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2.01 Isoprenoid Biosynthesis: Overview

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2.01 Isoprenoid Biosynthesis: Overview 2.01 Isoprenoid Biosynthesis: Overview DAVID E. CANE Brown University, Providence, RI, USA 1[90[0 INTRODUCTION 0 1[90[1 BIOSYNTHESIS OF ISOPENTENYL DIPHOSPHATE 2 1[90[1[0 Mevalonic Acid 2 1[90[1[1 The Deoxyxylulose Phosphate Pathway 2 1[90[2 ISOPENTENYL DIPHOSPHATE METABOLISM AND THE BIOCHEMISTRY OF CARBOCATIONS 3 1[90[2[0 Generation of Carbocations] Protonation of a Double Bond 4 1[90[2[0[0 ProtonationÐdeprotonation 4 1[90[2[0[1 ProtonationÐole_n alkylation 4 1[90[2[1 Generation of Carbocations] Protonation of an Epoxide 5 1[90[2[2 Generation of Carbocations] Ionization of an Allylic Diphosphate 6 1[90[2[2[0 Isoprenoid diphosphate chain elon`ation 6 1[90[2[2[1 Isoprenoid diphosphate isomerization and cyclization 7 1[90[2[2[2 Isoprenoid diphosphate chain couplin` 8 1[90[2[2[3 Isoprenoid diphosphate alkylation of heteroatoms 09 1[90[2[3 Reactions of Carbocations 00 1[90[3 MULTIDISCIPLINARY APPROACHES TO THE STUDY OF ISOPRENOID BIOSYNTHESIS 00 1[90[4 REFERENCES 01 1[90[0 INTRODUCTION Isoprenoid natural products are found in essentially all forms of life[0 Although the function of the vast majority of the tens of thousands of known isoprenoids is still largely unknown\ the demonstrated functions include mediation of cell!wall and glycoprotein biosynthesis "dolichol diphosphates#\ electron transport and redox chemistry "ubiquinones#\ photooxidative protection and photosynthetic light harvesting "carotenoids#\ contribution to lipid membrane structure "chol! esterol in eukaryotes\ archaebacterial lipids#\ modi_cation of proteins involved in signal transduction "prenylated proteins#\ modi_cation of t!RNA "N 5!isopentenyladenine# intercellular signaling and developmental control "estrogens\ gibberellins#\ interspecies defense "microbeÐmicrobe\ plantÐ microbe\ plantÐinsect# as antibiotics and phytoalexins "trichothecin\ capsidiol#\ to interspecies attack "e[g[\ fungalÐplant# "trichothecanes and gibberellins#\ among a myriad of activities[ Numerous other isoprenoids exhibit potent\ medicinally useful\ physiological activities whose relationship to their native function is still obscure\ for example the widely used diterpene gingkolides "cardiovascular agent# and taxoids "antitumor compound# "Figure 0#[ 0 2.02 Biosynthesis of Mevalonic Acid from Acetyl-CoA DANIEL A. BOCHAR, JON A. FRIESEN, CYNTHIA V. STAUFFACHER, and VICTOR W. RODWELL Purdue University, West Lafayette, IN, USA 1[91[0 INTRODUCTION 05 1[91[0[0 Acetyl!CoA to Mevalonate 05 1[91[0[1 Acetoacetyl!CoA Synthase 05 1[91[0[2 HMG!CoA Synthase 06 1[91[0[3 HMG!CoA Reductase 06 1[91[1 ACETOACETYL!CoA SYNTHASE 06 1[91[1[0 The Acetoacetyl!CoA Synthase Reaction is a Classical Claisen Condensation 06 1[91[1[1 Cells Elaborate Multiple Enzymes that Catalyze Acetoacetyl!CoA Biosynthesis 07 1[91[1[2 Several Cloned cDNAs Encode Cytosolic Acetoacetyl!CoA Synthases 07 1[91[1[3 A Bacterial Acetoacetyl!CoA Synthase Functions in Poly"b!hydroxybutyrate# Synthesis 07 1[91[1[4 Catalysis Involves a Histidine and an Acylated Cysteinyl Intermediate 08 1[91[1[5 Crystal Structure of a b!Ketothiolase 08 1[91[2 HMG!CoA