Molecular Functions of Alr2890 and PatR in the Coordination of Photosynthesis and Nitrogen Fixation

• Applicant: Dr. Manuel Brenes-Álvarez
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 573729313

Nostocales Cyanobacteria perform oxygenic photosynthesis in vegetative cells and facultatively, nitrogen fixation in heterocysts, morphologically distinct specialized cells. In an R-DeeP fractionation experiment, hundreds of RNA-dependent proteins were identified in the model Nostoc 7120 that previously were mainly uncharacterized. This proposal targets Alr2890 and PatR, two of these proteins that interact with RNA directly and have several outstanding features. The Alr2890 protein contains a canonical S4 RNA-binding domain. Homologs of Alr2890 exist in all cyanobacteria, eukaryotic algae, and plants where it has been found in thylakoid membrane and active photosystem II preparations. This suggests that Alr2890 and its homologs have a function in photosynthesis for an RNA-binding protein that has been conserved over millions of years of evolution from cyanobacteria to land plants. PatR possesses two OB-fold domains in tandem that may bind DNA and RNA and regulate the expression of heterocyst-specific genes by a non-canonical mechanism involving the sRNAs Yfr1 and NsiR1. The project will use classical genetic approaches and advanced RNA technology to characterize the functionality of Alr2890 and PatR at the molecular level. We will use CLIP-seq to identify the RNA partners of Alr2890 and perform RNA-seq analysis of the Δalr2890 strain to infer the biological relevance of binding RNA. Through a combination of targeted and random mutagenesis, and binding affinity measurements, the DNA- and RNA-binding activities of PatR will be characterized biochemically. Sequence analysis of ΔpatR suppressor mutants will provide insight into the molecular mechanisms downstream of PatR. These data will be complemented by transcriptomic and proteomic analyses of gene expression, as well as advanced confocal microscopy (RNA FISH) to decipher the regulatory networks the new RNA-binding proteins are involved in. The anticipated results will lead to novel insight into the coordination between photosynthesis and the post-transcriptional regulation of gene expression, and unravel functional details of a previously unanticipated regulatory axis linking transcription and post-transcriptional regulation. Both of these aspects present substantial potential for conceptual advancement.

• DFG Programme: Research Grants