Transcription Regulation of Abiotic Stress Responses in Rice: A Combined Action of Transcription

20 Pages·2011·0.34 MB·English

OMICS AJournalofIntegrativeBiology
Volume15,Number12,2011
ªMaryAnnLiebert,Inc.
DOI:10.1089/omi.2011.0095
Transcription Regulation of Abiotic Stress
Responses in Rice: A Combined Action of Transcription
Factors and Epigenetic Mechanisms
Ana Paula Santos, Taˆnia Serra, Duarte D. Figueiredo, Pedro Barros, Tiago Lourenc¸o,
Subhash Chander, Maria Margarida Oliveira, and Nelson J.M. Saibo
Abstract
Plant growth and crop production are highly reduced by adverse environmental conditions and rice is partic-
ularlysensitivetoabioticstresses.Plantshavedevelopedanumberofdifferentmechanismstorespondandtryto
adapt to abiotic stress. Plant response to stress such as drought, cold, and high salinity, implies rapid and
coordinated changes at transcriptional level of entire gene networks. During the last decade many transcription
factors, belonging to different families, have been shown to act as positive or negative regulators of stress
responsive genes, thus playing an extremely important role in stress signaling. More recently, epigenetic mech-
anisms have been also involved in the regulation of the stress responsive genes. In this review, we have per-
formedacomprehensiveanalysisofthericetranscriptionfactorsreportedsofarasbeinginvolvedinabioticstress
responses. The impact of abiotic stresses on epigenomes is also addressed. Finally, we update the connections
made so far between DNA-binding transcription factors (TFs), and epigenetic mechanisms (DNA methylation
and histones methylation or acetylation) emphasizing an integrative view of transcription regulation.
Introduction NAC, MYB, and WRKY have been described as playing a
major role in abiotic stress tolerance (Century et al., 2008;
Rice production is severely affected by adverse envi- Hirayama and Shinozaki, 2010; Saibo et al., 2009). In rice,
ronmental conditions, such as drought, submergence, threemajorstrategieshavebeenusedtoidentifyTFsassoci-
andsalinity,andtheclimatechangeisexpectedtoraisecar- ated with abiotic stress responses: comparative genomics—
bon dioxide levels, temperatures, and to increase the fre- abiotic stress-responsive genes from Arabidopsis and maize
quencyofflooding.Giventhatriceisoneoftheworld’smost wereusedtoidentifyriceorthologs;forwardgenetics—genes
important staple food, providing 30% of the calories con- relatedwithtraits,suchasdroughtorhypoxiatolerance,were
sumedinAsiancountries,itisimportanttobetterunderstand identified through association mapping; genome-wide ex-
the molecular mechanisms underlying tolerance to abiotic pression profiles—transcriptome analysis using microarrays
stresses. Plant response to environmental changes is associ- have been used to identify novel abiotic stress responsive
ated with changes in signaling molecules [e.g., sugars, hor- genes.
mones,calcium,reactiveoxygenspecies(ROS),nitrousoxide Chromatinremodelingandnuclearorganizationhasbeen
(NO)] (Tuteja and Sopory, 2008), but also with large-scale alsoinvolvedinplantresponsetostress(Kimetal.,2010).For
genomic restructuring (McClintock, 1984), including trans- example,inriceandwheatthesalinityandheat-shockstresses
poson activation (Cheng et al., 2006), and rapid changes on caused decondensation of interphase ribosomal chromatin
gene expression patterns (e.g., genes encoding transcription (Santos et al., 2011). Heterochromatin maintenance mecha-
factors)(Wangetal.,2011a). nismsmayrepresstranscriptionundernormalconditionsbut,
Manytranscriptionfactors(TFs)fromdifferentplantshave under stress, those mechanisms may fail causing chromatin
been shown to play central roles in abiotic stress responses. remodelingandnovelpatternsofgeneexpression(Arnholdt-
The ability of TFs in acting as master regulators has been Schmitt,2004;MadlungandComai,2004).
regardedasasustainableapproachtomodifycomplextraits Environmentalepigeneticsreferstotheimpactofstresses
incropplants(Centuryetal.,2008).Inthepreviousdecade, on epigenetic marks in the genome, with consequences on
diverse TF families such as AP2/ERF, bZIP, Zn-finger, gene expression control (Chinnusamy and Zhu, 2009). An
InstitutodeTecnologiaQu´ımicaeBiolo´gica,UniversidadeNovadeLisboaandInstitutodeBiologiaExperimentaleTecnolo´gica,Oeiras.
Portugal.
839
840 SANTOSET AL.
epigeneticmemorycanbeachievedthroughtheinterplayof canbedistinguishedbytheirDNAbindingspecificity.DREB
several molecular mechanisms such as DNA methylation, proteins interact with the DRE/CRT cis-element usually
posttranslational modifications of the N-terminal regions of present in the promoter of genes involved in cold, drought,
nucleosomecorehistoneproteinsandchromatinremodeling and high salinity responses. ERF proteins usually interact
(Zhang,2008).Althoughmanyproteinshavebeenshownto with the GCC box element present in several pathogenesis-
modulatetheepigeneticresponse toenvironmental stresses, related(PR)genes;nevertheless,otherreportshavesuggested
namely,TF-interactingproteins,onlyafewwerealreadyre- that this TFs can also bind to DRE elements (Sakuma et al.,
ported in rice. Rice epigenetic factors have been identified 2002; Xu et al., 2008b). In rice, most AP2/ERF proteins in-
mainlythroughcomparativegenomics. volved in biotic and abiotic stress responses belong to the
Inthisreview wediscuss themost recentfindings on the ERF or DREB subfamilies. The ERF proteins were initially
transcriptionalcontrolofabioticstressresponseswithspecial designated ethylene-responsive element binding proteins
focusonrice.First,acomprehensiveupdatedlistoftherice (EREBPs) due to their putative involvement in ethylene re-
TFs is described and then epigenetic changes occurring in sponses(OhmetakagiandShinshi,1995).Theseproteinswere
responsetoabioticstressarereferred.Thediscussionsection able to bind to the GCC box element present in PR genes,
ismainlydedicatedtothecrosstalkbetweenTFsandepige- suggesting a role in disease resistance responses (Gutterson
neticmechanismsunderlyingregulationofgeneexpressionin andReuber,2004;OhmetakagiandShinshi,1995;Zhouetal.,
abioticstressresponses. 1997).StudiesinArabidopsis,tobacco,andtomatohaveshown
that overexpression of ERF genes conferred resistance to
Rice Transcription FactorsKnown ToBeInvolved fungal and bacterial pathogens (Xu et al., 2008b). Recent
inAbiotic Stress Responses studies have also revealed the role of some ERF proteins in
abiotic stress responses. OsBIERF2 (BENZOTHIADIAZOLE-
Many rice TFs, belonging to different families, have been
INDUCEDERF2)overexpressioninriceenhancedtolerance
showntobeinvolvedinabioticstress(e.g.,drought,salinity,
to drought, high salinity, and low temperature (Oh et al.,
cold, heat, and hypoxia) responses. Although numerous re-
2009).Infieldconditions,thesametransgenicplantsshowed
ports are only based on gene expression analysis (Supple-
increased grain yield under drought stress conditions. ERF
mentaryTableS1),anumberofabioticstress-relatedTFshave
proteinsidentifiedinricewereshowntobeinvolvedinboth
alreadybeenfunctionallycharacterizedthroughtransgenic/
bioticandabioticstressresponses.OsBIERF1,OsBIERF3,and
mutant lines (Table 1). Although Supplementary Table S1
OsBIERF4 were induced by pathogen infection and also by
onlyincludesvalidatedgeneexpressiondata,ourdiscussion
cold,drought,andsaltstress(SupplementaryTableS1)(Cao
willmainlyconsiderTable1.ThetotalnumberofTFfamily
et al., 2005, 2006). Moreover, overexpression of OsBIERF3
members(inriceandotherplantspecieswithcompletedse-
enhanceddiseaseresistanceagainstviralandbacterialpath-
quencedgenomes)isshowninSupplementaryTableS2.
