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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
A Promoter Transcription start
Physcomitrella patens TGTGTAATAATAAGTTTTAATACCTGCCCCAGAG-AACTTCTCTATCATAGTCGTTCCGGTTCTAAAC---TGATCGAAA------------------------AGGAGT-- Marchantia polymorpha TGTGTCATAATAAATTTGAAGACCTGCCT-AGGT-AATTTCTGTATAATAGTTGTTCCAGTTTTAAAC---TGA--GAAA------------------------GAGATCTA Psilotum nudum TGTGTCATAATAAATTTGAATACCTGCCCTAGGT-AACTTCTGTATTATAGTTGCTCCAGTTTTAAAC---TGAA-AAAA------------------------AAGATC-A Sorghum bicolor TATGTCATAATAGATCCGAACACTTGCCTTGGATTGACTTCAATAT-ATAATTGCTCCAGTGAATAAC---TAAAAAAAA---ATAGAAGGACGGTAGATAGTAAAGAAA-- Oryza sativa TATGTCATAATAGATCCGAACACTTGCCTCAGATTGACTTCAATAT-ATAATTGCTCCAGTGAATAAC---TAAAAAAAA---ATAGAAGGACGGTAGATAGTAAAGAAA-- Polupus trichocarpa TATGTCATAATAGATCCGAACACTTGCCCTGGATCGACTTCCAGATCATAATTGCTCTAGTGAATAAC---TAACGAAAC---------------TAGATA-----GAAA-- Arabidopsis thaliana TATGTCATAATAGATCCGAACACTTGCCCCAGATCGACTTCCAGATCATAATTGCTCTAGTGAATAAC---TAAAGAAAATAGATGAATAGATGGAAGATAGAAGAGAAAGA Selaginella m. CATGCCATACTGAGATCGAGTACCCGCCCGAG-----CTCCCGCATCATAGCTGCTCCGGTCTCGGACGAATGAGTGGAA-----------------------GGTGTAGTT
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Shine Dalgarno Start Physcomitrella patens --AGTC--TT----------TAAAG---ATTTCCTAGAAGTTTCCTATTAA---------TTGCTGGCAGGT-TGTTGCTATTCCTCGTCTCGAGAGAGGAGAATCTCAATG Marchantia polymorpha AAAGTT--ATA---------TATGG---ATCTCTCAGAAGTTTACTAATTA---------TTGTTGGTAGGT-TTTTCCTATGCCTCGTCTGAAGAGAGGAGAACCTCGATG Psilotum nudum AAAGTTGGATAATAAAATAATAAGT---ATCTTTTAGAAGTTTACTATTCA---------TTATTGGTGGGT-TTTTCCTATGCCTCGTCTGAAGAGAGGAGAACCTCGATG Sorghum bicolor AGGACTAATCA---------TAATATCTATCTTTAAAAGATTCAATAAAAA-------GACAGTTGGCGGGTCTCTTTGTATGTCTTGTCCGGAAAGAGGAGGA-CTTAATG Oryza sativa AGGACTAATCA---------TAATATCTATCTTTCAAAGGTTCACTAAAAA-------G----TTGGCGGGTCTCTTTGTATGTCTTGTCCGGAAAGAGGAGGA-CTTAATG Polupus trichocarpa AAAACTAATTA---------GAAAA---ATCTCTCATGGGTTCACTAATTACTT----GACTGTTGGCGGGTCTCTTTGTATGTGTTGTCCGGAAAGAGGAGGA-CTCAATG Arabidopsis thaliana AAAAAAAATTC---------TAAG---TATCTATCATCGGTTCACTAATTACTTGAGTGACTGTTGGCGGGTTTCTTTGTATGTGTTGTCCGGAAAGAGGAGGA-CTCAATG Selaginella m. GGGGGAAATTC---------CGAAG-----CTCACGGGAGTTTACTAATCA---------CTATCGGCGGGT-TTCTTCTGTGCTTCATCCGGAAAGGGGAGAACCCCGACG
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B Promoter Transcription start
Arabidopsis thaliana TATGTCA----------TAATAGATCCGAACACTTGCCCCAGATCGACTTCCAGATCATAATTG----CTCTAG-----TGAATAACTAAAGAAAATAGATGAATAGATGGAAGAT Populus trichocarpa TATGTCA----------TAATAGATCCGAACACTTGCCCTGGATCGACTTCCAGATCATAATTG----CTCTAG-----TGAATAACTAACGAAACTAGAT--------------- Physcomitrella patens TGTGTCA----------TAATAAATTTGAATACCTGCCCTAGGTA-ACTTCTGTATTATAGTTG----CTCCAG-----TTTTAAACTGAA-AAAAAAGATCAAAAG--------- Chlorella vulgaris AATATC-----------TTTAAAATAAGTAAAAATAATTTGTAAACCAATAAAAAATATATTTA----TGGTAT-----AATATAACATATGATGTAAAAAAAACTA--------- Thalassiosira