Abstract
Over the last two decades, the development of an extensive set of molecular biology, genetic engineering, and computational toolboxes has allowed us to tease out emergent phenomena from microbial systems. In the IB IN DEPTH special section on fungal biology in this issue of Industrial Biotechnology, Drs. Scott Baker, Pacific Northwest National Laboratory, (Richland, WA) and Adrian Tsang, Centre for Structural and Functional Genomics, Concordia University (Montreal, Canada) have pulled together several exciting research articles on how these toolboxes are being deployed to gain a better understanding of fungal biology and biotechnology. At the core of many microorganisms' power to transform industrial biotechnology is metabolism and our ability to manipulate their metabolic pathways. However, metabolic processes are integrated with and an extension of the complex environment that microorganisms populate and transform. Pools of metabolites and trace metals must be tapped and utilized to support growth and activities. Thus, understanding how fungi interact with their respective environments is essential to understanding physiological response and the transformational power of fungi. In addition, the great diversity of fungi in the microbial worlds offers tremendous opportunities to advance our understanding of biological phenomena and for biotechnological development. Thus these expansive toolboxes are enabling successes achieved in unraveling some of the secrets of fungal biology and deploying these discoveries for innovative biotechnological solutions.
In this issue of IB, we present interviews with two colleagues who have been very active in the fungal biotechnology space: Dr. Randy Berka, Novozymes, Inc. (Davis, CA), and Dr. Igor Grigoriev, US Department of Energy Joint Genome Institute (Walnut Creek, CA). Dr. Berka has had a long and productive research and development career focused on fungal biology and industrial biotechnology. As we have seen time and time again, high throughput sequencing technologies have played an important role in expanding our knowledge base and providing the genomic blueprints for some of our old and familiar microbial friends as well as novel fungal species. As noted by Dr. Berka, these blueprints are valuable tools for developing a broad spectrum of biotechnological solutions. Dr. Grigoriev underscores the role of high throughput sequencing technologies in the diversification of portfolios of fungal species that can be deployed for innovative industrial biotechnology applications. He also illustrates a familiar theme that many of our research discoveries and technological innovations reveal: how much more there is to learn about our old and familiar friends.
The “integrative approaches” theme for understanding and deploying fungal biology is explored further in the review article by Drs. Mhairi Workman, Mikael R. Andersen, and Jette Thykaer of the Department of Systems Biology, Technical University of Denmark, Lyngby. They tell a compelling story of how quantitative physiology, the omics, metabolic engineering, and systems biology are being integrated to expand our knowledge of filamentous fungi, and how this knowledge can be used for “improving cell factories.” In an article by Chauve et al., we delve into another example of knowledge integration in an effort to understand the role β-glucosidases and cellobiohydrolases play in the deconstruction of lignocellulosic materials. The authors propose an integrated modeling framework that couples Michaelis-Menten kinetics for a β-glucosidase with the Langmuir kinetics of a cellobiohydrolase to explore the processive deconstruction of cellulose.
Trichoderma reesei has been an important industrial microbiological system for understanding the biochemistry of cell wall-degrading enzymes dating back to its discovery on the Solomon Islands during World War II. The strain QM6 was the basis of several classical mutagenesis efforts to create a hyper-producer of cell wall-degrading enzymes such as T. reesei RUT-C30. The original research article by Koike et al. in this issue presents the results of a comparative genomic study of QM6 and RUT-C30 to understand better the genomic basis that underlies the high protein production and secretion capability of RUT-C30. Given the importance of integrative toolboxes for biotechnology development our readers should expect more articles on how these toolboxes are evolving and being used in industrial biotechnology development.
Our Catalyzing Innovation features in this issue focus on regional and integrative approaches for supporting the growth of the industrial biotechnology sector. We hear from IB Editorial Board member Dr. Peter Punt and his colleagues at TNO (Zeist/Delft, The Netherlands) and RTD Services (Vienna, Austria) on efforts in the European community to develop a fully sustainable biobased economy. Core to this initiative is the integration of biotechnology, conversion, and separation technologies by several stakeholders and partners in the BioConSepT consortium. The goal of this consortium is to support biochemical production development in Europe through a Knowledge Based Bio-Economy. As noted in my previous editorials, the integration of science, technology, and stakeholders is an essential part of driving biotechnology innovation globally. Another exciting example of the integration of researchers, stakeholders, and economic development groups is provided by Jackie Robin of Ag-West Bio (Saskatoon, Saskatchewan). She describes an exciting research and development ecology involving the University of Saskatchewan (Saskatoon), Agriculture Canada, and the Canadian National Research Council. The Saskatchewan Ministry of the Economy is also an important driver in this effort to add the commercial translation of science and technology that comes out of this innovation ecology by providing business programs and services. As noted by Ms. Robin, communication is essential to leverage resources, expertise, and technology to drive participation in regional and global bioeconomies.
Continuing with our effort to introduce readers to the IB Editorial Board we offer an interview with Dr. Jose Moran-Mirabal, Assistant Professor, Department of Chemistry and Chemical Biology, McMaster University (Hamilton, Canada). Dr. Moran-Mirabal has been a close collaborator in our effort to deploy nano-confinement methods and advanced imaging technology to study the nano-scale behavior of cell wall-degrading enzymes. He is one of the few young researchers who have the unique preparation and capability to explore phenomena at the interface of the biological and physical worlds. His previous research experiences and his current research activities reflect his appreciation and understanding of how vital multidisciplinary approaches to research are essential to integrative approaches to biological discovery and biotechnological innovation. He represents one of the best young minds stepping up to the challenges of deploying industrial biotechnology for sustainable human development.
Speaking of sustainability, we include an Industrial Report in this issue from Roger A. Sedjo, Brent Sohngen, and Anne Riddle of the nonprofit and nonpartisan organization Resources of the Future (Washington, DC) entitled “Wood Bioenergy and Land Use: A Challenge to the Searchinger Hypothesis.” The goal of the report is to broaden the discussion on direct and in-direct land use with a focus on “traditional industrial forests and supplemental dedicated fuelwood plantations.” The report “finds that these sources can economically produce large levels of biomass without compromising crop production, thereby mitigating the land conversion and carbon emissions effects posited by the Searchinger Hypothesis.” Given the on-going debate on sustainability and biomass production there is a need to hear the diverse voices on this topic in our effort to develop integrative solutions for agricultural and forestry-based bioindustries.
Yes, there are many integrative approaches that are important to industrial biotechnology development. Our goal is to share these approaches and the outcomes of their deployment with our readers!