The summary for research seminar.docx
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The summary for research seminar.docx
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Thesummaryforresearchseminar
Thesummaryforresearchseminar
1.Introduction
Sedimentinleachatecollectionpondsisanextremeenvironmentwithconsiderablyhighofammoniumandorganicmatterconcentration.Therefore,theremightbesomespecificmicroognaismswhichmetabolizeindifferentialpathwayinthisspecialhabitat,especiallycarbonandnitrogentransformingmicroorganismswhichcouldbearhighamountsoforganicmattersandammonium.
Anaerobicmetabolicpathwaysallowunicellularorganismstotolerateorcolonizeanoxicenvironments.Overthepasttenyears,genomesequencingprojectshavebroughtanewlightontheextentofanaerobicmetabolismineukaryotes.Asurprisingdevelopmenthasbeenthatfree-livingunicellularalgaecapableofphotoautotrophiclifestyleare,intermsoftheirenzymaticrepertoire,amongthebestequippedeukaryotesknownwhenitcomestoanaerobicenergymetabolism.Someofthesealgaearemarineorganisms,commonintheoceans,othersaremoretypicallysoilinhabitants.Allthesespeciesareimportantfromtheecological,biotechnological,andevolutionaryperspectives.Intheunicellularalgaesurveyedhere,mixed-acidtypefermentationsarewidespreadwhileanaerobicrespiration,whichismoretypicalofeukaryoticheterotrophs,appearstoberare.
Thepresenceandfunctionofmitochondriaineukaryotesthatinhabitanaerobicenvironmentswaslongabiochemicalandevolutionarypuzzle.Majorinsightsintothephylogeneticdistribution,biochemistry,andevolutionarysignificanceoforganellesinvolvedinATPsynthesis(energymetabolism)ineukaryotesthatthriveinanaerobicenvironmentsforallorpartoftheirlifecycleshaveaccruedinrecentyears.Underpinnedbymanyexcitingadvances,twocentralthemesofthisprogresshaveunfolded.First,thefindingthatallknowneukaryoticgroupspossessanorganelleofmitochondrialoriginhasmappedtheoriginofmitochondriatotheoriginofknowneukaryoticgroups.Second,thephylogenyofeukaryaerobesandanaerobeshasbeenfoundtointerleaveacrossthediversityofeukaryoticgroups,erasingwhatwasoncethoughttobeamajorevolutiondividebetweeneukaryoticaerobesandtheiranaerobicrelativesDatafromgene,genome,andenvironmentalsequencingprojectsarerapidlyaccumulatingforeukaryotesthatliveinanaerobichabitats,givingcluesastowhatgenestheypossess.However,ithasbeenrepeatedlystressedandremainstruethatonlyforcomparativelyfeworganismsarespecificbiochemicaldataavailableconcerningtheenzymesandpathwaysthatareactuallyusedbytheorganismsandthemetabolicendproductsthatareexcretedbythemintheiranaerobichabitats.Similarly,thebiochemicalrolethattheirorganellesplayinATPsynthesisisknownforcompareativelyfewwell-studiedspecies.Eventhespectrumoforganellesspecifiedbytheterm“mitochondria”haschangedinrecentyears.Traditionally,thetermmitochondriareferstotheclassicaldouble-membrane-bounded,oxygen-respiring,crista-bearingorganellesfromratliverthatharbortheenzymesoftheKrebscycle(alsoknownasthecitricacidortricarboxylicacid[TCA]cycle)andoxidativephosphorylationandthatsynthesize,andexporttothecytosol,ATPwiththehelpofproton-pumpingelectrontransportchaincomplexes,ATPsynthases,andADP/ATPcarriers.Basedonthosecasestudies,wewillfocushereontheenzymes,pathways,andendproductsofcoreATPsynthesisineukaryoticanaerobesandtheparticipationofmitochondriatherein.
Thepresenceofacoreanaerobicmetabolismamongthealgaeprovidesinsightsintoitsevolutionaryorigin,whichtracestotheeukaryotecommonancestor.ThepredictedfermentativeenzymesoftenexhibitanaminoacidextensionattheN-terminus,suggestingthattheseproteinsmightbecompartmentalizedinthecell,likelyinthechloroplastorthemitochondrion.ThegreenalgaeChlamydomonasreinhardtiiandChlorellaNC64havethemostextendedsetoffermentativeenzymesreportedsofar.Amongtheeukaryoteswithsecondaryplastids,thediatomThalassiosirapseudonanahasthemostpronouncedanaerobiccapabilitiesasyet.Fromthestandpointsofgenomic,transcriptomic,andbiochemicalstudies,anaerobicenergymetabolisminC.reinhardtiiremainsthebestcharacterizedamongphotosyntheticprotists.ThisarticleispartofaSpecialIssueentitled:
Theevolutionaryaspectsofbioenergeticsystems.
2.lifewithoutoxygen
LifewithoutoxygeniscommononEarth.Oxygenshortageinbiotopescanresultfromgeochemicalorphysicalcircumstancesbutalsofrombacterialactivities.Anoxiacanbetransientorprotracted,extendingfromdiurnalperiodstomonthsoryearsormillenniaormore.Examplesofdiurnalanoxiaincludetidalzones,whilemarineoxygenminimumzonescanremainanoxicformanyyears,andseafloorbrinescanremainanoxicfor50,000 yearsormore;allofthesehabitatsharborricheukaryoticfloras.Survivalinanoxichabitatsrequiresmeansofanaerobicenergymetabolism,whicharefarmorevariedinprokaryotesthanineukaryotes.Thischapterwillfocusmainlyonphotosyntheticeukaryoteswhichaboundinanoxicenvironmentsand,anaerobicenergymetabolisminheterotrophiceukaryoteshavingbeenreviewedindepthrecently.
