Biocatalysis and Biodegradation

Abstract

1. General Concepts in Biodegradation and BiocatalysisDefinition of TermsScope of the Book: from Microbiology to Chemistry and Back AgainFurther Resources in Biocatalysis and Biodegradation2. A History of Concepts in Biodegradation and Microbial CatalysisThe Beginnings of Biodegradation on EarthEarly Human Observations of Biodegradation and BiocatalysisEarly Scientific Studies on Biodegradation and the Spontaneous Generation DebateMicrobial Pure Cultures from NatureEarly History of the Study of Diverse Metabolic Activities of MicrobesUnity of Metabolism in Living ThingsOxygen and OxygenasesHistory of Anaerobic BiocatalysisMolecular Genetics and Regulation Industrial Applications: Two Early Examples [box]Microbes in Organic SynthesisSummary 3. Identifying Novel Microbial Catalysis by Enrichment Culture and ScreeningWhy Use Enrichment Culture?The General Method The Pervasiveness of Enrichment Culture [box]Selection of Conditions and MediumScreening for Specific Biocatalytic ReactionsSummary4. Microbial Diversity: Catabolism of Organic Compounds Is Broadly DistributedThe Importance of Microbial (Bio)diversity Prokaryotes versus Eukaryotes: Fundamental Differences in Biodegradation [box]Fungi in Biocatalysis and BiodegradationDistribution in the Prokaryotic World of Biodegradative and Novel Biocatalytic CapabilitiesSpecialized Biodegradation by Microorganisms with Specialized MetabolismsAerobic versus Anaerobic Microorganisms in BiodegradationRepresentative Microorganisms with Broad Catabolic Abilities Pseudomonas putida F1 Sphingomonas yanoikuyae B1 Rhodococcus spp. Cunninghamella elegansMicrobial Consortia in BiodegradationGlobal Biodegradation and the Supraorganism ConceptSummary5. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its DiversityMicrobial Global Cycling of the ElementsFacts and Fallacies: Natural Products versus Synthetic Chemicals and Their BiodegradationAdvocating a Discontinuation of Use of the Term 'Xenobiotic' with Respect to Biodegradation [box]An Organic Functional Group ClassificationOrganic Functional Groups Found in NatureRing Compounds Found in NatureOrganic Functional Groups: What Is Known with Respect to Biodegradation and Microbial Biocatalysis?6. Physiological Processes: Enzymes, Emulsification, Uptake, and ChemotaxisGeneral Physiological Responses to Environmental ChemicalsEnzymes Enzyme Classification [box]Enzyme Substrate SpecificityUptake: Getting Substrates to the EnzymesEmulsification: Overcoming Poor Availability of SubstrateOrganic-Solvent ResistanceChemotaxis: Getting to the SubstratesSummary7. Evolution of Catabolic Enzymes and PathwaysHistoryMajor Protein Families in Microbial BiocatalysisPrinciples of Evolution Applied to Microbial Catabolism Where Do New Catabolic Enzymes Come From? [box]Gene Transfer in the Evolution of Catabolic PathwaysCase Study: Enzyme Evolution in the Aminohydrolase Protein SuperfamilySummary8. Metabolic Logic and Pathway MapsIntroductionC1 Metabolism MetamapC2 MetamapCycloalkane MetamapBTEX Metamap: Aerobic MetabolismBTEX Metamap: Anaerobic MetabolismPAH MetamapHeterocyclic Ring MetamapTriazine Ring MetamapOrganohalogen MetamapOrganometallic MetamapSummary9. Predicting Microbial Biocatalysis and BiodegradationWhy Is It Necessary To Predict Biodegradation Pathways?Biodegradation Prediction SystemsDefining the Trunk PathwaysDefining the Organic Functional Groups Relevant to Microbial CatabolismThe Basis for Predicting Microbial Biocatalysis and BiodegradationBeyond Two Functional Groups: the Need for HeuristicsSummary10. Microbial Biotechnology: Chemical Production and BioremediationHistorical and Conceptual ProgressRecent TrendsConverting Biomass to Glucose [box]End Products of Fermentation: PharmaceuticalsMicrobial Catalysis To Produce Chiral ProductsChiral Synthesis of DichloropropBiocatalysis for Non-Medicinal, Non-Chiral Specialty ChemicalsBiotechnological Waste RecyclingCase Study of Bioremediation: Atrazine in SoilSummary11. The Impact of Genomics on Microbial CatalysisGenome Sizes and OrganizationThe Present Impact of GenomicsFunctional Genomics in the Context of Microbial BiocatalysisInadvertent Deception in Modern Biochemistry TextbooksThe Case for Reverse Functional Genomics and New Discovery in BiocatalysisSummary12. The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?Microbial Enzyme Diversity Evidence for Enormous Unexplored Metabolic DiversityExperiments Suggesting that Novel Biocatalytic Reactions Are UbiquitousEnzyme Plasticity and New BiocatalystsSummary13. Big Questions and Future ProspectsThe Questions and Some Thoughts on Their Ultimate AnswersSummaryAPPENDIXESA. Books and Journals Relevant to Biodegradation and BiocatalysisB. Useful Internet Resources in Biodegradation and Biocatalysis