skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships

Abstract

Background Cytochrome P450s form an important group of enzymes involved in xenobiotics degradation and metabolism, both primary and secondary. These enzymes are also useful in industry as biotechnological tools for bioconversion and a few are reported to be involved in pathogenicity. Trichoderma spp. are widely used in industry and agriculture and are known for their biosynthetic potential of a large number of secondary metabolites. For realising the full biosynthetic potential of an organism, it is important to do a genome-wide annotation and cataloguing of these enzymes. Results Here, we have studied the genomes of seven species (T. asperellum, T. atroviride, T. citrinoviride, T. longibrachiatum, T. reesei , T. harzianum and T. virens) and identified a total of 477 cytochrome P450s. We present here the classification, evolution and structure as well as predicted function of these proteins. This study would pave the way for functional characterization of these groups of enzymes and will also help in realization of their full economic potential. Conclusion Our CYPome annotation and evolutionary studies of the seven Trichoderma species now provides opportunities for exploration of research-driven strategies to select Trichoderma species for various applications especially in relation to secondary metabolism and degradation of environmental pollutants.

Authors:
 [1];  [1];  [1];  [2];  [2];  [2];  [3];  [1]
  1. Bhabha Atomic Research Centre (BARC), Mumbai (India)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Technische Univ. Wien, Vienna (Austria)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1544287
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Fungal Biology and Biotechnology
Additional Journal Information:
Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2054-3085
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Chadha, Sonia, Mehetre, Sayaji T., Bansal, Ravindra, Kuo, Alan, Aerts, Andrea, Grigoriev, Igor V., Druzhinina, Irina S., and Mukherjee, Prasun K. Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships. United States: N. p., 2018. Web. doi:10.1186/s40694-018-0056-3.
Chadha, Sonia, Mehetre, Sayaji T., Bansal, Ravindra, Kuo, Alan, Aerts, Andrea, Grigoriev, Igor V., Druzhinina, Irina S., & Mukherjee, Prasun K. Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships. United States. doi:10.1186/s40694-018-0056-3.
Chadha, Sonia, Mehetre, Sayaji T., Bansal, Ravindra, Kuo, Alan, Aerts, Andrea, Grigoriev, Igor V., Druzhinina, Irina S., and Mukherjee, Prasun K. Mon . "Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships". United States. doi:10.1186/s40694-018-0056-3. https://www.osti.gov/servlets/purl/1544287.
@article{osti_1544287,
title = {Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships},
author = {Chadha, Sonia and Mehetre, Sayaji T. and Bansal, Ravindra and Kuo, Alan and Aerts, Andrea and Grigoriev, Igor V. and Druzhinina, Irina S. and Mukherjee, Prasun K.},
abstractNote = {Background Cytochrome P450s form an important group of enzymes involved in xenobiotics degradation and metabolism, both primary and secondary. These enzymes are also useful in industry as biotechnological tools for bioconversion and a few are reported to be involved in pathogenicity. Trichoderma spp. are widely used in industry and agriculture and are known for their biosynthetic potential of a large number of secondary metabolites. For realising the full biosynthetic potential of an organism, it is important to do a genome-wide annotation and cataloguing of these enzymes. Results Here, we have studied the genomes of seven species (T. asperellum, T. atroviride, T. citrinoviride, T. longibrachiatum, T. reesei , T. harzianum and T. virens) and identified a total of 477 cytochrome P450s. We present here the classification, evolution and structure as well as predicted function of these proteins. This study would pave the way for functional characterization of these groups of enzymes and will also help in realization of their full economic potential. Conclusion Our CYPome annotation and evolutionary studies of the seven Trichoderma species now provides opportunities for exploration of research-driven strategies to select Trichoderma species for various applications especially in relation to secondary metabolism and degradation of environmental pollutants.},
doi = {10.1186/s40694-018-0056-3},
journal = {Fungal Biology and Biotechnology},
number = 1,
volume = 5,
place = {United States},
year = {2018},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

