One-Carbon Feedstocks for Sustainable Bioproduction (Advances in Biochemical Engineering/Biotechnology, 180)

"This book offers a comprehensive review of the latest developments, challenges and trends in C1-based (one-carbon based) bioproduction, and it presents an authoritative account of one-carbon compounds as promising alternative microbial feedstocks. The book starts with a perspective on the future of C1 compounds as alternative feedstocks for microbial growth, and their vital role in the establishment of a sustainable circular carbon economy, followed by several chapters in which expert contributors discuss about the recent strategies and address key challenges regarding one or more C1 feedstocks. The book covers topics such as acetogenic production from C1 feedstocks, aerobic carboxydotrophic bacteria potential in industrial biotechnology, bioconversion of methane to value-added compounds, combination of electrochemistry and biology to convert C1 compounds, and bioprocesses based on C1-mixotrophy. Particular attention is given to the current metabolic engineering, systems biology, and synthetic biology strategies applied in this field"--Back cover In Memory of Arren Bar-Even Introduction: The Future Belongs to the One-Carbons Contents Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology 1 Introduction 2 Carboxydotrophic Candidates for Aerobic Gas Fermentation Approaches 2.1 Afipia Carboxidovorans 2.2 Hydrogenophaga Pseudoflava 2.3 Other Carboxydotrophic Bacteria 2.4 Synthetic Carboxydotrophy 3 The Aerobic Carboxydotrophic Metabolism and Biochemical Traits of Key Enzymes 3.1 Oxygen-Insensitive CO Dehydrogenase 3.2 Hydrogenases 3.3 Branched Respiratory Chain 3.4 Calvin-Benson-Bassham (CBB) Cycle 4 Genomic Organization of Genes Relevant for the Autotrophic Lifestyle of Aerobic Carboxydotrophs 4.1 Genetic Organization of Genes Coding for CO Dehydrogenase 4.2 Genetic Organization of Genes Coding for Hydrogenase 4.3 Genetic Organization of Genes Coding for Proteins of the CBB Cycle 5 Genetic and Metabolic Engineering Tools of Carboxydotrophic Bacteria 6 Conclusion and Outlook References Process Engineering Aspects for the Microbial Conversion of C1 Gases 1 C1-Gases as Microbial Carbon Source 2 Gas Fermentations with Acetogenic Microorganisms 2.1 Autotrophic Growth and Low Gas Solubilities in Water 2.2 Gas-Liquid Mass Transfer at Low Volumetric Power Input 2.3 Autotrophic Growth Kinetics 2.4 Autotrophic Gas Fermentation in Bubble Column Reactors 2.5 Continuous Gas Fermentation Processes 2.6 Enlarging the Product Spectrum of Gas Fermentation by Co-cultivation 2.7 Requirements for Syngas Purification in Gas Fermentation 3 Conversion of CO2 with Microalgae 3.1 Open Photobioreactors for Microalgae Mass Production 3.2 Requirements for Combustion Gas Purification for Photoautotrophic Processes 4 Conclusions References Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks 1 Introduction 2 Genomes of Acetogenic Bacteria 2.1 Moorella thermoacetica 2.2 Acetobacterium woodii 2.3 Clostridium ljungdahlii 2.4 Comparative Genomic Analysis of Acetogens 3 Transcriptome of Acetogenic Bacteria 3.1 The Wood-Ljungdahl Pathway 3.2 The Energy Conservation 4 Translational Response of Acetogens 5 Genome-Scale Model of Acetogens 6 Conclusion References Systems Metabolic Engineering of Methanotrophic Bacteria for Biological Conversion of Methane to Value-Added Compounds 1 Methane and Methanotrophic Bacteria 1.1 Methane Status 1.2 Overview of Methanotrophs 1.3 Methane Oxidation Pathway 1.4 Methane Assimilation Pathway 2 Synthetic Biology Tools for Methanotrophic Bacteria 2.1 Vector Systems for Methanotrophs 2.2 Gene Transfer (Insertion/Deletion) Techniques 2.3 Future Genetic Tool Development 3 Systems Biology and Metabolic Modeling of Methane Metabolism 3.1 Multi-omics System-Level Investigation of