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Genome-wide analysis of the Zn(II)2Cys6 zinc cluster-encoding gene family in Aspergillus flavus

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Abstract

Proteins with a Zn(II)2Cys6 domain, Cys-X2-Cys-X6-Cys-X5-12-Cys-X2-Cys-X6-9-Cys (hereafter, referred to as the C6 domain), form a subclass of zinc finger proteins found exclusively in fungi and yeast. Genome sequence databases of Saccharomyces cerevisiae and Candida albicans have provided an overview of this family of genes. Annotation of this gene family in most fungal genomes is still far from perfect and refined bioinformatic algorithms are urgently needed. Aspergillus flavus is a saprophytic soil fungus that can produce the carcinogenic aflatoxin. It is the second leading causative agent of invasive aspergillosis. The 37-Mb genome of A. flavus is predicted to encode 12,000 proteins. Two and a half percent of the total proteins are estimated to contain the C6 domain, more than twofold greater than those estimated for yeast, which is about 1 %. The variability in the spacing between cysteines, C3-C4 and C5-C6, in the zinc cluster enables classification of the domains into distinct subgroups, which are also well conserved in Aspergillus nidulans. Sixty-six percent (202/306) of the A. flavus C6 proteins contain a specific transcription factor domain, and 7 % contain a domain of unknown function, DUF3468. Two A. nidulans C6 proteins containing the DUF3468 are involved in asexual conidiation and another two in sexual differentiation. In the anamorphic A. flavus, a homolog of the latter lacks the C6 domain. A. flavus being heterothallic and reproducing mainly through conidiation appears to have lost some components involved in homothallic sexual development. Of the 55 predicted gene clusters thought to be involved in production of secondary metabolites, only about half have a C6-encoding gene in or near the gene clusters. The features revealed by the A. flavus C6 proteins likely are common for other ascomycete fungi.

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References

  • Abe Y, Ono C, Hosobuchi M, Yoshikawa H (2002) Functional analysis of mlcR, a regulatory gene for ML-236B (compactin) biosynthesis in Penicillium citrinum. Mol Genet Genomics 268:352–361

    Article  CAS  Google Scholar 

  • Akache B, Wu K, Turcotte B (2001) Phenotypic analysis of genes encoding yeast zinc cluster proteins. Nucleic Acids Res 29:2181–2190

    Article  CAS  Google Scholar 

  • Andrianopoulos A, Hynes MJ (1990) Sequence and functional analysis of the positively acting regulatory gene amdR from Aspergillus nidulans. Mol Cell Biol 10:3194–3203

    CAS  Google Scholar 

  • Baum JA, Geever R, Giles NH (1987) Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain. Mol Cell Biol 7:1256–1266

    CAS  Google Scholar 

  • Bayram O, Krappmann S, Ni M, Bok JW, Helmstaedt K, Valerius O, Braus-Stromeyer S, Kwon NJ, Keller NP, Yu JH, Braus GH (2008) VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism. Science 320:1504–1506

    Article  CAS  Google Scholar 

  • Bergmann S, Schumann J, Scherlach K, Lange C, Brakhage AA, Hertweck C (2007) Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol 3:213–217

    Article  CAS  Google Scholar 

  • Beri RK, Whittington H, Roberts CF, Hawkins AR (1987) Isolation and characterization of the positively acting regulatory gene QUTA from Aspergillus nidulans. Nucleic Acids Res 15:7991–8001

    Article  CAS  Google Scholar 

  • Bibbins M, Crepin VF, Cummings NJ, Mizote T, Baker K, Mellits KH, Connerton IF (2002) A regulator gene for acetate utilisation from Neurospora crassa. Mol Genet Genomics 267:498–505

    Article  CAS  Google Scholar 

  • Bluhm BH, Kim H, Butchko RA, Woloshuk CP (2008) Involvement of ZFR1 of Fusarium verticillioides in kernel colonization and the regulation of FST1, a putative sugar transporter gene required for fumonisin biosynthesis on maize kernels. Mol Plant Pathol 9:203–211

    Article  CAS  Google Scholar 

  • Bok JW, Chung D, Balajee SA, Marr KA, Andes D, Nielsen KF, Frisvad JC, Kirby KA, Keller NP (2006) GliZ, a transcriptional regulator of gliotoxin biosynthesis, contributes to Aspergillus fumigatus virulence. Infect Immun 74:6761–6768

