Comparative molecular evolution of Trichoderma chitinases in response to mycoparasitic interactions

Evolutionary Bioinformatics

Volumn 2010, Issue 6, 2010, Pages 1-26

  Ihrmark, Katarina ^a   Asmail, Nashwan ^a   Ubhayasekera, Wimal ^a,b,c   Melin, Petter ^a   Stenlid, Jan ^a   Karlsson, Magnus ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b LUND UNIVERSITY   (Sweden)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Chitinase; Mycoparasitism; Protein evolution; Trichoderma

Indexed keywords

CHITINASE; SIGNAL PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CODON; CODON USAGE; ENZYME SUBSTRATE COMPLEX; GENE DOSAGE; GENE NUMBER; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; HYPOCREA; HYPOCREA ATROVIRIDIS; HYPOCREA JECORINA; HYPOCREA VIRENS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHYLOGENY; TRICHODERMA;

HYPOCREA ATROVIRIDIS; TRICHODERMA;

EID: 77951266103     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article

References (68)

1. Hjeljord L, Tronsmo A. In: Harman GE, Kubicek CP, editors. Trichoderma and Gliocladium. Taylor and Francis. 1998; p. 131-51.
2. Harman GE, Howell CR, Viterbo A, Chet I, Lorito M. Trichoderma species- Opportunistic, avirulent plant symbionts. Nature Rev Microbiol. 2004;2:43-56.
3. Chet I, Harman GE, Baker R. Trichoderma hamatum-Its hyphal interactions with Rhizoctonia solani and Pythium spp. Microb Ecol. 1981; 7:29-38.
4. Schirmbock M, Lorito M, Wang YL, et al. Parallel formation and synergism of hydrolytic enzymes and peptaibol antibiotics, molecular mechanisms involved in the antagonistic action of Trichoderma harzianum against phytopathogenic fungi. Appl Environ Microb. 1994;60:4364-70.
5. Howell CR. Mechanisms employed by Trichoderma species in the biological control of plant diseases: The history and evolution of current concepts. Plant Dis. 2003;87:4-10.
6. Benitez T, Rincon AM, Limon MC, Codon AC. Biocontrol mechanisms of Trichoderma strains. Int Microbiol. 2004;7:249-60.
7. Karlsson M, Stenlid J. Comparative evolutionary histories of the fungal chitinase gene family reveal non-random size expansions and contractions due to adaptive natural selection. Evol Bioinform. 2008:47-60.
8. Duo-Chuan L. Review of fungal chitinases. Mycopathologia. 2006; 161:345-60.
9. Seidl V. Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions. Fungal Biol Rev. 2008;22:36-42.
10. Seidl V, Huemer B, Seiboth B, Kubicek CP. A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases. FEBS J. 2005;272:5923-39.
11. Seidl V, Gruber S, López-Mondéjar R, Zach S, Kubicek CP. The chitinolytic machinery of the mycoparasitic fungus Trichoderma atroviride. Proc 9th Int Conf Eur Chitin Soc. 2009. In press.
12. Karlsson M, Stenlid J. Evolution of family 18 glycoside hydrolases:Diversity, domain structures and phylogenetic relationships. J Mol Microbiol Biotechnol. 2009;16:208-23.
13. Limon MC, Margolles-Clark E, Benitez T, Penttila M. Addition of substrate- binding domains increases substrate-binding capacity and specific activity of a chitinase from Trichoderma harzianum. FEMS Microbiol Lett. 2001;198:57-63.
14. Klemsdal SS, Clarke JHL, Hoell IA, Eijsink VGH, Brurberg MB. Molecular cloning, characterization, and expression studies of a novel chitinase gene (ech30) from the mycoparasite Trichoderma atroviride strain P 1. FEMS Microbiol Lett. 2006;256:282-9.
15. Kim DJ, Baek JM, Uribe P, Kenerley CM, Cook DR. Cloning and characterization of multiple glycosyl hydrolase genes from Trichoderma virens. Curr Genet. 2002;40:374-84.
16. Viterbo A, Montero M, Ramot O, et al. Expression regulation of the endochitinase chit36 from Trichoderma asperellum (T. harzianum T-203). Curr Genet. 2002;42:114-22.
