The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics

BMC Genomics

Joseph W. Spatafora²  Kathryn E. Bushley³  C. Alisha Quandt¹ 

[1] Present address: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA;Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA;Department of Plant Biology, University of Minnesota, St. Paul, MN, USA

关键词: Lineage sorting;    Mycoparasites;    Hypocreales;    Secondary metabolism;   

Others  :  1221850
DOI  :  10.1186/s12864-015-1777-9

 received in 2015-01-15, accepted in 2015-07-14,  发布年份 2015

【 摘 要 】

Background

Two major mycoparasitic lineages, the family Hypocreaceae and the genus Tolypocladium, exist within the fungal order, Hypocreales. Peptaibiotics are a group of secondary metabolites almost exclusively described from Trichoderma species of Hypocreaceae. Peptaibiotics are produced by nonribosomal peptide synthetases (NRPSs) and have antibiotic and antifungal activities. Tolypocladium species are mainly truffle parasites, but a few species are insect pathogens.

Results

The draft genome sequence of the truffle parasite Tolypocladium ophioglossoides was generated and numerous secondary metabolite clusters were discovered, many of which have no known putative product. However, three large peptaibiotic gene clusters were identified using phylogenetic analyses. Peptaibiotic genes are absent from the predominantly plant and insect pathogenic lineages of Hypocreales, and are therefore exclusive to the largely mycoparasitic lineages. Using NRPS adenylation domain phylogenies and reconciliation of the domain tree with the organismal phylogeny, it is demonstrated that the distribution of these domains is likely not the product of horizontal gene transfer between mycoparasitic lineages, but represents independent losses in insect pathogenic lineages. Peptaibiotic genes are less conserved between species of Tolypocladium and are the product of complex patterns of lineage sorting and module duplication. In contrast, these genes are more conserved within the genus Trichoderma and consistent with diversification through speciation.

Conclusions

Peptaibiotic NRPS genes are restricted to mycoparasitic lineages of Hypocreales, based on current sampling. Phylogenomics and comparative genomics can provide insights into the evolution of secondary metabolite genes, their distribution across a broader range of taxa, and their possible function related to host specificity.

