marinus MED4 were differentially

regulated by light and suggested that this differential phasing, which is in agreement with the idea that they compete for the same core RNA polymerase, contribute to the variety of diel gene expression patterns observed within the whole transcriptome. In order to gain insight into the selleck inhibitor effects of UV irradiation on the diel RNA accumulation patterns of these expression regulators in PCC9511, we studied the expression of two group II sigma factors (rpoD4 and rpoD8). Necrostatin-1 in vitro Their patterns of expression, which are globally consistent with those reported earlier [14, 36], suggests that rpoD8 is maximally expressed shortly after dawn and one can hypothesize that its gene product (RpoD8) could selleckchem control the expression of genes upregulated in the morning (such as phrA, uvrA and umuC). Similarly, rpoD4 RNA levels peak at LDT, and

it is possible that RpoD4 could control the expression of genes expressed during this period (such as recA, sepF and lexA). The presence of UV radiation appeared to affect the expression patterns of both sigma factor genes. For rpoD8, because the daily amplitudes of variation were relatively modest (given that FC values ranging between -1 and +1 meant that genes were not differentially expressed; see methods), the differences observed during the light period might not be significant. In contrast, for rpoD4, there was a clear decrease in its relative expression at 15:00 Florfenicol in HL+UV compared

to HL conditions, which could potentially result in a delay in the expression of the whole set of genes under the control of this sigma factor. It has been proposed that the RpoD2 sigma factor of Synechococcus sp. strain PCC7942 is involved in a circadian clock output pathway [85]. There is no direct ortholog of of the rpoD2 gene in MED4 (and hence PCC9511), but one or several of the five sigma factors of this strain might have a similar function. The observed down-regulation of the circadian clock core oscillator kaiB gene at noon under HL+UV conditions could result in a modification of the diel expression patterns of one or several of these sigma factors, which in turn modified the expression of genes under their control (see above). Another gene known to convey the circadian clock output signal is sasA, which encodes a sensory histidine kinase. Like kaiB, it is maximally expressed during the night and its expression dramatically decreased at the beginning of the light period. However, while in HL it recovered its expression just after noon, this recovery took much longer in the presence of UV radiation, which could also potentially affect expression of the whole transcriptome. Indeed, SasA plays a key role in chromosome condensation and superhelicity status, which are known to regulate global gene expression and separation of replicated chromosomes [86].