p. AAATTCGCTAATTATTGTTTATTAACAGTGTAATTTAATTGTAAGACAAAAAATTGTATAAATT----TTCTTTTTGAGAAAATGAAAAATCGTGTATAATATATAA--------- Euglena gracilis ------------------AAAACTTAAGTTCTAATTACATTTATAATTTATTTAACTTTAAGTG----AGTTGG-------TAGCTCAGTTGGTAGAGCACTCGG----------- Chara vulgaris TTTG----------AAATCAAAAAAGAGTACAAAAT-------------TTTTACAAATGG--------TCCATTAAGCGCTCTATATATATG--CCATACTACAGG--------- Coccomyxa spec. GGAGGGGC-----CCACGCCCAAGGGCGTTCCGTCGGACGGGAAGCCCCTTTCACTAAACGGGGGGGAGGCCTTGTCCCGTGAGACATGGTAGGCCCAGACGGCGAG---------
Shine Dalgarno Start Arabidopsis thaliana AGAAGAGAAAGAAAAAAAAATTCTAAGTATCTATCATCGGTTCACTAATTACTTGAGTGACTGTTGGCGGGTTTCTTTGTATGTGTTGTCCGG-AAAGAGGAGGAC---TCAATG Populus trichocarpa -------AGAAAAAAACTAATTAGAAAAATCTCTCATGGGTTCACTAATTACTT----GACTGTTGGCGGGTCTCTTTGTATGTGTTGTCCGG-AAAGAGGAGGAC---TCAATG Physcomitrell apatens -------TTGGATAATAAAATAATAAGTATCTTTTAGAAGTTTACTATT--CAT-------TATTGGTGGGTTT-TTCCTATGCCTCGTCTGA-AGAGAGGAGAACC--TCGATG Chlorella vulgaris -------TTGATTTTCTTAACCG-CTATTTTTTTTAAAAAT--ACTGTGGTAAG----ATTTTAAAAAAGATAATTTCGGT----AATTCAAA-TAAGGAGAATTTTTCGCCATG Thalassiosira p. -------TGAAAACTCGTATTTAACAAATAGCTAAAAAAATTAACTATTTTTTA----TTTTTTATGAGAGTTTCATAGATTTCCGTCTCCCA-AAAGGAGAAAAT----CAATG Euglena gracilis ------CTTTTAACCGATCGGTCCTGGGTTCGAATCCCAGCCAACTCATTTTTA-----ATTTTGTGTAGGTGT-----------ATGATAAT-TTAATCGAAAAT---TATATG Chara vulgaris -----TATGAAAGTCTGCTTGAATT---AATTATAGTTGTTCTAGTGATACATT----CAAAAGGAAAAAGATAGTTGTTGATTATTGACATATTTTTATTTTATATTTTGTATG Coccomyxa spec. -----AGGGAGAGTCCCACAGGCCTGGCAGCATCTGTTGTTCTGCTGAAGGGTT----TGAGATAGGAGGGCTGAGTCTCTTTTATAGTATTTGTTTTTAGGAGAAATTCG-ATG
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
Supplemental Figure 2. Conservation of the psaA 5’ UTR in Embryophyta. (A) Sequence alignment of the psaA 5’ UTR of dicots, monocots, the fern-like vascular plant Psilotum nudum, the spikermoss Selaginella moellendorffii and mosses. The psaA promoter and conserved regions of the psaA 5’ UTR in embryophyta are labeled in blue and yellow, respectively. The start codon is labeled in green. Stars indicate identical nucleotides. The bars under the alignment represent the probes psaA-1-1 (blue), psaA-1-2 (red), and psaA-1-3 (green) used in EMSA experiments shown in Figure 7C. Accession numbers are indicated in the Method section. (B) Sequence alignment of the psaA 5’ UTR of vascular plants, Physcomitrella, the diatom Thalassiosia pseudonana, Euglena gracilis, and diverse green algae.
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