【 授权许可】

   
2015 Quandt et al.

【 图 表 】

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【 参考文献 】

• [1]Sung G-H, Hywel-Jones NL, Sung J-M, Luangsa-Ard JJ, Shrestha B, Spatafora JW. Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Stud Mycol. 2007; 57:5-59.
• [2]Spatafora JW, Sung G-H, Sung J-M, Hywel-Jones NL, White JF. Phylogenetic evidence for an animal pathogen origin of ergot and the grass endophytes. Mol Ecol. 2007; 16:1701-11.
• [3]Kepler RM, Sung G-H, Harada Y, Tanaka K, Tanaka E, Hosoya T et al.. Host jumping onto close relatives and across kingdoms by Tyrannicordyceps (Clavicipitaceae) gen. nov. and Ustilaginoidea (Clavicipitaceae). Am J Bot. 2012; 99:552-61.
• [4]Kepler R, Ban S, Nakagiri A, Bischoff J, Hywel-Jones N, Owensby CA et al.. The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: an application of One Fungus One Name. Fungal Biol. 2013; 117:611-22.
• [5]Hjeljord L, Tronsmo A: Trichoderma and Gliocladium in biological control: an overview. In Trichoderma Gliocladium. Enzymes Biological Control and Commercial Applications. Edited by Harman GE, Kubicek CP; 2002:115–133
• [6]Durand H, Clanet M, Tiraby G. Genetic improvement of Trichoderma reesei for large scale cellulase production. Enzyme Microb Technol. 1988; 10:341-6.
• [7]Sukumaran RK, Singhania RR, Pandey A. Microbial cellulases: Production, applications and challenges. J Scientific and Industrial Reseach. 2005; 64:832-44.
• [8]Quandt CA, Kepler RM, Gams W, Araujo JPM, Ban S, Evans HC et al.. Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium. IMA Fungus. 2014; 5:121-34.
• [9]Landvik S, Shailer NFJ, Eriksson OE. SSU rDNA sequence support for a close relationship between the Elaphomycetales and the Eurotiales and Onygenales. Mycoscience. 1996; 37:237-41.
• [10]LoBuglio KF, Berbee ML, Taylor JW. Phylogenetic origins of the asexual mycorrhizal symbiont Cenococcum geophilum Fr. and other mycorrhizal fungi among the ascomycetes. Mol Phylogenet Evol. 1996; 6:287-94.
• [11]Mains EB. Species of Cordyceps parasitic on Elaphomyces. Bull Torrey Bot Club. 1957; 84:243-51.
• [12]Kobayasi Y, Shimizu D. Monographic studies on Cordyceps 1. Group parasitic on Elaphomyces. Bull Natl Sci Museum, Tokyo. 1960; 5:69-85.
• [13]Sung G-H, Poinar GO, Spatafora JW. The oldest fossil evidence of animal parasitism by fungi supports a Cretaceous diversification of fungal-arthropod symbioses. Mol Phylogenet Evol. 2008; 49:495-502.
• [14]Borel JF. History of the discovery of cyclosporin and of its early pharmacological development. Wien Klin Wochenschr. 2002; 114:433.
• [15]Keller NP, Turner G, Bennett JW. Fungal secondary metabolism - from biochemistry to genomics. Nat Rev Microbiol. 2005; 3:937-47.
• [16]Isaka M, Kittakoop P, Thebtaranonth Y: Secondary Metabolites of Clavicipitalean Fungi. In Clavicipitalean Fungi Evolutionary Biology, Chemistry, Biocontrol And Cultural Impacts. Edited by White JF, Bacon CW, Hywel-Jones NL, Spatafora JW. New York, NY: Marcel Dekker; 2003:355–98.
• [17]Desjardins AE, Proctor RH. Molecular biology of Fusarium mycotoxins. Int J Food Microbiol. 2007; 119:47-50.
• [18]Molnár I, Gibson DM, Krasnoff SB. Secondary metabolites from entomopathogenic Hypocrealean fungi. Nat Prod Rep. 2010; 27:1241-75.
• [19]Marahiel MA, Stachelhaus T, Mootz HD. Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis. Chem Rev. 1997; 97:2651-74.
• [20]Bushley KE, Turgeon BG. Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships. BMC Evol Biol. 2010; 10:26. BioMed Central Full Text
• [21]Wei X, Yang F, Straney DC. Multiple non-ribosomal peptide synthetase genes determine peptaibol synthesis in Trichoderma virens. Can J Microbiol. 2005; 51:423-9.
• [22]Jenke-Kodama H, Sandmann A, Müller R, Dittmann E. Evolutionary implications of bacterial polyketide synthases. Mol Biol Evol. 2005; 22:2027-39.
• [23]Fischbach MA, Walsh CT, Clardy J. The evolution of gene collectives: How natural selection drives chemical innovation. Proc Natl Acad Sci. 2008; 105:4601-8.
• [24]Zhang YQ, Wilkinson H, Keller NP, Tsitsigiannis D, An Z. Secondary metabolite gene clusters. In: Handbook of industrial microbiology. An Z, editor. Dekker, New York; 2004: p.355-386.
• [25]Hoffmeister D, Keller NP. Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep. 2007; 24:393-416.
• [26]Chugh JK, Wallace BA: Peptaibols : models for ion channels Sequence alignments into subfamilies (SFs). 2001:565–570.
• [27]Fox RO, Richards FM. A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5-A resolution. Nature. 1982; 300:325-30.
