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Amenaghawon AN, Ayere JE, Amune UO, Otuya IC, Abuga EC, Anyalewechi CL, Okoro OV, Okolie JA, Oyefolu PK, Eshiemogie SO, Osahon BE, Omede M, Eshiemogie SA, Igemhokhai S, Okedi MO, Kusuma HS, Muojama OE, Shavandi A, Darmokoesoemo H. A comprehensive review of recent advances in the applications and biosynthesis of oxalic acid from bio-derived substrates. ENVIRONMENTAL RESEARCH 2024; 251:118703. [PMID: 38518912 DOI: 10.1016/j.envres.2024.118703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/12/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024]
Abstract
Organic acids are important compounds with numerous applications in different industries. This work presents a comprehensive review of the biological synthesis of oxalic acid, an important organic acid with many industrial applications. Due to its important applications in pharmaceuticals, textiles, metal recovery, and chemical and metallurgical industries, the global demand for oxalic acid has increased. As a result, there is an increasing need to develop more environmentally friendly and economically attractive alternatives to chemical synthesis methods, which has led to an increased focus on microbial fermentation processes. This review discusses the specific strategies for microbial production of oxalic acid, focusing on the benefits of using bio-derived substrates to improve the economics of the process and promote a circular economy in comparison with chemical synthesis. This review provides a comprehensive analysis of the various fermentation methods, fermenting microorganisms, and the biochemistry of oxalic acid production. It also highlights key sustainability challenges and considerations related to oxalic acid biosynthesis, providing important direction for further research. By providing and critically analyzing the most recent information in the literature, this review serves as a comprehensive resource for understanding the biosynthesis of oxalic acid, addressing critical research gaps, and future advances in the field.
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Affiliation(s)
- Andrew Nosakhare Amenaghawon
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria.
| | - Joshua Efosa Ayere
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria
| | - Ubani Oluwaseun Amune
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Chemical Engineering, Faculty of Engineering, Edo State University, Uzairue, Edo State, Nigeria
| | - Ifechukwude Christopher Otuya
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Chemical Engineering, Faculty of Engineering, Delta State University of Science and Technology, Ozoro, Delta State, Nigeria
| | - Emmanuel Christopher Abuga
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria
| | - Chinedu Lewis Anyalewechi
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Chemical Engineering, Faculty of Engineering, Federal Polytechnic Oko, Anambra State, Nigeria
| | - Oseweuba Valentine Okoro
- BioMatter Unit - École polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50 - CP 165/61, 1050 Brussels, Belgium
| | - Jude A Okolie
- Engineering Pathways, Gallogly College of Engineering, University of Oklahoma, Norman, OK 73019, USA
| | - Peter Kayode Oyefolu
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Steve Oshiokhai Eshiemogie
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Blessing Esohe Osahon
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria
| | - Melissa Omede
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria
| | - Stanley Aimhanesi Eshiemogie
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria
| | - Shedrach Igemhokhai
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Petroleum Engineering, University of Benin, Benin City, Edo State, Nigeria
| | - Maxwell Ogaga Okedi
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University, Tallahassee, FL 2310-6046, USA
| | - Heri Septya Kusuma
- Department of Chemical Engineering, Faculty of Industrial Technology, Universitas Pembangunan Nasional "Veteran" Yogyakarta, Indonesia.
| | - Obiora Ebuka Muojama
- Bioresources Valorization Laboratory, Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin City, Edo State, Nigeria; Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, AL, 35487-0203, USA
| | - Amin Shavandi
- BioMatter Unit - École polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50 - CP 165/61, 1050 Brussels, Belgium
| | - Handoko Darmokoesoemo
- Department of Chemistry, Faculty of Science and Technology, Airlangga University, Mulyorejo, Surabaya 60115, Indonesia.
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Tang M, Wang Y, Wang K, Zhou Y, Zhao E, Zhang H, Zhang M, Yu H, Zhao X, Li G. Codon Optimization Enables the Geneticin Resistance Gene to Be Applied Efficiently to the Genetic Manipulation of the Plant Pathogenic Fungus Botrytis cinerea. PLANTS (BASEL, SWITZERLAND) 2024; 13:324. [PMID: 38276781 PMCID: PMC10821057 DOI: 10.3390/plants13020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Botrytis cinerea can infect almost all of the important horticultural crops and cause severe economic losses globally every year. Modifying candidate genes and studying the phenotypic changes are among the most effective ways to unravel the pathogenic mechanism of this crop killer. However, few effective positive selection markers are used for B. cinerea genetic transformation, which limits multiple modifications to the genome, especially genes involving redundant functions. Here, we optimized a geneticin resistance gene, BcNPTII, based on the codon usage preference of B. cinerea. We found that BcNPTII can greatly increase the transformation efficiency of B. cinerea under G418 selection, with approximately 30 times higher efficiency than that of NPTII, which is applied efficiently to transform Magnaporthe oryzae. Using the gene replacement method, we successfully knocked out the second gene BOT2, with BcNPTII as the selection marker, from the mutant ΔoahA, in which OAHA was first replaced by the hygromycin resistance gene HPH in a field strain. We obtained the double knockout mutant ΔoahA Δbot2. Our data show that the codon-optimized BcNPTII is an efficient positive selection marker for B. cinerea transformation and can be used for various genetic manipulations in B. cinerea, including field wild-type strains.
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Affiliation(s)
- Maoyao Tang
- College of Plant Sciences, Jilin University, Changchun 130062, China; (M.T.); (Y.W.); (K.W.); (M.Z.); (H.Y.); (X.Z.)
| | - Yangyizhou Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China; (M.T.); (Y.W.); (K.W.); (M.Z.); (H.Y.); (X.Z.)
| | - Kexin Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China; (M.T.); (Y.W.); (K.W.); (M.Z.); (H.Y.); (X.Z.)
| | - Yuanhang Zhou
- Research Management Department, Changchun Academy of Forestry, Changchun 130021, China;
| | - Enshuang Zhao
- College of Computer Science and Technology, Jilin University, Changchun 130012, China; (E.Z.); (H.Z.)
| | - Hao Zhang
- College of Computer Science and Technology, Jilin University, Changchun 130012, China; (E.Z.); (H.Z.)
| | - Mingzhe Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China; (M.T.); (Y.W.); (K.W.); (M.Z.); (H.Y.); (X.Z.)
| | - Hang Yu
- College of Plant Sciences, Jilin University, Changchun 130062, China; (M.T.); (Y.W.); (K.W.); (M.Z.); (H.Y.); (X.Z.)
| | - Xi Zhao
- College of Plant Sciences, Jilin University, Changchun 130062, China; (M.T.); (Y.W.); (K.W.); (M.Z.); (H.Y.); (X.Z.)
| | - Guihua Li
- College of Plant Sciences, Jilin University, Changchun 130062, China; (M.T.); (Y.W.); (K.W.); (M.Z.); (H.Y.); (X.Z.)
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Alruwaili A, Rashid GMM, Sodré V, Mason J, Rehman Z, Menakath AK, Cheung D, Brown SP, Bugg TDH. Elucidation of microbial lignin degradation pathways using synthetic isotope-labelled lignin. RSC Chem Biol 2023; 4:47-55. [PMID: 36685258 PMCID: PMC9811514 DOI: 10.1039/d2cb00173j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Pathways by which the biopolymer lignin is broken down by soil microbes could be used to engineer new biocatalytic routes from lignin to renewable chemicals, but are currently not fully understood. In order to probe these pathways, we have prepared synthetic lignins containing 13C at the sidechain β-carbon. Feeding of [β-13C]-labelled DHP lignin to Rhodococcus jostii RHA1 has led to the incorporation of 13C label into metabolites oxalic acid, 4-hydroxyphenylacetic acid, and 4-hydroxy-3-methoxyphenylacetic acid, confirming that they are derived from lignin breakdown. We have identified a glycolate oxidase enzyme in Rhodococcus jostii RHA1 which is able to oxidise glycolaldehyde via glycolic acid to oxalic acid, thereby identifying a pathway for the formation of oxalic acid. R. jostii glycolate oxidase also catalyses the conversion of 4-hydroxyphenylacetic acid to 4-hydroxybenzoylformic acid, identifying another possible pathway to 4-hydroxybenzoylformic acid. Formation of labelled oxalic acid was also observed from [β-13C]-polyferulic acid, which provides experimental evidence in favour of a radical mechanism for α,β-bond cleavage of β-aryl ether units.
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Affiliation(s)
- Awatif Alruwaili
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - Goran M. M. Rashid
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - Victoria Sodré
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - James Mason
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - Zainab Rehman
- Department of Physics, University of WarwickCoventryCV4 7ALUK
| | | | - David Cheung
- Department of Physics, University of WarwickCoventryCV4 7ALUK
| | - Steven P. Brown
- Department of Physics, University of WarwickCoventryCV4 7ALUK
| | - Timothy D. H. Bugg
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
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Qiu Z, Wang X, Wang S, Cai N, Huang J, Wang M, Shu L, Li T. Transcriptome Analysis Revealed the Mechanism of Inhibition of Saprophytic Growth of Sparassis latifolia by Excessive Oxalic Acid. Cells 2022; 11:cells11223636. [PMID: 36429064 PMCID: PMC9688073 DOI: 10.3390/cells11223636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Sparassis latifolia, a highly valued edible fungus, is a crucial medicinal and food resource owing to its rich active ingredients and pharmacological effects. Excessive oxalic acid secreted on a pine-sawdust-dominated substrate inhibits its mycelial growth, and severely restricts the wider development of its cultivation. However, the mechanism underlying the relationship between oxalic acid and slow mycelial growth remains unclear. The present study reported the transcriptome-based response of S. latifolia induced by different oxalic acid concentrations. In total, 9206 differentially expressed genes were identified through comparisons of three groups; 4587 genes were down-regulated and 5109 were up-regulated. Transcriptome analysis revealed that excessive oxalic acid mainly down-regulates the expression of genes related to carbohydrate utilization pathways, energy metabolism, amino acid metabolism, protein synthesis metabolism, glycan biosynthesis, and signal transduction pathways. Moreover, genes encoding for wood-degrading enzymes were predominantly down-regulated in the mycelia treated with excessive oxalic acid. Taken together, the study results provide a speculative mechanism underlying the inhibition of saprophytic growth by excessive oxalic acid and a foundation for further research on the growth of S. latifolia mycelia.
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Affiliation(s)
- Zhiheng Qiu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
| | - Xinyi Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
| | - Shuang Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
| | - Nuo Cai
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
| | - Jing Huang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
| | - Miaoyue Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
| | - Lili Shu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
- Correspondence: (L.S.); (T.L.); Tel.: +86-024-88487143 (L.S.)
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang 110866, China
- Correspondence: (L.S.); (T.L.); Tel.: +86-024-88487143 (L.S.)