A HCF145 SRPBCC1 (134 AA) At VWNVLTDYERLADFIPNLVWSGRIPCPHP-----GRIWLEQRGLQRALYWHIEARVVLDLHECLDSPNGRELHFSMVDGDFKKFEGKWSVKS-GIRSVGTVLSYEVNVIPRF---NFPAIFLERIIRSDLPVNLRAVARQAEKGm VWNALTDYEHLADFIPNLVWSGRIPCPYP-----GRIWLEQRGFQRAMYWHIEARVVLDLQEVVNSAWDRELHFSMVDGDFKKFDGKWSVKS-GTRSSTAILSYEVNVIPRF---NFPAIFLERIIRSDLPVNLRALAYRAERPt VWNSLTDYERLADFIPNLVCSGRIPCPHP-----GRVWLEQRGLQRALYWHIEARVVLDLQEFPHSANNRELHFSMVDGDFKKFEGKWSLRS-GTRHGTTTLSYEVNVMPRY---NFPAIFLERIIGSDLPVNLRALACRAERBd VWRIITDYERLAEFVPNLVHSGRIPCPHE-----GRIWLEQRGLQQALYWHIEARVVLDLREVPDAVNGRELHFSMVDGDFKKFEGKWSVRS-GPRSASAILLYEVNVIPRF---NFPSIFLERIIRSDLPVNLRALAFRSEKOs VWRVITDYERLAEFIPNLVHSGRIPCPHQ-----GRVWLEQRGLQQALYWHIEARVVLDLKEVPDAVNGRELHFSMVDGDFKKFEGKWSIRS-GPRSSSAILLYEVNVIPRF---NFPAIFLERIIRSDLPVNLGALACRAENSb LWQVITDYERLADFIPNLVQSGTIPCPHE-----GRIWLEQRGLQQALYWHIEARVVLDLQEIHDSINGRELHFSMVDGDFKKFEGKWSIRS-GPRSSSAVLLYEVNVIPRF---NFPAIFLEKIIRSDLPVNLGALACRAEKSm VWEVLTDYERLAEFIPNLIHSARIPCPYP-----GRIWLLQRGLHTAMYWHIEATVVLDLEEFPHLTDGRSLQFCMVDGDFKKYAGRWLLQA-GTRPGTTDLHYEVNVIPRL---LLPGVFVEGIIKSDLPVNLRAIAERAEK Pp VWEVLTDYGRLAEFIPNLTRSEQIPCPHP-----GRTWLLQEGKQSAMYWQIEARVVLDLEEFLDAKDGRELRFSMVDGDFKRYVGRWYLRP-DVRPGTIILHYEVNVTPRL---LFPAAFVEKIIKSDLPTNLRAIAARAED:*. :*** :**:*:*** * ****: ** ** *.* : *:**:*** *****.* . .*:*.*******:: *:* :: . * * ***** ** :*. *:* ******* ** *:* ::* Cs VWAVLTDYDRLVEFVPNLEVCEKLPGGSA-----TRYRLRQQGCSQSLYLRLEASAVLDVQEVKGPLGRRELRFAMVESPNLKFSGQWTVEPDPTVRDGRSLGTTKLRYEIS---VAPKWSIPSTLVSKVVKSGLPANICAIA Cv VWRVLTNYERLADFVPNLESCERLPSPRT-----GRVWIRQRGCSQGVLWRLEAEAVIAVEEVRLPLGRREARFNMVDGDFKEMSGRWVVEPDP---SSAVGMATLLRFDIT---VQPKISLPSSVVSYVVRAGLPANIQAVS
HCF145 SRPBCC2 (129-130 AA) At VWKVLTSYESLPEIVPNLAISKILSRDNN----KVRI--LQEGCKGLLYMVLHARAVLDLHEIRE----QEIRFEQVEGDFDSLEGKWIFEQLGSHHTLLKYTVESKMRKDS---FLSEAIMEEVIYEDLPSNLCAIRDYIEK Gm VWNILTAYETLPKIVPNLAISKVVSRDNN----KVRI--LQEGCKGLLYMVLHARVVLDLCEYLE----QEISFEQVEGDFDSFRGKWIFEQLGNHHTLLKYSVESKMRKDT---FLSEAIMEEVIYEDLPSNLSAIRDYIEN Pt VWNVLTAYESLPEFVPNLAISKILSRENN----KVRI--LQEGCKGLLYMVLHARVVLDLCEHLE----QEISFEQVEGDFDSFQGKWILEQLGSHHTLLKYNVESKTHRDT---FLSEAIMEEVIYEDLPSNLCAIRDYIEK Bd VWNVLTAYE-LPEIIPNLAISRILLRDNN-----VRI--LQEGCKGLLYMVLHARVVM-LREKLE----REISFEQVEGDFFSFKGKWRLEQLGDQHTLLKYMVETKMHKDT---FLSESILEEVIYEDLPSNLCAIRDYVEK Os VWNILTAYEKLPEFVPNLAISRIIRRDNN----KVRI--LQEGCKGLLYMVLHARVVMDLREKLE----REISFEQVEGDFYSFKGKWRLEQLGDQHTLLKYMVETKMHKDT---FLSESILEEVIYEDLPSNLCAIRDYIEK Sb VWNVLTAYENLPEFVPNLAISRIVLRDNN----KVRI--MQEGCKGLLYMVLHARVVMDLREKFE----QEIRFEQVEGDFYSFKGKWRLEQLGDQHTLLKYMVETKMHRDT---FLSESILEEVIYEDLPSNLCAIRDYIEK Sm VWNVLTSYETLSEFVPNLSSSKIVSRHGN----HARV--LQEGCKCLLYMVLHARVVLELQELPP----NEITFQQVEGDFDVFSGKWTLESLGAEHTLLRYSVDMKMHNDF---LLPREIIEEIVYEDLPENLCAIRARVEL Pp VWAVLTAYESLQEFIPNLAICKVLTREKN----KVRL--LQEGCKCLLYMVLHARVILDLWERPQ----YEILFQQVEGDFDSFQGKWTLEPLGAQHTLLKYLVDTKMHKDS---LLAEALVEEVIYEDLPANLCAIRDRVEL **::**:** * :::***: .::: *. * :.*: :***** *********.:: * ** *:*.**** : *** :* ** .****:* *: * :.* :*.. ::**::***** *:.*** :* Cs VWDVLTDYEALPEFVPNLAVCERLPVPAGMESRLTRL--RQVGFKDMVFMQLHAEAVLDLHERPH----REIQFRAVAGDFGVLQGKFMLSEPERKETHLKYAVEVKIPRSTPMMGLLEPILERMVYEDIPFNLAALKQR Cv VWDVLTDYNRLAEFIPNLAVSQRIALPSNAPANIIRI--RQVGYKRMLYMCLHAESVLDLIEKPQ----GEIQFRQVAGDFERFQGKWMLQGLPLSGNSSSTTSDAEPSASQTQLKYAVEIVIPRSTRMLGVLEPLLERT
