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Comparative functional characterization of a novel benzoate hydroxylase cytochrome P450 of Fusarium oxysporum. Enzyme Microb Technol 2014; 70:58-65. [PMID: 25659633 DOI: 10.1016/j.enzmictec.2014.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/19/2014] [Accepted: 12/24/2014] [Indexed: 01/13/2023]
Abstract
FoCYP53A19, a novel cytochrome P450 capable of performing benzoate hydroxylation, was identified and characterized from the ascomycete Fusarium oxysporum f.sp. lycopersici. Comparative functional analysis of FoCYP53A19 with the heterologous and homologous cytochrome P450 reductases (CPR) such as Saccharomyces cerevisiae (ScCPR), Candida albicans (CaCPR) and F. oxysporum (FoCPR) revealed novel catalytic properties. The catalytic efficiency and substrate specificity of FoCYP53A19 were significantly influenced and altered by the source of the reductase employed. The yeast reconstitution system of FoCYP53A19 with ScCPR performed the hydroxylation of benzoic acid (BA) and demethylation of 3-methoxybenzoic acid (3-MBA); but when reconstituted with CaCPR, FoCYP53A19 performed only the essential hydroxylation of fungal benzoate catabolism. Remarkably, FoCYP53A19 with its homologous reductase FoCPR, not only demonstrated the improved conversion rates of BA and 3-MBA, but also exhibited activity toward the hydroxylation of 3-hydroxybenzoic acid. The electron transfer compatibility and the coupling efficiency between the homologous FoCYP-FoCPR system are significant and it favored enhanced monooxygenase activity with broader substrate specificity.
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202
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Golicz AA, Martinez PA, Zander M, Patel DA, Van De Wouw AP, Visendi P, Fitzgerald TL, Edwards D, Batley J. Gene loss in the fungal canola pathogen Leptosphaeria maculans. Funct Integr Genomics 2014; 15:189-96. [PMID: 25421464 DOI: 10.1007/s10142-014-0412-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/29/2014] [Accepted: 11/04/2014] [Indexed: 12/31/2022]
Abstract
Recent comparisons of the increasing number of genome sequences have revealed that variation in gene content is considerably more prevalent than previously thought. This variation is likely to have a pronounced effect on phenotypic diversity and represents a crucial target for the assessment of genomic diversity. Leptosphaeria maculans, a causative agent of phoma stem canker, is the most devastating fungal pathogen of Brassica napus (oilseed rape/canola). A number of L. maculans genes are known to be present in some isolates but lost in the others. We analyse gene content variation within three L. maculans isolates using a hybrid mapping and genome assembly approach and identify genes which are present in one of the isolates but missing in the others. In total, 57 genes are shown to be missing in at least one isolate. The genes encode proteins involved in a range of processes including oxidative processes, DNA maintenance, cell signalling and sexual reproduction. The results demonstrate the effectiveness of the method and provide new insight into genomic diversity in L. maculans.
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Affiliation(s)
- Agnieszka A Golicz
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
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203
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Jawallapersand P, Mashele SS, Kovačič L, Stojan J, Komel R, Pakala SB, Kraševec N, Syed K. Cytochrome P450 monooxygenase CYP53 family in fungi: comparative structural and evolutionary analysis and its role as a common alternative anti-fungal drug target. PLoS One 2014; 9:e107209. [PMID: 25222113 PMCID: PMC4164535 DOI: 10.1371/journal.pone.0107209] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 08/08/2014] [Indexed: 01/14/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are heme-thiolate proteins whose role as a drug target against pathogenic microbes has been explored because of their stereo- and regio-specific oxidation activity. We aimed to assess the CYP53 family's role as a common alternative drug target against animal (including human) and plant pathogenic fungi and its role in fungal-mediated wood degradation. Genome-wide analysis of fungal species revealed the presence of CYP53 members in ascomycetes and basidiomycetes. Basidiomycetes had a higher number of CYP53 members in their genomes than ascomycetes. Only two CYP53 subfamilies were found in ascomycetes and six subfamilies in basidiomycetes, suggesting that during the divergence of phyla ascomycetes lost CYP53 P450s. According to phylogenetic and gene-structure analysis, enrichment of CYP53 P450s in basidiomycetes occurred due to the extensive duplication of CYP53 P450s in their genomes. Numerous amino acids (103) were found to be conserved in the ascomycetes CYP53 P450s, against only seven in basidiomycetes CYP53 P450s. 3D-modelling and active-site cavity mapping data revealed that the ascomycetes CYP53 P450s have a highly conserved protein structure whereby 78% amino acids in the active-site cavity were found to be conserved. Because of this rigid nature of ascomycetes CYP53 P450s' active site cavity, any inhibitor directed against this P450 family can serve as a common anti-fungal drug target, particularly toward pathogenic ascomycetes. The dynamic nature of basidiomycetes CYP53 P450s at a gene and protein level indicates that these P450s are destined to acquire novel functions. Functional analysis of CYP53 P450s strongly supported our hypothesis that the ascomycetes CYP53 P450s ability is limited for detoxification of toxic molecules, whereas basidiomycetes CYP53 P450s play an additional role, i.e. involvement in degradation of wood and its derived components. This study is the first report on genome-wide comparative structural (gene and protein structure-level) and evolutionary analysis of a fungal P450 family.
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Affiliation(s)
- Poojah Jawallapersand
- Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, Free State, South Africa
| | - Samson Sitheni Mashele
- Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, Free State, South Africa
| | - Lidija Kovačič
- Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
- Department of Molecular Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Jure Stojan
- Faculty of Medicine, Institute of Biochemistry, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Radovan Komel
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Suresh Babu Pakala
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur, Andhra Pradesh, India
| | - Nada Kraševec
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- * E-mail: (KS); (NK)
| | - Khajamohiddin Syed
- Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, Free State, South Africa
- * E-mail: (KS); (NK)
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204
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Virginio ED, Kubitschek-Barreira PH, Batista MV, Schirmer MR, Abdelhay E, Shikanai-Yasuda MA, Lopes-Bezerra LM. Immunoproteome of Aspergillus fumigatus using sera of patients with invasive aspergillosis. Int J Mol Sci 2014; 15:14505-30. [PMID: 25141105 PMCID: PMC4159865 DOI: 10.3390/ijms150814505] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/24/2014] [Accepted: 08/08/2014] [Indexed: 01/31/2023] Open
Abstract
Invasive aspergillosis is a life-threatening lung or systemic infection caused by the opportunistic mold Aspergillus fumigatus. The disease affects mainly immunocompromised hosts, and patients with hematological malignances or who have been submitted to stem cell transplantation are at high risk. Despite the current use of Platelia™ Aspergillus as a diagnostic test, the early diagnosis of invasive aspergillosis remains a major challenge in improving the prognosis of the disease. In this study, we used an immunoproteomic approach to identify proteins that could be putative candidates for the early diagnosis of invasive aspergillosis. Antigenic proteins expressed in the first steps of A. fumigatus germination occurring in a human host were revealed using 2-D Western immunoblots with the serum of patients who had previously been classified as probable and proven for invasive aspergillosis. Forty antigenic proteins were identified using mass spectrometry (MS/MS). A BLAST analysis revealed that two of these proteins showed low homology with proteins of either the human host or etiological agents of other invasive fungal infections. To our knowledge, this is the first report describing specific antigenic proteins of A. fumigatus germlings that are recognized by sera of patients with confirmed invasive aspergillosis who were from two separate hospital units.
