DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Yu X., Li L., Li L., Guo M., Chory J., Yin Y. A yeast one hybrid assay was used using a tadem E2 site (CACTTG) as binding site within a yeast minimal promoter. yin@iastate.edu, chory@salk.edu 27-Aug-2008: Contacted by JYOTI. jyoti Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 1 hybrid one hybrid yeast one-hybrid yeast one hybrid one-hybrid 1 hybrid yeast one-hybrid one-hybrid yeast one hybrid nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Yu X., Li L., Li L., Guo M., Chory J., Yin Y. A yeast one hybrid assay was used using a tadem E2 site (CACTTG) as binding site within a yeast minimal promoter. yin@iastate.edu, chory@salk.edu Accepted 2008-SEP-14 by JYOTI. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 jyoti IMEx Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Yu X., Li L., Li L., Guo M., Chory J., Yin Y. A yeast one hybrid assay was used using a tadem E2 site (CACTTG) as binding site within a yeast minimal promoter. yin@iastate.edu, chory@salk.edu 27-Aug-2008: Contacted by JYOTI. jyoti Only protein-protein interactions in vitro In vitro pull down pull down anti tag western anti tag western blot anti tag western Yu X., Li L., Li L., Guo M., Chory J., Yin Y. Experimental details were obtaned from Yin et al (2002) PMID 12007405 (provided as reference 14 in text) A yeast one hybrid assay was used using a tadem E2 site (CACTTG) as binding site within a yeast minimal promoter. yin@iastate.edu, chory@salk.edu Accepted 2008-SEP-14 by JYOTI. 27-Aug-2008: Contacted by JYOTI. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 jyoti IMEx Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Yu X., Li L., Li L., Guo M., Chory J., Yin Y. A yeast one hybrid assay was used using a tadem E2 site (CACTTG) as binding site within a yeast minimal promoter. yin@iastate.edu, chory@salk.edu 27-Aug-2008: Contacted by JYOTI. jyoti Only protein-protein interactions arath-leaf Arabidopsis thaliana leaf leaf leaf bifc bimolecular fluorescence complementation bifc tag fluorescence tag visualisation by fluorescence tag fluorescence Yu X., Li L., Li L., Guo M., Chory J., Yin Y. A yeast one hybrid assay was used using a tadem E2 site (CACTTG) as binding site within a yeast minimal promoter. yin@iastate.edu, chory@salk.edu Accepted 2008-SEP-14 by JYOTI. 27-Aug-2008: Contacted by JYOTI. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 jyoti IMEx q9ln63-1 Protein BRASSINAZOLE-RESISTANT 2 BZR2 BES1 BIS1 Protein 107 Protein BIN2 SUBSTRATE 1 Protein BRI1-EMS-SUPPRESSOR 1 F18O14_4 At1g19350 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MTSDGATSTSAAAAAAAMATRRKPSWRERENNRRRERRRRAVAAKIYTGLRAQGNYNLPKHCDNNEVLKALCSEAGWVVEEDGTTYRKGHKPLPGDMAGSSSRATPYSSHNQSPLSSTFDSPILSYQVSPSSSSFPSPSRVGDPHNISTIFPFLRNGGIPSSLPPLRISNSAPVTPPVSSPTSRNPKPLPTWESFTKQSMSMAAKQSMTSLNYPFYAVSAPASPTHHRQFHAPATIPECDESDSSTVDSGHWISFQKFAQQQPFSASMVPTSPTFNLVKPAPQQLSPNTAAIQEIGQSSEFKFENSQVKPWEGERIHDVAMEDLELTLGNGKAHS 