SYNTHASE 08 1[91[2[0 Chemistry of the HMG!CoA Synthase Reaction 08 1[91[2[1 Substrate Speci_city 08 1[91[2[2 Isozymes Perform Distinct Physiolo`ic Roles 10 1[91[2[3 Cytosolic HMG!CoA Synthases Function in Isoprenoid Bio`enesis 10 1[91[2[4 Cloned cDNAs Encode Cytosolic HMG!CoA Synthases 10 1[91[2[5 Catalysis Involves an Active Site Cysteine 11 1[91[2[6 Inhibitors of HMG!CoA Synthase Activity 11 1[91[2[7 Formation of HMG!CoA May Involve a Dual!function Enzyme 11 1[91[3 HMG!CoA REDUCTASE 11 1[91[3[0 The HMG!CoA Reductase Reaction 11 1[91[3[1 Biosynthetic HMG!CoA Reductases 12 1[91[3[2 Pseudomonas mevalonii Elaborates a Biode`radative HMG!CoA Reductase 13 1[91[3[3 Domain Structure of HMG!CoA Reductases 13 1[91[3[4 HMG!CoA Reductase and Cholesterol Homeostasis 13 1[91[3[5 Dru`s that Control Cholesterol Biosynthesis Tar`et HMG!CoA Reductase 14 1[91[3[6 Plants Elaborate Multiple HMG!CoA Reductase Isozymes 15 1[91[3[7 Plant HMG!CoA Reductase Isozymes Ful_ll Discrete Physiolo`ic Functions 15 1[91[3[8 Stimuli Elicit Differential Effects on Plant HMG!CoA Reductase Isozymes 15 1[91[3[09 Yeast also Synthesizes HMG!CoA Reductase Isozymes 16 1[91[3[00 Animals do not Appear to Elaborate HMG!CoA Reductase Isozymes 16 1[91[3[01 Puri_ed HMG!CoA Reductases 16 1[91[3[02 Crystallo`raphic Structure of Pseudomonas mevalonii HMG!CoA Reductase 17 1[91[3[03 Ternary Complex Structures Reveal a Substrate!induced Closure of the Flap Domain 17 1[91[3[04 The Small Domain of Pseudomonas mevalonii HMG!CoA Reductase has an Unusual NAD!bindin` Fold 18 1[91[3[05 Determinants of Coenzyme Speci_city of the Pseudomonas mevalonii Enzyme 18 1[91[3[06 Catalysis Involves Two Reductive Sta`es 29 04 2.03 A Mevalonate-independent Route to Isopentenyl Diphosphate MICHEL ROHMER Universite´ Louis Pasteur, Strasbourg, France 1[92[0 INTRODUCTION 34 1[92[0[0 Isoprenoids 34 1[92[0[1 The AcetateÐMevalonate Pathway*the Role of IPP 35 1[92[1 BACTERIAL TRITERPENOIDS OF THE HOPANE SERIES] THE TOOLS FOR THE DISCOVERY OF THE MEVALONATE!INDEPENDENT PATHWAY 36 1[92[1[0 Hopanoid Structures 36 1[92[1[1 Distribution and Role of Bacterial Hopanoids 36 1[92[1[2 Incorporation of 02C!Labeled Acetate into Bacterial Hopanoids 37 1[92[2 ELUCIDATION OF THE NONMEVALONATE PATHWAY] THE ORIGIN OF THE CARBON ATOMS OF ISOPRENIC UNITS IN BACTERIA 49 1[92[2[0 Incorporation of 02C!Labeled Glucose into the Isoprenoids of Z[ mobilis and M[ fujisawaense via the EntnerÐDoudoroff Pathway] Ori`in of the Carbon Atoms of Isoprenic Units 49 1[92[2[1 A Rearran`ement is Required for Formation of the Isoprenic Skeleton 40 1[92[2[2 Incorporation of 02C!Labeled Glucose into the Isoprenoids of E[ coli and Alicyclobacillus acidoterrestris via the EmbdenÐMeyerhofÐParnas Pathway 41 1[92[2[3 Incorporation of 02C!Labeled Acetate via the Glyoxylate and Tricarboxylic Acid Cycles 41 1[92[2[4 The Absence of Key Enzymes of the Mevalonate Pathway in Bacteria Possessin` the Alternative Pathway 42 1[92[3 THE PRECURSORS OF IPP IN THE MEVALONATE!INDEPENDENT PATHWAY 43 1[92[3[0 Glyceraldehyde 2!Phosphate and Pyruvate as First Precursors 43 1[92[3[1 Hypothetical Bio`enetic Scheme for the Mevalonate Independent Pathway 44 1[92[3[2 D!0!Deoxyxylulose 4!Phosphate\ a Key Intermediate for Several Biosynthetic Routes 44 1[92[3[3 1!C!Methyl!D!erythritol 