title: Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome.
abstract: BACKGROUND
  The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated "omics" approaches.
  
  
  RESULTS
  The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization.
  
  
  CONCLUSIONS
  The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity.
authors: Laboratório de Genômica e Expressão, Departamento de Genética Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CEP: 13083-970, Campinas, São Paulo, Brasil.
authors: Alinne Batista
authors: AB
authors: Ambrosio
authors: Leandro Costa
authors: LC
authors: do Nascimento
authors: Bruno V
authors: BV
authors: Oliveira
authors: Paulo José P L
authors: PJ
authors: Teixeira
authors: Ricardo A
authors: RA
authors: Tiburcio
authors: Daniela P
authors: DP
authors: Toledo Thomazella
authors: Adriana F P
authors: AF
authors: Leme
authors: Marcelo F
authors: MF
authors: Carazzolle
authors: Ramon O
authors: RO
authors: Vidal
authors: Piotr
authors: P
authors: Mieczkowski
authors: Lyndel W
authors: LW
authors: Meinhardt
authors: Gonçalo A G
authors: GA
authors: Pereira
authors: Odalys G
authors: OG
authors: Cabrera
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D002099:Cacao / Q000235:genetics / Q000382:microbiology; D019295:Computational Biology; D004272:DNA, Mitochondrial / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D054629:Genome, Mitochondrial; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000235:genetics*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020543:Proteome / Q000032:analysis / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins; D020543:Proteome
references: J Biomed Biotechnol. 2010;2010:932527
references: 20589070
references: J Antimicrob Chemother. 2004 May;53(5):743-9
references: 15044422
references: Plant Cell. 1999 Sep;11(9):1717-30
references: 10488238
references: J Proteome Res. 2009 Nov;8(11):5120-31
references: 19764775
references: Biochim Biophys Acta. 2006 May-Jun;1757(5-6):604-10
references: 16624249
references: Sci Rep. 2012;2:322
references: 22435085
references: Mol Plant Pathol. 2001 Nov 1;2(6):319-25
references: 20573021
references: Nat Rev Mol Cell Biol. 2010 Sep;11(9):655-67
references: 20729931
references: Genetics. 2002 Apr;160(4):1451-60
references: 11973300
references: Cell. 2008 Jul 11;134(1):112-23
references: 18614015
references: Phytopathology. 2007 Dec;97(12):1648-9
references: 18943727
references: PLoS One. 2010 Nov 18;5(11):e14048
references: 21124976
references: Fungal Genet Biol. 2011 May;48(5):526-36
references: 21145408
references: Nihon Ishinkin Gakkai Zasshi. 2009;50(3):167-74
references: 19654450
references: New Phytol. 2012 Jun;194(4):1025-1034
references: 22443281
references: Nucleic Acids Res. 2010 Jun;38(10):e112
references: 20150413
references: Phytopathology. 2011 May;101(5):555-66
references: 21190423
references: Mycologia. 2005 Jan-Feb;97(1):57-69
references: 16389957
references: Free Radic Res. 2006 Apr;40(4):339-47
references: 16517498
references: Pest Manag Sci. 2004 Jan;60(1):3-7
references: 14727735
references: Gene. 2008 Aug 1;419(1-2):7-15
references: 18538510
references: Fungal Biol. 2012 May;116(5):551-62
references: 22559916
references: Plant Cell. 2002 Aug;14(8):1869-83
references: 12172028
references: Nucleic Acids Res. 2009 Dec;37(22):7509-18
references: 19843606
references: Science. 1997 Sep 5;277(5331):1453-62
references: 9278503
references: PLoS Biol. 2004 Jun;2(6):e160
references: 15208715
references: J Mol Biol. 1996 Feb 9;255(5):688-701
references: 8636971
references: Nat Protoc. 2007;2(4):953-71
references: 17446895
references: Trends Microbiol. 1998 Jan;6(1):1-3
references: 9481814
references: Annu Rev Phytopathol. 2012;50:267-94
references: 22726121
references: PLoS One. 2012;7(1):e29343
references: 22235287
references: J Biol Chem. 1990 Dec 5;265(34):20715-8
references: 2249981
references: Mol Genet Genomics. 2011 Aug;286(2):143-59
references: 21750919
references: Science. 2006 Jul 21;313(5785):314-8
references: 16857931
references: Phytopathology. 2003 Oct;93(10):1274-84
references: 18944327
references: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references: 9023104
references: Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18730-5
references: 18000048
