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Xin R, Feng X, Zhang H, Wang Y, Duan M, Xie T, Dong L, Yu Q, Huang L, Zhou F. Seven non-differentially expressed 'dark biomarkers' show transcriptional dysregulation in chronic lymphocytic leukemia. Per Med 2023. [PMID: 36705049 DOI: 10.2217/pme-2022-0123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aim: Transcriptional regulation is actively involved in the onset and progression of various diseases. This study used the feature-engineering approach model-based quantitative transcription regulation to quantitatively measure the correlation between mRNA and transcription factors in a reference dataset of chronic lymphocytic leukemia (CLL) transcriptomes. Methods: A comprehensive investigation of transcriptional regulation changes in CLL was conducted using 973 samples in six independent datasets. Results & conclusion: Seven mRNAs were detected to have significantly differential model-based quantitative transcription regulation values but no differential expression between CLL patients and controls. We called these genes 'dark biomarkers' because their original expression levels did not show differential changes in the CLL patients. The overlapping lncRNAs might have contributed their transcripts to the expression miscalculations of these dark biomarkers.
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Affiliation(s)
- Ruihao Xin
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China.,College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Xin Feng
- School of Science, Jilin Institute of Chemical Technology, Jilin,132000, China.,Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Hang Zhang
- College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Yueying Wang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Tunyang Xie
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Lin Dong
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Qiong Yu
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Lan Huang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
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2
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Vita F, Giuntoli B, Bertolini E, Taiti C, Marone E, D'Ambrosio C, Trovato E, Sciarrone D, Zoccali M, Balestrini R, Scaloni A, Mondello L, Mancuso S, Alessio M, Alpi A. Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments. BMC Genomics 2020; 21:90. [PMID: 31996138 PMCID: PMC6988325 DOI: 10.1186/s12864-020-6522-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments. RESULTS Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were able to identify proteins specifically linked to the sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in sulfur metabolism. Finally, geographical specificities were associated with the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through proton transfer reaction-mass spectrometry (PTR-MS) and gas-chromatography-mass spectrometry (GC-MS). In particular, a partial least squares-discriminant analysis (PLS-DA) model built from the latter data was able to return high confidence predictions of sample source. CONCLUSIONS Results provide a characterization of white fruiting bodies by a wide range of different molecules, suggesting the role for specific compounds in the responses and adaptation to distinct environments.
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Affiliation(s)
- Federico Vita
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy. .,A.R.E.A. Foundation, via Tavoleria 28, 56125, Pisa, Italy.
| | - Beatrice Giuntoli
- Department of Biology, Università di Pisa, via L. Ghini 13, 56126, Pisa, Italy.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.,Present address: Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO, 63132, USA
| | - Cosimo Taiti
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy
| | - Elettra Marone
- Faculty of Biosciences and Technologies for Agriculture Food and Environment, University of Teramo, Via R. Balzarini 1, 64100, Teramo, Italy
| | - Chiara D'Ambrosio
- Proteomics and Mass Spectrometry Laboratory, I.S.P.A.A.M., National Research Council, 80147, Napoli, Italy
| | - Emanuela Trovato
- Chromaleont Srl, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Danilo Sciarrone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Mariosimone Zoccali
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Raffaella Balestrini
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Viale P.A. Mattioli 25, 10125, Torino, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, I.S.P.A.A.M., National Research Council, 80147, Napoli, Italy
| | - Luigi Mondello
- Chromaleont Srl, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Stefano Mancuso