ogens,andimprovedtolerancetodroughtandhighsalinity
(Cao et al., 2005). Multifunctional ERF genes responding to
AP2/ERF family
bioticandabioticstressstimuliwerealsoidentifiedinpepper,
The AP2/ERF (APETALA2/ethylene response factor) CaPF1 (Capsicum annuum Pathogen and Freezing Tolerance-
familyoftranscriptionfactorsischaracterizedbythepresence RelatedProtein)(Xuetal.,2007),andwheat,TaERF1(Yietal.,
of the highly conserved AP2 DNA-binding domain (Dietz 2004).TheERFsubfamilyalsoincludesgeneswhoseexpres-
et al., 2010). This family was initially characterized as plant sionisinducedbyhypoxia.SUB1A,SUB1B,andSUB1Cbe-
specific; nevertheless, there are evidences suggesting that a long to the quantitative trait locus Submergence-1 (Sub1)
horizontal transfer of anHNH-AP2 endonuclease from bac- involved in rice submergence tolerance. SUB1A has two al-
teriaorvirusesmayberelatedtotheoriginofthisTFfamily lelesandwasshowntobepresentonlyinindicacultivars.The
(Magnanietal.,2004).SeveralAP2/ERFTFshavebeeniso- allele carried by the cultivar will define its susceptibility to
latedfromvariousplantssuchasrice(Dubouzetetal.,2003), submergence(Fukaoetal.,2006).IntrogressionofSUB1Ain
Arabidopsis (Sakuma et al., 2002), tobacco (Wu et al., 2007), japonicacultivarsincreasedtolerancetosubmergenceandalso
wheat(Agarwaletal.,2006),andpoplar(Dietzetal.,2010). todroughtstress(Fukaoetal.,2011).
Based on the similarity of the DNA binding domains, this Transcription factors belonging to the DREB subfamily
familyisdividedinfivesubfamilies:AP2,RAV,ERF,DREB, havebeenextensivelystudiedinseveralplants,suchasAra-
and ‘‘others’’ (Sakuma et al., 2002). The AP2 subfamily con- bidopsis,rice,wheat,tomato,andbarley(Agarwaletal.,2006;
tainstwoAP2DNA-bindingdomainsandismainlyinvolved Dietzetal.,2010;Yamaguchi-ShinozakiandShinozaki,2006).
inplantdevelopment(Dietzetal.,2010).Proteinscontaininga Based on studies in Arabidopsis this subfamily was further
singleAP2domainandaB3DNAbindingdomainareclas- dividedintwosubclasses,DREB1/CBFandDREB2,accord-
sified as members of the RAV subfamily. In Arabidopsis, ing to their transcriptional response to abiotic stress condi-
membersofthissubfamilywereshowntobemainlyinvolved tions (Agarwal et al., 2006; Yamaguchi-Shinozaki and
inplantdevelopment,butmayalsohaveafunctioninabiotic Shinozaki, 2006). The initially identified DREB1/CBF genes,
stressresponses(Swaminathanetal.,2008;Wooetal.,2010). DREB1A,DREB1B,andDREB1Cwererapidlyandtransiently
Inrice,aRAV-likegenewasidentified,RAVL1,andshownto inducedbycold,butnotbydroughtorhighsaltstress,sug-
coordinate the brassinosteroid biosynthetic and signaling gestingthatinArabidopsistheymaybeinvolvedincoldstress
pathways, indicating a putative function in plant develop- responses. Contrastingly, DREB2 genes, DREB2A and
ment(Jeetal.,2010). DREB2B,wereinducedbydroughtandhighsalt,butnotby
The DREB and ERF regulatory proteins contain a single cold,indicatingaputativefunctioninthetolerancetodrought
AP2DNA-bindingdomain,beingcharacterizedasregulators and high salt stress (Agarwal et al., 2006; Nakashima et al.,
of biotic and/or abiotic stress responses. These subfamilies 2009).TheidentificationofnewmembersoftheDREB1/CBF
olerance Reference (Dubouzetetal.,2003;Itoetal.,2006;Fukaoetal.,2011)(Dubouzetetal.,2003;Itoetal.,2006;Qinetal.,2007;GuthaandReddy,2008) (Dubouzetetal.,2003;Zhangetal.,2009) (Chenetal.,2008;Fukaoetal.,2011)(Wangetal.,2008) (Chenetal.,2008) (Dubouzetetal.,2003;Matsukuraetal.,2010) (Chenetal.,2008;Matsukuraetal.,2010) (Chenetal.,2008;Matsukuraetal.,2010)(Zhaoetal.,2010) (Caoetal.,2006;Ohetal.,2009)(Caoetal.,2005;Caoetal.,2006;Ohetal.,2009;Fukaoetal.,2011)(Huetal.,2008b) (Fukaoetal.,2006;Xuetal.,2006;FukaoandBailey-Serres,2008;Fukaoetal.,2011;Pena-Castroetal.,2011)(Vanninietal.,2004;Mattanaetal.,2005;Vanninietal.,2006;Vanninietal.,2007;Pasqualietal.,2008;AgarwalandJha,2010)(Suetal.,2010) continued()
bioticStressT Crosstalk Possibleroleinbioticstressresponses(wounding).Involvedinbioticstressresponsesandradicalscavenging. ND ND ND ND ND ND ND ND ND Involvedinbioticstressresponses. Possibleroleinethyleneresponses.Involvedinplantdevelopment,carbohydratemetabolism,ethyleneandGAsignalling.Involvedinbioticstressresponses. Involvedinsugarmetabolism.
A
arding Targets ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND Amy3andOsDREB1B.
g a
e
R
Transgenic/MutantLines, Functionalanalysis ArabidopsisOXinenhancessalt,droughtandfreezingtolerance.OXinriceimprovessalt,droughtandcoldtolerance.OXinriceimprovestolerancetosalt,coldandArabidopsisdrought.OXinimprovesfreezingandheattolerance.OXintobaccoimprovesdrought,salt,andfreezingtolerance.ArabidopsisOXinimprovescoldandsalttoleranceanddecreasessensitivitytoABA.OXinriceslightlyimprovesdroughttolerance.ArabidopsisOXinandriceimprovessalt,droughtandcoldtolerance.OXinriceimprovesdroughttolerance. ArabidopsisOXindidnotinducetargetstress-induciblegenes. ArabidopsisOXindidnotinducephenotypicalchanges;inriceimproveddroughttolerance. ArabidopsisOXinimproveddroughtandheatOsDREB2B2tolerance.stress-inducibleexpressionimproveddroughttolerance.RiceknockdownlineshypersensitivetoABAandslightlysensitivetodrought.OXinriceslightlyimprovesdroughttolerancebutdidnotaffectABAsensitivity.OXinriceimprovessalt,droughtandlowtemperaturetolerance.OXinriceimprovessaltanddroughttolerance.OXintobaccoimprovessalttolerance. Riceknockdownlinesdidnotshowphenotypicalchanges.OXinjaponicariceimprovessubmergencetolerance.Introgressioninjaponicariceimprovesdroughtandsubmergencetolerance.OXinriceincreasesABAArabidopsissensitivity.OXindecreasesABAsensitivity.ArabidopsisOverexpressioninandappleimprovescoldanddroughttolerance.Overexpressionintomatoimprovesdroughttolerance. OXinriceimprovedcoldtolerance.Riceknockdownlinesdisplayedcoldsensitivity.
h
haracterized,Throug Molecularstudies invitroBindstoDREandactivatestranscriptioninriceprotoplasts. GUSexpressiondrivenbyOsDREB1Bpromoterinresponsetocold,ABA,drought,salt,methylviologen,andsalicylicacid.BindstoDREandLTREandactivatestranscriptioninyeast. BindstoDREandactivatestranscriptioninyeast.BindstoDREandactivatestranscriptioninyeast.invitroBindstoDREandactivatestranscriptioninyeast.invitroBindstoDREandactivatestranscriptioninriceprotoplasts.NosignificantDREtransactivationinArabidopsisprotoplastsandwiththeGAL4systeminriceprotoplasts.OsDREB2B2bindstoDREandactivatestranscriptioninArabidopsisprotoplasts. OsDREB2B1didnotbindtoDREinArabidopsisprotoplasts. ND ND invitroBindstoGCC-box. ND ND PAL2Osmyb4transactivatesthe,ScD9SADcoldinduciblepromoters aOsDREB1BAmy3Bindstotheandpromoterandrepressestranscription.
