Engineering the Genetic Code: Expanding the Amino Acid Repertoire for the Design of Novel Proteins

309 Pages·2005·3.16 MB·English

by  Dr. Nediljko Budisa(auth.)

NediljkoBudisa
EngineeringtheGenetic
Code
EngineeringtheGeneticCode. NediljkoBudisa
Copyright82006WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:3-527-31243-9
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Nediljko Budisa
Engineering the Genetic Code
Expanding the Amino Acid Repertoire
for the Design of Novel Proteins
NediljkoBudisa 9 AllbookspublishedbyWiley-VCHarecarefully
Max-Planck-InstituteofBiochemistry produced.Nevertheless,authors,editors,and
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82006WILEY-VCHVerlagGmbH&Co.KGaA,
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ISBN-13: 978-3-527-31243-6
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V
Thisbookisdedicatedtomyscientificparents:
Prof.RobertHuber
Prof.LuisMoroder
Prof.DieterOesterhelt
EngineeringtheGeneticCode. NediljkoBudisa
Copyright82006WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:3-527-31243-9
VII
Foreword
,,VielleichtistdiephysikalischundchemischorientierteBiologieimAugenblickdie
zukunftsreichsteallerRealwissenschaften.‘‘
CarlFriedrichFreiherrvonWeizsa¨cker
Fromthelecture:,,WiewirddieWissenschaftdieWeltvera¨ndern?‘‘,Munich1969.
The emerging field of chemical biology is based on blending chemistry with mo-
lecularbiology,aprocessthatislargelystimulatedbythemostrecentadvancesin
genetic code engineering. While common methods of protein engineering and
site-directed mutagenesis allow to identify contributions of particular amino acids
tothestructure and/orfunction ofproteins viapermutationof thetwentycanoni-
calaminoacids,expansionofthegeneticcodeofferstheperspectivesofenriching
this alphabet of building blocks with noncanonical a-amino acids of unique bio-
physical and chemical properties. In fact, chemistry should allow the access to a
nearlyinfinitearrayofdiversestructuralelementsforthedesignofnovelproteins
orforincorporationofnewchemicalfunctionalitiesthatcanbeexploitedatwillfor
bioorthogonal posttranslational protein tagging and transformations to study and
to enrich the chemistry of living cells. At the present stage of this forefront re-
search a comprehensive treatise on the state of the art was indeed required, and
the book Engineering of the Genetic Code, authored by our previous student and
now colleague Dr. Nediljko Budisa who decisively contributed to advances in the
field, elegantly fulfils this need. Since our own reseach addresses structure and
function of biomolecules, we are fascinated by the new perspectives offered and
we witness the fast development of this challenging field of research. We trust
thatthecriticaltreatmentandnovelconcepts describedinBudisa’sbook Engineer-
ing of the Genetic Code will provide stimulus and guidance for scientists, research-
ers, teachers and students to learn about and apply this fascinating research area
anditsinnovativetoolsfortheirquestionsattheinterfaceofchemistryandbiology.
RobertHuber
LuisMoroder
DieterOesterhelt
EngineeringtheGeneticCode. NediljkoBudisa
Copyright82006WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:3-527-31243-9
IX
Contents
Foreword VII
Preface XV
1 Introduction 1
1.1 ClassicalApproachestoProteinModification 1
