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Kasirajan L, Kamaraj K. Optimization of laccase enzyme from Flammulina velutipes using response surface methodology box-behnken design. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01378-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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2
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Secretome of Paenibacillus sp. S-12 provides an insight about its survival and possible pathogenicity. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01032-4. [PMID: 36642775 DOI: 10.1007/s12223-023-01032-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
Our aim in this study was to characterize and investigate the secretome of Paenibacillus sp. S-12 by nanoLC-MS/MS tool-based analysis of trypsin digested culture supernatant proteins. Using a bioinformatics and combined approach of mass spectrometry, we identified 657 proteins in the secretome. Bioinformatic tools such as PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb were used for the subcellular localization and categorization of secretome on basis of signal peptides. Among the identified proteins, more than 25% of the secretome proteins were associated with virulence proteins including flagellar, adherence, and immune modulators. Gene ontology analysis using Blast2GO tools categorized 60 proteins of the secretome into biological processes, cellular components, and molecular functions. KEGG pathway analysis identified the enzymes or proteins involved in various biosynthesis and degradation pathways. Functional analysis of secretomes reveals a large number of proteins involved in the uptake and exchange of nutrients, colonization, and chemotaxis. A good number of proteins were involved in survival and defense mechanism against oxidative stress, the production of toxins and antimicrobial compounds. The present study is the first report of the in-depth protein profiling of Paenibacillus bacterium. In summary, the current findings of Paenibacillus sp. S-12 secretome provide basic information to understand its survival and the possible pathogenic mechanism.
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Lopes da Silva F, Aquino EN, Costa da Cunha D, Vieira Hamann PR, Magalhães TB, Steindorff AS, Ulhoa CJ, Noronha EF. Analysis of Trichoderma harzianum TR 274 secretome to assign candidate proteins involved in symbiotic interactions with Phaseolus vulgaris. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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HANIF SHAHNAZ, JABEEN KHAJISTA, AKHTAR NAUREEN, IQBAL SUMERA. GC-MS analysis & antifungal activity of Datura metel L. against Rhizoctonia solani Kuhn. AN ACAD BRAS CIENC 2022; 94:e20200851. [DOI: 10.1590/0001-3765202220200851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/25/2020] [Indexed: 11/21/2022] Open
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5
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Abuduaini X, Aili A, Lin R, Song G, Huang Y, Chen Z, Zhao H, Luo Q, Zhao H. The Lethal Effect of Bacillus subtilis Z15 Secondary Metabolites on Verticillium dahliae. Nat Prod Commun 2021. [DOI: 10.1177/1934578x20986728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Bacillus subtilis Z15 (BS-Z15), isolated from cotton rhizosphere soil, inhibits Verticillium dahliae and suppresses cotton Verticillium wilt in pot experiments. We investigated the influence of environmental factors, pH, temperature, ultraviolet light, protease, and incubation time on the stability of BS-Z15 secondary metabolites (SMs), and the mechanism underlying the cytotoxicity of BS-Z15 SMs on V. dahliae. BS-Z15 and its fermentation broth inhibited V. dahliae, and this effect was mediated by its SMs. These were shown to be stable to the influence of the above environmental factors. BS-Z15 SMs decreased the viability of V. dahliae conidia in a time-dependent manner. Scanning electron microscopy showed that BS-Z15 and its SMs resulted in flattened and depressed conidia. BS-Z15 SMs induced morphological abnormalities in the hyphae, which showed rough aberrant structures, reduced conidiophore production, and accelerated aging. Flow cytometry using Hoechst/propidium iodide double staining revealed that BS-Z15 SMs induced necrosis in V. dahliae in a time-dependent manner. Fluorescence microscopy showed that BS-Z15 SMs did not induce apoptotic bodies in the conidia of V. dahliae but caused significant changes in karyotypes, accompanied by nuclear lysis and nucleic-acid diffusion, which may play important roles in necrosis. In addition, 0.3 mg/mL BS-Z15 SMs had no effect on either the mitochondrial membrane potential or the synthesis of proapoptotic proteins, indicating that the SMs did not induce apoptosis in V. dahliae. Their lethal effect on V. dahliae was by inducing necrosis in its conidia and hyphae. BS-Z15 SMs thus have potential as biological pesticides to control Verticillium wilt in cotton.
