Regulatory RNAs in Cyanobacteria

High throughput sequencing of transcriptomes (RNA-Seq) has revolutionized our vision of the complexity of bacterial transcriptomes, showing the presence of abundant small non-coding RNAs (sRNAs), as well as pervasive antisense transcription. Non-coding RNAs are currently recognized as post-transcriptional regulators of virtually every aspect of bacterial physiology and essential elements of the regulatory circuits operated by most known transcriptional regulators.

Photosynthetic cyanobacteria are organisms with a versatile metabolism, minimal nutritional requirements and a remarkable ability to adapt to changing environments. As an example, their major “nutrient”, sunlight, is subjected to daily cycles of light and darkness as well as to changes in its intensity depending on time of day and time of year. In addition, complex cyanobacteria such as Nostoc sp., our model organism, are able to carry out several cell differentiation processes. One of those, differentiation of heterocysts (cells specialized in fixation of atmospheric nitrogen), takes place in response to the deficiency in combined nitrogen.

Our current work deals with the analysis of processes leading to adaptation to the nutritional stress of nitrogen deficiency, including heterocyst differentiation, from the perspective of the implication of regulatory RNAs. We are applying global approaches, including transcriptomic analysis by RNA-Seq (Mitschke et al, 2011), or the design of algorithms for the prediction of sRNAs in cyanobacterial genomes (Brenes-Álvarez et al., 2016). Our studies involve the analysis of small regulatory RNAs under control of NtcA, the global regulator of nitrogen assimilation in cyanobacteria (such as NsiR4, Klähn et al., 2015, or NsrR1, Álvarez-Escribano et al., 2018), or under control of HetR, a specific regulator of cell differentiation (such as NsiR1, Brenes-Álvarez et al., 2020). The image below shows that NsiR1 is a very early marker of heterocyst differentiation (Muro-Pastor 2014).


Differentiation of heterocysts (cells marked with white asterisks) involves transcriptional patterns that are exclusive of these cells specialized in nitrogen fixation. The confocal fluorescence images show the expression of green fluorescent protein from the promoter of NsiR1, a small non-coding RNA whose induction takes place at very early stages in cells initiating differentiation (cell marked with a red asterisk).


We have recently identified new elements of the HetR regulon, including several non-coding transcripts (Brenes-Álvarez et al., 2019). One of them, transcribed antisense to the glpX gene specifically in heterocysts, would contribute to the metabolic reprogramming taking place in these differentiated cells (Olmedo-Verd et al., 2019).  

Our work is carried out in collaboration with Wolfgang R. Hess (Genetics and Experimental Bioinformatics, University of Freiburg, Germany).

Ministerio de Ciencia e Innovación (PID2019-105526GB-IOO)
Ministerio de Economía, Industria y Competitividad (BFU2016-74943-C2-1-P)
Ministerio de Economía y Competitividad (BFU2013-48282-C2-1-P)
Ministerio de Ciencia e Innovación (BFU2010-14821)

