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Baldin C, Segreto R, Bazafkan H, Schenk M, Millinger J, Schreiner U, Flatschacher D, Speckbacher V, Pierson S, Alilou M, Atanasova L, Zeilinger S. Are1-mediated nitrogen metabolism is associated with iron regulation in the mycoparasite Trichoderma atroviride. Microbiol Res 2024; 289:127907. [PMID: 39348793 DOI: 10.1016/j.micres.2024.127907] [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: 06/10/2024] [Revised: 08/27/2024] [Accepted: 09/11/2024] [Indexed: 10/02/2024]
Abstract
Trichoderma atroviride is a mycoparasitic fungus with antagonistic activity against fungal pathogens and is used as a pathogen control agent alternative to synthetic fungicides. Sensing nutrient availability in the environment and adjusting metabolism for optimal growth, development and reproduction is essential for adaptability and is relevant to its mycoparasitic activity. During mycoparasitism, secondary metabolites are produced to weaken the fungal prey and support the attack. Are1-like proteins act as major GATA-type transcription factors in the activation of genes subject to nitrogen catabolite repression. Since the quality and quantity of nitrogen has been proven particularly relevant in remodeling the biosynthesis of secondary metabolites in fungi, we decided to functionally characterize Are1, the ortholog of Aspergillus nidulans AreA, in T. atroviride. We show that the growth of the T. atroviride ∆are1 mutant is impaired in comparison to the wild type on several nitrogen sources. Deletion of are1 enhanced sensitivity to oxidative and cell-wall stressors and altered the mycoparasitic activity. We were able to identify for the first time a link between Are1 and iron homeostasis via a regulatory mechanism that does not appear to be strictly linked to the nitrogen source, but rather to an independent role of the transcription factor.
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Affiliation(s)
- Clara Baldin
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Rossana Segreto
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Hoda Bazafkan
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Martina Schenk
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Julia Millinger
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Ulrike Schreiner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | | | - Siebe Pierson
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Mostafa Alilou
- Department of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Lea Atanasova
- Department of Food Science and Technology, University of Natural Resources and Life Science (BOKU), Vienna, Austria
| | - Susanne Zeilinger
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria.
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2
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Kushwah AS, Dixit H, Upadhyay V, Verma SK, Prasad R. The study of iron- and copper-binding proteome of Fusarium oxysporum and its effector candidates. Proteins 2024; 92:1097-1112. [PMID: 38666709 DOI: 10.1002/prot.26696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron-binding proteins (IBPs) and copper-binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high-throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron-binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate-binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen-host interactions. The insights gained from this report on the role of metal ions in plant-pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.
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Affiliation(s)
- Ankita Singh Kushwah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi, North Campus, Delhi, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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3
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Wang J, Zhou Y, Wang P, Zhao L, Zhang H, Qu H, Xu F. Inhibitory Effect and Mechanism of Carvacrol against Black Mold Disease Agent Alternaria alternata in Goji Berries. J Fungi (Basel) 2024; 10:402. [PMID: 38921388 PMCID: PMC11204410 DOI: 10.3390/jof10060402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
Alternaria alternata, as a main decay fungus of goji berry, can produce mycotoxins such as alternariol (AOH), alternariol monomethyl ether (AME), and tenuazonic acid (TeA). Carvacrol (CVR) has exhibited a broad-spectrum antifungal activity in vitro. We assumed that CVR can also be applied to control Alternaria rot on goji berries and mycotoxins produced by the pathogens. To investigate whether CVR impacts the accumulation of mycotoxins and cell membrane damage of A. alternata, the antifungal activity of CVR on the fungal growth and mycotoxin production was evaluated in this study. The results showed that the minimum inhibitory concentration (MIC) of CVR against A. alternata was 0.12 µL/mL. Meanwhile, the destruction of plasma membrane integrity, cytoplasmic leakage, intracellular oxidative damage, and inhibitory effect in vivo were also observed in A. alternata treated with CVR. Moreover, CVR significantly reduced the accumulation of AOH, AME, and TeA. Transcriptomic profiling was performed by means of comparative RNA-Seq analysis to research the gene expression level of A. alternata, which attested to significant changes in nitrogen metabolism, carbon utilization, fatty acid oxidation, and antioxidant enzymes in CVR-treated A. alternata. This study suggests a new understanding of the molecular mechanism of response to CVR treatment in A. alternata, indicating that CVR is a novel antifungal agent with the potential to be applied to various fungi.