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Santos-Carballal D, de Leeuw NH. Catalytic formation of oxalic acid on the partially oxidised greigite Fe 3S 4(001) surface. Phys Chem Chem Phys 2022; 24:20104-20124. [PMID: 35983830 DOI: 10.1039/d2cp00333c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Greigite (Fe3S4), with its ferredoxin-like 4Fe-4S redox centres, is a naturally occurring mineral capable of acting as a catalyst in the conversion of carbon dioxide (CO2) into low molecular-weight organic acids (LMWOAs), which are of paramount significance in several soil and plant processes as well as in the chemical industry. In this paper, we report the reaction between CO2 and water (H2O) to form oxalic acid (H2C2O4) on the partially oxidised greigite Fe3S4(001) surface by means of spin-polarised density functional theory calculations with on-site Coulomb corrections and long-range dispersion interactions (DFT+U-D2). We have calculated the bulk phase of Fe3S4 and the two reconstructed Tasker type 3 terminations of its (001) surface, whose properties are in good agreement with available experimental data. We have obtained the relevant phase diagram, showing that the Fe3S4(001) surface becomes 62.5% partially oxidised, by replacing S by O atoms, in the presence of water at the typical conditions of calcination [Mitchell et al. Faraday Discuss. 2021, 230, 30-51]. The adsorption and co-adsorption of the reactants on the partially oxidised Fe3S4(001) surface are exothermic processes. We have considered three mechanistic pathways to explain the formation of H2C2O4, showing that the coupling of the C-C bond and second protonation are the elementary steps with the largest energy penalty. Our calculations suggest that the partially oxidised Fe3S4(001) surface is a mineral phase that can catalyse the formation of H2C2O4 under favourable conditions, which has important implications for natural ecosystems and is a process that can be harnessed for the industrial manufacture of this organic acid.
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Affiliation(s)
| | - Nora H de Leeuw
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK. .,Department of Earth Sciences, Utrecht University, Princetonplein 8A, 3584 CD Utrecht, The Netherlands.
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Excessive Oxalic Acid Secreted by Sparassis latifolia Inhibits the Growth of Mycelia during Its Saprophytic Process. Cells 2022; 11:cells11152423. [PMID: 35954267 PMCID: PMC9368360 DOI: 10.3390/cells11152423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Sparassis latifolia is an edible and medicinal mushroom in Asia commercially cultivated on substrates containing pine sawdust. Its slow mycelial growth rate greatly increases the cultivation cycle. In this study, we mainly studied the role of oxalic acid (OA) secreted by S. latifolia in its saprophytic process. Our results show that crystals observed on the mycelial surface contained calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD) according to X-ray diffraction (XRD). Vegetative mycelia secreted large amounts of OA during extended culture periods. However, high concentrations of OA decreased the mycelial growth rate significantly. Moreover, the degradation of lignocellulose was significantly inhibited under high concentrations of OA. These changes could be attributed to the significantly decreased activities of lignocellulose-degrading enzymes. In conclusion, by establishing a link between OA secretion by the mycelium and the slow growth rate of its saprophytic process, this work provides fundamental information for shortening the cultivation cycle of S. latifolia.
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Chen H, He S, Zhang S, A R, Li W, Liu S. The Necrotroph Botrytis cinerea BcSpd1 Plays a Key Role in Modulating Both Fungal Pathogenic Factors and Plant Disease Development. FRONTIERS IN PLANT SCIENCE 2022; 13:820767. [PMID: 35845699 PMCID: PMC9280406 DOI: 10.3389/fpls.2022.820767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Botrytis cinerea is a necrotrophic microbe that causes gray mold disease in a broad range of hosts. In the present study, we conducted molecular microbiology and transcriptomic analyses of the host-B. cinerea interaction to investigate the plant defense response and fungal pathogenicity. Upon B. cinerea infection, plant defense responses changed from activation to repression; thus, the expression of many defense genes decreased in Arabidopsis thaliana. B. cinerea Zn(II)2Cys6 transcription factor BcSpd1 was involved in the suppression of plant defense as ΔBcSpd1 altered wild-type B05.10 virulence by recovering part of the defense responses at the early infection stage. BcSpd1 affected genes involved in the fungal sclerotium development, infection cushion formation, biosynthesis of melanin, and change in environmental pH values, which were reported to influence fungal virulence. Specifically, BcSpd1 bound to the promoter of the gene encoding quercetin dioxygenase (BcQdo) and positively affected the gene expression, which was involved in catalyzing antifungal flavonoid degradation. This study indicates BcSpd1 plays a key role in the necrotrophic microbe B. cinerea virulence toward plants by regulating pathogenicity-related compounds and thereby suppressing early plant defense.
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Affiliation(s)
| | | | | | | | | | - Shouan Liu
- Laboratory of Molecular Plant Pathology, Jilin University, Changchun, China
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Wu X, Lyu Y, Ren H, Zhou F, Zhang X, Zhao X, Zhang G, Yang H. Degradation of oxalic acid by Trichoderma afroharzianum and its correlation with cell wall degrading enzymes in antagonising Botrytis cinerea. J Appl Microbiol 2022; 133:2680-2693. [PMID: 35543356 DOI: 10.1111/jam.15617] [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: 03/25/2022] [Revised: 04/30/2022] [Accepted: 05/07/2022] [Indexed: 11/27/2022]
Abstract
AIM Oxalic acid (OA) is one of the pathogenic factors of Botrytis cinerea. Trichoderma afroharzianum exerts both antagonistic and oxalate-degrading effects on B. cinerea. This study aimed to investigate the relationship between the elimination of OA by T. afroharzianum and its antagonistic effects on B. cinerea. METHODS AND RESULTS Reversed-phase high performance liquid chromatogram (RP-HPLC) analysis showed that T. afroharzianum LTR-2 eliminated 10- or 20-mmol/L OA within 120 h, with the degradation being particularly efficient at the concentration of 20 mmol/L. RNA-seq analysis showed that the oxalate decarboxylase (OXDC) gene Toxdc, β-1,3-exoglucanase gene Tglu, and aspartic protease gene Tpro of LTR-2 were significantly upregulated after treatment with 20-mmol/L OA. RT-qPCR analysis showed that under the conditions of confrontation, Toxdc and three cell wall degrading enzyme (CWDE) genes were upregulated before physical contact with B. cinerea. In addition, RT-qPCR analysis showed that OA synthesis in B. cinerea was not significantly affected by LTR-2. CONCLUSIONS The results revealed a correlation between OA degradation and mycoparasitism in T. afroharzianum when antagonizing B. cinerea at transcriptional level. SIGNIFICANCE AND IMPACT OF THE STUDY The relationship between OA degradation by T. afroharzianum and its effects against B. cinerea provide a new perspective on the antagonism of T. afroharzianum against B. cinerea. In addition, this study provides theoretical data for the scientific application of T. afroharzianum in the field of biocontrol.
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Affiliation(s)
- Xiaoqing Wu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
| | - Yuping Lyu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - He Ren
- Shandong New Times Pharmaceutical Co., Ltd., Linyi 273400, China
| | - Fangyuan Zhou
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
| | - Xinjian Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
| | - Xiaoyan Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
| | - Guangzhi Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
| | - Hetong Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, China
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Jiao W, Liu X, Li Y, Li B, Du Y, Zhang Z, Chen Q, Fu M. Organic acid, a virulence factor for pathogenic fungi, causing postharvest decay in fruits. MOLECULAR PLANT PATHOLOGY 2022; 23:304-312. [PMID: 34820999 PMCID: PMC8743014 DOI: 10.1111/mpp.13159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Decay due to fungal infection is a major cause of postharvest losses in fruits. Acidic fungi may enhance their virulence by locally reducing the pH of the host. Several devastating postharvest fungi, such as Penicillium spp., Botrytis cinerea, and Sclerotinia sclerotiorum, can secrete gluconic acid, oxalic acid, or citric acid. Emerging evidence suggests that organic acids secreted by acidic fungi are important virulence factors. In this review, we summarized the research progress on the biosynthesis of organic acids, the role of the pH signalling transcription factor PacC in regulating organic acid, and the action mechanism of the main organic acid secreted via postharvest pathogenic fungi during infection of host tissues. This paper systematically demonstrates the relationships between tissue acidification and postharvest fungal pathogenicity, which will motivate the study of host-pathogen interactions and provide a better understanding of virulence mechanisms of the pathogens so as to design new technical strategies to prevent postharvest diseases.
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Affiliation(s)
- Wenxiao Jiao
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Xin Liu
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Youyuan Li
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Boqiang Li
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Yamin Du
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Zhanquan Zhang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Qingmin Chen
- College of Food Science and EngineeringShandong Agricultural and Engineering UniversityJinanChina
| | - Maorun Fu
- College of Food Science and EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
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Rana K, Yuan J, Liao H, Banga SS, Kumar R, Ding Y, Qian W. Host-induced gene silencing reveals the role of Sclerotinia sclerotiorum oxaloacetate acetylhydrolase gene in fungal oxalic acid accumulation and virulence. Microbiol Res 2022; 258:126981. [DOI: 10.1016/j.micres.2022.126981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/13/2021] [Accepted: 02/08/2022] [Indexed: 02/01/2023]
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Abstract
Whole-cell immobilization by entrapment in natural polymers can be a tool for morphological control and facilitate biomass retention. In this study, the possibility of immobilizing the filamentous fungus Aspergillus oryzae for l-malic acid production was evaluated with the two carbon sources acetate and glucose. A. oryzae conidia were entrapped in alginate, agar, and κ-carrageenan and production was monitored in batch processes in shake flasks and 2.5-L bioreactors. With glucose, the malic acid concentration after 144 h of cultivation using immobilized particles was mostly similar to the control with free biomass. In acetate medium, production with immobilized conidia of A. oryzae in shake flasks was delayed and titers were generally lower compared to cultures with free mycelium. While all immobilization matrices were stable in glucose medium, disintegration of bead material and biomass detachment in acetate medium was observed in later stages of the fermentation. Still, immobilization proved advantageous in bioreactor cultivations with acetate and resulted in increased malic acid titers. This study is the first to evaluate immobilization of A. oryzae for malic acid production and describes the potential but also challenges regarding the application of different matrices in glucose and acetate media.
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Zhao JJ, Zhang YF, Zhao TL, Li H, Yao QZ, Fu SQ, Zhou GT. Abiotic Formation of Calcium Oxalate under UV Irradiation and Implications for Biomarker Detection on Mars. ASTROBIOLOGY 2022; 22:35-48. [PMID: 35020413 DOI: 10.1089/ast.2020.2416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A major objective in the exploration of Mars is to test the hypothesis that the planet has ever hosted life. Biogenic compounds, especially biominerals, are believed to serve as biomarkers in Raman-assisted remote sensing missions. However, the prerequisite for the development of these minerals as biomarkers is the uniqueness of their biogenesis. Herein, tetragonal bipyramidal weddellite, a type of calcium oxalate, is successfully achieved by UV-photolyzing pyruvic acid (PA). The as-prepared products are identified and characterized by micro-Raman spectroscopy and field emission scanning electron microscopy. Persistent mineralization of weddellite is observed with altering key experimental parameters, including pH, Ca2+ and PA concentrations. In particular, the initial concentration of PA can significantly influence the morphology of weddellite crystal. Oxalate acid is commonly of biological origin; thus calcium oxalate is considered to be a biomarker. However, our results reveal that calcium oxalate can be harvested by a UV photolysis pathway. Moreover, prebiotic sources of organics (e.g., PA, glycine, alanine, and aspartic acid) have been proven to be available through abiotic pathways. Therefore, our results may provide a new abiotic pathway of calcium oxalate formation. Considering that calcium oxalate minerals have been taken as biosignatures for the origin and early evolution of life on Earth and astrobiological investigations, its formation and accumulation by the photolysis of abiological organic compounds should be taken into account.
