Table S3Properties of homologs of TDFs products from P. chlamydosporiaIMI 380407 and IMI 331547, for most significant HCA clusters.
Isolate cluster / TDF products / Biochemical activity / ReferencesIMI 380407 cluster I
Mg-dependent phosphatase (MDP) / Member of the haloacid dehalogenase-like hydrolases (HAD) superfamily. Acts as a fructosamine-6-phosphatase in protein dephosphorylation. / Selengut 2001
Major facilitator MFS1 transporter / Single-polypeptide secondary carriers transporting solutes across internal membranes or facilitating transmembrane uptake of nutrients (sugars, Krebs cycle metabolites or organophosphates-phosphate exchangers). Oligosaccharides permease. / Pao et al. 1998
Fungal transcription factor / Tubby protein. Membrane anchored transcription factors, involved in modulation of phosphoinositide based cell signals. / Bateman et al. 2009
IMI 380407 cluster II
Subgroup 1
GTPase activating protein, Rga6 / Regulator ofcell wall formation; possible negative regulator of Rho1, a further GTPase active in actin cytoskeleton organization and cell wall formation. / Nakano et al. 2001
Chromosome segregation protein / Functional role in DNA replication, recombination and repair, sensing double-strand breaks and damage checkpoints. / Borde 2007
GAL-4 transcription regulator / Transcriptional regulator for galactose-induced genes. Involved in tyrosine or glycerophospholipids metabolism, alkaloid biosynthesis II pathways, degradation of limonene, pinene, benzoate (via CoA ligation), lysine, methylnaphthalene and ethylbenzene, phenylalanine or histidine metabolism. Down regulates synthesis at the mitochondrial level. In Sordaria macrospora, a GAL4-like C6 Zn finger protein is involved in sexual development and fruiting body production. / Johnston 1987;
Lodiet al. 1991;
Masloff et al. 2002
Polyprotein, transposon related / Acting as a protease, integrase and reverse transcriptase. / Ranson et al. 1999
Subgroup 2
Metal homeostasis protein BSD2 / Involved in heavy metal ions homeostasis, control of transport and trafficking of Smf1p and Smf2p metaltransporters to vacuoles, for degrading. Effective in copper detoxification processes, preventing metal hyperaccumulation. / Liu and Culotta 1994
ATP-binding cassette, ABC transporter (MDR family) / Gene superfamily of transmembrane translocation enzymes requiring ATP hydrolysis for transport. Implicated in cellular efflux of toxic compounds. Control transport of cytotoxic products, ie folic acid antimetabolites and reduced folates in malignant cells. In S. cerevisiae are involvedin efflux of sex pheromones and mitochondrial iron homeostasis. Mediates pleiotropic drug resistance in yeasts, as cells lacking ABC pumps are hypersensitive to antifungal drugs. / Assaraf 2006;
Bauer et al. 1999;
Sipos and Kuchler006
IMI 380407 cluster IV
Glycosyltransferases / Transfer monosaccharide moieties from donors to acceptor molecules, i.e. oligo and polysaccharides, or glycoconjugates. / Breton et al. 2006
Reducing polyketide synthase / Catalysing radicicols (resorcilic acid lactones). Inhibits the Hsp90 molecular chaperone. / Reeves et al. 2008
Patatin-like phospholipases / Stress related enzymes. InS. cerevisiaemobilize triacylglycerol lipases from lipid storage particles. Deacylating phospholipase and lysophospholipase involved in phosphatidylcholine turnover also harbor a patatin-like domain. / Köhler et al. 2006
Nucleoporins / Protein complexes crossing the nuclear envelope, active in mitosis, control of gene expression, oncogenesis and cell cycle. / Bapteste et al. 2005;
De Souza et al. 2004
IMI 380407 cluster V
Chaperonin GroEL / Molecular chaperone, ubiquitous multisubunit double-ring complexes harbouring nascent or denatured polypeptides in their central chamber, facilitating protein folding through ATP hydrolysis, stabilization and preventing aggregation. / Ranson et al. 1999
Fot5 transposase / Transposable element close to Six, a Fusarium oxysporum f. sp. lycopersici gene coding for a 12 kDa protein required for I-3-mediated resistance in tomato. / Rep et al. 2004
IMI 331547 cluster I
Phytase / Hydrolytic enzyme involved in phosphate metabolism through the phytate (myo-inositol hexakisphosphate) degradation, release of free inorganic phosphate units and chelated divalent metals. / Lei and Stahl 2001
IMI 331547 cluster II
Phospholipase D1 / Ca2+-dependent phosphatidylethanolamine hydrolase. Catalyzes hydrolysis of phospholipids at distal phosphodiester bond to yield phosphatidic acid (PA) and free polar head groups. / Hong et al. 2003
Monoxygenase / Involved in redox-linked regulation of K+ channels. / Anantharaman et al. 2001
NCS, nucleoside transporters / Mediates cellular uptake and release of nucleosides and nucleoside analogues at the membrane level. / Loewen et al. 2002
Mycrocyle conidiation protein (Mmc) / In M. anisopliae is involved in metabolic pathways related to expression of a large number of genes, coding for stress related proteins, protein metabolism and normal conidiation pathways. / Zhangand Xia 2008
RNA dependent RNA polymerase / Found in several classes of organisms, including other fungi.Polymerize directly from RNA in post-transcriptional gene silencing(PTGS). In N. crassa acts as a rate limiting factor in PTGS. / Forrest et al. 2004, Pfaffl et al. 2002
