Biocatalysis and Biodegradation

Designed for use as a textbook and resource for professional scientists working in the areas of industrial microbiology, environmental microbiology, and biodegradation, this important new volume details both the fundamental concepts of the microbial transformation of organic compounds as well as its application for biotechnology and biodegradation. It offers comprehensive coverage of microbial catabolism from the group that developed the Biocatalysis/Biodegradation Database on the Web and discusses the logic of catabolism, which is important in the context of genome annotation and predicting biodegradation reactions.

Foreword

xi

David Gibson

Preface

xxi

General Concepts in Biodegradation and Biocatalysis

1

(6)

Definition of Terms

2

(3)

Further Resources in Biocatalysis and Biodegradation

5

(2)

A History of Concepts in Biodegradation and Microbial Catalysis

7

(20)

The Beginnings of Biodegradation on Earth

7

(2)

Early Human Observations of Biodegradation and Biocatalysis

9

(1)

Early Scientific Studies on Biodegradation and the Spontaneous-Generation Debate

9

(3)

Microbial Pure Cultures from Nature

12

(1)

Early History of the Study of Diverse Metabolic Activities of Microbes

13

(1)

Unity of Metabolism in Living Things

14

(1)

Oxygen and Oxygenases

15

(3)

History of Anaerobic Biocatalysis

18

(1)

Molecular Genetics and Regulation

19

(3)

Microbes in Organic Synthesis

22

(1)

Summary

23

(4)

Identifying Novel Microbial Catalysis by Enrichment Culture and Screening

27

(12)

Why Use Enrichment Culture?

28

(2)

The General Method

30

(3)

Selection of Conditions and Medium

33

(1)

Screening for Specific Biocatalytic Reactions

34

(1)

Summary

35

(4)

Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed

39

(32)

The Importance of Microbial (Bio) diversity

39

(2)

Fungi in Biocatalysis and Biodegradation

41

(2)

Distribution in the Prokaryotic World of Biodegradative and Novel Biocatalytic Capabilities

43

(9)

Specialized Biodegradation by Microorganisms with Specialized Metabolisms

52

(1)

Aerobic versus Anaerobic Microorganisms in Biodegradation

52

(2)

Representative Microorganisms with Broad Catabolic Abilities

54

(7)

Microbial Consortia in Biodegradation

61

(1)

Global Biodegradation and the Supraorganism Concept

62

(3)

Summary

65

(6)

Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity

71

(24)

Microbial Global Cycling of the Elements

72

(2)

Facts and Fallacies: Natural Products versus Synthetic Chemicals and Their Biodegradation

74

(2)

An Organic Functional Group Classification

76

(2)

Organic Functional Groups Found in Nature

78

(1)

Ring Compounds Found in Nature

79

(9)

Organic Functional Groups: What Is Known with Respect to Biodegradation and Microbial Biocatalysis?

88

(3)

Summary

91

(4)

Physiological Processes: Enzymes, Emulsification, Uptake, and Chemotaxis

95

(20)

General Physiological Responses to Environmental Chemicals

96

(1)

Enzymes

97

(2)

Enzyme Substrate Specificity

99

(1)

Uptake: Getting Substrates to the Enzymes

100

(4)

Emulsification: Overcoming Poor Availability of Substrate

104

(1)

Organic-Solvent Resistance

105

(2)

Chemotaxis: Getting to the Substrates

107

(2)

Summary

109

(6)

Evolution of Catabolic Enzymes and Pathways

115

(20)

History

116

(2)

Major Protein Families in Microbial Biocatalysis

118

(3)

Principles of Evolution Applied to Microbial Catabolism

121

(4)

Gene Transfer in the Evolution of Catabolic Pathways

125

(2)

Case Study: Enzyme Evolution in the Aminohydrolase Protein Superfamily

127

(4)

Summary

131

(4)

Metabolic Logic and Pathway Maps

135

(22)

Overview

135

(3)

C1 Metamap

138

(2)

C2 Metamap

140

(1)

Cycloalkane Metamap

141

(2)

BTEX Metamap: Aerobic Metabolism

143

(2)

BTEX Metamap: Anaerobic Metabolism

145

(1)

PAH Metamap

145

(2)

Heterocyclic-Ring Metamap

147

(1)

Triazine-Ring Metamap

148

(2)

Organohalogen Metamap

150

(2)

Organometallic Metamap

152

(1)

Summary

153

(4)

Predicting Microbial Biocatalysis and Biodegradation

157

(14)

Why Is It Necessary To Predict Biodegradation Pathways?

158

(1)

Biodegradation Prediction Systems

159

(2)

Defining the Trunk Pathways

161

(2)

Defining the Organic Functional Groups Relevant to Microbial Catabolism

163

(1)

The Basis for Predicting Microbial Biocatalysis and Biodegradation

164

(2)

Beyond Two Functional Groups: the Need for Heuristics

166

(2)

Summary

168

(3)

Microbial Biotechnology: Chemical Production and Bioremediation

171

(20)

Historical and Conceptual Progress

171

(2)

Recent Trends

173

(1)

End Products of Fermentation: Pharmaceuticals

174

(1)

Microbial Catalysis To Produce Chiral Products

175

(3)

Chiral Synthesis of Dichloroprop

178

(2)

Biocatalysis for Non-Medicinal, Non-Chiral Specialty Chemicals

180

(3)

Biotechnological Waste Recycling

183

(1)

Case Study of Bioremediation: Atrazine in Soil

184

(5)

Summary

189

(2)

The Impact of Genomics on Microbial Catalysis

191

(14)

Genome Sizes and Organization

191

(6)

The Present Impact of Genomics

197

(1)

Functional Genomics in the Context of Microbial Biocatalysis

197

(5)

Inadvertent Deception in Modern Biochemistry Textbooks

202

(1)

The Case for Reverse Functional Genomics and New Discovery in Biocatalysis

202

(1)

Summary

203

(2)

The Extent of Microbial Catalysis and Biodegradation: Are Microbes Infallible?

205

(8)

Microbial Enzyme Diversity

206

(3)

Experiments Suggest that Novel Biocatalytic Reactions Are Ubiquitous

209

(1)

Enzyme Plasticity and New Biocatalysts

210

(1)

Summary

211

(2)

Big Questions and Future Prospects

213

(10)

The Questions and Some Thoughts on Their Ultimate Answers

213

(3)

Summary

216

(1)

Appendixes

A. Books and Journals Relevant to Biodegradation and Biocatalysis

217

(2)

B. Useful Internet Resources in Biodegradation and Biocatalysis

219

(4)

Index

223

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Biocatalysis and Biodegradation

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