Supplemental Data. Manavski et al. (2015). Plant Cell /tpc

Transkriptio

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2 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 * * *** 2

3 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. 3

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5 A HCF145 SRPBCC1 (134 AA) At VWNVLTDYERLADFIPNLVWSGRIPCPHP-----GRIWLEQRGLQRALYWHIEARVVLDLHECLDSPNGRELHFSMVDGDFKKFEGKWSVKS-GIRSVGTVLSYEVNVIPRF---NFPAIFLERIIRSDLPVNLRAVARQAEK Gm VWNALTDYEHLADFIPNLVWSGRIPCPYP-----GRIWLEQRGFQRAMYWHIEARVVLDLQEVVNSAWDRELHFSMVDGDFKKFDGKWSVKS-GTRSSTAILSYEVNVIPRF---NFPAIFLERIIRSDLPVNLRALAYRAER Pt VWNSLTDYERLADFIPNLVCSGRIPCPHP-----GRVWLEQRGLQRALYWHIEARVVLDLQEFPHSANNRELHFSMVDGDFKKFEGKWSLRS-GTRHGTTTLSYEVNVMPRY---NFPAIFLERIIGSDLPVNLRALACRAER Bd VWRIITDYERLAEFVPNLVHSGRIPCPHE-----GRIWLEQRGLQQALYWHIEARVVLDLREVPDAVNGRELHFSMVDGDFKKFEGKWSVRS-GPRSASAILLYEVNVIPRF---NFPSIFLERIIRSDLPVNLRALAFRSEK Os VWRVITDYERLAEFIPNLVHSGRIPCPHQ-----GRVWLEQRGLQQALYWHIEARVVLDLKEVPDAVNGRELHFSMVDGDFKKFEGKWSIRS-GPRSSSAILLYEVNVIPRF---NFPAIFLERIIRSDLPVNLGALACRAEN Sb LWQVITDYERLADFIPNLVQSGTIPCPHE-----GRIWLEQRGLQQALYWHIEARVVLDLQEIHDSINGRELHFSMVDGDFKKFEGKWSIRS-GPRSSSAVLLYEVNVIPRF---NFPAIFLEKIIRSDLPVNLGALACRAEK Sm VWEVLTDYERLAEFIPNLIHSARIPCPYP-----GRIWLLQRGLHTAMYWHIEATVVLDLEEFPHLTDGRSLQFCMVDGDFKKYAGRWLLQA-GTRPGTTDLHYEVNVIPRL---LLPGVFVEGIIKSDLPVNLRAIAERAEK Pp VWEVLTDYGRLAEFIPNLTRSEQIPCPHP-----GRTWLLQEGKQSAMYWQIEARVVLDLEEFLDAKDGRELRFSMVDGDFKRYVGRWYLRP-DVRPGTIILHYEVNVTPRL---LFPAAFVEKIIKSDLPTNLRAIAARAED :*. :*** :**:*:*** * ****: ** ** *.* : *:**:*** *****.*..*:*.*******:: *:* ::. * * ***** ** :*. *:* ******* ** *:* ::* Cs VWAVLTDYDRLVEFVPNLEVCEKLPGGSA-----TRYRLRQQGCSQSLYLRLEASAVLDVQEVKGPLGRRELRFAMVESPNLKFSGQWTVEPDPTVRDGRSLGTTKLRYEIS---VAPKWSIPSTLVSKVVKSGLPANICAIA Cv VWRVLTNYERLADFVPNLESCERLPSPRT-----GRVWIRQRGCSQGVLWRLEAEAVIAVEEVRLPLGRREARFNMVDGDFKEMSGRWVVEPDP---SSAVGMATLLRFDIT---VQPKISLPSSVVSYVVRAGLPANIQAVS HCF145 SRPBCC2 ( 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 RNA binding motif TMR1 (68 AA) At EVLKSEILKFISEHGQE-GFMPMRKQLRLHGRVDIEKAITRMGGFRRIALMMNLSLAYKHRKPKGYWDN Vascular plants: Gm KVLESELLKFIAEHGQE-GFMPMRKQLRLHGRVDIEKAITRMGGFRKIATILNLSLAYKHRKPKGYWDN At: Arabidopsis thaliana At5g08720 Pt DVLKSELLKFISEHGQE-GFMPMRKQLRLHGRVDIEKAITRMGGFRRIATLMNLSLAYKHRKPKGYWDN Gm: Glycine max XM_ Bd EVLKSELGSFISKYGQN-GFMPKRKHLRTHGRVDIEKAITRMGGFRKIASIMNLSLSYKNRKPRGYWDN Pt: Populus trichocarpa XM_ Os EVLKSELEKFIAKYGQD-GFMPKRKHLRLHGRVDIEKAITRMGGFRKIASIMNLSLSYKNRKPRGYWDN Bd: Brachypodium distachyon XM_ Sb EVLKSELENFIAEYGQY-GFMPKRKHLRSHGRVDIEKAITRMGGFRKIASIMNLSLSYKNRKPRGYWDN Os: Oryza sativa Os03g Sm KVLERELEGFVAKAGKE-RVMPVRAELRKNGRVDLEKAIRRFGGFRSIAERLNMSLAYKRRKPRGFWQN Sb: Sorghum bicolor XM_ Pp NILQQELLKFIAEKGTK-GVMPLRCELREAGRVDLEKAITRNGGFGPVASKLNLSLAYKERKPRGYWDN Sm: Selaginella moellendorffii XM_ :*: *: *::: *.** *.** ****:**** * *** :* :*:**:**.***:*:*:* Pp: Physcomitrella patens XM_ Cs EDFGLLAAELERCFGGT-GTMPTRAQLRAITRTDLEKAMVAHGGPAAVAKRMGWKLAYKAKAPRGYWDK Cv VGRKCRLPYLAFSPVLE-ALCPQKMTLYGAGRYDIARAVERWGGLYELAGELGYAVTGSRKPGFSEWQE Green Algae: HHHHHHHHHHHHHH HHHHHHH-HHHHHHHHHH---HHHHHHH Cs: Coccomyxa subellipsoidea XM_ RNA binding motif TMR2 (67-69 AA) Cv: Chlorella variabilis XM_ At ENLQEEIGRFQQSWGMDPSFMPSRKSFERAGRYDIARALEKWGGLHEVSRLLALNVRHPNRQLNSRKDN Gm ENLQEEISRFQRGWGIDPSFMPSRKSFERAGRYDIARALEKWGGLHEVSRLLSLKVRQRSRQDNLAKDK Pt ENLQEEISRFQRSWGMDLSFMPSRKSFERAGRYDIARALEKWGGLHEVSRLLALKVRHPNRQANSIKDR Bd ENLQEEI-RFQ-NWGIDPSYMPSRKSFERAGRYDIARALEKWGGIQEVSRLLSLEPRRPRRQADSDSEK Os ENLQEEIRRFQKNWGMDPAYMPSRKSFERAGRYDIARALEKWGGVHEVSRLLSLELRRPRRRANSDDES Sb ENLQEEISRFQKSWGMDPSYMPSRKSFERAGRYDIARALEKWGGVQEVSRLLSLKLRRPRRQGDLDDES Sm ENLKREIQLFQKKLRSDPSRMPSRRTLERAGRY-IARALEKWGGLHEVAKVLNLQTKRKRCLEEPEEGW Pp QNVHKEILLFQKEHGNDRTTMPTRQSLERAGRYDLARSLEKWGGLREVARVLGLQVKKRQKSRTAKTDV :*::.** ** * : **:*:::****** :**:******::**:::* *: :: Cs KNVEREIAEFCEQEGLPPRIMPLKMDFVRANRYDLAHVVERWGGLSELAELLEYQACTCRSVSPHVCKE CV HISELAASTGLSGREGLFELASKTYAARRSMQGSVDGGEDMALADILTADAVGARAASANSKASAENGA HHHHHHHHHHHHHH HHHHHHH-HHHHHHHHHH---HHHHHHH C 5