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Affiliation(s)
- Junjie Wang
- Key Laboratory of Storage and Processing of Plant Agro-Products, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (P.W.); (L.Z.); (H.Q.); (F.X.)
| | - Yueli Zhou
- Key Laboratory of Storage and Processing of Plant Agro-Products, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (P.W.); (L.Z.); (H.Q.); (F.X.)
| | - Peng Wang
- Key Laboratory of Storage and Processing of Plant Agro-Products, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (P.W.); (L.Z.); (H.Q.); (F.X.)
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Lunaike Zhao
- Key Laboratory of Storage and Processing of Plant Agro-Products, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (P.W.); (L.Z.); (H.Q.); (F.X.)
| | - Huaiyu Zhang
- Key Laboratory of Storage and Processing of Plant Agro-Products, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (P.W.); (L.Z.); (H.Q.); (F.X.)
| | - Huan Qu
- Key Laboratory of Storage and Processing of Plant Agro-Products, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (P.W.); (L.Z.); (H.Q.); (F.X.)
| | - Fei Xu
- Key Laboratory of Storage and Processing of Plant Agro-Products, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (P.W.); (L.Z.); (H.Q.); (F.X.)
- Physical and Chemical Laboratory of Ningxia Center for Disease Control and Prevention, Yinchuan 750021, China
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Kerkaert JD, Huberman LB. Regulation of nutrient utilization in filamentous fungi. Appl Microbiol Biotechnol 2023; 107:5873-5898. [PMID: 37540250 PMCID: PMC10983054 DOI: 10.1007/s00253-023-12680-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
Organisms must accurately sense and respond to nutrients to survive. In filamentous fungi, accurate nutrient sensing is important in the establishment of fungal colonies and in continued, rapid growth for the exploitation of environmental resources. To ensure efficient nutrient utilization, fungi have evolved a combination of activating and repressing genetic networks to tightly regulate metabolic pathways and distinguish between preferred nutrients, which require minimal energy and resources to utilize, and nonpreferred nutrients, which have more energy-intensive catabolic requirements. Genes necessary for the utilization of nonpreferred carbon sources are activated by transcription factors that respond to the presence of the specific nutrient and repressed by transcription factors that respond to the presence of preferred carbohydrates. Utilization of nonpreferred nitrogen sources generally requires two transcription factors. Pathway-specific transcription factors respond to the presence of a specific nonpreferred nitrogen source, while another transcription factor activates genes in the absence of preferred nitrogen sources. In this review, we discuss the roles of transcription factors and upstream regulatory genes that respond to preferred and nonpreferred carbon and nitrogen sources and their roles in regulating carbon and nitrogen catabolism. KEY POINTS: • Interplay of activating and repressing transcriptional networks regulates catabolism. • Nutrient-specific activating transcriptional pathways provide metabolic specificity. • Repressing regulatory systems differentiate nutrients in mixed nutrient environments.