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Affiliation(s)
- Emylli D Virginio
- Laboratory of Cellular Mycology and Proteomics, Biology Institute, University of Rio de Janeiro State (UERJ), Rio de Janeiro 20550-013, Brazil.
| | - Paula H Kubitschek-Barreira
- Laboratory of Cellular Mycology and Proteomics, Biology Institute, University of Rio de Janeiro State (UERJ), Rio de Janeiro 20550-013, Brazil.
| | - Marjorie Vieira Batista
- Laboratory of Immunology (LIM 48), Clinics Hospital and Department of Infectious and Parasitic Diseases, Faculty of Medicine, University of São Paulo, São Paulo 05403-000, Brazil.
| | - Marcelo R Schirmer
- National Cancer Institute, Center for Bone Marrow Transplants, Rio de Janeiro 20230-130, Brazil.
| | - Eliana Abdelhay
- National Cancer Institute, Center for Bone Marrow Transplants, Rio de Janeiro 20230-130, Brazil.
| | - Maria A Shikanai-Yasuda
- Laboratory of Immunology (LIM 48), Clinics Hospital and Department of Infectious and Parasitic Diseases, Faculty of Medicine, University of São Paulo, São Paulo 05403-000, Brazil.
| | - Leila M Lopes-Bezerra
- Laboratory of Cellular Mycology and Proteomics, Biology Institute, University of Rio de Janeiro State (UERJ), Rio de Janeiro 20550-013, Brazil.
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205
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Yap HYY, Chooi YH, Firdaus-Raih M, Fung SY, Ng ST, Tan CS, Tan NH. The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties. BMC Genomics 2014; 15:635. [PMID: 25073817 PMCID: PMC4129116 DOI: 10.1186/1471-2164-15-635] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/23/2014] [Indexed: 12/28/2022] Open
Abstract
Background The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden or Tiger milk mushroom (Polyporales, Basidiomycota) is a valuable folk medicine for indigenous peoples in Southeast Asia. Despite the increasing interest in this ethnobotanical mushroom, very little is known about the molecular and genetic basis of its medicinal and nutraceutical properties. Results The de novo assembled 34.3 Mb L. rhinocerotis genome encodes 10,742 putative genes with 84.30% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed a close evolutionary relationship of L. rhinocerotis to Ganoderma lucidum, Dichomitus squalens, and Trametes versicolor in the core polyporoid clade. The L. rhinocerotis genome encodes a repertoire of enzymes engaged in carbohydrate and glycoconjugate metabolism, along with cytochrome P450s, putative bioactive proteins (lectins and fungal immunomodulatory proteins) and laccases. Other genes annotated include those encoding key enzymes for secondary metabolite biosynthesis, including those from polyketide, nonribosomal peptide, and triterpenoid pathways. Among them, the L. rhinocerotis genome is particularly enriched with sesquiterpenoid biosynthesis genes. Conclusions The genome content of L. rhinocerotis provides insights into the genetic basis of its reported medicinal properties as well as serving as a platform to further characterize putative bioactive proteins and secondary metabolite pathway enzymes and as a reference for comparative genomics of polyporoid fungi. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-635) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui-Yeng Y Yap
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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206
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Gao S, Li Y, Gao J, Suo Y, Fu K, Li Y, Chen J. Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus. BMC Genomics 2014; 15:627. [PMID: 25056288 PMCID: PMC4124159 DOI: 10.1186/1471-2164-15-627] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 07/17/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China. Genome sequencing of the pathogen will provide important information for globally understanding its virulence mechanism. RESULTS We report the genome sequences of a highly virulent C. lunata strain. Phylogenomic analysis indicates that C. lunata was evolved from Bipolaris maydis (Cochliobolus heterostrophus). The highly virulent strain has a high potential to evolve into other pathogenic stains based on analyses on transposases and repeat-induced point mutations. C. lunata has a smaller proportion of secreted proteins as well as B. maydis than entomopathogenic fungi. C. lunata and B. maydis have a similar proportion of protein-encoding genes highly homologous to experimentally proven pathogenic genes from pathogen-host interaction database. However, relative to B. maydis, C. lunata possesses not only many expanded protein families including MFS transporters, G-protein coupled receptors, protein kinases and proteases for transport, signal transduction or degradation, but also many contracted families including cytochrome P450, lipases, glycoside hydrolases and polyketide synthases for detoxification, hydrolysis or secondary metabolites biosynthesis, which are expected to be crucial for the fungal survival in varied stress environments. Comparative transcriptome analysis between a lowly virulent C. lunata strain and its virulence-increased variant induced by resistant host selection reveals that the virulence increase of the pathogen is related to pathways of toxin and melanin biosynthesis in stress environments, and that the two pathways probably have some overlaps. CONCLUSIONS The data will facilitate a full revelation of pathogenic mechanism and a better understanding of virulence differentiation of C. lunata.
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Affiliation(s)
- Shigang Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
| | - Yaqian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
| | - Jinxin Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
| | - Yujuan Suo
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
| | - Kehe Fu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
| | - Yingying Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
,Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 P. R. China
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207
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Wawrzyn GT, Quin MB, Choudhary S, López-Gallego F, Schmidt-Dannert C. Draft genome of Omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in Basidiomycota. ACTA ACUST UNITED AC 2014; 19:772-83. [PMID: 22726691 DOI: 10.1016/j.chembiol.2012.05.012] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/08/2012] [Accepted: 05/15/2012] [Indexed: 02/06/2023]
Abstract
The secondary metabolome of Basidiomycota represents a largely uncharacterized source of pharmaceutically relevant natural products. Terpenoids are the primary class of bioactive compounds isolated from mushrooms. The Jack O'Lantern mushroom Omphalotus olearius was identified 50 years ago as a prolific producer of anticancer illudin sesquiterpenoids; however, to date there have been exceptionally few studies into the biosynthesis of these important compounds. Here, we report the draft genome sequence of O. olearius, which reveals a diverse network of sesquiterpene synthases and two metabolic gene clusters associated with illudin biosynthesis. Characterization of the sesquiterpene synthases enabled a comprehensive survey of all currently available Basidiomycota genomes, thereby creating a predictive resource for terpenoid natural product biosynthesis in these organisms. Our results will facilitate discovery and biosynthetic production of unique pharmaceutically relevant bioactive compounds from Basidiomycota.
