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Ng IS, Zheng X, Chen BY, Chi X, Lu Y, Chang CS. Proteomics approach to decipher novel genes and enzymes characterization of a bioelectricity-generating and dye-decolorizing bacterium Proteus hauseri ZMd44. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0340-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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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Pereira-Medrano AG, Margesin R, Wright PC. Proteome characterization of the unsequenced psychrophile Pedobacter cryoconitis using 15N metabolic labeling, tandem mass spectrometry, and a new bioinformatic workflow. Proteomics 2012; 12:775-89. [PMID: 22539428 DOI: 10.1002/pmic.201100159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Organisms without a sequenced genome and lacking a complete protein database encounter an added level of complexity to protein identification and quantitation. De novo sequencing, new bioinformatics tools, and mass spectrometry (MS) techniques allow for advances in this area. Here, the proteomic characterization of an unsequenced psychrophilic bacterium, Pedobacter cryoconitis, is presented employing a novel workflow based on (15) N metabolic labelling, 2DE, MS/MS, and bioinformatics tools. Two bioinformatics pipelines, based on nitrogen constraint (N-constraint), ortholog searching, and de novo peptide sequencing with N-constraint similarity database search, are compared based on proteome coverage and throughput. Results demonstrate the effect of different growth temperatures (1°C, 20°C) and different carbon sources (glucose, maltose) on the proteome. Seventy-six and 69 proteins were identified and validated from the glucose- and maltose-grown bacterium, respectively, from which 21 and 22 were differentially expressed at different growth temperatures. Differentially expressed proteins are involved in stress response and carbohydrate metabolism, with higher expression at 20°C than at 1°C, while antioxidants were upregulated at 1°C. This study provides an alternative workflow to identify, validate, and quantify proteins from unsequenced organisms distantly related to other species in the protein database. Furthermore, it provides further understanding on bacterial adaptation mechanisms to cold environments, and a comparative proteomic analyses with other psychrophilic microorganisms.
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Affiliation(s)
- Ana G Pereira-Medrano
- Biological and Environmental Systems Group, The ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, UK
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Gonzalez-Fernandez R, Jorrin-Novo JV. Contribution of Proteomics to the Study of Plant Pathogenic Fungi. J Proteome Res 2011; 11:3-16. [DOI: 10.1021/pr200873p] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Raquel Gonzalez-Fernandez
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence, ceiA3, 14071 Cordoba, Spain
| | - Jesus V. Jorrin-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence, ceiA3, 14071 Cordoba, Spain
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de Vries RP, Benoit I, Doehlemann G, Kobayashi T, Magnuson JK, Panisko EA, Baker SE, Lebrun MH. Post-genomic approaches to understanding interactions between fungi and their environment. IMA Fungus 2011; 2:81-6. [PMID: 22679591 PMCID: PMC3317359 DOI: 10.5598/imafungus.2011.02.01.11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 05/18/2011] [Indexed: 01/22/2023] Open
Abstract
Fungi inhabit every natural and anthropogenic environment on Earth. They have highly varied life-styles including saprobes (using only dead biomass as a nutrient source), pathogens (feeding on living biomass), and symbionts (co-existing with other organisms). These distinctions are not absolute as many species employ several life styles (e.g. saprobe and opportunistic pathogen, saprobe and mycorrhiza). To efficiently survive in these different and often changing environments, fungi need to be able to modify their physiology and in some cases will even modify their local environment. Understanding the interaction between fungi and their environments has been a topic of study for many decades. However, recently these studies have reached a new dimension. The availability of fungal genomes and development of post-genomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post-)genomic approaches to better understand fungal interactions with their environments.
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Affiliation(s)
- Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Proteomics of plant pathogenic fungi. J Biomed Biotechnol 2010; 2010:932527. [PMID: 20589070 PMCID: PMC2878683 DOI: 10.1155/2010/932527] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 02/03/2010] [Accepted: 03/01/2010] [Indexed: 12/15/2022] Open
Abstract
Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular) and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.