6 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 [ and NetSurfP [ are shown below the alignment. For schematic presentation see Figure 3. (C) Abbreviations of organisms and accession numbers used in the alignments. 6

7 A Np: Csp: Cst: Ds: Gs: Pt: Vv: At: Os: Bd: Sb: Si: Sm: Pp: Cr: Cs: Pm: Ss: AtM1: AtM2: Ct: Pa: EKIWKVLTDYEALPDFLPNLAKSRLIEHPNGG-IRLEQVGSQ-RLLNFNFSARVVLDLEECFP REINFR-MVEGDFKGFSGSWCLEPYSLG EYIGTNLCYTIQV--WPKLTMPVGIIENRLSKDLRLNL EKTWQVLTDYEALADFIPNLIKSRLLEHPDGG-IRLEQIGSQ-RLLNFNFCARVVLDLEEYFL KEINFR-MIEGDFKGFSGSWCLKPYSFG DLVGTDLCYTIQV--WPKLTMPLKIIEPRLTNDMHVNL EKIWQILTDYESLADFIPNLAQSRLLAHPQGG-IRLEQIGSQ-RLLNFKFCARVVLDLEELFP KEINFQ-MVEGDFKGFSGKWCLEPYSLG AAQGTNLCYTIQV--WPKLTMPISILENRLSNDLRLNL EAVWQVLTDYESLPEFIPSLEKSQRLEHPEGEKVRLEQVGKQ-RLFKVNFSARVVLDLTEMPP SRIDFE-MVEGDFKAFSGYWSLEEADQ KTELIYSIFV--WPPRTMPVSLIERRLSLDLSLNL KAVWDLLTDYEHLAEFIPNLAVSRLRYHPQGG-IRLEQEGVQ-SVLGFRFRASVILDMYEKFS EDRAEIDFVLADSQDFDVFEGSWLMYPMKR NWTHLIYQVTV--QPKRFVPVQAVEWRIREDVPSNL DTVWKILTDYEKLADFIPGLAVSKLIDKKDKF-ARLYQIGQQNLAFGLKFNAKAILDCYERDLQTLAS----GEKRDIEFK-MTEGDFQFFEGMWSIEQLAK----PKTEDSVGQEYETTLSYLVDV--KPKMWLPVNLIEGRICKEIKSNL HTVWSILTDYEGLADFIPGLAVSQLVEKGEKF-ARLFQIGQQDLAFGLKFNAKGIVDCYEKDLESLPF----GEKRDIEFK-MIEGDFQIFEGKWSIEQRNTNT-WEGKDSSVGQEFYTTLTYVVDV--EPKRWLPVYLVEGRLSREIKMNL DSVWSVLTDYEKLSDFIPGLVVSELVEKEGNR-VRLFQMGQQNLALGLKFNAKAVLDCYEKELEVLPH----GRRREIDFK-MVEGDFQLFEGKWSIEQLDKGI-HGEALDLQFKDFRTTLAYTVDV--KPKMWLPVRLVEGRLCKEIRTNL DAVWATLTDYEGLAGFIPGLSECRLLDQSDCF-ARLYQVGEQDLALGFKFNARGTIDCYEGELQLLP---AGARRREIAFN-MIDGDFKVFEGNWSVQEEVD-----GGEISADQEFQTILSYVVEL--EPKLWVPVRLLEGRICNEIKTNL EAVWATLTDYEGLAGFIPGLSECRLLHQDAAF-ARLYQVGEQDLALGFKFNAKGTIDCYEGEMEVLP---AGARRREIAFN-MVEGDFKVFEGKWSVEEVEDSL-DEGGENPTGQEFQTTLSYVVEL--EPKLWVPVRLLEGRICKEIKTNL EAVWATLTDYEGLADFIPGLSECRLLDQHDGF-ARIYQVGEQDLALGFKFNAKGTIDCYEGDMEVLPD--AGARRREIAFN-MIDGDFKLFQGKWSVEEVDGSI-VEGGGNSEEQEFQTTLSYLLEL--EPKLWVPVRLLEGRICSEIKNNL EAVWATLTDYEGLADFIPGLSECRLLDQAQGF-ARLYQVGEQDLALGFKFNAKGTIDCYEGDLESLPDAQGNARRREIAFN-MIDGDFKVFQGKWSVQESVEQEQGGGDSDEGQESQTTTLSYLVEL--EPKLWVPVRLLEGRICSEIKNNL