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Affiliation(s)
- Grayson T Wawrzyn
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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208
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Syed K, Shale K, Pagadala NS, Tuszynski J. Systematic identification and evolutionary analysis of catalytically versatile cytochrome p450 monooxygenase families enriched in model basidiomycete fungi. PLoS One 2014; 9:e86683. [PMID: 24466198 PMCID: PMC3899305 DOI: 10.1371/journal.pone.0086683] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/13/2013] [Indexed: 01/08/2023] Open
Abstract
Genome sequencing of basidiomycetes, a group of fungi capable of degrading/mineralizing plant material, revealed the presence of numerous cytochrome P450 monooxygenases (P450s) in their genomes, with some exceptions. Considering the large repertoire of P450s found in fungi, it is difficult to identify P450s that play an important role in fungal metabolism and the adaptation of fungi to diverse ecological niches. In this study, we followed Sir Charles Darwin's theory of natural selection to identify such P450s in model basidiomycete fungi showing a preference for different types of plant components degradation. Any P450 family comprising a large number of member P450s compared to other P450 families indicates its natural selection over other P450 families by its important role in fungal physiology. Genome-wide comparative P450 analysis in the basidiomycete species, Phanerochaete chrysosporium, Phanerochaete carnosa, Agaricus bisporus, Postia placenta, Ganoderma sp. and Serpula lacrymans, revealed enrichment of 11 P450 families (out of 68 P450 families), CYP63, CYP512, CYP5035, CYP5037, CYP5136, CYP5141, CYP5144, CYP5146, CYP5150, CYP5348 and CYP5359. Phylogenetic analysis of the P450 family showed species-specific alignment of P450s across the P450 families with the exception of P450s of Phanerochaete chrysosporium and Phanerochaete carnosa, suggesting paralogous evolution of P450s in model basidiomycetes. P450 gene-structure analysis revealed high conservation in the size of exons and the location of introns. P450s with the same gene structure were found tandemly arranged in the genomes of selected fungi. This clearly suggests that extensive gene duplications, particularly tandem gene duplications, led to the enrichment of selective P450 families in basidiomycetes. Functional analysis and gene expression profiling data suggest that members of the P450 families are catalytically versatile and possibly involved in fungal colonization of plant material. To our knowledge, this is the first report on the identification and comparative-evolutionary analysis of P450 families enriched in model basidiomycetes.
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Affiliation(s)
- Khajamohiddin Syed
- Department of Life Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, Free State, South Africa
- * E-mail:
| | - Karabo Shale
- Department of Life Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, Free State, South Africa
| | | | - Jack Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
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209
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Junttila S, Laiho A, Gyenesei A, Rudd S. Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen. BMC Genomics 2013; 14:870. [PMID: 24325588 PMCID: PMC3878897 DOI: 10.1186/1471-2164-14-870] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/14/2013] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Lichens are symbiotic organisms with a fungal and an algal or a cyanobacterial partner. Lichens inhabit some of the harshest climates on earth and most lichen species are desiccation-tolerant. Lichen desiccation-tolerance has been studied at the biochemical level and through proteomics, but the underlying molecular genetic mechanisms remain largely unexplored. The objective of our study was to examine the effects of dehydration and rehydration on the gene expression of Cladonia rangiferina. RESULTS Samples of C. rangiferina were collected at several time points during both the dehydration and rehydration process and the gene expression intensities were measured using a custom DNA microarray. Several genes, which were differentially expressed in one or more time points, were identified. The microarray results were validated using qRT-PCR analysis. Enrichment analysis of differentially expressed transcripts was also performed to identify the Gene Ontology terms most associated with the rehydration and dehydration process. CONCLUSIONS Our data identify differential expression patterns for hundreds of genes that are modulated during dehydration and rehydration in Cladonia rangiferina. These dehydration and rehydration events clearly differ from each other at the molecular level and the largest changes to gene expression are observed within minutes following rehydration. Distinct changes are observed during the earliest stage of rehydration and the mechanisms not appear to be shared with the later stages of wetting or with drying. Several of the most differentially expressed genes are similar to genes identified in previous studies that have investigated the molecular mechanisms of other desiccation-tolerant organisms. We present here the first microarray experiment for any lichen species and have for the first time studied the genetic mechanisms behind lichen desiccation-tolerance at the whole transcriptome level.
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Affiliation(s)
- Sini Junttila
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Asta Laiho
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Attila Gyenesei
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Stephen Rudd
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
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210
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Fungal microsomes in a biotransformation perspective: protein nature of membrane-associated reactions. Appl Microbiol Biotechnol 2013; 97:10263-73. [DOI: 10.1007/s00253-013-5347-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 12/27/2022]
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211
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Design, synthesis, and evaluations of antifungal activity of novel phenyl(2H-tetrazol-5-yl)methanamine derivatives. J Chem Biol 2013; 7:29-35. [PMID: 24432136 DOI: 10.1007/s12154-013-0103-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 08/22/2013] [Indexed: 10/26/2022] Open
Abstract
Fungal infections pose a continuous and serious threat to human health and life. The intrinsic resistance has been observed in many genera of fungi. Many fungal infections are caused by opportunistic pathogens that may be endogenous (Candida infections) or acquired from the environment (Cryptococcus and Aspergillus infections). So, new therapeutic strategies are needed to combat various fungal infections. Fluconazole shows good antifungal activity with relatively low toxicity and is preferred as first line antifungal therapy, but it has suffered from severe drug resistance. So, there is a need to design novel analogues by modification of fluconazole-like structure. A novel series of phenyl(2H-tetrazol-5-yl)methanamine derivatives were synthesized by reaction of α-amino nitrile with sodium azide and ZnCl2 in presence of isopropyl alcohol. They were evaluated for antifungal activity against Candida albicans and Aspergillus niger and subjected to docking study against 1EA1.
