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ScienceDirect Editorial overview: Chemical biotechnology: The expansion of chemical biotechnology Curt R Fischer and Steffen Schaffer Current Opinion in Biotechnology 2014, 30:v–vii For a complete overview see the Issue doi:10.1016/j.copbio.2014.10.009 0958-1669/# 2014 Elsevier Ltd. All rights reserved.
Curt R Fischer
Ginkgo Bioworks, Boston, MA, USA e-mail: [email protected] Curt Fischer received his doctorate in chemical engineering at the Massachusetts Institute of Technology in 2009, where he focused on metabolic engineering, and biofuels production. He completed postdoctoral work at the University of California in microbial ecology and stableisotope-based mass spectrometry. Since 2011 he has been a biological engineer at Ginkgo Bioworks, designing and engineering organisms for a variety of industrial applications from fine chemicals to energy.
As joint co-editors of COBIOT’s special feature on Chemical Biotechnology, we are pleased to present this issue’s anthology. Chemical Biotechnology as we define it encompasses the use of live organisms or biochemical components to produce small-molecule chemicals. This field is expanding - not only in popularity among researchers, but also in several other important dimensions. This issue highlights key fronts in the expansion. The chemical diversity of the products is increasing, and the same is true of substrates. Additionally, processes that were new just a decade ago are now reaching the commercial scales. Lastly, new ideas on process intensification and the combination of chemical and biochemical process steps are emerging. The spectrum ranges from molecule discovery and screening (Luo, Cobb and Zhao) through enzyme engineering (Keasling et al.), design and optimization of whole cell biocatalysts (Ladkau, Schmid and Bu¨hler) to process integration (Balskus et al.; Nielsen et al.) and process design (Jansen and van Gulik; Porro et al.). Several reviews describe the progress been made with respect to certain products and product groups such as amino acids and their derivatives (Wendisch), polyhydroxyalkanoates (Wang, Yin and Che), glycolipids and lipopeptides (Geys, Soetaert and van Bogaert), succinic acid (Jansen and van Gulik) as well as the structurally and functionally diverse group of secondary metabolites (Zhao). Finally a variety of different application areas of industrial biotechnology such as commercial production of chemicals (Wendisch; Wang, Yin and Chen; Soetaert and van Bogaert; Jansen and van Gulik; Zhao), waste water treatment (Johnson) or biomining (Johnson) will be addressed.
Steffen Schaffer Keasling et al. highlight recent progress on engineering nature’s ‘‘assembly line’’ enzymes, the modular polyketide synthases, and propose a new broadly applicable strategy for improving these enzymes’ engineerability. Polyketides are of interest not only as natural products and antibiotics, but with better engineering could be tailored to make new molecular structures, with a variety of potential industrial applications.
Synthetic Biology Science & Technology, Evonik Industries, CREAVIS Science to Business, Marl, Germany e-mail: [email protected] Steffen Schaffer received his diploma in Biology from the University of Greifswald (Germany) and his Ph.D. in Molecular Microbiology from the University of Ulm (Germany). After heading a research team between 1999 and 2004 at the Juelich www.sciencedirect.com
Zhao et al. focus on the idea that new molecular structures do not necessarily require enzyme engineering; instead, they focus on the continuing explosion in sequencing capabilities, which in microbial genomes has revealed a vast menagerie of natural product biosynthesis gene clusters, with not known product. Improvements in chemical analysis coupled with the new genomic information are enabling researchers to more easily find complex natural products features than ever before. While the two previous papers touch on identification and characterization of the enzymatic machinery required to synthesize a given molecule or to catalyze a desired enzymatic step as well the engineering of such enzymes to Current Opinion in Biotechnology 2014, 30:v–vii
vi Chemical biotechnology
Research Center (Germany), he joined Evonik Industries (at that time the former Degussa) in 2004. He has been with Evonik since in various positions and is currently appointed Director Synthetic Biology in the strategic R&D unit Creavis. In that role he is responsible for development of whole-cell biocatalysts to be employed in commercial bioprocesses for production of chemicals.