ETVWGVLTDYEGLADFIPGLASSKVLERRENG-AQLLQIGEQELALGVKFRAKGVIEVTELPLELLDNG----CRRDIGFD-MVEGDFNLFRGIWRIEQILHG VEDATTQTSLTYILEV--QPKIWIPVALLEGRLQKEVSNNL EAVWGVLTDYDHLADHIPGLAESSVLQRRSNG-ARLKQIGQKNFALGVKFKAKAVVEVTEEAAQDLDDG----TLRDLHFE-TVEGDFQVFKGTWRMLEKSLE SNDAKVETYLSYILEV--QPKRWMPVALIEGVLGQEITCNL SAVWLALSDYDNLGKFIPSLVENRCLERGGRT-AVLYQVGAQDVAMGVKFSA-ALASVEALFP-YPLTSAPGVSSSDITFE-LVEGDFQAFRGVWRMQQT GEATTLLSYALFV--KPQAWLPVALIQGRIENEVVRNL EVIWGALTDYDSLGTFIPGLAENRCLERRAQG-AQLLQIGEQEIAFGAKFRARVVLDIEEHWSGVPG 35 aa HDIAFC-ACEGDFQVFRGVWRIQEGSR GEGSSRLSYALFV--RPQIWLPVRLVQGRIESEIKNNL DSLWSVLTDYDRLNLYIPNLLSSKKIFQKGNN-VHLKQVGAQ-DFLGMKFSAEVTIDLFEN KELGLLKFN-LIKGDFRKFEGSWKIQNIKNTS TNSLIYDLTV--QGCQWMPIGMIEKRLKKDLSENL DELWEVLTDYENLSKFIPNLSSSQLVHREGHT-VRLQQVGSQ-QLLGLRFSAQVQLELTEF RSEGLLSFK-MVKGDFRRFEGAWRVNELADG CSLVYELTV--QGCIGMPIALIEERLRDDLSSNL QSVWNVLTDYERLADFIPNLVWSGRIPCPHPGRIWLEQRGLQ-RALYWHIEARVVLDLHECLDSPNG RELHFS-MVDGDFKKFEGKWSVKSGIR SVGTVLSYEVNV--IPRFNFPAIFLERIIRSDLPVNL CEVWKVLTSYESLPEIVPNLAIS-KILSRDNNKVRILQEGCK-GLLYMVLHARAVLDLHEIRE QEIRFE-QVEGDFDSLEGKWIFEQ-LG SHHTLLKYTVESKMRKDSFLSEAIMEEVIYEDLPSNL KHVWAAITDYNNHKSFVPKLIDSGLISDNGRE-QVMFERGKTGIFLFRKTVYIKLSLQGEY PKRLDFH-QIEGDFKVYEGDWLIERASDG KGSILTFRAKIKPDFFAPAMFVRKVQQNDLPMVL ETIWNLLTDYNNLSTIIPKVIDSRLIEDNGSH-KIIDQTGKSGILFIEKSVRIVLKVTEKF PNALLFE-MVEGDFSTYTGSWSFRPGSSR EQTFVSWQTDFKPTFFAPPFLVSFLQHQDLPVVM * *:.*: : :*.: : * * : : : :. : *.. ** : * *. : : :.. :: : :: ** B AtM1: Arabidopsis thaliana HCF145 SRPBCC1 AtM2: Arabidopsis thaliana HCF145 SRPBCC2 Np: Nostoc punctiforme PCC73102 Csp: Calothrix sp. PCC7507 Cst: Cylindrospermum stagnale PCC7417 Ds: Dactylococcopsis salina PCC8305 Gs: Galdieria sulphuraria Pt: Populus trichcarpa Vv: Vitis vinifera At: Arabidopsis thaliana Os: Oryza sativa Bd: Brachypodium distachyon Sb: Sorghum bicolor Si: Setaria italica Sm: Selaginella moellendorffii Pp: Physcomitrella patens Cr: Chlamydomonas reinhardtii Cs: Coccomyxa subellipsoidea Pm: Prochlorococcus marinus sp. AS9601 Ss: Synechococcus sp. CC9902 Ct: Chlorobium tepidum Pa: Prosthecochloris aestuarii C At5g08720 At5g08720 CP CP CP CP XM_ XM_ XM_ At4g01650 AK XM_ XM_ XM_ XM_ XM_ XM_ XM_ CP CP AE CP