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy
| | - Massimo Alessio
- Division of Genetics and Cell Biology, IRCCS-Ospedale San Raffaele, Milan, Italy
| | - Amedeo Alpi
- A.R.E.A. Foundation, via Tavoleria 28, 56125, Pisa, Italy
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3
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Dulermo T, Lazar Z, Dulermo R, Rakicka M, Haddouche R, Nicaud JM. Analysis of ATP-citrate lyase and malic enzyme mutants of Yarrowia lipolytica points out the importance of mannitol metabolism in fatty acid synthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1107-17. [PMID: 25959598 DOI: 10.1016/j.bbalip.2015.04.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 12/20/2022]
Abstract
The role of the two key enzymes of fatty acid (FA) synthesis, ATP-citrate lyase (Acl) and malic enzyme (Mae), was analyzed in the oleaginous yeast Yarrowia lipolytica. In most oleaginous yeasts, Acl and Mae are proposed to provide, respectively, acetyl-CoA and NADPH for FA synthesis. Acl was mainly studied at the biochemical level but no strain depleted for this enzyme was analyzed in oleaginous microorganisms. On the other hand the role of Mae in FA synthesis in Y. lipolytica remains unclear since it was proposed to be a mitochondrial NAD(H)-dependent enzyme and not a cytosolic NADP(H)-dependent enzyme. In this study, we analyzed for the first time strains inactivated for corresponding genes. Inactivation of ACL1 decreases FA synthesis by 60 to 80%, confirming its essential role in FA synthesis in Y. lipolytica. Conversely, inactivation of MAE1 has no effects on FA synthesis, except in a FA overaccumulating strain where it improves FA synthesis by 35%. This result definitively excludes Mae as a major key enzyme for FA synthesis in Y. lipolytica. During the analysis of both mutants, we observed a negative correlation between FA and mannitol level. As mannitol and FA pathways may compete for carbon storage, we inactivated YlSDR, encoding a mannitol dehydrogenase converting fructose and NADPH into mannitol and NADP+. The FA content of the resulting mutant was improved by 60% during growth on fructose, demonstrating that mannitol metabolism may modulate FA synthesis in Y. lipolytica.
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Affiliation(s)
- Thierry Dulermo
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Zbigniew Lazar
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France; Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37/41, 51-630 Wroclaw, Poland
| | - Rémi Dulermo
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Magdalena Rakicka
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France; Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37/41, 51-630 Wroclaw, Poland
| | - Ramedane Haddouche
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France.
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4
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Saltarelli R, Ceccaroli P, Buffalini M, Vallorani L, Casadei L, Zambonelli A, Iotti M, Badalyan S, Stocchi V. Biochemical characterization and antioxidant and antiproliferative activities of different Ganoderma collections. J Mol Microbiol Biotechnol 2015; 25:16-25. [PMID: 25662590 DOI: 10.1159/000369212] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to conduct a molecular and biochemical characterization and to compare the antioxidant and antiproliferative activities of four Ganoderma isolates belonging to Ganoderma lucidum (Gl-4, Gl-5) and Ganoderma resinaceum (F-1, F-2) species. The molecular identification was performed by ITS and IGS sequence analyses and the biochemical characterization by enzymatic and proteomic approaches. The antioxidant activity of the ethanolic extracts was compared by three different methods and their flavonoid contents were also analyzed by high-performance liquid chromatography. The antiproliferative effect on U937 cells was determined by MTT assay. The studied mycelia differ both in the enzymatic activities and protein content. The highest content in total phenol and the highest antioxidant activity for DPPH free radical scavenging and chelating activity on Fe(2+) were observed with the Gl-4 isolate of G. lucidum. The presence of quercetin, rutin, myricetin, and morin as major flavonoids with effective antioxidant activity was detected. The ethanolic extracts from mycelia of G. lucidum isolates possess a substantial antiproliferative activity against U937 cells in contrast to G. resinaceum in which the antiproliferative effects were insignificant. This study provides a comparison between G. lucidum and G. resinaceum mycelial strains, and shows that G. resinaceum could be utilized to obtain several bioactive compounds.