C
a
ly poxi ND ND ND ND ND ND ND ND ND ND ND ND ND + 0 ND
nctional abioticstress ABAHy -/0 0 0 - + ND 0 ND ND + 0 - 0 - 0 -
Fu nder Heat ND + ND ND ND ND + 0 + ND ND ND ND ND 0 0
s u
tionFactor Geneexpression DroughtSalt ++ ++ 00 -ND ++ NDND ++ 00 ++ +ND ++ ++ 00 +ND 00 +0
rip Cold + + 0 ND + ND 0 + + 0 0 + + ND + +
c
s
n y
ceTra TFFamil AP2/ERF MYB
Ri
Listof1. Gene OsDREB1A OsDREB1B OsDREB1D OsDREB1E OsDREB1F OsDREB1G OsDREB2A OsDREB2BASform1 OsDREB2BASform2 ARAG1 OsBIERF2,AP37,OsERF3OsBIERF3,AP59 OsRAF SUB1A OsMYB4 MYBS3
e
Tabl Locus Os09g35030 Os09g35010 Os06g06970 Os04g48350 Os01g73770 Os08g43210 Os01g07120 Os05g27930 Os05g27930 Os04g46410 Os01g58420 Os02g43790 Os03g08470 BGIOSGA038325 Os04g43680 Os10g41200
841
Reference Daietal.,2007;Maetal.,2009) Huangetal.,2009b;SongandMatsuoka,2009) Huangetal.,2007) Huangetal.,2009a) Xuetal.,2008a) Zouetal.,2007,2008;Luetal.,2009) Shobbaretal.,2008;Luetal.,2009;Hossainetal.,2010b)Xiangetal.,2008;Luetal.,2009) Shobbaretal.,2008;Luetal.,2009;Hossainetal.,2010a)Yangetal.,2011) Shobbaretal.,2008;Luetal.,2009)Ramamoorthyetal.,2008;Wuetal.,2009)Qiuetal.,2004;Qiuetal.,2007;Caietal.,2008;Qiuetal.,2009)Qiuetal.,2004;Ryuetal.,2006;Shimonoetal.,2007;QiuandYu,2009) Qiuetal.,2004;Songetal.,2009) continued()
( ( ( ( ( ( ( ( ( ( ( ( ( ( (
Crosstalk Involvedincell-cycleregulation. InvolvedinH2O2-inducedstomataclosure. ND ND ND Roleinfertility:Involvedinpollendevelopment. GA3antagonizesgeneinductionbyABA.InducedbyACCandMeJA.InducedbyACC. InducedbyACC. Involvedinauxinsignalling.InducedbyACCandMeJAND Bioticstress Bioticstress ND
Targets OsCycB1 CytochromeP45071D10,Peroxidase24PrecursorND OsP5CSandOsProT. ND ND ND ND ND Os01g50100,Os08g29660LEA3Rab16and ND PR1aAOS2LOX,,,OsWRKY24,424551,,,74 GSTandacytochromeP450 ND
Functionalanalysis OXinriceimprovescoldtolerance.OXinArabidopsisimprovescold,droughtandsalttolerance.SeedgerminationinsensitivetoABA.Ricemutantisdrought-andsalt-tolerant,hasthickerleaves,lowerstomatadensityandclosedstomata. OXintobaccoandriceimprovessalttolerance. OXinriceimprovescoldanddroughttoleranceandcausesABA-hypersensitivity.OXinriceimprovessaltanddroughttolerance.OXinriceincreasessensitivitytosalt.RNAilineshavedecreasedfertility,increasedtolerancetosaltanddrought.OXinArabidopsisresultsinABAhypersensitivity. Ricemutantsaremoresensitivetosalinityanddehydration. OXinriceinducestolerancetodroughtandsalt,hypersensitivitytoABA.Mutanthaslowtolerancetosaltanddrought,anddecreasedsensitivitytoABA.Ricemutantismoresensitivetosalt,droughtandoxidativestress,andhasreducedsensitivitytoABA. ArabidopsisMutantisABA-insensitive.OXinabi5rescuesABAinsensitivephenotype.OXinriceimprovesdroughttolerance. OXinricewithpromHSP101–tolerancetoheatanddrought. OXinriceleadstohighersensitivitytosaltandcold.Enhancedresistancetobioticstress. OXinriceleadstoenhancedresistancetoblastinfectionviaBTH-inducibleArabidopsisresponses.OXinleadstoenhancedtolerancetodroughtandhighsalinity.DecreasedsensitivitytoABAingerminationandseedlinggrowth.ArabidopsisOXinleadstoenhancedosmoticstresstolerance.Theresultsarenotclear.
