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Characterization of the effects of terminators and introns on recombinant gene expression in the basidiomycete Ceriporiopsis subvermispora. J Microbiol 2020; 58:1037-1045. [DOI: 10.1007/s12275-020-0213-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 01/06/2023]
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2
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Shimizu T, Kanematsu S, Yaegashi H. Draft Genome Sequence and Transcriptional Analysis of Rosellinia necatrix Infected with a Virulent Mycovirus. PHYTOPATHOLOGY 2018; 108:1206-1211. [PMID: 29688132 DOI: 10.1094/phyto-11-17-0365-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the molecular mechanisms of pathogenesis is useful in developing effective control methods for fungal diseases. The white root rot fungus Rosellinia necatrix is a soilborne pathogen that causes serious economic losses in various crops, including fruit trees, worldwide. Here, using next-generation sequencing techniques, we first produced a 44-Mb draft genome sequence of R. necatrix strain W97, an isolate from Japan, in which 12,444 protein-coding genes were predicted. To survey differentially expressed genes (DEGs) associated with the pathogenesis of the fungus, the hypovirulent W97 strain infected with Rosellinia necatrix megabirnavirus 1 (RnMBV1) was used for a comprehensive transcriptome analysis. In total, 545 and 615 genes are up- and down-regulated, respectively, in R. necatrix infected with RnMBV1. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEGs suggested that primary and secondary metabolism would be greatly disturbed in R. necatrix infected with RnMBV1. The genes encoding transcriptional regulators, plant cell wall-degrading enzymes, and toxin production, such as cytochalasin E, were also found in the DEGs. The genetic resources provided in this study will accelerate the discovery of genes associated with pathogenesis and other biological characteristics of R. necatrix, thus contributing to disease control.
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Affiliation(s)
- Takeo Shimizu
- First, second, and third authors: Division of Apple Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 92-24 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
| | - Satoko Kanematsu
- First, second, and third authors: Division of Apple Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 92-24 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
| | - Hajime Yaegashi
- First, second, and third authors: Division of Apple Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 92-24 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
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3
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Systematic functional analysis of kinases in the fungal pathogen Cryptococcus neoformans. Nat Commun 2016; 7:12766. [PMID: 27677328 PMCID: PMC5052723 DOI: 10.1038/ncomms12766] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/01/2016] [Indexed: 12/15/2022] Open
Abstract
Cryptococcus neoformans is the leading cause of death by fungal meningoencephalitis; however, treatment options remain limited. Here we report the construction of 264 signature-tagged gene-deletion strains for 129 putative kinases, and examine their phenotypic traits under 30 distinct in vitro growth conditions and in two different hosts (insect larvae and mice). Clustering analysis of in vitro phenotypic traits indicates that several of these kinases have roles in known signalling pathways, and identifies hitherto uncharacterized signalling cascades. Virulence assays in the insect and mouse models provide evidence of pathogenicity-related roles for 63 kinases involved in the following biological categories: growth and cell cycle, nutrient metabolism, stress response and adaptation, cell signalling, cell polarity and morphology, vacuole trafficking, transfer RNA (tRNA) modification and other functions. Our study provides insights into the pathobiological signalling circuitry of C. neoformans and identifies potential anticryptococcal or antifungal drug targets. Cryptococcus neoformans is the leading cause of death by fungal meningoencephalitis. Here, the authors study the roles played by 129 putative kinases in the growth and virulence of C. neoformans, identifying potential targets for development of anticryptococcal drugs.