    Article  CAS  Google Scholar 

  • Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ (2011) Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet 7:e1001287

    Article  CAS  Google Scholar 

  • Brakhage AA (2012) Regulation of fungal secondary metabolism. Nat Rev Microbiol 11:21–32

    Article  Google Scholar 

  • Brown DW, Butchko RA, Busman M, Proctor RH (2007) The Fusarium verticillioides FUM gene cluster encodes a Zn(II)2Cys6 protein that affects FUM gene expression and fumonisin production. Eukaryot Cell 6:1210–1218

    Article  CAS  Google Scholar 

  • Brown DW, Yu JH, Kelkar HS, Fernandes M, Nesbitt TC, Keller NP, Adams TH, Leonard TJ (1996) Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans. Proc Natl Acad Sci U S A 93:1418–1422

    Article  CAS  Google Scholar 

  • Burger G, Strauss J, Scazzocchio C, Lang BF (1991) nirA, the pathway-specific regulatory gene of nitrate assimilation in Aspergillus nidulans, encodes a putative GAL4-type zinc finger protein and contains four introns in highly conserved regions. Mol Cell Biol 11:5746–5755

    CAS  Google Scholar 

  • Chang P-K, Ehrlich KC, Yu J, Bhatnagar D, Cleveland TE (1995) Increased expression of Aspergillus parasiticus aflR, encoding a sequence-specific DNA-binding protein, relieves nitrate inhibition of aflatoxin biosynthesis. Appl Environ Microbiol 61:2372–2377

    CAS  Google Scholar 

  • Chang P-K, Horn BW, Dorner JW (2009) Clustered genes involved in cyclopiazonic acid production are next to the aflatoxin biosynthesis gene cluster in Aspergillus flavus. Fungal Genet Biol 46:176–182

    Article  CAS  Google Scholar 

  • Chang P-K, Scharfenstein LL, Mack B, Ehrlich KC (2012) Deletion of the Aspergillus flavus orthologue of A. nidulans fluG reduces conidiation and promotes production of sclerotia but does not abolish aflatoxin biosynthesis. Appl Environ Microbiol 78:7557–7563

    Article  CAS  Google Scholar 

  • Chang P-K, Scharfenstein LL, Wei Q, Bhatnagar D (2010) Development and refinement of a high-efficiency gene-targeting system for Aspergillus flavus. J Microbiol Methods 81:240–246

    Article  CAS  Google Scholar 

  • Chen H, Lee MH, Daub ME, Chung KR (2007) Molecular analysis of the cercosporin biosynthetic gene cluster in Cercospora nicotianae. Mol Microbiol 64:755–770

    Article  CAS  Google Scholar 

  • Chen YP, Yuan GF, Hsieh SY, Lin YS, Wang WY, Liaw LL, Tseng CP (2010) Identification of the mokH gene encoding transcription factor for the upregulation of monacolin K biosynthesis in Monascus pilosus. J Agric Food Chem 58:287–293

    Article  CAS  Google Scholar 

  • Chiang YM, Szewczyk E, Davidson AD, Entwistle R, Keller NP, Wang CC, Oakley BR (2010) Characterization of the Aspergillus nidulans monodictyphenone gene cluster. Appl Environ Microbiol 76:2067–2074

    Article  CAS  Google Scholar 

  • Chiang YM, Szewczyk E, Davidson AD, Keller N, Oakley BR, Wang CC (2009) A gene cluster containing two fungal polyketide synthases encodes the biosynthetic pathway for a polyketide, asperfuranone, in Aspergillus nidulans. J Am Chem Soc 131:2965–2970

    Article  CAS  Google Scholar 

  • D'Souza CA, Lee BN, Adams TH (2001) Characterization of the role of the FluG protein in asexual development of Aspergillus nidulans. Genetics 158:1027–1036

    Google Scholar 

  • Endo H, Kajiwara S, Tsunoka O, Shishido K (1994) A novel cDNA, priBc, encoding a protein with a Zn(II)2Cys6 zinc cluster DNA-binding motif, derived from the basidiomycete Lentinus edodes. Gene 139:117–121

    Article  CAS  Google Scholar 

  • Felenbok B, Sequeval D, Mathieu M, Sibley S, Gwynne DI, Davies RW (1988) The ethanol regulon in Aspergillus nidulans: characterization and sequence of the positive regulatory gene alcR. Gene 73:385–396

