Rachhpal S. Kahlon Editor Pseudomonas: Molecular and Applied Biology Pseudomonas : Molecular and Applied Biology ThiSisaFMBlankPage Rachhpal S. Kahlon Editor Pseudomonas : Molecular and Applied Biology Editor RachhpalS.Kahlon DepartmentofMicrobiology PunjabAgriculturalUniversity Ludhiana,Punjab India ISBN978-3-319-31197-5 ISBN978-3-319-31198-2 (eBook) DOI10.1007/978-3-319-31198-2 LibraryofCongressControlNumber:2016940046 #SpringerInternationalPublishingSwitzerland2016 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthis book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained hereinorforanyerrorsoromissionsthatmayhavebeenmade. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAGSwitzerland Fondly dedicated to Iqbal Kahlon ThiSisaFMBlankPage Preface Inthe early 1970s, when Ijoined the bandwagon ofPseudomonasasapostdoc at theTechnicalUniversityofDenmark,Copenhagen,Pseudomonaswasconsidered asavaguelydefinedgenuscomprisingsoil-bornesaprophytes,attimesassociated with wound infection. However, with the developments in molecular biology, geneticengineering,PCR,DNA,andgenomesequencingsupportedbytechnologi- cal developments and computer-based databases, Pseudomonas has attained the position of a model organism for in silico modeling and systems biology where largechunksofunwantedDNAsegmentcanbereplacedbydesiredones.Presently, itisanimportantorganismforbiotechnologicalproductionofnovelchemicalsand pharmaceuticalsaswellasforscientificpursuitsforexploringnewareasofitsvast activities. This volume was planned with a view to provide concise and comprehensive information to young graduates, teachers, and research workers to visualize the potentialofthisimportantanddiversegroup. ThefirstchapteronPhylogenyandMolecularTaxonomyhas been contributed by distinguished scientists, Elena Garcia-Valdes and Jorge Lalucat, who discuss howthetaxonomyofPseudomonashasundergoneachangeandthemembersthat were not true Pseudomonas were assigned to other subclasses of Proteobacteria. Pseudomonas aeruginosa an opportunistic pathogen is notorious for hospital- acquired infection, multiple drug resistance, and a cause of CF of lungs.Quorum sensing and the mechanism of pathogenesis and virulence have been discussed. Two chapters on cell envelope and metabolic network highlight the structure and functionof cell envelope, particularly the outer membrane andthe vast metabolic potential of Pseudomonas. Mono- and di-oxygenases are the key enzymes for degradation of recalcitrant molecules, and a chapter on these has been included. One chapter is dedicated to genome and comparative genomics of important species. Also a chapter on “in silico” modeling and use of bioinformatics and databases has been included. Two chapters on applied biology elaborate on com- mercialexploitationforproductionofnovelmoleculesandbiopolymers.Theother highlightstheirroleindegradationoforganicchemicalpollutantsandbioremedia- tion.ThelasttwodealwithPseudomonas–plantinteractions:oneexclusivelydeals with plant pathogenesis by Pseudomonas syringae and the other elaborates their roleonbiocontrolofplantdiseasesanddirectandindirectplantgrowthpromotion. vii viii Preface Iwouldliketoplace onrecord myappreciationandthankstoAlena andJorge who were the first to accept my request to contribute a chapter on phylogeny and taxonomy.Thisactedasacatalystandwasasourceofencouragement.Iamequally grateful to Drs Levin, Parveen Sharma, Nagina, Swaranjit, Prince Sharma, and Saini and their colleagues for their outstanding contributions and making this volumepossible. I owe a great deal to my family, particularly my wife, Sukhdeep, for her all-round support and help. I do hope to compensate my lovely grandchildren AbhayandAmiebygivingthemmoretimenow. FinancialsupportbywayofgrantfromtheDepartmentofScienceandTechnol- ogy,GovernmentofIndia,NewDelhi,isacknowledgedwiththanks.Iamgrateful toPrincipal,SCDGovtCollege,Ludhiana,andProfDrBMSarwar,Head,Deptof Botany,forimplementationandsmoothfunctioningoftheprojectattheiresteemed institute. Lastly, I am grateful to my mentors, students, friends, and relatives who have beenpartofthisbeautifuljourney.TimelyhelpofMr.GurdeepSinghforcomputer typingisacknowledgedwiththanks. Ludhiana,Punjab,India RachhpalS.Kahlon December14,2015 Contents 1 Pseudomonas:MolecularPhylogenyandCurrentTaxonomy. . . . . 1 ElenaGarc´ıa-Valde´sandJorgeLalucat 2 CellEnvelope:MolecularArchitectureandFunction. . . . . . . . . . . 25 RachhpalS.Kahlon 3 Pseudomonas:TheVersatileandAdaptiveMetabolicNetwork. . . 81 PartapBirSingh,HarvinderSinghSaini,andRachhpalS.Kahlon 4 Pseudomonas:GenomeandComparativeGenomics. . . . . . . . . . . . 127 RachhpalS.Kahlon 5 PseudomonasOxygenases:NatureandFunction. . . . . . . . . . . . . . . 193 AbhaShukla,BrijdeepSingh,SwaranjitSinghCameotra, andRachhpalS.Kahlon 6 QuorumSensinginPseudomonasaeruginosa:Mechanismand RegulationofVirulence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231 SajalSarabhai,AmanjotKaur,NeenaCapalash,andPrinceSharma 7 InSilicoComparativeAnalysisofTypeVISecretionSystemsin PseudomonasputidaLS46. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 ParveenKumarSharma,JilagamazhiFu,RichardSparling, andDavidBernardLevin 8 PseudomonasforIndustrialBiotechnology. . . . . . . . . . . . . . . . . . . 281 RachhpalS.Kahlon 9 BiodegradationandBioremediationofOrganicChemicalPollutants byPseudomonas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343 RachhpalS.Kahlon ix