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Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi. G3-GENES GENOMES GENETICS 2015; 5:2539-45. [PMID: 26416668 PMCID: PMC4683626 DOI: 10.1534/g3.115.020057] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Magnaporthaceae is a family of ascomycetes that includes three fungi of great economic importance: Magnaporthe oryzae, Gaeumannomyces graminis var. tritici, and Magnaporthe poae. These three fungi cause widespread disease and loss in cereal and grass crops, including rice blast disease (M. oryzae), take-all disease in wheat and other grasses (G. graminis), and summer patch disease in turf grasses (M. poae). Here, we present the finished genome sequence for M. oryzae and draft sequences for M. poae and G. graminis var. tritici. We used multiple technologies to sequence and annotate the genomes of M. oryzae, M. poae, and G. graminis var. tritici. The M. oryzae genome is now finished to seven chromosomes whereas M. poae and G. graminis var. tritici are sequenced to 40.0× and 25.0× coverage respectively. Gene models were developed by the use of multiple computational techniques and further supported by RNAseq data. In addition, we performed preliminary analysis of genome architecture and repetitive element DNA.
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5
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Nishida H. Relationship between chromosomal GC content and isoelectric points of histones in fungi. J GEN APPL MICROBIOL 2015; 61:24-6. [PMID: 25833677 DOI: 10.2323/jgam.61.24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hiromi Nishida
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University
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6
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Jung KW, Yang DH, Maeng S, Lee KT, So YS, Hong J, Choi J, Byun HJ, Kim H, Bang S, Song MH, Lee JW, Kim MS, Kim SY, Ji JH, Park G, Kwon H, Cha S, Meyers GL, Wang LL, Jang J, Janbon G, Adedoyin G, Kim T, Averette AK, Heitman J, Cheong E, Lee YH, Lee YW, Bahn YS. Systematic functional profiling of transcription factor networks in Cryptococcus neoformans. Nat Commun 2015; 6:6757. [PMID: 25849373 PMCID: PMC4391232 DOI: 10.1038/ncomms7757] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/24/2015] [Indexed: 02/06/2023] Open
Abstract
Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall biological and pathogenic regulatory circuits remain elusive, particularly due to the presence of an evolutionarily divergent set of transcription factors (TFs). Here, we report the construction of a high-quality library of 322 signature-tagged gene-deletion strains for 155 putative TF genes previously predicted using the DNA-binding domain TF database, and examine their in vitro and in vivo phenotypic traits under 32 distinct growth conditions. At least one phenotypic trait is exhibited by 145 out of 155 TF mutants (93%) and ∼85% of them (132/155) are functionally characterized for the first time in this study. The genotypic and phenotypic data for each TF are available in the C. neoformans TF phenome database (http://tf.cryptococcus.org). In conclusion, our phenome-based functional analysis of the C. neoformans TF mutant library provides key insights into transcriptional networks of basidiomycetous fungi and human fungal pathogens.
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Affiliation(s)
- Kwang-Woo Jung
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Dong-Hoon Yang
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Shinae Maeng
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Kyung-Tae Lee
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Yee-Seul So
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Joohyeon Hong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Hyo-Jeong Byun
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Hyelim Kim
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Soohyun Bang
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Min-Hee Song
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Jang-Won Lee
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Min Su Kim
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Seo-Young Kim
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Je-Hyun Ji
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Goun Park
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Hyojeong Kwon
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Suyeon Cha
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Gena Lee Meyers
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Li Li Wang
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Jooyoung Jang
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Guilhem Janbon
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, Paris F-75015, France
| | - Gloria Adedoyin
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Taeyup Kim
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Anna K. Averette
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Eunji Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, Center for Fungal Pathogenesis, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
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Meyer V, Fiedler M, Nitsche B, King R. The Cell Factory Aspergillus Enters the Big Data Era: Opportunities and Challenges for Optimising Product Formation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 149:91-132. [PMID: 25616499 DOI: 10.1007/10_2014_297] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living with limits. Getting more from less. Producing commodities and high-value products from renewable resources including waste. What is the driving force and quintessence of bioeconomy outlines the lifestyle and product portfolio of Aspergillus, a saprophytic genus, to which some of the top-performing microbial cell factories belong: Aspergillus niger, Aspergillus oryzae and Aspergillus terreus. What makes them so interesting for exploitation in biotechnology and how can they help us to address key challenges of the twenty-first century? How can these strains become trimmed for better growth on second-generation feedstocks and how can we enlarge their product portfolio by genetic and metabolic engineering to get more from less? On the other hand, what makes it so challenging to deduce biological meaning from the wealth of Aspergillus -omics data? And which hurdles hinder us to model and engineer industrial strains for higher productivity and better rheological performance under industrial cultivation conditions? In this review, we will address these issues by highlighting most recent findings from the Aspergillus research with a focus on fungal growth, physiology, morphology and product formation. Indeed, the last years brought us many surprising insights into model and industrial strains. They clearly told us that similar is not the same: there are different ways to make a hypha, there are more protein secretion routes than anticipated and there are different molecular and physical mechanisms which control polar growth and the development of hyphal networks. We will discuss new conceptual frameworks derived from these insights and the future scientific advances necessary to create value from Aspergillus Big Data.
