Biogenesis of Fatty Acids, Lipids and Membranes PDF
Preview Biogenesis of Fatty Acids, Lipids and Membranes
Handbook of Hydrocarbon and Lipid Microbiology Series Editors: Kenneth N. Timmis (Editor-in-Chief) Matthias Boll · Otto Geiger · Howard Goldfine · Tino Krell Sang Yup Lee · Terry J. McGenity · Fernando Rojo Diana Z. Sousa · Alfons J. M. Stams · Robert Steffan · Heinz Wilkes Otto Geiger Editor Biogenesis of Fatty Acids, Lipids and Membranes Handbook of Hydrocarbon and Lipid Microbiology SeriesEditors KennethN.Timmis(Editor-in-Chief) TerryJ.McGenity EmeritusProfessor SchoolofBiologicalSciences InstituteofMicrobiology UniversityofEssex TechnicalUniversityBraunschweig WivenhovePark,UK Braunschweig,Germany FernandoRojo MatthiasBoll CSICCampusdeCantoblanco InstituteofBiology/Microbiology CentroNacionaldeBiotecnología UniversityofFreiburg Madrid,Spain Freiburg,Germany DianaZ.Sousa OttoGeiger LaboratoryofMicrobiology CentrodeCienciasGenómicas WageningenUniversity UniversidadNacionalAutónomade Wageningen,TheNetherlands México AlfonsJ.M.Stams Cuernavaca,Morelos,Mexico LaboratoryofMicrobiology HowardGoldfine WageningenUniversity DepartmentofMicrobiology Wageningen,TheNetherlands UniversityofPennsylvaniaPerelman RobertSteffan SchoolofMedicine CapeCoral,FL,USA Philadelphia,PA,USA HeinzWilkes TinoKrell ICBM DepartmentofEnvironmental CarlvonOssietzkyUniversity Protection Oldenburg,Niedersachsen,Germany EstacionExperimentaldelZaidin Granada,Granada,Spain SangYupLee Dept.Chem.Engineer.&BioProcess KoreaAdv.Inst.Science&Techn. Taejon,Korea(Republicof) This handbook is the unique and definitive resource of current knowledge on the diverse and multifaceted aspects of microbial interactions with hydrocarbons and lipids, the microbial players, the physiological mechanisms and adaptive strategies underlying microbial life and activities at hydrophobic material:aqueous liquid interfaces, and the multitude of health, environmental and biotechnological conse- quencesoftheseactivities. ScientificAdvisoryBoard Victor de Lorenzo, Eduardo Diaz, Otto Geiger, Ian Head, Sang Yup Lee, Terry McGenity,ColinMurrell,BalbinaNogales,RogerPrince,JuanLuisRamos,Wilfred Röling,ElioraRon,BurkhardTümmler,JanRoelofvanderMeer,WillyVerstraete, FriedrichWiddel,HeinzWilkesandMichailYakimov. Moreinformationaboutthisseriesathttp://www.springer.com/series/13884 Otto Geiger Editor Biogenesis of Fatty Acids, Lipids and Membranes With161Figuresand19Tables Editor OttoGeiger CentrodeCienciasGenómicas UniversidadNacionalAutónomadeMéxico Cuernavaca,Morelos,Mexico ISBN978-3-319-50429-2 ISBN978-3-319-50430-8(eBook) ISBN978-3-319-50431-5(printandelectronicbundle) https://doi.org/10.1007/978-3-319-50430-8 LibraryofCongressControlNumber:2018961436 #SpringerNatureSwitzerlandAG2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsorthe editorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforanyerrors oromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaims inpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG. Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland This work is dedicated to my extended German-Mexican family: Gertrud, Hanna, Jörg, Johannes, and Sofia Geiger Isabel M. López Lara, Otto Antonio, and Carmen Geiger López Preface Nucleicacidscarrytheinformationandproteinsdomostofthework,butthereisno life without membranes. Biological membranes are composed of proteins and amphiphiliclipids,i.e.,agroupofmoleculesconsistingofhydrophobichydrocarbon chainswhichareconnectedtoahydrophilicheadgroup.Inanaqueousenvironment, amphiphilic lipids tend to aggregate, and, if their molecular shape is more or less cylindrical,theyassembleintolipidbilayersasencounteredinmostmembranes.In thisvolumeoftheHandbook,thebiochemistryofthebiogenesisofmembranesand oftheirbuildingblocks,fattyacids,andmembranelipidswillbecoveredaswellas theirgeneticsandfunctionalgenomics.Examplesofmembranehomeostasisempha- size theflexibilityandadjustabilityofbiologicalmembranes. Foramore complete picture, we also tried to include the biogenesis of other lipid-derived biomolecules encounteredinmicrobes. Biological membranes show remarkable features, such as regions of distinct fluidity,givingrisetowhatisknownaslipidraftsormicrodomains.Thebilayerof most biological membranes seems to be asymmetric, as the inner leaflet usually shows a different lipid composition than the outer leaflet. Lipid composition of biological membranes depends on physiological conditions experienced by an organism; composition is not a constant and maybe changed upon adjusting to other physiological conditions, employing lipid remodeling