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Affiliation(s)
- Roberta Saltarelli
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
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Patel TK, Krasnyanski SF, Allen GC, Louws FJ, Panthee DR, Williamson JD. Tomato Plants Overexpressing a Celery Mannitol Dehydrogenase (MTD) Have Decreased Susceptibility to <i>Botrytis cinerea</i>. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajps.2015.68116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Urbanova V, Kohring GW, Klein T, Wang Z, Mert O, Emrullahoglu M, Buran K, Demir AS, Etienne M, Walcarius A. Sol-gel Approaches for Elaboration of Polyol Dehydrogenase-Based Bioelectrodes. ACTA ACUST UNITED AC 2013. [DOI: 10.1524/zpch.2013.0324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
This review describes the input of sol-gel chemistry to the immobilization of polyol dehydrogenases on electrodes, for applications in bioelectrocatalysis. The polyol dehydrogenases are described and their application for biosensing, biofuel cell and electrosynthesis are briefly discussed. The immobilization of proteins via sol-gel approaches is described, including a discussion on the difficulty to maintain the activity of proteins in a silica matrix and the strategies developed to offer a proper environment to the proteins by developing optimal organic-inorganic hybrid materials. Finally, the co-immobilization of the NAD
+
co-factor and of mediators for the elaboration of reagentless devices is presented, based on published and original data. All-in-all, sol-gel approaches appear to be a very promising for development of original electrochemical applications involving dehydrogenases in near future.
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Affiliation(s)
- Veronika Urbanova
- CNRS and Université de Lorraine, Lab. de Chimie Physique et Microbiologie, Villers-les-Nancy, Frankreich
| | | | - Tobias Klein
- Saarland University, Microbiology, Saarbrücken, Deutschland
| | - Zhijie Wang
- CNRS and Université de Lorraine, Lab. de Chimie Physique et Microbiologie, Villers-les-Nancy, Frankreich
| | - Olcay Mert
- Middle East Technical University, Department of Chemistry, Ankara, Türkei
| | | | - Kerem Buran
- Middle East Technical University, Department of Chemistry, Ankara, Türkei
| | - Ayhan S. Demir
- Middle East Technical University, Department of Chemistry, Ankara, Türkei
| | | | - Alain Walcarius
- CNRS and Université de Lorraine, Lab. de Chemie Physique et Microbiologie, Villers-les-Nancy, Frankreich
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7
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Calmes B, Guillemette T, Teyssier L, Siegler B, Pigné S, Landreau A, Iacomi B, Lemoine R, Richomme P, Simoneau P. Role of mannitol metabolism in the pathogenicity of the necrotrophic fungus Alternaria brassicicola. FRONTIERS IN PLANT SCIENCE 2013; 4:131. [PMID: 23717316 PMCID: PMC3652318 DOI: 10.3389/fpls.2013.00131] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/20/2013] [Indexed: 05/29/2023]
Abstract
In this study, the physiological functions of fungal mannitol metabolism in the pathogenicity and protection against environmental stresses were investigated in the necrotrophic fungus Alternaria brassicicola. Mannitol metabolism was examined during infection of Brassica oleracea leaves by sequential HPLC quantification of the major soluble carbohydrates and expression analysis of genes encoding two proteins of mannitol metabolism, i.e., a mannitol dehydrogenase (AbMdh), and a mannitol-1-phosphate dehydrogenase (AbMpd). Knockout mutants deficient for AbMdh or AbMpd and a double mutant lacking both enzyme activities were constructed. Their capacity to cope with various oxidative and drought stresses and their pathogenic behavior were evaluated. Metabolic and gene expression profiling indicated an increase in mannitol production during plant infection. Depending on the mutants, distinct pathogenic processes, such as leaf and silique colonization, sporulation, survival on seeds, were impaired by comparison to the wild-type. This pathogenic alteration could be partly explained by the differential susceptibilities of mutants to oxidative and drought stresses. These results highlight the importance of mannitol metabolism with respect to the ability of A. brassicicola to efficiently accomplish key steps of its pathogenic life cycle.
