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Chen L, Champramary S, Sahu N, Indic B, Szűcs A, Nagy G, Maróti G, Pap B, Languar O, Vágvölgyi C, Nagy LG, Kredics L, Sipos G. Dual RNA-Seq Profiling Unveils Mycoparasitic Activities of Trichoderma atroviride against Haploid Armillaria ostoyae in Antagonistic Interaction Assays. Microbiol Spectr 2023; 11:e0462622. [PMID: 37140425 PMCID: PMC10269595 DOI: 10.1128/spectrum.04626-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Armillaria ostoyae, a species among the destructive forest pathogens from the genus Armillaria, causes root rot disease on woody plants worldwide. Efficient control measures to limit the growth and impact of this severe underground pathogen are under investigation. In a previous study, a new soilborne fungal isolate, Trichoderma atroviride SZMC 24276 (TA), exhibited high antagonistic efficacy, which suggested that it could be utilized as a biocontrol agent. The dual culture assay results indicated that the haploid A. ostoyae-derivative SZMC 23085 (AO) (C18/9) is highly susceptible to the mycelial invasion of TA. In the present study, we analyzed the transcriptome of AO and that of TA in in vitro dual culture assays to test the molecular arsenal of Trichoderma antagonism and the defense mechanisms of Armillaria. We conducted time-course analysis and functional annotation and analyzed enriched pathways and differentially expressed genes including biocontrol-related candidate genes from TA and defense-related candidate genes from AO. The results indicated that TA deployed several biocontrol mechanisms when confronted with AO. In response, AO initiated multiple defense mechanisms to protect against the fungal attack. To our knowledge, the present study offers the first transcriptome analysis of a biocontrol fungus attacking AO. Overall, this study provides insights that aid the further exploration of plant pathogen-biocontrol agent interaction mechanisms. IMPORTANCE Armillaria species can survive for decades in the soil on dead woody debris, develop rapidly under favorable conditions, and harmfully infect newly planted forests. Our previous study found Trichoderma atroviride to be highly effective in controlling Armillaria growth; therefore, our current work explored the molecular mechanisms that might play a key role in Trichoderma-Armillaria interactions. Direct confrontation assays combined with time course-based dual transcriptome analysis provided a reliable system for uncovering the interactive molecular dynamics between the fungal plant pathogen and its mycoparasitic partner. Furthermore, using a haploid Armillaria isolate allowed us to survey the deadly prey-invading activities of the mycoparasite and the ultimate defensive strategies of its prey. Our current study provides detailed insights into the essential genes and mechanisms involved in Armillaria defense against Trichoderma and the genes potentially involved in the efficiency of Trichoderma to control Armillaria. In addition, using a sensitive haploid Armillaria strain (C18/9), with its complete genome data already available, also offers the opportunity to test possible variable molecular responses of Armillaria ostoyae toward diverse Trichoderma isolates with various biocontrol abilities. Initial molecular tests of the dual interactions may soon help to develop a targeted biocontrol intervention with mycoparasites against plant pathogens.