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Affiliation(s)
- Joshua D Kerkaert
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Lori B Huberman
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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5
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MacCready JS, Roggenkamp EM, Gdanetz K, Chilvers MI. Elucidating the Obligate Nature and Biological Capacity of an Invasive Fungal Corn Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:411-424. [PMID: 36853195 DOI: 10.1094/mpmi-10-22-0213-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Tar spot is a devasting corn disease caused by the obligate fungal pathogen Phyllachora maydis. Since its initial identification in the United States in 2015, P. maydis has become an increasing threat to corn production. Despite this, P. maydis has remained largely understudied at the molecular level, due to difficulties surrounding its obligate lifestyle. Here, we generated a significantly improved P. maydis nuclear and mitochondrial genome, using a combination of long- and short-read technologies, and also provide the first transcriptomic analysis of primary tar spot lesions. Our results show that P. maydis is deficient in inorganic nitrogen utilization, is likely heterothallic, and encodes for significantly more protein-coding genes, including secreted enzymes and effectors, than previous determined. Furthermore, our expression analysis suggests that, following primary tar spot lesion formation, P. maydis might reroute carbon flux away from DNA replication and cell division pathways and towards pathways previously implicated in having significant roles in pathogenicity, such as autophagy and secretion. Together, our results identified several highly expressed unique secreted factors that likely contribute to host recognition and subsequent infection, greatly increasing our knowledge of the biological capacity of P. maydis, which have much broader implications for mitigating tar spot of corn. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Joshua S MacCready
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Emily M Roggenkamp
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Kristi Gdanetz
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
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Luo Z, Chen Q, Su Y, Hu S, Keyhani NO, Wang J, Zhu C, Zhou T, Pan Y, Bidochka MJ, Zhang Y. The AreA Nitrogen Catabolite Repression Activator Balances Fungal Nutrient Utilization and Virulence in the Insect Fungal Pathogen Beauveria bassiana. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:646-659. [PMID: 36584226 DOI: 10.1021/acs.jafc.2c07047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In many fungi, the AreA GATA-type transcription factor mediates nitrogen catabolite repression affecting fungal development and, where applicable, virulence. Here, we investigated the functions of AreA in the fungal entomopathogen and plant endophyte Beauveria bassiana using knockdown of gene expression. The antiAreA mutants were impaired in nitrogen utilization and showed increased sensitivities to osmotic stressors but increased tolerances to oxidative/hypoxia stresses. Repression of BbAreA caused overall minimal effects on fungal virulence. The minor effects on virulence appeared to be due in part to competing secondary effects where host defense phenoloxidase activity was significantly decreased, but production of the fungal metabolite oosporein was increased and hyphal body development was impaired. Knockdown of BbAreA expression also resulted in impairment in ability of the fungus to associate with host plants. These data implicate that BbAreA likely acts as a regulator to balance fungal nutrient utilization, pathogenicity, and mutualism, facilitating the fungal occupation of host niches.
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Affiliation(s)
- Zhibing Luo
- Biotechnology Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Qiyan Chen
- Biotechnology Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yufeng Su
- Biotechnology Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Shasha Hu
- Department of Biological Sciences, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Nemat O Keyhani
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| | - Junyao Wang
- Biotechnology Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chenhua Zhu
- Biotechnology Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Teng Zhou
- Biotechnology Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yunxia Pan
- College of Engineering and Technology, Southwest University, Chongqing 400715, P. R. China
| | - Michael J Bidochka
- Department of Biological Sciences, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Yongjun Zhang
- Biotechnology Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, P. R. China
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7
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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Chutrakul C, Panchanawaporn S, Vorapreeda T, Jeennor S, Anantayanon J, Laoteng K. The Exploring Functional Role of Ammonium Transporters of Aspergillus oryzae in Nitrogen Metabolism: Challenges towards Cell Biomass Production. Int J Mol Sci 2022; 23:7567. [PMID: 35886914 PMCID: PMC9319855 DOI: 10.3390/ijms23147567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
Ammonium is a source of fermentable inorganic nitrogen essential for the growth and development of filamentous fungi. It is involved in several cellular metabolic pathways underlying nitrogen transport and assimilation. Ammonium can be transferred into the cell by an ammonium transporter. This study explored the role of ammonium transporters in nitrogen metabolism and cell biomass production in Aspergillus oryzae strain BCC 7051. Specific sequences encoding ammonium transporters (Amts) in A. oryzae were identified using genomic analysis. Four of the identified ammonium transporter genes, aoamt1-aoamt4, showed similarity in deduced amino acid sequences to the proteins in the ammonium transporter/methylammonium permease (AMT/MEP) family. Transcriptional analysis showed that the expression of aoamt2 and aoamt3 was ammonium-dependent, and was highly upregulated under ammonium-limited conditions. Their functional roles are characterized by genetic perturbations. The gene disruption and overexpression of aoamt3 indicated that the protein encoded by it was a crucial ammonium transporter associated with nitrogen metabolism and was required for filamentous growth. Compared with the wild type, the aoamt3-overexpressing strain showed superior growth performance, high biomass yield, and low glucose consumption. These results shed light on further improvements in the production of potent bioproducts by A. oryzae by manipulating the ammonium uptake capacity and nitrogen metabolism.