improve or modify its properties, the article by Ladkau, Schmid and Bu¨hler is taking the next step and describes different strategies to use these enzymes/enzyme sets as native or synthetically assembled multi-step pathways to produce value-added compounds. Grafting these pathways onto the metabolic network present in microbial host cells allows for production of these molecules from unrelated and, more importantly, low-cost substrates, but is also adding an additional level of complexity as integration of heterologous pathways into the hosts biochemical network often leads to unexpected and undesirable interactions. Wallace and Balskus highlight a variety of ways in which new innovations in chemical catalysis can be combined with biochemical or whole-cell catalysis in situ to create better, more efficient syntheses of chemical products. Incompatibilities of chemical catalysts with enzymes can be overcome through clever scaffolding or compartmentalization. And they point out that many times interactions between chemical catalysis and cellular metabolism can be interesting control points for engineering intervention, introducing the concept of biocompatible chemistry for the purpose. Nielsen et al. discuss this idea of combining chemical catalysis and biocatalysis in the context of lipids and polymers. They discuss in particular how traditional catalysts for the dehydration, polymerization, decarboxylation, and oxidation reactions can be adapted to upgrading lipids for fuel applications. These same catalysts are also useful in converting biological monomers into polymers and into existing, large-market polymer precursors. Real-world development of the number of new bioprocesses for the manufacture of chemicals which have been introduced into the market during the last decade as well as the growth rate of those products which have made this step, has been significantly lagging behind corresponding projections. Porro et al. attempt in their contribution to pinpoint those criteria to be most predictive of the probability of commercial success of a bioprocess-derived chemical. They conclude that the completely different raw material bases of classical chemical processes versus bioprocesses will often create problems if we are to replicate the petrochemical product tree by attempting to replace the underlying chemical processes with novel bioprocesses, because the boundary conditions of bioprocesses such as driving force, metabolic balance or product toxicity may be far from optimal. Thus, they suggest to re-analyze, which products can meaningfully be made by biotechnology and which cannot and in the latter case, which alternative molecules may fill in here. Several companies have announced launching production of succinic acid in commercial facilities. These include Succinity, a BASF/Purac Joint Venture, BioAmber, Myriant and Reverdia, a DSM/Roquette Joint Venture. Though the commercial success of the individual processes and the product in general remains to be proven, the fact that several major chemical companies have been investing significant amounts of money in construction of commercial plants indicates that there is enough potential to these investments. In their article Jansen and van Gulik cover the process designs developed and scaled-up by the individual players with respect to the choice of raw materials, biocatalyst characteristics, and process design. The focus however is on giving an overview of the applied downstream-purification strategies, a unit operation significantly impacting overall production costs, and pointing out their advantages as well as disadvantages and respective impact on manufacturing costs.
Current Opinion in Biotechnology 2014, 30:v–vii
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Editorial overview Fischer and Schaffer vii
After ethanol, amino acids for food and feed applications are the largest product group produced by biotechnological processes, the annual production volume of the two largest products glutamic acid and lysine being in the range of several million tons. Thus, amino acid fermentation has significantly contributed to establish biotechnology as an essential pillar of the chemical industry. The article by Wendisch described recent progress in improvement of bio-catalysts for production of certain amino acids as well as amino acid derivatives such as diacids, diamines and aminocarboxylic acids which can be used as monomers for polyamides and polyesters, but also dipeptides and keto acids. Increasing customer awareness with respect to sustainability issues and to a lesser degree changes in regulatory frameworks have motivated Consumer Care companies to review their ingredients portfolios and increase the amount of those produced by sustainable processes. This also applies to detergents. While bio-based surfactants are known for many years none of them has made it yet into commercial products apart from niche markets where customers are willing to pay a premium for more sustainable products. Geys, Soetaert and van Bogaert review the progress being made in recent years to move biosurfactants (different types of glycolipids and certain lipopeptides) into mass applications by improving their availability and lowering manufacturing costs. While short-chain polyhydroxyalkanoates (PHAs) such as polylactate and polyhydroxybutyrate have been commercialized already several years ago by companies such as Purac, NatureWorks and Metabolix, market penetration is still very low, which is probably due to a combination of several factors, most eminent a lag in performance versus
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price relationship if compared to established polymers. Wang, Yin and Chen present their perspectives on both issues. The authors discuss approaches in order to lower manufacturing costs by following novel routes in process design and employing low-cost feed-stocks. With respect to product performance, the authors suggest approaches to reliably adjust the composition of copolymers and to modify PHA properties by introducing additional functional groups. Wilmes et al. review progress on creating lipid biomass, but not from the usual substrates of sugars or cellulosics. Instead wastewater is their substrate of choice. Lipid formation in wastewater is a natural process - but the precise genetics and regulation involved in the formation of intracellular lipid bodies has been difficult to study until recently, in part because of the complex, diverse population of microbes involved in wastewater processing. Finally, Johnson reviews an existing, large-scale processing of chemical biotechnology that has received little attention in academic circles. ‘‘Biomining’’, or the use of microbial metabolism to extract desirable metals from ores, is increasingly used to extract copper from sulfidic ores. In fact, more kilograms of copper ore were bioleached for Cu recovery in 2010 than kilograms of plant biomass used for ethanol production in the US. This thoroughly understudied area is just beginning to be applied to the recovery of other metals such as nickel and other metals. We would like to thank all the contributors to this issue, and hope readers enjoy this snapshot of chemical biotechnology in 2014.