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Affiliation(s)
- Xieerwanimu Abuduaini
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, P. R. China
| | - Ailina Aili
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, P. R. China
| | - Rongrong Lin
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, P. R. China
| | - Ganggang Song
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, P. R. China
| | - Yu Huang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, P. R. China
| | - Zhongyi Chen
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, P. R. China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, P. R. China
| | - Heping Zhao
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, P. R. China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, P. R. China
| | - Qin Luo
- Tumor Hospital Affiliated Xinjiang Medical University, Urumqi, Xinjiang, P. R. China
| | - Huixin Zhao
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, P. R. China
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6
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Krishnaswamy A, Barnes N, Lotlikar NP, Damare SR. An Improved Method for Protein Extraction from Minuscule Quantities of Fungal Biomass. Indian J Microbiol 2019; 59:100-104. [PMID: 30728637 PMCID: PMC6328415 DOI: 10.1007/s12088-018-0752-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 06/20/2018] [Indexed: 11/30/2022] Open
Abstract
Filamentous fungi are ubiquitous eukaryotes having chitin as a major constituent of the cell wall. Chitin is tough to lyse due to which the intracellular fungal proteins are not readily accessible. The problem is further enhanced when the biomass to be analyzed for protein studies is too little due to the extreme experimental parameters under consideration such as increased or lowered pH, temperature, hydrostatic pressure, nutrients, etc. The method described here is capable of obtaining proteins from minuscule quantities of biomass (~5 mg lyophilized biomass). In this study, different lysing conditions and varied composition of extraction buffers were tried to obtain maximum protein of high quality. Lysis with zirconium beads in a combination buffer system (Tris-MgCl2 buffer, urea buffer I and urea buffer II) was best for extracting proteins from the fungal isolates used. The protocol described here provides for a simple and quick method for extraction of high-quality proteins from very less biomass that could be extended to other tough to lyse biological material also.
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Affiliation(s)
- Akhila Krishnaswamy
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Natasha Barnes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
- Present Address: Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Nikita P. Lotlikar
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Samir R. Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
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7
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Optimization of protein extraction and two-dimensional gel electrophoresis profiles for the identification of Cordyceps sinensis and other similar species. PLoS One 2018; 13:e0202779. [PMID: 30133529 PMCID: PMC6105017 DOI: 10.1371/journal.pone.0202779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/08/2018] [Indexed: 11/19/2022] Open
Abstract
Given that Chinese materia medica (CMM) is expensive and rare, people take tremendous risk to adulterate and falsify Cordyceps sinensis with counterfeit species with similar morphological features. It is thus essential to develop new methods to identify the authenticity of Cordyceps sinensis. It is hypothesized in this study that Cordyceps sinensis possesses certain protein biomarkers distinct from its counterfeits, which can be identified by proteomic technologies for authentication purposes. This is the first study that aims to optimize the conditions for extracting proteins from Cordyceps sinensis, a hybrid of fungal-animal CMM, and to compare the two-dimensional gel electrophoresis (2-DE) profiles between different Cordyceps species. Two different protein extraction buffer systems, namely, phenol/sodium dodecyl sulfate (SDS) buffer or lysis buffer, were evaluated, where the preparation using lysis buffer yielded better protein content. The results also showed that extraction with lysis buffer without pre- or post-washing of samples was the most effective protocol, with over 220% of protein yield and 819 protein spots detected on a 2-DE gel. Moreover, the results demonstrated that Cordyceps sinensis possesses protein biomarkers distinct from its counterfeits, and these biomarkers are not source- or origin-dependent, strongly supporting the feasibility of using identified biomarkers as indicators for authentication of Cordyceps species. The findings of this study warrant further investigations on the structural identification of protein biomarkers of Cordyceps species.
