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Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira MEDS, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LVG, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodríguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter MEMT, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CMDA, Birren BW, Cuomo CA. Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PLoS Genet 2011; 7:e1002345. [PMID: 22046142 PMCID: PMC3203195 DOI: 10.1371/journal.pgen.1002345] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/30/2011] [Indexed: 12/29/2022] Open
Abstract
Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.
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Affiliation(s)
| | - Mia D. Champion
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jason W. Holder
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Jonathan Goldberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Alexandre M. Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | | | | | - Ana Maria Garcia
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - David I. Heiman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Matthew R. Henn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chinnappa D. Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Henry León-Narváez
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Larissa V. G. Longo
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Li-Jun Ma
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Iran Malavazi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Alisson L. Matsuo
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Flavia V. Morais
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Instituto de Pesquisa y Desenvolvimento, Universidade do Vale do Paraíba, São José dos Campos, Brazil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sabrina Rodríguez-Brito
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Sharadha Sakthikumar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Silvia M. Salem-Izacc
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sean M. Sykes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Milene C. Vallejo
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeremy Zucker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Maria Sueli Felipe
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, Ribeirão Preto, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol – CTBE, São Paulo, Brazil
| | - Brian J. Haas
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Juan G. McEwen
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Gustavo Nino-Vega
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia, e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gioconda San-Blas
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | | | - Bruce W. Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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Li D, Sirakova T, Rogers L, Ettinger WF, Kolattukudy PE. Regulation of constitutively expressed and induced cutinase genes by different zinc finger transcription factors in Fusarium solani f. sp. pisi (Nectria haematococca). J Biol Chem 2002; 277:7905-12. [PMID: 11756444 DOI: 10.1074/jbc.m108799200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cutin monomers, generated by the low levels of constitutively expressed cutinase, induce high levels of cutinase that can help pathogenic fungi to penetrate into the host through the cuticle whose major structural polymer is cutin. We cloned three highly homologous cutinase genes, cut1, cut2, and cut3, from Fusarium solani f. pisi (Nectria haematococca). Amino acid sequence deduced from the nucleotide sequence of cut1 and cut2/3 matched with that of the peptides from cutinase 1 and cutinase 2, respectively, isolated from F. solani pisi grown on cutin as the sole carbon source. Induction of beta-glucuronidase gene fused to the promoters of the cutinases integrated into F. solani pisi genome indicates that cut2 is constitutively expressed and induced under starvation, whereas cut1 is highly induced by cutin monomers. A palindrome binding protein (PBP) previously cloned binds only to palindrome 1 of cut1 promoter but not palindrome 1 of cut2/3 which contains two base substitutions. PBP is thought to interfere with the binding of CTF1 alpha, the transcription factor involved in induction, to cut1 promoter and thus keep cut1 gene repressed until induced by cutin monomers. Because PBP cannot bind palindrome 1 of cut2, this gene is not repressed. CTF1 alpha does not transactivate cut2 promoter. A new Cys(6)Zn(2) motif-containing transcription factor, CTF1 beta, that binds palindrome 2 was cloned and sequenced. In yeast, CTF1 beta transactivates cut2 promoter but not cut1 promoter unless its palindrome 1 is mutated, unlike CTF1 alpha which transactivates cut1. Thus, CTF1 beta is involved in the constitutive expression of cut2 that causes production of low levels of cutin monomers that strongly induce cut1 using CTF1 alpha as the transcription factor.
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Affiliation(s)
- Daoxin Li
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Abstract
Polyesters occur in higher plants as the structural component of the cuticle that covers the aerial parts of plants. This insoluble polymer, called cutin, attached to the epidermal cell walls is composed of interesterified hydroxy and hydroxy epoxy fatty acids. The most common chief monomers are 10,16-dihydroxy C16 acid, 18-hydroxy-9,10 epoxy C18 acid, and 9,10,18-trihydroxy C18 acid. These monomers are produced in the epidermal cells by omega hydroxylation, in-chain hydroxylation, epoxidation catalyzed by P450-type mixed function oxidase, and epoxide hydration. The monomer acyl groups are transferred to hydroxyl groups in the growing polymer at the extracellular location. The other type of polyester found in the plants is suberin, a polymeric material deposited in the cell walls of a layer or two of cells when a plant needs to erect a barrier as a result of physical or biological stress from the environment, or during development. Suberin is composed of aromatic domains derived from cinnamic acid, and aliphatic polyester domains derived from C16 and C18 cellular fatty acids and their elongation products. The polyesters can be hydrolyzed by pancreatic lipase and cutinase, a polyesterase produced by bacteria and fungi. Catalysis by cutinase involves the active serine catalytic triad. The major function of the polyester in plants is as a protective barrier against physical, chemical, and biological factors in the environment, including pathogens. Transcriptional regulation of cutinase gene in fungal pathogens is being elucidated at a molecular level. The polyesters present in agricultural waste may be used to produce high value polymers, and genetic engineering might be used to produce large quantities of such polymers in plants.
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Affiliation(s)
- P E Kolattukudy
- Ohio State University, 206 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, USA.
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Pinot F, Benveniste I, Salaün JP, Loreau O, Noël JP, Schreiber L, Durst F. Production in vitro by the cytochrome P450 CYP94A1 of major C18 cutin monomers and potential messengers in plant-pathogen interactions: enantioselectivity studies. Biochem J 1999; 342 ( Pt 1):27-32. [PMID: 10432296 PMCID: PMC1220432 DOI: 10.1042/0264-6021:3420027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The major C(18) cutin monomers are 18-hydroxy-9,10-epoxystearic and 9,10,18-trihydroxystearic acids. These compounds are also known messengers in plant-pathogen interactions. We have previously shown that their common precursor 9,10-epoxystearic acid was formed by the epoxidation of oleic acid in Vicia sativa microsomes (Pinot, Salaün, Bosch, Lesot, Mioskowski and Durst (1992) Biochem. Biophys. Res. Commun. 184, 183-193). Here we determine the chirality of the epoxide produced as (9R,10S) and (9S,10R) in the ratio 90:10 respectively. We further show that microsomes from yeast expressing the cytochrome P450 CYP94A1 are capable of hydroxylating the methyl terminus of 9,10-epoxystearic and 9,10-dihydroxystearic acids in the presence of NADPH to form the corresponding 18-hydroxy derivatives. The reactions were not catalysed by microsomes from yeast transformed with a void plasmid or in absence of NADPH. After incubation of a synthetic racemic mixture of 9,10-epoxystearic acid with microsomes of yeast expressing CYP94A1, the chirality of the residual epoxide was shifted to 66:34 in favour of the (9S,10R) enantiomer. Both enantiomers were incubated separately and V(max)/K(m) values of 16 and 3.42 ml/min per nmol of P450 for (9R, 10S) and (9S,10R) respectively were determined, demonstrating that CYP94A1 is enantioselective for the (9R,10S) enantiomer, which is preferentially formed in V. sativa microsomes. Compared with the epoxide, the diol 9,10-dihydroxystearic acid was a much poorer substrate for the omega-hydroxylase, with a measured V(max)/K(m) of 0.33 ml/min per nmol of P450. Our results indicate that the activity of CYP94A1 is strongly influenced by the stereochemistry of the 9, 10-epoxide and the nature of substituents on carbons 9 and 10, with V(max)/K(m) values for epoxide>>oleic acid>diol.
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Affiliation(s)
- F Pinot
- Institut de Biologie Moléculaire des Plantes-CNRS UPR406, Département d'Enzymologie Cellulaire et Moléculaire, 28 rue Goethe, F-67083 Strasbourg Cedex, France.
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