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Affiliation(s)
- Chanikul Chutrakul
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Sarocha Panchanawaporn
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Tayvich Vorapreeda
- Biochemical Engineering and Systems Biology Research Group (IBEG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), at King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand;
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Jutamas Anantayanon
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
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9
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Anta-Fernández F, Santander-Gordón D, Becerra S, Santamaría R, Díaz-Mínguez JM, Benito EP. Nitric Oxide Metabolism Affects Germination in Botrytis cinerea and Is Connected to Nitrate Assimilation. J Fungi (Basel) 2022; 8:jof8070699. [PMID: 35887455 PMCID: PMC9324006 DOI: 10.3390/jof8070699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Nitric oxide regulates numerous physiological processes in species from all taxonomic groups. Here, its role in the early developmental stages of the fungal necrotroph Botrytis cinerea was investigated. Pharmacological analysis demonstrated that NO modulated germination, germ tube elongation and nuclear division rate. Experimental evidence indicates that exogenous NO exerts an immediate but transitory negative effect, slowing down germination-associated processes, and that this effect is largely dependent on the flavohemoglobin BCFHG1. The fungus exhibited a “biphasic response” to NO, being more sensitive to low and high concentrations than to intermediate levels of the NO donor. Global gene expression analysis in the wild-type and ΔBcfhg1 strains indicated a situation of strong nitrosative and oxidative stress determined by exogenous NO, which was much more intense in the mutant strain, that the cells tried to alleviate by upregulating several defense mechanisms, including the simultaneous upregulation of the genes encoding the flavohemoglobin BCFHG1, a nitronate monooxygenase (NMO) and a cyanide hydratase. Genetic evidence suggests the coordinated expression of Bcfhg1 and the NMO coding gene, both adjacent and divergently arranged, in response to NO. Nitrate assimilation genes were upregulated upon exposure to NO, and BCFHG1 appeared to be the main enzymatic system involved in the generation of the signal triggering their induction. Comparative expression analysis also showed the influence of NO on other cellular processes, such as mitochondrial respiration or primary and secondary metabolism, whose response could have been mediated by NmrA-like domain proteins.
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Affiliation(s)
- Francisco Anta-Fernández
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37008 Salamanca, Spain; (F.A.-F.); (S.B.); (J.M.D.-M.)
| | - Daniela Santander-Gordón
- Facultad de Ingeniería y Ciencias Aplicadas (FICA), Carrera de Ingeniería en Biotecnología, Universidad de las Américas (UDLA), Quito 170513, Ecuador;
| | - Sioly Becerra
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37008 Salamanca, Spain; (F.A.-F.); (S.B.); (J.M.D.-M.)
| | - Rodrigo Santamaría
- Department of Computer Science, University of Salamanca, 37008 Salamanca, Spain;
| | - José María Díaz-Mínguez
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37008 Salamanca, Spain; (F.A.-F.); (S.B.); (J.M.D.-M.)
| | - Ernesto Pérez Benito
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37008 Salamanca, Spain; (F.A.-F.); (S.B.); (J.M.D.-M.)