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212
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Tralau T, Luch A. The evolution of our understanding of endo-xenobiotic crosstalk and cytochrome P450 regulation and the therapeutic implications. Expert Opin Drug Metab Toxicol 2013; 9:1541-54. [DOI: 10.1517/17425255.2013.828692] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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213
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Johnson EA. Biotechnology of non-Saccharomyces yeasts—the basidiomycetes. Appl Microbiol Biotechnol 2013; 97:7563-77. [DOI: 10.1007/s00253-013-5046-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/05/2013] [Accepted: 06/07/2013] [Indexed: 12/24/2022]
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214
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Sartori D, Massi FP, Ferranti LS, Fungaro MHP. Identification of Genes Differentially Expressed Between Ochratoxin-Producing and Non-Producing Strains of Aspergillus westerdijkiae. Indian J Microbiol 2013; 54:41-5. [PMID: 24426165 DOI: 10.1007/s12088-013-0408-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/12/2013] [Indexed: 10/26/2022] Open
Abstract
Approximately 70 % of Aspergillus westerdijkiae strains are able to produce ochratoxin A (OTA), a nephrotoxic and carcinogenic mycotoxin which have been found in cereal and food commodities. Despite of its importance there is, up to now, no information available about which genes are differentially expressed between A. westerdijkiae ochratoxin-producing and non-producing strains. Using cDNA RDA approach we successfully sequenced 231 raw ESTs expected to be enriched in the ochratoxin-producing strain. BLASTX searches against the public databases showed that of these, 205 ESTs (79 %) exhibited significant similarities with proteins of known functions, 28 ESTs (11 %) had matches to hypothetical proteins, and the remaining 27 ESTs (10 %) had no significant hits. EST alignment resulted in a total of 14 non-redundant consensus sequences. Three putative genes encoding oxidoreductases were validated as up-expressed in the OTA producer strain using RT-qPCR approach. The expression of the putative genes encoding a cytochrome P450 family protein, 3-hydroxyphenylacetate-6-hydroxylase, and endoplasmic reticulum oxidoreductin were higher (32-, 2.8- and 20-fold respectively) in the OTA producer strain compared to the non-producer strain.
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Affiliation(s)
- Daniele Sartori
- Universidade Estadual de Londrina, P.O. Box 6001, Londrina, 86051-990 Brazil
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215
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Engineering and application of P450 monooxygenases in pharmaceutical and metabolite synthesis. Curr Opin Chem Biol 2013; 17:271-5. [DOI: 10.1016/j.cbpa.2013.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 11/21/2022]
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216
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Bao D, Gong M, Zheng H, Chen M, Zhang L, Wang H, Jiang J, Wu L, Zhu Y, Zhu G, Zhou Y, Li C, Wang S, Zhao Y, Zhao G, Tan Q. Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome. PLoS One 2013; 8:e58294. [PMID: 23526973 PMCID: PMC3602538 DOI: 10.1371/journal.pone.0058294] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/01/2013] [Indexed: 12/01/2022] Open
Abstract
Volvariella volvacea, the edible straw mushroom, is a highly nutritious food source that is widely cultivated on a commercial scale in many parts of Asia using agricultural wastes (rice straw, cotton wastes) as growth substrates. However, developments in V. volvacea cultivation have been limited due to a low biological efficiency (i.e. conversion of growth substrate to mushroom fruit bodies), sensitivity to low temperatures, and an unclear sexuality pattern that has restricted the breeding of improved strains. We have now sequenced the genome of V. volvacea and assembled it into 62 scaffolds with a total genome size of 35.7 megabases (Mb), containing 11,084 predicted gene models. Comparative analyses were performed with the model species in basidiomycete on mating type system, carbohydrate active enzymes, and fungal oxidative lignin enzymes. We also studied transcriptional regulation of the response to low temperature (4°C). We found that the genome of V. volvacea has many genes that code for enzymes, which are involved in the degradation of cellulose, hemicellulose, and pectin. The molecular genetics of the mating type system in V. volvacea was also found to be similar to the bipolar system in basidiomycetes, suggesting that it is secondary homothallism. Sensitivity to low temperatures could be due to the lack of the initiation of the biosynthesis of unsaturated fatty acids, trehalose and glycogen biosyntheses in this mushroom. Genome sequencing of V. volvacea has improved our understanding of the biological characteristics related to the degradation of the cultivating compost consisting of agricultural waste, the sexual reproduction mechanism, and the sensitivity to low temperatures at the molecular level which in turn will enable us to increase the industrial production of this mushroom.
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Affiliation(s)
- Dapeng Bao
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Ming Gong
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Mingjie Chen
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Liang Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Hong Wang
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Jianping Jiang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Lin Wu
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Gang Zhu
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Yan Zhou
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Chuanhua Li
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Shengyue Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Yan Zhao
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Guoping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Qi Tan
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Shanghai, P. R. China
- Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, P. R. China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, P. R. China
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Gan P, Ikeda K, Irieda H, Narusaka M, O'Connell RJ, Narusaka Y, Takano Y, Kubo Y, Shirasu K. Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. THE NEW PHYTOLOGIST 2013; 197:1236-1249. [PMID: 23252678 DOI: 10.1111/nph.12085] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/05/2012] [Indexed: 05/04/2023]
Abstract
Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease-causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate-degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage-specific gene expression profiles of expanded classes of potential pathogenicity genes.
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Affiliation(s)
- Pamela Gan
- Plant Science Center, RIKEN, Yokohama, Japan
| | - Kyoko Ikeda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroki Irieda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mari Narusaka
- Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Okayama, Japan
| | | | - Yoshihiro Narusaka
- Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Okayama, Japan
| | | | - Yasuyuki Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Ken Shirasu
- Plant Science Center, RIKEN, Yokohama, Japan
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218
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Wang M, Gu B, Huang J, Jiang S, Chen Y, Yin Y, Pan Y, Yu G, Li Y, Wong BHC, Liang Y, Sun H. Transcriptome and proteome exploration to provide a resource for the study of Agrocybe aegerita. PLoS One 2013; 8:e56686. [PMID: 23418592 PMCID: PMC3572045 DOI: 10.1371/journal.pone.0056686] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/14/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Agrocybe aegerita, the black poplar mushroom, has been highly valued as a functional food for its medicinal and nutritional benefits. Several bioactive extracts from A. aegerita have been found to exhibit antitumor and antioxidant activities. However, limited genetic resources for A. aegerita have hindered exploration of this species. METHODOLOGY/PRINCIPAL FINDINGS To facilitate the research on A. aegerita, we established a deep survey of the transcriptome and proteome of this mushroom. We applied high-throughput sequencing technology (Illumina) to sequence A. aegerita transcriptomes from mycelium and fruiting body. The raw clean reads were de novo assembled into a total of 36,134 expressed sequences tags (ESTs) with an average length of 663 bp. These ESTs were annotated and classified according to Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Gene expression profile analysis showed that 18,474 ESTs were differentially expressed, with 10,131 up-regulated in mycelium and 8,343 up-regulated in fruiting body. Putative genes involved in polysaccharide and steroid biosynthesis were identified from A. aegerita transcriptome, and these genes were differentially expressed at the two stages of A. aegerita. Based on one-dimensional gel electrophoresis (1-DGE) coupled with electrospray ionization liquid chromatography tandem MS (LC-ESI-MS/MS), we identified a total of 309 non-redundant proteins. And many metabolic enzymes involved in glycolysis were identified in the protein database. CONCLUSIONS/SIGNIFICANCE This is the first study on transcriptome and proteome analyses of A. aegerita. The data in this study serve as a resource of A. aegerita transcripts and proteins, and offer clues to the applications of this mushroom in nutrition, pharmacy and industry.