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Affiliation(s)
- Liqiong Chen
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Simang Champramary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
| | - Neha Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Boris Indic
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
| | - Attila Szűcs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | | | - Bernadett Pap
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Omar Languar
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - György Sipos
- Functional Genomics and Bioinformatics Group, Institute of Forest and Natural Resource Management, Faculty of Forestry, University of Sopron, Sopron, Hungary
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Longsaward R, Pengnoo A, Kongsawadworakul P, Viboonjun U. A novel rubber tree PR-10 protein involved in host-defense response against the white root rot fungus Rigidoporus microporus. BMC Plant Biol 2023; 23:157. [PMID: 36944945 PMCID: PMC10032002 DOI: 10.1186/s12870-023-04149-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/28/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND White root rot disease in rubber trees, caused by the pathogenic fungi Rigidoporus microporus, is currently considered a major problem in rubber tree plantations worldwide. Only a few reports have mentioned the response of rubber trees occurring at the non-infection sites, which is crucial for the disease understanding and protecting the yield losses. RESULTS Through a comparative proteomic study using the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) technique, the present study reveals some distal-responsive proteins in rubber tree leaves during the plant-fungal pathogen interaction. From a total of 12 selected differentially expressed protein spots, several defense-related proteins such as molecular chaperones and ROS-detoxifying enzymes were identified. The expression of 6 candidate proteins was investigated at the transcript level by Reverse Transcription Quantitative PCR (RT-qPCR). In silico, a highly-expressed uncharacterized protein LOC110648447 found in rubber trees was predicted to be a protein in the pathogenesis-related protein 10 (PR-10) class. In silico promoter analysis and structural-related characterization of this novel PR-10 protein suggest that it plays a potential role in defending rubber trees against R. microporus infection. The promoter contains WRKY-, MYB-, and other defense-related cis-acting elements. The structural model of the novel PR-10 protein predicted by I-TASSER showed a topology of the Bet v 1 protein family, including a conserved active site and a ligand-binding hydrophobic cavity. CONCLUSIONS A novel protein in the PR-10 group increased sharply in rubber tree leaves during interaction with the white root rot pathogen, potentially contributing to host defense. The results of this study provide information useful for white root rot disease management of rubber trees in the future.
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Affiliation(s)
- Rawit Longsaward
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Ashara Pengnoo
- Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai Campus, Songkhla, 90110, Thailand
- Natural Biological Control Research Center, National Research Council of Thailand, 196 Phahonyothin Road, Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Panida Kongsawadworakul
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Unchera Viboonjun
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Zhou Q, Yin X, Zhang H, Wang Y. MicroRNA-like RNA Functions Are Required for the Biosynthesis of Active Compounds in the Medicinal Fungus Sanghuangporus vaninii. Microbiol Spectr 2022; 10:e0021922. [PMID: 36301126 DOI: 10.1128/spectrum.00219-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
miRNA-like RNAs (milRNAs) have been recognized as sequence-specific regulators of posttranscriptional regulation of gene expression in eukaryotes. However, the functions of hundreds of fungal milRNAs in the biosynthesis of metabolic components are obscure. Sanghuangporus produces diverse bioactive compounds and is widely used in Asian countries. Here, genes encoding two Dicers, four Argonautes, and four RdRPs were identified and characterized in Sanghuangporus vanini. Due to the lack of an efficient gene manipulation system, the efficacy of spray-induced gene silencing (SIGS) was determined in S. vanini, which showed efficient double-stranded RNA (dsRNA) uptake and gene silencing efficiency. SIGS-mediated gene knockdown showed that SVRDRP-3, SVRDRP-4, SVDICER-1, and SVDICER-2 were critical for mycelial biomass, flavonoid, triterpenoid, and polysaccharide production. Illumina deep sequencing was performed to characterize the milRNAs from S. vanini mycelium and fruiting body. A total of 31 milRNAs were identified, out of which, SvmilR10, SvmilR17, and SvmilR33 were Svrdrp-4- and Svdicer-1-dependent milRNAs. Importantly, SIGS-mediated overexpression of SvmilR10 and SvmilR33 resulted in significant changes in the yields of flavonoids, triterpenoids, and polysaccharides. Further analysis showed that these milRNA target genes encoding the retrotransposon-derived protein PEG1 and histone-lysine N-methyltransferase were potentially downregulated in the milRNA overexpressing strain. Our results revealed that S. vanini has high external dsRNA and small RNA uptake efficiency and that milRNAs may play crucial regulatory roles in the biosynthesis of bioactive compounds. IMPORTANCE Fungi can take up environmental RNA that can silence fungal genes with RNA interference, which prompts the development of SIGS. Efficient dsRNA and milRNA uptake in S. vanini, successful dsRNA-targeted gene block, and the increase in intracellular miRNA abundance showed that SIGS technology is an effective and powerful tool for the functional dissection of fungal genes and millRNAs. We found that the RdRP, Dicer, and Argonaute genes are critical for mycelial biomass and bioactive compound production. Our study also demonstrated that overexpressed SVRDRP-4- and SVDICER-1-dependent milRNAs (SvmilR10 and SvmilR33) led to significant changes in the yields of the three active compounds. This study not only provides the first report on SIGS-based gene and milRNA function exploration, but also provides a theoretical platform for exploration of the functions of milRNAs involved in biosynthesis of metabolic compounds in fungi.