B C RNA binding motif TMR1 (68 AA) At EVLKSEILKFISEHGQE-GFMPMRKQLRLHGRVDIEKAITRMGGFRRIALMMNLSLAYKHRKPKGYWDN Vascular plants:Gm KVLESELLKFIAEHGQE-GFMPMRKQLRLHGRVDIEKAITRMGGFRKIATILNLSLAYKHRKPKGYWDN At: Arabidopsis thaliana At5g08720Pt DVLKSELLKFISEHGQE-GFMPMRKQLRLHGRVDIEKAITRMGGFRRIATLMNLSLAYKHRKPKGYWDN Gm: Glycine max XM_003528024Bd EVLKSELGSFISKYGQN-GFMPKRKHLRTHGRVDIEKAITRMGGFRKIASIMNLSLSYKNRKPRGYWDN Pt: Populus trichocarpa XM_002307027Os EVLKSELEKFIAKYGQD-GFMPKRKHLRLHGRVDIEKAITRMGGFRKIASIMNLSLSYKNRKPRGYWDN Bd: Brachypodium distachyon XM_003559134Sb EVLKSELENFIAEYGQY-GFMPKRKHLRSHGRVDIEKAITRMGGFRKIASIMNLSLSYKNRKPRGYWDN Os: Oryza sativa Os03g0837900Sm KVLERELEGFVAKAGKE-RVMPVRAELRKNGRVDLEKAIRRFGGFRSIAERLNMSLAYKRRKPRGFWQN Sb: Sorghum bicolor XM_002466088 Pp NILQQELLKFIAEKGTK-GVMPLRCELREAGRVDLEKAITRNGGFGPVASKLNLSLAYKERKPRGYWDN Sm: Selaginella moellendorffii XM_002987569 .:*: *: *::: * .** * .** ****:**** * *** :* :*:**:**.***:*:*:* Pp: Physcomitrella patens XM_001783694 Cs EDFGLLAAELERCFGGT-GTMPTRAQLRAITRTDLEKAMVAHGGPAAVAKRMGWKLAYKAKAPRGYWDK Cv VGRKCRLPYLAFSPVLE-ALCPQKMTLYGAGRYDIARAVERWGGLYELAGELGYAVTGSRKPGFSEWQE Green Algae: HHHHHHHHHHHHHH---------HHHHHHH-HHHHHHHHHH---HHHHHHH------------------ Cs: Coccomyxa subellipsoidea XM_005645014 RNA binding motif TMR2 (67-69 AA) Cv: Chlorella variabilis XM_005849478 At ENLQEEIGRFQQSWGMDPSFMPSRKSFERAGRYDIARALEKWGGLHEVSRLLALNVRHPNRQLNSRKDN Gm ENLQEEISRFQRGWGIDPSFMPSRKSFERAGRYDIARALEKWGGLHEVSRLLSLKVRQRSRQDNLAKDK Pt ENLQEEISRFQRSWGMDLSFMPSRKSFERAGRYDIARALEKWGGLHEVSRLLALKVRHPNRQANSIKDR Bd ENLQEEI-RFQ-NWGIDPSYMPSRKSFERAGRYDIARALEKWGGIQEVSRLLSLEPRRPRRQADSDSEK Os ENLQEEIRRFQKNWGMDPAYMPSRKSFERAGRYDIARALEKWGGVHEVSRLLSLELRRPRRRANSDDES Sb ENLQEEISRFQKSWGMDPSYMPSRKSFERAGRYDIARALEKWGGVQEVSRLLSLKLRRPRRQGDLDDESSm ENLKREIQLFQKKLRSDPSRMPSRRTLERAGRY-IARALEKWGGLHEVAKVLNLQTKRKRCLEEPEEGW Pp QNVHKEILLFQKEHGNDRTTMPTRQSLERAGRYDLARSLEKWGGLREVARVLGLQVKKRQKSRTAKTDV :*::.** ** * : **:*:::****** :**:******::**:::* *: ::Cs KNVEREIAEFCEQEGLPPRIMPLKMDFVRANRYDLAHVVERWGGLSELAELLEYQACTCRSVSPHVCKE CV HISELAASTGLSGREGLFELASKTYAARRSMQGSVDGGEDMALADILTADAVGARAASANSKASAENGA HHHHHHHHHHHHHH---------HHHHHHH-HHHHHHHHHH---HHHHHHH------------------
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
Supplemental Figure 4. Conservation of the Tandem Repeated SRPBCC and TMR motifs in HCF145. (A) Alignment of tandem repeated HCF145 motifs SRPBCC1 and SRPBCC2. The number of amino acids (aa) is indicated. Acidic and basic amino acids are labeled in red and blue, respectively. Highly conserved amino acids in both motifs are boxed in yellow. (B) Alignment of tandem repeated RNA binding TMR motifs 1 and 2. The number of amino acids (aa) is indicated. Highly conserved amino acids in both TMR motifs are boxed in yellow. The predicted helices (Jpred [http://www.compbio.dundee.ac.uk/jpred/] and NetSurfP [http://www.cbs.dtu.dk/services/NetSurfP]) are shown below the alignment. For schematic presentation see Figure 3. (C) Abbreviations of organisms and accession numbers used in the alignments.