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Complete primary structure of a newly characterized galactose-specific lectin from the seeds of Dolichos lablab. Glycoconj J 2008; 26:161-72. [DOI: 10.1007/s10719-008-9173-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 07/24/2008] [Accepted: 07/28/2008] [Indexed: 11/25/2022]
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Qin G, Tian S, Chan Z, Li B. Crucial role of antioxidant proteins and hydrolytic enzymes in pathogenicity of Penicillium expansum: analysis based on proteomics approach. Mol Cell Proteomics 2006; 6:425-38. [PMID: 17194899 DOI: 10.1074/mcp.m600179-mcp200] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Penicillium expansum, a widespread filamentous fungus, is a major causative agent of fruit decay and may lead to the production of mycotoxin that causes harmful effects on human health. In this study, we compared the cellular and extracellular proteomes of P. expansum in the absence and presence of borate, which affects the virulence of the fungal pathogen. The differentially expressed proteins were identified using ESI-Q-TOF-MS/MS. Several proteins related to stress response (glutathione S-transferase, catalase, and heat shock protein 60) and basic metabolism (glyceraldehyde-3-phosphate dehydrogenase, dihydroxy-acid dehydratase, and arginase) were identified in the cellular proteome. Catalase and glutathione S-transferase, the two antioxidant enzymes, exhibited reduced levels of expression upon exposure to borate. Because catalase and glutathione S-transferase are related to oxidative stress response, we further investigated the reactive oxygen species (ROS) levels and oxidative protein carbonylation (damaged proteins) in P. expansum. Higher amounts of ROS and carbonylated proteins were observed after borate treatment, indicating that catalase and glutathione S-transferase are important in scavenging ROS and protecting cellular proteins from oxidative damage. Additionally to find secretory proteins that contribute to the virulence, we studied the extracellular proteome of P. expansum under stress condition with reduced virulence. The expression of three protein spots were repressed in the presence of borate and identified as the same hydrolytic enzyme, polygalacturonase.
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Affiliation(s)
- Guozheng Qin
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Samyn B, Sergeant K, Carpentier S, Debyser G, Panis B, Swennen R, Van Beeumen J. Functional Proteome Analysis of the Banana Plant (Musa spp.) Using de Novo Sequence Analysis of Derivatized Peptides. J Proteome Res 2006; 6:70-80. [PMID: 17203950 DOI: 10.1021/pr0601943] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the use of chemical derivatization with MALDI-MS/MS analysis for de novo sequence analysis. Using three frequently used homology-based search algorithms, we were able to identify more than 40 proteins from banana, a nonmodel plant with unsequenced genome. Furthermore, this approach allowed the identification of different isoforms. We also observed that the identification score obtained varied according to the position of the peptide sequences in the query using the MS-Blast algorithm.
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Affiliation(s)
- Bart Samyn
- Department of Biochemistry, Physiology and Microbiology, Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.
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Linke D, Bouws H, Peters T, Nimtz M, Berger RG, Zorn H. Laccases of Pleurotus sapidus: characterization and cloning. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:9498-505. [PMID: 16302768 DOI: 10.1021/jf052012f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Peanut shells, a major waste stream of food processing, served as a renewable substrate for inducing the production of laccases by basidiomycetes. Of 46 surface cultures examined, 29 showed laccase activity under the experimental conditions. The edible fungus Pleurotus sapidus was selected as the most active producer, immobilized on the shells, and cultivated in the fed-batch mode. A continuous rise in laccase activity was found, indicating the inducibility of laccase secretion by the peanut shells and the reusability of the mycelium. Two laccase isoenzymes were purified by decoupled 2-D electrophoresis, and amino acid sequence information was obtained by electrospray ionization tandem mass spectrometry. cDNAs of the corresponding gene and another laccase were cloned and sequenced using a PCR-based screening of a synthesized P. sapidus cDNA library. Data bank searches against public databases returned laccases of P. ostreatus and P. sajor-caju as the best hits. The potential use of laccases by the food industry is discussed.
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Affiliation(s)
- Diana Linke
- Zentrum Angewandte Chemie, Institut für Lebensmittelchemie der Universität Hannover, Wunstorfer Strasse 14, D-30453 Hannover, Germany
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Matis M, Zakelj-Mavric M, Peter-Katalinić J. Global Analysis of the Hortaea werneckii Proteome: Studying Steroid Response in Yeast. J Proteome Res 2005; 4:2043-51. [PMID: 16335949 DOI: 10.1021/pr050195f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The response of the halophilic black yeast Hortaea werneckii to the steroid hormone progesterone has been studied at the protein level using fluorescent two-dimensional differential gel electrophoresis (2D-DIGE) technology in combination with mass spectrometry. Data on protein identification from this study reveal molecular mechanisms of the response to progesterone. In particular, the overexpression of Pck2 and Pac2 in the stimulated cells indicates the interactions of progesterone with the cell growth and reproduction signaling pathways.
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Affiliation(s)
- Maja Matis
- Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, Georgia 30912, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447509 DOI: 10.1002/cfg.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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