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Affiliation(s)
- Jia-Jian Zhao
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, P.R. China
| | - Yi-Fan Zhang
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, P.R. China
| | - Tian-Lei Zhao
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, P.R. China
| | - Han Li
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, P.R. China
| | - Qi-Zhi Yao
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, P.R. China
| | - Sheng-Quan Fu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, P.R. China
| | - Gen-Tao Zhou
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, P.R. China
- CAS Center for Excellence in Comparative Planetology, University of Science and Technology of China, Hefei, P.R. China
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13
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Cui K, He L, Zhao Y, Mu W, Lin J, Liu F. Comparative Analysis of Botrytis cinerea in Response to the Microbial Secondary Metabolite Benzothiazole Using iTRAQ-Based Quantitative Proteomics. PHYTOPATHOLOGY 2021; 111:1313-1326. [PMID: 33325724 DOI: 10.1094/phyto-11-20-0503-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Benzothiazole is a microbial volatile compound with strong antifungal activity against the phytopathogenic fungus Botrytis cinerea, but its mode of action against fungi remains largely unknown. Understanding the molecular mechanisms underlying its activity could aid the design and synthesis of similar compounds against pathogenic fungi. Based on the results of morphological and antifungal activity assays, B. cinerea was exposed to 2.5 µl/liter of benzothiazole for 12, 24, and 48 h, and an isobaric tags for relative and absolute quantitation-based quantitative proteomic analysis showed that 378 out of 5,110 identified proteins were differentially expressed proteins (DEPs). The majority of these DEPs were associated with carbohydrate metabolism, oxidation reduction processes, and energy production. Further analysis showed that benzothiazole inhibited mitochondrial membrane organization and decreased the mitochondrial membrane potential of B. cinerea. In addition, the key enzymes of the glyoxylate cycle were downregulated after benzothiazole treatment, and a biochemical analysis indicated that inhibition of the glyoxylate cycle by benzothiazole blocked nutrient availability and interfered with adenosine triphosphate generation. This study provides markers for future research of the molecular responses of B. cinerea to benzothiazole stress.
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Affiliation(s)
- Kaidi Cui
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
| | - Leiming He
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, People's Republic of China
| | - Yunhe Zhao
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
| | - Wei Mu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
| | - Jin Lin
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
| | - Feng Liu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
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Wang CY, Lou XY, Cai Z, Zhang MZ, Jia C, Qin JC, Yang YW. Supramolecular Nanoplatform Based on Mesoporous Silica Nanocarriers and Pillararene Nanogates for Fungus Control. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32295-32306. [PMID: 34196538 DOI: 10.1021/acsami.1c08582] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Synthetic fungicides have been widely used to protect crops from fungal diseases. However, excessive use of synthetic fungicides leads to the generation of fungicide resistance in fungal pathogens. Recently, smart cargo delivery systems have been introduced for the construction of a pesticide delivery nanoplatform, benefiting from their controlled release performance. Herein, a fungal pathogen microenvironment-responsive supramolecular fungicide nanoplatform has been designed and constructed, using quaternary ammonium salt (Q)-modified mesoporous silica nanoparticles (MSN-Q NPs) as nanocarriers loaded with berberine hydrochloride (BH) and carboxylatopillar[5]arene (CP[5]A) as nanogates to form BH-loaded CP[5]A@MSN-Q NPs for effective inhibition of Botrytis cinerea. CP[5]A as nanogates can endow the fungicide nanoplatform with pH stimuli-responsive release features for the control of fungicide release. The loaded BH, as a natural plant fungicide, provides an ecofriendly alternative to synthetic fungicides for controlling B. cinerea. Interestingly, we use oxalic acid (OA) secreted by B. cinerea as a trigger so that BH can be released from the fungicide nanoplatform on demand under pathogen microenvironments for controlling B. cinerea. The experimental results indicate that the fabricated fungicide nanoplatform could effectively inhibit the mycelial growth and spore germination, providing a new way for the management of B. cinerea in actual application.
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Affiliation(s)
- Chao-Yi Wang
- College of Chemistry and College of Plant Science, Jilin University, Changchun 130012, P. R. China
| | - Xin-Yue Lou
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Zhi Cai
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ming-Zhe Zhang
- College of Plant Science, Jilin University, Changchun 130012, P. R. China
| | - Chengguo Jia
- College of Plant Science, Jilin University, Changchun 130012, P. R. China
| | - Jian-Chun Qin
- College of Plant Science, Jilin University, Changchun 130012, P. R. China
| | - Ying-Wei Yang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
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15
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Laothanachareon T, Bruinsma L, Nijsse B, Schonewille T, Suarez-Diez M, Tamayo-Ramos JA, Martins dos Santos VAP, Schaap PJ. Global Transcriptional Response of Aspergillus niger to Blocked Active Citrate Export through Deletion of the Exporter Gene. J Fungi (Basel) 2021; 7:jof7060409. [PMID: 34071072 PMCID: PMC8224569 DOI: 10.3390/jof7060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus niger is the major industrial citrate producer worldwide. Export as well as uptake of citric acid are believed to occur by active, proton-dependent, symport systems. Both are major bottlenecks for industrial citrate production. Therefore, we assessed the consequences of deleting the citT gene encoding the A. niger citrate exporter, effectively blocking active citrate export. We followed the consumption of glucose and citrate as carbon sources, monitored the secretion of organic acids and carried out a thorough transcriptome pathway enrichment analysis. Under controlled cultivation conditions that normally promote citrate secretion, the knock-out strain secreted negligible amounts of citrate. Blocking active citrate export in this way led to a reduced glucose uptake and a reduced expression of high-affinity glucose transporter genes, mstG and mstH. The glyoxylate shunt was strongly activated and an increased expression of the OAH gene was observed, resulting in a more than two-fold higher concentration of oxalate in the medium. Deletion of citT did not affect citrate uptake suggesting that citrate export and citrate uptake are uncoupled from the system.
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Affiliation(s)
- Thanaporn Laothanachareon
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani 12120, Thailand
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Tom Schonewille
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Juan Antonio Tamayo-Ramos
- International Research Center in Critical Raw Materials-ICCRAM, University of Burgos, 09001 Burgos, Spain;
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- LifeGlimmer GmbH, 12163 Berlin, Germany
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
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16
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Lv Z, He Z, Hao L, Kang X, Ma B, Li H, Luo Y, Yuan J, He N. Genome Sequencing Analysis of Scleromitrula shiraiana, a Causal Agent of Mulberry Sclerotial Disease With Narrow Host Range. Front Microbiol 2021; 11:603927. [PMID: 33519746 PMCID: PMC7840784 DOI: 10.3389/fmicb.2020.603927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Scleromitrula shiraiana is a necrotrophic fungus with a narrow host range, and is one of the main causal pathogens of mulberry sclerotial disease. However, its molecular mechanisms and pathogenesis are unclear. Here, we report a 39.0 Mb high-quality genome sequence for S. shiraiana strain SX-001. The S. shiraiana genome contains 11,327 protein-coding genes. The number of genes and genome size of S. shiraiana are similar to most other Ascomycetes. The cross-similarities and differences of S. shiraiana with the closely related Sclerotinia sclerotiorum and Botrytis cinerea indicated that S. shiraiana differentiated earlier from their common ancestor. A comparative genomic analysis showed that S. shiraiana has fewer genes encoding cell wall-degrading enzymes (CWDEs) and effector proteins than that of S. sclerotiorum and B. cinerea, as well as many other Ascomycetes. This is probably a key factor in the weaker aggressiveness of S. shiraiana to other plants. S. shiraiana has many species-specific genes encoding secondary metabolism core enzymes. The diversity of secondary metabolites may be related to the adaptation of these pathogens to specific ecological niches. However, melanin and oxalic acid are conserved metabolites among many Sclerotiniaceae fungi, and may be essential for survival and infection. Our results provide insights into the narrow host range of S. shiraiana and its adaptation to mulberries.
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Affiliation(s)
- Zhiyuan Lv
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ziwen He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Lijuan Hao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xin Kang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Hongshun Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yiwei Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Jianglian Yuan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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17
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Chroumpi T, Mäkelä MR, de Vries RP. Engineering of primary carbon metabolism in filamentous fungi. Biotechnol Adv 2020; 43:107551. [DOI: 10.1016/j.biotechadv.2020.107551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
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18
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Recovering Secondary REE Value from Spent Oil Refinery Catalysts Using Biogenic Organic Acids. Catalysts 2020. [DOI: 10.3390/catal10091090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Spent catalysts produced by oil refinery industries are regarded as an important secondary source for valuable metals. In particular, spent fluid catalytic cracking (FCC) catalysts represent a potential source for rare earth elements (REEs). This study aimed to exploit the leachability of spent FCC catalysts as a secondary source for La, by using an alternative organic acid lixiviant produced under optimized fungal fermentation conditions. The first chemical leaching tests revealed that citric acid (>100 mM) is a comparable alternative lixiviant to conventional inorganic acids (1 M) and that the La dissolution behavior changed significantly with different types of organic acids. The initial fungal fermentation conditions (e.g., inoculum level, substrate concentration, pH) largely affected the resultant biogenic acid composition, and its manipulation was possible in order to almost solely ferment citric acid (~130 mM) while controlling the production of unwanted oxalic acid. The performance of actual biogenic acids (direct use of cell-free spent media) and artificially reconstituted biogenic acids (a mixture of chemical reagents) was nearly identical, achieving a final La dissolution of ~74% at a pulp density of 5%. Overall, the microbiological fermentation of organic acids could become a promising approach to supply an efficient and environmentally benign alternative lixiviant for REE scavenging from spent FCC catalyst wastes.
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Wang Y, Wang Y. Oxalic Acid Metabolism Contributes to Full Virulence and Pycnidial Development in the Poplar Canker Fungus Cytospora chrysosperma. PHYTOPATHOLOGY 2020; 110:1319-1325. [PMID: 32154765 DOI: 10.1094/phyto-10-19-0381-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Poplar Cytospora canker, which is mainly caused by Cytospora chrysosperma, is one of the most destructive and widespread tree diseases worldwide. Although oxalic acid (OA) is demonstrated as an important virulence determinant in several necrotrophic fungi, specific functions of OA during pathogenesis remain controversial. Here, we identified three genes (CcOah, CcOdc1, and CcOdc2) directly involved in OA biosynthesis and catabolism in C. chrysosperma. We demonstrated that CcOah is required for OA biogenesis. All three genes were found to be highly upregulated during early infection stages of the poplar stem. The deletion of any of the three genes led to an obvious reduction of pycnidial production but no abnormality of hyphal growth and morphology. Furthermore, the individual deletion strain exhibited significantly limited lesion sizes on poplar twigs and leaves. Exogenous application of OA or citric acid can complement the virulence defects of ΔCcOah and ΔCcOdc1 strains. We further found that the ΔCcOah strain strongly promoted reactive oxygen species burst of poplar leaves during infection. Finally, induced secretion of OA was observed by monitoring color change of the plates after poplar stem extracts were added in the cultures; however, we failed to quantify OA concentration by high-performance liquid chromatography. Taken together, the present results provide insights into the function of OA acting as an important virulence factor of C. chrysosperma.