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Affiliation(s)
- Vera Meyer
- Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355, Berlin, Germany,
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Choi J, Cheong K, Jung K, Jeon J, Lee GW, Kang S, Kim S, Lee YW, Lee YH. CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. Nucleic Acids Res 2012. [PMID: 23193288 PMCID: PMC3531191 DOI: 10.1093/nar/gks1163] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In 2007, Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr/) was publicly open with 65 genomes corresponding to 58 fungal and Oomycete species. The CFGP provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since 2007, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants and 105 animals. In addition, the number of tools in Favorite increased to 27. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, several systematic platforms designed to support studies on selected gene families have been developed. Most of them are connected through Favorite to allow of sharing data across the platforms.
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Affiliation(s)
- Jaeyoung Choi
- Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea
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Moktali V, Park J, Fedorova-Abrams ND, Park B, Choi J, Lee YH, Kang S. Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes. BMC Genomics 2012; 13:525. [PMID: 23033934 PMCID: PMC3505482 DOI: 10.1186/1471-2164-13-525] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 09/28/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable "CYPomes" ranging from one to more than 300 CYPs. Despite the rapid growth of sequenced fungal and oomycete genomes and the resulting influx of predicted CYPs, the vast majority of CYPs remain functionally uncharacterized. To facilitate the curation and functional and evolutionary studies of CYPs, we previously developed Fungal Cytochrome P450 Database (FCPD), which included CYPs from 70 fungal and oomycete species. Here we present a new version of FCPD (1.2) with more data and an improved classification scheme. RESULTS The new database contains 22,940 CYPs from 213 species divided into 2,579 clusters and 115 clans. By optimizing the clustering pipeline, we were able to uncover 36 novel clans and to assign 153 orphan CYP families to specific clans. To augment their functional annotation, CYP clusters were mapped to David Nelson's P450 databases, which archive a total of 12,500 manually curated CYPs. Additionally, over 150 clusters were functionally classified based on sequence similarity to experimentally characterized CYPs. Comparative analysis of fungal and oomycete CYPomes revealed cases of both extreme expansion and contraction. The most dramatic expansions in fungi were observed in clans CYP58 and CYP68 (Pezizomycotina), clans CYP5150 and CYP63 (Agaricomycotina), and family CYP509 (Mucoromycotina). Although much of the extraordinary diversity of the pan-fungal CYPome can be attributed to gene duplication and adaptive divergence, our analysis also suggests a few potential horizontal gene transfer events. Updated families and clans can be accessed through the new version of the FCPD database. CONCLUSIONS FCPD version 1.2 provides a systematic and searchable catalogue of 9,550 fungal CYP sequences (292 families) encoded by 108 fungal species and 147 CYP sequences (9 families) encoded by five oomycete species. In comparison to the first version, it offers a more comprehensive clan classification, is fully compatible with Nelson's P450 databases, and has expanded functional categorization. These features will facilitate functional annotation and classification of CYPs encoded by newly sequenced fungal and oomycete genomes. Additionally, the classification system will aid in studying the roles of CYPs in the evolution of fungal adaptation to specific ecological niches.