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Pawlik A, Stefanek S, Janusz G. Properties, Physiological Functions and Involvement of Basidiomycetous Alcohol Oxidase in Wood Degradation. Int J Mol Sci 2022; 23. [PMID: 36430286 DOI: 10.3390/ijms232213808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
Extensive research efforts have been devoted to describing yeast alcohol oxidase (AO) and its promoter region, which is vastly applied in studies of heterologous gene expression. However, little is known about basidiomycetous AO and its physiological role in wood degradation. This review describes several alcohol oxidases from both white and brown rot fungi, highlighting their physicochemical and kinetic properties. Moreover, the review presents a detailed analysis of available AO-encoding gene promoter regions in basidiomycetous fungi with a discussion of the manipulations of culture conditions in relation to the modification of alcohol oxidase gene expression and changes in enzyme production. The analysis of reactions catalyzed by lignin-modifying enzymes (LME) and certain lignin auxiliary enzymes (LDA) elucidated the possible involvement of alcohol oxidase in the degradation of derivatives of this polymer. Combined data on lignin degradation pathways suggest that basidiomycetous AO is important in secondary reactions during lignin decomposition by wood degrading fungi. With numerous alcoholic substrates, the enzyme is probably engaged in a variety of catalytic reactions leading to the detoxification of compounds produced in lignin degradation processes and their utilization as a carbon source by fungal mycelium.
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Maiden NA, Syd Ali N, Ahmad K, Atan S, Wong MY. Growth and physiological responses of Hevea brasiliensis to Rigidoporus microporus infection. J RUBBER RES 2022. [DOI: 10.1007/s42464-022-00156-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sun YF, Lebreton A, Xing JH, Fang YX, Si J, Morin E, Miyauchi S, Drula E, Ahrendt S, Cobaugh K, Lipzen A, Koriabine M, Riley R, Kohler A, Barry K, Henrissat B, Grigoriev IV, Martin FM, Cui BK. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. J Fungi (Basel) 2022; 8:jof8030311. [PMID: 35330313 PMCID: PMC8955403 DOI: 10.3390/jof8030311] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.
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Affiliation(s)
- Yi-Fei Sun
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Annie Lebreton
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jia-Hui Xing
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Yu-Xuan Fang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829 Cologne, Germany
| | - Elodie Drula
- INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France;
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Kelly Cobaugh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
- Department of Biological Sciences, King Abdulaziz University, Jeddah 999088, Saudi Arabia
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
- Department of Microbial and Plant Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Francis M. Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
| | - Bao-Kai Cui
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
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Wang P, Xu J, Wu G, Liu T, Yang ZL. Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition. J Fungi (Basel) 2021; 7:679. [PMID: 34436218 DOI: 10.3390/jof7080679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Saprophytic fungi (SPF) play vital roles in ecosystem dynamics and decomposition. However, because of the complexity of living systems, our understanding of how SPF interact with each other to decompose organic matter is very limited. Here we studied their roles and interactions in the decomposition of highly specialized substrates between the two genera Auriscalpium and Strobilurus fungi-colonized fallen pinecones of the same plant sequentially. We obtained the genome sequences from seven fungal species with three pairs: A. orientale-S. luchuensis, A. vulgare-S. stephanocystis and A. microsporum-S. pachcystidiatus/S. orientalis on cones of Pinus yunnanensis, P. sylvestris and P. armandii, respectively, and the organic profiles of substrate during decomposition. Our analyses revealed evidence for both competition and cooperation between the two groups of fungi during decomposition, enabling efficient utilization of substrates with complementary profiles of carbohydrate active enzymes (CAZymes). The Auriscalpium fungi are highly effective at utilizing the primary organic carbon, such as lignin, and hemicellulose in freshly fallen cones, facilitated the invasion and colonization by Strobilurus fungi. The Strobilurus fungi have genes coding for abundant CAZymes to utilize the remaining organic compounds and for producing an arsenal of secondary metabolites such as strobilurins that can inhibit other fungi from colonizing the pinecones.
