Class of cyclic ribosomal peptide synthetic genes in filamentous fungi

Fungal Genetics and Biology

Volumn 86, Issue , 2016, Pages 58-70

  Nagano, Nozomi ^a,b   Umemura, Myco ^c   Izumikawa, Miho ^d   Kawano, Jin ^c   Ishii, Tomoko ^e   Kikuchi, Moto ^e   Tomii, Kentaro ^a,b   Kumagai, Toshitaka ^f   Yoshimi, Akira ^g   Machida, Masayuki ^c   Abe, Keietsu ^g   Shin ya, Kazuo ^a   Asai, Kiyoshi ^a,b,h  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b Biological Network Team   (Japan)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^d Japan Biological Informatics Consortium   (Japan)

^e Technology Research Association of Highly Efficient Gene Design   (Japan)

^f Fermlab Inc   (Japan)

^g TOHOKU UNIVERSITY   (Japan)

^h UNIVERSITY OF TOKYO   (Japan)

Author keywords

Aspergilli; Genome analyses; Ribosomal peptide synthetic pathways; Secondary metabolites

Indexed keywords

AMINO TERMINAL SEQUENCE; ARTICLE; ASPERGILLUS FLAVUS; CONTROLLED STUDY; FUNGAL GENE; FUNGAL STRAIN; GENE CLUSTER; GENE SEQUENCE; GENOME ANALYSIS; MUSHROOM; NONHUMAN; PRIORITY JOURNAL; USTYA GENE; USTYB GENE; AMINO ACID SEQUENCE; CHEMISTRY; FUNGAL GENOME; GENETICS; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; RIBOSOME;

CYCLOPEPTIDE; SYNTHETIC DNA; USTILOXIN B;

AMINO ACID SEQUENCE; ASPERGILLUS FLAVUS; GENES, FUNGAL; GENES, SYNTHETIC; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PEPTIDES, CYCLIC; RIBOSOMES;

EID: 84950279555     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2015.12.010     Document Type: Article

References (39)

1. Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
3. Arnison P.G., et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat. Prod. Rep. 2013, 30:108-160.
4. Cacho R.A., et al. Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi. Front. Microbiol. 2015, 5:774.
5. Cerqueira G.C., et al. The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 2014, 42:D705-D710.
6. Finn R.D., et al. Pfam: the protein families database. Nucleic Acids Res. 2014, 42:D222-D230.
7. Furihata K., Seto H. Constant time HMBC (CT-HMBC), a new HMBC technique useful for improving separation of cross peaks. Tetrahedron Lett. 1998, 39:7337-7340.
8. Heiman M.G., et al. The Golgi-resident protease Kex2 acts in conjunction with Prm1 to facilitate cell fusion during yeast mating. J. Cell Biol. 2007, 176:209-222.
9. Houbraken J., et al. Modern taxonomy of biotechnologically important Aspergillus and Penicillium species. Adv. Appl. Microbiol. 2014, 86:199-249.
10. Jalving R., et al. Characterization of the kexin-like maturase of Aspergillus niger. Appl. Environ. Microbiol. 2000, 66:363-368.
11. Keller N.P., et al. Fungal secondary metabolism - from biochemistry to genomics. Nat. Rev. Microbiol. 2005, 3:937-947.
12. Khaldi N., et al. SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet. Biol. 2010, 47:736-741.
13. Koiso Y., et al. Ustiloxin: a phytotoxin and a mycotoxin from false smut balls on rice panicles. Tetrahedron Lett. 1992, 33:4157-4160.
14. Koiso Y., et al. Ustiloxins, antimitotic cyclic peptides from false smut balls on rice panicles caused by Ustilaginoidea virens. J. Antibiot. (Tokyo) 1994, 47:765-773.
15. Koiso Y., et al. Isolation and structure of an antimitotic cyclic peptide, ustiloxin F: chemical interrelation with a homologous peptide, ustiloxin B. J. Antibiot. (Tokyo) 1998, 51:418-422.
16. Li Y., et al. Ustiloxins, new antimitotic cyclic peptides: interaction with porcine brain tubulin. Biochem. Pharmacol. 1995, 49:1367-1372.
17. Ludueńa R.F., et al. Interaction of ustiloxin A with bovine brain tubulin. Biochem. Pharmacol. 1994, 47:1593-1599.
18. Ma L.J., et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010, 464:367-373.
19. Magrane, M., UniProt Consortium, 2011. UniProt Knowledgebase: A Hub of Integrated Protein Data. Database (Oxford) 2011, bar009.
20. Medema M.H., et al. AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 2011, 39:W339-W346.
21. Mizutani O., et al. Modified Cre-loxP recombination in Aspergillus oryzae by direct introduction of Cre recombinase for marker gene rescue. Appl. Environ. Microbiol. 2012, 78:4126-4133.
22. Möller S., et al. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 2001, 17:646-653.
23. Morita H., et al. Serine-type carboxypeptidase KexA of Aspergillus oryzae has broader substrate specificity than Saccharomyces cerevisiae Kex1 and is required for normal hyphal growth and conidiation. Appl. Environ. Microbiol. 2012, 78:8154-8157.
24. Nagano N., et al. Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database. Proteins 2007, 66:147-159.
25. Nagano N., et al. EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Res. 2015, 43:D453-D458.
26. Nielsen H., et al. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997, 10:1-6.
27. Oman T.J., van der Donk W.A. Follow the leader: the use of leader peptides to guide natural product biosynthesis. Nat. Chem. Biol. 2010, 6:9-18.
28. Petersen T.N., et al. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8:785-786.
29. Sievers F., et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011, 7:539.
30. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197.
31. Tsukui T., et al. Ustiloxins, fungal cyclic peptides, are ribosomally synthesised in Ustilaginoidea virens. Bioinformatics 2015, 31:981-985.
32. Tuteja R. Type I signal peptidase: an overview. Arch. Biochem. Biophys. 2005, 441:107-111.
33. Umemura M., et al. MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data. PLoS ONE 2013, 8:e84028.
34. Umemura M., et al. Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus. Fungal Genet. Biol. 2014, 68:23-30.
35. Vallee B.L., Auld D.S. Active-site zinc ligands and activated H2O of zinc enzymes. Proc. Natl. Acad. Sci. USA 1990, 87:220-224.
36. Wagner J.C., Wolf D.H. Hormone (pheromone) processing enzymes in yeast. The carboxy-terminal processing enzyme of the mating pheromone alpha-factor, carboxypeptidase ysc alpha, is absent in alpha-factor maturation-defective kex1 mutant cells. FEBS Lett. 1987, 221:423-426.
37. Ward J.J., et al. The DISOPRED server for the prediction of protein disorder. Bioinformatics 2004, 20:2138-2139.
38. Wiemann P., Keller N.P. Strategies for mining fungal natural products. J. Ind. Microbiol. Biotechnol. 2014, 41:301-313.
39. Yu J., et al. Aspergillus flavus genomics as a tool for studying the mechanism of aflatoxin formation. Food Addit. Contam. Part A: Chem. Anal. Control Expo. Risk Assess. 2008, 25:1152-1157.