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Affiliation(s)
- Venkatesh Moktali
- Integrative Biosciences program in Bioinformatics & Genomics, The Pennsylvania State University, University Park, PA, USA
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Choi J, Vogl AW, Kronstad JW. Regulated expression of cyclic AMP-dependent protein kinase A reveals an influence on cell size and the secretion of virulence factors in Cryptococcus neoformans. Mol Microbiol 2012; 85:700-15. [PMID: 22717009 DOI: 10.1111/j.1365-2958.2012.08134.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyclic AMP-dependent protein kinase A (PKA) regulates elaboration of the virulence factors melanin and polysaccharide capsule in Cryptococcus neoformans. A mutation in PKA1 encoding the catalytic subunit is known to reduce virulence in mice while a defect in PKR1 encoding the regulatory subunit enhances disease. Here, we constructed strains with galactose-inducible and glucose-repressible versions of PKA1 and PKR1 by inserting the GAL7 promoter upstream of the genes. As expected, no capsule was found in dextrose-containing media for the P(GAL7):PKA1 strain, whereas a large capsule was formed on cells grown in galactose. Along with capsule thickness, high PKA activity also influenced cell size, ploidy and vacuole enlargement, as observed in previous reports of giant/titan cell formation. We employed the regulated strains to test the hypothesis that PKA influences secretion and found that elevated PKA expression positively regulates extracellular protease activity and negatively regulates urease secretion. Furthermore, proper PKA regulation and activity were required for wild-type levels of melanization and laccase activity, as well as correct localization of the enzyme. The latter phenotype is consistent with the discovery that PKA regulates the organization of intracellular membrane compartments. Overall, these results indicate that PKA influences secretion pathways directly related to virulence factor elaboration.
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Affiliation(s)
- Jaehyuk Choi
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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11
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RAPYD — Rapid Annotation Platform for Yeast Data. J Biotechnol 2011; 155:118-26. [DOI: 10.1016/j.jbiotec.2010.10.076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/13/2010] [Accepted: 10/22/2010] [Indexed: 01/07/2023]
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Abadio AKR, Kioshima ES, Teixeira MM, Martins NF, Maigret B, Felipe MSS. Comparative genomics allowed the identification of drug targets against human fungal pathogens. BMC Genomics 2011; 12:75. [PMID: 21272313 PMCID: PMC3042012 DOI: 10.1186/1471-2164-12-75] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 01/27/2011] [Indexed: 11/16/2022] Open
Abstract
Background The prevalence of invasive fungal infections (IFIs) has increased steadily worldwide in the last few decades. Particularly, there has been a global rise in the number of infections among immunosuppressed people. These patients present severe clinical forms of the infections, which are commonly fatal, and they are more susceptible to opportunistic fungal infections than non-immunocompromised people. IFIs have historically been associated with high morbidity and mortality, partly because of the limitations of available antifungal therapies, including side effects, toxicities, drug interactions and antifungal resistance. Thus, the search for alternative therapies and/or the development of more specific drugs is a challenge that needs to be met. Genomics has created new ways of examining genes, which open new strategies for drug development and control of human diseases. Results In silico analyses and manual mining selected initially 57 potential drug targets, based on 55 genes experimentally confirmed as essential for Candida albicans or Aspergillus fumigatus and other 2 genes (kre2 and erg6) relevant for fungal survival within the host. Orthologs for those 57 potential targets were also identified in eight human fungal pathogens (C. albicans, A. fumigatus, Blastomyces dermatitidis, Paracoccidioides brasiliensis, Paracoccidioides lutzii, Coccidioides immitis, Cryptococcus neoformans and Histoplasma capsulatum). Of those, 10 genes were present in all pathogenic fungi analyzed and absent in the human genome. We focused on four candidates: trr1 that encodes for thioredoxin reductase, rim8 that encodes for a protein involved in the proteolytic activation of a transcriptional factor in response to alkaline pH, kre2 that encodes for α-1,2-mannosyltransferase and erg6 that encodes for Δ(24)-sterol C-methyltransferase. Conclusions Our data show that the comparative genomics analysis of eight fungal pathogens enabled the identification of four new potential drug targets. The preferred profile for fungal targets includes proteins conserved among fungi, but absent in the human genome. These characteristics potentially minimize toxic side effects exerted by pharmacological inhibition of the cellular targets. From this first step of post-genomic analysis, we obtained information relevant to future new drug development.