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Affiliation(s)
- Yuanyuan Wang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Yonglin Wang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
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20
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Singh NK, Paz E, Kutsher Y, Reuveni M, Lers A. Tomato T2 ribonuclease LE is involved in the response to pathogens. MOLECULAR PLANT PATHOLOGY 2020; 21:895-906. [PMID: 32352631 PMCID: PMC7280031 DOI: 10.1111/mpp.12928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/05/2020] [Accepted: 02/15/2020] [Indexed: 05/16/2023]
Abstract
T2 ribonucleases (RNases) are RNA-degrading enzymes that function in various cellular processes, mostly via RNA metabolism. T2 RNase-encoding genes have been identified in various organisms, from bacteria to mammals, and are most diverse in plants. The existence of T2 RNase genes in almost every organism suggests an important biological function that has been conserved through evolution. In plants, T2 RNases are suggested to be involved in phosphate scavenging and recycling, and are implicated in defence responses to pathogens. We investigated the function of the tomato T2 RNase LE, known to be induced by phosphate deficiency and wounding. The possible involvement of LE in pathogen responses was examined. Expression analysis showed LE induction during fungal infection and by stimuli known to be associated with pathogen inoculation, including oxalic acid and hydrogen peroxide. Analysis of LE-suppressed transgenic tomato lines revealed higher susceptibility to oxalic acid, a cell death-inducing factor, compared to the wild type. This elevated sensitivity of LE-suppressed lines was evidenced by visual signs of necrosis, and increased ion leakage and reactive oxygen species levels, indicating acceleration of cell death. Challenge of the LE-suppressed lines with the necrotrophic pathogen Botrytis cinerea resulted in accelerated development of disease symptoms compared to the wild type, associated with suppressed expression of pathogenesis-related marker genes. The results suggest a role for plant endogenous T2 RNases in antifungal activity.
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Affiliation(s)
- Naveen Kumar Singh
- Department of Postharvest Science, Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
| | - Einat Paz
- Department of Postharvest Science, Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
- The Robert H. Smith Faculty of Agricultural, Food and Environment SciencesHebrew University of JerusalemRehovotIsrael
| | - Yaarit Kutsher
- Plant Science Institute, the Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
| | - Moshe Reuveni
- Plant Science Institute, the Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
| | - Amnon Lers
- Department of Postharvest Science, Volcani CenterAgricultural Research OrganizationRishon LeZionIsrael
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21
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Zhang M, Sun C, Liu Y, Feng H, Chang H, Cao S, Li G, Yang S, Hou J, Zhu‐Salzman K, Zhang H, Qin Q. Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection-related development and host penetration. MOLECULAR PLANT PATHOLOGY 2020; 21:834-853. [PMID: 32301267 PMCID: PMC7214349 DOI: 10.1111/mpp.12934] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/04/2019] [Accepted: 02/19/2020] [Indexed: 05/28/2023]
Abstract
Simultaneous transcriptome analyses of both host plants and pathogens, and functional validation of the identified differentially expressed genes (DEGs) allow us to better understand the mechanisms underlying their interactions. Here, we analyse the mixed transcriptome derived from Botrytis cinerea (the causal agent of grey mould) infected tomato leaves at 24 hr after inoculation, a critical time point at which the pathogen has penetrated and developed in the leaf epidermis, whereas necrotic symptoms have not yet appeared. Our analyses identified a complex network of genes involved in the tomato-B. cinerea interaction. The expression of fungal transcripts encoding candidate effectors, enzymes for secondary metabolite biosynthesis, hormone and reactive oxygen species (ROS) production, and autophagy-related proteins was up-regulated, suggesting that these genes may be involved in the initial infection processes. Specifically, tomato genes involved in phytoalexin production, stress responses, ATP-binding cassette transporters, pathogenesis-related proteins, and WRKY DNA-binding transcription factors were up-regulated. We functionally investigated several B. cinerea DEGs via gene replacement and pathogenicity assays, and demonstrated that BcCGF1 was a novel virulence-associated factor that mediates fungal development and virulence via regulation of conidial germination, conidiation, infection structure formation, host penetration, and stress adaptation. The fungal infection-related development was controlled by BcCGF-mediated ROS production and exogenous cAMP restored the mutant infection-related development. Our findings provide new insights into the elucidation of the simultaneous tactics of pathogen attack and host defence. Our systematic elucidation of BcCGF1 in mediating fungal pathogenesis may open up new targets for fungal disease control.
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Affiliation(s)
- Ming‐Zhe Zhang
- College of Plant SciencesKey Laboratory of Zoonosis ResearchMinistry of EducationJilin UniversityChangchun, JilinChina
| | - Chen‐Hao Sun
- College of Plant SciencesJilin UniversityChangchun, JilinChina
| | - Yue Liu
- College of Plant SciencesKey Laboratory of Zoonosis ResearchMinistry of EducationJilin UniversityChangchun, JilinChina
| | - Hui‐Qiang Feng
- College of Plant SciencesKey Laboratory of Zoonosis ResearchMinistry of EducationJilin UniversityChangchun, JilinChina
| | - Hao‐Wu Chang
- College of Computer Science, Technology, Symbol Computation and Knowledge EngineeringMinistry of EducationJilin UniversityChangchun, JilinChina
| | - Sheng‐Nan Cao
- College of Plant SciencesJilin UniversityChangchun, JilinChina
| | - Gui‐Hua Li
- College of Plant SciencesJilin UniversityChangchun, JilinChina
| | - Song Yang
- College of Plant SciencesJilin UniversityChangchun, JilinChina
| | - Jie Hou
- College of Plant SciencesJilin UniversityChangchun, JilinChina
- College of ForestryBeiHua UniversityJinlinChina
| | - Keyan Zhu‐Salzman
- Department of EntomologyNorman Borlaug CenterTexas A&M UniversityCollege StationTXUSA
| | - Hao Zhang
- College of Computer Science, Technology, Symbol Computation and Knowledge EngineeringMinistry of EducationJilin UniversityChangchun, JilinChina
| | - Qing‐Ming Qin
- College of Plant SciencesKey Laboratory of Zoonosis ResearchMinistry of EducationJilin UniversityChangchun, JilinChina
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22
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Petrasch S, Silva CJ, Mesquida-Pesci SD, Gallegos K, van den Abeele C, Papin V, Fernandez-Acero FJ, Knapp SJ, Blanco-Ulate B. Infection Strategies Deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a Function of Tomato Fruit Ripening Stage. FRONTIERS IN PLANT SCIENCE 2019; 10:223. [PMID: 30881367 PMCID: PMC6405687 DOI: 10.3389/fpls.2019.00223] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 02/08/2019] [Indexed: 05/12/2023]
Abstract
Worldwide, 20-25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply chain due to rotting by fungal pathogens. Most postharvest pathogens exhibit necrotrophic or saprotrophic lifestyles, resulting in decomposition of the host tissues and loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit or remain quiescent until host conditions stimulate a successful infection. Previous research on infections of fruit has mainly been focused on the host's genetic and physicochemical factors that inhibit or promote disease. Here, we investigated if fruit pathogens can modify their own infection strategies in response to the ripening stage of the host. To test this hypothesis, we profiled global gene expression of three fungal pathogens that display necrotrophic behavior-Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer-during interactions with unripe and ripe tomato fruit. We assembled and functionally annotated the transcriptomes of F. acuminatum and R. stolonifer as no genomic resources were available. Then, we conducted differential gene expression analysis to compare each pathogen during inoculations versus in vitro conditions. Through characterizing patterns of overrepresented pathogenicity and virulence functions (e.g., phytotoxin production, cell wall degradation, and proteolysis) among the differentially expressed genes, we were able to determine shared strategies among the three fungi during infections of compatible (ripe) and incompatible (unripe) fruit tissues. Though each pathogen's strategy differed in the details, interactions with unripe fruit were commonly characterized by an emphasis on the degradation of cell wall components, particularly pectin, while colonization of ripe fruit featured more heavily redox processes, proteolysis, metabolism of simple sugars, and chitin biosynthesis. Furthermore, we determined that the three fungi were unable to infect fruit from the non-ripening (nor) tomato mutant, confirming that to cause disease, these pathogens require the host tissues to undergo specific ripening processes. By enabling a better understanding of fungal necrotrophic infection strategies, we move closer to generating accurate models of fruit diseases and the development of early detection tools and effective management strategies.
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Affiliation(s)
- Stefan Petrasch
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Christian J. Silva
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Saskia D. Mesquida-Pesci
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Karina Gallegos
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Casper van den Abeele
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Victor Papin
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Ecole Nationale Supérieure Agronomique de Toulouse, Toulouse, France
| | - Francisco J. Fernandez-Acero
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Microbiology Laboratory, Institute of Viticulture and Agri-Food Research, Marine and Environmental Sciences Faculty, University of Cádiz, Cádiz, Spain
| | - Steven J. Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Barbara Blanco-Ulate
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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23
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Palmieri F, Estoppey A, House GL, Lohberger A, Bindschedler S, Chain PSG, Junier P. Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions. ADVANCES IN APPLIED MICROBIOLOGY 2018; 106:49-77. [PMID: 30798804 DOI: 10.1016/bs.aambs.2018.10.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oxalic acid is the most ubiquitous and common low molecular weight organic acid produced by living organisms. Oxalic acid is produced by fungi, bacteria, plants, and animals. The aim of this review is to give an overview of current knowledge about the microbial cycling of oxalic acid through ecosystems. Here we review the production and degradation of oxalic acid, as well as its implications in the metabolism for fungi, bacteria, plants, and animals. Indeed, fungi are well known producers of oxalic acid, while bacteria are considered oxalic acid consumers. However, this framework may need to be modified, because the ability of fungi to degrade oxalic acid and the ability of bacteria to produce it, have been poorly investigated. Finally, we will highlight the role of fungi and bacteria in oxalic acid cycling in soil, plant and animal ecosystems.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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24
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Liang X, Rollins JA. Mechanisms of Broad Host Range Necrotrophic Pathogenesis in Sclerotinia sclerotiorum. PHYTOPATHOLOGY 2018; 108:1128-1140. [PMID: 30048598 DOI: 10.1094/phyto-06-18-0197-rvw] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Among necrotrophic fungi, Sclerotinia sclerotiorum is remarkable for its extremely broad host range and for its aggressive host tissue colonization. With full genome sequencing, transcriptomic analyses and the increasing pace of functional gene characterization, the factors underlying the basis of this broad host range necrotrophic pathogenesis are now being elucidated at a greater pace. Among these, genes have been characterized that are required for infection via compound appressoria in addition to genes associated with colonization that regulate oxalic acid (OA) production and OA catabolism. Moreover, virulence-related secretory proteins have been identified, among which are candidates for manipulating host activities apoplastically and cytoplasmically. Coupled with these mechanistic studies, cytological observations of the colonization process have blurred the heretofore clear-cut biotroph versus necrotroph boundary. In this review, we reexamine the cytology of S. sclerotiorum infection and put more recent molecular and genomic data into the context of this cytology. We propose a two-phase infection model in which the pathogen first evades, counteracts and subverts host basal defense reactions prior to killing and degrading host cells. Spatially, the pathogen may achieve this via the production of compatibility factors/effectors in compound appressoria, bulbous subcuticular hyphae, and primary invasive hyphae. By examining the nuances of this interaction, we hope to illuminate new classes of factors as targets to improve our understanding of broad host range necrotrophic pathogens and provide the basis for understanding corresponding host resistance.
