Fungal Biotechnology for Biofuel Production

Book Series: Mycology: Current and Future Developments

Volume 1

by

Roberto N. Silva

DOI: 10.2174/97816810807411150101
eISBN: 978-1-68108-074-1, 2016
ISBN: 978-1-68108-075-8
ISSN: 2452-0772 (Print)
ISSN: 2452-0780 (Online)



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Mycology: Current and Future Development is a book series that brings together t...[view complete introduction]

Table of Contents

Foreword

- Pp. i

Christian P. Kubicek

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Preface

- Pp. ii

Roberto Nascimento Silva

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List of Contributors

- Pp. iii-vii (5)

Roberto Nascimento Silva

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The Panorama for Biofuels Biotechnology: Present and Future

- Pp. 3-22 (20)

Renato Graciano de Paula, Amanda Cristina Campos Antoniêto and Roberto N. Silva

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Enzymes and Accessory Proteins Involved in the Hydrolysis of Lignocellulosic Biomass for Bioethanol Production

- Pp. 23-56 (34)

Carolina Araújo Barcelos, Vanessa Alves Rocha, Cláudia Groposo, Aline Machado de Castro and Nei Pereira Jr

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Enzymes Prospection from Fungi and Biomass Pretreatment for Biorefinery Application

- Pp. 57-81 (25)

Maria de Lourdes T.M. Polizeli, Rosane M. Peralta, Adelar Bracht, Michele Michelin and Alexandre F. Somera

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Transcriptional Regulation and Responses in Filamentous Fungi Exposed to Lignocellulose

- Pp. 82-127 (46)

Paul Daly, Jolanda M. van Munster, Roxane Raulo and David B. Archer

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Fungal Metabolic Engineering for Biofuel Production

- Pp. 128-147 (20)

Daniel P. Kiesenhofer, Astrid R. Mach-Aigner and Robert L. Mach

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Heterologous Expression of Carbohydrate-Active Enzymes in Filamentous Fungi

- Pp. 148-201 (54)

Marcelo Ventura Rubio, Robson Tramontina, Thiago Augusto Gonçalves, Cristiane Akemi Uchima, Fernando Segato, Fabio Marcio Squina and André Ricardo de Lima Damasio

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Protein Engineering Strategies to Improve Efficiency in Biomass Degradation

- Pp. 202-221 (20)

Lucas F. Ribeiro, Tina Xiong, Pricila Hauk and Liliane F.C. Ribeiro

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Engineering Saccharomyces cerevisiae for Efficient D-Xylose and L-Arabinose Fermentation

- Pp. 222-242 (21)

Mekonnen M. Demeke, Maria R. Foulquié-Moreno and Johan M. Thevelein

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Application of Fungal Lipases in Biodiesel Production: Technical and Economic Aspects Influencing the Enzymatic Route

- Pp. 243-275 (33)

Denise M.G. Freire, Erika C.G. Aguieiras and Elisa D. Cavalcanti-Oliveira

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Immobilization of Plant Cell Wall Degrading Enzymes

- Pp. 276-315 (40)

César Rafael Fanchini Terrasan, Eliane Pereira Cipolatti, Livia Tereza de Andrade Souza, Rosana Oliveira Henriques, Sonia Moreno-Pérez, Wilson Galvão de Morais Junior, Amadi Onyetugo Chioma, José Manuel Guisan and Benevides Costa Pessela

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Large Scale Production of Cellulases for Biomass Degradation

- Pp. 316-328 (13)

Rosymar C. de Lucas, Mariana Cereia and Marisa A. de L. Coral

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Fungal Consortia for Conversion of Lignocellulose into Bioproducts

- Pp. 329-365 (37)

Marta Zoglowek, Gustav H. Hansen, Peter S. Lübeck and Mette Lübeck

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From Genomes to Transcriptomes and Secretomes: A Fungal Perspective with Insights into Biorefinery Applications

- Pp. 366-394 (29)

Carlaile F.O. Nogueira, Gabriela L. Berto, Gustavo H. Goldman, Rolf A. Prade and Fernando Segato

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Systems and Synthetic Biology Approaches for Fungal Engineering

- Pp. 395-418 (24)

