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1.
PLoS One ; 6(11): e28231, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-22140558

RESUMEN

Nonribosomal peptides (NRPs) and polyketides (PKs) are ecologically important secondary metabolites produced by bacteria and fungi using multidomain enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. Previous phylogenetic analyses of fungal NRPSs and PKSs have suggested that a few of these genes were acquired by fungi via horizontal gene transfer (HGT) from bacteria, including a hybrid NPS/PKS found in Cochliobolus heterostrophus (Dothideomycetes, Ascomycota). Here, we identify this hybrid gene in fungi representing two additional classes of Ascomycota (Aspergillus spp., Microsporum canis, Arthroderma spp., and Trichophyton spp., Eurotiomycetes; Chaetomium spp. and Metarhizium spp., Sordariomycetes) and use phylogenetic analyses of the most highly conserved domains from NRPSs (adenylation (A) domain) and PKSs (ketoacyl synthase (KS) domain) to examine the hypothesis that the hybrid NPS7/PKS24 was acquired by fungi from bacteria via HGT relatively early in the evolution of the Pezizomycotina. Our results reveal a unique ancestry of the A domain and KS domain in the hybrid gene relative to known fungal NRPSs and PKSs, provide strong evidence for HGT of the hybrid gene from a putative bacterial donor in the Burkholderiales, and suggest the HGT event occurred early in the evolution of the filamentous Ascomycota.


Asunto(s)
Ascomicetos/enzimología , Ascomicetos/genética , Bacterias/enzimología , Bacterias/genética , Transferencia de Gen Horizontal/genética , Péptido Sintasas/genética , Sintasas Poliquetidas/genética , Datos de Secuencia Molecular , Péptido Sintasas/química , Filogenia , Sintasas Poliquetidas/química , Estructura Terciaria de Proteína
2.
PLoS Genet ; 5(8): e1000618, 2009 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-19714214

RESUMEN

The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.


Asunto(s)
Cromosomas Fúngicos/genética , Genoma Fúngico , Nectria/genética , Composición de Base , Cromosomas Fúngicos/química , Hongos/clasificación , Hongos/genética , Duplicación de Gen , Nectria/química , Nectria/clasificación , Filogenia
3.
Science ; 317(5843): 1400-2, 2007 Sep 07.
Artículo en Inglés | MEDLINE | ID: mdl-17823352

RESUMEN

We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.


Asunto(s)
Fusarium/genética , Genoma Fúngico , Polimorfismo Genético , ADN de Hongos , Evolución Molecular , Fusarium/fisiología , Hordeum/microbiología , Datos de Secuencia Molecular , Enfermedades de las Plantas/microbiología , Mutación Puntual , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN
4.
Eukaryot Cell ; 6(7): 1189-99, 2007 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-17513566

RESUMEN

Coccidioides species, the fungi responsible for the valley fever disease, are known to reproduce asexually through the production of arthroconidia that are the infectious propagules. The possible role of sexual reproduction in the survival and dispersal of these pathogens is unexplored. To determine the potential for mating of Coccidioides, we analyzed genome sequences and identified mating type loci characteristic of heterothallic ascomycetes. Coccidioides strains contain either a MAT1-1 or a MAT1-2 idiomorph, which is 8.1 or 9 kb in length, respectively, the longest reported for any ascomycete species. These idiomorphs contain four or five genes, respectively, more than are present in the MAT loci of most ascomycetes. Along with their cDNA structures, we determined that all genes in the MAT loci are transcribed. Two genes frequently found in common sequences flanking MAT idiomorphs, APN2 and COX13, are within the MAT loci in Coccidioides, but the MAT1-1 and MAT1-2 copies have diverged dramatically from each other. Data indicate that the acquisition of these genes in the MAT loci occurred prior to the separation of Coccidioides from Uncinocarpus reesii. An analysis of 436 Coccidioides isolates from patients and the environment indicates that in both Coccidioides immitis and C. posadasii, there is a 1:1 distribution of MAT loci, as would be expected for sexually reproducing species. In addition, an analysis of isolates obtained from 11 soil samples demonstrated that at three sampling sites, strains of both mating types were present, indicating that compatible strains were in close proximity in the environment.