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8
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Sathesh-Prabu C, Lee YK. Genetic Variability and Proteome Profiling of a Radiation Induced Cellulase Mutant Mushroom Pleurotus florida. Pol J Microbiol 2018; 65:271-277. [PMID: 29334071 DOI: 10.5604/17331331.1215606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the genetic similarity changes between a mutant mushroom (Pleurotus florida, designated as PfCM4) having increased cellulolytic activity developed through radiation mutagenesis and its wild type by amplified fragment length polymorphism (AFLP). On average, 23 AFLP fragments were amplified per primer combination, and a total of 286 polymorphic fragments (78.57% polymorphism) with maximal fragment length of 1365 base pairs (bp) were obtained. The genetic similarity between wild type and PfCM4 was found to be 22.30%. In addition, mycelial and secreted protein profiling by 2D-PAGE showed at least three and five different protein spots in the range of 25 kD to 100 kD, respectively, in PfCM4. It seems that the variation in genetic similarity and different expression of both mycelial and secreted proteins in PfCM4 in comparison to the wild type could likely be correlated with its increased cellulolytic activity effected by the irradiation.
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Affiliation(s)
- Chandran Sathesh-Prabu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Young-Keun Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
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9
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Liu L, Wu R, Zhang J, Shang N, Li P. D-Ribose Interferes with Quorum Sensing to Inhibit Biofilm Formation of Lactobacillus paraplantarum L-ZS9. Front Microbiol 2017; 8:1860. [PMID: 29018429 PMCID: PMC5622935 DOI: 10.3389/fmicb.2017.01860] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/12/2017] [Indexed: 01/31/2023] Open
Abstract
Biofilms help bacteria survive under adverse conditions, and the quorum sensing (QS) system plays an important role in regulating their activities. Quorum sensing inhibitors (QSIs) have great potential to inhibit pathogenic biofilm formation and are considered possible replacements for antibiotics; however, further investigation is required to understand the mechanisms of action of QSIs and to avoid inhibitory effects on beneficial bacteria. Lactobacillus paraplantarum L-ZS9, isolated from fermented sausage, is a bacteriocin-producing bacteria that shows potential to be a probiotic starter. Since exogenous autoinducer-2 (AI-2) promoted biofilm formation of the strain, expression of genes involved in AI-2 production was determined in L. paraplantarum L-ZS9, especially the key gene luxS. D-Ribose was used to inhibit biofilm formation because of its AI-2 inhibitory activity. Twenty-seven differentially expressed proteins were identified by comparative proteomic analysis following D-ribose treatment and were functionally classified into six groups. Real-time quantitative PCR showed that AI-2 had a counteractive effect on transcription of the genes tuf, fba, gap, pgm, nfo, rib, and rpoN. Over-expression of the tuf, fba, gap, pgm, and rpoN genes promoted biofilm formation of L. paraplantarum L-ZS9, while over-expression of the nfo and rib genes inhibited biofilm formation. In conclusion, D-ribose inhibited biofilm formation of L. paraplantarum L-ZS9 by regulating multiple genes involved in the glycolytic pathway, extracellular DNA degradation and transcription, and translation. This research provides a new mechanism of QSI regulation of biofilm formation of Lactobacillus and offers a valuable reference for QSI application in the future.
