Figure S1: Sequence alignment of various PcpcB promoters.
Dots represent nucleotides that are conserved among these evolutionarily distant promoters.
Conserved regions of the PcpcB promoter informed the design of the tet operator promoters. The
gray highlighted sequences indicate the tet operators, and the underlined sequences indicate
which nucleotides are consistent with the PcpcB sequence. PEZ1 included a 12-bp region that was
largely conserved among the PcpcBpromoters. PEZ2 included a less-conserved region that was
predicted to be the -35 of the PcpcB promoter. PEZ3 has the same design as PEZ2, but reintroduces
the conserved G nucleotide present in the PcpcB promoters and PEZ1.
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Figure S2: Ethanol and aTc do not impact growth of Synechococcus sp. strain PCC 7002.
Growth rate of WT Synechococcus sp. strain PCC 7002 in standard growth conditions in
untreated media, media with 1000 ng/mL aTc solution or equal volume 50% ethanol (used in
preparation of aTc solution).There is no defect in growth associated with the addition of aTc or
ethanol to the media mixture at the relevant concentrations.
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Figure S3: Predicted RNA secondary structures for RNA-OUT sequences used in this study.
Expression of the RNA-OUT sRNA under different tet operator promoters led to changes in the
predicted structure of the hairpins formed from the RNA-OUT sequence. The different
transcription start sites of the PEZ promoters used to express RNA-OUT led to additional
nucleotides on the 5’ end of the sequence. In the case of PEZ3, these extraneous base pairs interact
to form an additional stem loop structure, which could impede the RNA-OUT unfolding process
that ultimately blocks the transcription of the reporter gene. The box indicates the part of the
hairpin structure that directly interacts with the RNA-IN 5’ UTR upon initial contact.
Page 3 of 4
3.5
3
OD730
2.5
2
WT
1.5
∆Hfq
1
0.5
0
0
20
40
Hours
60
80
Figure S4: Hfq disruption does not impact growth rate under standard conditions
Growth rate of WT Synechococcus sp. strain PCC 7002 versus ∆hfq under standard growth
conditions. There is no defect in growth associated with the interruption of hfq.
Page 4 of 4