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Affiliation(s)
- Xiaofei Liang
- First author: State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University; and second author: Department of Plant Pathology, University of Florida, P.O. Box 110680, Gainesville 32611-0680
| | - Jeffrey A Rollins
- First author: State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University; and second author: Department of Plant Pathology, University of Florida, P.O. Box 110680, Gainesville 32611-0680
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25
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Yin Y, Wu S, Chui C, Ma T, Jiang H, Hahn M, Ma Z. The MAPK kinase BcMkk1 suppresses oxalic acid biosynthesis via impeding phosphorylation of BcRim15 by BcSch9 in Botrytis cinerea. PLoS Pathog 2018; 14:e1007285. [PMID: 30212570 PMCID: PMC6136818 DOI: 10.1371/journal.ppat.1007285] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) cassette of the cell wall integrity (CWI) pathway is primarily responsible for orchestrating changes of cell wall. However, functions of this cassette in other cellular processes are not well understood. Here, we found that the Botrytis cinerea mutant of MAPK kinase (BcMkk1) displays more serious defects in mycelial growth, conidiation, responses to cell wall and oxidative stresses, but possesses less reduced virulence than the mutants of its upstream (BcBck1) and downstream (BcBmp3) kinases. Interestingly, BcMkk1, but not BcBck1 and BcBmp3, negatively regulates production of oxalic acid (OA) and activity of extracellular hydrolases (EHs) that are proposed to be virulence factors of B. cinerea. Moreover, we obtained evidence that BcMkk1 negatively controls OA production via impeding phosphorylation of the Per-Arnt-Sim (PAS) kinase BcRim15 by the Ser/Thr kinase BcSch9. In addition, the fungal Pro40 homolog BcPro40 was found to interact simultaneously with three MAPKs, implying that BcPro40 is a scaffold protein of the CWI pathway in B. cinerea. Taken together, results of this study reveal that BcMkk1 negatively modulates virulence via suppressing OA biosynthesis in B. cinerea, which provides novel insight into conserved and species-specific functions of the MAPK kinase in fungi. Botrytis cinerea causes pre- and postharvest diseases in more than 200 economically important crops. In this study, the roles of cell wall integrity (CWI)-related MAPK kinase BcMkk1in regulating B. cinerea virulence were investigated using genetic and biochemical approaches. We found that the MAPK kinase BcMkk1 positively regulates virulence via the CWI pathway. Unexpectedly, BcMkk1 also negatively regulates fungal virulence via restraining oxalic acid production, by impeding phosphorylation of the PAS kinase BcRim15 mediated by the kinase BcSch9. To our knowledge, this is the first report that a MAPK kinase can negatively modulate fungal virulence on host plants. Our results provide novel insight into biological functions of a MAPK kinase in fungal pathogenesis.
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Affiliation(s)
- Yanni Yin
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Sisi Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chaonan Chui
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Tianling Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huixian Jiang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Matthias Hahn
- Department of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- * E-mail:
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Müller N, Leroch M, Schumacher J, Zimmer D, Könnel A, Klug K, Leisen T, Scheuring D, Sommer F, Mühlhaus T, Schroda M, Hahn M. Investigations on VELVET regulatory mutants confirm the role of host tissue acidification and secretion of proteins in the pathogenesis of Botrytis cinerea. THE NEW PHYTOLOGIST 2018; 219:1062-1074. [PMID: 29790574 DOI: 10.1111/nph.15221] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/11/2018] [Indexed: 05/03/2023]
Abstract
The Botrytis cinerea VELVET complex regulates light-dependent development and virulence. The goal of this study was to identify common virulence defects of several VELVET mutants and to reveal their molecular basis. Growth, differentiation, physiology, gene expression and infection of fungal strains were analyzed, and quantitative comparisons of in planta transcriptomes and secretomes were performed. VELVET mutants showed reduced release of citric acid, the major acid secreted by the wild-type, whereas no significant role for oxalic acid was observed. Furthermore, a common set of infection-related and secreted proteins was strongly underexpressed in the mutants. Quantitative secretome analysis with 15 N metabolic labeling revealed a correlation of changes in protein and mRNA levels between wild-type and mutants, indicating that transcript levels determine the abundance of secreted proteins. Infection sites kept at low pH partially restored lesion expansion and expression of virulence genes by the mutants. Drastic downregulation of proteases in the mutants was correlated with incomplete degradation of cellular host proteins at the infection site, but no evidence was obtained that aspartyl proteases are required for lesion formation. The B. cinerea VELVET complex controls pathogenic differentiation by regulating organic acid secretion, host tissue acidification, gene expression and protein secretion.
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Affiliation(s)
- Nathalie Müller
- Department of Biology, Plant Pathology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Michaela Leroch
- Department of Biology, Plant Pathology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Julia Schumacher
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, 48143, Münster, Germany
| | - David Zimmer
- Department of Biology, Computational Systems Biology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Anne Könnel
- Department of Biology, Plant Pathology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Klaus Klug
- Department of Biology, Plant Pathology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Thomas Leisen
- Department of Biology, Plant Pathology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - David Scheuring
- Department of Biology, Plant Pathology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Frederik Sommer
- Department of Biology, Molecular Biotechnology & Systems Biology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Department of Biology, Computational Systems Biology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Michael Schroda
- Department of Biology, Molecular Biotechnology & Systems Biology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Matthias Hahn
- Department of Biology, Plant Pathology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
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27
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Bar-Even A. Daring metabolic designs for enhanced plant carbon fixation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:71-83. [PMID: 29907311 DOI: 10.1016/j.plantsci.2017.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/16/2017] [Accepted: 12/16/2017] [Indexed: 05/07/2023]
Abstract
Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., "low hanging fruit". Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco's catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon. While the barriers for implementing these elaborated metabolic architectures are quite significant, if we truly want to revolutionize carbon fixation, only daring engineering efforts will lead the way.
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Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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28
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Cai X, Ge C, Xu C, Wang X, Wang S, Wang Q. Expression Analysis of Oxalate Metabolic Pathway Genes Reveals Oxalate Regulation Patterns in Spinach. Molecules 2018; 23:E1286. [PMID: 29861493 PMCID: PMC6100029 DOI: 10.3390/molecules23061286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 11/17/2022] Open
Abstract
Spinach (Spinacia oleracea L.) is one of most important leafy vegetables because of its high nutritional value and high oxalate content, which can be toxic with negative effects on human nutrition. Ammonium and nitrate can effectively regulate oxalate accumulation, although the mechanisms underlying the oxalate biosynthesis and regulation are still undetermined in plants. In the present study, we identified 25 putative genes that are involved in the oxalate biosynthetic and degradation pathway, before analyzing the oxalate content and the expression levels of the corresponding proteins under normal growth conditions, with or without ammonium and nitrate treatments, using high and low oxalate-accumulated spinach genotypes. The two cultivars exhibited different profiles of total oxalate and soluble oxalate accumulation. The high oxalate concentrations in spinach were as a result of the high transcription levels of the genes that are involved in oxalate biosynthesis under normal growth conditions, such as SoGLO2, SoGLO3, three SoOXACs, SoMLS, SoMDH1, SoMDH2, and SoMDH4. The results revealed that the ammonium and nitrate were able to control the oxalate content in leaves, possibly because of the different transcription levels of the genes. The oxalate content is regulated by complex regulatory mechanisms and is varied in the different varieties of spinach. The results from this research may be used to assist the investigation of the mechanism of oxalate regulation and breeding for reduced oxalate content in spinach.
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Affiliation(s)
- Xiaofeng Cai
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai 200234, China.
| | - Chenhui Ge
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai 200234, China.
| | - Chenxi Xu
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai 200234, China.
| | - Xiaoli Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai 200234, China.
| | - Shui Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai 200234, China.
| | - Quanhua Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai 200234, China.
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29
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Rodenburg SYA, Terhem RB, Veloso J, Stassen JHM, van Kan JAL. Functional Analysis of Mating Type Genes and Transcriptome Analysis during Fruiting Body Development of Botrytis cinerea. mBio 2018; 9:e01939-17. [PMID: 29440571 PMCID: PMC5821092 DOI: 10.1128/mbio.01939-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023] Open
Abstract
Botrytis cinerea is a plant-pathogenic fungus producing apothecia as sexual fruiting bodies. To study the function of mating type (MAT) genes, single-gene deletion mutants were generated in both genes of the MAT1-1 locus and both genes of the MAT1-2 locus. Deletion mutants in two MAT genes were entirely sterile, while mutants in the other two MAT genes were able to develop stipes but never formed an apothecial disk. Little was known about the reprogramming of gene expression during apothecium development. We analyzed transcriptomes of sclerotia, three stages of apothecium development (primordia, stipes, and apothecial disks), and ascospores by RNA sequencing. Ten secondary metabolite gene clusters were upregulated at the onset of sexual development and downregulated in ascospores released from apothecia. Notably, more than 3,900 genes were differentially expressed in ascospores compared to mature apothecial disks. Among the genes that were upregulated in ascospores were numerous genes encoding virulence factors, which reveals that ascospores are transcriptionally primed for infection prior to their arrival on a host plant. Strikingly, the massive transcriptional changes at the initiation and completion of the sexual cycle often affected clusters of genes, rather than randomly dispersed genes. Thirty-five clusters of genes were jointly upregulated during the onset of sexual reproduction, while 99 clusters of genes (comprising >900 genes) were jointly downregulated in ascospores. These transcriptional changes coincided with changes in expression of genes encoding enzymes participating in chromatin organization, hinting at the occurrence of massive epigenetic regulation of gene expression during sexual reproduction.IMPORTANCE Fungal fruiting bodies are formed by sexual reproduction. We studied the development of fruiting bodies ("apothecia") of the ubiquitous plant-pathogenic ascomycete Botrytis cinerea The role of mating type genes in apothecium development was investigated by targeted mutation. Two genes are essential for the initiation of sexual development; mutants in these genes are sterile. Two other genes were not essential for development of stipes; however, they were essential for stipes to develop a disk and produce sexual ascospores. We examined gene expression profiles during apothecium development, as well as in ascospores sampled from apothecia. We provide the first study ever of the transcriptome of pure ascospores in a filamentous fungus. The expression of numerous genes involved in plant infection was induced in the ascospores, implying that ascospores are developmentally primed for infection before their release from apothecia.
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Affiliation(s)
- Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Wageningen University, Bioinformatics Group, Wageningen, The Netherlands
| | - Razak B Terhem
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Javier Veloso
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Department of Plant Physiology, Faculty of Sciences, University of A Coruña, A Coruña, Spain
| | - Joost H M Stassen
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
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30
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Ren H, Wu X, Lyu Y, Zhou H, Xie X, Zhang X, Yang H. Selection of reliable reference genes for gene expression studies in Botrytis cinerea. J Microbiol Methods 2017; 142:71-75. [PMID: 28917607 DOI: 10.1016/j.mimet.2017.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/30/2017] [Accepted: 09/10/2017] [Indexed: 01/06/2023]
Abstract
Botrytis cinerea is an important plant pathogen causing grey mold disease in a wide range of plant species. The aim of this study was to identify reliable reference genes that can be used for the analysis of relative gene expression in B. cinerea with quantitative real-time reverse transcription PCR (qRT-PCR). Six commonly used housekeeping genes including actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ubiquitin (UBQ), ubiquitin-conjugating enzyme (UCE), α-tubulin (α-TUB) and β-tubulin (β-TUB) were selected to test their expression stabilities in B. cinerea treated with different concentration of oxalic acid (1, 5 and 10mM) and confronted with antagonistic Trichoderma afroharzianum. Four in silico algorithms (geNorm, BestKeeper, NormFinder and Comparative ΔCt) were applied to evaluate the expression stabilities of these genes, and the UBQ gene was identified as the most stably expressed. It was used to normalize the expression levels of three genes related to oxalic acid production (NADPH, VEL1 and OAH) when B. cinerea was challenged by T. afroharzianum. The results of this study are useful for gene expression analysis in B. cinerea.