7B0AA929FED4748B e2-arath-dna E2 site (CACTTG) nucleic acid nucleic acid arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress CACTTGCACTTGCACTTG 3AD4AF696505FC37 elf6_arath Probable lysine-specific demethylase ELF6 JMJ11 PKDM9B Early flowering 6 Jumonji domain-containing protein 11 Probable lysine-specific histone demethylase ELF6 F21E1.160 ELF6 At5g04240 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MGNVEIPNWLKALPLAPVFRPTDTEFADPIAYISKIEKEASAFGICKIIPPLPKPSKKYVFYNLNKSLLKCPELVSDVDISKVCKEDRAVFTTRQQELGQTVKKNKGEKGKSNSQRSGVKQVWQSGGVYTLDQFEAKSKAFYKTQLGTVKELAPVVIEALFWKAALEKPIYIEYANDVPGSAFGEPEDHFRHFRQRKRRGRGFYQRKTENNDPSGKNGEKSSPEVEKAPLASTSLSSQDSSKQKNMDIVDEMEGTAGWKLSNSSWNLQMIARSPGSVTRFMPDDIPGVTSPMVYIGMLFSWFAWHVEDHELHSMNYLHTGSPKTWYAVPCDYALDFEEVIRKNSYGRNIDQLAALTQLGEKTTLVSPEMIVASGIPCCRLVQNPGEFVVTFPRSYHVGFSHGFNCGEAANFGTPQWLNVAKEAAVRRAAMNYLPMLSHQQLLYLLTMSFVSRVPRSLLPGGRSSRLRDRQREEREFLVKRAFVEDILNENKNLSVLLREPGSRLVMWDPDLLPRHSALALAAAGVAGASAVSPPAVAKKELEEGHSELQNKEKTSLLEELSLFMEKLNDVYYDDDDGLLNDFQVDTGTLPCVACGVLGFPFMSVVQPSEKALKDLSERQGETDAQEIMTLSSEKSDCEWKTSSRYIRPRIFCLEHTIELQRLLQSRGGLKFLVICHKDFQKFKAHAAIVAEEVKVPFSYDDVLLESASQEELSLIDLAIEDEEKYEHSVDWTSELGINLRYCVKVRKNSPTKKIQHALSLGGLFSDTSQMLDFTTIRWLQRKSRSKAKPSSTSSFTPCEHLEVKADGKLRDNLDSQTGKKEEKIIQYSRKKKLNPKPSAEQVQELATLAKSKDFDKTCKNFSSRSHLDSAIRSEMNSEIGDSGRVIGVSFSINPCSSSFTVGHGQEHPEITVKFGSDLDGNVTNSLSMVNGDSADLTLTSISREQHQGHSMTSNNNGSNSGSHVVASQTILVSTGDNHDGPRKLSGDYVCSDVSVRGIQEAVEMSDQEFGEPRSTVTNIEDEQQSQIVKPTQREAVFGDHEQVEGAEAVSTRENLCSEIILHTEHSSAHVGMEIPDINTASENLVVDMTHDGEPLESSDILSSSNGDEASSNGLQVLNDELSMESEVSSSENTEVIEAPNSMGEAKKKRKIESESETNDNPESSIGFIRSPCEGLRSRGKRKATCETSLKHTETSDEEKKPIAKRLKKTPKACSGSRQQEVPTTTHPNRCYLEGCKMTFESKAKLQTHKRNRCTHEGCGKKFRAHKYLVLHQRVHKDERPFECSWKGCSMTFKWQWARTEHLRLHTGERPYICKVDGCGLSFRFVSDYSRHRRKTMHYVT 40CB360D273989DC ref6_arath Lysine-specific demethylase REF6 Jumonji domain-containing protein 12 Lysine-specific histone demethylase REF6 Protein RELATIVE OF EARLY FLOWERING 6 T29H11_50 JMJ12 PKDM9A At3g48430 REF6 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MAVSEQSQDVFPWLKSLPVAPEFRPTLAEFQDPIAYILKIEEEASRYGICKILPPLPPPSKKTSISNLNRSLAARAAARVRDGGFGACDYDGGPTFATRQQQIGFCPRKQRPVQRPVWQSGEEYSFGEFEFKAKNFEKNYLKKCGKKSQLSALEIETLYWRATVDKPFSVEYANDMPGSAFIPLSLAAARRRESGGEGGTVGETAWNMRAMSRAEGSLLKFMKEEIPGVTSPMVYVAMMFSWFAWHVEDHDLHSLNYLHMGAGKTWYGVPKDAALAFEEVVRVHGYGEELNPLVTFSTLGEKTTVMSPEVFVKAGIPCCRLVQNPGEFVVTFPGAYHSGFSHGFNFGEASNIATPEWLRMAKDAAIRRAAINYPPMVSHLQLLYDFVLALGSRVPTSINPKPRSSRLKDKARSEGERLTKKLFVQNIIHNNELLSSLGKGSPVALLPQSSSDISVCSDLRIGSHLITNQENPIQLKCEDLSSDSVVVDLSNGLKDTVSVKEKFTSLCERSRNHLASTEKDTQETLSDAERRKNDAAVALSDQRLFSCVTCGVLSFDCVAIVQPKEAAARYLMSADCSFFNDWTAASGSANLGQAARSLHPQSKEKHDVNYFYNVPVQTMDHSVKTGDQKTSTTSPTIAHKDNDVLGMLASAYGDSSDSEEEDQKGLVTPSSKGETKTYDQEGSDGHEEARDGRTSDFNCQRLTSEQNGLSKGGKSSLLEIALPFIPRSDDDSCRLHVFCLEHAAEVEQQLRPFGGINLMLLCHPEYPRIEAEAKIVAEELVINHEWNDTEFRNVTREDEETIQAALDNVEAKGGNSDWTVKLGVNLSYSAILSRSPLYSKQMPYNSIIYKAFGRSSPVASSPSKPKVSGKRSSRQRKYVVGKWCGKVWMSHQVHPFLLEQDLEGEESERSCHLRVAMDEDATGKRSFPNNVSRDSTTMFGRKYCRKRKIRAKAVPRKKLTSFKREDGVSDDTSEDHSYKQQWRASGNEEESYFETGNTASGDSSNQMSDPHKGIIRHKGYKEFESDDEVSDRSLGEEYTVRACAASESSMENGSQHSMYDHDDDDDDIDRQPRGIPRSQQTRVFRNPVSYESEDNGVYQQSGRISISNRQANRMVGEYDSAENSLEERGFCSTGKRQTRSTAKRIAKTKTVQSSRDTKGRFLQEFASGKKNEELDSYMEGPSTRLRVRHQKPSRGSLETKPKKIGKKRSGNASFSRVATEKDVEEKEEEEEEEENEEEECAAYQCNMEGCTMSFSSEKQLMLHKRNICPIKGCGKNFFSHKYLVQHQRVHSDDRPLKCPWKGCKMTFKWAWSRTEHIRVHTGARPYVCAEPDCGQTFRFVSDFSRHKRKTGHSVKKTNKR A45A5801285EBA16 bzr2_arath Protein BRASSINAZOLE-RESISTANT 2 BZR2 BES1 BIS1 At1g19350 F18O14_4 Protein BRI1-EMS-SUPPRESSOR 1 Protein BIN2 SUBSTRATE 1 Protein 107 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MTSDGATSTSAAAAAAAMATRRKPSWRERENNRRRERRRRAVAAKIYTGLRAQGNYNLPKHCDNNEVLKALCSEAGWVVEEDGTTYRKGHKPLPGDMAGSSSRATPYSSHNQSPLSSTFDSPILSYQVSPSSSSFPSPSRVGDPHNISTIFPFLRNGGIPSSLPPLRISNSAPVTPPVSSPTSRNPKPLPTWESFTKQSMSMAAKQSMTSLNYPFYAVSAPASPTHHRQFHAPATIPECDESDSSTVDSGHWISFQKFAQQQPFSASMVPTSPTFNLVKPAPQQLSPNTAAIQEIGQSSEFKFENSQVKPWEGERIHDVAMEDLELTLGNGKAHS DIP protein Q9LN63 original sequence version: 82 DIP protein Q9LN63 original sequence version: 47 DIP protein Q9LN63 original sequence version: 60 DIP protein Q9LN63 original sequence version: 79 DIP protein Q9LN63 original sequence version: 99 7B0AA929FED4748B ref6-dna 1 5 unspecified role unspecified role bait bait 7 unspecified role unspecified role prey prey c-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain 8 unspecified role unspecified role ancillary ancillary direct interaction direct interaction Figure 1 ELF6 and REF6 interact with BES1 at the C termini in yeast. The authors concluded that BES1 and REF6 interact. at5g04240-dna 1 8 unspecified role unspecified role ancillary ancillary 5 unspecified role unspecified role bait bait 6 unspecified role unspecified role prey prey c-terminal sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined [EBI-1798441]Certain and ragged-n-terminus positions must always be strictly superior to 0 and inferior or equal to the protein sequence length. Actual positions : 1340-1340, sequence length 1327 [EBI-1798441]1147-1340 direct interaction direct interaction Figure 1 ELF6 and REF6 interact with BES1 at the C termini in yeast. The authors concluded that BES1 interacts with ELF6. bzr2-dna 1 4 unspecified role unspecified role prey prey 5 unspecified role unspecified role bait bait direct interaction direct interaction Figure 1 Whereas ELF6-C alone had little effect on reporter gene expression, BES1 by itself can activate reporter gene expression. elf6-bzr2-1 2 6 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role prey prey n-terminal mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain in vitro In vitro direct interaction direct interaction Figure 2 Deletion of the N-terminal 41 amino acid of BES1 (BES1ΔN) disrupted the interaction between BES1 and ELF6-C or REF6-C (Fig. 2 A). The fragment containing the first 41 residues