  • Álvarez-Escribano, I., Brenes-Álvarez, M., Olmedo-Verd, E., Georg, J., Hess, W. R., Vioque, A. and Muro-Pastor, A. M. (2021) NsiR3, a nitrogen stress-inducible small RNA, regulates proline oxidase expression in the cyanobacterium Nostoc sp. PCC 7120. The FEBS Journal 288: 1614-1629.
    doi: 10.1111/febs.15516
  • Brenes-Álvarez, M. Minguet, M., Vioque, A. and Muro-Pastor A. M. (2020) NsiR1, a small RNA with multiple copies, modulates heterocyst differentiation in the cyanobacterium Nostoc sp. PCC 7120. Environmental Microbiology 22: 3325-3338.
    doi: 10.1111/1462-2920.15103
  • Brenes-Álvarez, M., Vioque, A. and Muro-Pastor A. M. (2020) The integrity of the cell wall and its remodeling during heterocyst differentiation is regulated by phylogenetically conserved sRNA Yfr1 in Nostoc sp. PCC 7120. mBio 11: e02599-19.
    doi: 10.1128/mBio.02599-19
  • Bižić, M., Klintzsch, T., Ionescu, D., Hindiyeh, M. Y., Günthel, M., Muro-Pastor, A. M., Eckert, W., Urich, T., Keppler, F. and Grossart, H.-P. (2020) Aquatic and terrestrial Cyanobacteria produce methane. Science Advances, 6: eaax5343.
    doi: 10.1126/sciadv.aax5343
  • Muro-Pastor A.M. and W. R. Hess. (2020) Regulatory RNA at the crossroads of carbon and nitrogen metabolism in photosynthetic cyanobacteria. BBA- Gene Regulatory Mechanims.1863: 194477.
    doi: 10.1016/j.bbagrm.2019.194477
  • Olmedo-Verd, E., Brenes-Álvarez, M., Vioque A. and Muro-Pastor, A. M. (2019) A heterocyst-specific antisense RNA contributes to metabolic reprogramming in Nostoc sp. PCC 7120. Plant and Cell Physiology 60: 1646-1655.
    doi: 10.1093/pcp/pcz087
  • Brenes-Álvarez, M., Mitschke, J., Olmedo-Verd, E., Georg, J., Hess, W. R., Vioque, A. and Muro-Pastor, A. M. (2019) Elements of the heterocyst‐specific transcriptome unravelled by co‐expression analysis in Nostoc sp. PCC 7120. Environmental Microbiology 21: 2544-2558.
    doi: 10.1111/1462-2920.14647
  • Hou, S., Brenes-Álvarez, M., Reinmann, V., Alkhnbashi, O. S., Backofen, R., Muro-Pastor, A. M., and Hess, W. R. (2019) CRISPR-Cas systems in multicellular cyanobacteria. RNA Biology 16: 518-529.
    doi: 10.1080/15476286.2018.1493330
  • Álvarez-Escribano, I., Vioque, A. and Muro-Pastor A. M. (2018) NsrR1, a nitrogen stress-repressed sRNA, contributes to the regulation of nblA in Nostoc sp. PCC 7120. Frontiers Microbiology 9, 2267.
    doi: 10.3389/fmicb.2018.02267
  • Muro-Pastor, A.M., Brenes-Álvarez, M., and Vioque, A. (2017). A combinatorial strategy of alternative promoter use during differentiation of a heterocystous cyanobacterium. Environmental Microbiology Reports 9: 449-458.
    doi: 10.1111/1758-2229.12555
  • Brenes-Álvarez, M., Olmedo-Verd, E., Vioque, A., and Muro-Pastor, A.M. (2016). Identification of conserved and potentially regulatory small RNAs in heterocystous cyanobacteria. Frontiers Microbiology 7, 48.
    doi: 10.3389/fmicb.2016.00048.
  • Klähn, S., Schaal, C., Georg, J., Baumgartner, D., Knippen, G., Hagemann, M., Muro-Pastor, A.M., and Hess, W.R. (2015). The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7. Proc. Natl. Acad. Sci. USA 112, E6243-6252.
    doi: 10.1073/pnas.1508412112.
  • Muro-Pastor, A.M. (2014). The heterocyst-specific NsiR1 small RNA is an early marker of cell differentiation in cyanobacterial filaments. mBio 5, e01079-01014.
    doi: 10.1128/mBio.01079-14.
  • Muro-Pastor, A.M., and Hess, W.R. (2012). Heterocyst differentiation: from single mutants to global approaches. Trends Microbiol. 20, 548-557.
    doi: 10.1016/j.tim.2012.07.005.
  • Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135.
    doi: 10.1073/pnas.1112724108.
  • Ionescu, D., Voβ, B., Oren, A., Hess, W.R., and Muro-Pastor, A.M. (2010). Heterocyst-specific transcription of NsiR1, a non-coding RNA encoded in a tandem array of direct repeats in cyanobacteria. Journal Molecular Biology 398, 177-188.
    doi: 10.1016/j.jmb.2010.03.010.