Asunto(s)
Coccidioides , Genes del Tipo Sexual de los Hongos , Genoma Fúngico , Reproducción , Coccidioides/genética , Coccidioides/fisiología , ADN-(Sitio Apurínico o Apirimidínico) Liasa/clasificación , ADN-(Sitio Apurínico o Apirimidínico) Liasa/genética , ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , Proteínas Fúngicas/clasificación , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Proteínas de la Membrana/clasificación , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Proteínas Nucleares/clasificación , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Filogenia , Transcripción Genética
5.
Fungal Genet Biol ; 43(11): 775-88, 2006 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-16857399

RESUMEN

Coccidioides posadasii is a dimorphic fungal pathogen of humans and other mammals. The switch between saprobic and parasitic growth involves synthesis of new cell walls of which chitin is a significant component. To determine whether particular subsets of chitin synthases (CHSes) are responsible for production of chitin at different stages of differentiation, we have isolated six CHS genes from this fungus. They correspond, together with another reported CHS gene, to single members of the seven defined classes of chitin synthases (classes I-VII). Using Real-Time RT-PCR we show their pattern of expression during morphogenesis. CpCHS2, CpCHS3, and CpCHS6 are preferentially expressed during the saprobic phase, while CpCHS1 and CpCHS4 are more highly expressed during the parasitic phase. CpCHS5 and CpCHS7 expression is similar in both saprobic and parasitic phases. Because C. posadasii contains single members of the seven classes of CHSes found in fungi, it is a good model to investigate the putatively different roles of these genes in fungal growth and differentiation.


Asunto(s)
Quitina Sintasa/genética , Coccidioides/genética , Proteínas Fúngicas/genética , Regulación Enzimológica de la Expresión Génica , Regulación Fúngica de la Expresión Génica , Animales , Secuencia de Bases , Quitina Sintasa/clasificación , Coccidioides/enzimología , Coccidioides/crecimiento & desarrollo , Coccidioides/patogenicidad , Proteínas Fúngicas/biosíntesis , Perfilación de la Expresión Génica/métodos , Regulación Enzimológica de la Expresión Génica/genética , Regulación Fúngica de la Expresión Génica/genética , Humanos , Datos de Secuencia Molecular , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos
6.
Mol Plant Microbe Interact ; 19(2): 139-49, 2006 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-16529376

RESUMEN

Cochliobolus heterostrophus race T, causal agent of southern corn leaf blight, requires T-toxin (a family of C35 to C49 polyketides) for high virulence on T-cytoplasm maize. Production of T-toxin is controlled by two unlinked loci, Tox1A and Tox1B, carried on 1.2 Mb of DNA not found in race O, a mildly virulent form of the fungus that does not produce T-toxin, or in any other Cochliobolus spp. or closely related fungus. PKS1, a polyketide synthase (PKS)-encoding gene at Tox1A, and DEC1, a decarboxylase-encoding gene at Tox1B, are necessary for T-toxin production. Although there is evidence that additional genes are required for T-toxin production, efforts to clone them have been frustrated because the genes are located in highly repeated, A+T-rich DNA. To overcome this difficulty, ligation specificity-based expression analysis display (LEAD), a comparative amplified fragment length polymorphism/gel fractionation/capillary sequencing procedure, was applied to cDNAs from a near-isogenic pair of race T (Tox1+) and race O (Tox1-) strains. This led to discovery of PKS2, a second PKS-encoding gene that maps at Tox1A and is required for both T-toxin biosynthesis and high virulence to maize. Thus, the carbon chain of each T-toxin family member likely is assembled by action of two PKSs, which produce two polyketides, one of which may act as the starter unit for biosynthesis of the mature T-toxin molecule.


Asunto(s)
Ascomicetos/enzimología , Macrólidos/metabolismo , Micotoxinas/biosíntesis , Sintasas Poliquetidas/genética , Factores de Virulencia/biosíntesis , Ascomicetos/patogenicidad , Mapeo Cromosómico , Cromosomas de las Plantas/genética , ADN Complementario/genética , Eliminación de Gen , Perfilación de la Expresión Génica , Pruebas de Sensibilidad Microbiana , Complejos Multienzimáticos , Micotoxinas/química , Filogenia , Sintasas Poliquetidas/química , Plantones/microbiología , Análisis de Secuencia de ADN , Especificidad de la Especie , Zea mays/anatomía & histología , Zea mays/microbiología
7.
Eukaryot Cell ; 4(3): 545-55, 2005 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-15755917

RESUMEN

Nonribosomal peptides, made by nonribosomal peptide synthetases, have diverse biological activities, including roles as fungal virulence effectors. Inspection of the genome of Cochliobolus heterostrophus, a fungal pathogen of maize and a member of a genus noted for secondary metabolite production, revealed eight multimodular nonribosomal peptide synthase (NPS) genes and three monomodular NPS-like genes, one of which encodes a nonribosomal peptide synthetase/polyketide synthase hybrid enzyme presumed to be involved in synthesis of a peptide/polyketide molecule. Deletion of each NPS gene and phenotypic analyses showed that the product of only one of these genes, NPS6, is required for normal virulence on maize. NPS6 is also required for resistance to hydrogen peroxide, suggesting it may protect the fungus from oxidative stress. This and all other nps mutants had normal growth, mating ability, and appressoria. Real-time PCR analysis showed that expression of all NPS genes is low (relative to that of actin), that all (except possibly NPS2) are expressed during vegetative growth, and that expression is induced by nitrogen starvation. Only NPS6 is unfailingly conserved among euascomycete fungi, including plant and human pathogens and saprobes, suggesting the possibility that NPS6 activity provides oxidative stress protection during both saprobic and parasitic growth.


