Industrial Biotransformations

Second, Completely Revised and Extended Edition

Edited byAndreas Liese, Karsten Seelbach, Christian Wandrey

InnodataFile Attachment3527607900.jpg

Industrial Biotransformations

Edited byA. Liese, K. Seelbach, C. Wandrey

Further Titles of Interest

Aehle, W. (Ed.)

Enzymes in IndustryProduction and Applications

Second, Completely Revised Edition

2004

ISBN 3-527-29592-5

Bommarius, A. S., Riebel, B. R.

BiocatalysisFundamentals and Applications

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ISBN 3-527-30344-8

Buchholz, K., Kasche, V., Bornscheuer, U. T.

Biocatalysts and Enzyme Technology

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ISBN 3-527-30497-5

Jördening, H.-J., Winter, J. (Eds.)

Environmental Biotechnology

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ISBN 3-527-30585-8

Brakmann, S., Schwienhorst, A. (Eds.)

Evolutionary Methods in BiotechnologyClever Tricks for Directed Evolution

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ISBN 3-527-30799-0

Industrial Biotransformations

Second, Completely Revised and Extended Edition

Edited byAndreas Liese, Karsten Seelbach, Christian Wandrey

Editors

Prof. Dr. Andreas LieseTechnische Universität Hamburg-HarburgInstitute of BiocatalysisDenickestr. 1521073 HamburgGermany

Dr. Karsten SeelbachSiegwerk Druckfarben AGAlfred-Keller-Str. 5553721 SiegburgGermany

Prof. Dr. Christian WandreyForschungszentrum JülichInstitute of Biotechnology52425 JülichGermany

First Edition 2000Second, Completely Revised andExtended Edition 2006

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© 2006 WILEY-VCH Verlag GmbH & Co. KGaA,Weinheim

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ISBN-13: 978-3-527-31001-2ISBN-10: 3-527-31001-0

V

Preface to the first edition IX

Preface to the second edition XI

List of Contributors XII

1 History of Industrial Biotransformations – Dreams and Realities 1Durda Vasic-Racki

1.1 From the “Flower of Vinegar” to Recombinant E. Coli – The History ofMicrobial Biotransformations 1

1.2 From Gastric Juice to SweetzymeT – The History of EnzymaticBiotransformations 11

1.3 From Wine Bottle to a State-of-the-Art Facility – The History ofBiochemical Engineering 23

1.4 Advantages of Biotransformations Over Classical Chemistry-Enzymesare proteins, things of beauty and a joy forever 29

2 The Enzyme Classification 37Christoph Hoh and Murillo Villela Filho

2.1 Enzyme Nomenclature 372.2 Enzyme Classes 392.2.1 EC 1 Oxidoreductases 402.2.2 EC 2 Transferases 462.2.3 EC 3 Hydrolases 492.2.4 EC 4 Lyases 542.2.5 EC 5 Isomerases 562.2.6 EC 6 Ligases 59

Contents

VI

3 Retrosynthetic Biocatalysis 63Junhua Tao, Alan Pettman, and Andreas Liese

3.1 Alkanes 633.2 Alkenes 643.3 Amines 643.4 Alcohols 653.5 Aldehydes 673.6 Ketones 683.7 Epoxides 683.8 Diols 693.9 Carboxylic Acids 703.10 Esters 723.11 Amides 723.12 Imines 733.13 Amino Acids 743.14 Hydroxy Acids 773.15 a-Hydroxy Ketones 793.16 b-Hydroxy Aldehydes, Ketones or Carboxylic Acids 803.17 Cyanohydrins, Hemithioacetals and Hemiaminals 813.18 Sulfoxides and Sulfones 823.19 Halides 823.20 Aromatics (Ring Functionalization) 833.21 Cyclic Compounds 843.22 Carbohydrates 843.23 Peroxides 853.24 Isomers 853.25 Examples of Retrosynthetic Biotransformations 863.25.1 Example 1 863.25.2 Example 2 87

4 Optimization of Industrial Enzymes by Molecular Engineering 93Thorsten Eggert

4.1 Introduction 934.2 Learning from Nature 954.3 Enzyme Production Using Bacterial Expression Hosts 954.4 Improvements to Enzymes by Molecular Engineering Techniques 984.4.1 Rational Enzyme Design 984.4.2 Directed Evolution 1004.4.3 Random Mutagenesis Methods 1024.5 Identification of Improved Enzyme Variants 1054.6 Conclusions and Future Prospects 108

Contents

VII

5 Basics of Bioreaction Engineering 115Nagaraj N. Rao, Stephan Lütz, Karsten Seelbach, and Andreas Liese

5.1 Definitions 1165.1.1 Process Definitions 1165.1.2 Definitions of Unit Operations 1215.2 Biocatalyst Kinetics 1245.2.1 Types of Biocatalysts 1245.2.2 Enzyme Structure 1245.2.3 Kinetics 1255.3 Basic Reactor Types and their Modes of Operation 1305.3.1 Mass and Energy Balances 1335.4 Biocatalyst Recycling and Recovery 1355.4.1 Entrapment 1375.4.2 Cross-linking 1395.4.3 Covalent Binding 1395.4.4 Membrane Filtration 1405.5 Reaction Parameters 1405.6 Scale-up of Bioreactors 1415.7 Recent Developments and Trends 141