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Affiliation(s)
- Benoit Calmes
- SFR 4207 QUASAV, UMR 1345 IRHS, Université d'AngersAngers Cedex, France
- SFR 4207 QUASAV, INRA, UMR 1345 IRHSAngers Cedex, France
- SFR 4207 QUASAV, Agrocampus-Ouest, UMR 1345 IRHSAngers Cedex, France
| | - Thomas Guillemette
- SFR 4207 QUASAV, UMR 1345 IRHS, Université d'AngersAngers Cedex, France
- SFR 4207 QUASAV, INRA, UMR 1345 IRHSAngers Cedex, France
- SFR 4207 QUASAV, Agrocampus-Ouest, UMR 1345 IRHSAngers Cedex, France
| | - Lény Teyssier
- SFR 4207 QUASAV, UMR 1345 IRHS, Université d'AngersAngers Cedex, France
- SFR 4207 QUASAV, INRA, UMR 1345 IRHSAngers Cedex, France
- SFR 4207 QUASAV, Agrocampus-Ouest, UMR 1345 IRHSAngers Cedex, France
| | - Benjamin Siegler
- Plateforme d'Ingénierie et Analyses Moléculaires, Université d'AngersAngers Cedex, France
| | - Sandrine Pigné
- SFR 4207 QUASAV, UMR 1345 IRHS, Université d'AngersAngers Cedex, France
- SFR 4207 QUASAV, INRA, UMR 1345 IRHSAngers Cedex, France
- SFR 4207 QUASAV, Agrocampus-Ouest, UMR 1345 IRHSAngers Cedex, France
| | - Anne Landreau
- SONAS EA 921, SFR 4207, QUASAV UFR des Sciences Pharmaceutiques et d'Ingénierie de la Santé, Université d'AngersAngers Cedex, France
| | | | - Rémi Lemoine
- Ecologie, Biologie des Interactions, UMR 7267 CNRS/Université de PoitiersPoitiers, France
| | - Pascal Richomme
- SONAS EA 921, SFR 4207, QUASAV UFR des Sciences Pharmaceutiques et d'Ingénierie de la Santé, Université d'AngersAngers Cedex, France
| | - Philippe Simoneau
- SFR 4207 QUASAV, UMR 1345 IRHS, Université d'AngersAngers Cedex, France
- SFR 4207 QUASAV, INRA, UMR 1345 IRHSAngers Cedex, France
- SFR 4207 QUASAV, Agrocampus-Ouest, UMR 1345 IRHSAngers Cedex, France
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8
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Vita F, Lucarotti V, Alpi E, Balestrini R, Mello A, Bachi A, Alessio M, Alpi A. Proteins from Tuber magnatum Pico fruiting bodies naturally grown in different areas of Italy. Proteome Sci 2013; 11:7. [PMID: 23375047 PMCID: PMC3608153 DOI: 10.1186/1477-5956-11-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 12/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A number of Tuber species are ecologically important. The fruiting bodies of some of these also have value as a cooking ingredient due to the fact that they possess exceptional flavor and aromatic properties. In particular, T. magnatum fruiting bodies (commonly known as truffles), are greatly appreciated by consumers. These grow naturally in some parts of Italy. However, the quality of these fruiting bodies varies significantly depending on the area of origin due to differences in environmental growth conditions. It is therefore useful to be able to characterize them. A suitable method to reach this goal is to identify proteins which occur in the fruiting bodies that are specific to each area of origin. In this work protein profiles are described for samples coming from different areas and collected in two successive years. To our knowledge this is the first time that proteins of T. magnatum have been thoroughly examined. RESULTS Using two dimensional electrophoresis, reproducible quantitative differences in the protein patterns (total 600 spots) of samples from different parts of Italy (accession areas) were revealed by bioinformatic analysis. 60 spots were chosen for further analysis, out of which 17 could probably be used to distinguish a sample grown in one area from a sample grown in another area. Mass spectrometry (MS) protein analysis of these seventeen spots allowed the identification of 17 proteins of T. magnatum. CONCLUSIONS The results indicate that proteomic analysis is a suitable method for characterizing those differences occurring in samples and induced by the different environmental conditions present in the various Italian areas where T. magnatum can grow. The positive protein identification by MS analysis has proved that this method can be applied with success even in a species whose genome, at the moment, has not been sequenced.