- Correspondence:
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10
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Ibrahim ABM, Mahmoud GA, Cordes DB, Slawin AMZ. Pb (II) and Hg (II) Thiosemicarbazones for Inhibiting the Broad‐Spectrum Pathogen
Cladosporium sphaerospermum
ASU18 (MK387875) and Altering Its Antioxidant System. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - David B. Cordes
- EaStCHEM School of Chemistry University of St Andrews Fife U.K
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11
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Recent advances in metabolic regulation and bioengineering of gibberellic acid biosynthesis in Fusarium fujikuroi. World J Microbiol Biotechnol 2022; 38:131. [PMID: 35689127 DOI: 10.1007/s11274-022-03324-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/29/2022] [Indexed: 12/24/2022]
Abstract
The plant growth hormone gibberellic acid (GA3), as one of the representative secondary metabolites, is widely used in agriculture, horticulture and brewing industry. GA3 is detected in both plants and several fungi with the ability to stimulate plant growth. Currently, the main mode of industrial production of GA3 is depended on the microbial fermentation via long-period submerged fermentation using Fusarium fujikuroi as the only producing strain, qualified for its natural productivity. However, the demand of large-sale industrialization of GA3 was still restricted by the low productivity. The biosynthetic route of GA3 in F. fujikuroi is now well-defined. Furthermore, the multi-level regulation mechanisms involved in the whole network of GA3 production have also been gradually unveiled by the past two decades based on the identification and characterization of several global regulators and their mutual functions. Combined with the quick development of genetic manipulation techniques, the rational modification of producing strain F. fujikuroi development become practical for higher productivity achievement. Herein, we review the latest advances in the molecular regulation of GA3 biosynthesis in F. fujikuroi and conclude a comprehensive network involving nitrogen depression, global regulator, histone modification and G protein signaling pathway. Correspondingly, the bioengineering strategies covering conventional random mutation, genetic manipulating platform development, metabolic edition and fermentation optimization were also systematically proposed.
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12
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Hanrahan-Tan DG, Henderson L, Kertesz MA, Lilje O. The Effects of Nitrogen and Phosphorus on Colony Growth and Zoospore Characteristics of Soil Chytridiomycota. J Fungi (Basel) 2022; 8:jof8040341. [PMID: 35448572 PMCID: PMC9024642 DOI: 10.3390/jof8040341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 01/03/2023] Open
Abstract
The Chytridiomycota phylum contributes to nutrient cycling and the flow of energy between trophic levels in terrestrial and aquatic ecosystems yet remains poorly described or absent from publications discussing fungal communities in these environments. This study contributes to the understanding of three species of soil chytrids in vitro—Gaertneriomyces semiglobifer, Spizellomyces sp. and Rhizophlyctis rosea—in the presence of elevated concentrations of nitrogen and phosphorus and with different sources of nitrogen. Colony growth was measured after 4 weeks as dry weight and total protein. To determine the impacts on zoospore reproduction, motility, lipid content, and attachment to organic substrates, 4- and 8-week incubation times were investigated. Whilst all isolates were able to assimilate ammonium as a sole source of nitrogen, nitrate was less preferred or even unsuitable as a nutrient source for G. semiglobifer and R. rosea, respectively. Increasing phosphate concentrations led to diverse responses between isolates. Zoospore production was also variable between isolates, and the parameters for zoospore motility appeared only to be influenced by the phosphate concentration for Spizellomyces sp. and R. rosea. Attachment rates increased for G. semiglobifer in the absence of an inorganic nitrogen source. These findings highlight variability between the adaptive responses utilised by chytrids to persist in a range of environments and provide new techniques to study soil chytrid biomass and zoospore motility by total protein quantification and fluorescent imaging respectively.
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Affiliation(s)
- Deirdre G. Hanrahan-Tan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
- Correspondence: (D.G.H.-T.); (O.L.)
| | - Linda Henderson
- Department of Planning and Environment, Locked Bag 5022, Parramatta, NSW 2124, Australia;
| | - Michael A. Kertesz
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Osu Lilje
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
- Correspondence: (D.G.H.-T.); (O.L.)