8 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. 8

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10 Vascular Plants Arabidopsis thaliana HCF145 At5g FMPMRKQLRLHGRVDIEKAIT--RMGGFRRIALMMNL-SLAYKHRKPKGYWD 2. FMPSRKSFERAGRYDIARALE--KWGGLHEVSRLLAL-NVRHPNRQLNSRKD Green algae Chlorella variabilis XM_ 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_ Coccomyxaceae 1. RMPSCTELREAGAFTLYSAISK--HGGVGAFARQLGLDP----KRRDSGYWE 2. GMPTIQDLQRSGHNSLIKAINH--WGGRSAVARRLGLACSPTRRLMTLGDLS 3. VMPSRTQLLEAGRPDLLQAVKR--MGGFKRVAAALELAF----LPARRGRSA Ostreococcus lucimarinus XM_ Mamiellophyceae 1. CMPTREQLR-GGRHWDAIQQIE-SLGGFVKVAQLLDWSG---AKTRPRGYWT 2. RMPSQKSLRDAGRADIVNALKR--FGGAEKVAASMGLEFGSGNKRSSASARG Red algae Cyanidioschyzon merolae XM_ Cyanidiales TMPTAGQLAAHHRSDLIRAIRK--HGGFPKVAEQLGLK----AHRRPNGYWN Cyanidioschyzon merolae XM_ Cyanidiales VMPPERILAKAGRFDLIISIEY--HGGSRAVAEICELRDSASWEYVLEMRDL EMPSIAELQRQGREDLARLIRR--HGGPLVFAARFGLYVPPSRRRREADLKW Cyanidioschyzon merolae XM_ 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_ 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 10

