Regulatory RNAs in Cyanobacteria

Cyanobacteria are photosynthetic 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, including differentiation of heterocysts (specialized cells devoted to fixation of atmospheric nitrogen in the absence of combined nitrogen).

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 transcriptional regulators. Our current work aims at understanding the regulation of adaptation to different stress situations, from the perspective of the implication of regulatory RNAs. We are applying global approaches, including RNA-Seq (Mitschke et al, 2011), design of algorithms for the prediction of sRNAs in cyanobacterial genomes (Brenes-Álvarez et al., 2016) or construction of co-expression networks (Brenes-Álvarez et al., 2019). 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).


Differentiation of heterocysts (cells marked with triangles) involves transcriptional patterns that are exclusive of these cells specialized in nitrogen fixation. The confocal fluorescence image shows the expression of green fluorescent protein from the promoter of NsiR2, a small non-coding RNA whose induction takes place at very early stages in cells initiating differentiation (cell marked with an asterisk).


Our recent work describes several examples of post-transcriptioinal regulation operated by non-coding RNAs especifically in heterocysts. Trancription of an antisense to gene glpX exclusively in heterocysts (Olmedo-Verd et al., 2019) or the differential transcription of two small RNAs, NsiR3 (Álvarez-Escribano et al., 2021) and NsiR4 (Brenes-Álvarez et al., 2021) contribute to the metabiolic reprogramming and reduction of photosynthetic activity that takes place in heterocysts versus the adjacent vegetative cells.

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-I00)
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)

  • Brenes-Álvarez, M., Olmedo-Verd, E., Vioque, A and  Muro-Pastor, A. M. (2021) A nitrogen stress inducible small RNA regulates CO2 fixation in Nostoc. Plant Physiology 187: 787-798
  • 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.