TableContinued1.() Molecularstudies OsCycB1Bindstothepromoterinvitro. BindstoconservedDNAmotifandactivatestranscription. Constitutivelyexpressedinleaves,culms,rootsandspikesinadultplants.Activatestranscription. ND Expressedinmaturepollen.Twospliceforms,withdifferenttransactivationandDNAbindingactivity.BindstoG-box.BothproteinsinteractwitheachotherandwithOsVP1.BindstoABREandactivatestranscription.Expressedinschlerenchymaandepidermalsilicacellsandimmatureleafs.Expressedmainlyinleaves.Activatestranscription. Expressedinroots,shoots,stem,matureleave,flagleave,andpanicle.BindstoABREandactivatestranscription.Expressedmainlyincoleoptilesandprimaryroots.BindstoABRE.BindstoABREandactivatestranscription.Expressedmainlyinpaniclesundercontrolconditions ND Inducedbybenzothiadiazole(BHT).Expressedinalltissuesundercontrolconditions. ND
a
poxi ND ND ND ND ND ND + ND ND ND ND ND ND ND ND
bioticstress ABAHy ND ND + ND 0 + + + + ND +/0 ND ND +-0// +
a
nder Heat ND ND ND ND ND ND ND ND ND + ND + - + 0
u
Geneexpression DroughtSalt ++ NDND +ND +0 ++ +-+/ ++ ++ ++ ++ ++ +ND ++ ++/0/0 ++
Cold + ND + + 0 +-/ + +/0 + ND + ND - +-/ 0
TFFamily ZincFinger-C2H2 bZIP WRKY
Gene OsMYB3R-2 DST ZFP182 ZFP245 ZFP252 OsABI5,OsbZIP10 OsABF1,OsbZIP12 OsbZIP23 OsABF3,OsABF2OsbZIP46 ABL1 OsbZIP72,OsABF4OsWRKY11 OsWRKY13 WRKY45 OsWRKY08(OsWRKY8v2)
Locus Os01g62410 Os03g57240 Os03g60560 Os07g39870 Os12g39400 Os01g64000 Os01g64730 Os02g52780 Os06g10880 Os06g10880 Os09g28310 Os01g43650 Os01g54600(EF143611indica–) Os05g25770 Os05g50610
842
Reference (Xieetal.,2005;Yuetal.,2010) (Huetal.,2008a),(Takasakietal.,2010),(Nakashimaetal.,2007),(Ohnishietal.,2005)(Huetal.,2006),(Linetal.,2007) (Gaoetal.,2010)(Fangetal.,2008)(Yokotanietal.,2009) (Jeongetal.,2010) (Zhengetal.,2009)(Fangetal.,2008)(Takasakietal.,2010) (Baniwaletal.,2004;Yokotanietal.,2008;Liuetal.,2009;Mittaletal.,2009;Liuetal.,2010)(Yokotanietal.,2008;Mittaletal.,2009;Liuetal.,2010)(Zhouetal.,2009)
Crosstalk Auxintransportpathway.Sugarsignalling.Bioticstress(overexpressionincreasestolerancetoblastdisease) ND ND ND ND ND ND ND ND
Targets HVA22 ND ND ND ND ND ND OsLEA3 ND ND ND
Functionalanalysis ArabidopsisOXinleadstoenhancedsensitivitytoABA,saltandosmoticstressesandsugarstarvationOXinrice:improvedtolerancetocold,dehydrationandsalt.MoresensitivetoABA. OXinrice:improvedtolerancetodroughtandsalt.MoresensitivetoABA,withincreasedstomataclosure. ArabidopsisOXthegenearehypersensitivetoABAandmoretoleranttodehydration.ArabidopsisOXinresultedinthermotoleranceandhighergerminationrateundersalinitystressOXinriceunderGOS2(constitutivepromoter)andtheRCc3(root-specific)increasedtheplanttolerancetodrought,highsalinity,andlowtemperatureatthevegetativestage. OXinriceenhancestolerancetodroughtandhigh-salinityOXinrice–tolerancetohighsalinityanddrought ArabidopsisOXinwithhigherbasalthermotolerance,notacquired. ArabidopsisOXinresultedinthermotolerancetotransientheatandsalttolerance. ArabidopsisOXinresultedinconferredincreasedtolerancetosaltandosmoticstress.
TableContinued1.() Molecularstudies Expressedinaleuronecells.Promotestranscription. Inducedbywounding.Tissue-specificexpressionaccordingtostress.Transcriptionalactivator Particularlyinducedinstomataguardcells.Inducedbyblast,MeJAandethylene.Activatestranscription.ND Increasedexpressionmainlyinroots.Activatestranscription. Expressedinrootandpanicles.RCc3:OsNAC10plantsshowedenhanceddroughttoleranceatthereproductivestageduetodifferencesinexpressionofOsNAC10-dependenttargetgenesinrootsandleavesExpressedinrootsandleaves.Activatestranscription.Northernblot.ShowstranscriptionalactivityinyeastbutnotinriceprotoplastsExpressinleaves&flowers(qRT-PCR) Activatestranscription DREB1A/Stress-responsivegenesCBF3RD29ACOR15A,,andKIN1wereupregulatedintransgenicplants ulated,respectively.
g
nderabioticstress HeatABAHypoxia ++ND +NDND +NDND NDNDND 0NDND +NDND +NDND +NDND +NDND +NDND NDNDND gulationandnotre
u e
Geneexpression DroughtSalt ++ ++ ++ ++ +0 ++ ++ ++ ++ ++ NDND ulation,downr
Cold 0 + + 0 0 0 + + 0 0 ND pregd.
use
TFFamily NAC HSF HLH spondtoverexpres
reo
AC6 corOX,
Gene OsWRKY72 SNAC2/OsN SNAC1/OsNAC19 OsNAC52/ONAC088ONAC063 OsNAC10 ONAC045 OsNAC5 OsHSF7/OsHsfA2d OsHsfA2e OsbHLH2/OsICE1 nus,andzerodetermined;
Locus Os11g29870 Os01g66120 Os03g60080 Os05g34830 Os08g33910 Os11g03300 Os11g03370 Os11g08210 Os03g06630 Os03g58160 Os11g32100 Plus,miND,not
843
844 SANTOSET AL.
subclass, DREB1D and DREB1F, which respond to drought Arabidopsis(Liaoetal.,2008).Inrice,onlyafewstudiesreport
andsaltstress,respectively,maysuggestacrosstalkbetween theinvolvementofMYBproteinsinabioticandbioticstress
DREB1/CBFandDREB2pathwaysinresponsetothoseabi- responses. Response to cold seems to be a common feature
otic stresses (Haake et al., 2002; Nakashima et al., 2009; amongthebestcharacterizedriceMYBproteins.
Sakuma et al., 2002). In rice, several DREB1 and DREB2 or- RiceMYBS3proteincontainsasingleMYBrepeat(MYB1R)
thologswereshowntoplayaroleinabioticstressresponses. anditsgeneexpressionisrepressedbyABAandinducedby
The rice DREB1A orthologs, OsDREB1A and OsDREB1B, coldandsalt(Suetal.,2010).MYBS3overexpressioninrice
weredifferentlyexpressedinresponsetoabioticstress.Rice significantlyincreasestolerancetocoldandRNAinterference
geneswereinducedbycold,butalsobydroughtandhighsalt lines displayed enhanced sensitivity to this abiotic stress
conditions(Dubouzetetal.,2003;Itoetal.,2006).OsDREB1B suggestingaroleofMYBS3inricecoldresponses.Moreover,
wasalsoshowntorespondtoheatstress,suggestingarolein microarrayanalysisandtransactivationassaysrevealedthat
the response to this abiotic stress (Qin et al., 2007). Further- MYBS3 represses the cold signaling pathway dependent on
more, the overexpression of OsDREB1A and OsDREB1B in theDREB1/CBFregulon(Suetal.,2010).
riceresultedintolerancephenotypessimilarlytoArabidopsis MYB3R subfamily proteins are known to be involved in
plants overexpressing the DREB1A (Ito et al., 2006; Naka- cell-cycle regulation through the transcriptional control of
shima et al., 2009). Rice DREB2 genes, OsDREB2A and Os- cyclins. However, some studies revealed that TFs from this
DREB2B,showedasimilarresponsetodroughtandsalt,but subfamilymightplayaroleinabioticstressresponses(Feller
OsDREB2Bwasalsoinducedbycold,suggestingaputative etal.,2011).OsMYB3R-2geneexpressionisinducedbycold,
role of DREB2 proteins in cold responses (Matsukura et al., drought, and high salinity and its overexpression in Arabi-
2010).Furthermore,OsDREB2Bwasshowntoberegulatedat dopsis has significantly enhanced cold tolerance (Dai et al.,
the posttranscriptional level by alternative splicing (Matsu- 2007).OsMYB3R-2wasalsoshowntotargetcyclingenesin-
kuraetal.,2010).Asimilarmechanismofregulationwasalso volved in the G2/M transition and thereby regulates the
foundfor DREB2proteins in barley,wheat, and maize(Na- progressofthecellcycleduringcoldstress(Maetal.,2009).