    Article  CAS  Google Scholar 

  • Fox EM, Gardiner DM, Keller NP, Howlett BJ (2008) A Zn(II)2Cys6 DNA binding protein regulates the sirodesmin PL biosynthetic gene cluster in Leptosphaeria maculans. Fungal Genet Biol 45:671–682

    Article  CAS  Google Scholar 

  • Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Penalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438:1105–1115

    Article  CAS  Google Scholar 

  • Gardner KH, Pan T, Narula S, Rivera E, Coleman JE (1991) Structure of the binuclear metal-binding site in the GAL4 transcription factor. Biochemistry 30:11292–11302

    Article  CAS  Google Scholar 

  • Georgianna DR, Fedorova ND, Burroughs JL, Dolezal AL, Bok JW, Horowitz-Brown S, Woloshuk CP, Yu J, Keller NP, Payne GA (2010) Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters. Mol Plant Pathol 11:213–226

    Article  CAS  Google Scholar 

  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274:563–567

    Article  Google Scholar 

  • Gomi K, Akeno T, Minetoki T, Ozeki K, Kumagai C, Okazaki N, Iimura Y (2000) Molecular cloning and characterization of a transcriptional activator gene, amyR, involved in the amylolytic gene expression in Aspergillus oryzae. Biosci Biotechnol Biochem 64:816–827

    Article  CAS  Google Scholar 

  • Hidalgo P, Ansari AZ, Schmidt P, Hare B, Simkovich N, Farrell S, Shin EJ, Ptashne M, Wagner G (2001) Recruitment of the transcriptional machinery through GAL11P: structure and interactions of the GAL4 dimerization domain. Genes Dev 15:1007–1020

    Article  CAS  Google Scholar 

  • Hong M, Fitzgerald MX, Harper S, Luo C, Speicher DW, Marmorstein R (2008) Structural basis for dimerization in DNA recognition by Gal4. Structure 16:1019–1026

    Article  CAS  Google Scholar 

  • Horn BW, Moore GG, Carbone I (2009) Sexual reproduction in Aspergillus flavus. Mycologia 101:423–429

    Article  Google Scholar 

  • Huang X, Li HM (2009) Cloning and bioinformatic analysis of lovastatin biosynthesis regulatory gene lovE. Chin Med J (Engl) 122:1800–1805

    CAS  Google Scholar 

  • Imazaki I, Kurahashi M, Iida Y, Tsuge T (2007) Fow2, a Zn(II)2Cys6-type transcription regulator, controls plant infection of the vascular wilt fungus Fusarium oxysporum. Mol Microbiol 63:737–753

    Article  CAS  Google Scholar 

  • Johnston M (1987) A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. Microbiol Rev 51:458–476

    CAS  Google Scholar 

  • Keegan L, Gill G, Ptashne M (1986) Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science 231:699–704

    Article  CAS  Google Scholar 

  • Keller S, Macheleidt J, Scherlach K, Schmaler-Ripcke J, Jacobsen ID, Heinekamp T, Brakhage AA (2011) Pyomelanin formation in Aspergillus fumigatus requires HmgX and the transcriptional activator HmgR but is dispensable for virulence. PLoS One 6:e26604

    Article  CAS  Google Scholar 

  • Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND (2010) SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47:736–741

    Article  CAS  Google Scholar 

  • Kihara J, Moriwaki A, Tanaka N, Tanaka C, Ueno M, Arase S (2008) Characterization of the BMR1 gene encoding a transcription factor for melanin biosynthesis genes in the phytopathogenic fungus Bipolaris oryzae. FEMS Microbiol Lett 281:221–227

    Article  CAS  Google Scholar 

  • Kim JE, Jin J, Kim H, Kim JC, Yun SH, Lee YW (2006) GIP2, a putative transcription factor that regulates the aurofusarin biosynthetic gene cluster in Gibberella zeae. Appl Environ Microbiol 72:1645–1652

    Article  CAS  Google Scholar 

  • Lee BN, Adams TH (1996) fluG and flbA function interdependently to initiate conidiophore development in Aspergillus nidulans through brlAβ activation. EMBO J 15:299–309

    CAS  Google Scholar 

  • Lee BY, Han SY, Choi HG, Kim JH, Han KH, Han DM (2005) Screening of growth- or development-related genes by using genomic library with inducible promoter in Aspergillus nidulans. J Microbiol 43:523–528