17. de las Mercedes Dana M, Carmen Limón M, Mejias R, et al. Regulation of chitinase 33 (chit33) gene expression in Trichoderma harzianum. Curr Genet. 2001;38:335-42.
18. Zeilinger S, Galhaup C, Payer K, et al. Chitinase gene expression during mycoparasitic interaction of Trichoderma harzianum with its host. Fungal Genet Biol. 1999;26:131-40.
19. Bishop JG, Dean AM, Mitchell-Olds T. Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution. Proc Natl Acad Sci U S A. 2000;97:5322-7.
20. Tiffin P. Comparative evolutionary histories of chitinase genes in the genus Zea and family Poaceae. Genetics. 2004;167:1331-40.
21. Gardes M, Bruns TD. Its primers with enhanced specificity for basidiomycetes- Application to the identification of mycorrhizae and rusts. Mol Ecol. 1993;2:113-8.
22. White TJ, Bruns T, Lee S, Taylor J. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, Editors PCR protocols: A guide to methods and applications. San Diego:Academic; 1990;315-22.
23. Druzhinina IS, Kopchinskiy AG, Komon M, et al. An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genet Biol. 2005;42:813-28.
24. Hall TA. BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95-8.
25. Rozen S, Skaletsky H. In: Krawetz S, Misener S, editors. Bioinformatics methods and protocols:Methods in molecular biology. Totowa: Humana Press; 2000;365-86.
26. De Bie T, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution. Bioinformatics. 2006;22:1269-71.
27. Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 2005;15:1153-60.
28. Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
29. Zdobnov EM, Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17:847-8.
30. Thompson JD, Higgins DG, Gibson TJ. Clustal-W-Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673-80.
31. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol. 2007;24:1596-9.
32. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comp Appl Biosci. 1992;8:275-82.
33. Larkin MA, Blackshields G, Brown NP, et al. Clustal W and clustal X version 2.0. Bioinformatics. 2007;23:2947-8.
34. Lee T. Reverse conservation analysis reveals the specificity determining residues of cytochrome P450 family 2 (CYP 2). Evol Bioinform. 2008;4:7-16.
35. Mayrose I, Graur D, Ben-Tal N, Pupko T. Comparison of site-specific rateinference methods for protein sequences: Empirical bayesian methods are superior. Mol Biol Evol. 2004;21:1781-91.
36. Pupko T, Bell R, Mayrose I, Glaser F, Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics. 2002;18:S71-7.
37. Peden JF. Analysis of codon usage. Nottingham: University of Nottingham; 1999.
38. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. Gen- Bank. Nucleic Acids Res. 2008;36:D25-30.
39. Karplus K, Katzman S, Shackleford G, et al. SAM-T04: what is new in protein-structure prediction for CASP 6. Proteins. 2005;61:135-42.
40. Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res. 2000;28:235-42.
41. Kleywegt GJ, Zou JY, Kjeldgaard M, Jones TA. In: Rossmann MG, Arnold E, editors. International tables for crystallography, Vol. F. Crystallography of biological macromolecules. Dordrecht: Kluwer Academic; 2001;353-6,366-7.
42. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallogr A. 1991;47:110-9.
43. Rao FV, Houston DR, Boot RG, et al. Specificity and affinity of natural product cyclopentapeptide inhibitors against A. fumigatus, human, and bacterial chitinases. Chem Biol. 2005;12:65-76.
44. Cavada BS, Moreno FBB, da Rocha BAM, et al. cDNA cloning and 1.75 angstrom crystal structure determination of PPL2, an endochitinase and N-acetylglucosamine-binding hemagglutinin from Parkia platycephala seeds. FEBS J. 2006;273:3962-74.