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
A Np: EKIWKVLTDYEALPDFLPNLAKSRLIEHPNGG-IRLEQVGSQ-RLLNFNFSARVVLDLEECFP------------REINFR-MVEGDFKGFSGSWCLEPYSLG-----------EYIGTNLCYTIQV--WPKLTMPVGIIENRLSKDLRLNLCsp: EKTWQVLTDYEALADFIPNLIKSRLLEHPDGG-IRLEQIGSQ-RLLNFNFCARVVLDLEEYFL------------KEINFR-MIEGDFKGFSGSWCLKPYSFG-----------DLVGTDLCYTIQV--WPKLTMPLKIIEPRLTNDMHVNLCst: EKIWQILTDYESLADFIPNLAQSRLLAHPQGG-IRLEQIGSQ-RLLNFKFCARVVLDLEELFP------------KEINFQ-MVEGDFKGFSGKWCLEPYSLG-----------AAQGTNLCYTIQV--WPKLTMPISILENRLSNDLRLNLDs: EAVWQVLTDYESLPEFIPSLEKSQRLEHPEGEKVRLEQVGKQ-RLFKVNFSARVVLDLTEMPP------------SRIDFE-MVEGDFKAFSGYWSLEEADQ---------------KTELIYSIFV--WPPRTMPVSLIERRLSLDLSLNLGs: KAVWDLLTDYEHLAEFIPNLAVSRLRYHPQGG-IRLEQEGVQ-SVLGFRFRASVILDMYEKFS---------EDRAEIDFVLADSQDFDVFEGSWLMYPMKR--------------NWTHLIYQVTV--QPKRFVPVQAVEWRIREDVPSNLPt: DTVWKILTDYEKLADFIPGLAVSKLIDKKDKF-ARLYQIGQQNLAFGLKFNAKAILDCYERDLQTLAS----GEKRDIEFK-MTEGDFQFFEGMWSIEQLAK----PKTEDSVGQEYETTLSYLVDV--KPKMWLPVNLIEGRICKEIKSNLVv: HTVWSILTDYEGLADFIPGLAVSQLVEKGEKF-ARLFQIGQQDLAFGLKFNAKGIVDCYEKDLESLPF----GEKRDIEFK-MIEGDFQIFEGKWSIEQRNTNT-WEGKDSSVGQEFYTTLTYVVDV--EPKRWLPVYLVEGRLSREIKMNLAt: DSVWSVLTDYEKLSDFIPGLVVSELVEKEGNR-VRLFQMGQQNLALGLKFNAKAVLDCYEKELEVLPH----GRRREIDFK-MVEGDFQLFEGKWSIEQLDKGI-HGEALDLQFKDFRTTLAYTVDV--KPKMWLPVRLVEGRLCKEIRTNLOs: DAVWATLTDYEGLAGFIPGLSECRLLDQSDCF-ARLYQVGEQDLALGFKFNARGTIDCYEGELQLLP---AGARRREIAFN-MIDGDFKVFEGNWSVQEEVD-----GGEISADQEFQTILSYVVEL--EPKLWVPVRLLEGRICNEIKTNLBd: EAVWATLTDYEGLAGFIPGLSECRLLHQDAAF-ARLYQVGEQDLALGFKFNAKGTIDCYEGEMEVLP---AGARRREIAFN-MVEGDFKVFEGKWSVEEVEDSL-DEGGENPTGQEFQTTLSYVVEL--EPKLWVPVRLLEGRICKEIKTNLSb: EAVWATLTDYEGLADFIPGLSECRLLDQHDGF-ARIYQVGEQDLALGFKFNAKGTIDCYEGDMEVLPD--AGARRREIAFN-MIDGDFKLFQGKWSVEEVDGSI-VEGGGNSEEQEFQTTLSYLLEL--EPKLWVPVRLLEGRICSEIKNNLSi: EAVWATLTDYEGLADFIPGLSECRLLDQAQGF-ARLYQVGEQDLALGFKFNAKGTIDCYEGDLESLPDAQGNARRREIAFN-MIDGDFKVFQGKWSVQESVEQEQGGGDSDEGQESQTTTLSYLVEL--EPKLWVPVRLLEGRICSEIKNNLSm: ETVWGVLTDYEGLADFIPGLASSKVLERRENG-AQLLQIGEQELALGVKFRAKGVIEVTELPLELLDNG----CRRDIGFD-MVEGDFNLFRGIWRIEQILHG--------VEDATTQTSLTYILEV--QPKIWIPVALLEGRLQKEVSNNLPp: EAVWGVLTDYDHLADHIPGLAESSVLQRRSNG-ARLKQIGQKNFALGVKFKAKAVVEVTEEAAQDLDDG----TLRDLHFE-TVEGDFQVFKGTWRMLEKSLE--------SNDAKVETYLSYILEV--QPKRWMPVALIEGVLGQEITCNLCr: SAVWLALSDYDNLGKFIPSLVENRCLERGGRT-AVLYQVGAQDVAMGVKFSA-ALASVEALFP-YPLTSAPGVSSSDITFE-LVEGDFQAFRGVWRMQQT--------------GEATTLLSYALFV--KPQAWLPVALIQGRIENEVVRNLCs: EVIWGALTDYDSLGTFIPGLAENRCLERRAQG-AQLLQIGEQEIAFGAKFRARVVLDIEEHWSGVPG 35 aa HDIAFC-ACEGDFQVFRGVWRIQEGSR------------GEGSSRLSYALFV--RPQIWLPVRLVQGRIESEIKNNLPm: DSLWSVLTDYDRLNLYIPNLLSSKKIFQKGNN-VHLKQVGAQ-DFLGMKFSAEVTIDLFEN-----------KELGLLKFN-LIKGDFRKFEGSWKIQNIKNTS-------------TNSLIYDLTV--QGCQWMPIGMIEKRLKKDLSENLSs: DELWEVLTDYENLSKFIPNLSSSQLVHREGHT-VRLQQVGSQ-QLLGLRFSAQVQLELTEF-----------RSEGLLSFK-MVKGDFRRFEGAWRVNELADG---------------CSLVYELTV--QGCIGMPIALIEERLRDDLSSNL AtM1: QSVWNVLTDYERLADFIPNLVWSGRIPCPHPGRIWLEQRGLQ-RALYWHIEARVVLDLHECLDSPNG--------RELHFS-MVDGDFKKFEGKWSVKSGIR-------------SVGTVLSYEVNV--IPRFNFPAIFLERIIRSDLPVNLAtM2: CEVWKVLTSYESLPEIVPNLAIS-KILSRDNNKVRILQEGCK-GLLYMVLHARAVLDLHEIRE------------QEIRFE-QVEGDFDSLEGKWIFEQ-LG-------------SHHTLLKYTVESKMRKDSFLSEAIMEEVIYEDLPSNLCt: KHVWAAITDYNNHKSFVPKLIDSGLISDNGRE-QVMFERGKTGIFLFRKTVYIKLSLQGEY-------------PKRLDFH-QIEGDFKVYEGDWLIERASDG---------------KGSILTFRAKIKPDFFAPAMFVRKVQQNDLPMVL Pa: ETIWNLLTDYNNLSTIIPKVIDSRLIEDNGSH-KIIDQTGKSGILFIEKSVRIVLKVTEKF-------------PNALLFE-MVEGDFSTYTGSWSFRPGSSR---------------EQTFVSWQTDFKPTFFAPPFLVSFLQHQDLPVVM
* *:.*: : :*.: : * * : : : : . : * .. ** : * * . : : : . . :: : :: **
B C
AtM1: Arabidopsis thaliana HCF145 SRPBCC1 At5g08720 AtM2: Arabidopsis thaliana HCF145 SRPBCC2 At5g08720 Np: Nostoc punctiforme PCC73102 CP001037 Csp: Calothrix sp. PCC7507 CP003943 Cst: Cylindrospermum stagnale PCC7417 CP003642 Ds: Dactylococcopsis salina PCC8305 CP003944 Gs: Galdieria sulphuraria XM_005707359 Pt: Populus trichcarpa XM_002320890 Vv: Vitis vinifera XM_002280685 At: Arabidopsis thaliana At4g01650 Os: Oryza sativa AK059198 Bd: Brachypodium distachyon XM_003567477 Sb: Sorghum bicolor XM_002459131 Si: Setaria italica XM_004971363 Sm: Selaginella moellendorffii XM_002987229 Pp: Physcomitrella patens XM_001775661 Cr: Chlamydomonas reinhardtii XM_001699680 Cs: Coccomyxa subellipsoidea XM_005645755 Pm: Prochlorococcus marinus sp. AS9601 CP000551 Ss: Synechococcus sp. CC9902 CP000097 Ct: Chlorobium tepidum AE006470 Pa: Prosthecochloris aestuarii CP001108
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
Supplemental Figure 5. Conservation of the SRPBCC Motif in HCF145-L Proteins of Photosynthetic Organisms. (A) Multiple alignment of HCF145-L proteins in photosynthetic organisms. HCF145 motifs SRPBCC1 (AtM1) and SRPBCC2 (AtM2) are included. Acidic and basic amino acids are labeled in red and blue, respectively. Highly conserved amino acids are boxed in yellow. For schematic presentation see Figure 3. (B) Abbreviations of organisms and accession numbers used in the alignment. (C) Unrooted phylogram of all sequence motifs used in the alignment analyzed by the maximum likelihood method. Bootstrap values (based on 1000 iterations) are shown for corresponding nodes. The scale bar is an idicator for the evolutionary distance in substitutions per site.