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Affiliation(s)
- Man Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Bianli Gu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
- Molecular Diagnosis Center, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People's Republic of China
| | - Jie Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Shuai Jiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yijie Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yalin Yin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yongfu Pan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Guojun Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yamu Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Barry Hon Cheung Wong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
- Department of Clinical Immunology, Guangdong Medical College, Dongguan, People's Republic of China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, People's Republic of China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, People's Republic of China
- * E-mail:
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219
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Cools HJ, Hammond-Kosack KE. Exploitation of genomics in fungicide research: current status and future perspectives. MOLECULAR PLANT PATHOLOGY 2013; 14:197-210. [PMID: 23157348 PMCID: PMC6638899 DOI: 10.1111/mpp.12001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Every year, fungicide use to control plant disease caused by pathogenic fungi increases. The global fungicide market is now worth more than £5.3 billion, second only to the herbicide market in importance. In the UK, over 5500 tonnes of fungicide were applied to crops in 2010 (The Food and Environment Research Agency, Pesticide Usage Statistics), with 95.5% of the wheat-growing area receiving three fungicide sprays. Although dependence on fungicides to produce food securely, reliably and cheaply may be moderated in the future by further developments in crop biotechnology, modern crop protection will continue to require a diversity of solutions, including effective and safe chemical control. Therefore, investment in exploiting the increasingly available genome sequences of the most devastating fungal and oomycete phytopathogenic species should bring an array of new opportunities for chemical intervention. To date, the impact of whole genome research on the development, introduction and stewardship of fungicides has been limited, but ongoing improvements in computational analysis, molecular biology, chemical genetics, genome sequencing and transcriptomics will facilitate the development and registration of the future suite of crop protection chemicals.
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Affiliation(s)
- Hans J Cools
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
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220
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Thakur K, Chawla V, Bhatti S, Swarnkar MK, Kaur J, Shankar R, Jha G. De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PLoS One 2013; 8:e53937. [PMID: 23349770 PMCID: PMC3547962 DOI: 10.1371/journal.pone.0053937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022] Open
Abstract
Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.
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Affiliation(s)
- Karnika Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vandna Chawla
- Studio of Computational Biology & Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Shammi Bhatti
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Mohit Kumar Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Gopaljee Jha
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
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221
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Morel M, Meux E, Mathieu Y, Thuillier A, Chibani K, Harvengt L, Jacquot JP, Gelhaye E. Xenomic networks variability and adaptation traits in wood decaying fungi. Microb Biotechnol 2013; 6:248-63. [PMID: 23279857 PMCID: PMC3815920 DOI: 10.1111/1751-7915.12015] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/05/2012] [Accepted: 11/08/2012] [Indexed: 01/08/2023] Open
Abstract
Fungal degradation of wood is mainly restricted to basidiomycetes, these organisms having developed complex oxidative and hydrolytic enzymatic systems. Besides these systems, wood-decaying fungi possess intracellular networks allowing them to deal with the myriad of potential toxic compounds resulting at least in part from wood degradation but also more generally from recalcitrant organic matter degradation. The members of the detoxification pathways constitute the xenome. Generally, they belong to multigenic families such as the cytochrome P450 monooxygenases and the glutathione transferases. Taking advantage of the recent release of numerous genomes of basidiomycetes, we show here that these multigenic families are extended and functionally related in wood-decaying fungi. Furthermore, we postulate that these rapidly evolving multigenic families could reflect the adaptation of these fungi to the diversity of their substrate and provide keys to understand their ecology. This is of particular importance for white biotechnology, this xenome being a putative target for improving degradation properties of these fungi in biomass valorization purposes.
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Affiliation(s)
- Mélanie Morel
- Université de Lorraine, IAM, UMR 1136, IFR 110 EFABA, Vandoeuvre-lès-Nancy, F-54506, France.
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New Insights into the Use of Filamentous Fungi and Their Degradative Enzymes as Tools for Assessing the Ecotoxicity of Contaminated Soils During Bioremediation Processes. SOIL BIOLOGY 2013. [DOI: 10.1007/978-3-642-33811-3_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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223
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Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:205-20. [DOI: 10.1016/j.bbapap.2012.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 01/11/2023]
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Syed K, Yadav JS. P450 monooxygenases (P450ome) of the model white rot fungus Phanerochaete chrysosporium. Crit Rev Microbiol 2012; 38:339-63. [PMID: 22624627 PMCID: PMC3567848 DOI: 10.3109/1040841x.2012.682050] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phanerochaete chrysosporium, the model white rot fungus, has been the focus of research for the past about four decades for understanding the mechanisms and processes of biodegradation of the natural aromatic polymer lignin and a broad range of environmental toxic chemicals. The ability to degrade this vast array of xenobiotic compounds was originally attributed to its lignin-degrading enzyme system, mainly the extracellular peroxidases. However, subsequent physiological, biochemical, and/or genetic studies by us and others identified the involvement of a peroxidase-independent oxidoreductase system, the cytochrome P450 monooxygenase system. The whole genome sequence revealed an extraordinarily large P450 contingent (P450ome) with an estimated 149 P450s in this organism. This review focuses on the current status of understanding on the P450 monooxygenase system of P. chrysosproium in terms of pre-genomic and post-genomic identification, structural and evolutionary analysis, transcriptional regulation, redox partners, and functional characterization for its biodegradative potential. Future research on this catalytically diverse oxidoreductase enzyme system and its major role as a newly emerged player in xenobiotic metabolism/degradation is discussed.