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Affiliation(s)
- Lei Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China
| | - Ruiyun Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jinlan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Nan Shang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Pinglan Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China
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10
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Verwaaijen B, Wibberg D, Kröber M, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A. The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.). PLoS One 2017; 12:e0177278. [PMID: 28486484 PMCID: PMC5423683 DOI: 10.1371/journal.pone.0177278] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/25/2017] [Indexed: 12/19/2022] Open
Abstract
The necrotrophic pathogen Rhizoctonia solani is one of the most economically important soil-borne pathogens of crop plants. Isolates of R. solani AG1-IB are the major pathogens responsible for bottom-rot of lettuce (Lactuca sativa L.) and are also responsible for diseases in other plant species. Currently, there is lack of information regarding the molecular responses in R. solani during the pathogenic interaction between the necrotrophic soil-borne pathogen and its host plant. The genome of R. solani AG1-IB (isolate 7/3/14) was recently established to obtain insights into its putative pathogenicity determinants. In this study, the transcriptional activity of R. solani AG1-IB was followed during the course of its pathogenic interaction with the host plant lettuce under controlled conditions. Based on visual observations, three distinct pathogen-host interaction zones on lettuce leaves were defined which covered different phases of disease progression on tissue inoculated with the AG1-IB (isolate 7/3/14). The zones were defined as: Zone 1-symptomless, Zone 2-light brown discoloration, and Zone 3-dark brown, necrotic lesions. Differences in R. solani hyphae structure in these three zones were investigated by microscopic observation. Transcriptional activity within these three interaction zones was used to represent the course of R. solani disease progression applying high-throughput RNA sequencing (RNA-Seq) analysis of samples collected from each Zone. The resulting three transcriptome data sets were analyzed for their highest expressed genes and for differentially transcribed genes between the respective interaction zones. Among the highest expressed genes was a group of not previously described genes which were transcribed exclusively during early stages of interaction, in Zones 1 and 2. Previously described importance of up-regulation in R. solani agglutinin genes during disease progression could be further confirmed; here, the corresponding genes exhibited extremely high transcription levels. Most differentially higher expressed transcripts were found within Zone 2. In Zone 3, the zone with the strongest degree of interaction, gene transcripts indicative of apoptotic activity were highly abundant. The transcriptome data presented in this work support previous models of the disease and interaction cycle of R. solani and lettuce and may influence effective techniques for control of this pathogen.
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Affiliation(s)
- Bart Verwaaijen
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Magdalena Kröber
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Zrenner
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Hanna Bednarz
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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11
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Zhang B, Qin Y, Han Y, Dong C, Li P, Shang Q. Comparative proteomic analysis reveals intracellular targets for bacillomycin L to induce Rhizoctonia solani Kühn hyphal cell death. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1152-1159. [PMID: 27267622 DOI: 10.1016/j.bbapap.2016.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 04/29/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
Abstract
Bacillomycin L, a natural iturinic lipopeptide produced by Bacillus amyloliquefaciens, is characterized by strong antifungal activity against a variety of agronomically important filamentous fungi including Rhizoctonia solani Kühn. To further understand its antifungal actions, proteomes were comparatively studied within R. solani hyphal cells treated with or without bacillomycin L. The results show that 39 proteins were alternatively expressed within cells in response to this lipopeptide, which are involved in stress response, carbohydrate, amino acid and nucleotide metabolism, cellular component organization, calcium homeostasis, protein degradation, RNA processing, gene transcription, and others, suggesting that, in addition to inducing cell membrane permeabilization, iturin exhibits antibiotic activities by targeting intracellular molecules. Based on these results, a model of action of bacillomycin L against R. solani hyphal cells was proposed. Our study provides new insight into the antibiotic mechanisms of iturins.
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Affiliation(s)
- Bao Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuxuan Qin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing 100083, China
| | - Yuzhu Han
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Chunjuan Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pinglan Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing 100083, China.
| | - Qingmao Shang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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12
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Lakshman DK, Roberts DP, Garrett WM, Natarajan SS, Darwish O, Alkharouf N, Pain A, Khan F, Jambhulkar PP, Mitra A. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with Roles in Plant Cell Wall Degradation and Virulence. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3101-3110. [PMID: 27019116 DOI: 10.1021/acs.jafc.5b05735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rhizoctonia solani AG 4 is a soilborne necrotrophic fungal plant pathogen that causes economically important diseases on agronomic crops worldwide. This study used a proteomics approach to characterize both intracellular proteins and the secretome of R. solani AG 4 isolate Rs23A under several growth conditions, the secretome being highly important in pathogenesis. From over 500 total secretome and soluble intracellular protein spots from 2-D gels, 457 protein spots were analyzed and 318 proteins positively matched with fungal proteins of known function by comparison with available R. solani genome databases specific for anastomosis groups 1-IA, 1-IB, and 3. These proteins were categorized to possible cellular locations and functional groups and for some proteins their putative roles in plant cell wall degradation and virulence. The majority of the secreted proteins were grouped to extracellular regions and contain hydrolase activity.