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
Vascular Plants Arabidopsis thaliana HCF145 At5g08720 1. FMPMRKQLRLHGRVDIEKAIT--RMGGFRRIALMMNL-SLAYKHRKPKGYWD 2. FMPSRKSFERAGRYDIARALE--KWGGLHEVSRLLAL-NVRHPNRQLNSRKD Green algae Chlorella variabilis XM_005846292 Chlorellales 1. TMPTSAQLEAAGRRDLVAAVRA--AGGFLEVAQALGLR----SQRKPAGYWE 2. VMPSRSALQAAGRYDLHHAVML--HGGYTVASQSLDR----------RPAWP 3. CLPTASQLLEAGRGDLYQASRW--GGGAIVRRGGFCA-------AGQALGWE 4. RMPTHLQLASAGRHDLKYALQL--HGSASIAAM-LGLQ------GNTQGAHN Bathycoccus prasinos CCO17813 Mamiellales 1. GMPSKRSLEKENRKDLIKRVEK--LFGYDWLTMAVLLDF--EPFRKPFYYWD 2. VMPTRRDLIDARRWDLHHAVVL--HGGYGAVAKTLKWPR--ARWAEDRHLLN 3. RLPSALELRNVGRDDLARHMVE--HGGPVTVAKRMRMKP-------GKGAWI 4. YMPTDEELINAGRHDLRYRVKE--IGSATVAKYAKLQNRTEKMSLAEARAFL Coccomyxa subellipsoidea C-169 XP_005645828 Coccomyxaceae 1. RMPSCTELREAGAFTLYSAISK--HGGVGAFARQLGLDP----KRRDSGYWE 2. GMPTIQDLQRSGHNSLIKAINH--WGGRSAVARRLGLACSPTRRLMTLGDLS 3. VMPSRTQLLEAGRPDLLQAVKR--MGGFKRVAAALELAF----LPARRGRSA Ostreococcus lucimarinus XM_001415510 Mamiellophyceae 1. CMPTREQLR-GGRHWDAIQQIE-SLGGFVKVAQLLDWSG---AKTRPRGYWT 2. RMPSQKSLRDAGRADIVNALKR--FGGAEKVAASMGLEFGSGNKRSSASARG Red algae Cyanidioschyzon merolae XM_005538035 Cyanidiales
TMPTAGQLAAHHRSDLIRAIRK--HGGFPKVAEQLGLK----AHRRPNGYWN Cyanidioschyzon merolae XM_005538049 Cyanidiales
VMPPERILAKAGRFDLIISIEY--HGGSRAVAEICELRDSASWEYVLEMRDL EMPSIAELQRQGREDLARLIRR--HGGPLVFAARFGLYVPPSRRRREADLKW
Cyanidioschyzon merolae XM_005538687 Cyanidiales 1. YMPTSNELREAKRSDLVRAIIV--HGGYAKVAERCGL--QPHR--RSFGYWR 2. RMPTYNELVAAKKRILAYAIAE--NGGFLEVARRMNLQLSSDE-----TPWR 3. RFPRQQDLVRLGRYDLDWAIHRW-HGGYTRLAAELGYLRSRLPC-KPRNFWS 4. RMPNRKELEALDRHDLIYAIRK--FGGFLTVATKLGLSRDALTHTRPRGYWS 5. IMPRLEQLRMYNREDLINAIHR--HGGAANVARRLHLFWY-----GPKTFWR 6. KMPTQQELISAGRVDVAYGVHL--HGGVYEVARRLRLQVLDPP--RAPFYWN 7. VMPTSMTIVRSGRRDLAAAIRR--HGGWDAFARRLNLRPAAPK--RPKGYWN 8. FVRNYAADFVRRPGDDEDDPDAAGKIAYSDVSEILAGNVGNKRCRTVVGAIR 9. VMPTAEELRLDGRADLVFACERI-HGGLATVARGLGWPLLAER--LPPESLK 10. EMPTEADLLRTGGIDIHEAIVC--HGGYVEVARSLNLRHPEDP---EWTDWS Galdieria sulphuraria XM_005705295 Cyanidiales 1. SVHLLQVKKSGGECPLPRSSTKCYYGGGTPSFELLVP-20aa-VRDVRGYWK 2. RMPSANELRKSGRYALALAISSH-HGGFHAVAREIGLQPNHHS----SGYWD 3. YMPTYHQLLKARRLDLAKAIHK--YGGFPAVAEKLGR---IPN--KRRKYWH 4. QLPTMTLLSTCKRWDLMGAIRL--HGGLYEVSRKTQIPLSKSTR-QPRGYWS 5. IVPTLSNLKRNQRQDLVEAIRK--HGGVQTVAAKLYMLRQSKR--KAKGYWN 6. VMPLGHELRRHQRRDLCYAIQL--HGGFSVVAGKLHL---NWI--GPISFWR 7. RMPTLNDLVIRGRVDLAFGIRL--HHGFPAVAKAFGLEWTIPS--RPRMYWN 8. YMPSNETLYQLGRGDLADAIRD--TKGWVYYAKRLGLVPHYRCI-SSHKLWK 9. AVASVEELYRDGRGDIAFAIMKY-HQGATQLAHRLKWKAPHMRP-LPPAYYR 10. LMPSKKELFQTGYRDLVFVIYR--HGGFQKVACRMGWTIHEDNP-HWLTQWL Cyanobacteria Microcoleus sp. PCC 7113 AFZ22266 Oscillatoriales 1. VMPKAAQLRQLGRYDLA-MAISKYHGGYRSVASRLGLTYT----GQRFGYWH 2. VMPSRQQLEQAGEKPLAAAIG-LHGGVL-AVARRLGFKLP--YGRKPRGYWK 3. VMPTREQLVQIQRAELISAIA-TNGGWP-SVARRFGL------ANPNKGYTS
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
Supplemental Figure 7. Multiple Alignment of Transcript Binding Motif Repeats (TMR) Present in Representative TMR Proteins of Photosynthetic Organisms in Eukaryotes and Cyanobacteria. The consensus sequence MP-x(4)-L-x(3)-GR-x-DL-x(2)-AI-x(2-4)-HGG-x(3)-VA-x(2)-LGL-x(5-27)-GYW is colored in yellow. Acidic and basic amino acids are labeled in red and blue, respectively. For schematic presentation see Figure 3.