45. Hurtado-Guerrero R, van Aalten DMF. Structure of Saccharomyces cerevisiae chitinase 1 and screening-based discovery of potent inhibitors. Chem Biol. 2007;14:589-99.
46. Kraulis PJ. Molscript-a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr. 1991;24:946-50.
47. Harris M, Jones TA. Molray-a web interface between O and the POV-Ray ray tracer. Acta Crystallogr D. 2001;57:1201-3.
48. Pond SLK, Frost SDW. Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 2005;22:1208-22.
49. Pond SLK, Frost SDW, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21:676-9.
50. Pond SLK, Frost SDW. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005;21:2531-3.
51. Pond SLK, Frost SDW. A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol. 2005;22:223-34.
52. Lanave C, Preparata G, Saccone C, Serio G. A new method for calculating evolutionary substitution rates. J Mol Evol. 1984;20:86-93.
53. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci. 1986;17:57-86.
54. Rodriguez F, Oliver JL, Marin A, Medina JR. The general stochastic-model of nucleotide substitution. J Theor Biol. 1990;142:485-501.
55. Poon A, Lewis F, Pond SLK, Frost S. An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comp Biol. 2007;3:e231.
56. Marchler-Bauer A, Anderson JB, Cherukuri PF, et al. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 2005;33: D192-6.
57. Druzhinina I, Kubicek CP. Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters. J Zhejiang Univ. 2005;6B:100-12.
58. Wapinski I, Pfeffer A, Friedman N, Regev A. Natural history and evolutionary principles of gene duplication in fungi. Nature. 2007;449:54-U36.
59. Hoell IA, Klemsdal SS, Vaaje-Kolstad G, Horn SJ, Eijsink VGH. Overexpression and characterization of a novel chitinase from Trichoderma atroviride strain P 1. Biochim Biophys Acta Prot Proteom. 2005;1748:180-90.
60. Delacruz J, Hidalgogallego A, Lora JM, et al. Isolation and characterization of 3 chitinases from Trichoderma harzianum. Eur J Biochem. 1992;206:859-67.
61. Boer H, Munck N, Natunen J, et al. Differential recognition of animal type beta 4-galactosylated and alpha 3-fucosylated chito-oligosaccharides by two family 18 chitinases from Trichoderma harzianum. Glycobiology. 2004;14:1303-13.
62. Haran S, Schickler H, Oppenheim A, Chet I. Differential expression of Trichoderma harzianum chitinases during mycoparasitism. Phytopathology. 1996;86:980-5.
63. Carsolio C, Gutierrez A, Jimenez B, Vanmontagu M, Herreraestrella A. Characterization of Ech-42, a Trichoderma harzianum endochitinase gene expressed during mycoparasitism. Proc Natl Acad Sci U S A. 1994; 91:10903-7.
64. Garcia I, Lora JM, Delacruz J, et al. Cloning and characterization of a chitinase (Chit42) cdna from the mycoparasitic fungus Trichoderma harzianum. Curr Genet. 1994;27:83-9.
65. Mach RL, Peterbauer CK, Payer K, et al. Expression of two major chitinase genes of Trichoderma atroviride (T. harzianum P1) is triggered by different regulatory signals. Appl Environ Microbiol. 1999;65:1858-63.
66. Carsolio C, Benhamou N, Haran S, et al. Role of the Trichoderma harzianum endochitinase gene, ech42, in mycoparasitism. Appl Environ Microbiol. 1999;65:929-35.
67. Woo SL, Donzelli B, Scala F, et al. Disruption of the ech42 (endochitinaseencoding) gene affects biocontrol activity in Trichoderma harzianum P 1. Mol Plant Microbe In. 1999;12:419-29.
68. Baek JM, Howell CR, Kenerley CM. The role of an extracellular chitinase from Trichoderma virens Gv29-8 in the biocontrol of Rhizoctonia solani. Curr Genet. 1999;35:41-50.