Gerardo Ruiz Amores, María-Eugenia Guazzaroni, Letícia Magalhães Arruda and Rafael Silva-Rocha

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Subject Index

- Pp. 419-428 (10)

Roberto Nascimento Silva

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Foreword

Today’s chemical technology is still strongly dependent on fossil starting materials, fuel production being only one but a dominant example. Yet environmental concerns and political constraints have put the replacement of fossil carbon sources in industrial processes by compounds that are available in even larger amounts, but whose utilization can be performed in a carbon dioxide neutral way, at a top place in the list of technological advances of the 21st century. Quantitatively, this requirement can only be fulfilled by plant biomass since plants use carbon dioxide fixation via photosynthesis as the sole source of carbon. Furthermore, the dry plant biomass consists mainly of three polymers (cellulose, hemicelluloses and lignin), which – after depolymerization to the monomer constituents (hexoses, pentoses and phenylpropan substances) – can be used as a basis for the industrial production of ethanol or platform chemicals by fermentation or biocatalysis (biorefinery). Clearly, the production of these monomeric constituents by reliable processes and in high amounts that satisfy economic requirements and avoiding the production of hazardous byproducts is essential to the biorefinery concept. There is general consent that this can only be achieved by enzymatic hydrolysis.

Yet biological processes are slow on technological scales. Therefore, the composition of the enzymes used, their properties and the kinetics of the hydrolysis process are still major areas which need improvement and optimization. To do this on a science-driven basis, however, more basic knowledge is needed. Almost all of the enzymes used are derived from fungi. Fungi, the fifth kingdom, play a predominant role in the degradation of lignocellulose biomass in nature, and consequently some of them have therefore served as models or workhorses for the production of the respective enzymes for plant biomass hydrolysis in academic laboratories and on an industrial scale. This book therefore presents an overview of the progress and latest achievements in the understanding of these processes at genomic, transcriptomic and proteomic levels which are indispensable prerequisites for further improvement of the process, and highlights areas for further research development.

Christian P. Kubicek
Research Division Biotechnology and Microbiology,
Institute of Chemical Engineering,
Technische Universität Wien,
Gumpendorferstraße 1a, 1060 Vienna,
Austria


Preface

The world is going through major environmental changes and new energy demands are required. With the imminent shortage of energy sources based on fossil, new renewable energy source have been used for both purposes as fuel as well for industrial power generation. However, to access these renewable matrices, it is necessary a full understanding of the process in order to reach biofuels at low cost. In this sense, biotechnology comes as a new science that combines biology of various knowledge areas such as biochemistry, microbiology, enzymology, molecular and systems biology. The use of microorganisms in the processing of biomass in order to produce biofuels such as ethanol or biodiesel, as well as derivatives with biotechnological potential has been an alternative to implement the so-called biorefinery.

In the following chapters of this work the current panorama of biofuel and the using of fungi in biotechnology for the production of bioethanol and biodiesel will be discussed. In this sense, an overview of the process and the global biofuels market will be presented, followed by the basic biology of degradation of plant biomass, enzymology and regulation of gene expression of genes encoding enzymes that degrade plant biomass. In a second step, the processes already established will be presented in biorefinery such as large-scale production of hydrolytic enzymes as well as the general and specific aspects of biodiesel production. Subsequently, the presentation of enzymes used in the degradation of biomass in its immobilized form and the exploration of new enzymes will be discussed in addition to the benefits of using consortium of microorganisms for use in biorefinery. Finally the current situation of biomass degradation processes and production of biofuel within the scope of ‘omics’ sciences and the integration of these processes from the point of view of synthetic and systems biology will be discussed.

We hope this book will contribute both in the academic field but also in the industrial area to the understanding and implementation of biofuel production worldwide.