kashimaetal.,2009).MostoftheDREBsareinvolvedinABA- TheR2R3-MYBproteinsarethelargestgroupofplantMYB
independent stress responses; however, some studies have proteins, including hundreds of members throughout the
reported DREBs that are responsive to ABA (Haake et al., plant kingdom (Feller et al., 2011). The functions of these
2002; Yamaguchi-Shinozaki and Shinozaki, 2006). For in- proteinsaremainlyrelatedtoregulationofplantmorphology
stance, OsDREB1F and ABA RESPONSIVE AP2-LIKE and metabolism, but a role in biotic and abiotic stress re-
(ARAG1) gene expression was shown to be upregulated in sponses has also been reported. OsMYB4 was shown to be
response to ABA. Moreover, the ARAG1 knockdown line involved in the regulation of both types of stress responses
displayedhypersensitivitytoABAanddrought,suggestinga and its overexpression confers varying levels of tolerance
roleofthisTFintheABA-dependentdroughtstressresponse depending on thespecies (Agarwaland Jha, 2010).Itsover-
(Zhaoetal.,2010).Interestingly,apossibleroleofriceDREB expressioninArabidopsisincreasesplanttolerancetocoldand
proteins in biotic stress responses was reported. OsDREB1B drought and the resistance to biotic stress (Mattana et al.,
overexpressionintobaccoimprovedplantresistancetovirus 2005; Vannini et al., 2004, 2006). Tomato plants over-
infection and induced the expression of several PR genes expressing this TF displayed a higher tolerance to drought
(GuthaandReddy,2008).OnlyfewDREBproteinswerein- andincreasedresistancetobioticstress,butnoalterationon
volvedinbioticstressresponses.InArabidopsis,DREB2Agene coldsensitivity(Vanninietal.,2007).Intheapple,enhanced
expression was upregulated in ACTIVATED DISEASE RE- tolerance to drought and cold was reported in transgenic
SISTANCE 1 (ADR1) overexpression lines (Agarwal et al., plantsoverexpressingOsMYB4(Pasqualietal.,2008).Besides
2006). thedifferenttolerancelevelsobservedindifferenttransgenic
hosts,theincreaseindroughttoleranceseemstobeacommon
featureinallplantsoverexpressingOsMYB4.
MYBfamily
Although several MYB proteins have been identified in
MYBtranscriptionfactorsarecharacterizedbythepresence rice,sofaronlyafewOsMYBshavebeenfunctionallychar-
of MYB repeats (R) involved in DNA-binding and protein- acterizedfortheirroleinabioticstressresponses(Table1).The
protein interactions (Feller et al., 2011). MYB proteins were data already gathered suggest that rice MYBs play an im-
initially identified in animals, but similar proteins are re- portantroleinthecoldstressresponsemechanisms.
portedininsects,plants(SupplementaryTableS2)andfungi
(Strackeetal.,2001).Inplants,MYBproteinscanbeclassified
Zinc fingers
intothreesubfamilies,R-MYB,R2R3-MYB,andR1R2R3-MYB
(MYB3R) depending on the presence of one, two, or three Thezinc-fingerproteinsplayamajorroleinmanycellular
tandemMYBrepeats,respectively(Felleretal.,2011).Several pathways and are present in all eukaryotic organisms. Zn
members of this family were identified in rice, Arabidopsis, fingerTFshavebeenimplicatedindistinctpathways,suchas
maize, and soybean, and shown to be involved in a wide nutrient homeostasis and root development (Devaiah et al.,
varietyofcell processes,suchascell cycleand cellmorpho- 2007), flower development (Wu et al., 2008), carbohydrate
genesis(Felleretal.,2011;JinandMartin,1999;Strackeetal., metabolism (Tanaka et al., 2009) and light and hormonal
2001). MYB proteins were also reported to be involved in signaling(Feurtadoetal.,2011).
biotic and abiotic stress responses. Studies in soybean re- TheC2H2-typeZnfingerTFsareoneofthemostabundant
vealed that GmMYB76, GmMYB92, and GmMYB177 are in- Zn finger TFs and have been described as involved in the
ducedbyseveralabioticstressconditionsandoverexpression responseofdifferentplantstoabioticstressconditions(Mit-
of these TFs improves tolerance to salt and freezing in tleretal.,2006;Sakamotoetal.,2004;Vogeletal.,2005).These
TFSAND EPIGENETIC MECHANISMS IN ABIOTICSTRESS RESPONSES 845
TFs,alsoreferredtoasTFIIIA-typefinger,arecharacterized PyACGTGG/TC) (Choi et al., 2000; Guiltinan et al., 1990;
bytwocysteinandtwohistidineresiduesthatbindtoazinc Hoboetal.,1999a;Unoetal.,2000).Thiscis-actingelement
iontoformastructurethatbindstothemajorgrooveofDNA wasinitiallyidentifiedinwheat(Guiltinanetal.,1990)and
(PavletichandPabo,1991).ThefirstofsuchTFsidentifiedin rice(Mundyetal.,1990)andwaslatershowntobepresentin
plantswasthepetuniaZPT2-1,azinc-fingerproteinTFIIIA- the promoters of many ABA-responsive genes. The role of
type(Takatsujietal.,1992).Inrice,despitethehighnumberof bZIP TFs in ABA-signaling was further supported by the
genes encoding C2H2-type Zn finger TFs (Agarwal et al., findings that the overexpression of these TFs causes ABA-
2007),onlyafewhavebeenfunctionallycharacterized:ZINC- hypersensitivityintransgenicplants(Fujitaetal.,2005;Kang
FINGER PROTEINS 182 (ZFP182), ZFP245, ZFP252 and etal.,2002;Zouetal.,2007;Xiangetal.,2008).Inmostcases,
DROUGHT SALT TOLERANCE (DST) (Huang et al., 2007, theoverexpressionofOsbZIPsinriceimprovestoleranceto
2009a,2009b;Xuetal.,2008a).Theoverexpressionofthefirst abioticstressconditions,namely,highsalinityanddrought,
three of these TFsin rice plants yielded similarphenotypes: whereas its downregulation/knockout leads to higher sen-
increasedtolerancetoabioticstressconditions(Huangetal., sitivity (see Table 1). Nevertheless, rice plants over-
2007,2009a;Xuetal.,2008a).TheDSTprotein,ontheother expressingOsABI5/OsbZIP10areanexception,becausethey
hand,seemstohaveadifferentroleinabioticstresssignaling, werereportedtobemoresensitivetosalinitythanthewild-
becausericeplantsharboringamutationinitsgenearemore type(Zouetal.,2008).Itisalsointerestingtonotethat,most
toleranttoabioticstressesthanthewild-typeplants(Huang rice genes coding for bZIP TFs involved in abiotic stress
etal.,2009b).AsshowninTable1andalsoinSupplementary signaling are induced by ABA and bind to the ABRE cis-
TableS1,genescodingfordifferentC2H2-typeTFsinriceare element(Table1).Theseresultsindicatethat,inrice,abiotic
differentially regulated by several abiotic stress conditions. stress signaling though bZIP TFs preferably occurs in an
ThismeansthattheseTFsmostlikelyhaverolesindifferent ABA-dependent manner. Moreover, the bZIP-mediated
signalingpathwaysmediatingabioticstressresponses. ABA signaling pathway seems to be conserved in several
There is much crosstalk between different families of TFs plant species, both monocots and dicots. For example, the
involvedinabioticstresssignaling.C2H2-typeTFshavebeen homologousproteinsTRAB1(riceTRANSCRIPTIONFAC-
particularly described as interacting with the DREB1/CBF TOR RESPONSIBLE FOR ABA REGULATION 1), HvABI5
regulon. For example, Arabidopsis plants overexpressing (barley ABA INSENSITIVE 5), and ABI5 (Arabidopsis ABA
DREB1A/CBF3 were found to have altered levels of ZAT10/ INSENSITIVE 5) interact respectively with their counter-
STZ (Maruyama et al., 2004). This interaction is further parts OsVP1 (rice VP1- VIVIPAROUS 1), HvVP1 (barley
supported by the finding that ZAT12, a transcriptional re- VP1),andAtABI3(ArabidopsisABAINSENSITIVE3),which
pressoralsodescribedasaregulatorofseveralabioticstress- are themselves homologues, to modulate ABA-dependent
responsivegenesinArabidopsis(Davletovaetal.,2005),hasa geneexpression(CasarettoandHo,2003;Hoboetal.,1999b;
regulon partly overlapping that of DREB1C/CBF2 (Vogel Nakamuraetal.,2001).
