P_IIsignal transduction proteins: nitrogen regulation and beyond

Abstract

The P(II) proteins are one of the most widely distributed families of signal transduction proteins in nature. They are pivotal players in the control of nitrogen metabolism in bacteria and archaea, and are also found in the plastids of plants. Quite remarkably, P(II) proteins control the activities of a diverse range of enzymes, transcription factors and membrane transport proteins, and in recent years the extent of these interactions has been recognized to be much greater than heretofore described. Major advances have been made in structural studies of P(II) proteins, including the solution of the first structures of P(II) proteins complexed with their targets. We have also begun to gain insights into how the key effector molecules, 2-oxoglutarate and ATP/ADP, influence the activities of P(II) proteins. In this review, we have set out to summarize our current understanding of P(II) biology and to consider where future studies of these extraordinarily adaptable proteins might lead us.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

“…First, 10 GOV contigs encoded P-II, a nitrogen metabolism regulator that is widespread across bacteria and archaea (Fig. 3B) 35,36 . Functional P-II genes contain a conserved C-terminal motif, and a conserved Y residue that is uridylylated under nitrogen-limiting conditions 35 .…”

“…3B) 35,36 . Functional P-II genes contain a conserved C-terminal motif, and a conserved Y residue that is uridylylated under nitrogen-limiting conditions 35 . One AMG clade (P-II-3) lacked this conversed Y residue leaving its function ambiguous, whereas 3 clades (P-II-1, P-II-2, and P-II-4) displayed both conserved motifs and were also predicted to have structures similar to bona fide P-II, which suggests these AMGs are functional ( Supplementary Fig.…”

“…7). In bacteria, such an arrangement is a signature of P-II-like genes that specifically activate alternative nitrogen production and ammonia uptake pathways during nitrogen starvation 35,36 . Third, one GOV contig included amoC, the gene coding for the subunit C of ammonia monooxygenase, suggesting a role in ammonia oxidation 37,38 .…”

“…Thus, we hypothesize that viruses utilize DsrC-5 or SoxYZ to boost sulfur oxidation rates when infecting sulfur oxidizers in low-nutrient conditions, and P-II under high-nutrient conditions favorable for normal host growth. The latter could be particularly useful to viruses by activating expensive and stress-inducing alternative N-producing pathways typically only used under N-starvation conditions 35,36 . Consistent with this, metatranscriptomes from three low-nutrient stations (11_SRF in Mediterranean Sea, 39_DCM in Arabian Sea, and 151_SRF in Atlantic Ocean) revealed expression of viral homologs of dsrC and soxYZ but not of viral P-II (Extended Data Table 1).…”

ATPase as a switch in P II signal transduction

“…The signaling protein P II , highly conserved in archaea, bacteria, and plants, is an example of beauty in biology (1). P II is relatively small, a homotrimer with each subunit of just 12-13 kDa; yet it binds to several effectors and exercises its regulatory roles by interacting with its partners that can be enzymes, transcriptional factors, or membrane transport proteins.…”