Supplemental Data. Manavski et al. (2015). › content › suppl › 2015 › 08 › 26 ›...

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

** *** * * ** *** * * * ** *** * ** ** ** ** * *

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

* ** ** * ** *** * * * * * ** * ** **** * * * *

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 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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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 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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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 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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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 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 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 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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Supplemental Data. Manavski et al. (2015). › content › suppl › 2015 › 08 › 26 ›...

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