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Affiliation(s)
- Khajamohiddin Syed
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Jagjit S Yadav
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
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Lah L, Haridas S, Bohlmann J, Breuil C. The cytochromes P450 of Grosmannia clavigera: Genome organization, phylogeny, and expression in response to pine host chemicals. Fungal Genet Biol 2012; 50:72-81. [PMID: 23111002 DOI: 10.1016/j.fgb.2012.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/29/2012] [Accepted: 10/16/2012] [Indexed: 01/04/2023]
Abstract
Grosmannia clavigera is a fungal associate of the mountain pine beetle (Dendroctonus ponderosae) and a pathogen of lodgepole pine (Pinus contorta) that must overcome terpenoid oleoresin and phenolic defenses of host trees. G. clavigera responds to monoterpene influx with complementary mechanisms that include export and the use of these compounds as a carbon source. Cytochromes P450 (CYPs) may also be involved in the metabolism of host defense compounds. We have identified and phylogenetically classified G. clavigera CYPs (CYPome). We show that although the G. clavigera CYPome has contracted in evolution, certain CYP families have expanded by duplication. We analyzed RNA-seq data for CYP expression following treatment with terpenes and pine phloem extracts to identify CYPs potentially involved in detoxification of these pine defense compounds. We also used transcriptome analysis of G. clavigera grown on monoterpenes, triglycerides or oleic acid as a carbon source to identify up-regulated CYPs that may be involved in the utilization of these compounds to support fungal growth. Finally, we identify secondary metabolite biosynthetic gene clusters that contain CYPs, and CYPs in clusters that may be involved in conversion of host chemicals.
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Affiliation(s)
- Ljerka Lah
- Department of Wood Sciences, University of British Columbia, Vancouver, BC, Canada
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226
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Loto I, Gutiérrez MS, Barahona S, Sepúlveda D, Martínez-Moya P, Baeza M, Cifuentes V, Alcaíno J. Enhancement of carotenoid production by disrupting the C22-sterol desaturase gene (CYP61) in Xanthophyllomyces dendrorhous. BMC Microbiol 2012; 12:235. [PMID: 23075035 PMCID: PMC3552872 DOI: 10.1186/1471-2180-12-235] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/12/2012] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Xanthophyllomyces dendrorhous is a basidiomycetous yeast that synthesizes astaxanthin, which is a carotenoid with a great biotechnological impact. The ergosterol and carotenoid synthesis pathways are derived from the mevalonate pathway, and in both pathways, cytochrome P450 enzymes are involved. RESULTS In this study, we isolated and described the X. dendrorhous CYP61 gene, which encodes a cytochrome P450 involved in ergosterol biosynthesis. This gene is composed of nine exons and encodes a 526 amino acid polypeptide that shares significant percentages of identity and similitude with the C22-sterol desaturase, CYP61, from other fungi. Mutants derived from different parental strains were obtained by disrupting the CYP61 gene with an antibiotic selection marker. These mutants were not able to produce ergosterol and accumulated ergosta-5,8,22-trien-3-ol and ergosta-5,8-dien-3-ol. Interestingly, all of the mutants had a more intense red color phenotype than their respective parental strains. The carotenoid composition was qualitatively and quantitatively analyzed by RP-HPLC, revealing that the carotenoid content was higher in the mutant strains without major changes in their composition. The expression of the HMGR gene, which encodes an enzyme involved in the mevalonate pathway (3-hydroxy-3-methylglutaryl-CoA reductase), was analyzed by RT-qPCR showing that its transcript levels are higher in the CYP61 mutants. CONCLUSIONS These results suggest that in X. dendrorhous, ergosterol regulates HMGR gene expression by a negative feedback mechanism and in this way; it contributes in the regulation of the carotenoid biosynthesis.
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Affiliation(s)
- Iris Loto
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
| | - María Soledad Gutiérrez
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
| | - Salvador Barahona
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
| | - Dionisia Sepúlveda
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
| | - Pilar Martínez-Moya
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
| | - Marcelo Baeza
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
| | - Víctor Cifuentes
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
| | - Jennifer Alcaíno
- Laboratorio de Genética. Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile
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227
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Meux E, Morel M, Lamant T, Gérardin P, Jacquot JP, Dumarçay S, Gelhaye E. New substrates and activity of Phanerochaete chrysosporium Omega glutathione transferases. Biochimie 2012; 95:336-46. [PMID: 23063695 DOI: 10.1016/j.biochi.2012.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/04/2012] [Indexed: 01/30/2023]
Abstract
Omega glutathione transferases (GSTO) constitute a family of proteins with variable distribution throughout living organisms. It is notably expanded in several fungi and particularly in the wood-degrading fungus Phanerochaete chrysosporium, raising questions concerning the function(s) and potential redundancy of these enzymes. Within the fungal families, GSTOs have been poorly studied and their functions remain rather sketchy. In this study, we have used fluorescent compounds as activity reporters to identify putative ligands. Experiments using 5-chloromethylfluorescein diacetate as a tool combined with mass analyses showed that GSTOs are able to cleave ester bonds. Using this property, we developed a specific activity-based profiling method for identifying ligands of PcGSTO3 and PcGSTO4. The results suggest that GSTOs could be involved in the catabolism of toxic compounds like tetralone derivatives. Biochemical investigations demonstrated that these enzymes are able to catalyze deglutathionylation reactions thanks to the presence of a catalytic cysteine residue. To access the physiological function of these enzymes and notably during the wood interaction, recombinant proteins have been immobilized on CNBr Sepharose and challenged with beech wood extracts. Coupled with GC-MS experiments this ligand fishing method allowed to identify terpenes as potential substrates of Omega GST suggesting a physiological role during the wood-fungus interactions.
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Affiliation(s)
- Edgar Meux
- UMR 1136 INRA-UHP Interactions Arbres/Micro-Organismes, IFR110 Ecosystèmes Forestiers, Agroressources, Bioprocédés et Alimentation, Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France
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228
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Large scale expressed sequence tag (EST) analysis of Metarhizium acridum infecting Locusta migratoria reveals multiple strategies for fungal adaptation to the host cuticle. Curr Genet 2012; 58:265-79. [DOI: 10.1007/s00294-012-0382-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Revised: 09/21/2012] [Accepted: 09/21/2012] [Indexed: 12/18/2022]
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229
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Abstract
Diverse oxygenation patterns of natural products generated by secondary metabolic pathways in microorganisms and plants are largely achieved through the tailoring reactions catalysed by cytochrome P450 enzymes (P450s). P450s are a large family of oxidative hemoproteins found in all life forms from prokaryotes to humans. Understanding the reactivity and selectivity of these fascinating C-H bond-activating catalysts will advance their use in generating valuable pharmaceuticals and products for medicine, agriculture and industry. A major strength of this P450 group is its set of established enzyme-substrate relationships, the source of the most detailed knowledge on how P450 enzymes work. Engineering microbial-derived P450 enzymes to accommodate alternative substrates and add new functions continues to be an important near- and long-term practical goal driving the structural characterization of these molecules. Understanding the natural evolution of P450 structure-function should accelerate metabolic engineering and directed evolutionary approaches to enhance diversification of natural product structures and other biosynthetic applications.