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Affiliation(s)
- He Ren
- College of Life Science, Shandong University of Technology, Zibo 255000, Shandong Province, People's Republic of China; Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Xiaoqing Wu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Yuping Lyu
- College of Life Science, Shandong University of Technology, Zibo 255000, Shandong Province, People's Republic of China; Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Hongzi Zhou
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Xueying Xie
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
| | - Xinjian Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China.
| | - Hetong Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Shandong Academy of Sciences, Jinan 250014, Shandong Province, People's Republic of China
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31
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Odoni DI, van Gaal MP, Schonewille T, Tamayo-Ramos JA, Martins Dos Santos VAP, Suarez-Diez M, Schaap PJ. Aspergillus niger Secretes Citrate to Increase Iron Bioavailability. Front Microbiol 2017; 8:1424. [PMID: 28824560 PMCID: PMC5539119 DOI: 10.3389/fmicb.2017.01424] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 11/13/2022] Open
Abstract
Aspergillus niger has an innate ability to secrete various organic acids, including citrate. The conditions required for A. niger citrate overproduction are well described, but the physiological reasons underlying extracellular citrate accumulation are not yet fully understood. One of the less understood culture conditions is the requirement of growth-limiting iron concentrations. While this has been attributed to iron-dependent citrate metabolizing enzymes, this straightforward relationship does not always hold true. Here, we show that an increase in citrate secretion under iron limited conditions is a physiological response consistent with a role of citrate as A. niger iron siderophore. We found that A. niger citrate secretion increases with decreasing amounts of iron added to the culture medium and, in contrast to previous findings, this response is independent of the nitrogen source. Differential transcriptomics analyses of the two A. niger mutants NW305 (gluconate non-producer) and NW186 (gluconate and oxalate non-producer) revealed up-regulation of the citrate biosynthesis gene citA under iron limited conditions compared to iron replete conditions. In addition, we show that A. niger can utilize Fe(III) citrate as iron source. Finally, we discuss our findings in the general context of the pH-dependency of A. niger organic acid production, offering an explanation, besides competition, for why A. niger organic acid production is a sequential process influenced by the external pH of the culture medium.
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Affiliation(s)
- Dorett I Odoni
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Merlijn P van Gaal
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands.,Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
| | - Tom Schonewille
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Juan A Tamayo-Ramos
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands.,LifeGlimmer GmBHBerlin, Germany
| | - Maria Suarez-Diez
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
| | - Peter J Schaap
- Laboratory of System and Synthetic Biology, Wageningen University & ResearchWageningen, Netherlands
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Regulation of conidiation in Botrytis cinerea involves the light-responsive transcriptional regulators BcLTF3 and BcREG1. Curr Genet 2017; 63:931-949. [PMID: 28382431 DOI: 10.1007/s00294-017-0692-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 01/25/2023]
Abstract
Botrytis cinerea is a plant pathogenic fungus with a broad host range. Due to its rapid growth and reproduction by asexual spores (conidia), which increases the inoculum pressure, the fungus is a serious problem in different fields of agriculture. The formation of the conidia is promoted by light, whereas the formation of sclerotia as survival structures occurs in its absence. Based on this observation, putative transcription factors (TFs) whose expression is induced upon light exposure have been considered as candidates for activating conidiation and/or repressing sclerotial development. Previous studies reported on the identification of six light-responsive TFs (LTFs), and two of them have been confirmed as crucial developmental regulators: BcLTF2 is the positive regulator of conidiation, whose expression is negatively regulated by BcLTF1. Here, the functional characterization of the four remaining LTFs is reported. BcLTF3 has a dual function, as it represses conidiophore development by repressing bcltf2 in light and darkness, and is moreover essential for conidiogenesis. In bcltf3 deletion mutants conidium initials grow out to hyphae, which develop secondary conidiophores. In contrast, no obvious functions could be assigned to BcLTF4, BcLTF5 and BcLTF6 in these experiments. BcREG1, previously reported to be required for virulence and conidiogenesis, has been re-identified as light-responsive transcriptional regulator. Studies with bcreg1 overexpression strains indicated that BcREG1 differentially affects conidiation by acting as a repressor of BcLTF2-induced conidiation in the light and as an activator of a BcLTF2-independent conidiation program in the dark.
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Seifbarghi S, Borhan MH, Wei Y, Coutu C, Robinson SJ, Hegedus DD. Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus. BMC Genomics 2017; 18:266. [PMID: 28356071 PMCID: PMC5372324 DOI: 10.1186/s12864-017-3642-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/18/2017] [Indexed: 11/17/2022] Open
Abstract
Background Sclerotinia sclerotiorum causes stem rot in Brassica napus, which leads to lodging and severe yield losses. Although recent studies have explored significant progress in the characterization of individual S. sclerotiorum pathogenicity factors, a gap exists in profiling gene expression throughout the course of S. sclerotiorum infection on a host plant. In this study, RNA-Seq analysis was performed with focus on the events occurring through the early (1 h) to the middle (48 h) stages of infection. Results Transcript analysis revealed the temporal pattern and amplitude of the deployment of genes associated with aspects of pathogenicity or virulence during the course of S. sclerotiorum infection on Brassica napus. These genes were categorized into eight functional groups: hydrolytic enzymes, secondary metabolites, detoxification, signaling, development, secreted effectors, oxalic acid and reactive oxygen species production. The induction patterns of nearly all of these genes agreed with their predicted functions. Principal component analysis delineated gene expression patterns that signified transitions between pathogenic phases, namely host penetration, ramification and necrotic stages, and provided evidence for the occurrence of a brief biotrophic phase soon after host penetration. Conclusions The current observations support the notion that S. sclerotiorum deploys an array of factors and complex strategies to facilitate host colonization and mitigate host defenses. This investigation provides a broad overview of the sequential expression of virulence/pathogenicity-associated genes during infection of B. napus by S. sclerotiorum and provides information for further characterization of genes involved in the S. sclerotiorum-host plant interactions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3642-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shirin Seifbarghi
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.,Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - M Hossein Borhan
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. .,Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada.
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AbuQamar S, Moustafa K, Tran LS. Mechanisms and strategies of plant defense against Botrytis cinerea. Crit Rev Biotechnol 2017; 37:262-274. [PMID: 28056558 DOI: 10.1080/07388551.2016.1271767] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Biotic factors affect plant immune responses and plant resistance to pathogen infections. Despite the considerable progress made over the past two decades in manipulating genes, proteins and their levels from diverse sources, no complete genetic tolerance to environmental stresses has been developed so far in any crops. Plant defense response to pathogens, including Botrytis cinerea, is a complex biological process involving various changes at the biochemical, molecular (i.e. transcriptional) and physiological levels. Once a pathogen is detected, effective plant resistance activates signaling networks through the generation of small signaling molecules and the balance of hormonal signaling pathways to initiate defense mechanisms to the particular pathogen. Recently, studies using Arabidopsis thaliana and crop plants have shown that many genes are involved in plant responses to B. cinerea infection. In this article, we will review our current understanding of mechanisms regulating plant responses to B. cinerea with a particular interest on hormonal regulatory networks involving phytohormones salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and abscisic acid (ABA). We will also highlight some potential gene targets that are promising for improving crop resistance to B. cinerea through genetic engineering and breeding programs. Finally, the role of biological control as a complementary and alternative disease management will be overviewed.
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Affiliation(s)
- Synan AbuQamar
- a Department of Biology , United Arab Emirates University , Al-Ain , UAE
| | - Khaled Moustafa
- b Conservatoire National des Arts et Métiers , Paris , France
| | - Lam Son Tran
- c Plant Abiotic Stress Research Group & Faculty of Applied Sciences , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,d Signaling Pathway Research Unit , RIKEN Center for Sustainable Resource Science , Yokohama , Kanagawa , Japan
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Bar-Even A. Formate Assimilation: The Metabolic Architecture of Natural and Synthetic Pathways. Biochemistry 2016; 55:3851-63. [PMID: 27348189 DOI: 10.1021/acs.biochem.6b00495] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formate may become an ideal mediator between the physicochemical and biological realms, as it can be produced efficiently from multiple available sources, such as electricity and biomass, and serve as one of the simplest organic compounds for providing both carbon and energy to living cells. However, limiting the realization of formate as a microbial feedstock is the low diversity of formate-fixing enzymes and thereby the small number of naturally occurring formate-assimilation pathways. Here, the natural enzymes and pathways supporting formate assimilation are presented and discussed together with proposed synthetic routes that could permit growth on formate via existing as well as novel formate-fixing reactions. By considering such synthetic routes, the diversity of metabolic solutions for formate assimilation can be expanded dramatically, such that different host organisms, cultivation conditions, and desired products could be matched with the most suitable pathway. Astute application of old and new formate-assimilation pathways may thus become a cornerstone in the development of sustainable strategies for microbial production of value-added chemicals.
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Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology , Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Jongkon N, Chotpatiwetchkul W, Gleeson MP. Probing the Catalytic Mechanism Involved in the Isocitrate Lyase Superfamily: Hybrid Quantum Mechanical/Molecular Mechanical Calculations on 2,3-Dimethylmalate Lyase. J Phys Chem B 2015. [PMID: 26224328 DOI: 10.1021/acs.jpcb.5b04732] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The isocitrate lyase (ICL) superfamily catalyzes the cleavage of the C(2)-C(3) bond of various α-hydroxy acid substrates. Members of the family are found in bacteria, fungi, and plants and include ICL itself, oxaloacetate hydrolase (OAH), 2-methylisocitrate lyase (MICL), and (2R,3S)-dimethylmalate lyase (DMML) among others. ICL and related targets have been the focus of recent studies to treat bacterial and fungal infections, including tuberculosis. The catalytic process by which this family achieves C(2)-C(3) bond breaking is still not clear. Extensive structural studies have been performed on this family, leading to a number of plausible proposals for the catalytic mechanism. In this paper, we have applied quantum mechanical/molecular mechanical (QM/MM) methods to the most recently reported family member, DMML, to assess whether any of the mechanistic proposals offers a clear energetic advantage over the others. Our results suggest that Arg161 is the general base in the reaction and Cys124 is the general acid, giving rise to a rate-determining barrier of approximately 10 kcal/mol.
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Affiliation(s)
- Nathjanan Jongkon
- Department of Social and Applied Science, College of Industrial Technology, King Mongkut's University of Technology, North Bangkok , Bangkok 10800, Thailand
| | - Warot Chotpatiwetchkul
- Department of Chemistry, Faculty of Science, Kasetsart University , Chatuchak, Bangkok 10903, Thailand
| | - M Paul Gleeson
- Department of Chemistry, Faculty of Science, Kasetsart University , Chatuchak, Bangkok 10903, Thailand
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Bar-Even A, Milo R, Noor E, Tawfik DS. The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness. Biochemistry 2015. [DOI: 10.1021/acs.biochem.5b00621] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Elad Noor
- Institute
of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
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Liang X, Liberti D, Li M, Kim YT, Hutchens A, Wilson R, Rollins JA. Oxaloacetate acetylhydrolase gene mutants of Sclerotinia sclerotiorum do not accumulate oxalic acid, but do produce limited lesions on host plants. MOLECULAR PLANT PATHOLOGY 2015; 16:559-71. [PMID: 25285668 PMCID: PMC6638444 DOI: 10.1111/mpp.12211] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The oxaloacetate acetylhydrolase (OAH, EC 3.7.1.1)-encoding gene Ss-oah1 was cloned and functionally characterized from Sclerotinia sclerotiorum. Ss-oah1 transcript accumulation mirrored oxalic acid (OA) accumulation with neutral pH induction dependent on the pH-responsive transcriptional regulator Ss-Pac1. Unlike previously characterized ultraviolet (UV)-induced oxalate-deficient mutants ('A' mutants) which retain the capacity to accumulate OA, gene deletion Δss-oah1 mutants did not accumulate OA in culture or during plant infection. This defect in OA accumulation was fully restored on reintroduction of the wild-type (WT) Ss-oah1 gene. The Δss-oah1 mutants were also deficient in compound appressorium and sclerotium development and exhibited a severe radial growth defect on medium buffered at neutral pH. On a variety of plant hosts, the Δss-oah1 mutants established very restricted lesions in which the infectious hyphae gradually lost viability. Cytological comparisons of WT and Δss-oah1 infections revealed low and no OA accumulation, respectively, in subcuticular hyphae. Both WT and mutant hyphae exhibited a transient association with viable host epidermal cells at the infection front. In summary, our experimental data establish a critical requirement for OAH activity in S. sclerotiorum OA biogenesis and pathogenesis, but also suggest that factors independent of OA contribute to the establishment of primary lesions.
