A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria

Abstract

As the key enzyme of bacterial nitrogen assimilation, glutamine synthetase (GS) is tightly regulated. In cyanobacteria, GS activity is controlled by the interaction with inactivating protein factors IF7 and IF17 encoded by the genes gifA and gifB, respectively. We show that a glutamine-binding aptamer within the gifB 5′ UTR of Synechocystis sp. PCC 6803 is critical for the expression of IF17. Binding of glutamine induced structural re-arrangements in this RNA element leading to enhanced protein synthesis in vivo and characterizing it as a riboswitch. Mutagenesis showed the riboswitch mechanism to contribute at least as much to the control of gene expression as the promoter-mediated transcriptional regulation. We suggest this and a structurally related but distinct element, to be designated type 1 and type 2 glutamine riboswitches. Extended biocomputational searches revealed that glutamine riboswitches are exclusively but frequently found in cyanobacterial genomes, where they are primarily associated with gifB homologs. Hence, this RNA-based sensing mechanism is common in cyanobacteria and establishes a regulatory feedback loop that couples the IF17-mediated GS inactivation to the intracellular glutamine levels. Together with the previously described sRNA NsiR4, these results show that non-coding RNA is an indispensable component in the control of nitrogen assimilation in cyanobacteria.

The Distinctive Regulation of Cyanobacterial Glutamine Synthetase

“…This suggested that IF17 synthesis might be also controlled by a ncRNA, namely by a glutamine riboswitch. In Synechocystis it was experimentally proven that the glutamine binding aptamer present in the 5’UTR of gifB undergoes structural modulations, which in turn impact the production of IF17 [127]. These results unequivocally demonstrated that the described glnA aptamer represents the metabolite-sensing domain of a glutamine-binding riboswitch, thus renaming to type 1 glutamine riboswitch was proposed.…”

“…Recently, detailed analysis revealed a widespread occurrence of the glnA aptamer in cyanobacterial strains. The DP aptamer, however, is apparently restricted to the monophyletic group of marine picocyanobacteria where it frequently exists in multiple copies [127]. Within the available cyanobacterial genome sequences the aptamers were mainly found to be associated with genes encoding for proteins, which harbor the domain of unknown function 4278 (DUF4278).…”

“…Investigation of a DP aptamer of a Prochlorococcus strain revealed that these elements are also part of functional glutamine riboswitches and activate gene expression upon glutamine binding similar to the type 1 glutamine riboswitch. Hence, for those containing the DP aptamer the designation type 2 glutamine riboswitch was suggested [127].…”

Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)

“…Likewise, the sRNA IsaR1 contributes to the adjustment of iron-sulfur cluster biosynthesis, photosynthetic electron transport and photosystem (PS) I gene expression in the acclimation response to low iron (Georg et al, 2017). Moreover, two different types of ncRNAs, the sRNA NsiR4 and the glutamine type I riboswitch, were found to control cyanobacterial nitrogen assimilation in ways that differ considerably from the archetypical model developed for E. coli (Klähn et al, 2015(Klähn et al, , 2018. Despite the observed abundance of riboregulatory processes, no RBPs functionally similar to ProQ, CsrA and Hfq could be identified in cyanobacteria.…”

Small protein 26 interacts and enhances glutamine synthetase activity in Methanosarcina mazei

“…8C). Those so-called inactivating factors (IF7 and IF17) are expressed under N sufficiency combining transcriptional regulation but also posttranscriptional regulation by regulatory RNAs, an asRNA (NsiR4) in case of IF7 (Klahn et al (2015)) and a recently discovered glutamine-binding riboswitch in case of IF17 (Klahn et al (2018)).…”