6 Processes 147Andreas Liese, Karsten Seelbach, Arne Buchholz, and Jürgen Haberland

Oxireductases EC 1 153Transferases EC 2 264Hydrolases EC 3 273Lyases EC 4 447Isomerases EC 5 503

7 Quantitative Analysis of Industrial Biotransformation 515Adrie J. J. Straathof

IndexIndex of enzyme name 521Index of strain 526Index of company 531Index of starting material 536Index of product 545

Contents

IX

Preface to the first edition

The main incentive in writing this book was to gather information on one-stepbiotransformations that are of industrial importance. With this collection, wewant to illustrate that more enzyme-catalyzed processes have gained practical sig-nificance than their potential users are conscious of. There is still a prejudice thatbiotransformations are only needed in cases where classical chemical synthesisfails. Even the conviction that the respective biocatalysts are not available and, ifso, then too expensive, unstable and only functional in water, still seems to bewidespread. We hope that this collection of industrial biotransformations will infuture influence decision-making of synthesis development in such a way that itmight lead to considering the possible incorporation of a biotransformation stepin a scheme of synthesis.

We therefore took great pains in explicitly describing the substrates, the cata-lyst, the product and as much of the reaction conditions as possible of the pro-cesses mentioned. Wherever flow schemes were available for publication or couldbe generated from the reaction details, this was done. Details of some process pa-rameters are still incomplete, since such information is only sparingly available.We are nevertheless convinced that the details are sufficient to convey a feeling forthe process parameters. Finally, the use of the products is described and a few pro-cess-relevant references are made.

We would go beyond the scope of this foreword, should we attempt to thank allthose who were kind enough to supply us with examples. Of course, we only pub-lished openly available results (including the patent literature) or used personallyconveyed results with the consent of the respective authors. We are aware of thefact that far more processes exist and that by the time the book is published,many process details will be outdated. Nonetheless, we believe that this compila-tion with its overview character will serve the above-mentioned purpose. Thisawareness could be augmented if the reader, using his or her experience, wouldtake the trouble of filling out the printed worksheet at the end of this book withsuggestions that could lead to an improvement of a given process or the incor-poration of a further industrial process into the collection.

Requesting our industrial partners to make process schemes and parametersmore accessible did not please them very much. Even so, we are asking our part-ners once again to disclose more information than they have done in the past. In

many instances, far more knowledge of industrial processes has been gained thanis publicly available. Our objective is to be able to make use of these “well knownsecrets” as well. We would like to express our gratitude to all those who suppliedus with information in a progress-conducive manner. Thanks also go to thosewho did not reject our requests completely and at least supplied us with a photo-graph in compensation for the actually requested information.

The book begins with a short historical overview of industrial biotransforma-tions. Since the process order of the compilation is in accordance with the enzymenomenclature system, the latter is described in more detail. We also include achapter on reaction engineering to enable an easier evaluation of the processes.The main part of the book, as you would expect, is the compilation of the indus-trial biotransformations. The comprehensive index will allow a facile search forsubstrates, enzymes and products.

We sincerely hope that this book will be of assistance in the academic as well asthe industrial field, when one wants to get an insight into industrial biotransfor-mations. We would be very thankful to receive any correction suggestions orfurther comments and contributions. At least we hope to experience a triggereffect that would make it worth while for the readership, the authors and the edi-tors to have a second edition succeeding the first.

We are indebted to several coworkers for screening literature and compilingdata, especially to Jürgen Haberland, Doris Hahn, Marianne Hess, Wolfgang Lan-ters, Monika Lauer, Christian Litterscheid, Nagaraj Rao, Durda Vasic-Racki, Mur-illo Villela Filho, Philomena Volkmann and Andrea Weckbecker.

We thank especially Uta Seelbach for drawing most of the figures during longnights, as well as Nagaraj Rao and the “enzyme group” (Nils Brinkmann, LasseGreiner, Jürgen Haberland, Christoph Hoh, David Kihumbu, Stephan Laue, Tho-mas Stillger and Murillo Villela Filho).

And last but not least we thank our families for their support and tolerance dur-ing the time that we invested in our so called ‘book project’.

Preface to the first editionX

XI

Preface to the second edition

After more than five years since the first edition of “Industrial Biotransforma-tions” many new examples have become industrially relevant, others have lostimportance. Therefore we had to enlarge the chapter “Processes” by 20%. If newinformation about the processes of the first edition was available, this informationwas incorporated. All processes were checked with respect to the literature(including patent literature). We have included all the valuable corrections sugges-tions or further comments and contributions of many readers. This might per-haps be of great importance for the reader of the second edition. Expecting that afirst edition could not be perfect, we stated in the preface to the first edition: “Wewould be very thankful to receive any correction suggestions or further commentsand contributions. At least we hope to experience a trigger effect that would makeit worthwhile for the readership, the authors and the editors to have a second edi-tion succeeding the first.” We were astonished how carefully many readerschecked the information given. So the reader of the second edition will not onlyhave an enlarged chapter “Processes”, but also an updated version with – memust admit – many useful corrections. The best criticism will be given by anexperienced reader. We hope very much that the “old” and the “new” readers willrealize that the second edition is more than a remake of the first edition.