1.2 PeptideSynthesis,SemisynthesisandChemistryofTotalProtein
Synthesis 2
1.3 ChemoselectiveLigationsCombinedwithBiochemicalMethods 5
1.4 MethodsandApproachesofClassicalProteinEngineering 5
1.5 GeneticallyEncodedProteinModifications–ReprogrammingProtein
Translation 6
1.6 BasicDefinitionsandTaxonomy 8
References 10
2 ABriefHistoryofanExpandedAminoAcidRepertoire 13
2.1 The‘‘GoldenYears’’ofMolecularBiologyandTripletCode
Elucidation 13
2.2 EarlyExperimentsontheIncorporationofAminoAcidAnalogsin
Proteins 15
2.3 TestTube(Cell-free)SynthesisofProteinsandEarlyIncorporation
Experiments 18
2.4 NoncanonicalAminoAcidsasToolsforStudyingCellMetabolism,
Physiology,ProteinProcessingandTurnover 19
2.5 ProblemofProofsandFormalCriteriaforNoncanonicalAminoAcid
Incorporation 23
2.6 RecentRenaissance–GeneticCodeEngineering 26
References 28
3 BasicFeaturesoftheCellularTranslationApparatus 31
3.1 NaturalLaws,GeneticInformationandthe‘‘CentralDogma’’of
MolecularBiology 31
3.2 CellularInvestmentsinRibosome-mediatedProteinSynthesis 33
3.3 MolecularArchitectureofAARS 34
EngineeringtheGeneticCode. NediljkoBudisa
Copyright82006WILEY-VCHVerlagGmbH&Co.KGaA,Weinheim
ISBN:3-527-31243-9
X Contents
3.4 StructureandFunctionofthetRNAMolecule 40
3.5 AminoacylationReaction 44
3.6 AARS:tRNAInteractions–IdentitySets 45
3.7 TranslationalProofreading 48
3.8 RibosomalDecoding–ABriefOverview 50
3.9 CodonBiasandtheFidelityofProteinSynthesis 51
3.10 PreprogrammedContext-dependentRecoding:fMet,Sec,Pyl,etc. 53
3.11 BeyondBasicCoding–PosttranslationalModifications 56
References 59
4 AminoAcidsandCodons–CodeOrganizationandProteinStructure 66
4.1 BasicFeaturesandAdaptiveNatureoftheUniversalGeneticCode 66
4.2 MetabolismandIntracellularUptakeofCanonicalAminoAcids 68
4.3 PhysicochemicalPropertiesofCanonicalAminoAcids 69
4.4 ReasonsfortheOccurrenceofOnly20AminoAcidsintheGenetic
Code 73
4.5 WhatPropertiesofAminoAcidsareBestPreservedbytheGenetic
Code? 74
4.6 EvolutionaryLegacy:DualNatureofConservedCodeandFiniteNumber
ofProteinFolds 77
4.7 NaturalVariationsinAssignmentofCodonsoftheUniversalGenetic
Code 79
4.7.1 NucleosideModificationsandCodonReassignments 81
4.8 CodonReassignmentConceptsPossiblyRelevanttoCode
Engineering 81
4.8.1 GenomeSize,Composition,ComplexityandCodonReassignments 81
4.8.2 StopCodonTakeover,CodonCaptureandCodonAmbiguity 83
References 85
5 ReprogramingtheCellularTranslationMachinery 90
5.1 EnzymeSpecificityofAminoacyl-tRNASynthetases(AARS)andCode
Interpretation 90
5.1.1 LivingCellsasPlatformsforAminoAcidRepertoireExpansion 90
5.1.2 Uptake,ToxicityandMetabolicFateofNoncanonicalAminoAcids 91
5.1.2.1 GeneralConsiderations 91
5.1.2.2 AminoAcidTransport 93
5.1.2.3 MetabolicConversionsandToxicityofAnalogsandSurrogates 94
5.1.3 ConstrainsandLevelsinCodeEngineering 95
5.1.4 AuxotrophismandNaturalAARSwithManipulatedFunctions 95
5.1.4.1 Proteome-wideReplacements:‘‘UnnaturalMicroorganisms’’ 97
5.1.4.2 SubstitutionsattheLevelofSingleProteins–SelectivePressure
Incorporation(SPI) 100
5.1.4.3 KineticControl–EnhancedSystemforProteinTranslation 102
5.1.4.4 ExtensionoftheExistingSpecificitiesofAARS 104
5.1.4.5 AARSwithanAttenuatedEditingFunction 106
Contents XI
5.1.5 BeyondAuxotrophism:TowardsAARSwithDeNovoSubstrate
Specificity 108
5.1.5.1 KineticIssuesofOrthogonalAARS:CatalyticEfficiencyand
Selectivity 111
5.2 ReassigningCodingandNoncodingUnits 113