of BES1 was sufficient for the interaction, although the binding was much weaker (BES1 1�41). The authors concluded that "both the zinc fingers and the fragment immediately upstream of zinc fingers of ELF6 and REF6 contributed to the interaction with BES1". ref6-bzr2-1 2 8 unspecified role unspecified role prey prey region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain n-terminal mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range in vitro In vitro 7 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 2 Deletion of the N-terminal 41 amino acid of BES1 (BES1ΔN) disrupted the interaction between BES1 and ELF6-C or REF6-C (Fig. 2 A). The fragment containing the first 41 residues of BES1 was sufficient for the interaction, although the binding was much weaker (BES1 1�41). The authors concluded that "both the zinc fingers and the fragment immediately upstream of zinc fingers of ELF6 and REF6 contributed to the interaction with BES1". bzr2-elf6-1 3 6 unspecified role unspecified role neutral component neutral component n-terminal N-terminal EYFP yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component c-terminal C-terminus of EYFP yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminal required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain in vitro In vitro direct interaction direct interaction Figure 3 ELF6 interacts with BES1 in Arabidopsis mesophyll protoplasts, as shown by BiFC. the proteins interacted in the nucleus. elf6-bzr2-2 2 6 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role prey prey n-terminal mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain in vitro In vitro 42 46 direct interaction direct interaction Figure 2 Deletion of the N-terminal 41 amino acid of BES1 (BES1ΔN) disrupted the interaction between BES1 and ELF6-C or REF6-C (Fig. 2 A). The fragment containing the first 41 residues of BES1 was sufficient for the interaction, although the binding was much weaker (BES1 1�41). The authors concluded that "both the zinc fingers and the fragment immediately upstream of zinc fingers of ELF6 and REF6 contributed to the interaction with BES1". ref6-bzr2-2 2 8 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain n-terminal mbp tag maltose binding protein tag maltose binding protein tag maltose binding protein tag mbp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range in vitro In vitro 7 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) 52 49 direct interaction direct interaction Figure 2 Deletion of the N-terminal 41 amino acid of BES1 (BES1ΔN) disrupted the interaction between BES1 and ELF6-C or REF6-C (Fig. 2 A). The fragment containing the first 41 residues of BES1 was sufficient for the interaction, although the binding was much weaker (BES1 1�41). The authors concluded that "both the zinc fingers and the fragment immediately upstream of zinc fingers of ELF6 and REF6 contributed to the interaction with BES1".