Methanotrophs 3.1.1 Genomics 3.1.2 Transcriptomics 3.1.3 Proteomics 3.1.4 Metabolomics 3.2 Metabolic Modeling of Methane Metabolism 4 Production of Value-Added Compounds from Methane Using Methanotrophic Biocatalysts 4.1 Rational Engineering Strategies of Methanotrophic Bacteria 4.2 Production of Value-Added Chemicals and Fuels Using Engineered Biocatalysts 4.2.1 Organic Acids Lactic Acid C-4 Carboxylic Acids Hydroxycarboxylic Acids 4.2.2 Short-Chain Diols Isobutanol 2,3-Butanediol (2,3-BDO) 1,2-Propanediol (1,2-PDO) 4.2.3 Fatty Acids 4.2.4 Polyhydroxyalkanoates (PHAs) 4.2.5 Secondary Metabolites Isoprene Limonene Carotenoids Ectoine α-Humulene 4.2.6 Amino Acids-Derived Products Cadaverine Putrescine Shinorine 5 Perspectives References Developing Synthetic Methylotrophs by Metabolic Engineering-Guided Adaptive Laboratory Evolution 1 Introduction 2 Rational Design and Evolution of Methanol-Dependent Strains 2.1 Engineering with Compromised RuMP Cycle 2.2 Engineering with Complete RuMP Cycle 2.3 Evolution for Improved Methanol Assimilation and Tolerance 3 ME-ALE for Creating Fully Synthetic Methylotrophs 4 Key Factors Affecting the Efficiency of Synthetic Methylotrophy 4.1 Toxicity of Methanol and Formaldehyde 4.2 Formaldehyde Generation and Assimilation 4.3 Redox and Energy Balance 5 Conclusion and Future Perspectives References Bioconversion of Methanol by Synthetic Methylotrophy 1 Introduction 2 Modification and Redesign Based on Natural Methanol Assimilation Pathway 2.1 The RuMP Pathway 2.1.1 Optimization of the Catalytic Ability of Key Enzymes 2.1.2 Enhancement of the Precursor Ru5P Regeneration 2.2 The Serine Cycle 2.3 The XuMP Pathway 2.4 The Reductive Glycine Pathway 3 Designing Artificial Methanol Assimilation Pathways 4 Concluding Remarks and Future Perspectives References Aerobic Utilization of Methanol for Microbial Growth and Production 1 Methanol Assimilatory Pathways Compatible with Aerobic Growth 1.1 The Ribulose Monophosphate Pathway 1.2 The Dihydroxyacetone Pathway 1.3 The Calvin-Benson-Bassham Cycle 1.4 The Serine Cycle 2 Aerobic Methylotrophic Microorganisms 2.1 Bacillus methanolicus 2.2 Pichia pastoris 2.3 Methylobacterium extorquens 2.4 Cupriavidus necator 2.5 Other Methylotrophic Bacteria 3 Strain Engineering of Methylotrophs 3.1 Amino Acids 3.2 Organic Acids 3.3 Alcohols 3.4 Isoprenoids and Polyketides 3.5 Polyhydroxybutyrate and Heterologous Proteins 3.6 Single-Cell Protein 4 Advantages and Challenges of Methanol Fermentations 4.1 Growth Media Composition 4.2 Basic Bioprocess Design and Setup 4.3 Parameters and Approaches for Bioprocess Control 4.4 Scale-Up 5 Outlook on Technological and Market Developments 5.1 CRISPR Tools for Methylotrophic Strain Engineering 5.2 Adaptive Laboratory Evolution to Improve Methylotrophic Producing Strains 5.3 Synthetic Microbial Consortia for Process Intensification 5.4 One Methylotrophic Production Host Yielding Two or More Products References Empower C1: Combination of Electrochemistry and Biology to Convert C1 Compounds 1 Introduction 2 Electrochemical Treatment of C1-Compounds Followed by Biosynthesis 2.1 Electrochemical Conversion of C1 Compounds in General 2.1.1 Carbon Monoxide 2.1.2 Formic Acid/Formate 2.1.3 Formaldehyde, Methanol, and Methane 2.2 Bridging Electrochemical Reduction and Bioconversion 2.2.1 Uncoupled Systems 2.2.2 Coupled Systems 3 Direct Bioelectrosynthesis from C1 Compounds 3.1 General Aspects of Bioelectrosynthesis 3.2 Bioelectrosynthesis from CO2 with Methanogenic Cultures 3.3 Bioelectrosynthesis from CO2 with Acetogenic Cultures 3.4 Bioelectrosynthesis from CO2 with Other Microorganisms and Mixed Cultures 3.5 Co- and Mixed Cultures to Convert CO2 in Bioelectrosynthetic Processes 4 Challenges and Chances 5 Conclusion References Extracellular Electrons Powered Microbial CO2 Upgrading: Microbial