CYPome of the conifer pathogen Heterobasidion irregulare: Inventory, phylogeny, and transcriptional analysis of the response to biocontrol
journal, February 2017


Trichoderma: the genomics of opportunistic success
journal, September 2011

  • Druzhinina, Irina S.; Seidl-Seiboth, Verena; Herrera-Estrella, Alfredo
  • Nature Reviews Microbiology, Vol. 9, Issue 10
  • DOI: 10.1038/nrmicro2637

Metazoan cytochrome P450 evolution
journal, November 1998

  • Nelson, David R.
  • Comparative Biochemistry and Physiology Part C: Pharmacology, Toxicology and Endocrinology, Vol. 121, Issue 1-3
  • DOI: 10.1016/S0742-8413(98)10027-0

Identification and characterization of a pathogenicity-related gene VdCYP1 from Verticillium dahliae
journal, June 2016

  • Zhang, Dan-Dan; Wang, Xin-Yan; Chen, Jie-Yin
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep27979

Involvement of Trichoderma Trichothecenes in the Biocontrol Activity and Induction of Plant Defense-Related Genes
journal, May 2012

  • Malmierca, M. G.; Cardoza, R. E.; Alexander, N. J.
  • Applied and Environmental Microbiology, Vol. 78, Issue 14
  • DOI: 10.1128/AEM.00385-12

AliView: a fast and lightweight alignment viewer and editor for large datasets
journal, August 2014


Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium
journal, June 2002

  • Ward, T. J.; Bielawski, J. P.; Kistler, H. C.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 14
  • DOI: 10.1073/pnas.142307199

Cytochrome P450 enzymes in the fungal kingdom
journal, January 2011

  • Črešnar, B.; Petrič, Š.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1814, Issue 1
  • DOI: 10.1016/j.bbapap.2010.06.020

Secondary metabolism in Trichoderma – Chemistry meets genomics
journal, June 2016

  • Zeilinger, Susanne; Gruber, Sabine; Bansal, Ravindra
  • Fungal Biology Reviews, Vol. 30, Issue 2
  • DOI: 10.1016/j.fbr.2016.05.001

P450 monooxygenases (P450ome) of the model white rot fungus Phanerochaete chrysosporium
journal, March 2012


CYP56 (Dit2p) in Candida albicans: Characterization and Investigation of Its Role in Growth and Antifungal Drug Susceptibility
journal, July 2008

  • Melo, N. R.; Moran, G. P.; Warrilow, A. G. S.
  • Antimicrobial Agents and Chemotherapy, Vol. 52, Issue 10
  • DOI: 10.1128/AAC.00446-08

The cytochromes P450 of Grosmannia clavigera: Genome organization, phylogeny, and expression in response to pine host chemicals
journal, January 2013


Identification of novel gene clusters for secondary metabolism in Trichoderma genomes
journal, March 2016


Inactivation of a cytochrome P-450 is a determinant of trichothecene diversity in Fusarium species
journal, August 2002


Characterization of the sterol 14α-demethylases of Fusarium graminearum identifies a novel genus-specific CYP51 function
journal, February 2013

  • Fan, Jieru; Urban, Martin; Parker, Josie E.
  • New Phytologist, Vol. 198, Issue 3
  • DOI: 10.1111/nph.12193

The CYPome (Cytochrome P450 complement) of Aspergillus nidulans
journal, March 2009

  • Kelly, Diane E.; Kraševec, Nada; Mullins, Jonathan
  • Fungal Genetics and Biology, Vol. 46, Issue 1
  • DOI: 10.1016/j.fgb.2008.08.010

CDD: a Conserved Domain Database for the functional annotation of proteins
journal, November 2010

  • Marchler-Bauer, A.; Lu, S.; Anderson, J. B.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq1189

The sporulation-specific enzymes encoded by the DIT1 and DIT2 genes catalyze a two-step reaction leading to a soluble LL-dityrosine-containing precursor of the yeast spore wall.
journal, May 1994

  • Briza, P.; Eckerstorfer, M.; Breitenbach, M.
  • Proceedings of the National Academy of Sciences, Vol. 91, Issue 10
  • DOI: 10.1073/pnas.91.10.4524

Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us?
journal, February 2013

  • Kelly, Steven L.; Kelly, Diane E.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1612
  • DOI: 10.1098/rstb.2012.0476

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species
journal, February 2016

  • Schmoll, Monika; Dattenböck, Christoph; Carreras-Villaseñor, Nohemí
  • Microbiology and Molecular Biology Reviews, Vol. 80, Issue 1
  • DOI: 10.1128/MMBR.00040-15

The P450 Gene Superfamily: Recommended Nomenclature
journal, February 1987


Structural domains of P450-containing monooxygenase systems
journal, January 1995


A P450-centric view of plant evolution: P450-centric evolution
journal, March 2011


Identification and heterologous expression of the cytochrome P450 oxidoreductase from the white-rot basidiomycete Coriolus versicolor
journal, July 2002

  • Ichinose, H.; Wariishi, H.; Tanaka, H.
  • Applied Microbiology and Biotechnology, Vol. 59, Issue 6
  • DOI: 10.1007/s00253-002-1083-8

WebLogo: A Sequence Logo Generator
journal, May 2004

  • Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
  • Genome Research, Vol. 14, Issue 6, p. 1188-1190
  • DOI: 10.1101/gr.849004

Pigments of rat liver microsomes
journal, June 1958


Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability
journal, April 2008


Functional Analysis of the Cytochrome P450 Monooxygenase Gene bcbot1 of Botrytis cinerea Indicates That Botrydial Is a Strain-Specific Virulence Factor
journal, June 2005

  • Siewers, Verena; Viaud, Muriel; Jimenez-Teja, Daniel
  • Molecular Plant-Microbe Interactions, Vol. 18, Issue 6
  • DOI: 10.1094/MPMI-18-0602

Origins of P450 diversity
journal, February 2013

  • Sezutsu, Hideki; Le Goff, Gaëlle; Feyereisen, René
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1612
  • DOI: 10.1098/rstb.2012.0428

Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes
journal, August 2005


Catalytic Reaction of Basidiomycete Lentinula edodes Cytochrome P450, Le. CYP1 Enzyme Produced in Yeast
journal, January 2004

  • Akiyama, Ryoko; Kajiwara, Susumu; Shishido, Kazuo
  • Bioscience, Biotechnology, and Biochemistry, Vol. 68, Issue 1
  • DOI: 10.1271/bbb.68.79

Fungal secondary metabolism — from biochemistry to genomics
journal, December 2005

  • Keller, Nancy P.; Turner, Geoffrey; Bennett, Joan W.
  • Nature Reviews Microbiology, Vol. 3, Issue 12, p. 937-947
  • DOI: 10.1038/nrmicro1286

Prediction and analysis of the modular structure of cytochrome P450 monooxygenases
journal, January 2010

  • Sirim, Demet; Widmann, Michael; Wagner, Florian
  • BMC Structural Biology, Vol. 10, Issue 1
  • DOI: 10.1186/1472-6807-10-34

Confidence Limits on Phylogenies: an Approach Using the Bootstrap
journal, July 1985


Functional Characterization of TvCyt2, a Member of the p450 Monooxygenases From Trichoderma virens Relevant During the Association With Plants and Mycoparasitism
journal, March 2018

  • Ramírez-Valdespino, Claudia A.; Porras-Troncoso, Maria Daniela; Corrales-Escobosa, Alma Rosa
  • Molecular Plant-Microbe Interactions, Vol. 31, Issue 3
  • DOI: 10.1094/MPMI-01-17-0015-R

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
journal, September 2017

  • Katoh, Kazutaka; Rozewicki, John; Yamada, Kazunori D.
  • Briefings in Bioinformatics, Vol. 20, Issue 4
  • DOI: 10.1093/bib/bbx108

Fusarium oxysporum Fatty-acid Subterminal Hydroxylase (CYP505) Is a Membrane-bound Eukaryotic Counterpart of Bacillus megaterium Cytochrome P450BM3
journal, September 2000