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Affiliation(s)
- Federico Vita
- Department of Crop Plant Biology, University of Pisa, via Mariscoglio 34, 56124 Pisa, Italy.
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9
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Ceccaroli P, Buffalini M, Saltarelli R, Barbieri E, Polidori E, Ottonello S, Kohler A, Tisserant E, Martin F, Stocchi V. Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum. THE NEW PHYTOLOGIST 2011; 189:751-764. [PMID: 21039570 DOI: 10.1111/j.1469-8137.2010.03520.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
• Primary carbohydrate metabolism plays a special role related to carbon/nitrogen exchange, as well as metabolic support of fruiting body development, in ectomycorrhizal macrofungi. In this study, we used information retrieved from the recently sequenced Tuber melanosporum genome, together with transcriptome analysis data and targeted validation experiments, to construct the first genome-wide catalogue of the proteins supporting carbohydrate metabolism in a plant-symbiotic ascomycete. • More than 100 genes coding for enzymes of the glycolysis, pentose phosphate, tricarboxylic acid, glyoxylate and methylcitrate pathways, glycogen, trehalose and mannitol metabolism and cell wall precursor were annotated. Transcriptional regulation of these pathways in different stages of the T. melanosporum lifecycle was investigated using whole-genome oligoarray expression data together with real-time reverse transcription-polymerase chain reaction analysis of selected genes. • The most significant results were the identification of methylcitrate cycle genes and of an acid invertase, the first enzyme of this kind to be described in a plant-symbiotic filamentous fungus. • A subset of transcripts coding for trehalose, glyoxylate and methylcitrate enzymes was up-regulated in fruiting bodies, whereas genes involved in mannitol and glycogen metabolism were preferentially expressed in mycelia and ectomycorrhizas, respectively. These data indicate a high degree of lifecycle stage specialization for particular branches of carbohydrate metabolism in T. melanosporum.
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Affiliation(s)
- P Ceccaroli
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - M Buffalini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - R Saltarelli
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - E Barbieri
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - E Polidori
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - S Ottonello
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Viale G.P. Usberti 23/A, 43100 Parma, Italy
| | - A Kohler
- INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - E Tisserant
- INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - F Martin
- INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - V Stocchi
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
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10
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Deng Z, Cao L, Huang H, Jiang X, Wang W, Shi Y, Zhang R. Characterization of Cd- and Pb-resistant fungal endophyte Mucor sp. CBRF59 isolated from rapes (Brassica chinensis) in a metal-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2011; 185:717-24. [PMID: 20956060 DOI: 10.1016/j.jhazmat.2010.09.078] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 09/20/2010] [Accepted: 09/23/2010] [Indexed: 05/08/2023]
Abstract
To better understand the characteristics of fungal endophytes in the development of effective phytoremediation of heavy metals, the objectives of this study were to isolate a fungal endophyte tolerant Cd and Pb from rape roots grown in a heavy metal-contaminated soil, to characterize the metal-resistant fungal endophyte, and to assess its potential applications in removal of Cd and Pb from contaminated solutions and experimental soil. The isolate CBRF59 was identified as Mucor sp. based on morphological characteristics and phylogenetic analysis. From a Cd solution of 2.0mM, the maximum biosorption capacity of Cd by dead biomass of Mucor sp. CBRF59 was 108 mg g(-1). Under the same conditions, the bioaccumulation capacity of Cd by active biomass of the strain was 173 mg g(-1). The bioaccumulation capacity of Pb by active biomass of the strain was significantly lower than that by dead biomass in the initial Pb concentrations from 1.0 to 2.0mM. The ratio of Pb to Cd and initial pH values in the mixed Cd+Pb solutions affected the bioaccumulation and biosorption capacities of the metals by CBRF59. The addition of the active mycelia of CBRF59 significantly increased the availability of soil Pb and Cd by 77% and 11.5-fold, respectively. The results showed that the endophytic fungus was potentially applicable for the decontamination of metal-polluted media.
