Supplementary Material s64

SUPPLEMENTARY MATERIAL

Table S1. Extended HLR1 sequences within the intergenic region upstream of hli genes from various species. Positionb relative to the translational Organism Gene Extended HLR1a start site strand Synechococcus sp. SYNW1449 (hli1) GTAACATTgtTTTACTTT -11 + WH8102 SYNW0817 (hli4) TTTACACTccGTAGCAAT -16 +

Thermosynechococcu tsr0446 GTAACAATtcTTTACCAA -53 - s elongatus BP-1 (CAB/ELIP/HLIP superfamily) tsl0446 (putative high TTGAGAATccTTAACAAT -79 - light-inducible protein) tsl0446 (putative high GTTACCTGtgGTTACATC -733 - light-inducible protein) Prochlorococcus PMM1135 (hli14) TTTACATTatTTAATACTtgtGTTACATTaaTTAACAAT -53 + marinus MED4 (HL- PMM1399 (hli6) TTTACATTcaTTAATAGTtgtGTTATATTtgTTTACATA -53 + Adapted Strain) PMM0818 (hli16) TTTACATTcaTTAATAGTtgtGTTATATTtgTTTACATA -53 + PMM0690 (hli21) GTTACATTtaTTAATAAT -14 + PMM1404 (hli5) TTTACAGAaaGTAATATTaatGTTATATTtgTTTACGTA -17 + PMM1404 (hli5) TTTAGATAtcTTAACACA -97 - PMM1384 (hli12) GTTACATTaaTGTCCAAA -119 - PMM1384 (hli12) GTTATATTtaTTAATATA -16 + PMM1118 (hli4) TTTACAAAccTTCATATAtcctGTTACACTatTTAATATA -18 + PMM1317 (hli13) TTTGCATAtaTTTCCAAT -229 +

Prochlorococcus PMT0051 (similar to GTTACGTTccTTCATAAT -74 - marinus MIT9313 high light inducible (LL-Adapted Strain) protein)

Anabaena variabilis Ava_1411 GTTATATTaaTTTACATA -58 + ATCC 29413 (CAB/ELIP/HLIP superfamily) Ava_2916 TTTACAATagTTAATATAtctGTTACAGTtcTTAACAGA -140 + (CAB/ELIP/HLIP superfamily) Ava_0175 ATTACAATttGTTAAAAA -178 + (CAB/ELIP/HLIP- related) Ava_3554 TTCAACATctGTTACATTacGTTACAGA -68 + (CAB/ELIP/HLIP superfamily)

Cyanophora paradoxa CypaCp098 (ycf17) GTTACAAAtgTTTACATA -30 + (red alga) CypaCp098 (ycf17) GTTACTATagTTTACTTT -369 + chloroplast P-SSM2 Cyanophage PSSM2_272 (hli01) GTTACACTtcTTTACAAA -53 +

P-SSM4 Cyanophage PSSM4_177 (hli01) TGTACATAacTTTACATTagTTAACAAT +2 + PSSM4_177 (hli01) TTGACAAAacTTTACAAT -39 + PSSM4_178 (hli02) TTTACATTagTTAACAAT -232 + aThe extended HLR1 sites listed were determined (using the ScanACE program (as described in the Methods section)) to be good matches to a motif generated using, as input, the set of all of the 18-bp direct repeats spaced two nucleotides apart (as shown in Figure 3) for S. elongatus PCC 7942 hliA and nblA and all the Synechocystis PCC 6803 genes shown in Figure 3; the non-conserved central two nucleotides were excluded as active columns. bWith respect to the rightmost residue of the given sequence. Table S2. DspA-regulated genes from Synechocystis PCC 6803 newly identified as bearing an extended HLR1 motif within the intergenic region upstream.

Positionb relative to the Gene Extended HLR1a translational start site Strand ssr2016 unknown GTTACATTtaTTTACATA -90 + sll1797 ycf21 GTTACAAAacTTTACATT -34 - ssr2016 unknown TTTACAAAaaTTTACAAA -111 + slr1634 unknown TTTACATTtgTTAACAAT -355 - ssl3446 unknown TTAACATAagTTTACAAA -187 - sll1783 unknown TTTACAAAtaTTTACATG -159 - sll1541 unknown GTTACATTtcTTTACTTT -35 - sll0819 psaF GTTACGATtaTTTACAAT -211 + slr1634 unknown TTTATAATtaTTTACATT -142 - slr0611 sds TTTACGAAagTTTACATA -43 - sll1626 LexA GATACAAAatTTTACATT -102 - repressor slr0897 probable TTTACAATtaGTTGCATT -204 - endoglucanase aThe extended HLR1 sites listed were determined (using the ScanACE program (as described in the Methods section)) to be good matches to a motif generated using, as input, the set of all of the 18-bp direct repeats spaced two nucleotides apart (as shown in Figure 3) for the Synechocystis PCC 6803 genes shown in Figure 3; the non-conserved central two nucleotides were excluded as active columns. bWith respect to the rightmost residue of the given sequence. Figure S1. Transcriptional start site mapping for Synechocystis PCC 6803 hliA, hliB, hliC, and hliD genes. The sets of lanes TCGA are the sequencing ladders used to measure the primer extension reaction products for each of the genes. Asterisks indicate the locations of the major primer extension products denoting the transcriptional start sites. The sequences of the non- coding strands as read from the sequencing ladders are given with the transcriptional start sites shown in italics.