Cystathionine--lyase / Involved in cysteine release through cystathionine catabolism (cephalosporin biosynthesis). / Kosalková et al. 2001
IMI 331547 cluster III
Arrestin (S-antigen domain protein) / Involved in pH signalling in Aspergillus nidulans. Arrestin-like proteins in S. cerevisiae show a detoxification role, conferring resistance to dinitrobenzene. Interacting with cytoplasmic proteins and intracellular signaling pathways. / Herranz et al. 2005;
Mo et al. 2008;
Shinoda and Kikuchi 2007
Dihydrolipoamide dehydrogenase (LPD1) / Flavoprotein (E3) component of the pyruvate, alpha-ketoglutarate and branched-chain alpha-ketoacid dehydrogenase complexes involved in oxidation-reduction in the metabolic process, located in mitochondrial inner membrane. / Jang et al.1997
Tyrosyl-DNA phosphodiesterase / Phospholipase D family member. Hydrolyses the topoisomerase 1- DNA bonds; involved in DNA damage repair in yeasts. / Interthal et al.2001;
Pouliot et al. 1999
bZIP transcription factor domain / Transcriptional regulators of stress response and cell proliferation, through sequence specific DNA interactions. Involved in yeasts sexual differentiation and stationary phase. In Podospora control apoptosis and cell death. / Dementhon et al. 2004, Deppmann et al. 2006
Frequency clock protein / Gene family of nuclear transcription factors. In N.crassa organize the circadian clock acting as nuclear transcription factor. Involved in circadian conidiation, light and temperature reaction and circadian rhythm regulation. / Lewis et al. 1997; Nowrousian et al. 2003
References
Anantharaman V, Koonin EV, Aravind L (2001) Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule binding domains. J Mol Biol 307:1271-1292
Assaraf YG (2006) The role of multidrug resistance efflux transporters in antifolate resistance and folate homeostasis. Drug Res Updates 9: 227-246
Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Söding J (2009) Phospholipid scramblases and tubby like proteins belong to anew superfamily of membrane tethered transcription factors. Bioinformatics 5:159-162
Bapteste E, Charlebois RL, MacLeod D, Brochier C (2005) The two tempos of nuclear pore complex evolution: highly adaptingproteins in an ancient frozen structure. Gen Biol 6 (Article No 10 R85).
Bauer BE, Wolfger H, Kuchler K, (1999) Inventory and function of yeast ABC proteins: about sex, stress, pleiotropic drug and heavy metal resistance. Biochim Biophys Acta 1461:217-236
Borde V (2007) The multiple roles of the Mre11 complex for meiotic recombination. Chromosome Res 15:551-563
Breton C, Šnajdrová L, Jeanneau C, Koca J, Imberty A (2006) Structures and mechanisms of glycosyltransferases. Glycobiol 16(Article No 29R-37R)
Dementhon K, Saupe SJ, Clavé C (2004) Characterization of IDI-4, a bZIP transcription factor inducing autophagy and cell death in the fungus Podospora anserina. Mol Microbiol 53:1625-1640
Deppmann CD, Alvania RS, Taparowsky EJ (2006) Cross-species annotation of basic leucine zipper factor interactions: insight into the evolution of closed interaction networks. Mol Biol Evol 23:1480-1492
De Souza CP, Osmani AH, Hashmi SB, Osmani SA (2004) Partial nuclear pore complex disassembly during closed mitosis in Aspergillus nidulans. Curr Biol 14:1973-1984
Forrest EC, Cogoni C, Macino G (2004) The RNA-dependent RNA polymerase, QDE-1, is a rate-limiting factor in post-transcriptional gene silencing in Neurospora crassa. Nucl Acids Res 32:2123-2128
Interthal H, Pouliot JJ, Champoux JJ (2001) The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the phospholipase D superfamily. Proc Natl Acad Sci USA 98:12009-12014
Jang YJ, Chung KS, Park C, Yoo H.S (1997) Fission yeast dihydrolipoamide dehydrogenase gene is involved in G1/S cell cycle progression. Biochim Biophys Acta 1358:229-239
Johnston M (1987) A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. Microbiol Rev51:458-476
Köhler GA, Brenot A, Haas-Stapleton E, Agabian N, Deva R, Nigam S (2006) Phospholipase A2 and Phospholipase B activities in fungi. Biochim Biophys Acta 1761:1391-1399
Kosalková K, Marcos AT, Martín JF (2001) A moderate amplification of the mecB gene encoding cystathionine--lyase stimulates cephalosporin biosynthesis in Acremonium chrysogenum. J Ind Microbiol Biotechnol 27:252-258
Lei XG, Stahl CH (2001) Biotechnological development of effective phytases for mineral nutrition and environmental protection. Appl Microbiol Biotechnol 57:474-481
Lewis MT,Morgan LW, Feldman JF (1997) Analysis of frequency (frq) clock gene homologs: evidence for a helix-turn-helix transcription factor. Mol Gen Genom 253:401-414
Loewen SK, Ng AML, Mohabir NN, Baldwin SA, Cass CE, Young JD (2003) Functional characterization of a H+/nucleoside co-transporter (CaCNT) from Candida albicans, a fungal member of the concentrative nucleoside transporter (CNT) family of membrane proteins. Yeast20:661-675
Herranz S, Rodriguez JM, Bussink HJ, Sanchez-Ferrero JC, Arst HN, Penalva MA, Vincent O (2005) Arrestin-related proteins mediate pH signaling in fungi. Proc Natl Acad Sci USA102:12141-12146.