etal.,2005).Moreover,ZAT12wasalsodescribedasanega- Other than abiotic stress signaling, bZIP TFs have been
tive regulator of DREB1A/CBF3 and DREB1B/CBF1 (Vogel described as involved in other signaling pathways, such as
et al., 2005). In rice, plants overexpressing ZFP252 were re- lightsignaling(Chattopadhyayetal.,1998),floralarchitecture
portedtohavealteredlevelsofOsDREB1A(Xuetal.,2008a). (Maier et al., 2009), hormone signaling (Fukazawa et al.,
C2H2-type TFs are therefore signaling components that can 2000),andpollendevelopment (Iven etal.,2010).Ascanbe
belocatedeitherup-ordownstreamtheDREB1/CBFgenes. seeninTable1andSupplementaryTableS1,ricegenescoding
Other types of Zn fingers, such as the Zn finger Homeo- for bZIP TFs are regulated at the transcriptional level by
Domain TFs (ZF-HD), have been reported to have a role in severalhormones,suchasauxins(Yangetal.,2011),gibber-
abiotic stress signaling in plants. These proteins are charac- ellins(Shobbaretal.,2008),andethylene(intheformofACC)
terizedbythepresenceofZnfinger-likemotifsupstreamofa (Lu et al., 2009). This is indicative of a crosstalk between
homeodomain (Windhovel et al., 2001). These TFs act in severalsignalingpathways,mediatedbybZIPTFs.
concertwithNACTFsinArabidopsis,toregulatetheexpres- Another group of bZIP TFs that has been implicated in
sionofabioticstress-relatedgenes(Tranetal.,2006).Inrice, abioticstressresponsesaretheHDZIPTFs.Theseproteinsare
however, the involvement of these TFs in stress signaling characterized by the presence of a homeodomain directly
is yet to be described. Up to now, only microarray data is before the bZIP domain (Ruberti et al., 1991). These HDZIP
available on the transcriptional regulation of these genes in domainsareresponsibleforhomo-andheterodimerizationof
rice(Jainetal.,2008). the TFs, and also for the DNA-binding specificity (Meijer
etal.,2000).Theseproteinsareplant-specificanddonotoccur
inotherEukaryotes.SimilartobZIPs,HDZIPTFshavebeen
Leucine zippers
implicated in several cellular processes, such as hormone
bZIP proteins are a large family of TFs, present in all eu- (Ilegemsetal.,2010)andlightsignaling(Wangetal.,2003),
karyotes,andthatarecharacterizedbythepresenceofabasic and also in plant development (Vernoud et al., 2009). Even
region,responsibleforDNA-binding,andofaleucinezipper, thoughtherearesomereportsontheinvolvementofHDZIPs
involved in protein homo- and heterodimerization (Jakoby inabioticstresssignaling,onlyafewoftheseTFshavesofar
et al., 2002). Many bZIP TFs have been linked to the ABA- been characterized. The heterologous expression of the sun-
dependentsignalingpathwayinseveralplantspecies,suchas flowergeneHahb-4inArabidopsisledtoplantsthatweremore
rice, Arabidopsis, and maize (Choi et al., 2000; Hobo et al., toleranttowaterstress(Dezaretal.,2005).Moreover,inthe
1999a;Unoetal.,2000;Zhangetal.,2011).TheroleofbZIPsin drought-resistantspeciesCraterostigmaplantagineum,allgenes
thispathwaywasrevealedbythereportsthatTFsbelonging coding for the seven HDZIP TFs identified respond to
to this family bind to the ABA Responsive Element (ABRE; drought stressat thetranscriptional level (Deng et al.,2002;
846 SANTOSET AL.
Franketal.,1998),whichisastrongindicationthattheseTFs compared to wild-type plants (Wu et al., 2009). When
play an important role in abiotic stress signaling. In rice, OsWRKY08 was overexpressed in Arabidopsis, besides an
however, other than gene expression studies (Agalou et al., improvementofprimaryrootgrowthinthetransgenicplants
2008;Jainetal.,2008),notmuchisknownaboutthefunction underosmoticstress,noclearphenotyperegardingsurvival
ofHDZIPsinthestresssignalingpathways.Nevertheless,itis underabioticstresswasshown(Qiuetal.,2004;Songetal.,
interestingtonotethatdroughtisthestresstowhichmostof 2009). OsWRKY72 was known to be involved in the ABA
thegenescodingforHDZIPsrespond(SupplementaryTable signaling (Xie et al., 2005) and its overexpression in Arabi-
S1).This,togetherwithpreviousdatafromotherplantspecies dopsis increased sensitivity to ABA, salt, and osmotic stress
(Dengetal.,2002;Dezaretal.,2005;Franketal.,1998),seems (Yu et al., 2010). Although the salt and osmotic stress phe-
tosupportaprominentroleoftheseTFsinwaterstresssig- notype was not obvious, there is a clear function of OsWR-
naling.Itisalsonoteworthythatsome,butnotallofHDZIP- KY72 in ABA signaling and a crosstalk with the sugar
codinggenes,respondtothehormoneABA(Dengetal.,2002; metabolism and auxin transport pathways (Yu et al., 2010).
Dezar et al., 2005; Johannesson et al., 2003). This probably OsWRKY13(Qiuetal.,2007)andOsWRKY45(Shimonoetal.,
meansthatHDZIPsplayaroleinbothABA-dependentand- 2007; Qiu and Yu, 2009) were also shown to be involved in
independentsignalingpathways. bioticstressresistance,whereasOsWRKY08,OsWRKY11,and
OsWRKY72werenotinvestigatedfortheirputativeinvolve-
mentinbioticstressresponse(Table1).
WRKY family
Although few reports have clearly demonstrated the
The WRKY family of TF is one of the largest and oldest WRKYTFsfunctioninabioticstressinrice,theysuggestthat
families of transcriptional regulators in the plant kingdom WRKYTFsaremainlyinvolvedinosmoticstress-relatedre-
(Rushtonetal.,2010).However,thefirstdescriptionsofthis sponses(Table1).TheoverexpressionofWRKYriceTFscan
TF family came out on the mid-1990s (Ishiguro and Naka- induceeitherimprovedtoleranceorhighersensitivitytothe
mura,1994;Rushtonetal.,1995).WRKYTFsareexclusiveof stress,thusactingaspositiveornegativeregulatorsinstress
plantsandcanbefoundfromgreenalgaetolandplants.The signallingpathways(Rushtonetal.,2010).