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Affiliation(s)
- Zujun Deng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
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11
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Novel insights into mannitol metabolism in the fungal plant pathogen Botrytis cinerea. Biochem J 2010; 427:323-32. [DOI: 10.1042/bj20091813] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order to redefine the mannitol pathway in the necrotrophic plant pathogen Botrytis cinerea, we used a targeted deletion strategy of genes encoding two proteins of mannitol metabolism, BcMTDH (B. cinerea mannitol dehydrogenase) and BcMPD (B. cinerea mannitol-1-phosphate dehydrogenase). Mobilization of mannitol and quantification of Bcmpd and Bcmtdh gene transcripts during development and osmotic stress confirmed a role for mannitol as a temporary and disposable carbon storage compound. In order to study metabolic fluxes, we followed conversion of labelled hexoses in wild-type and ΔBcmpd and ΔBcmtdh mutant strains by in vivo NMR spectroscopy. Our results revealed that glucose and fructose were metabolized via the BcMPD and BcMTDH pathways respectively. The existence of a novel mannitol phosphorylation pathway was also suggested by the NMR investigations. This last finding definitively challenged the existence of the originally postulated mannitol cycle in favour of two simultaneously expressed pathways. Finally, physiological and biochemical studies conducted on double deletion mutants (ΔBcmpdΔBcmtdh) showed that mannitol was still produced despite a complete alteration of both mannitol biosynthesis pathways. This strongly suggests that one or several additional undescribed pathways could participate in mannitol metabolism in B. cinerea.
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Saltarelli R, Ceccaroli P, Iotti M, Zambonelli A, Buffalini M, Casadei L, Vallorani L, Stocchi V. Biochemical characterisation and antioxidant activity of mycelium of Ganoderma lucidum from Central Italy. Food Chem 2009. [DOI: 10.1016/j.foodchem.2009.02.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Dulermo T, Rascle C, Chinnici G, Gout E, Bligny R, Cotton P. Dynamic carbon transfer during pathogenesis of sunflower by the necrotrophic fungus Botrytis cinerea: from plant hexoses to mannitol. THE NEW PHYTOLOGIST 2009; 183:1149-1162. [PMID: 19500266 DOI: 10.1111/j.1469-8137.2009.02890.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The main steps for carbon acquisition and conversion by Botrytis cinerea during pathogenesis of sunflower cotyledon were investigated here. A sequential view of soluble carbon metabolites detected by NMR spectroscopy during infection is presented. Disappearance of plant hexoses and their conversion to fungal metabolites were investigated by expression analysis of an extended gene family of hexose transporters (Bchxts) and of the mannitol pathway, using quantitative PCR. In order to analyse the main fungal metabolic routes used by B. cinerea in real time, we performed, for the first time, in vivo NMR analyses during plant infection. During infection, B. cinerea converts plant hexoses into mannitol. Expression analysis of the sugar porter gene family suggested predominance for transcription induced upon low glucose conditions and regulated according to the developmental phase. Allocation of plant hexoses by the pathogen revealed a conversion to mannitol, trehalose and glycogen for glucose and a preponderant transformation of fructose to mannitol by a more efficient metabolic pathway. Uptake of plant hexoses by B. cinerea is based on a multigenic flexible hexose uptake system. Their conversion into mannitol, enabled by two simultaneously expressed pathways, generates a dynamic intracellular carbon pool.