Hong S, Horiuchi H, Ohta A (2003) Molecular cloning of a phospholipase D gene from Aspergillus nidulans and characterization of its deletion mutants. FEMS Microbiol Lett224:231-237
Lodi T, Donnini C, Ferrero I (1991) Catabolite repression by galactose in overexpressed GAL4 strains of Saccharomyces cerevisiae. J Gen Microbiol137:1039-1044
Liu XF, Culotta VC (1994)The requirement for yeast superoxide dismutase is bypassed through mutations in bsd2, a novel metal homeostasis gene. Mol Cell Biol 14:7037-7045
Masloff S, Jacobsen S, Pöggeler S, Kück U (2002) Functional analysis of the C6 zinc finger gene pro1 involved in fungal sexual development. Fungal Genet Biol 36:107-116
Mo W, Zhang L, Yang G, Zhai J, Hu Z, Chen Y, Chen X, Hui L, Huang R, Hu G (2008)Nuclear β-arrestin1 functions as a scaffold for the dephosphorylation of STAT1 and moderates the antiviral activity of IFN-γ. Mol Cell31:695-707
Nakano K, Mutoh T, MabuchiI (2001) Characterization of GTPase-activating proteins for the function of the Rho-family small GTPases in the fission yeast Schizosaccharomyces pombe. Gen Cells 6:1031-1042
NowrousianM, Duffield GE, Loros JJ, Dunlap JC (2003)The frequencygene is required for temperature-dependent regulation of many clock-controlled genes in Neurospora crassa. Genetics 164:923-933
Pao SS, Paulsen IT, Saier MH Jr (1998) Major facilitator superfamily. Microbiol Mol Biol Rev 62:1-34
Pfaffl MW, Horgan GW, Dempfle L (2002) Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in Real-Time PCR. Nucl Acids Res 30(Article No e36)
Pouliot JJ, Yao KC, Robertson CA, Nash HA (1999) Yeast gene for a Tyr-DNA phosphodiesterase that repairs Topoisomerase I complexes. Science 286:552-555
Ranson NA,White HE, Saibil HR (1999) Chaperonins. Biochem J 333:233-242
Reeves CD, Hu Z, Reid R, Kealey JT (2008) Genes for the biosynthesis of the fungal polyketides hypothemycin from Hypomyces subiculosus and radicicol from Pochonia chlamydosporia. Appl Env Microbiol 74:5121-5129
Rep M, Van der Does HC, Meijer M, Van Wijk R, Houterman PM, Dekker HL, De Koster CG, CornelissenBJC (2004) A small, cysteine-rich protein secreted by Fusarium oxysporum during colonization of xylem vessels is required for I-3-mediated resistance in tomato. Mol Microbiol 53:1373-1383
Selengut JD (2001) MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases. Biochemistry 40:12704-12711
Shinoda J, Kikuchi Y (2007) Rod1, an arrestin-related protein, is phosphorylated by Snf1-kinase in Saccharomyces cerevisiae. Biochem Biophys Res Comm 364:258-263
Sipos G, KuchlerK (2006) Fungal ATP-binding cassette (ABC) transporters in drug resistance and detoxification. Curr Drug Targets7:471-481
Zhang S, Xia Y (2008) Identification of genes preferentially expressed during microcycle conidiation of Metarhizium anisopliae using suppression subtractive hybridization. FEMS Microbiol Lett 286:71-77