Light‐sensingmecanismsinprokaryotes

Anoverviewandpossibleapplica9ons

Majorclassesofproteindomains

Proteindomain Chromophore

Bacteriorhodopsin:• Firstfoundinhaloarchaea• Quiteaneasymechanismtocreateaprotongradientthroughtheuseoflight(throughtheisomerisa9onofre9nal)• Absorbingmostlygreenlight

• SomeBacteriorhodopsin‐likegeneshavebeenfoundinotherorganisms.Therearenamedproteorhodopsins.TheyhavebeenexpressedinE.Coli

Bacteriophytochrome:• Foundinmanydifferenttypesofbacteria• Basedontheisomerisa9onofthechromophore• MostouputdomainareHKandEAL‐GGDEF(involvedincyclicdi‐GMPhydrolysis)• Absorbingredandfar‐redlight

Bacteriophytochrome Bilinderiva9ve

PYP p‐coumaricacid

PYPdomain:• Basedontheisomerisa9onofcoumaricacid• Mostrlyabsorbbluelight(maximumat446nm)• Usuallysingle‐domainedbutcanalsoformhybridswithHisKA,GGDEForEALoutputdomains

LOV Flavin

LOV‐family:• Firstdiscoveredinplantphototropinandmorerecentlyinbacteria• Basedonthetransi9onalforma9onofacovalentbondbetweenthecysteineandthechromophore(flavin)• ItisasubclassofthePASdomain(largeclasseofsensingandproteininterac9onbasedontheuseofaco‐factor)• NamedaZertheinputsignalofthisdomain(Light,OxygenandVoltage)• B.Sub-lishasaLOVdomain(inphotoreceptorYtvA)

BLUF Flavin

BLUF‐domain:• SimilarstruturewiththePASdomain• FoundinRhodobactersphaeroides• ThenamecomesfromeBlueLightsensingUsingFlavin• Logically,thisdomainsensebluelight• E.ColihasaBLUFdomain(morepreciselytheYgcFphotoreceptorprotein)

Cryptochrome FAD

Cryptochrome:• Foundinmanydifferentorganisms,likeplantsandanimalsaswellasinbacteria• Thechromophoreisaflavincombinedwithpterin• Absorbsintheviolet‐bluedomainofthespectrum• Lightac9vatesaphosophoryla9onwhichthenmighthavegeneregula9onoutput

BRregula9oninH.Salinarum

Weno9cethatinfullyaerobicand/ordarkcondi9ons,thebacteriadoesn’tsynthe9setheprotein

BacteriophytochromeandPSregula9oninC.Bradyrhizobium

Onceagainweseethattheexpressionofthephotosystemsgenesareregulatedbylightandoxygencondi9ons

Examplesofbacteriawithdomains

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

Advantages:•  Noninvasiveprocess,norisktoharmthecells(inoppositetochemicalinductors)

•  Fasterprocessthanchemicals(noneedtowaitfordiffusioninthereactorforexample)

•  Lightiseaslyproduced

Disadvantages:•  Thetwospectrumdomainsofthedifferentphotoreceptormustbeasfarawayas

possible(toreducetheriskofinterferences)

•  Somemechanismsareanaerobic‐dependant.Theconcentra9onofoxygenmustbekeptlow

Combina9onw/magnetotac9cbacteria

•  Fordiagnos9cs,orsamplescreening,wedon'talwaysneedthewholesetofreceptors‐‐>Subsetofreceptorsexpresseddependingonlight.

•  Regula9onbylightcouldalsopermitsalow‐budgetproject.Eg:usingLEDortranslucentpaper(permitu9liza9onofstandardbulb).

•  Oxygenlevelisverycri9calforvesicles'forma9oninmagnetotac9cbacteria‐‐>Weneedageneregula9onsystemwhichisrelatedtothelightdifferencesratherthantheaerobiccondi9on.

C.Bradyrhizobium

•  Theresultismorecorrelatedtothelightdifferencesthantheoxygenlevel:Far‐red‐‐>Expression;Red‐‐>Repression.

Fremyelladiplosiphon

•  Pigmentedproteinsdependonthecolorofambientlight‐‐>Insertreceptorgenesdownstreamofthepigmentedproteins.

Caulobactercrescentus•  Exposingcellsthatare

coordinatelyoverexpressingLovKandLovRtobluelightenhancestheafachmentcapacityofthesecells.

•  LightregulatesLovKkinaseac9vity.

•  LovRregulatescell‐surfaceafachment.

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.

TheBLUF‐EALproteinYcgFinE.coli

TheYcgFpathway:

receptor

Modulation of biofilm formation

The repressor: inhibited by interaction with YcgF

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

TheBLUF‐EALproteinYcgFinE.coli

Theprojectidea:

LinktheYcgFpathwaywiththebiofilmsubjectbypromo9ngthesecre9onofaproteinthatcouldgiveinteres9ngproper9estothefilmtotheYcgFpathway:useapromoterrepressedbyYcgE.

Protein X region upstream of YmgZ-ABC

YcgE

YcgF

Blue light

TheBLUF‐EALproteinYcgFinE.coli

Advantages:

•  Itisana9vepathwayinE.coli(whichiseasytomanipulate)

•  Thistypeofmucosalbiofilmis“naturally”inducedbybluelight:wecouldthinkofapplica9onsforanaqua9cenvironment

Possibleproblems:

•  Ar9clesveryrecent(January&April2009)sonotmuchinfoaboutthesequencesandproteins

•  Wewouldneedto“characterize”thetypeofbiofilmthebacteriaformwhentheYcgFpathwayisac9ve

•  Thepathwayseemstobepartofastress‐responsecircuit:therecouldbeinterferenceswithotherpathways

AninteresDngmoleculeforbiofilms:c‐di‐GMP

Themoleculeanditsroles:

AninteresDngmoleculeforbiofilms:c‐di‐GMP

Basic(leJ)andmorecomplexpathways(right,inE.coli):

AninteresDngmoleculeforbiofilms:c‐di‐GMP

Examplesofeffectsonc‐di‐GMPinvariousorganisms:

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