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Affiliation(s)
- Larissa M. Podust
- Department of Pathology, Molecular Structure Group and Center for Discovery and Innovation in Parasitic Diseases (CDIPD), University of California San Francisco, San Francisco, California, 94158, USA. Fax: 415 502 8193; Tel: 415 514 1381;
| | - David H. Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA. Fax: 734-615-3641; Tel: 734 615 9907;
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230
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Li S, Tietz DR, Rutaganira FU, Kells PM, Anzai Y, Kato F, Pochapsky TC, Sherman DH, Podust LM. Substrate recognition by the multifunctional cytochrome P450 MycG in mycinamicin hydroxylation and epoxidation reactions. J Biol Chem 2012; 287:37880-90. [PMID: 22952225 DOI: 10.1074/jbc.m112.410340] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The majority of characterized cytochrome P450 enzymes in actinomycete secondary metabolic pathways are strictly substrate-, regio-, and stereo-specific. Examples of multifunctional biosynthetic cytochromes P450 with broader substrate and regio-specificity are growing in number and are of particular interest for biosynthetic and chemoenzymatic applications. MycG is among the first P450 monooxygenases characterized that catalyzes both hydroxylation and epoxidation reactions in the final biosynthetic steps, leading to oxidative tailoring of the 16-membered ring macrolide antibiotic mycinamicin II in the actinomycete Micromonospora griseorubida. The ordering of steps to complete the biosynthetic process involves a complex substrate recognition pattern by the enzyme and interplay between three tailoring modifications as follows: glycosylation, methylation, and oxidation. To understand the catalytic properties of MycG, we structurally characterized the ligand-free enzyme and its complexes with three native metabolites. These include substrates mycinamicin IV and V and their biosynthetic precursor mycinamicin III, which carries the monomethoxy sugar javose instead of the dimethoxylated sugar mycinose. The two methoxy groups of mycinose serve as sensors that mediate initial recognition to discriminate between closely related substrates in the post-polyketide oxidative tailoring of mycinamicin metabolites. Because x-ray structures alone did not explain the mechanisms of macrolide hydroxylation and epoxidation, paramagnetic NMR relaxation measurements were conducted. Molecular modeling based on these data indicates that in solution substrate may penetrate the active site sufficiently to place the abstracted hydrogen atom of mycinamicin IV within 6 Å of the heme iron and ~4 Å of the oxygen of iron-ligated water.
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Affiliation(s)
- Shengying Li
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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231
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Xiao G, Ying SH, Zheng P, Wang ZL, Zhang S, Xie XQ, Shang Y, St Leger RJ, Zhao GP, Wang C, Feng MG. Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana. Sci Rep 2012; 2:483. [PMID: 22761991 PMCID: PMC3387728 DOI: 10.1038/srep00483] [Citation(s) in RCA: 430] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 06/15/2012] [Indexed: 12/14/2022] Open
Abstract
The ascomycete fungus Beauveria bassiana is a pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. We sequenced the genome of B. bassiana and a phylogenomic analysis confirmed that ascomycete entomopathogenicity is polyphyletic, but also revealed convergent evolution to insect pathogenicity. We also found many species-specific virulence genes and gene family expansions and contractions that correlate with host ranges and pathogenic strategies. These include B. bassiana having many more bacterial-like toxins (suggesting an unsuspected potential for oral toxicity) and effector-type proteins. The genome also revealed that B. bassiana resembles the closely related Cordyceps militaris in being heterothallic, although its sexual stage is rarely observed. A high throughput RNA-seq transcriptomic analysis revealed that B. bassiana could sense and adapt to different environmental niches by activating well-defined gene sets. The information from this study will facilitate further development of B. bassiana as a cost-effective mycoinsecticide.
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Affiliation(s)
- Guohua Xiao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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232
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Kristan K, Rižner TL. Steroid-transforming enzymes in fungi. J Steroid Biochem Mol Biol 2012; 129:79-91. [PMID: 21946531 DOI: 10.1016/j.jsbmb.2011.08.012] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 07/27/2011] [Accepted: 08/19/2011] [Indexed: 11/24/2022]
Abstract
Fungal species are a very important source of many different enzymes, and the ability of fungi to transform steroids has been used for several decades in the production of compounds with a sterane skeleton. Here, we review the characterised and/or purified enzymes for steroid transformations, dividing them into two groups: (i) enzymes of the ergosterol biosynthetic pathway, including data for, e.g. ERG11 (14α-demethylase), ERG6 (C-24 methyltransferase), ERG5 (C-22 desaturase) and ERG4 (C-24 reductase); and (ii) the other steroid-transforming enzymes, including different hydroxylases (7α-, 11α-, 11β-, 14α-hydroxylase), oxidoreductases (5α-reductase, 3β-hydroxysteroid dehydrogenase/isomerase, 17β-hydroxysteroid dehydrogenase, C-1/C-2 dehydrogenase) and C-17-C-20 lyase. The substrate specificities of these enzymes, their cellular localisation, their association with protein super-families, and their potential applications are discussed. Article from a special issue on steroids and microorganisms.
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Affiliation(s)
- Katja Kristan
- Institute of Biochemistry, University of Ljubljana, Ljubljana, Slovenia.
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233
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Ichinose H. Molecular and Functional Diversity of Fungal Cytochrome P450s. Biol Pharm Bull 2012; 35:833-7. [DOI: 10.1248/bpb.35.833] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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234
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Wang L, Chen W, Feng Y, Ren Y, Gu Z, Chen H, Wang H, Thomas MJ, Zhang B, Berquin IM, Li Y, Wu J, Zhang H, Song Y, Liu X, Norris JS, Wang S, Du P, Shen J, Wang N, Yang Y, Wang W, Feng L, Ratledge C, Zhang H, Chen YQ. Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One 2011; 6:e28319. [PMID: 22174787 PMCID: PMC3234268 DOI: 10.1371/journal.pone.0028319] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/05/2011] [Indexed: 12/15/2022] Open
Abstract
Mortierella alpina is an oleaginous fungus which can produce lipids accounting for up to 50% of its dry weight in the form of triacylglycerols. It is used commercially for the production of arachidonic acid. Using a combination of high throughput sequencing and lipid profiling, we have assembled the M. alpina genome, mapped its lipogenesis pathway and determined its major lipid species. The 38.38 Mb M. alpina genome shows a high degree of gene duplications. Approximately 50% of its 12,796 gene models, and 60% of genes in the predicted lipogenesis pathway, belong to multigene families. Notably, M. alpina has 18 lipase genes, of which 11 contain the class 2 lipase domain and may share a similar function. M. alpina's fatty acid synthase is a single polypeptide containing all of the catalytic domains required for fatty acid synthesis from acetyl-CoA and malonyl-CoA, whereas in many fungi this enzyme is comprised of two polypeptides. Major lipids were profiled to confirm the products predicted in the lipogenesis pathway. M. alpina produces a complex mixture of glycerolipids, glycerophospholipids and sphingolipids. In contrast, only two major sterol lipids, desmosterol and 24(28)-methylene-cholesterol, were detected. Phylogenetic analysis based on genes involved in lipid metabolism suggests that oleaginous fungi may have acquired their lipogenic capacity during evolution after the divergence of Ascomycota, Basidiomycota, Chytridiomycota and Mucoromycota. Our study provides the first draft genome and comprehensive lipid profile for M. alpina, and lays the foundation for possible genetic engineering of M. alpina to produce higher levels and diverse contents of dietary lipids.