references: J Proteome Res. 2010 Sep 3;9(9):4758-66
references: 20666496
references: Bioinformatics. 2009 Aug 1;25(15):1966-7
references: 19497933
references: Mol Ecol. 2004 Oct;13(10):2995-3005
references: 15367115
references: Methods. 2009 Jul;48(3):249-57
references: 19336255
references: Redox Rep. 2008;13(6):246-54
references: 19017464
references: Adv Drug Deliv Rev. 2001 Jul 2;49(1-2):3-26
references: 11377800
references: BMC Genomics. 2008 Nov 18;9:548
references: 19019209
references: Nat Genet. 2006 May;38(5):576-82
references: 16582907
references: BMC Bioinformatics. 2005 Jun 16;6:151
references: 15960857
references: Curr Genet. 1991 Feb;19(2):129-37
references: 1648454
references: Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13207-12
references: 14576278
references: Proteomics. 2006 Jan;6(1):72-80
references: 16294304
references: Nucleic Acids Res. 2010 Aug;38(14):4570-8
references: 20371516
references: Mol Plant Microbe Interact. 2011 Mar;24(3):368-76
references: 21077772
references: J Mol Evol. 2009 Oct;69(4):372-85
references: 19826748
references: Mol Plant Microbe Interact. 1997 Dec;10(9):1106-9
references: 9390425
references: Genome Biol. 2012 Jan 31;13(1):R4
references: 22293517
references: Mol Plant Pathol. 2001 Jul 1;2(4):241-55
references: 20573012
references: Eukaryot Cell. 2011 Nov;10(11):1376-83
references: 21926328
references: Mol Plant Pathol. 2009 Sep;10(5):703-15
references: 19694958
references: Proteomics. 2006 Apr;6 Suppl 1:S88-96
references: 16544282
references: Insect Mol Biol. 2011 Apr;20(2):141-52
references: 20958808
references: APMIS Suppl. 1998;84:5-14
references: 9850675
references: Bioinformatics. 2005 Sep 15;21(18):3674-6
references: 16081474
references: Nucleic Acids Res. 2000 Jan 1;28(1):263-6
references: 10592242
references: Nat Methods. 2008 Jul;5(7):621-8
references: 18516045
references: Proteomics. 2009 Jun;9(12):3222-32
references: 19562796
references: Curr Genet. 2006 Aug;50(2):125-36
references: 16733756
references: J Biol Chem. 2004 Apr 9;279(15):14473-6
references: 14973134
references: Cell. 2011 Aug 19;146(4):645-58
references: 21854988
references: Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6630-5
references: 15851668
references: Biochim Biophys Acta. 1995 May 24;1271(1):123-6
references: 7599197
references: Trends Microbiol. 2010 Nov;18(11):521-30
references: 20832322
references: J Proteome Res. 2011 May 6;10(5):2508-24
references: 21388144
references: Mutat Res. 1989 Jan;219(1):9-15
references: 2911274
references: Nucleic Acids Res. 2001 Sep 15;29(18):3757-74
references: 11557808
references: FEBS Lett. 2004 Jun 1;567(1):96-102
references: 15165900
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W20-5
references: 15215342
references: Mol Plant Microbe Interact. 2002 May;15(5):493-500
references: 12036280
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W585-7
references: 17517783
references: Nucleic Acids Res. 2000 Jan 1;28(1):27-30
references: 10592173
references: PLoS One. 2008 Jun 04;3(6):e2300
references: 18523684
references: Proteomics. 2006 Nov;6(22):5995-6007
references: 17051649
references: J Proteome Res. 2006 Jul;5(7):1543-54
references: 16823961
references: Phytopathology. 2011 Aug;101(8):1005-12
references: 21486144
references: PLoS One. 2009 Dec 22;4(12):e8407
references: 20027311
references: Annu Rev Biochem. 2007;76:723-49
references: 17263664
references: Cell. 2011 Jul 22;146(2):277-89
references: 21784248
references: Med Mycol. 2010 Feb;48(1):1-15
references: 19462332
references: Nature. 2003 Apr 24;422(6934):859-68
references: 12712197
references: Mycologia. 2005 Sep-Oct;97(5):1067-92
references: 16596958
references: J Proteome Res. 2012 Jan 1;11(1):279-91
references: 21939285
references: Fungal Genet Biol. 2008 May;45(5):628-37
references: 18226935
references: J Biol Chem. 2002 Aug 16;277(33):29810-6
references: 12065597
references: Mol Biol Evol. 2009 Oct;26(10):2299-315
references: 19597163
references: Apoptosis. 2007 May;12(5):1011-23
references: 17453165
references: Microbiology (Reading). 2000 Oct;146 ( Pt 10):2495-2508
references: 11021925
references: Plant Cell. 2004 Jan;16(1):241-56
references: 14671022
references: Biochim Biophys Acta. 2012 Sep-Oct;1819(9-10):992-7
references: 22172994