Roberto Nascimento Silva

Universidade de São Paulo

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Renato Graciano de Paula

Universidade Federal do Espírito Santo

Cirano José Ulhôa

Universidade Católica Dom Bosco

Rafael Silva‐Rocha

Cell Medica (Switzerland)

Andrei Stecca Steindorff

Joint Genome Institute

Amanda Cristina Campos Antoniêto

Universidade de São Paulo

Karoline Maria Vieira Nogueira

Universidade de São Paulo

Valdirene Neves Monteiro

Universidade Estadual de Goiás

Wellington Ramos Pedersoli

Universidade de São Paulo

Fausto Almeida

Universidade de São Paulo

Gustavo H. Goldman

Universidade de São Paulo

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Universidade de São Paulo

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Universidade de Ribeirão Preto

Universidade Federal de Goiás

Universidade Estadual de Campinas (UNICAMP)

Universidade de Brasília

Universidade Estadual Paulista (Unesp)

Universidade Federal do Rio de Janeiro

TU Wien

Brazilian Agricultural Research Corporation

Hospital Universitário da Universidade de São Paulo

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Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reeseiusing high-throughput genomic and proteomic analyses

Biotechnology for Biofuels (2014)

Lílian dos Santos Castro Wellington Ramos Pedersoli Amanda Cristina Campos Antoniêto Andrei Stecca Steindorff Rafael Silva‐Rocha

The filamentous fungus Trichoderma reesei is a major producer of lignocellulolytic enzymes utilized by bioethanol industries. However, to achieve low cost second generation bioethanol production on an industrial scale an efficient mix of hydrolytic enzymes is required for the deconstruction of plant biomass. In this study, we investigated the molecular basis for lignocellulose-degrading enzyme production T. reesei during growth in cellulose, sophorose, and glucose. We examined and compared the transcriptome and differential secretome (2D-DIGE) of T. reesei grown in cellulose, sophorose, or glucose as the sole carbon sources. By applying a stringent cut-off threshold 2,060 genes were identified as being differentially expressed in at least one of the respective carbon source comparisons. Hierarchical clustering of the differentially expressed genes identified three possible regulons, representing 123 genes controlled by cellulose, 154 genes controlled by sophorose and 402 genes controlled by glucose. Gene regulatory network analyses of the 692 genes differentially expressed between cellulose and sophorose, identified only 75 and 107 genes as being specific to growth in sophorose and cellulose, respectively. 2D-DIGE analyses identified 30 proteins exclusive to sophorose and 37 exclusive to cellulose. A correlation of 70.17% was obtained between transcription and secreted protein profiles. Our data revealed new players in cellulose degradation such as accessory proteins with non-catalytic functions secreted in different carbon sources, transporters, transcription factors, and CAZymes, that specifically respond in response to either cellulose or sophorose.

10.1186/1754-6834-7-41

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Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis

Frontiers in Microbiology (2016)

Lílian dos Santos Castro Renato Graciano de Paula Amanda Antoniêto Gabriela Félix Persinoti Rafael Silva‐Rocha

We defined the role of the transcriptional factor–XYR1–in the filamentous fungus Trichoderma reesei during cellulosic material degradation. In this regard, we performed a global transcriptome analysis using RNA-Seq of the ∆xyr1 mutant strain of T. reesei compared with the parental strain QM9414 grown in the presence of cellulose, sophorose, and glucose as sole carbon sources. We found that 5885 genes were expressed differentially under the three tested carbon sources. Of these, 322 genes were upregulated in the presence of cellulose, while 367 and 188 were upregulated in sophorose and glucose, respectively. With respect to genes under the direct regulation of XYR1, 30 and 33 are exclusive to cellulose and sophorose, respectively. The most modulated genes in the ∆xyr1 belong to Carbohydrate-Active Enzymes (CAZymes), transcription factors, and transporters families. Moreover, we highlight the downregulation of transporters belonging to the MFS and ABC transporter families. Of these, MFS members were mostly downregulated in the presence of cellulose. In sophorose and glucose, the expression of these transporters was mainly upregulated. Our results revealed that MFS and ABC transporters could be new players in cellulose degradation and their role was shown to be carbon source-dependent. Our findings contribute to a better understanding of the regulatory mechanisms of XYR1 to control cellulase gene expression in T. reesei in the presence of cellulosic material, thereby potentially enhancing its application in several biotechnology fields.