Roberto Nascimento Silva
Department of Biochemistry and Immunology,
Ribeirão Preto Medical School,
University of São Paulo (USP),
Ribeirão Preto, São Paulo,
Brazil

List of Contributors

Editor(s):
Roberto N. Silva
Department of Biochemistry and Immunology
Ribeirão Preto Medical School
University of São Paulo (USP)
Ribeirão Preto
SP
Brazil




Contributor(s):
Adelar Bracht
Department of Biochemistry
Universidade Estadual de Maringá
Maringa
Brazil


Alexandre F. Somera
Biology Department, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto
Universidade de São Paulo
Sao Paulo
Brazil


Aline Machado de Castro
Laboratories of Bioprocesses Development - Departament of Biochemical Engineering - School of Chemistry, Center of Technology
Federal University of Rio de Janeiro
Rio de Janeiro - RJ, 21941-901
Brazil


Amadi Onyetugo Chioma
Department of Microbiology, Faculty of Biological Sciences
University of Nigeria
Nsukka 410001
Nigeria


Amanda Cristina Campos Antoniêto
Department of Biochemistry and Immunology, Ribeirão Preto Medical School
University of São Paulo (USP)
Ribeirão Preto
SP
Brazil


André Ricardo de Lima Damásio
CTBE, Brazilian Bioethanol Science and Technology Laboratory, CNPEM
National Center for Research in Energy and Materials
Campinas-SP
Brazil
/
University of Campinas, IB - Institute of Biology, Department of Biochemistry and Tissue Biology
Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz
13083-862 Campinas/SP
Brazil


Astrid R. Mach-Aigner
Institute of Chemical Engineering
Vienna University of Technologyc
Vienna
Austria


Benevides Costa Pessela
Depto. Biotecnología y Microbiología de Alimentos. Instituto de Investigación en Ciencias de los Alimentos
CIAL. Consejo Superior de Investigaciones Científicas – CSIC Cantoblanco, Campus UAM, 28049
Madrid
España


Carlaile F. O. Nogueira
Department of Biotechnology, Escola de Engenharia de Lorena
University of São Paulo
Lorena
SP
Brazil


Carolina Araújo Barcelos
Laboratories of Bioprocesses Development - Departament of Biochemical Engineering - School of Chemistry, Center of Technology
Federal University of Rio de Janeiro
Rio de Janeiro - RJ, 21941-901
Brazil


César Rafael Fanchini Terrasan
Departamento de Biocatalisis Enzimática. Instituto de Catálisis y Petroleoquímica
ICP Consejo Superior de Investigaciones Científicas-CSIC
Madrid
España


Christian P. Kubicek
Research Area Biotechnology and Microbiology
Institute of Chemical Engineering
TU Wien Getreidemarkt 9—166.5
Vienna
Austria


Cláudia Groposo
Laboratories of Bioprocesses Development - Departament of Biochemical Engineering - School of Chemistry, Center of Technology
Federal University of Rio de Janeiro
Rio de Janeiro
RJ, 21941-901
Brazil


Cristiane Akemi Uchima
CTBE, Laboratório Nacional de Ciência e Tecnologia do Bioetanol, CNPEM
Centro Nacional de Pesquisa em Energia e Materiais
Campinas-SP
Brazil


Daniel P. Kiesenhofer
Institute of Chemical Engineering
Vienna University of Technology
Vienna
Austria


David B Archer
School of Life Science
University of Nottingham, University Park
Nottingham
NG7 2RD
UK


Denise M. G. Freire
Biochemistry Department, Chemistry Institute
Federal University of Rio de Janeiro
Rio de Janeiro
Brazil


Eliane Pereira Cipolatti
Depto. Biotecnología y Microbiología de Alimentos. Instituto de Investigación en Ciencias de los Alimentos
CIAL. Consejo Superior de Investigaciones Científicas – CSIC Cantoblanco, Campus UAM, 28049
Madrid
España
/
Dpto. Chemical and Food Engineering
Federal University of Santa Catarina (UFSC)
P.O. Box 476, 88040-900
Florianópolis
Brazil


Elisa D. Cavalcanti-Oliveira
Biochemistry Department, Chemistry Institute
Federal University of Rio de Janeiro
Rio de Janeiro
Brazil


Erika C. G. Aguieiras
Biochemistry Department, Chemistry Institute
Federal University of Rio de Janeiro
Rio de Janeiro
Brazil


Fabio Marcio Squina
CTBE, Brazilian Bioethanol Science and Technology Laboratory, CNPEM
National Center for Research in Energy and Materials
Campinas
SP
Brazil