Current Opinion in Biotechnology 2014, 30:v–vii
ScienceDirect Editorial overview: Chemical biotechnology: The expansion of chemical biotechnology Curt R Fischer and Steffen Schaffer Current Opinion in Biotechnology 2014, 30:v–vii For a complete overview see the Issue doi:10.1016/j.copbio.2014.10.009 0958-1669/# 2014 Elsevier Ltd. All rights reserved.
Curt R Fischer
Ginkgo Bioworks, Boston, MA, USA e-mail: [email protected] Curt Fischer received his doctorate in chemical engineering at the Massachusetts Institute of Technology in 2009, where he focused on metabolic engineering, and biofuels production. He completed postdoctoral work at the University of California in microbial ecology and stableisotope-based mass spectrometry. Since 2011 he has been a biological engineer at Ginkgo Bioworks, designing and engineering organisms for a variety of industrial applications from fine chemicals to energy.
As joint co-editors of COBIOT’s special feature on Chemical Biotechnology, we are pleased to present this issue’s anthology. Chemical Biotechnology as we define it encompasses the use of live organisms or biochemical components to produce small-molecule chemicals. This field is expanding - not only in popularity among researchers, but also in several other important dimensions. This issue highlights key fronts in the expansion. The chemical diversity of the products is increasing, and the same is true of substrates. Additionally, processes that were new just a decade ago are now reaching the commercial scales. Lastly, new ideas on process intensification and the combination of chemical and biochemical process steps are emerging. The spectrum ranges from molecule discovery and screening (Luo, Cobb and Zhao) through enzyme engineering (Keasling et al.), design and optimization of whole cell biocatalysts (Ladkau, Schmid and Bu¨hler) to process integration (Balskus et al.; Nielsen et al.) and process design (Jansen and van Gulik; Porro et al.). Several reviews describe the progress been made with respect to certain products and product groups such as amino acids and their derivatives (Wendisch), polyhydroxyalkanoates (Wang, Yin and Che), glycolipids and lipopeptides (Geys, Soetaert and van Bogaert), succinic acid (Jansen and van Gulik) as well as the structurally and functionally diverse group of secondary metabolites (Zhao). Finally a variety of different application areas of industrial biotechnology such as commercial production of chemicals (Wendisch; Wang, Yin and Chen; Soetaert and van Bogaert; Jansen and van Gulik; Zhao), waste water treatment (Johnson) or biomining (Johnson) will be addressed.
Steffen Schaffer Keasling et al. highlight recent progress on engineering nature’s ‘‘assembly line’’ enzymes, the modular polyketide synthases, and propose a new broadly applicable strategy for improving these enzymes’ engineerability. Polyketides are of interest not only as natural products and antibiotics, but with better engineering could be tailored to make new molecular structures, with a variety of potential industrial applications.
Synthetic Biology Science & Technology, Evonik Industries, CREAVIS Science to Business, Marl, Germany e-mail: [email protected] Steffen Schaffer received his diploma in Biology from the University of Greifswald (Germany) and his Ph.D. in Molecular Microbiology from the University of Ulm (Germany). After heading a research team between 1999 and 2004 at the Juelich www.sciencedirect.com
Zhao et al. focus on the idea that new molecular structures do not necessarily require enzyme engineering; instead, they focus on the continuing explosion in sequencing capabilities, which in microbial genomes has revealed a vast menagerie of natural product biosynthesis gene clusters, with not known product. Improvements in chemical analysis coupled with the new genomic information are enabling researchers to more easily find complex natural products features than ever before. While the two previous papers touch on identification and characterization of the enzymatic machinery required to synthesize a given molecule or to catalyze a desired enzymatic step as well the engineering of such enzymes to Current Opinion in Biotechnology 2014, 30:v–vii
vi Chemical biotechnology
Research Center (Germany), he joined Evonik Industries (at that time the former Degussa) in 2004. He has been with Evonik since in various positions and is currently appointed Director Synthetic Biology in the strategic R&D unit Creavis. In that role he is responsible for development of whole-cell biocatalysts to be employed in commercial bioprocesses for production of chemicals.