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Affiliation(s)
- Dilip K Lakshman
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Daniel P Roberts
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Wesley M Garrett
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Savithiry S Natarajan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Omar Darwish
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Nadim Alkharouf
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Arnab Pain
- Pathogen Genomics, KAUST , Thuwal, Saudi Arabia 23955
| | - Farooq Khan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | | | - Amitava Mitra
- Department of Plant Pathology, University of Nebraska , Lincoln, Nebraska 68583, United States
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13
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Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of Ganoderma spp. Protein J 2016; 35:100-6. [DOI: 10.1007/s10930-016-9656-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Ghosh P, Roy A, Hess D, Ghosh A, Das S. Deciphering the mode of action of a mutant Allium sativum Leaf Agglutinin (mASAL), a potent antifungal protein on Rhizoctonia solani. BMC Microbiol 2015; 15:237. [PMID: 26502719 PMCID: PMC4623900 DOI: 10.1186/s12866-015-0549-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background Mutant Allium sativum leaf agglutinin (mASAL) is a potent, biosafe, antifungal protein that exhibits fungicidal activity against different phytopathogenic fungi, including Rhizoctonia solani. Methods The effect of mASAL on the morphology of R.solani was monitored primarily by scanning electron and light microscopic techniques. Besides different fluorescent probes were used for monitoring various intracellular changes associated with mASAL treatment like change in mitochondrial membrane potential (MMP), intracellular accumulation of reactive oxygen species (ROS) and induction of programmed cell death (PCD). In addition ligand blot followed by LC-MS/MS analyses were performed to detect the putative interactors of mASAL. Results Knowledge on the mode of function for any new protein is a prerequisite for its biotechnological application. Detailed morphological analysis of mASAL treated R. solani hyphae using different microscopic techniques revealed a detrimental effect of mASAL on both the cell wall and the plasma membrane. Moreover, exposure to mASAL caused the loss of mitochondrial membrane potential (MMP) and the subsequent intracellular accumulation of reactive oxygen species (ROS) in the target organism. In conjunction with this observation, evidence of the induction of programmed cell death (PCD) was also noted in the mASAL treated R. solani hyphae. Furthermore, we investigated its interacting partners from R. solani. Using ligand blots followed by liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses, we identified different binding partners including Actin, HSP70, ATPase and 14-3-3 protein. Conclusions Taken together, the present study provides insight into the probable mode of action of the antifungal protein, mASAL on R. solani which could be exploited in future biotechnological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0549-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Prithwi Ghosh
- Division of Plant Biology, Bose Institute, Centenary Campus, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India.
| | - Amit Roy
- Division of Plant Biology, Bose Institute, Centenary Campus, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India. .,Present address: Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
| | - Daniel Hess
- The Protein Analysis Facility, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Anupama Ghosh
- Division of Plant Biology, Bose Institute, Centenary Campus, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India.
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India.
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15
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Kramer A, Beck HC, Kumar A, Kristensen LP, Imhoff JF, Labes A. Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant. PLoS One 2015; 10:e0140047. [PMID: 26460745 PMCID: PMC4603891 DOI: 10.1371/journal.pone.0140047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/21/2015] [Indexed: 11/19/2022] Open
Abstract
The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.
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Affiliation(s)
- Annemarie Kramer
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Hans Christian Beck
- Centre for Clinical Proteomics, Department for Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Abhishek Kumar
- Department for Botany and Molecular Biology, Institute of Botany, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Lars Peter Kristensen
- Centre for Clinical Proteomics, Department for Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Johannes F. Imhoff
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Antje Labes
- Research Unit Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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Wang L, Liu M, Liao M. Proteomic response of Rhizoctonia solani GD118 suppressed by Paenibacillus kribbensis PS04. World J Microbiol Biotechnol 2014; 30:3037-45. [PMID: 25164959 DOI: 10.1007/s11274-014-1730-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/22/2014] [Indexed: 11/24/2022]
Abstract
Rice sheath blight, caused by Rhizoctonia solani, is considered a worldwide destructive rice disease and leads to considerable yield losses. A bio-control agent, Paenibacillus kribbensis PS04, was screened to resist against the pathogen. The inhibitory effects were investigated (>80 %) by the growth of the hyphae. Microscopic observation of the hypha structure manifested that the morphology of the pathogenic mycelium was strongly affected by P. kribbensis PS04. To explore essentially inhibitory mechanisms, proteomic approach was adopted to identify differentially expressed proteins from R. solani GD118 in response to P. kribbensis PS04 using two-dimensional gel electrophoresis. Protein profiling was used to identify 13 differential proteins: 10 proteins were found to be down-regulated while 3 proteins were up-regulated. These proteins were involved in material and energy metabolism, antioxidant activity, protein folding and degradation, and cytoskeleton regulation. Among them, material and energy metabolism was differentially regulated by P. kribbensis PS04. Protein expression was separately inhibited by the bio-control agent in oxidation resistance, protein folding and degradation, and cytoskeleton regulation. Proteome changes of the mycelium assist in understanding how the pathogen was directly suppressed by P. kribbensis PS04.