WRKYTFsarecharacterizedbyaDNA-bindingdomainwith
approximately60a.a.,theWRKYdomain,whichcontainsan
NAC family
almost invariant WRKY amino acid sequence at the N ter-
minusandazinc-fingerlikemotifintheCterminus(Rushton TheNACTFfamilyisplantspecificandoneofthelargest
etal.,2010).TheWRKYTFfamilyisdividedintothreegroups TF families. NAC proteins contain a highly conserved N-
based on the number of WRKY domains (two domains in terminalDNA-bindingdomain(NACdomain)andavariable
GroupIandoneinGroupsIIandIII)andthestructureoftheir C-terminaldomainthatplaysamajorroleintheregulationof
zincfingers(C2HCinGroupIII).TheWRKYdomainhasbeen transcriptionasanactivatororrepressor.ThisTFfamilywas
crystallized(Yamasakietal.,2005)andtheproposedstructure originally named from three consensus sequences identified
is consistent with the cis-element where it should bind, the fromPetuniaandArabidopsis,bothwithsimilarDNA-binding
highly conserved W-box (TTGACC/T). Because this cis- domains, that is, NAC domain [NAM (no apical meristem),
elementisconserved,thespecificityforthedifferentTFsmust ATAF1-2 (Arabidopsis transcription activation factor), and
be obtained by the neighbouring areas of the W-box (Ciolk- CUC2(cup-shapedcotyledon)](Aidaetal.,1997,1999;Souer
owskietal.,2008).WRKYTFshavebeendescribedashavinga etal.,1996).NACTFshavebeeninvolvedinseveralaspectsof
roleintheregulationofbioticand/orabioticstressresponses, plant development such as formation of boundary cells of
germination, senescence, and developmental processes the meristem, transition between cell division and cell ex-
(Rushtonetal.,2010).Researchhashoweverbeenfocusedon pansion in stamen and petals, anther dehiscence, flowering,
biotic stress responses (Rushton et al., 2010; Shimono et al., lateralrootdevelopment,hormonesignaling,senescence,and
2007;Taoetal.,2009).AlthoughnovelWRKYTFshavebeen seed quality. Furthermore, this family was also found to
described,clearphenotypesaredifficulttoobtainbyreverse- participateintheresponsestopathogens,viralinfections,and
geneticsapproaches(Berrietal.,2009),whichmaybedueto environmentalstimuliofdifferentplantspecies(reviewedin
regulatoryredundancyamongthemembersofthisfamily. Olsenetal.,2005;Tranetal.,2010).
More than 100 WRKY family members, belonging to five Only a few members ofthis family weredescribed in the
mainphylogeneticgroups,havebeenpredicted/describedin lastdecadeofthe20thcentury.Thepostgenomicera,withthe
rice(Berrietal.,2009).Despitetheirwell-knownresponseto availabilityofhigh-qualitygenomesequencesofbothArabi-
biotic stress, some WRKY TFs have been reported as re- dopsisandrice,hasofferedanunprecedentedopportunityto
spondingtoabioticstress(Table1andSupplementaryTable identify complete TF families and their networks. Compre-
S1). They are mainly upregulated in response to drought, hensive genome-wide analyses of the NAC TF family sug-
salinity, and ABA, and downregulated in response to cold gestedthatthereareatleast117and151putativemembersof
(Berri et al., 2009; Ramamoorthy et al., 2008). Nevertheless, the NAC TF family in Arabidopsis and rice, respectively
despitetheextensivelistofriceWRKYTFsstudied,onlyafew (Nuruzzamanetal.,2010).Inrice,sequenceanalysisofNAC
havebeenfunctionallycharacterizedregardingtheirresponse TFs suggested that NAC family proteins could be classified
toabioticstress(Table1).OsWRKY13overexpressioninrice intotwomajorgroups,AandB,furthersubdividedintoseven
increasedsensitivitytosaltandcoldstress(Qiuetal.,2008), and nine subgroups, respectively. Group A consists of 65
whereasOsWRKY45enhancedtolerancetosaltanddrought OsNAC proteins havinglowhomologywiththeArabidopsis
in Arabidopsis (Qiu and Yu, 2009). The overexpression of NACs, whereas the 86 OsNAC genes assigned to group B
OsWRKY11,knowntobeinduced bydroughtandheat, en- showedhighhomologywiththeArabidopsisandotherNAC
hancedheat,anddroughttoleranceafterheatpretreatmentas proteins(Nuruzzamanetal.,2010).TheNACTFsrelatedto
TFSAND EPIGENETIC MECHANISMS IN ABIOTICSTRESS RESPONSES 847
development and stresses belong to group B. The OsNAC mostlydescribedasinvolvedinmechanisms related toheat
genesweredistributedalloverthe12ricechromosomesand stress(Charngetal.,2007;Schrammetal.,2008),HSFshave
36OsNACgeneswereobservedintandemduplication.This also been related to other stress response networks, such as
suggests that the NAC family increased rapidly during the oxidativestress(Lietal.,2005),chillingstress(Lietal.,2003)
course of evolution through tandem duplications of chro- andhigh-salinitystress(Yokotanietal.,2008).
mosomalregions(Fangetal.,2008;Nuruzzamanetal.,2010). Amongthe26HSFspredictedinrice,themembersofthe
Analysis of OsNAC gene promoter sequences revealed the class A are the most abundant and the best studied so far.
presenceof17cis-actingregulatoryDNAelementsknownto Recently, the gene expression of HSF family members has
beresponsivetoplanthormones(e.g.,auxin,gibberellicacid, been studied under different stress conditions such as heat,
andsalicylicacid)andenvironmentalstimuli(lightandcold) oxidative stress, drought, cold, and high-salinity (Liu et al.,
andrelatedwithseedspecificexpression(Fangetal.,2008). 2010;Mittaletal.,2009).Themembersofthisfamilyaredif-
Differentauthorshavereportedthedifferentialexpression ferentially expressed under abioticstress conditionsand are
of151NACgenesinmicroarrayanalysesofriceplantssub- developmentally regulated in diverse tissue types under
jectedtoabioticstress.Accordingtotheauthor,thenumberof controlconditions(Liuetal.,2010;Mittaletal.,2009).Inad-
differentiallyexpressedgeneswas15%(Fangetal.,2008)or dition,differentHSFclassescanberelatedtodifferentstres-
30% (Nuruzzaman et al., 2010), which may be due to the ses.Forexample,genesencodingHSFclassCmembersseem
different varieties used in the study and the number of tobemoreresponsivetocoldstress(Mittaletal.,2009)and
stresses analyzed. Among 20 OsNAC genes identified as re- classAmembersaremoreresponsivetoheatstress(Liuetal.,
sponsivetoabioticstress,only3areinducedbydrought,salt, 2010;Mittaletal.,2009).Infact,severalmembersoftheclassA
and cold,whereas the remaining genes were either induced respondextremelyfasttoheatstress,eventuallyactingasheat
by one or two stresses (Fang et al., 2008). On the basis of sensors.
individualstressresponses,5genesareinducedbydrought, ManyHSFgenesareknowntobedifferentiallyregulatedby
19genesbysalt,and16genesbycold(SupplementaryTable diverse abiotic stresses (Liu et al., 2010; Mittal et al., 2009),
S1). Moreover, all the 20 stress-inducible OsNAC genes however,onlytwomembersoftheHSFfamily(allfromclassA)
werefoundtocontainatleastoneofthestress-responsivecis- have been functionally characterized in overexpression/
elements such as ABRE (ABA-responsive element), DRE mutantanalyses(Table1).TheoverexpressionofOsHsfA2ein
(dehydration-responsive element), and LTRE (low tempera- Arabidopsisgreatlyenhancedthethermotoleranceoftransgenic
ture-responsiveelement)(Fangetal.,2008). plants during germination, vegetative, and flowering stage
DespitealltheresearchonriceNACTFgenes,sofaronly (Yokotani et al., 2008). In addition, transgenic plants also
seven members of the family (OsNAC5, OsNAC6/SNAC2, showed improved tolerance to high-salinity both at seedling
OsNAC10, OsNAC19/SNAC1, ONAC045, OsNAC52, and andvegetativestage.AnotherHSF,OsHSF7,wasidentifiedby
ONAC063) have been functionally characterized for abiotic Yeast-Onehybrid screeningusing a dimericHSEas bait(Liu
stresstolerance(Table1).ApartfromOsNAC063,whichisnot etal.,2009).TheoverexpressionofOsHSF7inArabidopsisdid
droughtstressinduced,alltheothergenesareinducedunder notleadtoahigherlevelofHSPs(HSFtargets)intransgenic
salt and droughtstress. The overexpression of each ofthese plants.Inaddition,thetransgenicplantsshowedahigherbasal
genes in rice and/or Arabidopsis improved tolerance to thermotolerancethanwild-typeplants.HSFsseemtoplayan
drought and salt (except OsNAC52) stress in transgenic importantroleintheresponsetohightemperatureandmaybe
plants. Among these seven OsNAC genes, at least five usefultoimproveheattoleranceincropplants.Itisknownthat
are induced by ABA (Table 1). Furthermore, transgenic a rise of+1(cid:2)C could leadto a 10% decline inrice yield(Peng
plants overexpressing OsNAC6/SNAC2, OsNAC19/SNAC1, etal.,2004).
