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Nogueira KMV, Mendes V, Kamath KS, Cheruku A, Oshiquiri LH, de Paula RG, Carraro C, Pedersoli WR, Pereira LMS, Vieira LC, Steindorff AS, Amirkhani A, McKay MJ, Nevalainen H, Molloy MP, Silva RN. Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei. Microb Cell Fact 2024; 23:22. [PMID: 38229067 DOI: 10.1186/s12934-023-02279-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose breakdown is crucial to induce the signaling cascade that triggers cellulase production. However, the sugar transporters involved in this process in T. reesei remain poorly identified and characterized. RESULTS To address this gap, this study used temporal membrane proteomics analysis to identify five known and nine putative sugar transporters that may be involved in cellulose degradation by T. reesei. Docking analysis pointed out potential ligands for the putative sugar transporter Tr44175. Further functional validation of this transporter was carried out in Saccharomyces cerevisiae. The results showed that Tr44175 transports a variety of sugar molecules, including cellobiose, cellotriose, cellotetraose, and sophorose. CONCLUSION This study has unveiled a transporter Tr44175 capable of transporting cellobiose, cellotriose, cellotetraose, and sophorose. Our study represents the first inventory of T. reesei sugar transportome once exposed to cellulose, offering promising potential targets for strain engineering in the context of bioethanol production.
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Affiliation(s)
- Karoline Maria Vieira Nogueira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Vanessa Mendes
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Karthik Shantharam Kamath
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Anusha Cheruku
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Letícia Harumi Oshiquiri
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria, ES, 29047-105, Brazil
| | - Claudia Carraro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Wellington Ramos Pedersoli
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Lucas Matheus Soares Pereira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Luiz Carlos Vieira
- Department of Molecular and Cell Biology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Helena Nevalainen
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil.
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Silva AC, Oshiquiri LH, de Morais Costa de Jesus LF, Maués DB, Silva RDN. The Cerato-Platanin EPL2 from Trichoderma reesei Is Not Directly Involved in Cellulase Formation but in Cell Wall Remodeling. Microorganisms 2023; 11:1965. [PMID: 37630525 PMCID: PMC10459490 DOI: 10.3390/microorganisms11081965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Trichoderma reesei is a saprophytic fungus that produces large amounts of cellulases and is widely used for biotechnological applications. Cerato-platanins (CPs) are a family of proteins universally distributed among Dikarya fungi and have been implicated in various functions related to fungal physiology and interaction with the environment. In T. reesei, three CPs are encoded in the genome: Trire2_111449, Trire2_123955, and Trire2_82662. However, their function is not fully elucidated. In this study, we deleted the Trire2_123955 gene (named here as epl2) in the wild-type QM6aΔtmus53Δpyr4 (WT) strain and examined the behavior of the Δepl2 strain compared with WT grown for 72 h in 1% cellulose using RNA sequencing. Of the 9143 genes in the T. reesei genome, 760 were differentially expressed, including 260 only in WT, 214 only in Δepl2, and 286 in both. Genes involved in oxidative stress, oxidoreductase activity, antioxidant activity, and transport were upregulated in the Δepl2 mutant. Genes encoding cell wall synthesis were upregulated in the mutant strain during the late growth stage. The Δepl2 mutant accumulated chitin and glucan at higher levels than the parental strain and was more resistant to cell wall stressors. These results suggest a compensatory effect in cell wall remodeling due to the absence of EPL2 in T. reesei. This study is expected to contribute to a better understanding of the role of the EPL2 protein in T. reesei and improve its application in biotechnological fields.
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Affiliation(s)
| | | | | | | | - Roberto do Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (A.C.S.); (L.H.O.); (L.F.d.M.C.d.J.); (D.B.M.)
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Antoniêto ACC, Nogueira KMV, Mendes V, Maués DB, Oshiquiri LH, Zenaide-Neto H, de Paula RG, Gaffey J, Tabatabaei M, Gupta VK, Silva RN. Use of carbohydrate-directed enzymes for the potential exploitation of sugarcane bagasse to obtain value-added biotechnological products. Int J Biol Macromol 2022; 221:456-471. [PMID: 36070819 DOI: 10.1016/j.ijbiomac.2022.08.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
Microorganisms, such as fungi and bacteria, are crucial players in the production of enzymatic cocktails for biomass hydrolysis or the bioconversion of plant biomass into products with industrial relevance. The biotechnology industry can exploit lignocellulosic biomass for the production of high-value chemicals. The generation of biotechnological products from lignocellulosic feedstock presents several bottlenecks, including low efficiency of enzymatic hydrolysis, high cost of enzymes, and limitations on microbe metabolic performance. Genetic engineering offers a route for developing improved microbial strains for biotechnological applications in high-value product biosynthesis. Sugarcane bagasse, for example, is an agro-industrial waste that is abundantly produced in sugar and first-generation processing plants. Here, we review the potential conversion of its feedstock into relevant industrial products via microbial production and discuss the advances that have been made in improving strains for biotechnological applications.
