PipX, the coactivator of NtcA, is a global regulator in cyanobacteria

Abstract

To modulate the expression of genes involved in nitrogen assimilation, the cyanobacterial P II -interacting protein X (PipX) interacts with the global transcriptional regulator NtcA and the signal transduction protein P II , a protein found in all three domains of life as an integrator of signals of the nitrogen and carbon balance. PipX can form alternate complexes with NtcA and P II , and these interactions are stimulated and inhibited, respectively, by 2-oxoglutarate, providing a mechanistic link between P II signaling and NtcA-regulated gene expression. Here, we demonstrate that PipX is involved in a much wider interaction network. The effect of pipX alleles on transcript levels was studied by RNA sequencing of S. elongatus strains grown in the presence of either nitrate or ammonium, followed by multivariate analyses of relevant mutant/control comparisons. As a result of this process, 222 genes were classified into six coherent groups of differentially regulated genes, two of which, containing either NtcA-activated or NtcA-repressed genes, provided further insights into the function of NtcA-PipX complexes. The remaining four groups suggest the involvement of PipX in at least three NtcA-independent regulatory pathways. Our results pave the way to uncover new regulatory interactions and mechanisms in the control of gene expression in cyanobacteria.nitrogen regulation | transcription | translation | photosynthesis

The Emergence of 2-Oxoglutarate as a Master Regulator Metabolite

“…In cyanobacteria, some of the functions of the P II protein in regulating nitrogen assimilation have been taken over by NtcA, a global transcriptional regulator belonging to the Crp-Fnr family (76)(77)(78) that senses the N status. As noted above, in cyanobacteria, high 2-OG levels are indicative of nitrogen deficiency (26).…”

“…2-OG binds to NtcA and acts as an allosteric effector by increasing the affinity of NtcA for specific DNA binding targets, resulting in transcriptional activation in vitro (79)(80)(81). Canonical NtcA binding sites are palindromic and, in promoters subject to activation, are frequently centered at position ϳϪ41.5 with respect to the transcriptional start site (77,82), similar to class II promoters activated by Crp and Fnr (83). However, unlike Crp, NtcA can also act as a repressor.…”

The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

“…Depending on the 2-OG level, which reflects the nitrogen status, PipX interacts with either NtcA or P II (15,16). For a schematic overview of the nitrogen regulatory network, see SI Appendix, Fig.…”

Role of Type 2 NAD(P)H Dehydrogenase NdbC in Redox Regulation of Carbon Allocation in Synechocystis

“…Thus, the up-regulation of the Cmp operon in DndbC was not caused by known regulating mechanisms. The regulators of the nitrogen assimilation genes PII and PipX (Llácer et al, 2010;Espinosa et al, 2014;for review, see Forchhammer, 2004) were reduced in the DndbC mutant (Table III), while the global nitrogen regulator NtcA remained unchanged (Supplemental Table S5). Decreased amounts of PII and PipX, which promote the deactivation of NtcA (Luque et al, 2004), as well as down-regulation of Sll0822, also an inducer of nitrogen transport (Ishii and Hihara, 2008;Yamauchi et al, 2011), could cause the low accumulation of nitrogen transporters induced by the NdbC deletion, particularly in LC.…”