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Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi

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Abstract

Fungi are key players in biotechnological applications. Although several studies focusing on fungal diversity and genetics have been performed, many details of fungal biology remain unknown, including how cellulolytic enzymes are modulated within these organisms to allow changes in main plant cell wall compounds, cellulose and hemicellulose, and subsequent biomass conversion. With the advent and consolidation of DNA/RNA sequencing technology, different types of information can be generated at the genomic, structural and functional levels, including the gene expression profiles and regulatory mechanisms of these organisms, during degradation-induced conditions. This increase in data generation made rapid computational development necessary to deal with the large amounts of data generated. In this context, the origination of bioinformatics, a hybrid science integrating biological data with various techniques for information storage, distribution and analysis, was a fundamental step toward the current state-of-the-art in the postgenomic era. The possibility of integrating biological big data has facilitated exciting discoveries, including identifying novel mechanisms and more efficient enzymes, increasing yields, reducing costs and expanding opportunities in the bioprocess field. In this review, we summarize the current status and trends of the integration of different types of biological data through bioinformatics approaches for biological data analysis and enzyme selection.

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Acknowledgements

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Funding

This work was supported by grants from the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP 2015/09202-0 and 2018/19660-4), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Biology Program 88882.160095/2013–01), and Conselho Nacional de Desenvolvimento Científico e Tecnológico for a Research Fellowship to APS (CNPq 312777/2018-3) and grants to CAS (CNPq Univeral 430350/2018-0). MACH received fellowship from FAPESP (2020/10536-9). AHA and RRR received PhD fellowships from FAPESP (2019/03232-6 and 2020/13420-1, respectively).

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Authors and Affiliations

  1. Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil

    Jaire A. Ferreira Filho, Rafaela R. Rosolen, Deborah A. Almeida, Paulo Henrique C. de Azevedo, Maria Lorenza L. Motta, Alexandre H. Aono, Clelton A. dos Santos, Maria Augusta C. Horta & Anete P. de Souza

  2. Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil

    Clelton A. dos Santos

  3. Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil

    Maria Augusta C. Horta

  4. Department of Plant Biology, Institute of Biology, UNICAMP, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil

    Anete P. de Souza

Authors
  1. Jaire A. Ferreira Filho
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  2. Rafaela R. Rosolen
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  3. Deborah A. Almeida
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  4. Paulo Henrique C. de Azevedo
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  5. Maria Lorenza L. Motta
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  6. Alexandre H. Aono
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  7. Clelton A. dos Santos
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  8. Maria Augusta C. Horta
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  9. Anete P. de Souza
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Contributions

APS and JAFF conceptualized the manuscript. JAFF, RRR, DAA, PHCA, MLLM, AHA, CAS, MACH and APS wrote the manuscript. JAFF, AHA and MLLM prepared the figures. JAFF and PHCA prepared the tables. CAS, MACH and APS revised the manuscript.

Corresponding author

Correspondence to Anete P. de Souza.

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Filho, J.A.F., Rosolen, R.R., Almeida, D.A. et al. Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. 3 Biotech 11, 475 (2021). https://doi.org/10.1007/s13205-021-03032-y

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  • DOI: https://doi.org/10.1007/s13205-021-03032-y

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