A combinatorial strategy of alternative promoter use during differentiation of a heterocystous cyanobacterium

Abstract

Heterocystous cyanobacteria such as Nostoc sp. are filamentous photosynthetic organisms that, in response to nitrogen deficiency, undergo a differentiation process transforming certain, semi-regularly spaced cells into heterocysts, devoted to nitrogen fixation. During transition to a nitrogen-fixing regime, growth of most vegetative cells in the filament is temporarily arrested due to nutritional deprivation, but developing heterocysts require intense transcriptional activity. Therefore, the coexistence of arrested vegetative cells and actively developing prospective heterocysts relies on the simultaneous operation of somewhat opposite transcriptional programs. We have identified genes with multiple nitrogen-responsive transcriptional starts appearing in seemingly paradoxical combinations. For instance, sigA, encoding the RNA polymerase housekeeping sigma factor, is transcribed from one major nitrogen stress-repressed promoter and from a second, nitrogen stress-induced promoter. Here, we show that both promoters are expressed with complementary temporal dynamics. Using a gfp reporter we also show that transcription from the inducible promoter takes place exclusively in differentiating heterocysts and is already detected before any morphological or fluorescence signature of differentiation is observed. Tandem promoters with opposite dynamics could operate a compensatory mechanism in which repression of transcription from the major promoter operative in vegetative cells is offset by transcription from a new promoter only in developing heterocyst.

Elements of the heterocyst‐specific transcriptome unravelled by co‐expression analysis in Nostoc sp. PCC 7120

“…S3B). Such early expression is consistent with previous observations for other elements, such as NsiR1 (Muro‐Pastor, ) or sigC (Muro‐Pastor et al ., ) that also appeared in the E‐DIF cluster.…”

“…The relatively homogeneous temporal dynamics observed for genes in the E‐DIF cluster points to a limited number of participating regulatory factors. Accordingly, the search for regulatory sequences that appear statistically enriched in the E‐DIF cluster led to the identification of the DIF1‐motif (TCCGGA) (Mitschke et al ., ) previously associated to early heterocyst‐specific expression (Muro‐Pastor, ; Muro‐Pastor et al ., ). A new motif (TTGGCAWWTTGGCA), which we have called DIF2, is present in the promoters of several transcripts (including sRNAs NsiR2 and NsiR8) that also belong to the early heterocyst‐specific transcriptome.…”

“…Genes encoding sigma factors SigC, SigE and SigG are transcribed heterocyst‐specifically (Aldea et al ., ), although the enhanced transcription of sigG in heterocysts might be a consequence of cell envelope stress during differentiation (Bell et al ., ). Furthermore, sigC is transcribed in very early stages of differentiation (Muro‐Pastor et al ., ). Whereas sigC or sigE mutants show a slight delay in differentiation (Khudyakov and Golden, ; Mella‐Herrera et al ., ) and both SigC and SigE are required for normal expression of heterocyst‐specific genes (Mella‐Herrera et al ., ; Ehira and Miyazaki, ), no single sigma factor is exclusively associated to heterocyst development, likely due to functional redundancy.…”

Ancient association of cyanobacterial multicellularity with the regulator HetR and an RGSGR pentapeptide‐containing protein (PatX)

“…Promoters with the DIF1 motif in the ‐35 region are induced early in heterocyst differentiation and are active in developing heterocysts (Yoon and Golden, ; Mitschke et al . ; Muro‐Pastor, ; Muro‐Pastor et al ., ).…”

The Integrity of the Cell Wall and Its Remodeling during Heterocyst Differentiation Are Regulated by Phylogenetically Conserved Small RNA Yfr1 in Nostoc sp. Strain PCC 7120

“…Two of the validated targets of Yfr1 (amiC2 and murC) are necessary for proper diazotrophic growth (11)(12)(13). In addition, mraY (also among the targets of Yfr1 validated in this study) has a complex promoter region in which one transcription start site is specifically upregulated in heterocysts (41), suggesting a role of this enzyme in heterocyst differentiation. Strain OE_Yfr1 was unable to grow in liquid medium without combined nitrogen and grew very poorly on solid medium without combined nitrogen (Fig.…”