Since the first edition was sold out earlier than we had expected, the publisherfound it scientifically – and economically – more reasonable to have a second edi-tion than to have a reprint of the first edition. Finally after all the additional workwas done we agreed with the publisher. Perhaps it is worth to be mentioned thatin the meantime also the first Chinese edition appeared.

The focus of the book is still the chapter “Processes”. Nevertheless all the otherchapters were carefully reevaluated. In the chapter “History of Industrial Biotrans-formations” we included a new part “History of Biochemical Engineering”.

Entirely new is the chapter “Retrosynthetic Biocatalysis”. The basic idea comesfrom classical organic chemistry, where a complex chemical structure is reducedto building blocks, which might even be commercially available. Similarly, onecan find out which easily available building blocks can be used for industrial bio-transformations. We hope that the reader will find this concept useful. Especiallywe hope that the classical organic chemistry becomes more part of biotechnologythis way.

XII Preface to the second edition

Entirely new is the chapter “Optimization of Industrial Enzymes by MolecularEngineering”. The field of technical evolution of enzymes has become so impor-tant that we think it is justified to have a chapter devoted to the interesting andrelevant findings in this field. There is no longer an “excuse” that there is no suffi-ciently stable, selective and active enzyme for a desired reaction. Technical evolu-tion of enzymes has become similarly important as screening of enzymes fromthe environment. The chapter “Basics of Bioreaction Engineering” has been care-fully checked and hopefully improved due to many valuable suggestions of thereaders. We hope that bioreaction engineering will be understood as of equalimportance for industrial biotransformations as enzyme engineering.

An additional short chapter is entitled “Quantitative Analysis of Industrial Bio-transformation”. Here the reader can find some quantitative information aboutthe fact that it is a prejudice to believe that only hydrolases in water are useful forindustrial biotransformations. Redox reactions and C-C-bond formations even inorganic solvents or biphasic systems are also industrially relevant today.

Our original understanding of “Industrial Biotransformations” was a one step reac-tion of industrial relevance. This definition might become less clear in the future,because also two or three step biotransformations are or might be included. So it willbecome more and more difficult to distinguish an industrial biotransformation froma fermentation process. This is especially true in the age of “designer bugs”, where amicroorganism is first grown and than used as a more or less “non-growing catalyst”for industrial biotransformation. But we should not bother too much with definitions.Our aim was and is to show that biotransformations are of great importance in theacademic and industrial fields. Since the first edition the field of “White Biotechnol-ogy” (formally known as Industrial Microbiology) has developed a lot. A quantativeunderstanding of complex microbial systems by means of the “polyomics” techniques(genomics, proteomics, and metabolomics) has improved so much that we canexpect recombinant pathways for industrial biotransformations used in a biocata-lysis under non-natural conditions. We can foresee that the technical evolutionnot only of biocatalyst but also of bioprocesses will lead to many more industrialbiotransformations. Thus, sooner or later we expect the burden/pleasure that wewill have to prepare a third edition of “Industrial Biotransformations”.

We would like to ask the reader again to help us with “correction suggestions orfurther comments and contributions”. The best compensation for all the work theauthor of a book can get is the feeling that it is read by colleagues who understandthe subject.

Last but not least we would like to mention in addition to the many coworkerswho have contributed to the first edition, now the additional valuable contribu-tions of many more who helped us to prepare the second edition, especially Karl-Heinz Drauz, Kurt Faber, Katja Goldberg, Udo Kragl, Peter Stahmann, TrevorLaird, John Villadsen, Ulrike Zimmermann. Especially we thank our families fortheir support during the time that we invested in the second edition of this book.

Dezember 2005 Andreas LieseKarsten SeelbachChristian Wandrey

XIII

List of Contributors

Dr. Arne BuchholzDSM Nutritional ProductsFeldbergstraße 879539 LörrachGermany

Dr. Thorsten EggertInstitut für MolekulareEnzymtechnologieder Heinrich-Heine-UniversitätDüsseldorfim Forschungszentrum Jülich52426 JülichGermany

Dr. Murillo Villela FilhoDegussa AGPoject House ProFermRodenbacher Chaussee 463457 Hanau-WolfgangGermany

Dr. Jürgen HaberlandDSM Nutritional ProductsEmil-Barell-Straße 3Bldg.50/R.20979639 Grenzach-WyhlenGermany

Dipl.-Chem. Christoph HohSanofi-Aventis Deutschland GmbHDiabel OperationsIndustriepark Höchst65926 Frankfurt am MainGermany

Prof. Dr. Andreas LieseHead of Institute of Biotechnology IITechnical University of Hamburg-HarburgDenickestr. 1521073 HamburgGermany

Dipl.-Chem. Stephan LützInstitut für BiotechnologieForschungszentrum Jülich GmbH52425 JülichGermany

Alan PettmanPfizer LimitedWalton OaksDorking RoadTadworthSurrey, KT20 7NSUK