• [28]Chugh JK, Bruckner H, Wallace BA. Model for a Helical Bundle Channel Based on the High-Resolution Crystal Structure of Trichotoxin _ A50E. Biochemistry. 2002; 41:12934-41.
• [29]Whitmore L, Wallace BA. The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Res. 2004; 32(Database issue):D593-4.
• [30]Röhrich CR, Iversen A, Jaklitsch WM, Voglmayr H, Berg A, Dörfelt H et al.. Hypopulvins, novel peptaibiotics from the polyporicolous fungus Hypocrea pulvinata, are produced during infection of its natural hosts. Fungal Biol. 2012; 116:1219-31.
• [31]Schirmbock M, Lorito M, Wang Y, Hayes CK, Arisan-atac I, Scala F 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 Microbiol. 1994; 60:4364-70.
• [32]Lorito M, Peterbauer C, Hayes CK, Harman GE. Synergistic interaction between fungal cell wall degrading enzymes and different antifungal compounds enhances inhibition of spore germination. Microbiology. 1994; 140(Pt 3):623-9.
• [33]Lorito M, Woo SL, D’Ambrosio M, Harman GE, Hayes CK, Kubicek CP et al.. Synergistic interaction between cell wall degrading enzymes and membrane affecting compounds. Mol Plant Microbe Interact. 1996; 9:206-13.
• [34]Wiest A, Grzegorski D, Xu B-W, Goulard C, Rebuffat S, Ebbole DJ et al.. Identification of peptaibols from Trichoderma virens and cloning of a peptaibol synthetase. J Biol Chem. 2002; 277:20862-8.
• [35]Mukherjee PK, Wiest A, Ruiz N, Keightley A, Moran-Diez ME, McCluskey K et al.. Two classes of new peptaibols are synthesized by a single non-ribosomal peptide synthetase of Trichoderma virens. J Biol Chem. 2011; 286:4544-54.
• [36]Degenkolb T, Agheheh RK, Dieckmann R, Neuhof T, Baker SE, Druzhinina IS et al.. The production of multiple small peptaibol families by single 14-module peptide synthetases in Trichoderma/Hypocrea. Chem Biodivers. 2012; 9:499-535.
• [37]Krishna K, Sukumar M, Balaram P, Unit MB. Structural chemistry and membrane modifying activity of the fungal polypeptides zervamicins, antiamoebins and efrapeptins. Pure Appl Chem. 1990; 62:1417-20.
• [38]Krasnoff SB, Gupta S. Efrapeptin production by Tolypocladium fungi (Deuteromycotina: Hyphomycetes): Intra- and interspecific variation. J Chem Ecol. 1992; 18:1727-41.
• [39]Bandani AR, Khambay BPS, Faull JL, Newton R, Deadman M, Butt TM. Production of efrapeptins by Tolypocladium species and evaluation of their insecticidal and antimicrobial properties. Mycol Res. 2000; 104:537-44.
• [40]Gupta S, Krasnoff SB, Roberts DW, Renwick JAA. Structure of Efrapeptins from the fungus Tolypocladium niveum: peptide inhibitors of mitochondrial ATPase. J Org Chem. 1992; 57:2306-13.
• [41]Nagaraj G, Uma MV, Shivayogi MS. Antimalarial Activities of Peptide Antibiotics Isolated from Fungi. Antimicrob Agents Chemother. 2001; 45:145-9.
• [42]Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE et al.. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol. 2008; 26:553-60.
• [43]Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M et al.. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 2011; 12:R40. BioMed Central Full Text
• [44]Zheng P, Xia Y, Xiao G, Xiong C, Hu X, Zhang S et al.. Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine. Genome Biol. 2011; 12:R116. BioMed Central Full Text
• [45]Xiao G, Ying S-H, Zheng P, Wang Z-L, Zhang S, Xie X-Q et al.. Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana. Sci Rep. 2012; 2:483.
• [46]Gao Q, Jin K, Ying SH, Zhang Y, Xiao G, Shang Y et al.. Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet. 2011; 7:e1001264.
• [47]Hu X, Zhang Y, Xiao G, Zheng P, Xia Y, Zhang X et al.. Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus. Chinese Sci Bull. 2013; 58:2846-54.
• [48]Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE et al.. The genome of Tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genet. 2013; 9: Article ID e1003496
• [49]Parra G, Bradnam K, Ning Z, Keane T, Korf I. Assessing the gene space in draft genomes. Nucleic Acids Res. 2009; 37:289-97.
• [50]Sedmera P, Havlicek V, Jegorov A, Segre AL. Cyclosporin D Hydroperoxide, a new metabolite of Tolypocladium terricola. Tetrahedron Lett. 1995; 36:6953-6.
• [51]Traber R, Dreyfuss MM. Occurrence of cyclosporins and cyclosporin-like peptolides in fungi. J Ind Microbiol. 1996; 17:397-401.
• [52]Wiemann P, Guo C-J, Palmer JM, Sekonyela R, Wang CCC, Keller NP. Prototype of an intertwined secondary-metabolite supercluster. Proc Natl Acad Sci U S A. 2013; 110:17065-70.
