light‐sensing mecanisms in prokaryotes2009.igem.org/wiki/images/4/48/light.pdf ·...
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Light‐sensingmecanismsinprokaryotes
Anoverviewandpossibleapplica9ons
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Majorclassesofproteindomains
Proteindomain Chromophore
Bacteriorhodopsin:• Firstfoundinhaloarchaea• Quiteaneasymechanismtocreateaprotongradientthroughtheuseoflight(throughtheisomerisa9onofre9nal)• Absorbingmostlygreenlight
• SomeBacteriorhodopsin‐likegeneshavebeenfoundinotherorganisms.Therearenamedproteorhodopsins.TheyhavebeenexpressedinE.Coli
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Bacteriophytochrome:• Foundinmanydifferenttypesofbacteria• Basedontheisomerisa9onofthechromophore• MostouputdomainareHKandEAL‐GGDEF(involvedincyclicdi‐GMPhydrolysis)• Absorbingredandfar‐redlight
Bacteriophytochrome Bilinderiva9ve
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PYP p‐coumaricacid
PYPdomain:• Basedontheisomerisa9onofcoumaricacid• Mostrlyabsorbbluelight(maximumat446nm)• Usuallysingle‐domainedbutcanalsoformhybridswithHisKA,GGDEForEALoutputdomains
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LOV Flavin
LOV‐family:• Firstdiscoveredinplantphototropinandmorerecentlyinbacteria• Basedonthetransi9onalforma9onofacovalentbondbetweenthecysteineandthechromophore(flavin)• ItisasubclassofthePASdomain(largeclasseofsensingandproteininterac9onbasedontheuseofaco‐factor)• NamedaZertheinputsignalofthisdomain(Light,OxygenandVoltage)• B.Sub-lishasaLOVdomain(inphotoreceptorYtvA)
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BLUF Flavin
BLUF‐domain:• SimilarstruturewiththePASdomain• FoundinRhodobactersphaeroides• ThenamecomesfromeBlueLightsensingUsingFlavin• Logically,thisdomainsensebluelight• E.ColihasaBLUFdomain(morepreciselytheYgcFphotoreceptorprotein)
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Cryptochrome FAD
Cryptochrome:• Foundinmanydifferentorganisms,likeplantsandanimalsaswellasinbacteria• Thechromophoreisaflavincombinedwithpterin• Absorbsintheviolet‐bluedomainofthespectrum• Lightac9vatesaphosophoryla9onwhichthenmighthavegeneregula9onoutput
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BRregula9oninH.Salinarum
Weno9cethatinfullyaerobicand/ordarkcondi9ons,thebacteriadoesn’tsynthe9setheprotein
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BacteriophytochromeandPSregula9oninC.Bradyrhizobium
Onceagainweseethattheexpressionofthephotosystemsgenesareregulatedbylightandoxygencondi9ons
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Examplesofbacteriawithdomains
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Possibleapplica9onsPhoto‐sequencedproteinsynthesis
• Useapre‐exis9nglight‐triggeredmechanism(inE.ColiorB.Sub-lis)toactonthesynthesisofaprotein(e.g.theYcgFmechanism).• Asecondlightreceptorcouldbeaddedfromanotherbacterium(ifpossibleattheotherendofthelightspectrume.g.bacteriophytochrome)thatwouldbelinkedtoanotherpathway(leadingtotheforma9onofanotherproduct/enzyme)• • IndustrialUse:havingafeedbackonthebacteria’sproduc9on.Asensorinthebioreactorcouldcalculatetheconcentra9onofaproduct(ortoxicbyproduct)andreportbacktothebacteria(inhibitateorac9vatetheproduc9on)throughlightcontrol• «Easy»andfastwayto«communicate»withthecell• Therewouldalsobethepossibilitytohaveasequencedproduc9on.Ainforma9csystemwouldswitchfromonelighttoanotherinducingoneorexpressionoranother
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Advantages:• Noninvasiveprocess,norisktoharmthecells(inoppositetochemicalinductors)
• Fasterprocessthanchemicals(noneedtowaitfordiffusioninthereactorforexample)
• Lightiseaslyproduced
Disadvantages:• Thetwospectrumdomainsofthedifferentphotoreceptormustbeasfarawayas
possible(toreducetheriskofinterferences)
• Somemechanismsareanaerobic‐dependant.Theconcentra9onofoxygenmustbekeptlow
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Combina9onw/magnetotac9cbacteria
• Fordiagnos9cs,orsamplescreening,wedon'talwaysneedthewholesetofreceptors‐‐>Subsetofreceptorsexpresseddependingonlight.