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Barrit T, Porcher A, Cukier C, Satour P, Guillemette T, Limami AM, Teulat B, Campion C, Planchet E. Nitrogen nutrition modifies the susceptibility of Arabidopsis thaliana to the necrotrophic fungus, Alternaria brassicicola. PHYSIOLOGIA PLANTARUM 2022; 174:e13621. [PMID: 34989007 DOI: 10.1111/ppl.13621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The impact of the form of nitrogen (N) source (nitrate versus ammonium) on the susceptibility to Alternaria brassicicola, a necrotrophic fungus, has been examined in Arabidopsis thaliana at the rosette stage. Nitrate nutrition was found to increase fungal lesions considerably. There was a similar induction of defence gene expression following infection under both N nutritions, except for the phytoalexin deficient 3 gene, which was overexpressed with nitrate. Nitrate also led to a greater nitric oxide production occurring in planta during the saprophytic growth and lower nitrate reductase (NIA1) expression 7 days after inoculation. This suggests that nitrate reductase-dependent nitric oxide production had a dual role, whereby, despite its known role in the generic response to pathogens, it affected plant metabolism, and this facilitated fungal infection. In ammonium-grown plants, infection with A. brassicicola induced a stronger gene expression of ammonium transporters and significantly reduced the initially high ammonium content in the leaves. There was a significant interaction between N source and inoculation (presence versus absence of the fungus) on the total amino acid content, while N nutrition reconfigured the spectrum of major amino acids. Typically, a higher content of total amino acid, mainly due to a stronger increase in asparagine and glutamine, is observed under ammonium nutrition while, in nitrate-fed plants, glutamate was the only amino acid which content increased significantly after fungal inoculation. N nutrition thus appears to control fungal infection via a complex set of signalling and nutritional events, shedding light on how nitrate availability can modulate disease susceptibility.
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Affiliation(s)
| | - Alexis Porcher
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, France
| | | | - Pascale Satour
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, France
| | | | - Anis M Limami
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, France
| | | | - Claire Campion
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, France
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14
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Khanal S, Schroeder L, Nava-Mercado OA, Mendoza H, Perlin MH. Role for nitrate assimilatory genes in virulence of Ustilago maydis. Fungal Biol 2021; 125:764-775. [PMID: 34537172 DOI: 10.1016/j.funbio.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/14/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
Ustilago maydis can utilize nitrate as a sole source of nitrogen. This process is initiated by transporting nitrate from the extracellular environment into the cell by a nitrate transporter and followed by a two-step reduction of nitrate to ammonium via nitrate reductase and nitrite reductase enzymes, respectively. Here, we characterize the genes encoding nitrate transporter, um03849 and nitrite reductase, um03848 in U. maydis based on their roles in mating and virulence. The deletion mutants for um03848, um03849 or both genes were constructed in mating compatible haploid strains 1/2 and 2/9. In addition, CRISPR-Cas9 gene editing technique was used for um03849 gene to create INDEL mutations in U. maydis mating strains. For all the mutants, phenotypes such as growth ability, mating efficiency and pathogenesis were examined. The growth of all the mutants was diminished when grown in a medium with nitrate as the source of nitrogen. Although no clear effects on haploid filamentation or mating were observed for either single mutant, double Δum03848 Δum03849 mutants showed reduction in mating, but increased filamentation on low ammonium, particularly in the 1/2 background. With respect to pathogenesis on the host, all the mutants showed reduced degrees of disease symptoms. Further, when the deletion mutants were paired with wild type of opposite mating-type, reduced virulence was observed, in a manner specific to the genetic background of the mutant's progenitor. This background specific reduction of plant pathogenicity was correlated with differential expression of genes for the mating program in U. maydis.
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Affiliation(s)
- Sunita Khanal
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Luke Schroeder
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | | | - Hector Mendoza
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA.
