Hfq Is Required for Optimal Nitrate Assimilation in the Cyanobacterium Anabaena sp. Strain PCC 7120

Abstract

Hfq is an RNA binding protein involved in posttranscriptional regulation of gene expression in bacteria. It acts by binding to regulatory small RNAs (sRNAs), which confer specificity for the regulation. Recently, orthologues of the Hfq protein were annotated in cyanobacterial genomes, although its capacity to regulate gene expression by interacting with sRNAs has not been yet demonstrated. Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that, in the absence of combined nitrogen, is able to fix atmospheric nitrogen by differentiating specialized cells called heterocysts. We have generated an hfq knockout mutant of Anabaena sp. PCC 7120. Deletion of this gene results in differentiation of heterocysts in the presence of nitrate, suggesting a defect in nitrate assimilation. We show that hfq mutant cells are affected in transport and use of nitrate and nitrite. An analysis of the expression of several genes in the nir operon, encoding different elements of the nitrate assimilation pathway, demonstrates a downregulation of their transcription in mutant cells. We also observed that genes ntcB and cnaT, involved in the regulation of the nir operon, show a lower expression in cells lacking Hfq. Finally, when hfq was reintroduced in the mutant, heterocyst differentiation was no longer observed in the presence of nitrate. Therefore, our results indicate that the RNA chaperone Hfq is involved in the regulation of the nir operon, although the mechanism for this regulation is still unknown.

Bacterial nitrate assimilation: gene distribution and regulation

“…It has been recently described that Hfq is required for optimal nitrate assimilation in the cyanobacterium Anabaena sp. strain PCC 7120 and hfq orthologues have been annotated in several cyanobacterial genomes [17]. In heterotrophic bacteria, any role of Hfq in the regulation of nitrate assimilation has yet to be esxtablished.…”

Transcriptome dynamics of a broad host-range cyanophage and its hosts

“…Normalization with a house-keeping gene has been shown to perform well for RNA-seq read counts (Bullard et al, 2010), and the rnpB gene was used for this purpose as the transcript levels of this gene were stable over the course of infection (Supplementary Figure S1), as has been shown previously during phage infection of Prochlorococcus . Transcript levels of this gene are stable across a variety of physiological conditions in cyanobacteria (for example see Mitschke et al, 2011), and hence this gene is often used as an internal control for cyanobacterial expression studies (for examples see references Holtzendorff et al, 2001;Muro-Pastor et al, 2001;Stork et al, 2005;Puerta-Fernández and Vioque, 2011). Reads from the bisulfite strand-specific libraries were used to estimate antisense transcripts (asRNA) length according to the coverage they produced for the phage genome.…”

Binding of the RNA chaperone Hfq to the type IV pilus base is crucial for its function in Synechocystis sp. PCC 6803

“…In the filamentous nitrogen‐fixing cyanobacterium Nostoc sp. PCC 7120, Hfq was found to be important for nitrate and nitrite assimilation (Puerta‐Fernández and Vioque, ). A Synechocystis Δhfq mutant showed a defect in type IV pilus (T4P) biogenesis and a decreased accumulation of several mRNAs centred on alterations in transcripts that are under the control of a cAMP receptor protein (CRP)‐like transcription factor (SyCRP1) (Dienst et al ., ) which is involved in T4P biogenesis (Yoshimura et al ., ).…”