Asunto(s)
Ascomicetos/enzimología , Ascomicetos/patogenicidad , Proteínas Fúngicas/metabolismo , Genes Fúngicos , Estrés Oxidativo , Péptido Sintasas/metabolismo , Secuencia de Aminoácidos , Ascomicetos/genética , Ascomicetos/fisiología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas Fúngicas/clasificación , Proteínas Fúngicas/genética , Regulación Fúngica de la Expresión Génica , Humanos , Peróxido de Hidrógeno/metabolismo , Datos de Secuencia Molecular , Oxidantes/metabolismo , Péptido Sintasas/clasificación , Péptido Sintasas/genética , Filogenia , Hojas de la Planta/microbiología , Alineación de Secuencia , Zea mays/anatomía & histología , Zea mays/microbiología
8.
Proc Natl Acad Sci U S A ; 100(26): 15670-5, 2003 Dec 23.
Artículo en Inglés | MEDLINE | ID: mdl-14676319

RESUMEN

Fungal type I polyketides (PKs) are synthesized by PK synthases (PKSs) and include well known secondary metabolites such as the anticholesterol drug lovastatin and the potent natural carcinogen aflatoxin. Other type I PKs are known to be virulence factors for some plant pathogens and pigments such as melanin. In this study, a phylogenomic approach was used to investigate the origin and diversity of fungal genes encoding putative PKSs that are predicted to synthesize type I PKs. The resulting genealogy, constructed by using the highly conserved PKS ketosynthase (KS) domain, indicated that: (i). Species within subphylum Pezizomycotina (phylum Ascomycota) but not early diverging ascomycetes, like Saccharomyces cerevisiae (Saccharomycotina) or Schizosaccharomyces pombe (Taphrinomycotina), had large numbers (7-25) of PKS genes. (ii). Bacteria and fungi had separate groups of PKS genes; the few exceptions are the likely result of horizontal gene transfer from bacteria to various sublineages of fungi. (iii). The bulk of genes encoding fungal PKSs fell into eight groups. Four groups were predicted to synthesize variously reduced PKs, and four groups were predicted to make unreduced PKs. (iv). Species within different classes of Pezizomycotina shared the same groups of PKS genes. (v). Different fungal genomes shared few putative orthologous PKS genes, even between closely related genomes in the same class or genus. (vi) The discontinuous distributions of orthologous PKSs among fungal species can be explained by gene duplication, divergence, and gene loss; horizontal gene transfer among fungi does not need to be invoked.


Asunto(s)
Ascomicetos/genética , Complejos Multienzimáticos/genética , Filogenia , Ascomicetos/clasificación , Ascomicetos/enzimología , Ascomicetos/patogenicidad , Bacterias/clasificación , Bacterias/genética , Bases de Datos de Ácidos Nucleicos , Bases de Datos de Proteínas , Duplicación de Gen , Variación Genética , Datos de Secuencia Molecular
9.
Proc Natl Acad Sci U S A ; 100(10): 5980-5, 2003 May 13.
Artículo en Inglés | MEDLINE | ID: mdl-12730371

RESUMEN

Insertional mutants of the fungal maize pathogen Cochliobolus heterostrophus were screened for altered virulence. One mutant had 60% reduction in lesion size relative to WT but no other detectable change in phenotype. Analysis of sequence at the insertion site revealed a gene (CPS1) encoding a protein with two AMP-binding domains. CPS1 orthologs were detected in all Cochliobolus spp. examined, in several other classes of ascomycete fungi, and in animals but not in basidiomycete fungi, bacteria, or plants. Phylogenetic analysis suggested that CPS1 represents a previously undescribed subset of adenylate-forming enzymes that have diverged from certain acyl-CoA ligases, which in bacteria are involved in biosynthesis of nonribosomal peptides or polyketidepeptide hybrids. Disruption of CPS1 caused reduced virulence of both race T and race O of C. heterostrophus on maize, of Cochliobolus victoriae on oats, and of Gibberella zeae on wheat. These results suggest that CPS1 functions as a general fungal virulence factor in plant pathogenic ascomycetes.