5.2.1 SenseCodonReassignment:MostCommonlyUsedSubstitutions 113
5.2.1.1 Tryptophan 114
5.2.1.2 Tyrosine 118
5.2.1.3 Phenylalanine 119
5.2.1.4 Histidine 122
5.2.1.5 Proline 124
5.2.1.6 Methionine 127
5.2.1.7 Leucine 130
5.2.1.8 ValineandIsoleucine 132
5.2.1.9 ArginineandCanavanine 133
5.2.1.10 LysineandLysyl-tRNASynthetases–EnzymeswithManyTalents 135
5.3 InVitroChemicalandEnzymatictRNAAminoacylation 137
5.3.1 ChemicaltRNAAcylationforSenseCodonReassignment 138
5.3.2 Ribozymes,RibosomesandMissenseSuppressions 140
5.4 NovelCodon–AnticodonBasePairs 142
5.4.1 InVitroandInVivoFrameshiftSuppressionof4-and5-base
Codons 142
5.4.2 TowardaThird,NoncanonicalBasePairinDNA 145
5.5 StopCodonTakeover 146
5.5.1 TheConceptofSuppressioninProteinTranslation 147
5.5.2 ChemicalAminoacylationofAmberSuppressortRNA 148
5.5.3 InVitroversusInVivoTranslationforExtensionoftheAminoAcid
Repertoire 150
5.5.4 GeneralLimitsofSuppression-basedApproaches 151
5.6 InVivoNonsenseSuppression-basedMethods 153
5.6.1 InSearchforOrthogonaltRNA 153
5.6.2 Species-specificAminoacylationFeaturesandOrthogonalAARS:tRNA
Pairs 154
5.6.3 OrthogonalAARS:tRNAPairsinE.coli 156
5.6.4 OrthogonalPairsinYeastandMammalianCells 158
5.7 OutlookandVisions 159
5.7.1 CouplingReprogrammedTranslationwithMetabolicEngineering
159
5.7.1.1 CatalyticPromiscuityandSyntheticCapacityExtensionofMetabolic
Pathways 159
5.7.1.2 ImportingNaturalProductMetabolicPathwaysandPossibleDeNovo
Design 160
5.7.2 ShuttleOrthogonalPairandHybridTranslationSystemswithCodon
Capture 162
References 165
XII Contents
6 ImplicationsandInsights:FromReprogrammedTranslationandCode
EvolutiontoArtificialLife 184
6.1 CodeEngineeringandSyntheticBiology 184
6.2 NovelFeaturesofProteinTranslationthathaveEmergedfromResearch
inCodeEngineering 185
6.2.1 CodeMalleability,CatalyticPromiscuityandtheAminoAcid‘‘Identity’’
Problem 185
6.2.2 ABarrierbetweenAllowableandNonpermissiveAminoAcids–An
IndexforEntryintheGeneticCode 187
6.2.3 ProteinStructuralTypesandAminoAcidSubstitutionCapacity 190
6.2.4 BuildingaDirectLinkbetweenMetabolismandReprogrammed
Translation 192
6.3 TheAminoAcidRepertoireanditsEvolution 193
6.3.1 ‘‘CopernicanTurn’’andtheLastSacrosanctinBiochemistry 193
6.3.2 SpontaneousTerrestrialandExtraterrestrialGenerationofAmino
Acids 194
6.3.3 MetabolicRoutesforAminoAcidSynthesesandCo-evolution
Theory 197
6.4 ArtificialGeneticSystemsandCodeEngineering 200
6.4.1 CellswithChemicallyAmbiguousProteomes–CodonReassignment
Issues 200
6.4.2 IsitPossibletoImprovetheAdaptiveFeaturesoftheGenetic
Code? 201
6.4.3 PossibilitiesforDeNovoDesignofOrganismswiththeir‘‘Own’’Genetic
Codes 203
6.4.4 CodeEngineeringandSociety–PhilosophicalandEthical
Implications 205
6.4.5 FutureChallenges,ChancesandRisks 207
References 208
7 SomePracticalPotentialsofReprogrammedCellularTranslation 213
7.1 PracticalChoiceofMethodsandSomeControversiesintheField 213
7.2 ThePlasticityoftheTranslationMachinery,AminoAcidGenericTypes
andProteinStructure 215
7.3 DNANucleotideAnalogs:FromSequencingtoExpandedCodeand
Therapy 217
7.4 NoncanonicalAminoAcidsinMaterialScience 217
7.5 IsomorphousReplacementandAtomicMutationsinStructuralBiology
andBiophysics 221
7.5.1 ProteinX-rayCrystallography 221
7.5.2 AtomicMutationsandPredictablePerturbationsintheProtein
Structure 223
7.5.3 ProteinsEnrichedwithChalcogen,HydroxylandAzaAnalogsand
SurrogatesofTrp 225