Genetic Transformation Systems in Fungi, Volume 2

274 Pages·2015·10.085 MB·English

by  Marco A. van den Berg, Karunakaran Maruthachalam (eds.)

Fungal Biology
Marco A. van den Berg
Karunakaran Maruthachalam E ditors
Genetic
Transformation
Systems in
Fungi, Volume 2
Fungal Biology
Series Editors:
Vijai Kumar Gupta, PhD
Molecular Glycobiotechnology Group, Department of Biochemistry,
School of Natural Sciences, National University of Ireland Galway,
Galway, Ireland
Maria G. Tuohy, PhD
Molecular Glycobiotechnology Group, Department of Biochemistry,
School of Natural Sciences, National University of Ireland Galway,
Galway, Ireland
For further volumes:
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Marco A. van den Berg
Karunakaran M aruthachalam
Editors
Genetic Transformation
Systems in Fungi,
Volume 2
Editors
Marco A. van den Berg, Ph.D. Karunakaran Maruthachalam, Ph.D.
Applied Biochemistry Department Global Marker Technology Lab
DSM Biotechnology Center (DuPont-Pioneer)
Delft , The Netherlands E.I.DuPont India Pvt Ltd
DuPont Knowledge Center
Hyderabad , Telangana , India
ISSN 2198-7777 ISSN 2198-7785 (electronic)
ISBN 978-3-319-10502-4 ISBN 978-3-319-10503-1 (eBook)
DOI 10.1007/978-3-319-10503-1
Springer Cham Heidelberg New York Dordrecht London
Library of Congress Control Number: 2014952786
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Pref ace
Fungi are a highly versatile class of microorganisms and their habitats are as
diverse. In nature, fungi play a crucial role in a range of degradation pro-
cesses, enabling recycling of valuable raw materials by wood decaying fungi
like the white rot fungus Phanerochaete chrysosporium. On the other hand,
fungi can be pests to food production like the rice blast fungus M agnaporthe
oryzae . Furthermore, mankind exploits the enzymatic opportunities of fungi
through classical industrial processes as ethanol production by the yeast
Saccharomyces cerevisiae and heterologous enzyme production by fi lamen-
tous fungi as Trichoderma reesei. All these stimulated an enormous number
of studies trying to understand as well as exploit the metabolic capabilities of
various fungal species.
O ne of the game-changing breakthroughs in fungal research was the
development of genetic transformation technology. This enabled researchers
to effi ciently modify the gene content of fungi and study the functional rele-
vance. Interestingly, the fi rst available method (protoplast or spheroplast
transformation) evolved from an existing classical method called protoplast
fusion, a process which also introduces DNA into a receiving cell however in
an uncontrolled way. This publication aims to give an overview of all existing
transformation methods used for yeasts and fungi.
V olume I describes in detail the different classical methods as electropora-
tion, protoplast, Agrobacterium mediated, lithium acetate and biolistic transfor-
mation as well as more recently developed methods. Transformation methods
do not describe the whole story; DNA must enter the cell, the nucleus, and
fi nally integrate in the genome, if required also at predetermined positions.
Several chapters will update on the current insights in these processes.
V olume II describes transformation-associated methods and tools as cell
fusion, repetitive elements, automation, analysis, markers, and vectors; this vol-
ume refl ects the many relevant elements at hand for the modern fungal researcher.
This publication is meant not only as reference material for the experienced
researcher, but also as introduction for the emerging scientist. Therefore, all
methods are supported by several illustrative example protocols from various
fungal species and laboratories around the world, which will be a good starting
position to develop a working protocol for other fungal species being studied.
Delft, The Netherlands Marco A. van den Berg
Hyderabad, Telangana, India Karunakaran Maruthachalam
v
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Contents
Part I Endogenous DNA: Cell Fusion
1 Anastomosis and Heterokaryon Formation ............................... 3
Martin Weichert and André Fleißner