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15
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John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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16
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Transcriptomic Insights into the Antifungal Effects of Magnolol on the Growth and Mycotoxin Production of Alternaria alternata. Toxins (Basel) 2020; 12:toxins12100665. [PMID: 33092244 PMCID: PMC7594048 DOI: 10.3390/toxins12100665] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/12/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023] Open
Abstract
Alternaria alternata is an important phytopathogen causing fruit black rot and also producing a variety of mycotoxins, such as alternariol (AOH) and alternariol monomethyl ether (AME) as two main contaminants. This could lead to economic losses of agricultural products as well as human health risks. In this study, magnolol extracted from the traditional Chinese herb, Mangnolia officinalis, exhibited an obvious antifungal property and could completely suppress the mycelial growth at 100 μM. Morphological differences of A. alternata were observed to be significantly shrunk and wrinkled after the exposure to magnolol. Furthermore, AOH and AME were no longer produced in response to 50 μM of magnolol. To uncover the antifungal and antimycotoxigenic mechanisms, the transcriptomic profiles of A. alternata—treated with or without magnolol—were evaluated. The clustered genes responsible for AOH and AME biosynthesis were obviously less transcribed under magnolol stress and this was further confirmed by qRT-PCR. The global regulators of carbon and nitrogen utilization, such as CreA and NmrA, were significantly down-regulated and this possibly caused the reduction in mycotoxins. In addition, fatty acid β-oxidation was regarded to contribute to polyketide mycotoxin production for the supply of precursor acetyl-CoA while the expression of these related genes was inhibited. The response to magnolol led to the marked alteration of oxidative stress and the down-expression of the mitogen-activated protein kinase (MAPK) signaling pathway from the transcriptome data and the determination of peroxidase (POD), superoxide dismutase (SOD) and glutathione (GSH) assays. This above might be the very reason for the growth supression and mycotoxin production of A. alternata by magnolol. This study provides new insights into its potential as an important active ingredient for the control of A. alternata and its mycotoxins in fruits and their products.
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17
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Liu Y, Li H, Li J, Zhou Y, Zhou Z, Wang P, Zhou S. Characterization of the promoter of the nitrate transporter-encoding gene nrtA in Aspergillus nidulans. Mol Genet Genomics 2020; 295:1269-1279. [PMID: 32561986 DOI: 10.1007/s00438-020-01700-x] [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: 12/23/2019] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
Aspergillus nidulans nrtA encodes a nitrate transporter that plays an important role in the [Formula: see text] assimilatory process. Many studies have focused on protein functions rather than gene regulation. The knowledge of nrtA[Formula: see text] uptake process, particularly in the regulation mechanism of transcription factors AreA and NirA on nrtA transcription, is very limited. Herein, we investigated the transcriptional regulation of nrtA in response to various N-sources in detail and characterized the promoter activity of nrtA. We confirmed that nrtA was induced by [Formula: see text] and repressed by preferred N-sources. Additionally, for the first time, we found that the transcription of nrtA increased under N-starvation conditions. AreA mediates nrtA transcription under both [Formula: see text] and N-starvation conditions, while NirA is effective only under [Formula: see text] conditions. All of the proposed AreA and NirA binding sites in the promoter region were capable of binding to their corresponding transcription factors in vitro. In vivo, all of the NirA binding sites showed regulation activities, but to AreA, only several of the initiation-codon-proximal binding sites participated in nrtA transcription. Moreover, the active binding sites contributed in different degrees of regulation strength to nrtA transcription, which is unrelated to the distance between the binding sites and initiation codon. These results provided an extensive map of nrtA promoter, defining the functional regulatory elements of A. nidulans nrtA.
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Affiliation(s)
- Yangyi Liu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Haoxiang Li
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jingyi Li
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yao Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, USA
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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18
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Espeso EA, Villarino M, Carreras M, Alonso-Guirado L, Alonso JM, Melgarejo P, Larena I. Altered nitrogen metabolism in biocontrol strains of Penicillium rubens. Fungal Genet Biol 2019; 132:103263. [PMID: 31419528 DOI: 10.1016/j.fgb.2019.103263] [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: 04/23/2019] [Revised: 07/31/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
The importance of the metabolic route of nitrogen in the fungus Penicillium rubens (strain PO212) is studied in relation to its biocontrol activity (BA). PO212 can resist a high concentration of chlorate anion and displays a classical nitrate-deficiency (nit-) phenotype resulting in poor colonial growth when nitrate is used as the main source of nitrogen. Analyses of genes implicated in nitrate assimilation evidenced the strong sequence conservation of PO212 and CH8 genome with penicillin producers such as reference strain P. rubens Wisconsin 54-1255, P2niaD18 and Pc3, however also revealed the presence of mutations. PO212 carries a mutation in the gene coding for zinc-binuclear cluster transcription factor NirA that specifically mediates the regulation of genes involved in nitrate assimilation. The nirA1 mutation causes an early stop of NirA factor, losing 66% of its sequence. The NirA1 mutant form is unable to mediate a nitrate-dependent regulation of nitrate and nitrite reductase coding genes. In this study, we study another isolate, CH8, with potential BA and nit- phenotype. A mutation in the nitrate permease coding gene crnA was found in CH8. An insertion of a guanine in the coding sequence cause a frameshift in CrnA with the loss of the last two transmembrane domains. Analysis of PO212 and CH8 isolates and complementation strains show the importance of NirA regulator in maintaining correct transcriptional levels of nitrate and nitrite reductases and suggest CrnA as the main nitrate transporter. the presence of alternative transporter for chlorate and the existence of a mechanism for preventing nitrite derived toxicity in Penicillum. BA of PO212 is partially altered when nirA1 mutation was complemented. This result and the finding of CH8, a novel biocontrol P. rubens strain with a nit- phenotype, suggest that nitrogen metabolism is a component of biocontrol capacity.