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Affiliation(s)
- Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Vanessa Mendes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - David Batista Maués
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Letícia Harumi Oshiquiri
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Hermano Zenaide-Neto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitória, ES 29047-105, Brazil
| | - James Gaffey
- Circular Bioeconomy Research Group, Shannon Applied Biotechnology Centre, Munster Technological University, Kerry, Ireland; BiOrbic, Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil.
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Oshiquiri LH, Gomes SL, Georg RC. Blastocladiella emersonii spliceosome is regulated in response to the splicing inhibition caused by the metals cadmium, cobalt and manganese. Fungal Biol 2020; 124:468-474. [PMID: 32389309 DOI: 10.1016/j.funbio.2020.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/08/2023]
Abstract
Blastocladiella emersonii is an aquatic fungus of the phylum Blastocladiomycota, localized near the base of the fungal tree. Previous studies have shown that B. emersonii responds to heat shock and cadmium exposure inducing the transcription of a high number of genes. EST sequencing from heat shocked and cadmium exposed B. emersonii cells has shown that exposure to cadmium causes strong splicing inhibition. Despite the knowledge about splicing inhibition by cadmium, it is still unclear if other metal contaminants can cause the same response. In the present study, we have demonstrated that the effect of cadmium exposure on splicing inhibition is much stronger than that of other divalent metals such as cobalt and manganese. Data presented here also indicate that intron retention occurs randomly among the fungal transcripts, as verified by analyzing differently affected transcripts. In addition, we identified in the genome of B. emersonii the genes encoding the snRNA splicing components U1, U2, U4, U5 and U6 and observed that spliceosome snRNAs are upregulated in the presence of metals, in particular snRNA U1 in cells under cadmium exposure. This observation suggests that snRNA upregulation might be a defense of the fungal cell against the metal stress condition.
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Affiliation(s)
- Letícia Harumi Oshiquiri
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Suely Lopes Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Raphaela Castro Georg
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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Oshiquiri LH, Dos Santos KRA, Ferreira Junior SA, Steindorff AS, Barbosa Filho JR, Mota TM, Ulhoa CJ, Georg RC. Trichoderma harzianum transcriptome in response to cadmium exposure. Fungal Genet Biol 2019; 134:103281. [PMID: 31626987 DOI: 10.1016/j.fgb.2019.103281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/18/2022]
Abstract
Cadmium (Cd) is a heavy metal present in the environment mainly as a result of industrial contamination that can cause toxic effects to life. Some microorganisms, as Trichoderma harzianum, a fungus used in biocontrol, are able to survive in polluted environments and act as bioremediators. Aspects about the tolerance to the metal have been widely studied in other fungi although there are a few reports about the response of T. harzianum. In this study, we determined the effects of cadmium over growth of T. harzianum and used RNA-Seq to identify significant genes and processes regulated in the metal presence. Cadmium inhibited the fungus growth proportionally to its concentration although the fungus exhibited tolerance as it continued to grow, even in the highest concentrations used. A total of 3767 (1993 up and 1774 down) and 2986 (1606 up and 1380 down) differentially expressed genes were detected in the mycelium of T. harzianum cultivated in the presence of 1.0 mg mL-1 or 2.0 mg mL-1 of CdCl2, respectively, compared to the absence of the metal. Of these, 2562 were common to both treatments. Biological processes related to cellular homeostasis, transcription initiation, sulfur compound biosynthetic and metabolic processes, RNA processing, protein modification and vesicle-mediated transport were up-regulated. Carbohydrate metabolic processes were down-regulated. Pathway enrichment analysis indicated induction of glutathione and its precursor's metabolism. Interestingly, it also indicated an intense transcriptional induction, especially by up-regulation of spliceosome components. Carbohydrate metabolism was repressed, especially the mycoparasitism-related genes, suggesting that the mycoparasitic ability of T. harzianum could be affected during cadmium exposure. These results contribute to the advance of the current knowledge about the response of T. harzianum to cadmium exposure and provide significant targets for biotechnological improvement of this fungus as a bioremediator and a biocontrol agent.
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Affiliation(s)
- Letícia Harumi Oshiquiri
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | | | | | - Andrei Stecca Steindorff
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | | | - Thuana Marcolino Mota
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | - Cirano José Ulhoa
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | - Raphaela Castro Georg
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil.
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