• [53]Kershaw M, Moorhouse E, Bateman R, Reynolds S, Charnley A. The role of destruxins in the pathogenicity of Metarhizium anisopliae for three species of insect. J Invertebr Pathol. 1999; 74:213-23.
• [54]Wang B, Kang Q, Lu Y, Bai L, Wang C. Unveiling the biosynthetic puzzle of destruxins in Metarhizium species. Proc Natl Acad Sci U S A. 2012; 109:1287-92.
• [55]Kneifel H, Konig WA, Loeffler W, Muller R. Ophiocordin, an antifungal antibiotic of Cordyceps ophioglossoides. Arch Microbiol. 1977; 113:121-30.
• [56]Boros C, Hamilton SM, Katz B, Kulanthaivel P. Comparison of Balanol from Verticillium balanoides and ophiocordin from Cordyceps ophioglossoides. J Antibiot (Tokyo). 1994; 47:1010-6.
• [57]Putri SP, Kinoshita H, Ihara F, Igarashi Y, Nihira T. Ophiosetin, a new tetramic acid derivative from the mycopathogenic fungus Elaphocordyceps ophioglossoides. J Antibiot (Tokyo). 2010; 63:195-8.
• [58]Sims JW, Fillmore JP, Warner DD, Schmidt EW. Equisetin biosynthesis in Fusarium heterosporum. Chem Commun (Camb). 2005;186–8.
• [59]Tsantrizos YS, Pischos S, Sauriol F, Widden P. Peptaibol metabolites of Tolypocladium geodes. Can J Chem. 1996; 172:165-72.
• [60]Lee S-J, Yeo W-H, Yun B-S, Yoo I-D. Isolation and sequence analysis of new peptaibol, boletusin, from Boletus spp. J Pept Sci. 1999; 5:374-8.
• [61]Lee S-J, Yun B-S, Cho D-H, Yoo I-D. Tylopeptins A and B, new antibiotic peptides from Tylopilus neofelleus. J Antibiot (Tokyo). 1999; 52:998-1006.
• [62]Young C, McMillan L, Telfer E, Scott B. Molecular cloning and genetic analysis of an indole-diterpene gene cluster from Penicillium paxilli. Mol Microbiol. 2001; 39:754-64.
• [63]Fleetwood DJ, Scott B, Lane GA, Tanaka A, Johnson RD. A complex ergovaline gene cluster in Epichloë endophytes of grasses. Appl Environ Microbiol. 2007; 73:2571-9.
• [64]Campbell MA, Staats M, van Kan JAL, Rokas A, Slot JC. Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia. 2013; 105:1126-34.
• [65]Mukherjee PK, Horwitz BA, Kenerley CM. Secondary metabolism in Trichoderma--a genomic perspective. Microbiology. 2012; 158(Pt 1):35-45.
• [66]FASTQ/A short-reads pre-processing tools. http://hannonlab. cshl.edu/fastx_toolkit/ webcite
• [67]Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-9.
• [68]Wgsim - read simulator for next generation sequencing. http://github. com/lh3/wgsim webcite
• [69]Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ et al.. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2011; 108:1513-8.
• [70]Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C et al.. Versatile and open software for comparing large genomes. Genome Biol. 2004; 5:R12. BioMed Central Full Text
• [71]Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B et al.. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008; 18:188-96.
• [72]Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I et al.. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29:644-52.
• [73]Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011; 27:764-70.
• [74]Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 2008; 18:1979-90.
• [75]Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004; 5:59. BioMed Central Full Text
• [76]Stanke M, Morgenstern B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 2005; 33(Web Server issue):W465-7.
• [77]RepeatMasker. http://www. repeatmasker.org webcite
• [78]Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005; 21 Suppl. 1:i351-8.
• [79]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol. 1990; 215:403-10.
• [80]Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome informatics. 2009; 23:205-11.
• [81]Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T. antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 2013; 41(Web Server issue):W204-12.
• [82]Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH et al.. SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol. 2010; 47:736-41.
• [83]Mesquite: a modular system for evolutionary analysis. http://mesquiteproject. org webcite
• [84]Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010; 5: Article ID e11147
• [85]Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32:1792-7.
• [86]Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006; 22:2688-90.
• [87]Robbertse B, Yoder RJ, Boyd A, Reeves J, Spatafora JW. Hal: an automated pipeline for phylogenetic analyses of genomic data. PLoS Curr. 2011; 3: Article ID RRN1213
• [88]Enright AJ, Van DS, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acid Res. 2002; 30:1575-84.
• [89]Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007; 56:564-77.