2 Induction of the Sexual Cycle in Filamentous Ascomycetes .... 23
Jos Houbraken and Paul S. Dyer
3 What Have We Learned by Doing Transformations
in N eurospora tetrasperma? ......................................................... 47
Durgadas P. Kasbekar
Part II Endogenous DNA: Repetitive Elements
4 Repeat-Induced Point Mutation: A Fungal-Specific,
Endogenous Mutagenesis Process............................................... 55
James K. Hane, Angela H. Williams, Adam P. Taranto,
Peter S. Solomon, and Richard P. Oliver
5 Calculating RIP Mutation in Fungal Genomes
Using RIPCAL ............................................................................. 69
James K. Hane
6 Fungal Transposable Elements ................................................... 79
Linda Paun and Frank Kempken
7 In Vivo Targeted Mutagenesis in Yeast Using
TaGTEAM .................................................................................... 97
Shawn Finney-Manchester and Narendra Maheshri
Part III Endogenous DNA: Gene Expression Control
8 RNA Silencing in Filamentous Fungi: From Basics
to Applications .............................................................................. 107
Nguyen Bao Quoc and Hitoshi Nakayashiki
vii
viii Contents
9 RNAi-Mediated Gene Silencing in the Beta-Lactam
Producer Fungi P enicillium chrysogenum and
Acremonium chrysogenum ........................................................... 125
Carlos García-Estrada and Ricardo V. Ullán
10 Controlling Fungal Gene Expression Using
the Doxycycline- Dependent Tet-ON System
in Aspergillus fumigatus ............................................................... 131
Michaela Dümig and Sven Krappmann
Part IV Tools and Applications: Selection Markers and Vectors
11 Expanding the Repertoire of Selectable Markers
for Aspergillus Transformation ................................................... 141
Khyati Dave, V. Lakshmi Prabha, Manmeet Ahuja,
Kashyap Dave, S. Tejaswini, and Narayan S. Punekar
12 Arginase (a gaA) as a Fungal Transformation Marker ............. 155
Kashyap Dave, Manmeet Ahuja, T.N. Jayashri,
Rekha Bisht Sirola, Khyati Dave, and Narayan S. Punekar
13 Transformation of Ascomycetous Fungi Using
Autonomously Replicating Vectors ............................................. 161
Satoko Kanematsu and Takeo Shimizu
14 A Recyclable and Bidirectionally Selectable Marker
System for Transformation of T richoderma ............................... 169
Thiago M. Mello-de-Sousa, Robert L. Mach,
and Astrid R. Mach-Aigner
15 Split-Marker-Mediated Transformation and Targeted
Gene Disruption in Filamentous Fungi ...................................... 175
Kuang-Ren Chung and Miin-Huey Lee
Part V Tools and Applications: High Throughput Experimentation
16 Integrated Automation for Continuous High-Throughput
Synthetic Chromosome Assembly and Transformation
to Identify Improved Yeast Strains for Industrial
Production of Biofuels and Bio-based Chemicals ..................... 183
Stephen R. Hughes and Steven B. Riedmuller
17 Imaging Flow Cytometry and High- Throughput
Microscopy for Automated Macroscopic Morphological
Analysis of Filamentous Fungi .................................................... 201
Aydin Golabgir, Daniela Ehgartner, Lukas Neutsch,
Andreas E. Posch, Peter Sagmeister, and Christoph Herwig
Contents ix
18 Yeast Cell Electroporation in Droplet-Based
Microfluidic Chip ......................................................................... 211
Qiuxian Cai and Chunxiong Luo
19 Identification of T-DNA Integration Sites:
TAIL-PCR and Sequence Analysis ............................................. 217
Jaehyuk Choi, Junhyun Jeon, and Yong-Hwan Lee
Part VI Tools and Applications: Comprehensive
Approaches in Selected Fungi
20 Genetic and Genomic Manipulations in A spergillus niger ....... 225
Adrian Tsang, Annie Bellemare, Corinne Darmond,
and Janny Bakhuis
21 Genetic Manipulation of M eyerozyma guilliermondii ............... 245
Nicolas Papon, Yuriy R. Boretsky, Vincent Courdavault,
Marc Clastre, and Andriy A. Sibirny
Index ...................................................................................................... 263