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Ruiz-Dueñas FJ, Barrasa JM, Sánchez-García M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, Ramírez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, Martínez AT. Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Mol Biol Evol 2021; 38:1428-1446. [PMID: 33211093 PMCID: PMC8480192 DOI: 10.1093/molbev/msaa301] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
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Affiliation(s)
| | - José M Barrasa
- Life Sciences Department, Alcalá University, Alcalá de Henares, Spain
| | | | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | | | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Rashid Babiker
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
| | | | - Remedios Pacheco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Guillermo Padilla
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Patricia Ferreira
- Biochemistry and Molecular and Cellular Biology Department and BIFI, Zaragoza University, Zaragoza, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Harald Kellner
- International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Cullen
- Forest Products Laboratory, US Department of Agriculture, Madison, WI, USA
| | - Francis Martin
- INRAE, Laboratory of Excellence ARBRE, Champenoux, France
| | - Marie-Noëlle Rosso
- INRAE, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, USA
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
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Basik AA, Sanglier JJ, Yeo CT, Sudesh K. Microbial Degradation of Rubber: Actinobacteria. Polymers (Basel) 2021; 13:polym13121989. [PMID: 34204568 PMCID: PMC8235351 DOI: 10.3390/polym13121989] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/25/2023] Open
Abstract
Rubber is an essential part of our daily lives with thousands of rubber-based products being made and used. Natural rubber undergoes chemical processes and structural modifications, while synthetic rubber, mainly synthetized from petroleum by-products are difficult to degrade safely and sustainably. The most prominent group of biological rubber degraders are Actinobacteria. Rubber degrading Actinobacteria contain rubber degrading genes or rubber oxygenase known as latex clearing protein (lcp). Rubber is a polymer consisting of isoprene, each containing one double bond. The degradation of rubber first takes place when lcp enzyme cleaves the isoprene double bond, breaking them down into the sole carbon and energy source to be utilized by the bacteria. Actinobacteria grow in diverse environments, and lcp gene containing strains have been detected from various sources including soil, water, human, animal, and plant samples. This review entails the occurrence, physiology, biochemistry, and molecular characteristics of Actinobacteria with respect to its rubber degrading ability, and discusses possible technological applications based on the activity of Actinobacteria for treating rubber waste in a more environmentally responsible manner.
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Affiliation(s)
- Ann Anni Basik
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Jean-Jacques Sanglier
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Chia Tiong Yeo
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Correspondence: ; Tel.: +60-4-6534367; Fax: +60-4-6565125
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10
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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Silva TC, Araujo ECG, Lins TRDS, Reis CA, Sanquetta CR, Rocha MPD. Non-Timber Forest Products in Brazil: A Bibliometric and a State of the Art Review. Sustainability 2020; 12:7151. [DOI: 10.3390/su12177151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Non-timber forest products (NTFPs) are a consolidated source of income and acquisition of inputs from forest environments. Therefore, the objective of this work was to carry out a collection of publications on NTFPs in Brazil, until 2019, available in the Scopus database, presenting a bibliometric review and the state of the art of this theme from the evaluation of these publications, discussing the challenges of Brazilian legislation on NTFPs. After screening the articles of interest, 196 documents were evaluated, in which they were observed institutions and authors, analyzing networks of citations and terms used, areas of forest sciences and sciences that encompass the most explored biomes and the most studied species. The results showed that the concern to research on NTFPs in Brazil began in the 1990s, with an increase in the number of publications over the years. Besides that, the research on NTFPs is multidisciplinary, with emphasis on the areas of Agricultural and Biological Sciences and Environmental Science. For better regulation of the process of exploration and management of NTFPs in Brazil, the need to create specific legislation that takes into account factors such as the phytogeographic domain the explored area, producing species, and the products and co-products obtained was observed.
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