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

Abstract

Summary Nitrogen is frequently limiting microbial growth in the environment. As a response, many filamentous cyanobacteria differentiate heterocysts, cells devoted to N2 fixation. Heterocyst differentiation is under the control of the master regulator HetR. Through the characterization of the HetR‐dependent transcriptome in Nostoc sp. PCC 7120, we identified the new candidate genes likely involved in heterocyst differentiation. According to their maximum induction, we defined E‐DIF (early in differentiation) and L‐DIF (late in differentiation) genes. Most of the genes known to be involved in the critical aspects of heterocyst differentiation or function were also classified into these groups, showing the validity of the approach. Using fusions to gfp, we verified the heterocyst‐specific transcription of several of the found genes, antisense transcripts and potentially trans‐acting sRNAs. Through comparative sequence analysis of promoter regions, we noticed the prevalence of the previously described DIF1 motif and identified a second motif, called DIF2, in other promoters of the E‐DIF cluster. Both motifs are widely conserved in heterocystous cyanobacteria. We assigned alr2522 as a third member, besides nifB and nifP, to the CnfR regulon. The elements identified here are of interest for understanding cell differentiation, engineering of biological nitrogen fixation or production of O2‐sensitive molecules in cyanobacteria.

Expression from DIF1-motif promoters of hetR and patS is dependent on HetZ and modulated by PatU3 during heterocyst differentiation

“…This result excluded HetP, but did not establish either HetR or HetZ, as the factor required for the induced expression of hetR and patS . More generally, the expression from DIF1 motif promoters is dependent on a functional hetR [33, 36]. In this study, we found that HetZ is more directly involved in the regulation of DIF1-motif promoters of hetR and patS .…”

Molecular circuit of heterocyst differentiation in cyanobacteria

“…A classical approach of inducing mutations and screening of Fox − mutant (Fox − mutant led to the development of a leaky heterocyst that can work only under an anaerobic condition) has led to the discovery of many key regulators. In recent years, a holistic approach has been used, where labeled RNAs are directly hybridized to the microarray, leading to the discovery of many new key players in the form of transcriptional profile in the heterocyst differentiation [12]. All of the genes related to heterocyst differentiation can be categorized as early in differentiation and late in differentiation, based upon their relative timing of the expression [12].…”

“…In recent years, a holistic approach has been used, where labeled RNAs are directly hybridized to the microarray, leading to the discovery of many new key players in the form of transcriptional profile in the heterocyst differentiation [12]. All of the genes related to heterocyst differentiation can be categorized as early in differentiation and late in differentiation, based upon their relative timing of the expression [12]. Recently, a crystal structure of alr1298, which codes for a pentapeptide repeat cytoplasmic protein, has been reported.…”

NsiR1, a small RNA with multiple copies, modulates heterocyst differentiation in the cyanobacterium Nostoc sp. PCC 7120

“…In Bacillus several sRNAs have been identified that are sporulation‐specific and with expression restricted to the forespore (Silvaggi et al ., 2006; Schmalisch et al ., 2010; Marchais et al ., 2011; Mars et al ., 2016). In heterocyst‐forming cyanobacteria, sRNAs and antisense RNAs with heterocyst‐specific expression have been identified (Ionescu et al ., 2010; Brenes‐Álvarez et al ., 2016; Brenes‐Álvarez et al ., 2019). A heterocyst‐specific antisense RNA is involved in carbon fixation shutdown in heterocysts (Olmedo‐Verd et al ., 2019).…”