Fernando Segato
EEL, Escola de Engenharia de Lorena, USP
Universidade de São Paulo
Lorena
SP
Brazil
/
Department of Biotechnology
Escola de Engenteria, de Lorena, University of Sao Paulo
Lorena
SP
Brazil


Gabriela L. Berto
Department of Biotechnology, Escola de Engenharia de Lorena
University of São Paulo
Lorena
SP
Brazil


Gerardo Ruiz Amores
FMRP
University of São Paulo
Ribeirao Preto
SP
Brazil


Gustav H. Hansen
Department of Systems Biology
Technical University of Denmark
Soeltofts Plads bldg. 223
DK-2800 Kgs. Lyngby
Denmark


Gustavo H. Goldman
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo
Ribeirão Preto
SP
Brazil


Johan M. Thevelein
Laboratory of Molecular Cell Biology
Institute of Botany and Microbiology
Leuven
KU
Belgium
/
Department of Molecular Microbiology
VIB, Kasteelpark Arenberg 31
B-3001 Leuven-Heverlee
Flanders
Belgium


Jolanda M van Munster
School of Life Sciences
University of Nottingham, University Park
Nottingham
NG7 2RD
UK


José Manuel Guisan
Departamento de Biocatalisis Enzimática. Instituto de Catálisis y Petroleoquímica
ICP Consejo Superior de Investigaciones Científicas-CSIC
Madrid
España


Letícia Magalhães Arruda
FMRP
University of São Paulo
Ribeirao Preto
SP
Brazil


Liliane F.C. Ribeiro
Department of Chemical, Biochemical and Environmental Engineering
University of Maryland
Baltimore County
Baltimore
USA


Livia Tereza de Andrade Souza
Depto. Biotecnología y Microbiología de Alimentos. Instituto de Investigación en Ciencias de los Alimentos
CIAL. Consejo Superior de Investigaciones Científicas – CSIC Cantoblanco, Campus UAM, 28049
Madrid
España
/
Institute of Biological Science
Federal University of Minas Gerais
Pampulha. Box 486, 31270-901
Belo Horizonte
Brazil


Lucas F. Ribeiro
Chemical and Biomolecular Engineering
Johns Hopkins University
Baltimore
USA


Marcelo Ventura Rubio
CTBE, Brazilian Bioethanol Science and Technology Laboratory, CNPEM
National Center for Research in Energy and Materials
Campinas
SP
Brazil
/
UNICAMP - University of Campinas, IB - Institute of Biology, Department of Biochemistry and Tissue Biology
Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz
13083-862 Campinas
SP
Brazil


Maria de Lourdes T. M. Polizeli
Biology Department, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto
Universidade de São Paulo
São Paulo
Brazil


Maria R. Foulquié-Moreno
Laboratory of Molecular Cell Biology
Institute of Botany and Microbiology
KU
Leuven
/
Department of Molecular Microbiology
VIB, Kasteelpark Arenberg 31
B-3001 Leuven-Heverlee
Flanders
Belgium


María-Eugenia Guazzaroni
FFCLRP
University of São Paulo
Ribeirao Preto
SP
Brazil


Mariana Cereia
Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto
Universidade de São Paulo
Sao Paulo
Brazil


Marisa A. de L. Coral
Novozymes Latin America Ltda
Araucária
PR
Brazil


Marta Zoglowek
Section for Sustainable Biotechnology
Aalborg University Copenhagen, A. C. Meyers Vænge 15
DK 2450 Copenhagen
SV
Denmark


Mekonnen M. Demeke
Laboratory of Molecular Cell Biology
Institute of Botany and Microbiology
KU
Leuven
/
Department of Molecular Microbiology
VIB, Kasteelpark Arenberg 31
B-3001 Leuven-Heverlee
Flanders
Belgium


Mette Lübeck
Section for Sustainable Biotechnology
Aalborg University Copenhagen, A. C. Meyers Vænge 15
DK 2450 Copenhagen
SV
Denmark


Michele Michelin
Biology Department, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto
Universidade de São Paulo
São Paulo
Brazil