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Affiliation(s)
- Liuqing Wang
- Key Laboratory of Natural Pesticide and Chemical Biology of Ministry of Education, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, 510642, People's Republic of China
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Rahmad N, Al-Obaidi JR, Rashid NMN, Zean NB, Yusoff MHYM, Shaharuddin NS, Jamil NAM, Saleh NM. Comparative proteomic analysis of different developmental stages of the edible mushroom Termitomyces heimii. Biol Res 2014; 47:30. [PMID: 25053143 PMCID: PMC4105490 DOI: 10.1186/0717-6287-47-30] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/25/2014] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Termitomyces heimii is a basidiomycete fungus that has a symbiotic relationship with termites, and it is an edible mushroom with a unique flavour and texture. T. heimii is also one of the most difficult mushrooms to cultivate throughout the world. Little is known about the growth and development of these mushrooms, and the available information is insufficient or poor. The purpose of this study was to provide a base of knowledge regarding the biological processes involved in the development of T. heimii. The proteomic method of 2 dimensional difference gel electrophoresis 2D-DIGE was used to determine and examine the protein profiles of each developmental stage (mycelium, primordium and fruiting body). Total proteins were extracted by TCA-acetone precipitation. RESULTS A total of 271 protein spots were detected by electrophoresis covering pH 3-10 and 10-250 kDa. Selected protein spots were subjected to mass spectrometric analyses with matrix-assisted laser desorption/ionisation (MALDI TOF/TOF). Nineteen protein spots were identified based on peptide mass fingerprinting by matching peptide fragments to the NCBI non-redundant database using MASCOT software. The 19 protein spots were categorised into four major groups through KEGG pathway analysis, as follows: carbohydrate metabolism, energy metabolism, amino acid metabolism and response to environmental stress. CONCLUSIONS The results from our study show that there is a clear correlation between the changes in protein expression that occur during different developmental stages. Enzymes related to cell wall synthesis were most highly expressed during fruiting body formation compared to the mycelium and primordial stages. Moreover, enzymes involved in cell wall component degradation were up-regulated in the earlier stages of mushroom development.
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Affiliation(s)
- Norasfaliza Rahmad
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Jameel R Al-Obaidi
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Noraswati Mohd Nor Rashid
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Ng Boon Zean
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | | | - Nur Syahidah Shaharuddin
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Nor Azreen Mohd Jamil
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Norihan Mohd Saleh
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
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Seo EY, Nam J, Kim HS, Park YH, Hong SM, Lakshman D, Bae H, Hammond J, Lim HS. Selective Interaction Between Chloroplast β-ATPase and TGB1L88 Retards Severe Symptoms Caused by Alternanthera mosaic virus Infection. THE PLANT PATHOLOGY JOURNAL 2014; 30:58-67. [PMID: 25288986 PMCID: PMC4174830 DOI: 10.5423/ppj.oa.09.2013.0097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 10/13/2013] [Accepted: 10/13/2013] [Indexed: 05/02/2023]
Abstract
The multifunctional triple gene block protein 1 (TGB1) of the Potexvirus Alternanthera mosaic virus (AltMV) has been reported to have silencing suppressor, cell-to-cell movement, and helicase functions. Yeast two hybrid screening using an Arabidopsis thaliana cDNA library with TGB1 as bait, and co-purification with TGB1 inclusion bodies identified several host proteins which interact with AltMV TGB1. Host protein interactions with TGB1 were confirmed by biomolecular fluorescence complementation, which showed positive TGB1 interaction with mitochondrial ATP synthase delta' chain subunit (ATP synthase delta'), light harvesting chlorophyll-protein complex I subunit A4 (LHCA4), chlorophyll a/b binding protein 1 (LHB1B2), chloroplast-localized IscA-like protein (ATCPISCA), and chloroplast β-ATPase. However, chloroplast β-ATPase interacts only with TGB1L88, and not with weak silencing suppressor TGB1P88. This selective interaction indicates that chloroplast β-ATPase is not required for AltMV movement and replication; however, TRV silencing of chloroplast β-ATPase in Nicotiana benthamiana induced severe tissue necrosis when plants were infected by AltMV TGB1L88 but not AltMV TGB1P88, suggesting that β-ATPase selectively responded to TGB1L88 to induce defense responses.