Whetherinaerobicoranaerobicenvironments,thechallengeofstayingalivemeansstayingfarfromequilibrium,andthatmeansmaintainingmetabolicfluxandredoxbalance.Inanaerobicenergymetabolism,justasinaerobicmetabolism,thegenerationofATPentailstheaccumulationofreducedcofactorssuchasNADHandFADH2thataregeneratedbycatabolicpathways,usuallyglycolysis,andthathavetobereoxidizedinaprocessthatinvolvesthetransferofelectronstosuitableacceptorsthatarethenexcretedbytheorganismtosustainmetabolicflux.Amongeukaryotes,anoxygenicphotosynthesishasnotbeendescribed,henceforeukaryotes,onlytwoprocessesareknowntomaintainredoxbalanceandconserveenergyunderanoxia:
i)fermentations,whichusuallyentailsubstratelevelphosphorylation(SLP),andii)anaerobicrespirationinvolvingchemiosmoticcoupling.Ineukaryoterespiration,electrons,usuallystemmingfromcarbohydratesandlipidsbutsometimesfromsulfide,enterviaNADHandFADH2themitochondrialelectrontransportchain,whichiscomprisedofmembraneproteins,theprostheticgroupsofwhichharborincreasinglypositivepotentialsinthecourseofelectronfluxtowardstheterminalacceptor.Electronfluxservestoestablishanelectrochemicalgradientacrosstheinnermitochondrialmembrane,resultinginaprotonmotiveforcethatdrivesATPsynthesis.Inanaerobicmitochondria,theterminalacceptorisnotO2,butisoftenfumarate.Fermentationsareprocessesinwhichtheterminalelectronacceptorisgeneratedbythecellthroughmetabolism.ATPisgeneratedviaSLP,whereanintermediatecontainsahighenergyphosphatebond(usuallyamixedanhydride)whichisusedtophosphorylateADP.SLPoccurswiththehelpofsoluble,ratherthanmembrane-associated,enzymes.Ineukaryotes,somefermentationpathwaysentailtheharnessingofchemiosmoticenergy,forexamplethereductionofendogenouslygeneratedfumaratetosuccinateintherespiratorychainofsomeanaerobicmitochondria.Overall,respirationandfermentationdifferwithrespecttotheenzymesemployedforcofactorreoxidationandtheenergyconservationprocessesinvolved.
Thebiochemistryofanaerobeshasbeenfarmoreextensivelystudiedinprokaryotesthanineukaryotes,probablybecausemostofwhatweknowabouteukaryoticenergymetabolismstemsfromstudiesofmulticellularorganisms,themajorityofwhicharespecializedtowardsoxygenastheterminalacceptor.Mostmulticellulareukaryotessuchasanimalsandplantscanonlywithstandshortperiodsofanoxia.Afewmetazoanswhichwithstandlongerperiodsofanoxiaoreventotalanoxiadoexist,astherecentlyreportedmarinesediment-dwellinganimalsLoriciferansindicate.Mostofthemetabolicdiversityineukaryotesisfoundamongunicellularspecies(protists),amongthemparasites(manyofwhichliveinoxygendeprivedenvironments)andphotosyntheticorganisms(microalgae),whichfrequentlyencounterhypoxicoranoxicconditionsintheirnaturalenvironments,e.g.soils,microbialmats,ormarineandfreshwatersediments.
Muchefforthasbeendevotedtothestudyofparasiteswiththegoalofidentifyingtargetstodevelopspecifictreatments,andacomprehensivereviewontheanaerobicpathwaysinheterotrophiceukaryoteshasbeenrecentlypublished.Comparedtomedicallyrelevantparasites,ourunderstandingofanaerobicenergymetabolisminphotosyntheticeukaryoteshasalwaysbeenmorelimited.Thiscircumstancehaschangedsomewhatoverthelasttenyears,withthegrowinginterestinmicroalgaeforbiotechnologicalapplications,forexampletheproductionofbiofuelssuchashydrogenandhydrocarbons.Hereweprovideanupdateontheknowledgeontheanaerobicmetabolicroutesoccurringinunicellulargreenalgae.Thesignificance/relevanceofthecompartmentalizationforsomeanaerobicpathwaysisconsideredastheevolutionaryoriginofthesepathwaysandtheimpactofphototrophyoriginsforanaerobicpathways.
3.Biogeochemicalimplication
Duringevolution,enzymesandpathwayscanreadilyundergorecompartmentationbetweenmitochondrial,cytosolic,andinthecaseofalgae,plastidiccompartments,astheexampleofADHElocalizationshiftforPolytomella(mitochondrial)vs.Chlamydomonas(chloroplast)underscores.Themovementofwholepathwaysfromonecompartmenttoanotherbecameevidentthroughstudiesofchloroplast-cytosolisoenzymes,studiesofdifferentiallocalizationofisoprenoidbiosynthesistoplastidsandthecytosolofalgae,starchmetabolisminalgae,peroxisomalpathways,andt
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