11 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. 11

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13 Supplemental Table 1. Oligonucleotides Used for PCR, RT-PCR, Primer Extension, Probe Generation, Genotyping, and other Applications. Primer name Primer sequence ATG-f-P 720-3UTR-r-P Cacc-145-for 145-rev. ex7-for ex8-for ex10-rev2 ex10-rev1 LBb1 PsaA80-mer At4-Kpn1-f At4-Kpn1-r Cacc-145-for 145-rev Fw-BclI-hcf145 Rev-SalI-hcf145-strep Rev-SalI-hcf145- strepa2 Fw-BclI-hcf145-B1 Rev-SalI-hcf145-strep psaa ATG rev 70-mer psaa 1 70-mer psaa 2 70-mer psaa 3 psba 80-mer T7_5UTRpsaA 3 T7_5UTR-psaA 2 psaa5utrrev HCF145-like 2-f HCF145-like 2-r LB4 B3-T7-petB-for petb-ex-rev atgtcagtgagcaagtttccacatctc tatctttgcgagttacaagactacac caccatgtcagtgagcaagtttccacatctc atattgaacccaattgatatcaagatc ctgaagcaatcatggaagagg agctttgatgatgaatctttcacttgc ggatgtctcacgttcaatgc aagacgagatacttcgtgtaatcctc gcgtggaccgcttgctgcaact ccacatctccattcaggatttcttggcccactattggccaaaccacctgagcactaggtccaatgtgagtagg atcactc ctgctttggtaccgctttccagatctag atcatggtacccaaccaattcgctaacaagacc caccatgtcagtgagcaagtttccacatctc atattgaacccaattgatatcaagatc atatattgatcacatagcggcgccggtag ataatagtcgacttatttttcgaactgcgggtggctccaagcgctatattgaacccaattgatatcaag ataatagtcgacttatttttcgaactgcgggtggctccaagcgctaatgtctctttgtagaccaggaat atatattgatcaagaggagagaaatcttcagag ataatagtcgacttatttttcgaactgcgggtggctccaagcgctatattgaacccaattgatatcaag gttccggcgaacgaataatcat tctattttctttagttattcactagagcaattatgatctggaagtcgatctggggcaagtgttcggatct aagtaattagtgaaccgatgatagatacttagaatttttttttctttctcttctatcttccatctattca gcgaacgaataatcattgagtcctcctctttccggacaacacatacaaagaaacccgccaacagtcactc gacggttttcagtgctagttatccagttacagaagcgaccccataggctttcgctttcgcgtctctctaaaattg cagtc taatacgactcactatagggagaagatccgaacacttgccc taatacgactcactatagggctaagtatctatcatcggttcac gtgaaccgatgatagatacttag ctcgacactgctagcttcttc tcgtaacaatctagaacagctttg cgtgtgccaggtgcccacggaatagt cgtaatacgactcactatagggactgaagctaactttgg taccggaatagcgtcaggtacac 13

14 Supplemental Table 1. continued Primer name Primer sequence 5 3 psaa 5' 1 pppsaa_f pppsaa_r pppsba_f pppsba_r pprps14_f pprps14_r ppycf3_f ppycf3_r npt5 npt3 pp5 f pp5 r pp3 f pp3 r ppf1 ppr1 ppf2 ppr2 ppf3 ppr3 EF1α-f EF1α-r Fw T7 psaa3_1 Fw T7 psaa3_2 Rev psaa3_1 Rev psaa3_2 taccggaatagcgtcaggtacac tggcgagcatctggaataacta tgtccagcaaccagaaaaagaa ttcattgcagctcctcctgtag aggatgttgtgttcagcttgga aaaaatatcaagattttcgtcactc tgcatgagccatttctcgta tgttgcagacattttactccgaat ccaatgctattgcttgtttcca agtgcattctttggacctccaatcggatcctgtcaaacactga gacaggaggcccgatctagtaa gctcgagtttttcagcaagatgtggccaacacaaatgaacagt tggaggtccaaagaatgcacta ttactagtcgggcctcctgtccacgtgtttcttgaaccagagg aggagatcttctagaaagatgtcgacctcatatgaatggccacgatgt atcagcagtgattctgccctaag gcggctgagtggctccttca aaattatcgcgcgcggtgtc tgatcatggtgagaagtgttgct ggtttgggaggttttgactgac cgtggagagacaacatcctttg agcgtggtatcacaattgac gatcgctcgatcatgttatc taatacgactcactatagggagacataattgctctagtgaataactaa taatacgactcactatagggagagaatagatggaagatagaagagaa ttagttattcactagagcaattatg ttctcttctatcttccatctattc 14