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Affiliation(s)
- E A Espeso
- Centro Investigaciones Biológicas, CSIC, Departamento de Biología Molecular y Celular, Ramiro de Maeztu, 9, Madrid 28040, Spain.
| | - M Villarino
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
| | - M Carreras
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
| | - L Alonso-Guirado
- Centro Investigaciones Biológicas, CSIC, Departamento de Biología Molecular y Celular, Ramiro de Maeztu, 9, Madrid 28040, Spain; Spanish National Cancer Research Centre CNIO, Genetic & Molecular Epidemiology Group, Madrid 28029, Spain(1).
| | - J M Alonso
- Centro Investigaciones Biológicas, CSIC, Departamento de Biología Molecular y Celular, Ramiro de Maeztu, 9, Madrid 28040, Spain
| | - P Melgarejo
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
| | - I Larena
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
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Borin GP, Carazzolle MF, Dos Santos RAC, Riaño-Pachón DM, Oliveira JVDC. Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30. Front Bioeng Biotechnol 2018; 6:151. [PMID: 30406095 PMCID: PMC6204389 DOI: 10.3389/fbioe.2018.00151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022] Open
Abstract
The biomass-degrading fungus Trichoderma reesei has been considered a model for cellulose degradation, and it is the primary source of the industrial enzymatic cocktails used in second-generation (2G) ethanol production. However, although various studies and advances have been conducted to understand the cellulolytic system and the transcriptional regulation of T. reesei, the whole set of genes related to lignocellulose degradation has not been completely elucidated. In this study, we inferred a weighted gene co-expression network analysis based on the transcriptome dataset of the T. reesei RUT-C30 strain aiming to identify new target genes involved in sugarcane bagasse breakdown. In total, ~70% of all the differentially expressed genes were found in 28 highly connected gene modules. Several cellulases, sugar transporters, and hypothetical proteins coding genes upregulated in bagasse were grouped into the same modules. Among them, a single module contained the most representative core of cellulolytic enzymes (cellobiohydrolase, endoglucanase, β-glucosidase, and lytic polysaccharide monooxygenase). In addition, functional analysis using Gene Ontology (GO) revealed various classes of hydrolytic activity, cellulase activity, carbohydrate binding and cation:sugar symporter activity enriched in these modules. Several modules also showed GO enrichment for transcription factor activity, indicating the presence of transcriptional regulators along with the genes involved in cellulose breakdown and sugar transport as well as other genes encoding proteins with unknown functions. Highly connected genes (hubs) were also identified within each module, such as predicted transcription factors and genes encoding hypothetical proteins. In addition, various hubs contained at least one DNA binding site for the master activator Xyr1 according to our in silico analysis. The prediction of Xyr1 binding sites and the co-expression with genes encoding carbohydrate active enzymes and sugar transporters suggest a putative role of these hubs in bagasse cell wall deconstruction. Our results demonstrate a vast range of new promising targets that merit additional studies to improve the cellulolytic potential of T. reesei strains and to decrease the production costs of 2G ethanol.
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Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
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Transcription Factors Controlling Primary and Secondary Metabolism in Filamentous Fungi: The β-Lactam Paradigm. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4020047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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