3!phosphate\ a Putative Intermediate 45 1[92[4 DISTRIBUTION OF THE MEVALONATE!INDEPENDENT PATHWAY 46 1[92[4[0 Distribution Amon` Prokaryotes 46 1[92[4[1 Distribution amon`st Phototrophic Eukaryotes] Al`ae and Hi`her Plants 59 1[92[5 CONCLUSIONS*FURTHER DEVELOPMENTS 51 1[92[6 REFERENCES 54 1[92[0 INTRODUCTION 1[92[0[0 Isoprenoids Isoprenoids belong to a huge family of natural products[0 Many of the ½11 999 known compounds are described in other chapters of this volume[ They include\ for instance\ essential metabolites such 34 35 A Mevalonate!independent Route to Isopentenyl Diphosphate as sterols acting as membrane stabilizers or as precursors of steroid hormones\ carotenoids of photosynthesizing organisms\ acyclic prenyl chains found in chlorophylls "phytol#\ in ubiquinone\ menaquinone\ or plastoquinone from electron transfer chains\ in prenylated proteins\ or in dolichols and polyprenols required for the biosynthesis of polysaccharides or protein glycosylation\ as well as a multitude of {{secondary|| metabolites of less obvious fundamental role in cell biology[ All isoprenoids share a common feature] they are formally derived from the branched C4 skeleton of isoprene[ The formation of isopentenyl diphosphate "IPP#\ i[e[\ of the biological equivalent of isoprene\ via the acetateÐmevalonate pathway\ has been largely documented and is described in detail in Chapter 1[91 of this volume[ However\ the main steps will be brie~y described here as they are required for the discussion of the topic presented in this chapter[ 1[92[0[1 The AcetateÐMevalonate Pathway*the Role of IPP The pioneering work of Bloch\ Lynen\ Cornforth\ and many others allowed an understanding of how living cells synthesize their isoprenoids from acetate\ activated as acetyl CoA "0# "Figure 0#[1Ð3 Two Claisen!type condensations yield successively acetoacetyl CoA "1# and hydroxymethylglutaryl CoA "2#[ An NADPH!dependent reductase catalyzes the _rst supposed committed step of isoprenoid biosynthesis\ the reduction of hydroxymethylglutaryl CoA to mevalonate "3#\ which was accepted until the mid!0889s as the universal precursor of isoprenoids[ Three successive phosphorylations followed by a decarboxylation yield _nally the branched _ve!carbon atom skeleton of IPP "4#[ O HO O O OO CH3 2 1 SCoA SCoA NADPH 2 CH3 SCoA SCoA OO– (1) (2) (3) HO 5 3 ATP OH 3 1 –CO2 OPP OPP OO– 4 2 (4) (5) (6) expected labeling pattern in isoprenoids OPP OPP from [2-13C]acetate from [1-13C]acetate Figure 0 The acetateÐmevalonate pathway for isoprenoid biosynthesis[ IPP can be considered as the universal building block for all isoprenoids\ even in the bacteria and the eukaryotes that have been shown to possess the mevalonate!independent route and that will be discussed in this chapter[ The role of IPP as isoprenoid precursor in eukaryotes has been extensively discussed[ We will therefore only focus on the data available from prokaryotic organisms[ IPP was always successfully incorporated into bacterial isoprenoids[ This is in accordance with its universal role\ shared with its isomer dimethylallyl diphosphate "5#\ as isoprenoid precursor[ Carbon!03! labeled IPP could be incorporated into ubiquinone\ menaquinone\ carotenoids\
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