improve or modify its properties, the article by Ladkau, Schmid and Bu¨hler is taking the next step and describes different strategies to use these enzymes/enzyme sets as native or synthetically assembled multi-step pathways to produce value-added compounds. Grafting these pathways onto the metabolic network present in microbial host cells allows for production of these molecules from unrelated and, more importantly, low-cost substrates, but is also adding an additional level of complexity as integration of heterologous pathways into the hosts biochemical network often leads to unexpected and undesirable interactions. Wallace and Balskus highlight a variety of ways in which new innovations in chemical catalysis can be combined with biochemical or whole-cell catalysis in situ to create better, more efficient syntheses of chemical products. Incompatibilities of chemical catalysts with enzymes can be overcome through clever scaffolding or compartmentalization. And they point out that many times interactions between chemical catalysis and cellular metabolism can be interesting control points for engineering intervention, introducing the concept of biocompatible chemistry for the purpose. Nielsen et al. discuss this idea of combining chemical catalysis and biocatalysis in the context of lipids and polymers. They discuss in particular how traditional catalysts for the dehydration, polymerization, decarboxylation, and oxidation reactions can be adapted to upgrading lipids for fuel applications. These same catalysts are also useful in converting biological monomers into polymers and into existing, large-market polymer precursors. Real-world development of the number of new bioprocesses for the manufacture of chemicals which have been introduced into the market during the last decade as well as the growth rate of those products which have made this step, has been significantly lagging behind corresponding projections. Porro et al. attempt in their contribution to pinpoint those criteria to be most predictive of the probability of commercial success of a bioprocess-derived chemical. They conclude that the completely different raw material bases of classical chemical processes versus bioprocesses will often create problems if we are to replicate the petrochemical product tree by attempting to replace the underlying chemical processes with novel bioprocesses, because the boundary conditions of bioprocesses such as driving force, metabolic balance or product toxicity may be far from optimal. Thus, they suggest to re-analyze, which products can meaningfully be made by biotechnology and which cannot and in the latter case, which alternative molecules may fill in here. Several companies have announced launching production of succinic acid in commercial facilities. These include Succinity, a BASF/Purac Joint Venture, BioAmber, Myriant and Reverdia, a DSM/Roquette Joint Venture. Though the commercial success of the individual processes and the product in general remains to be proven, the fact that several major chemical companies have been investing significant amounts of money in construction of commercial plants indicates that there is enough potential to these investments. In their article Jansen and van Gulik cover the process designs developed and scaled-up by the individual players with respect to the choice of raw materials, biocatalyst characteristics, and process design. The focus however is on giving an overview of the applied downstream-purification strategies, a unit operation significantly impacting overall production costs, and pointing out their advantages as well as disadvantages and respective impact on manufacturing costs.
Current Opinion in Biotechnology 2014, 30:v–vii
www.sciencedirect.com
Editorial overview Fischer and Schaffer vii
After ethanol, amino acids for food and feed applications are the largest product group produced by biotechnological processes, the annual production volume of the two largest products glutamic acid and lysine being in the range of several million tons. Thus, amino acid fermentation has significantly contributed to establish biotechnology as an essential pillar of the chemical industry. The article by Wendisch described recent progress in improvement of bio-catalysts for production of certain amino acids as well as amino acid derivatives such as diacids, diamines and aminocarboxylic acids which can be used as monomers for polyamides and polyesters, but also dipeptides and keto acids. Increasing customer awareness with respect to sustainability issues and to a lesser degree changes in regulatory frameworks have motivated Consumer Care companies to review their ingredients portfolios and increase the amount of those produced by sustainable processes. This also applies to detergents. While bio-based surfactants are known for many years none of them has made it yet into commercial products apart from niche markets where customers are willing to pay a premium for more sustainable products. Geys, Soetaert and van Bogaert review the progress being made in recent years to move biosurfactants (different types of glycolipids and certain lipopeptides) into mass applications by improving their availability and lowering manufacturing costs. While short-chain polyhydroxyalkanoates (PHAs) such as polylactate and polyhydroxybutyrate have been commercialized already several years ago by companies such as Purac, NatureWorks and Metabolix, market penetration is still very low, which is probably due to a combination of several factors, most eminent a lag in performance versus
www.sciencedirect.com
price relationship if compared to established polymers. Wang, Yin and Chen present their perspectives on both issues. The authors discuss approaches in order to lower manufacturing costs by following novel routes in process design and employing low-cost feed-stocks. With respect to product performance, the authors suggest approaches to reliably adjust the composition of copolymers and to modify PHA properties by introducing additional functional groups. Wilmes et al. review progress on creating lipid biomass, but not from the usual substrates of sugars or cellulosics. Instead wastewater is their substrate of choice. Lipid formation in wastewater is a natural process - but the precise genetics and regulation involved in the formation of intracellular lipid bodies has been difficult to study until recently, in part because of the complex, diverse population of microbes involved in wastewater processing. Finally, Johnson reviews an existing, large-scale processing of chemical biotechnology that has received little attention in academic circles. ‘‘Biomining’’, or the use of microbial metabolism to extract desirable metals from ores, is increasingly used to extract copper from sulfidic ores. In fact, more kilograms of copper ore were bioleached for Cu recovery in 2010 than kilograms of plant biomass used for ethanol production in the US. This thoroughly understudied area is just beginning to be applied to the recovery of other metals such as nickel and other metals. We would like to thank all the contributors to this issue, and hope readers enjoy this snapshot of chemical biotechnology in 2014.
Current Opinion in Biotechnology 2014, 30:v–vii