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Affiliation(s)
- Xiaofei Liang
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611-0680, USA
| | - Daniele Liberti
- Nunhems Netherlands BV, PO Box 4005, Haelen, 6080, AA, the Netherlands
| | - Moyi Li
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32610, USA
| | - Young-Tae Kim
- Environmental Biotechnology Research Centre, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 305-806, South Korea
| | - Andrew Hutchens
- University of Maryland Medical Center, 22 S. Greene Street, Baltimore, MD, 21201, USA
| | - Ron Wilson
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611-0680, USA
| | - Jeffrey A Rollins
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611-0680, USA
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Schumacher J, Simon A, Cohrs KC, Traeger S, Porquier A, Dalmais B, Viaud M, Tudzynski B. The VELVET Complex in the Gray Mold Fungus Botrytis cinerea: Impact of BcLAE1 on Differentiation, Secondary Metabolism, and Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:659-74. [PMID: 25625818 DOI: 10.1094/mpmi-12-14-0411-r] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Botrytis cinerea, the gray mold fungus, is an important plant pathogen. Field populations are characterized by variability with regard to morphology, the mode of reproduction (conidiation or sclerotia formation), the spectrum of secondary metabolites (SM), and virulence. Natural variation in bcvel1 encoding the ortholog of Aspergillus nidulans VeA, a member of the VELVET complex, was previously shown to affect light-dependent differentiation, the formation of oxalic acid (OA), and virulence. To gain broader insight into the B. cinerea VELVET complex, an ortholog of A. nidulans LaeA, BcLAE1, a putative interaction partner of BcVEL1, was studied. BcVEL1 but not its truncated versions interacts with BcLAE1 and BcVEL2 (VelB ortholog). In accordance with the expected common as well as specific functions of BcVEL1 and BcLAE1, the deletions of both genes result in similar though not identical phenotypes. Both mutants lost the ability to produce OA, to colonize the host tissue, and to form sclerotia. However, mutants differ with regard to aerial hyphae and conidia formation. Genome-wide expression analyses revealed that BcVEL1 and BcLAE1 have common and distinct target genes. Some of the genes that are underexpressed in both mutants, e.g., those encoding SM-related enzymes, proteases, and carbohydrate-active enzymes, may account for their reduced virulence.
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Affiliation(s)
| | - Adeline Simon
- 2 BIOGER, INRA, Avenue Lucien Brétignières, 78850 Grignon, France
| | - Kim C Cohrs
- 1 IBBP, WWU Münster, Schlossplatz 8, 48143 Münster, Germany
| | | | - Antoine Porquier
- 2 BIOGER, INRA, Avenue Lucien Brétignières, 78850 Grignon, France
- 3 Université Paris-Sud, 91405 Orsay, France
| | | | - Muriel Viaud
- 2 BIOGER, INRA, Avenue Lucien Brétignières, 78850 Grignon, France
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40
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Oxalate production by fungi: significance in geomycology, biodeterioration and bioremediation. FUNGAL BIOL REV 2014. [DOI: 10.1016/j.fbr.2014.05.001] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Yadav K, Kumar C, Archana G, Naresh Kumar G. Pseudomonas fluorescens ATCC 13525 containing an artificial oxalate operon and Vitreoscilla hemoglobin secretes oxalic acid and solubilizes rock phosphate in acidic alfisols. PLoS One 2014; 9:e92400. [PMID: 24705024 PMCID: PMC3976251 DOI: 10.1371/journal.pone.0092400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 02/21/2014] [Indexed: 11/18/2022] Open
Abstract
Oxalate secretion was achieved in Pseudomonas fluorescens ATCC 13525 by incorporation of genes encoding Aspergillus niger oxaloacetate acetyl hydrolase (oah), Fomitopsis plaustris oxalate transporter (FpOAR) and Vitreoscilla hemoglobin (vgb) in various combinations. Pf (pKCN2) transformant containing oah alone accumulated 19 mM oxalic acid intracellularly but secreted 1.2 mM. However, in the presence of an artificial oxalate operon containing oah and FpOAR genes in plasmid pKCN4, Pf (pKCN4) secreted 13.6 mM oxalate in the medium while 3.6 mM remained inside. This transformant solubilized 509 μM of phosphorus from rock phosphate in alfisol which is 4.5 fold higher than the Pf (pKCN2) transformant. Genomic integrants of P. fluorescens (Pf int1 and Pf int2) containing artificial oxalate operon (plac-FpOAR-oah) and artificial oxalate gene cluster (plac-FpOAR-oah, vgb, egfp) secreted 4.8 mM and 5.4 mM oxalic acid, released 329 μM and 351 μM P, respectively, in alfisol. The integrants showed enhanced root colonization, improved growth and increased P content of Vigna radiata plants. This study demonstrates oxalic acid secretion in P. fluorescens by incorporation of an artificial operon constituted of genes for oxalate synthesis and transport, which imparts mineral phosphate solubilizing ability to the organism leading to enhanced growth and P content of V. radiata in alfisol soil.
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Affiliation(s)
- Kavita Yadav
- Molecular Microbial Biochemistry Laboratory, Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Chanchal Kumar
- Molecular Microbial Biochemistry Laboratory, Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - G. Archana
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - G. Naresh Kumar
- Molecular Microbial Biochemistry Laboratory, Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
- * E-mail:
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Kobayashi K, Hattori T, Honda Y, Kirimura K. Oxalic acid production by citric acid-producing Aspergillus niger overexpressing the oxaloacetate hydrolase gene oahA. J Ind Microbiol Biotechnol 2014; 41:749-56. [PMID: 24615146 DOI: 10.1007/s10295-014-1419-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 02/11/2014] [Indexed: 12/01/2022]
Abstract
The filamentous fungus Aspergillus niger is used worldwide in the industrial production of citric acid. However, under specific cultivation conditions, citric acid-producing strains of A. niger accumulate oxalic acid as a by-product. Oxalic acid is used as a chelator, detergent, or tanning agent. Here, we sought to develop oxalic acid hyperproducers using A. niger as a host. To generate oxalic acid hyperproducers by metabolic engineering, transformants overexpressing the oahA gene, encoding oxaloacetate hydrolase (OAH; EC 3.7.1.1), were constructed in citric acid-producing A. niger WU-2223L as a host. The oxalic acid production capacity of this strain was examined by cultivation of EOAH-1 under conditions appropriate for oxalic acid production with 30 g/l glucose as a carbon source. Under all the cultivation conditions tested, the amount of oxalic acid produced by EOAH-1, a representative oahA-overexpressing transformant, exceeded that produced by A. niger WU-2223L. A. niger WU-2223L and EOAH-1 produced 15.6 and 28.9 g/l oxalic acid, respectively, during the 12-day cultivation period. The yield of oxalic acid for EOAH-1 was 64.2 % of the maximum theoretical yield. Our method for oxalic acid production gave the highest yield of any study reported to date. Therefore, we succeeded in generating oxalic acid hyperproducers by overexpressing a single gene, i.e., oahA, in citric acid-producing A. niger as a host.
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Affiliation(s)
- Keiichi Kobayashi
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan
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Δ(1)-pyrroline-5-carboxylate/glutamate biogenesis is required for fungal virulence and sporulation. PLoS One 2013; 8:e73483. [PMID: 24039956 PMCID: PMC3767830 DOI: 10.1371/journal.pone.0073483] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/22/2013] [Indexed: 11/19/2022] Open
Abstract
Proline dehydrogenase (Prodh) and Δ1-pyrroline-5-carboxylate dehydrogenase (P5Cdh) are two key enzymes in the cellular biogenesis of glutamate. Recombinant Prodh and P5Cdh proteins of the chestnut blight fungus Cryphonectria parasitica were investigated and showed activity in in vitro assays. Additionally, the C. parasitica Prodh and P5Cdh genes were able to complement the Saccharomyces cerevisiae put1 and put2 null mutants, respectively, to allow these proline auxotrophic yeast mutants to grow on media with proline as the sole source of nitrogen. Deletion of the Prodh gene in C. parasitica resulted in hypovirulence and a lower level of sporulation, whereas deletion of P5Cdh resulted in hypovirulence though no effect on sporulation; both Δprodh and Δp5cdh mutants were unable to grow on minimal medium with proline as the sole nitrogen source. In a wild-type strain, the intracellular level of proline and the activity of Prodh and P5Cdh increased after supplementation of exogenous proline, though the intracellular Δ1-pyrroline-5-carboxylate (P5C) content remained unchanged. Prodh and P5Cdh were both transcriptionally down-regulated in cells infected with hypovirus. The disruption of other genes with products involved in the conversion of arginine to ornithine, ornithine and glutamate to P5C, and P5C to proline in the cytosol did not appear to affect virulence; however, asexual sporulation was reduced in the Δpro1 and Δpro2 mutants. Taken together, our results showed that Prodh, P5Cdh and related mitochondrial functions are essential for virulence and that proline/glutamate pathway components may represent down-stream targets of hypovirus regulation in C. parasitica.
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Recovery of nickel from chromite overburden, Sukinda using Aspergillus niger supplemented with manganese. KOREAN J CHEM ENG 2012. [DOI: 10.1007/s11814-012-0142-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Schumacher J, Pradier JM, Simon A, Traeger S, Moraga J, Collado IG, Viaud M, Tudzynski B. Natural variation in the VELVET gene bcvel1 affects virulence and light-dependent differentiation in Botrytis cinerea. PLoS One 2012; 7:e47840. [PMID: 23118899 PMCID: PMC3485325 DOI: 10.1371/journal.pone.0047840] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/21/2012] [Indexed: 12/14/2022] Open
Abstract
Botrytis cinerea is an aggressive plant pathogen causing gray mold disease on various plant species. In this study, we identified the genetic origin for significantly differing phenotypes of the two sequenced B. cinerea isolates, B05.10 and T4, with regard to light-dependent differentiation, oxalic acid (OA) formation and virulence. By conducting a map-based cloning approach we identified a single nucleotide polymorphism (SNP) in an open reading frame encoding a VELVET gene (bcvel1). The SNP in isolate T4 results in a truncated protein that is predominantly found in the cytosol in contrast to the full-length protein of isolate B05.10 that accumulates in the nuclei. Deletion of the full-length gene in B05.10 resulted in the T4 phenotype, namely light-independent conidiation, loss of sclerotial development and oxalic acid production, and reduced virulence on several host plants. These findings indicate that the identified SNP represents a loss-of-function mutation of bcvel1. In accordance, the expression of the B05.10 copy in T4 rescued the wild-type/B05.10 phenotype. BcVEL1 is crucial for full virulence as deletion mutants are significantly hampered in killing and decomposing plant tissues. However, the production of the two best known secondary metabolites, the phytotoxins botcinic acid and botrydial, are not affected by the deletion of bcvel1 indicating that other factors are responsible for reduced virulence. Genome-wide expression analyses of B05.10- and Δbcvel1-infected plant material revealed a number of genes differentially expressed in the mutant: while several protease- encoding genes are under-expressed in Δbcvel1 compared to the wild type, the group of over-expressed genes is enriched for genes encoding sugar, amino acid and ammonium transporters and glycoside hydrolases reflecting the response of Δbcvel1 mutants to nutrient starvation conditions.