and OsNAC52 were reported to be hypersensitive to exoge-
nous ABA (Table 1), indicating that NAC TFs may be in- EpigeneticMechanisms andRegulation
volvedintheABAsignalingpathway. ofGeneExpression inAbiotic StressResponses
Thestress-inducibleNACTFsarepromisingcandidatesto
Epigeneticmechanismshaveakeyroleonplantplasticity
improve tolerance to abiotic stress, particularly to salt and
responses to unpredictable abiotic stresses. This review is
drought.However,sofaronlyafewmembersoftheNACTF
focused on DNA methylation and histone modification
familyhavebeenoverexpressedinrice.
changes associated to abiotic stress responses reported in
several plant species, including rice and Arabidopsis model
Heat-shockfactors plants.
Heat-shock transcription factors (HSFs), although present
DNAMethylation andAbiotic Stress
inalllivingorganismsknownsofar,aremostlyrepresentedin
plants(Baniwaletal.,2004).TheseTFsareknowntobindto Cytosine methylation is a conserved epigenetic mark in-
heat-shockelements(HSEs)inthepromoterregionsofheat- volvedingenomedefenseagainstendogenoustransposable
shockproteins(HSPs).TheHSEsareconstitutedbyapalin- elementsorviralDNAandinregulationofgeneexpression
dromic sequence, the conserved nGAAnnTTcn motif, to throughout plant development. The addition of a methyl
where HSFs can bind (Pelham, 1982). Plants HSFs are char- grouptocytosineresiduesiscatalyzedbymethyltransferases
acterized by a DNA-binding domain on the N-terminal, (MTases) and in plants this may occur in both asymmetric
oligomerization motif, nuclear localization signal, nuclear (CHH) and symmetric (CG and CHG) contexts. Four main
exportsignal,andanactivationdomain.Basedontheoligo- families of plant MTases have been identified so far, with
merization domain structure, HSFs are classified into three distinct functions in de novo and/or maintenance methyla-
different classes, A, B, and C (Kotak et al., 2004). Although tion: DOMAINS REARRANGED METHYLTRANSFERASE
848 SANTOSET AL.
(DRM), METHYLASE 1 (MET1), CHROMOMETHYL- butionalongplantgenomes(Lietal.,2008;Yanetal.,2010;
TRANSFERASE (CMT), and DNA methyltransferase homo- Zhang et al., 2006; Zilberman et al., 2007). Transcriptional
log 2 (Dnmt2) (reviewed by Zhang et al., 2010). The inactive heterochromatic regions, which contain highly
establishmentofDNAmethylationiscounteractedbypassive abundant transposable elements (TEs) and repetitive se-
or active demethylation. While in the first, metylated cyto- quences,containthehighestdensityofmethylatedcytosines.
sines are replaced with unmethylated ones during DNA In euchromatic regions, lower but still significant levels of
replication,activedemethylationinvolvesabaseexcisionre- cytosine methylation were also found. Surprisingly, in both
pairmechanism,mediatedbyDNAglycosylases,withoutthe Arabidopsis(Zhangetal.,2006;Zilbermanetal.,2007)andrice
occurrence of DNA replication (Ikeda and Kinoshita, 2009). (Lietal.,2008;Yanetal.,2010),DNAmethylationrelatedto
Additionally, DNA methylation is modulated by other activegeneswasmoreabundantintranscribedregionsthan
mechanisms, such as RNA-directed DNA methylation in promoters. In Arabidopsis, the transcript elongation effi-
(RdDM) pathway, mediated by siRNAs (Chan et al., 2005) ciencywasnegativelycorrelatedtotheextentofmethylation
andchromatinremodelingfactors(Meyer,2010;Zhangetal., withinthegenebody(Zilbermanetal.,2007).Onemightex-
2010).Alltogether,theseregulatorypathwaysprovideady- pectthatasimilarmechanismalsooccursinrice.
namic platform for establishment of DNA methylation pat- AbioticstressesmayinducechangesinDNAmethylation
terns, which may be crucial to guarantee the epigenomic levels,whichmaybeassociatedwithchromatinremodeling
plasticity and enablean efficient response todevelopmental andtranscriptionregulationofstressresponsivegenes(Table2).
cuesandenvironmentalstress.ThemechanisticeffectofDNA Genome-wide analyses in several plant species evidence a
methylationintranscriptionisstillunclearandseverallinesof globalrearrangementofDNAmethylationafterstressappli-
evidence suggest that the roles of cytosine methylation are cation,mostlyduetodemethylation(Ainaetal.,2004;Labra
equallydiverseandlikelyindividualizedfordifferentgenes etal.,2002;Wangetal.,2011b;Zhongetal.,2009).Theuseof
(Zhangetal.,2010).Methylatedcytosinesmayattractmethyl- AFLP-based methylation-sensitive approach (MSAP) re-
bindingproteins,whichinturnrecruithistonemodifiersand vealedthatsomeofthesechanges(methylation/demethyla-
chromatin remodeling proteins, forming a complex that can tion) are site-specific, because conserved patterns were
perturb the binding of transcription factors (Fransz and de observedbetweendistinctgenotypesortissues(Labraetal.,
Jong, 2002). High-resolution mapping of DNA methylation 2002;Wangetal.,2011b).Becausethistechniqueisrestricted
have uncovered some common aspects related to its distri- to CG methylation analysis through specific restriction
Table 2. PlantEpigenetic Landscape Modifications UnderAbioticStresses
Enrichement(+) depletion
Stress Plant Chromatinmark (-) nochange (0) Reference
Cold Zeamays 5-mC - (Stewardet al.,2002)
Arabidopsisthaliana H3K27me3 - (Kwonet al.,2009)
H3ac + (Pavangadkaret al.,2010)
Celllines: H3Ser10P + (Sokol et al.,2007)
Nicotiana (By2) H3Ser10PK14ac +
Arabidopsisthaliana (T87) H4ac +
Drought Pisumsativum 5-mC + (Labraet al., 2002)
Oryza sativa 5-mC - (Wanget al., 2011b)
Arabidopsisthaliana H3K23ac + (Kimet al.,2008b)
H3K27ac +
H3K4me3 +
Arabidopsisthaliana H3K4me3 + (vanDijk et al.,2010)
H3K4me2 +
H3K4me +
Salinity Lagunculariaracemosa 5-mC - (Lira-Medeiroset al., 2010)
Triticum aestivum 5-mC - (Zhong et al.,2009)
Nicotiana (By2) H3Ser10P; + (Sokol et al.,2007)
H3K14ac +
Arabidopsisthaliana H3K9ac + (Chen et al.,2010)
H3K14ac +
H3K4me3 +
H3K9me2 -
Heat Arabidopsisthaliana 5-mC 0 (Pecinkaet al.,2010a)
H3K9me2 -
H3K4me3 0/-
Hypoxia Oryza sativa H3K4me2 - (Tsujiet al., 2006)
H3ac +
H3K4me3 +
Aluminium Nicotiana tabacum 5-mC - (Choiand Sano, 2007)
UV Arabidopsisthaliana H3ac + (Lang-Mladek et al.,2010)