    CAS  Google Scholar 

  • Liu TD, Marzluf GA (2004) Characterization of pco-1, a newly identified gene which regulates purine catabolism in Neurospora. Curr Genet 46:213–227

    Article  CAS  Google Scholar 

  • Ma J, Ptashne M (1987a) The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80. Cell 50:137–142

    Article  CAS  Google Scholar 

  • Ma J, Ptashne M (1987b) Deletion analysis of GAL4 defines two transcriptional activating segments. Cell 48:847–853

    Article  CAS  Google Scholar 

  • MacPherson S, Larochelle M, Turcotte B (2006) A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 70:583–604

    Article  CAS  Google Scholar 

  • Maicas S, Moreno I, Nieto A, Gomez M, Sentandreu R, Valentin E (2005) In silico analysis for transcription factors with Zn(II)2C6 binuclear cluster DNA-binding domains in Candida albicans. Comp Funct Genomics 6:345–356

    Article  CAS  Google Scholar 

  • Marmorstein R, Carey M, Ptashne M, Harrison SC (1992) DNA recognition by GAL4: structure of a protein–DNA complex. Nature 356:408–414

    Article  CAS  Google Scholar 

  • Nakazawa T, Ishiuchi K, Praseuth A, Noguchi H, Hotta K, Watanabe K (2012) Overexpressing transcriptional regulator in Aspergillus oryzae activates a silent biosynthetic pathway to produce a novel polyketide. ChemBioChem 13:855–861

    Article  CAS  Google Scholar 

  • Nicholson MJ, Koulman A, Monahan BJ, Pritchard BL, Payne GA, Scott B (2009) Identification of two aflatrem biosynthesis gene loci in Aspergillus flavus and metabolic engineering of Penicillium paxilli to elucidate their function. Appl Environ Microbiol 75:7469–7481

    Article  CAS  Google Scholar 

  • Noguchi Y, Sano M, Kanamaru K, Ko T, Takeuchi M, Kato M, Kobayashi T (2009) Genes regulated by AoXlnR, the xylanolytic and cellulolytic transcriptional regulator, in Aspergillus oryzae. Appl Microbiol Biotechnol 85:141–154

    Article  CAS  Google Scholar 

  • Ogawa M, Kobayashi T, Koyama Y (2012) ManR, a novel Zn(II)2Cys6 transcriptional activator, controls the beta-mannan utilization system in Aspergillus oryzae. Fungal Genet Biol 49:987–995

    Article  CAS  Google Scholar 

  • Pan T, Coleman JE (1990) GAL4 transcription factor is not a "zinc finger" but forms a Zn(II)2Cys6 binuclear cluster. Proc Natl Acad Sci U S A 87:2077–2081

    Article  CAS  Google Scholar 

  • Payne GA, Nierman WC, Wortman JR, Pritchard BL, Brown D, Dean RA, Bhatnagar D, Cleveland TE, Machida M, Yu J (2006) Whole genome comparison of Aspergillus flavus and A. oryzae. Med Mycol 44(Suppl):9–11

    Article  Google Scholar 

  • Payne GA, Nystrom GJ, Bhatnagar D, Cleveland TE, Woloshuk CP (1993) Cloning of the afl-2 gene involved in aflatoxin biosynthesis from Aspergillus flavus. Appl Environ Microbiol 59:156–162

    CAS  Google Scholar 

  • Pildain MB, Frisvad JC, Vaamonde G, Cabral D, Varga J, Samson RA (2008) Two novel aflatoxin-producing Aspergillus species from Argentinean peanuts. Int J Syst Evol Microbiol 58:725–735

    Article  CAS  Google Scholar 

  • Reece RJ, Ptashne M (1993) Determinants of binding-site specificity among yeast C6 zinc cluster proteins. Science 261:909–911

    Article  CAS  Google Scholar 

  • Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, Koyama Y, Itoh T, Hattori M, Hanya Y (2011) Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239. DNA Res 18:165–176

    Article  CAS  Google Scholar 

  • Scazzocchio C (1994) The proline utilisation pathway, history and beyond. Prog Ind Microbiol 29:259–277

    CAS  Google Scholar 

  • Seo JA, Guan Y, Yu JH (2006) FluG-dependent asexual development in Aspergillus nidulans occurs via derepression. Genetics 172:1535–1544

