The nitrogen regulator PipX acts in cis to prevent operon polarity

Abstract

Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to important environmental challenges, like those imposed by the succession of days and nights. Not surprisingly, certain regulatory proteins are found exclusively in this phylum. One of these unique factors, PipX, provides a mechanistic link between signals of carbon/nitrogen and of energy, transduced by the signalling protein PII, and the control of gene expression by the global nitrogen regulator NtcA. Here we report a new regulatory function of PipX: enhancement in cis of pipY expression, a gene encoding a universally conserved protein involved in amino/keto acid and Pyridoxal phosphate homeostasis. In Synechococcus elongatus and many other cyanobacteria these genes are expressed as a bicistronic pipXY operon. Despite being cis-acting, polarity suppression by PipX is nevertheless reminiscent of the function of NusG paralogues typified by RfaH, which are non-essential operon-specific bacterial factors acting in trans to upregulate horizontally-acquired genes. Furthermore, PipX and members of the NusG superfamily share a TLD/KOW structural domain, suggesting regulatory interactions of PipX with the translation machinery. Our results also suggest that the cis-acting function of PipX is a sophisticated regulatory strategy for maintaining appropriate PipX-PipY stoichiometry.

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

“…Interestingly, the single occurrence of PipX in fraction 9 ( Figure 6B) might be linked to a recently suggested new functionality as an interactor with the translation machinery (Cantos et al, 2019).…”

The PII-NAGK-PipX-NtcA Regulatory Axis of Cyanobacteria: A Tale of Changing Partners, Allosteric Effectors and Non-covalent Interactions

“…The regulatory influence of PipX on PipY was originally detected in functional, gene expression and mutational studies (Labella et al, 2017 ). More recently it has been concluded (Cantos et al, 2018 ) that PipX enhances pipY expression in cis , preventing operon polarity, a function that might implicate additional interactions of PipX with the transcription and translation machineries, by analogy with the action of NusG paralogues, which are proteins bearing, as PipX, Tudor-like domains. It has been proposed (Cantos et al, 2018 ) that the cis -acting function of PipX might be a sophisticated strategy for keeping the appropriate PipX-PipY stoichiometry.…”

The default cyanobacterial linked genome: an interactive platform based on cyanobacterial linkage networks to assist functional genomics

“…Genetic and structural analyses suggest that PipX may perform additional roles [47‐49,53‐55]. In this context, the N‐terminal domain of PipX, whether in complex with either NtcA or PII [50], shows the same fold [54], a TLD/KOW motif found in the C‐terminal domain of the NusG family which is involved in interaction with the ribosome [54,56]. Furthermore, the C‐terminal domain of PipX contains an R‐rich basic patch that provides interaction determinants in noncanonical RNA‐binding proteins [57].…”