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
Supplemental Table 1. Oligonucleotides Used for PCR, RT-PCR, Primer Extension,
Probe Generation, Genotyping, and other Applications.
Primer name Primer sequence 5’ → 3’
720-ATG-f-P atgtcagtgagcaagtttccacatctc
720-3UTR-r-P tatctttgcgagttacaagactacac
Cacc-145-for caccatgtcagtgagcaagtttccacatctc
145-rev. atattgaacccaattgatatcaagatc
ex7-for ctgaagcaatcatggaagagg
ex8-for agctttgatgatgaatctttcacttgc
ex10-rev2 ggatgtctcacgttcaatgc
ex10-rev1 aagacgagatacttcgtgtaatcctc
LBb1 gcgtggaccgcttgctgcaact
PsaA80-mer ccacatctccattcaggatttcttggcccactattggccaaaccacctgagcactaggtccaatgtgagtagg
atcactc
At4-Kpn1-f ctgctttggtaccgctttccagatctag
At4-Kpn1-r atcatggtacccaaccaattcgctaacaagacc
Cacc-145-for caccatgtcagtgagcaagtttccacatctc
145-rev atattgaacccaattgatatcaagatc
Fw-BclI-hcf145 atatattgatcacatagcggcgccggtag
Rev-SalI-hcf145-strep ataatagtcgacttatttttcgaactgcgggtggctccaagcgctatattgaacccaattgatatcaag
Rev-SalI-hcf145-
strepA2
ataatagtcgacttatttttcgaactgcgggtggctccaagcgctaatgtctctttgtagaccaggaat
Fw-BclI-hcf145-B1 atatattgatcaagaggagagaaatcttcagag
Rev-SalI-hcf145-strep ataatagtcgacttatttttcgaactgcgggtggctccaagcgctatattgaacccaattgatatcaag
psaA ATG rev gttccggcgaacgaataatcat
70-mer psaA 1 tctattttctttagttattcactagagcaattatgatctggaagtcgatctggggcaagtgttcggatct
70-mer psaA 2 aagtaattagtgaaccgatgatagatacttagaatttttttttctttctcttctatcttccatctattca
70-mer psaA 3 gcgaacgaataatcattgagtcctcctctttccggacaacacatacaaagaaacccgccaacagtcactc
psbA 80-mer gacggttttcagtgctagttatccagttacagaagcgaccccataggctttcgctttcgcgtctctctaaaattg
cagtc
T7_5UTRpsaA 3 taatacgactcactatagggagaagatccgaacacttgccc
T7_5UTR-psaA 2 taatacgactcactatagggctaagtatctatcatcggttcac
psaA5UTRrev gtgaaccgatgatagatacttag
HCF145-like 2-f
HCF145-like 2-r
LB4
B3-T7-petB-for
petB-ex-rev
ctcgacactgctagcttcttc
tcgtaacaatctagaacagctttg
cgtgtgccaggtgcccacggaatagt
cgtaatacgactcactatagggactgaagctaactttgg
taccggaatagcgtcaggtacac
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Supplemental Data. Manavski et al. (2015). Plant Cell 10.1105/tpc.15.00234
Supplemental Table 1. continued
Primer name Primer sequence 5’ → 3’
psaA 5' 1 taccggaatagcgtcaggtacac
ppPsaA_F tggcgagcatctggaataacta
ppPsaA_R tgtccagcaaccagaaaaagaa
ppPsbA_F ttcattgcagctcctcctgtag
ppPsbA_R aggatgttgtgttcagcttgga
ppRps14_f aaaaatatcaagattttcgtcactc
ppRps14_r tgcatgagccatttctcgta
ppYcf3_f
ppYcf3_r
npt5’
tgttgcagacattttactccgaat
ccaatgctattgcttgtttcca
agtgcattctttggacctccaatcggatcctgtcaaacactga
npt3’ gacaggaggcccgatctagtaa
pp5’f gctcgagtttttcagcaagatgtggccaacacaaatgaacagt
pp5’r tggaggtccaaagaatgcacta
pp3’f ttactagtcgggcctcctgtccacgtgtttcttgaaccagagg
pp3’r aggagatcttctagaaagatgtcgacctcatatgaatggccacgatgt
ppF1 atcagcagtgattctgccctaag
ppR1 gcggctgagtggctccttca
ppF2 aaattatcgcgcgcggtgtc
ppR2 tgatcatggtgagaagtgttgct
ppF3 ggtttgggaggttttgactgac
ppR3 cgtggagagacaacatcctttg
EF1α-f agcgtggtatcacaattgac
EF1α-r
Fw T7 psaA3_1
Fw T7 psaA3_2
Rev psaA3_1
Rev psaA3_2
gatcgctcgatcatgttatc
taatacgactcactatagggagacataattgctctagtgaataactaa
taatacgactcactatagggagagaatagatggaagatagaagagaa
ttagttattcactagagcaattatg
ttctcttctatcttccatctattc
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