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Park B, Park J, Cheong KC, Choi J, Jung K, Kim D, Lee YH, Ward TJ, O'Donnell K, Geiser DM, Kang S. Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing. Nucleic Acids Res 2011; 39:D640-6. [PMID: 21087991 PMCID: PMC3013728 DOI: 10.1093/nar/gkq1166] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Revised: 10/21/2010] [Accepted: 10/31/2010] [Indexed: 11/16/2022] Open
Abstract
The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education.
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Affiliation(s)
- Bongsoo Park
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Jongsun Park
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Kyeong-Chae Cheong
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Jaeyoung Choi
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Kyongyong Jung
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Donghan Kim
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Yong-Hwan Lee
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Todd J. Ward
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Kerry O'Donnell
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - David M. Geiser
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
| | - Seogchan Kang
- Department of Plant Pathology, Integrative Biosciences Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA 16802, USA, Fungal Bioinformatics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea and United States Department of Agriculture-Agricultural Research Service, Bacterial Foodborne Pathogens and Mycology Research Unit, Peoria, IL 61604, USA
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Ma LJ, Fedorova ND. A practical guide to fungal genome projects: strategy, technology, cost and completion. Mycology 2010. [DOI: 10.1080/21501201003680943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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15
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Choi J, Park J, Kim D, Jung K, Kang S, Lee YH. Fungal secretome database: integrated platform for annotation of fungal secretomes. BMC Genomics 2010; 11:105. [PMID: 20146824 PMCID: PMC2836287 DOI: 10.1186/1471-2164-11-105] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2009] [Accepted: 02/11/2010] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD). DESCRIPTION A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository. CONCLUSIONS The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at http://fsd.snu.ac.kr/.
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Affiliation(s)
- Jaeyoung Choi
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Jongsun Park
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
| | - Donghan Kim
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Kyongyong Jung
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Seogchan Kang
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
- Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea
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16
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Lee W, Park J, Choi J, Jung K, Park B, Kim D, Lee J, Ahn K, Song W, Kang S, Lee YH, Lee S. IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes. BMC Genomics 2009; 10:148. [PMID: 19351385 PMCID: PMC2681477 DOI: 10.1186/1471-2164-10-148] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 04/07/2009] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data. RESULTS The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs. CONCLUSION The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site (http://www.imgd.org/).
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Affiliation(s)
- Wonhoon Lee
- Insect Biosystematics Laboratory, Seoul National University, Seoul 151–921, Korea
- Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151–921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
| | - Jongsun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151–921, Korea
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151–921, Korea
| | - Kyongyong Jung
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
| | - Bongsoo Park
- Department of Plant Pathology, Penn State University, University Park, PA 16802, USA
| | - Donghan Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151–921, Korea
| | - Jaeyoung Lee
- Insect Biosystematics Laboratory, Seoul National University, Seoul 151–921, Korea
| | - Kyohun Ahn
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
| | - Wonho Song
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
| | - Seogchan Kang
- Department of Plant Pathology, Penn State University, University Park, PA 16802, USA
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151–921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151–921, Korea
- Center for Agricultural Biomaterials, Seoul National University, Seoul 151–921, Korea
| | - Seunghwan Lee
- Insect Biosystematics Laboratory, Seoul National University, Seoul 151–921, Korea
- Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151–921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea
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