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Affiliation(s)
- Thierry Dulermo
- Génomique Fonctionnelle des Champignons Pathogènes des Plantes, UMR Microbiologie, Adaptation & Pathogénie, Université de Lyon, Lyon, F-69003, France; Université Lyon1-CNRS-INSA-BayerCropScience, 10 rue Raphaël Dubois, Bât Lwoff, Villeurbanne, F-69621, France
| | - Christine Rascle
- Génomique Fonctionnelle des Champignons Pathogènes des Plantes, UMR Microbiologie, Adaptation & Pathogénie, Université de Lyon, Lyon, F-69003, France; Université Lyon1-CNRS-INSA-BayerCropScience, 10 rue Raphaël Dubois, Bât Lwoff, Villeurbanne, F-69621, France
| | - Gaetan Chinnici
- Génomique Fonctionnelle des Champignons Pathogènes des Plantes, UMR Microbiologie, Adaptation & Pathogénie, Université de Lyon, Lyon, F-69003, France; Université Lyon1-CNRS-INSA-BayerCropScience, 10 rue Raphaël Dubois, Bât Lwoff, Villeurbanne, F-69621, France
| | - Elisabeth Gout
- UMR 5168 Réponse & Dynamique Cellulaires, Laboratoire de Physiologie Cellulaire Végétale, Université Joseph Fourier-CEA-CNRS-INRA, 17 rue des Martyrs, Grenoble F-38054, France
| | - Richard Bligny
- UMR 5168 Réponse & Dynamique Cellulaires, Laboratoire de Physiologie Cellulaire Végétale, Université Joseph Fourier-CEA-CNRS-INRA, 17 rue des Martyrs, Grenoble F-38054, France
| | - Pascale Cotton
- Génomique Fonctionnelle des Champignons Pathogènes des Plantes, UMR Microbiologie, Adaptation & Pathogénie, Université de Lyon, Lyon, F-69003, France; Université Lyon1-CNRS-INSA-BayerCropScience, 10 rue Raphaël Dubois, Bât Lwoff, Villeurbanne, F-69621, France
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Deveau A, Kohler A, Frey-Klett P, Martin F. The major pathways of carbohydrate metabolism in the ectomycorrhizal basidiomycete Laccaria bicolor S238N. THE NEW PHYTOLOGIST 2008; 180:379-390. [PMID: 18665900 DOI: 10.1111/j.1469-8137.2008.02581.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The primary carbohydrate metabolism of an ectomycorrhizal fungus and its transcriptional regulation has never been characterized at the genome scale although it plays a fundamental role in the functioning of the symbiosis. In this study, the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor S238N-H82 was explored to construct a comprehensive genome-wide inventory of pathways involved in primary carbohydrate metabolism. Several genes and gene families were annotated, including those of the glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, and trehalose and mannitol metabolism. The transcriptional regulation of these pathways was studied using whole-genome expression oligoarrays and quantitative polymerase chain reaction in free-living mycelium, ectomycorrhizas and fruiting bodies. Pathways of carbohydrate biosynthesis and catabolism are identical in L. bicolor compared with other sequenced saprotrophic basidiomycetes. Ectomycorrhiza and fruiting body development induced the regulation of a restricted set of transcripts of the glycolytic, mannitol and trehalose metabolisms.
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Affiliation(s)
- A Deveau
- UMR1136 INRA-Nancy Université Interactions Arbres/Micro-organismes, IFR110, Centre de Nancy, F-54280 Champenoux, France
| | - A Kohler
- UMR1136 INRA-Nancy Université Interactions Arbres/Micro-organismes, IFR110, Centre de Nancy, F-54280 Champenoux, France
| | - P Frey-Klett
- UMR1136 INRA-Nancy Université Interactions Arbres/Micro-organismes, IFR110, Centre de Nancy, F-54280 Champenoux, France
| | - F Martin
- UMR1136 INRA-Nancy Université Interactions Arbres/Micro-organismes, IFR110, Centre de Nancy, F-54280 Champenoux, France
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