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Affiliation(s)
- Eun-Young Seo
- Department of Applied Biology, Chungnam National University, Daejeon 305-764, Korea
| | - Jiryun Nam
- Department of Applied Biology, Chungnam National University, Daejeon 305-764, Korea
- Department of Bioscience II, Bio-Medical Science, Daejeon 305-301, Korea
| | - Hyun-Seung Kim
- Department of Applied Biology, Chungnam National University, Daejeon 305-764, Korea
| | - Young-Hwan Park
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
| | - Seok Myeong Hong
- Department of Medicine, Graduate School, Chung-Ang University, Seoul 156-756, Korea
| | - Dilip Lakshman
- USDA-ARS, US National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD 20705, USA
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
- Hanhong Bae, Phone) +82-51-455-5495, FAX) +82-51-455-5494, E-mail)
| | - John Hammond
- USDA-ARS, US National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD 20705, USA
- John Hammond, Phone) +1-301-504-5313, FAX) +301-504-5096, E-mail)
| | - Hyoun-Sub Lim
- Department of Applied Biology, Chungnam National University, Daejeon 305-764, Korea
- Co-corresponding authors. Hyoun-Sub Lim, Phone) +82-42-821-5766, FAX) +82-42-823-8679, E-mail)
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Alam M, Ghosh W. Optimization of a phenol extraction-based protein preparation method amenable to downstream 2DE and MALDI-MS based analysis of bacterial proteomes. Proteomics 2014; 14:216-21. [DOI: 10.1002/pmic.201300146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 10/25/2013] [Accepted: 11/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Masrure Alam
- Department of Microbiology; Bose Institute; Kolkata India
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20
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A phage-displayed chicken single-chain antibody fused to alkaline phosphatase detects Fusarium pathogens and their presence in cereal grains. Anal Chim Acta 2013; 764:84-92. [DOI: 10.1016/j.aca.2012.12.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 12/12/2012] [Accepted: 12/14/2012] [Indexed: 11/17/2022]
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21
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Natarajan. Analysis of Soybean Embryonic Axis Proteins by Two-Dimensional Gel Electrophoresis and Mass Spectrometry. ACTA ACUST UNITED AC 2013. [DOI: 10.6000/1927-5129.2013.09.41] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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22
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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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Abstract
Some fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of 'unknown function protein' as opposed to 'hypothetical protein' - once any protein has been identified by protein mass spectrometry. A combination of approaches including comparative proteomics, pathogen-induced protein expression and immunoproteomics are outlined, which, when used in combination with a variety of other techniques (e.g. functional genomics, microarray analysis, immunochemical and infection model systems), appear to yield comprehensive and definitive information on protein function in fungi. The relative advantages of proteomic, as opposed to transcriptomic-only, analyses are also described. In the future, combined high-throughput, quantitative proteomics, allied to transcriptomic sequencing, are set to reveal much about protein function in fungi.
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Affiliation(s)
- Sean Doyle
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Gusakov AV, Semenova MV, Sinitsyn AP. Mass spectrometry in the study of extracellular enzymes produced by filamentous fungi. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810140030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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