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Affiliation(s)
- Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yun Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Yan Ren
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Zhennan Gu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Hongchao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Michael J. Thomas
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Baixi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Isabelle M. Berquin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yang Li
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Jiansheng Wu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Huanxin Zhang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Yuanda Song
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Xiang Liu
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - James S. Norris
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Suriguga Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Peng Du
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Junguo Shen
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Na Wang
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Yanlin Yang
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Wei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Colin Ratledge
- Department of Biological Sciences, University of Hull, Hull, United Kingdom
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yong Q. Chen
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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235
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Zheng P, Xia Y, Xiao G, Xiong C, Hu X, Zhang S, Zheng H, Huang Y, Zhou Y, Wang S, Zhao GP, Liu X, St Leger RJ, Wang C. Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine. Genome Biol 2011; 12:R116. [PMID: 22112802 PMCID: PMC3334602 DOI: 10.1186/gb-2011-12-11-r116] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 11/10/2011] [Accepted: 11/23/2011] [Indexed: 01/10/2023] Open
Abstract
Background Species in the ascomycete fungal genus Cordyceps have been proposed to be the teleomorphs of Metarhizium species. The latter have been widely used as insect biocontrol agents. Cordyceps species are highly prized for use in traditional Chinese medicines, but the genes responsible for biosynthesis of bioactive components, insect pathogenicity and the control of sexuality and fruiting have not been determined. Results Here, we report the genome sequence of the type species Cordyceps militaris. Phylogenomic analysis suggests that different species in the Cordyceps/Metarhizium genera have evolved into insect pathogens independently of each other, and that their similar large secretomes and gene family expansions are due to convergent evolution. However, relative to other fungi, including Metarhizium spp., many protein families are reduced in C. militaris, which suggests a more restricted ecology. Consistent with its long track record of safe usage as a medicine, the Cordyceps genome does not contain genes for known human mycotoxins. We establish that C. militaris is sexually heterothallic but, very unusually, fruiting can occur without an opposite mating-type partner. Transcriptional profiling indicates that fruiting involves induction of the Zn2Cys6-type transcription factors and MAPK pathway; unlike other fungi, however, the PKA pathway is not activated. Conclusions The data offer a better understanding of Cordyceps biology and will facilitate the exploitation of medicinal compounds produced by the fungus.
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Affiliation(s)
- Peng Zheng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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236
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Mitochondria and fungal pathogenesis: drug tolerance, virulence, and potential for antifungal therapy. EUKARYOTIC CELL 2011; 10:1376-83. [PMID: 21926328 DOI: 10.1128/ec.05184-11] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, mitochondria have been identified as important contributors to the virulence and drug tolerance of human fungal pathogens. In different scenarios, either hypo- or hypervirulence can result from changes in mitochondrial function. Similarly, specific mitochondrial mutations lead to either sensitivity or resistance to antifungal drugs. Here, we provide a synthesis of this emerging field, proposing that mitochondrial function in membrane lipid homeostasis is the common denominator underlying the observed effects of mitochondria in drug tolerance (both sensitivity and resistance). We discuss how the contrasting effects of mitochondrial dysfunction on fungal drug tolerance and virulence could be explained and the potential for targeting mitochondrial factors for future antifungal drug development.
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237
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Lah L, Podobnik B, Novak M, Korošec B, Berne S, Vogelsang M, Kraševec N, Zupanec N, Stojan J, Bohlmann J, Komel R. The versatility of the fungal cytochrome P450 monooxygenase system is instrumental in xenobiotic detoxification. Mol Microbiol 2011; 81:1374-89. [PMID: 21810122 DOI: 10.1111/j.1365-2958.2011.07772.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Cytochromes P450 (CYPs) catalyse diverse reactions and are key enzymes in fungal primary and secondary metabolism, and xenobiotic detoxification. CYP enzymatic properties and substrate specificity determine the reaction outcome. However, CYP-mediated reactions may also be influenced by their redox partners. Filamentous fungi with numerous CYPs often possess multiple microsomal redox partners, cytochrome P450 reductases (CPRs). In the plant pathogenic ascomycete Cochliobolus lunatus we recently identified two CPR paralogues, CPR1 and CPR2. Our objective was to functionally characterize two endogenous fungal cytochrome P450 systems and elucidate the putative physiological roles of CPR1 and CPR2. We reconstituted both CPRs with CYP53A15, or benzoate 4-hydroxylase from C. lunatus, which is crucial in the detoxification of phenolic plant defence compounds. Biochemical characterization using RP-HPLC shows that both redox partners support CYP activity, but with different product specificities. When reconstituted with CPR1, CYP53A15 converts benzoic acid to 4-hydroxybenzoic acid, and 3-methoxybenzoic acid to 3-hydroxybenzoic acid. However, when the redox partner is CPR2, both substrates are converted to 3,4-dihydroxybenzoic acid. Deletion mutants and gene expression in mycelia grown on media with inhibitors indicate that CPR1 is important in primary metabolism, whereas CPR2 plays a role in xenobiotic detoxification.
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Affiliation(s)
- Ljerka Lah
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
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238
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Homology modeling, molecular docking and spectra assay studies of sterol 14α-demethylase from Penicillium digitatum. Biotechnol Lett 2011; 33:2005-11. [DOI: 10.1007/s10529-011-0657-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 05/24/2011] [Indexed: 10/18/2022]
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239
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Grogan G. Cytochromes P450: exploiting diversity and enabling application as biocatalysts. Curr Opin Chem Biol 2010; 15:241-8. [PMID: 21145278 DOI: 10.1016/j.cbpa.2010.11.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/03/2010] [Accepted: 11/08/2010] [Indexed: 01/21/2023]
Abstract
The remarkable chemical reactivity and substrate range displayed by cytochromes P450 (P450s) renders them attractive as potential catalysts for a host of challenging chemical reactions in industry. The opportunities afforded by these biocatalysts are increased by the availability of greater diversity provided by the genomic resource and the variant libraries of well-known P450s produced by rational and random engineering techniques. The exploitation of this enormous diversity will require novel tools in screening, to identify enzyme reactions of interest, and also in the enabling of these valuable activities through protein engineering and bioprocess optimisation.
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Affiliation(s)
- Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK.
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