Nei Pereira Jr
Laboratories of Bioprocesses Development - Departament of Biochemical Engineering - School of Chemistry
Center of Technology, Federal University of Rio de Janeiro
Rio de Janeiro
RJ, 21941-901
Brazil


Paul Daly
School of Life Sciences
University of Nottingham, University Park
Nottingham
NG7 2RD
UK


Peter S. Lübeck
Section for Sustainable Biotechnology
Aalborg University Copenhagen
A. C. Meyers Vænge 15
DK 2450 Copenhagen
SV
Denmark


Pricila Hauk
Institute for Bioscience and Biotechnology Research
University of Maryland
College Park
USA
/
Fischell Department of Bioengineering
University of Maryland
College Park
USA


Rafael Silva-Rocha
FMRP
University of São Paulo
Ribeirao Preto
Sao Paulo
Brazil


Renato Graciano de Paula
Department of Biochemistry and Immunology, Ribeirão Preto Medical School
University of São Paulo (USP)
Ribeirão Preto
SP
Brazil


Robert L. Mach
Institute of Chemical Engineering
Vienna University of Technology
Vienna
Austria


Roberto N. Silva
Department of Biochemistry and Immunology, Ribeirão Preto Medical School
University of São Paulo (USP)
Ribeirão Preto
Sao Paulo
Brazil


Robson Tramontina
CTBE, Brazilian Bioethanol Science and Technology Laboratory, CNPEM
National Center for Research in Energy and Materials
Campinas
SP
Brazil
/
UNICAMP - University of Campinas, IB - Institute of Biology, Department of Biochemistry and Tissue Biology
Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz
13083-862 Campinas
SP
Brazil


Rolf A. Prade
Department of Microbiology and Molecular Genetics
Oklahoma State University
Stillwater
OK
USA


Rosana Oliveira Henriques
Depto. Biotecnología y Microbiología de Alimentos. Instituto de Investigación en Ciencias de los Alimentos
CIAL. Consejo Superior de Investigaciones Científicas – CSIC Cantoblanco, Campus UAM, 28049
Madrid
España
/
Dpto. Chemical and Food Engineering
Federal University of Santa Catarina (UFSC)
P.O. Box 476, 88040-900
Florianópolis
Brazil


Rosane M. Peralta
Department of Biochemistry
Universidade Estadual de Maringá
Maringa
Brazil


Rosymar C. de Lucas
Universidade Federal do Parana
PR
Brazil
/
Novozymes, Araucária
PR
Brazil


Roxane Raulo
School of Life Sciences
University of Nottingham, University Park
Nottingham
NG7 2RD
UK


Sonia Moreno-Pérez
Depto. Biotecnología y Microbiología de Alimentos. Instituto de Investigación en Ciencias de los Alimentos
CIAL. Consejo Superior de Investigaciones Científicas – CSIC Cantoblanco, Campus UAM, 28049
Madrid
España
/
Departamento de Biocatalisis Enzimática. Instituto de Catálisis y Petroleoquímica
ICP Consejo Superior de Investigaciones Científicas-CSIC
Madrid
España


Thiago Augusto Gonçalves
CTBE, Brazilian Bioethanol Science and Technology Laboratory, CNPEM
National Center for Research in Energy and Materials
Campinas
SP
Brazil
/
UNICAMP - University of Campinas, IB - Institute of Biology, Department of Biochemistry and Tissue Biology
Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz
13083-862 Campinas
SP
Brazil


Tina Xiong
Chemical and Biomolecular Engineering
Johns Hopkins University
Baltimore
USA


Vanessa Alves Rocha
Laboratories of Bioprocesses Development - Departament Of Biochemical Engineering - School of Chemistry, Center of Technology
Federal University of Rio de Janeiro
Rio de Janeiro
Brazil


Wilson de Morais
Depto. Biotecnología y Microbiología de Alimentos. Instituto de Investigación en Ciencias de los Alimentos
CIAL. Consejo Superior de Investigaciones Científicas – CSIC Cantoblanco, Campus UAM, 28049
Madrid
España
/
School of Chemical Engineeringy
Federal University of Uberlândia. J, Campus Santa Mônica - Bloco 1K
38400-902, Uberlândia
Brazil




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