  • Kitazume, Tatsuya; Takaya, Naoki; Nakayama, Norikazu
  • Journal of Biological Chemistry, Vol. 275, Issue 50
  • DOI: 10.1074/jbc.M005617200

Transformation of Fatty Acids Catalyzed by Cytochrome P450 Monooxygenase Enzymes of Candida tropicalis
journal, October 2003


Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis
journal, June 2008


MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011

  • Tamura, K.; Peterson, D.; Peterson, N.
  • Molecular Biology and Evolution, Vol. 28, Issue 10
  • DOI: 10.1093/molbev/msr121

Cytochromes P450 as versatile biocatalysts
journal, June 2006


Accepted Trichoderma names in the year 2015
journal, September 2015


Cytochrome P450 and the Individuality of Species
journal, September 1999


Cytochrome P450 monooxygenases: perspectives for synthetic application
journal, July 2006


Genetically Closely Related but Phenotypically Divergent Trichoderma Species Cause Green Mold Disease in Oyster Mushroom Farms Worldwide
journal, September 2007

  • Komon-Zelazowska, M.; Bissett, J.; Zafari, D.
  • Applied and Environmental Microbiology, Vol. 73, Issue 22
  • DOI: 10.1128/AEM.01059-07

The cytochrome P450 complement (CYPome) of Mycosphaerella graminicola : CYPome of
journal, January 2013

  • Newsome, Alun W.; Nelson, David; Corran, Andrew
  • Biotechnology and Applied Biochemistry, Vol. 60, Issue 1
  • DOI: 10.1002/bab.1062

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes
journal, January 2012

  • Moktali, Venkatesh; Park, Jongsun; Fedorova-Abrams, Natalie D.
  • BMC Genomics, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2164-13-525

Cytochrome P450 of wood-rotting basidiomycetes and biotechnological applications: Cytochrome P450s of Basidiomycetes
journal, January 2013

  • Ichinose, Hirofumi
  • Biotechnology and Applied Biochemistry, Vol. 60, Issue 1
  • DOI: 10.1002/bab.1061

Fungal cytochrome P450 sterol 14α-demethylase (CYP51) and azole resistance in plant and human pathogens
journal, June 2012

  • Becher, Rayko; Wirsel, Stefan G. R.
  • Applied Microbiology and Biotechnology, Vol. 95, Issue 4
  • DOI: 10.1007/s00253-012-4195-9

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
journal, April 2011

  • Kubicek, Christian P.; Herrera-Estrella, Alfredo; Seidl-Seiboth, Verena
  • Genome Biology, Vol. 12, Issue 4
  • DOI: 10.1186/gb-2011-12-4-r40

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)
journal, May 2008

  • Martinez, Diego; Berka, Randy M.; Henrissat, Bernard
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1403

Complex regulation of secondary metabolism controlling pathogenicity in the phytopathogenic fungus Alternaria alternata
journal, March 2014

  • Takaoka, Shinya; Kurata, Mariko; Harimoto, Yoshiaki
  • New Phytologist, Vol. 202, Issue 4
  • DOI: 10.1111/nph.12754

P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature
journal, January 1996


The Cytochrome P450 Complement (CYPome) of Streptomyces coelicolor A3(2)
journal, April 2002

  • Lamb, David C.; Skaug, Tove; Song, Hong-Lin
  • Journal of Biological Chemistry, Vol. 277, Issue 27
  • DOI: 10.1074/jbc.M111109200

Fungal Cytochrome P450 Monooxygenases: Their Distribution, Structure, Functions, Family Expansion, and Evolutionary Origin
journal, June 2014

  • Chen, Wanping; Lee, Mi-Kyung; Jefcoate, Colin
  • Genome Biology and Evolution, Vol. 6, Issue 7
  • DOI: 10.1093/gbe/evu132

MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013

  • Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1183

Hydroxylation of bisphenol A by hyper lignin-degrading fungus Phanerochaete sordida YK-624 under non-ligninolytic condition
journal, October 2013


Trichoderma Research in the Genome Era
journal, August 2013