• Regula9onbylightcouldalsopermitsalow‐budgetproject.Eg:usingLEDortranslucentpaper(permitu9liza9onofstandardbulb).
• Oxygenlevelisverycri9calforvesicles'forma9oninmagnetotac9cbacteria‐‐>Weneedageneregula9onsystemwhichisrelatedtothelightdifferencesratherthantheaerobiccondi9on.
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C.Bradyrhizobium
• Theresultismorecorrelatedtothelightdifferencesthantheoxygenlevel:Far‐red‐‐>Expression;Red‐‐>Repression.
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Fremyelladiplosiphon
• Pigmentedproteinsdependonthecolorofambientlight‐‐>Insertreceptorgenesdownstreamofthepigmentedproteins.
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Caulobactercrescentus• Exposingcellsthatare
coordinatelyoverexpressingLovKandLovRtobluelightenhancestheafachmentcapacityofthesecells.
• LightregulatesLovKkinaseac9vity.
• LovRregulatescell‐surfaceafachment.
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TheBLUF‐EALproteinYcgFinE.coli
Afewfastfacts:
• YcgF:blue‐lightsensorofEscherichiacoli• BLUF:receptorsthatsenseBlueLightbyU9lizingFADasachromophore
• EAL:domaininvolvedinc‐di‐GMP(cyclicdi‐guanosinemonophosphate)hydrolysis
• c‐di‐GMP:globalsecondmessengerusedbybacteriatocontrolmul9cellularbehavior
The receptor in reality doesn’t interact with c-di-GMP, but instead functions as an anti-repressor in a pathway involved in biofilm formation/maturation.
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TheBLUF‐EALproteinYcgFinE.coli
TheYcgFpathway:
receptor
Modulation of biofilm formation
The repressor: inhibited by interaction with YcgF
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TheBLUF‐EALproteinYcgFinE.coli
TheYcgZ‐ABCoperoninEscherichiacoli:
Map position: 1215012-1215248
Map position: 1215291-1215563
Protein involved in biofilm formation
Map position: 1215592-1215858
Regulator of acid resistance
Map position: 1215971-1215219
Protein involved in biofilm formation
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TheBLUF‐EALproteinYcgFinE.coli
Theprojectidea:
LinktheYcgFpathwaywiththebiofilmsubjectbypromo9ngthesecre9onofaproteinthatcouldgiveinteres9ngproper9estothefilmtotheYcgFpathway:useapromoterrepressedbyYcgE.
Protein X region upstream of YmgZ-ABC
YcgE
YcgF
Blue light
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TheBLUF‐EALproteinYcgFinE.coli
Advantages:
• Itisana9vepathwayinE.coli(whichiseasytomanipulate)
• Thistypeofmucosalbiofilmis“naturally”inducedbybluelight:wecouldthinkofapplica9onsforanaqua9cenvironment
Possibleproblems:
• Ar9clesveryrecent(January&April2009)sonotmuchinfoaboutthesequencesandproteins
• Wewouldneedto“characterize”thetypeofbiofilmthebacteriaformwhentheYcgFpathwayisac9ve
• Thepathwayseemstobepartofastress‐responsecircuit:therecouldbeinterferenceswithotherpathways
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AninteresDngmoleculeforbiofilms:c‐di‐GMP
Themoleculeanditsroles:
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AninteresDngmoleculeforbiofilms:c‐di‐GMP
Basic(leJ)andmorecomplexpathways(right,inE.coli):
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AninteresDngmoleculeforbiofilms:c‐di‐GMP
Examplesofeffectsonc‐di‐GMPinvariousorganisms:
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References
• MichaelA.vanderHorst(2007)Photosensinginchemotrophic,non‐phototrophicbacteria:lettherebelightsensingtoo.TRENDSinMicrobiologyVol.15No.12
• ErinB.Purcell(2008)Photoregula9oninprokaryotes.CurrentOpinioninMicrobiology2008
• Tschowri,N.&Hengge,R.(2009)TheBLUF‐EALproteinYcgFactsasadirectan9‐repressorinabluelightresponseofE.coli.GenesDev.23,522‐534.
• HengeR.(2009)Principlesofci‐di‐GMPsignallinginbacteria.NatureReviews.7,263‐273.
• SchroederC.(2008)InfluenceofajoininghelixontheBLUFdomainoftheYcgFphotoreceptorfromEscherichiacoli.ChemBioChem.9,15,2463‐2473.
• Purcelletal.(2007)APhotosensorytwo‐componentsystemregulatesbacterialcellafachment.PNAS
• KehoeandGutu(2006)RespondingtoColor:TheRegula9onofComplementaryChroma9cAdapta9on.TheAnnualReviewofPlantBiology
• Wikipedia