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Affiliation(s)
- Julia Schumacher
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | | | | | - Stefanie Traeger
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Javier Moraga
- Organic Chemistry Department, Cádiz University, Puerto Real, Cádiz, Spain
| | | | - Muriel Viaud
- INRA, BIOGER, Grignon, France
- * E-mail: (MV); (BT)
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität Münster, Münster, Germany
- * E-mail: (MV); (BT)
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de Oliveira BV, Teixeira GS, Reis O, Barau JG, Teixeira PJPL, do Rio MCS, Domingues RR, Meinhardt LW, Paes Leme AF, Rincones J, Pereira GAG. A potential role for an extracellular methanol oxidase secreted by Moniliophthora perniciosa in Witches' broom disease in cacao. Fungal Genet Biol 2012; 49:922-32. [PMID: 23022488 DOI: 10.1016/j.fgb.2012.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 08/28/2012] [Accepted: 09/02/2012] [Indexed: 11/29/2022]
Abstract
The hemibiotrophic basidiomycete fungus Moniliophthora perniciosa, the causal agent of Witches' broom disease (WBD) in cacao, is able to grow on methanol as the sole carbon source. In plants, one of the main sources of methanol is the pectin present in the structure of cell walls. Pectin is composed of highly methylesterified chains of galacturonic acid. The hydrolysis between the methyl radicals and galacturonic acid in esterified pectin, mediated by a pectin methylesterase (PME), releases methanol, which may be decomposed by a methanol oxidase (MOX). The analysis of the M. pernciosa genome revealed putative mox and pme genes. Real-time quantitative RT-PCR performed with RNA from mycelia grown in the presence of methanol or pectin as the sole carbon source and with RNA from infected cacao seedlings in different stages of the progression of WBD indicate that the two genes are coregulated, suggesting that the fungus may be metabolizing the methanol released from pectin. Moreover, immunolocalization of homogalacturonan, the main pectic domain that constitutes the primary cell wall matrix, shows a reduction in the level of pectin methyl esterification in infected cacao seedlings. Although MOX has been classically classified as a peroxisomal enzyme, M. perniciosa presents an extracellular methanol oxidase. Its activity was detected in the fungus culture supernatants, and mass spectrometry analysis indicated the presence of this enzyme in the fungus secretome. Because M. pernciosa possesses all genes classically related to methanol metabolism, we propose a peroxisome-independent model for the utilization of methanol by this fungus, which begins with the extracellular oxidation of methanol derived from the demethylation of pectin and finishes in the cytosol.
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Affiliation(s)
- Bruno V de Oliveira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970 Campinas, SP, Brazil
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47
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Billon-Grand G, Rascle C, Droux M, Rollins JA, Poussereau N. pH modulation differs during sunflower cotyledon colonization by the two closely related necrotrophic fungi Botrytis cinerea and Sclerotinia sclerotiorum. MOLECULAR PLANT PATHOLOGY 2012; 13:568-78. [PMID: 22171786 PMCID: PMC6638627 DOI: 10.1111/j.1364-3703.2011.00772.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
During pathogenesis on sunflower cotyledons, Botrytis cinerea and Sclerotinia sclerotiorum show a striking resemblance in symptom development. Based on pH change profiles, the colonization process of both fungi can be divided into two stages. The first stage is associated with a pH decrease, resulting from an accumulation of citric and succinic acids. The second stage is correlated with a pH increase, resulting from an accumulation of ammonia. In this article, we also report that oxalic acid is produced at the late stage of the colonization process and that ammonia accumulation is concomitant with a decrease in free amino acids in decaying tissues. Sclerotinia sclerotiorum produces eight-fold more oxalic acid and two-fold less ammonia than B. cinerea. Consequently, during sunflower cotyledon colonization by B. cinerea, pH dynamics differ significantly from those of S. sclerotiorum. In vitro assays support the in planta results and show that decreases in pH are linked to glucose consumption. At different stages of the colonization process, expression profiles of genes encoding secreted proteases were investigated. This analysis highlights that the expression levels of the B. cinerea protease genes are higher than those of S. sclerotiorum. This work suggests that the overt similarities of S. sclerotiorum and B. cinerea symptom development have probably masked our recognition of the dynamic and potentially different metabolic pathways active during host colonization by these two necrotrophic fungi.
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Affiliation(s)
- Geneviève Billon-Grand
- Université Lyon 1, CNRS, BAYER SAS, UMR 5240 Microbiologie, Adaptation et Pathogénie, 14 impasse Pierre Baizet, BP 99163, F-69263 Lyon cedex 09, France.
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48
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Neelon K, Roberts MF, Stec B. Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS. Biophys J 2012; 101:2816-24. [PMID: 22261071 DOI: 10.1016/j.bpj.2011.10.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 10/13/2011] [Accepted: 10/24/2011] [Indexed: 12/11/2022] Open
Abstract
1-L-myo-inositol-phosphate synthase (mIPS) catalyzes the first step of the unique, de novo pathway of inositol biosynthesis. However, details about the complex mIPS catalytic mechanism, which requires oxidation, enolization, intramolecular aldol cyclization, and reduction, are not fully known. To gain further insight into this mechanism, we determined the crystal structure of the wild-type mIPS from Archaeoglobus fulgidus at 1.7 Å, as well as the crystal structures of three active-site mutants. Additionally, we obtained the structure of mIPS with a trapped 5-keto-glucose-6-phosphate intermediate at 2 Å resolution by a novel (to our knowledge) process of activating the crystal at high temperature. A comparison of all of the crystal structures of mIPS described in this work suggests a novel type of catalytic mechanism that relies on the forced atomic proximity of functional groups. The lysine cluster is contained in a small volume in the active site, where random motions of these side chains are responsible for the progress of the complex multistep reaction as well as for the low rate of catalysis. The mechanism requires that functional groups of Lys-274, Lys-278, Lys-306, and Lys-367 assume differential roles in the protonation/deprotonation steps that must occur during the mIPS reaction. This mechanism is supported by the complete loss of activity of the enzyme caused by the Leu-257 mutation to Ala that releases the lysine containment.
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Affiliation(s)
- Kelly Neelon
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
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49
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Evidence for a common toolbox based on necrotrophy in a fungal lineage spanning necrotrophs, biotrophs, endophytes, host generalists and specialists. PLoS One 2012; 7:e29943. [PMID: 22253834 PMCID: PMC3256194 DOI: 10.1371/journal.pone.0029943] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/08/2011] [Indexed: 12/21/2022] Open
Abstract
The Sclerotiniaceae (Ascomycotina, Leotiomycetes) is a relatively recently evolved lineage of necrotrophic host generalists, and necrotrophic or biotrophic host specialists, some latent or symptomless. We hypothesized that they inherited a basic toolbox of genes for plant symbiosis from their common ancestor. Maintenance and evolutionary diversification of symbiosis could require selection on toolbox genes or on timing and magnitude of gene expression. The genes studied were chosen because their products have been previously investigated as pathogenicity factors in the Sclerotiniaceae. They encode proteins associated with cell wall degradation: acid protease 1 (acp1), aspartyl protease (asps), and polygalacturonases (pg1, pg3, pg5, pg6), and the oxalic acid (OA) pathway: a zinc finger transcription factor (pac1), and oxaloacetate acetylhydrolase (oah), catalyst in OA production, essential for full symptom production in Sclerotinia sclerotiorum. Site-specific likelihood analyses provided evidence for purifying selection in all 8 pathogenicity-related genes. Consistent with an evolutionary arms race model, positive selection was detected in 5 of 8 genes. Only generalists produced large, proliferating disease lesions on excised Arabidopsis thaliana leaves and oxalic acid by 72 hours in vitro. In planta expression of oah was 10-300 times greater among the necrotrophic host generalists than necrotrophic and biotrophic host specialists; pac1 was not differentially expressed. Ability to amplify 6/8 pathogenicity related genes and produce oxalic acid in all genera are consistent with the common toolbox hypothesis for this gene sample. That our data did not distinguish biotrophs from necrotrophs is consistent with 1) a common toolbox based on necrotrophy and 2) the most conservative interpretation of the 3-locus housekeeping gene phylogeny--a baseline of necrotrophy from which forms of biotrophy emerged at least twice. Early oah overexpression likely expands the host range of necrotrophic generalists in the Sclerotiniaceae, while specialists and biotrophs deploy oah, or other as-yet-unknown toolbox genes, differently.
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50
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Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 2011; 7:e1002230. [PMID: 21876677 PMCID: PMC3158057 DOI: 10.1371/journal.pgen.1002230] [Citation(s) in RCA: 654] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/22/2011] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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Affiliation(s)
- Joelle Amselem
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Ernesto P. Benito
- Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | - Ronald P. de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Fillinger
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Elisabeth Fournier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD – INRA – SupAgro, Montpellier, France
| | - Lilian Gout
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Matthias Hahn
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Linda Kohn
- Biology Department, University of Toronto, Mississauga, Canada
| | - Nicolas Lapalu
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Kim M. Plummer
- Botany Department, La Trobe University, Melbourne, Australia
| | - Jean-Marc Pradier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Emmanuel Quévillon
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Adeline Simon
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Arjen ten Have
- Instituto de Investigaciones Biologicas – CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Bettina Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Paul Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Marion Andrew
- Biology Department, University of Toronto, Mississauga, Canada
| | | | | | - Rolland Beffa
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Isabelle Benoit
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Ourdia Bouzid
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Baptiste Brault
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mathias Choquer
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Jérome Collémare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Pascale Cotton
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Etienne G. Danchin
- Interactions Biotiques et Santé Plantes, UMR5240, INRA – Université de Nice Sophia-Antipolis – CNRS, Sophia-Antipolis, France
| | | | - Angélique Gautier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Corinne Giraud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Tatiana Giraud
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS – AgroParisTech, Orsay, France
| | - Celedonio Gonzalez
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Spain
| | - Sandrine Grossetete
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Ulrich Güldener
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | | | - Chinnappa Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Anne Lappartient
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Michaela Leroch
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Caroline Levis
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Evan Mauceli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cécile Neuvéglise
- Biologie Intégrative du Métabolisme Lipidique Microbien, UMR1319, INRA – Micalis – AgroParisTech, Thiverval-Grignon, France
| | - Birgitt Oeser
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Matthew Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Julie Poulain
- GENOSCOPE, Centre National de Séquençage, Evry, France
| | - Nathalie Poussereau
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Hadi Quesneville
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Christine Rascle
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Julia Schumacher
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Adrienne Sexton
- School of Botany, University of Melbourne, Melbourne, Australia
| | - Evelyn Silva
- Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Catherine Sirven
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Darren M. Soanes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Matt Templeton
- Plant and Food Research, Mt. Albert Research Centre, Auckland, New Zealand
| | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Hebrew University Jerusalem, Rehovot, Israel
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey A. Rollins
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Marc-Henri Lebrun
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Marty Dickman
- Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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