SUPPLEMENTARY MATERIAL

Table S1. Extended HLR1 sequences within the intergenic region upstream of hli genes from various species.

Organism / Gene /

Extended HLR1a

/ Positionb relative to the translational start site / strand
Synechococcus sp. WH8102 / SYNW1449 (hli1) / GTAACATTgtTTTACTTT / -11 / +
SYNW0817 (hli4) / TTTACACTccGTAGCAAT / -16 / +
Thermosynechococcus elongatus BP1 / tsr0446 (CAB/ELIP/HLIP superfamily) / GTAACAATtcTTTACCAA / -53 / -
tsl0446 (putative high light-inducible protein) / TTGAGAATccTTAACAAT / -79 / -
tsl0446 (putative high light-inducible protein) / GTTACCTGtgGTTACATC / -733 / -
Prochlorococcus marinus MED4 (HL-Adapted Strain) / PMM1135 (hli14) / TTTACATTatTTAATACTtgtGTTACATTaaTTAACAAT / -53 / +
PMM1399 (hli6) / TTTACATTcaTTAATAGTtgtGTTATATTtgTTTACATA / -53 / +
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 marinus MIT9313 (LL-Adapted Strain) / PMT0051 (similar to high light inducible protein) / GTTACGTTccTTCATAAT / -74 / -
Anabaena variabilis ATCC 29413 / Ava_1411 (CAB/ELIP/HLIP superfamily) / GTTATATTaaTTTACATA / -58 / +
Ava_2916 (CAB/ELIP/HLIP superfamily) / TTTACAATagTTAATATAtctGTTACAGTtcTTAACAGA / -140 / +
Ava_0175 (CAB/ELIP/HLIP-related) / ATTACAATttGTTAAAAA / -178 / +
Ava_3554 (CAB/ELIP/HLIP superfamily) / TTCAACATctGTTACATTacGTTACAGA / -68 / +
Cyanophora paradoxa (red alga) chloroplast / CypaCp098 (ycf17) / GTTACAAAtgTTTACATA / -30 / +
CypaCp098 (ycf17) / GTTACTATagTTTACTTT / -369 / +
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.

Gene / Extended HLR1a / Positionb relative to the 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 repressor / GATACAAAatTTTACATT / -102 / -
slr0897 probable endoglucanase / TTTACAATtaGTTGCATT / -204 / -

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.