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Huang Z, Wang Q, Khan IA, Li Y, Wang J, Wang J, Liu X, Lin F, Lu J. The Methylcitrate Cycle and Its Crosstalk with the Glyoxylate Cycle and Tricarboxylic Acid Cycle in Pathogenic Fungi. Molecules 2023; 28:6667. [PMID: 37764443 PMCID: PMC10534831 DOI: 10.3390/molecules28186667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
In fungi, the methylcitrate cycle converts cytotoxic propionyl-coenzyme A (CoA) to pyruvate, which enters gluconeogenesis. The glyoxylate cycle converts acetyl-CoA to succinate, which enters gluconeogenesis. The tricarboxylic acid cycle is a central carbon metabolic pathway that connects the methylcitrate cycle, the glyoxylate cycle, and other metabolisms for lipids, carbohydrates, and amino acids. Fungal citrate synthase and 2-methylcitrate synthase as well as isocitrate lyase and 2-methylisocitrate lyase, each evolved from a common ancestral protein. Impairment of the methylcitrate cycle leads to the accumulation of toxic intermediates such as propionyl-CoA, 2-methylcitrate, and 2-methylisocitrate in fungal cells, which in turn inhibits the activity of many enzymes such as dehydrogenases and remodels cellular carbon metabolic processes. The methylcitrate cycle and the glyoxylate cycle synergistically regulate carbon source utilization as well as fungal growth, development, and pathogenic process in pathogenic fungi.
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Affiliation(s)
- Zhicheng Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
| | - Qing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
| | - Irshad Ali Khan
- Department of Agriculture, The University of Swabi, Khyber 29380, Pakistan;
| | - Yan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
| | - Jing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.W.); (J.W.); (F.L.)
| | - Jiaoyu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.W.); (J.W.); (F.L.)
| | - Xiaohong Liu
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.W.); (J.W.); (F.L.)
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Jianping Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
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Tomazeli EC, Alfaro M, Zambonelli A, Garde E, Pérez G, Jiménez I, Ramírez L, Salman H, Pisabarro AG. Transcriptome Metabolic Characterization of Tuber borchii SP1-A New Spanish Strain for In Vitro Studies of the Bianchetto Truffle. Int J Mol Sci 2023; 24:10981. [PMID: 37446159 DOI: 10.3390/ijms241310981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots, and they are known for their peculiar aromas and flavors. The axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation has prompted searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) was isolated and cultured, and its transcriptome was analyzed under different in vitro culture conditions. The results showed that the highest growth of T. borchii SP1 was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22 °C. We analyzed the transcriptome of this strain cultured in different media to establish a framework for future comparative studies, paying particular attention to the central metabolic pathways, principal secondary metabolite gene clusters, and the genes involved in producing volatile aromatic compounds (VOCs). The results showed a transcription signal for around 80% of the annotated genes. In contrast, most of the transcription effort was concentrated on a limited number of genes (20% of genes account for 80% of the transcription), and the transcription profile of the central metabolism genes was similar in the different conditions analyzed. The gene expression profile suggests that T. borchii uses fermentative rather than respiratory metabolism in these cultures, even in aerobic conditions. Finally, there was a reduced expression of genes belonging to secondary metabolite clusters, whereas there was a significative transcription of those involved in producing volatile aromatic compounds.
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Affiliation(s)
- Emilia Chuina Tomazeli
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
- Bionanoplus, 31194 Oricain, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Alessandra Zambonelli
- Department of Agro-Food Sciences and Technologies, University of Bologna (UNIBO), 40126 Bologna, Italy
| | - Edurne Garde
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Gumer Pérez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Idoia Jiménez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | | | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
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Peraza-Reyes L, Berteaux-Lecellier V. Peroxisomes and sexual development in fungi. Front Physiol 2013; 4:244. [PMID: 24046747 PMCID: PMC3764329 DOI: 10.3389/fphys.2013.00244] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are versatile and dynamic organelles that are essential for the development of most eukaryotic organisms. In fungi, many developmental processes, such as sexual development, require the activity of peroxisomes. Sexual reproduction in fungi involves the formation of meiotic-derived sexual spores, often takes place inside multicellular fruiting bodies and requires precise coordination between the differentiation of multiple cell types and the progression of karyogamy and meiosis. Different peroxisomal functions contribute to the orchestration of this complex developmental process. Peroxisomes are required to sustain the formation of fruiting bodies and the maturation and germination of sexual spores. They facilitate the mobilization of reserve compounds via fatty acid β-oxidation and the glyoxylate cycle, allowing the generation of energy and biosynthetic precursors. Additionally, peroxisomes are implicated in the progression of meiotic development. During meiotic development in Podospora anserina, there is a precise modulation of peroxisome assembly and dynamics. This modulation includes changes in peroxisome size, number and localization, and involves a differential activity of the protein-machinery that drives the import of proteins into peroxisomes. Furthermore, karyogamy, entry into meiosis and sorting of meiotic-derived nuclei into sexual spores all require the activity of peroxisomes. These processes rely on different peroxisomal functions and likely depend on different pathways for peroxisome assembly. Indeed, emerging studies support the existence of distinct import channels for peroxisomal proteins that contribute to different developmental stages.
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Affiliation(s)
- Leonardo Peraza-Reyes
- CNRS, Institut de Génétique et Microbiologie, University Paris-Sud, UMR8621 Orsay, France
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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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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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Montanini B, Levati E, Bolchi A, Kohler A, Morin E, Tisserant E, Martin F, Ottonello S. Genome-wide search and functional identification of transcription factors in the mycorrhizal fungus Tuber melanosporum. THE NEW PHYTOLOGIST 2011; 189:736-750. [PMID: 21058951 DOI: 10.1111/j.1469-8137.2010.03525.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
• Developmental transitions associated with the life cycle of plant-symbiotic fungi, such as the ascomycete Tuber melanosporum, are likely to require an extensive reprogramming of gene expression brought about by transcription factors (TFs). To date, little is known about the transcriptome alterations that accompany developmental shifts associated with symbiosis or fruiting body formation. • Taking advantage of the black truffle genome sequence, we used a bioinformatic approach, coupled with functional analysis in yeast and transcriptome profiling, to identify and catalogue T. melanosporum TFs, the so-called 'regulome'. • The T. melanosporum regulome contains 102 homologs of previously characterized TFs, 57 homologs of hypothetical TFs, and 42 putative TFs apparently unique to Tuber. The yeast screen allowed the functional discovery of four TFs and the validation of about one-fifth of the in silico predicted TFs. Truffle proteins apparently unrelated to transcription were also identified as potential transcriptional regulators, together with a number of plant TFs. • Twenty-nine TFs, some of which associated with particular developmental stages, were found to be up-regulated in ECMs or fruiting bodies. About one-quarter of these up-regulated TFs are expressed at surprisingly high levels, thus pointing to a striking functional specialization of the different stages of the Tuber life cycle.
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Affiliation(s)
- Barbara Montanini
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
| | - Elisabetta Levati
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
| | - Angelo Bolchi
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
| | - Annegret Kohler
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Emmanuelle Morin
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Emilie Tisserant
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Francis Martin
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Simone Ottonello
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
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