Electrosynthesis and Artificial Photosynthesis 1 Introduction 2 Overview of Microbial Electrosynthesis 2.1 Fundamental 2.2 Inward Extracellular Electron Transfer 2.3 Microbial CO2 Fixation Metabolism 3 MES Biocathode Engineering for High Productivity 3.1 General Strategies from Microbial Electrode Point of View 3.2 Purposeful Strategies for Specific Requirements 4 Metabolic Engineering for High-Value Products 5 Artificial Photosynthesis for Solar-Driven CO2-to-Chemicals 5.1 Integrating Biocatalysts into Photoelectrochemical Devices 5.2 Photosensitizing Biocatalysts with Semiconducting Nanoparticles 6 Conclusion and Outlook References Understanding and Engineering Glycine Cleavage System and Related Metabolic Pathways for C1-Based Biosynthesis 1 Introduction 2 Reductive Glycine Pathway and GCS for C1 Fixation 3 Components and Interactions of GCS in Biological Networks 3.1 GCS Components and Biological Functions 3.2 Structural Features, Reaction Mechanisms, and Interactions of GCS Proteins 3.3 Lipoylation of H Protein and Lipoate-Protein Ligase A 4 Quantitative Analysis and Engineering of GCS-Related Reactions 4.1 Quantitative Analysis of H Protein Lipoylation by LplA 4.2 Quantitative Analysis of the Different Forms of Hlip for Kinetic Studies 4.3 Some Thoughts on Quantitative Study of the rGlyP 4.4 Engineering of GCS 5 Concluding Remarks References Engineering the Reductive Glycine Pathway: A Promising Synthetic Metabolism Approach for C1-Assimilation 1 Introduction 2 The Modules and Variants of the Reductive Glycine Pathway 2.1 The Core Module for Formate to Glycine Conversion 2.2 Glycine Conversion Modules via Serine 2.3 Glycine Conversion Modules via Glyoxylate 2.4 Glycine Conversion Modules via Acetyl-Phosphate 2.5 Modules for Supply of Reducing Power 2.6 Modules for Supply of ATP in Aerobic and Anaerobic Conditions 2.7 CO2 Reduction as an Alternative Substrate Module 2.8 An Extension Module for Methanol Assimilation 2.9 Possible Module for Methane Conversion 3 Metabolic Engineering Approaches and Achievements 3.1 Selection Schemes for the C1, GCS and Serine Modules 3.2 Selections for Full Biomass Assimilation and Full Formatotrophy via rGlyP 3.3 Other Selection Schemes and Considerations for Future Engineering 3.4 Pathway Module Confirmation by 13C-Labelling Studies 3.5 Non-growth Coupled Engineering Efforts 4 Comparing the rGlyP to Other C1-Pathways 4.1 Assessing the rGlyP for Formatotrophic Growth 4.2 Assessing the rGlyP for Growth on Methanol 4.3 Assessing the rGlyP for Autotrophic Growth 5 Outlook on Future Directions and Applications of the Reductive Glycine Pathway 5.1 Optimizing Inefficiencies in the rGlyP and the Central Metabolic Network 5.2 Engineering of the rGlyP in More Organisms 5.3 Developing Bioproduction Strains References Biosynthesis Based on One-Carbon Mixotrophy 1 Introduction 2 Acetogenic Mixotrophy 3 Methylotrophic Mixotrophy 4 Mixotrophy via Anaplerotic and Naturally Occurring Carbon Fixating Reactions 5 The Case of Mixotrophic Ethanol Biosynthesis 6 Concluding Remarks and Outlook References Conversion of Carbon Monoxide to Chemicals Using Microbial Consortia 1 Introduction 1.1 Syngas Fermentation for a Circular Economy 1.2 Microbes Using Carbon Monoxide for Growth 1.3 The Microbial Consortia Approach for Syngas Fermentation 2 CO Conversion by Open Mixed Cultures 2.1 Anaerobic Sludges as Biocatalysts for Syngas Fermentation 2.2 Syngas Biomethanation 2.3 Production of Ethanol 2.4 Production of Carboxylic Acids and Higher Alcohols 3 CO Conversion by Synthetic Co-cultures 3.1 Synthetic Co-cultures: A Win-Win 3.2 Production of Methane 3.3 Production of Carboxylic Acids and Alcohols 3.4 Production of Other Value-Added Chemicals 4 CO Conversion via Sequential Processes 5 Challenges and Opportunities of Syngas-Fermenting Microbial Communities 6 Conclusion References