10.3389/fmicb.2016.00175

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Citations (92)

New Insights in Trichoderma harzianum Antagonism of Fungal Plant Pathogens by Secreted Protein Analysis

Current Microbiology (2010)

Valdirene Neves Monteiro Roberto Nascimento Silva Andrei Stecca Steindorff Fábio T. Costa Eliane Ferreira Noronha

Macrophomina phaseolina

Trichoderma harzianum

Chitinase

Secretory protein

Proteome

Trichoderma

Fusarium solani

Fungal protein

10.1007/s00284-010-9611-8

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Fungal Extracellular Vesicles Associated with the Structuring and Remodelling of the Trichoderma harzianum Cell Wall

Research Square (Research Square) (2024)

Eriston Vieira Gomes Cirano José Ulhôa Rosa E. Cardoza Santiago Gutiérrez Roberto Nascimento Silva

Abstract Purpose The main structure of the fungal cell wall (CW) consists of crosslinked glucans, chitin, and glycoproteins. This structure is responsible for the cell shape. It also provides osmotic and physical protection to cells. However, sophisticated CW remodeling is required for fungal morphogenesis and reproduction. This requires remarkable dynamism of the fungal CW, which must combine contrasting properties, such as elasticity and stiffness. Different fungal species assemble their CWs in different ways. Extracellular vesicles (EVs) are a general term for cell-derived bilayered phospholipid membrane particles that enter the extracellular environment. EVs have a wide variety of origins, sizes, cargos, membrane compositions, and biological functions. Recent advances in this emerging field have contributed to the construction of a solid knowledge base that is rapidly evolving into the formulation of applied tools, including drug delivery systems and vaccine prototypes.

10.21203/rs.3.rs-4718177/v1

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CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Leonardo Martins‐Santana Renato Graciano de Paula Adriano Gomes Silva Douglas Christian Borges Lopes Roberto Nascimento Silva

Abstract Background Trichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Over the last decades, there have been a strong increase in the understanding of the regulatory network controlling cellulase-coding gene expression in response to a number of inducers and environmental signals. In this sense, the role of calcium and the Calcineurin-responsive protein (CRZ1) has been investigated in industrially relevant strains of T. reesei RUT-C30, but this system has not been investigated in wild-type reference strain of this fungus. Results Here, we investigated the role of CRZ1 and Ca 2+ signaling in the fungus T. reesei QM6a. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reesei Δ crzl strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca 2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei , suggesting the existence of additional Ca 2+ sensing mechanisms in this fungus. Conclusions This work presents new evidence on the regulatory role of CRZ1 and Ca 2+ sensing in the regulation of cellulolytic enzymes in T. reesei , evidencing significant and previously unknown function of this Ca 2+ sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca 2+ transport. Taken together, the data obtained here provide new evidence on the regulatory network of T. reesei related to plant biomass deconstruction.

10.1101/622647

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Citations (2)

CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a

Genetics and Molecular Biology (2020)

Leonardo Martins‐Santana Renato Graciano de Paula Adriano Gomes Silva Douglas Christian Borges Lopes Roberto Nascimento Silva

Trichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Here we investigated the role of CRZ1 and Ca2+signaling in the fungus T. reesei QM6a concerning holocellulases production. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reeseiAcrz1 strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei, highlighting the role of the major regulator Ca2+ on the signaling for holocellulases transcriptional control in the most part of cellulases genes here investigated. This work presents new evidence on the regulatory role of CRZ1 and Ca2+ sensing in the regulation of cellulolytic enzymes in T. reesei, evidencing significant and previously unknown function of this Ca2+sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca2+ transport.

10.1590/1678-4685-gmb-2019-0244

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Citations (29)

Expression analysis of the exo-β-1,3-glucanase from the mycoparasitic fungus Trichoderma asperellum

Microbiological Research (2008)

César Marcos Marcello Andrei Stecca Steindorff Silvana Petrofeza da Silva Roberto Nascimento Silva Luiz Artur Mendes Bataus

Glucanase

Trichoderma

10.1016/j.micres.2008.08.002

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Citations (81)

Expression analysis of the α-1,2-mannosidase from the mycoparasitic fungus Trichoderma harzianum

Biological Control (2015)

Paulo Roberto da Mota Marcela Suriani Ribeiro Raphaela de Castro Georg Gabrielle Rosa Silva Renato Graciano de Paula

Sclerotinia Sclerotiorum

Trichoderma harzianum

Chitinase

10.1016/j.biocontrol.2015.12.013

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Citations (8)

Editorial for Special Issue: Fungal Biology and Interactions

Microorganisms (2024)

Roberto Nascimento Silva Renato Graciano de Paula

As we conclude this Special Issue on fungal biology and interactions, it is only appropriate to reflect on the remarkable progress our scientific community has made in unraveling the mysteries of the fungal kingdom [...]

10.3390/microorganisms12020282

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Cytotoxic activity of l-lysine alpha-oxidase against leukemia cells

Seminars in Cancer Biology (2021)

Mariana Costa Nascimento Roberto Nascimento Silva

10.1016/j.semcancer.2021.09.015

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Citations (4)