and de novo lipid synthesis. There is lipid transfer between different membranes inside a cell, and finally, gradients of ions and charges across biological membranes are frequent features. In recent years, lipidomic and structural studies revealed the existence of many more membrane lipids, sometimes limited to very specialized microbes or organelles. Confronted with such complexity, it is obvious that experimental approaches to study biological membranes are demanding, not always satisfactory andstillneedtobeimprovedinmanycases.Weareonlybeginningtounderstandthe functioningandimportanceofbiologicalmembranes.Besideslipids,proteinsarethe other important components of biological membranes, and different functional associations, integrations, penetrations, and movements of proteins in connection with membranes are described, often endowing these membranes with special functionalproperties. Humans,animals,andplantsarethemostobviousandvisibleorganismsforuson our planet, and we are usually focused on them when thinking on our immediate vii viii Preface needsandpleasures.However,itis“themicrobes”whichguaranteeongoinglifeon earth, and we need to understand all aspects of their biology in order to help our planet. I hope that besides the experts, newcomers to the field will find the chapters of thisbookinterestingandunderstandableinthehopethat“hottopicsresearch”onthe biogenesis of fatty acids, lipids, and membranes will become accessible to a large readershipandhopefullytotheinterestedgeneralpublic. Finally,Iwouldliketothankthepeoplewhomadethisworkpossible: – Theeditorinchief,KennethTimmis,whodidawonderfuljobingettingmeon the way with this volume and who always had constructive inputs during the evolutionofthevolume – The people at Springer, especially Simone Giesler, Sharmila Thirumaniselvan, andSylviaBlago,whowereattheproductioninterfaceanddidallthemanuscript processing – Allthecontributorsofachaptertothisvolume – Finally,mywife,Isabel,ourson,OttoAntonio,andourdaughter,Carmen,who cametounderstandthatfamilyeffortswerenecessarytoreadythisvolumeforthe Handbook Thankyouallverymuch! OttoGeiger CentrodeCienciasGenómicas UniversidadNacionalAutónomadeMéxico Cuernavaca,Morelos,Mexico December2018 Acknowledgments IamgladthatduringmylifeIcoulddedicatemostofmytimetodowhatImostlike todo:researchinbiologicalsciences.Iliketothankmyteachersandfriendsforthe training and lessons they had inwaitfor me: Helmut Görisch, Harald Sobek, Rudi Müller, Karl-Heinz van Pée, and Franz Lingens at the University of Hohenheim, Eugene P. Kennedy at Harvard Medical School, as well as Ben Lugtenberg and HermanSpainkatLeidenUniversity.Iamgratefultothefundingagenciesthatmade research possible: Alexander von Humboldt Foundation, Deutsche Forschungsge- meinschaft, Howard Hughes Medical Institute, UC-Mexus Conacyt, MIT-Mexico CONACYTSeedFund,ConsejoNacionaldeCienciayTecnologíaMéxico(Ciencia Básica 253549, Fronteras de la Ciencia 118), Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica, and Universidad Nacional Autónoma de México.Iammostgratefultoallmycollaboratorsandespeciallythosewhopassed throughthelaboratoryandwithwhomIwasallowedtosharetheexcitingmoments of discovering some novelty. Special thanks to Lourdes Martínez-Aguilar and to IsabelLópez-Lara,and“GraciasMéxico!” ix Contents PartI BiochemistryofBiogenesisofFattyAcidsandLipids ...... 1 1 FattyAcids:Introduction ................................ 3 EricR.Moellering,VictoriaL.Prince,andRogerC.Prince 2 SynthesisofAcetyl-CoAfromCarbonDioxideinAcetogenic Bacteria .............................................. 25 A.WiechmannandV.Müller 3 FormationofFattyAcids ................................ 43 IsabelM.López-LaraandOttoGeiger 4 FormationofIsoprenoids ................................ 57 JordiPérez-Gil,ManuelRodríguez-Concepción,and ClaudiaE.Vickers 5 FormationofBacterialGlycerol-BasedMembraneLipids: Pathways,Enzymes,andReactions ........................ 87 OttoGeiger,ChristianSohlenkamp,andIsabelM.López-Lara 6 OrnithineLipidsandOtherAminoAcid-Containing AcyloxyacylLipids ..................................... 109 ChristianSohlenkamp 7 BacterialSphingolipidsandSulfonolipids ................... 123 OttoGeiger,JonathanPadilla-Gómez,andIsabelM.López-Lara 8 PhenolicLipidsSynthesizedbyTypeIIIPolyketideSynthases ... 139 AkimasaMiyanagaandYasuoOhnishi 9 LipidA .............................................. 151 RussellE.Bishop 10 LipoteichoicAcidSynthesisandFunctioninGram-Positive Bacteria .............................................. 163 OlafSchneewindandDominiqueMissiakas xi
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