    Article  CAS  Google Scholar 

  • Shimizu T, Kinoshita H, Nihira T (2007) Identification and in vivo functional analysis by gene disruption of ctnA, an activator gene involved in citrinin biosynthesis in Monascus purpureus. Appl Environ Microbiol 73:5097–5103

    Article  CAS  Google Scholar 

  • Suarez T, de Queiroz MV, Oestreicher N, Scazzocchio C (1995) The sequence and binding specificity of UaY, the specific regulator of the purine utilization pathway in Aspergillus nidulans, suggest an evolutionary relationship with the PPR1 protein of Saccharomyces cerevisiae. EMBO J 14:1453–1467

    CAS  Google Scholar 

  • Todd RB, Andrianopoulos A (1997) Evolution of a fungal regulatory gene family: the Zn(II)2Cys6 binuclear cluster DNA binding motif. Fungal Genet Biol 21:388–405

    Article  CAS  Google Scholar 

  • Todd RB, Murphy RL, Martin HM, Sharp JA, Davis MA, Katz ME, Hynes MJ (1997) The acetate regulatory gene facB of Aspergillus nidulans encodes a Zn(II)2Cys6 transcriptional activator. Mol Gen Genet 254:495–504

    Article  CAS  Google Scholar 

  • Tsuji G, Kenmochi Y, Takano Y, Sweigard J, Farrall L, Furusawa I, Horino O, Kubo Y (2000) Novel fungal transcriptional activators, Cmr1p of Colletotrichum lagenarium and Pig1p of Magnaporthe grisea, contain Cys2His2 zinc finger and Zn(II)2Cys6 binuclear cluster DNA-binding motifs and regulate transcription of melanin biosynthesis genes in a developmentally specific manner. Mol Microbiol 38:940–954

    Article  CAS  Google Scholar 

  • Vienken K, Fischer R (2006) The Zn(II)2Cys6 putative transcription factor NosA controls fruiting body formation in Aspergillus nidulans. Mol Microbiol 61:544–554

    Article  CAS  Google Scholar 

  • Vienken K, Scherer M, Fischer R (2005) The Zn(II)2Cys6 putative Aspergillus nidulans transcription factor repressor of sexual development inhibits sexual development under low-carbon conditions and in submersed culture. Genetics 169:619–630

    Article  CAS  Google Scholar 

  • Wiemann P, Willmann A, Straeten M, Kleigrewe K, Beyer M, Humpf HU, Tudzynski B (2009) Biosynthesis of the red pigment bikaverin in Fusarium fujikuroi: genes, their function and regulation. Mol Microbiol 72:931–946

    Article  CAS  Google Scholar 

  • Wight WD, Kim KH, Lawrence CB, Walton JD (2009) Biosynthesis and role in virulence of the histone deacetylase inhibitor depudecin from Alternaria brassicicola. Mol Plant Microbe Interact 22:1258–1267

    Article  CAS  Google Scholar 

  • Young C, McMillan L, Telfer E, Scott B (2001) Molecular cloning and genetic analysis of an indole-diterpene gene cluster from Penicillium paxilli. Mol Microbiol 39:754–764

    Article  CAS  Google Scholar 

  • Yu J, Chang P-K, Ehrlich KC, Cary JW, Bhatnagar D, Cleveland TE, Payne GA, Linz JE, Woloshuk CP, Bennett JW (2004) Clustered pathway genes in aflatoxin biosynthesis. Appl Environ Microbiol 70:1253–1262

    Article  CAS  Google Scholar 

  • Yuan GF, Fu YH, Marzluf GA (1991) nit-4, a pathway-specific regulatory gene of Neurospora crassa, encodes a protein with a putative binuclear zinc DNA-binding domain. Mol Cell Biol 11:5735–5745

    CAS  Google Scholar 

  • Yuan XL, Roubos JA, van den Hondel CA, Ram AF (2008) Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger. Mol Genet Genomics 279:11–26

    Article  CAS  Google Scholar 

  • Zhang S, Monahan BJ, Tkacz JS, Scott B (2004) Indole-diterpene gene cluster from Aspergillus flavus. Appl Environ Microbiol 70:6875–6883

    Article  CAS  Google Scholar 

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Chang, PK., Ehrlich, K.C. Genome-wide analysis of the Zn(II)2Cys6 zinc cluster-encoding gene family in Aspergillus flavus . Appl Microbiol Biotechnol 97, 4289–4300 (2013). https://doi.org/10.1007/s00253-013-4865-2

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