (Pubitemid 26360429)
30. Cuomo, C. A. &Birren, B. W. The fungal genome initiative and lessons learned from genome sequencing. Methods Enzymol. 470, 833-855 (2010)
31. Singh, K., Nizam, S., Sinha, M. &Verma, P. K. Comparative Transcriptome Analysis of the Necrotrophic Fungus Ascochyta rabiei during Oxidative Stress: Insight for Fungal Survival in the Host Plant. PLoS ONE 7, e33128. doi:10.1371/ journal.pone.0033128 (2012)
32. Altschul, S. F. et al. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nuc. Acids Res. 25, 3389-3402 (1997) (Pubitemid 27359211)
33. Eddy, S. R. Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 (2011)
34. Pei, J., Kim, B. H. &Grishin, N. V. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nuc. Acids Res. 36, 2295-2300 (2008) (Pubitemid 351567002)
35. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. and Evol. 17, 540-552 (2000) (Pubitemid 30210700)
36. Ronquist, F. &Huelsenbeck, J. P. Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003) (Pubitemid 37038874)
37. Alexandros, S. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models. Bioinformatics 21, 2688-2690 (2006)
38. Boc, A., Diallo Alpha, B. &Makarenkov, V. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nuc. Acids Res. 40, 573-W579 (2012)
39. Abascal, F., Zardoya, R. &Posada, D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105 (2005) (Pubitemid 40668057)
40. Voorrips, R. E. MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93, 77-78 (2002) (Pubitemid 34496540)
41. Nei, M. &Rooney, A. P. Concerted and birth-and-death evolution in multigene families. Annu Rev Genet. 39, 121-152 (2005) (Pubitemid 43011110)
42. Oberdorfer, G., Steinkellner, G., Stueckler, C., Faber, K. &Gruber, K. Stereopreferences of old yellow enzymes: structure correlations and sequence patterns in enoate reductases. ChemCatChem. 3, 1562-1566 (2011)