Asunto(s)
Ascomicetos/genética , Ascomicetos/patogenicidad , Avena/microbiología , Proteínas de la Membrana , Plantas/microbiología , Proteínas de Schizosaccharomyces pombe , Triticum/microbiología , Virulencia/genética , Animales , Ascomicetos/clasificación , Clonación Molecular , Eliminación de Gen , Glucosiltransferasas/genética , Humanos , Datos de Secuencia Molecular , Mutagénesis , Filogenia , Reacción en Cadena de la Polimerasa
10.
Nature ; 422(6934): 859-68, 2003 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-12712197

RESUMEN

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.


Asunto(s)
Genes Fúngicos/genética , Genoma Fúngico , Neurospora crassa/genética , Señalización del Calcio/genética , Metilación de ADN , Diterpenos/metabolismo , Evolución Molecular , Duplicación de Gen , Proteínas de Unión al GTP Heterotriméricas/metabolismo , Complejos Multienzimáticos/genética , Familia de Multigenes/genética , Mutagénesis/genética , Neurospora crassa/citología , Neurospora crassa/enzimología , Neurospora crassa/metabolismo , Enfermedades de las Plantas/microbiología , Interferencia de ARN , ARN Ribosómico/genética , Receptores de Superficie Celular/genética , Secuencias Repetitivas de Ácidos Nucleicos , Análisis de Secuencia de ADN , Transducción de Señal/genética
11.
Proc Natl Acad Sci U S A ; 99(20): 13324-9, 2002 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-12271140

RESUMEN

Using a genome-wide approach, we asked how many transporter genes contribute to symbiotic phosphate uptake and analyzed their evolutionary conservation. Considering the sequenced rice genome at hand, only the Oryza sativa phosphate transporter (OsPT) gene OsPT11 was specifically induced during the arbuscular mycorrhizal symbiosis. This induction was confined to the root system and was tightly correlated with the degree of root colonization by Glomus intraradices. OsPT11 activation was independent of the nutritional status of the plant and phosphate availability in the rhizosphere. Moreover, infection of roots with the fungal pathogens Rhizoctonia solani and Fusarium moniliforme did not activate OsPT11, corroborating the high signal specificity for OsPT11 activation in the arbuscular mycorrhizal symbiosis. OsPT11 expression complemented a defect in phosphate uptake in a yeast strain mutated in its high-affinity P(i) transporter (pho84), thereby confirming its function. Recently, a phosphate transporter gene in potato was shown to be induced during arbuscular mycorrhizal symbiosis. Assessment of the phylogenetic relationship of the rice and potato protein revealed that the rice is nonorthologous to the potato protein. Further, there are no structural commonalities in the promoter regions. Thus, although cytological and physiological features of the arbuscular mycorrhizal symbiosis seem to be conserved, the molecular components may differ significantly between distantly related plant species.


Asunto(s)
Oryza/genética , Proteínas de Transporte de Fosfato/genética , Proteínas de Plantas/genética , Proteínas de Plantas/fisiología , Simbiosis , Elementos Transponibles de ADN , ADN Complementario/metabolismo , Eliminación de Gen , Genoma de Planta , Cinética , Datos de Secuencia Molecular , Fósforo/metabolismo , Filogenia , Regiones Promotoras Genéticas , ARN/metabolismo , Saccharomyces cerevisiae/metabolismo , Factores de Tiempo
12.
Mol Ecol ; 11(7): 1191-6, 2002 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-12074726

RESUMEN

Our data on the intercontinental population biology of Letharia vulpina show an unexpected shift from a recombining North American population with unique haplotypes to genetically depauperate Swedish and Italian populations, each with many representatives of a single repeated haplotype. Analysis of eight loci in 47 individuals supported recombination in North American populations and showed almost no variation among European populations. We infer that a genetic bottleneck caused by limited long-distance dispersal accounts for the lack of genetic variation found in marginal populations. This lack of variation in the European populations makes it impossible to use population genetic means to distinguish clonal reproduction from self-fertilization or even outcrossing, but phenotype indicates that reproduction in the marginal populations is by clonal spread, via soredia and isidioid soredia.


Asunto(s)
Ascomicetos/genética , Variación Genética , Filogenia , Ascomicetos/crecimiento & desarrollo , California , ADN de Hongos/química , ADN de Hongos/genética , ADN Ribosómico/química , ADN Ribosómico/genética , Italia , Reacción en Cadena de la Polimerasa , Alineación de Secuencia , Análisis de Secuencia de ADN , Suecia
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