BackgroundPhosphate (Pi) and Nitrogen (N) are essential macronutrients required for plant growth and development. In Arabidopsis thaliana (Arabidopsis), the transcription factor PHR1 acts as a Pi central regulator. PHL1 is a homolog of PHR1 and also plays a role in maintaining Pi homeostasis. In rice (Oryza sativa), OsPHR1–4 are the orthologs of PHR1 and have been implicated in regulating sensing and signaling cascades governing Pi homeostasis.ResultsHere the role of OsPHR3 was examined in regulating the homeostasis of N under different Pi regimes. Deficiencies of different variants of N exerted attenuating effects on the relative expression levels of OsPHR3 in a tissue-specific manner. For the functional characterization of OsPHR3, its Tos17 insertion homozygous mutants i.e., osphr3–1, osphr3–2, and osphr3–3 were compared with the wild-type for various morphophysiological and molecular traits during vegetative (hydroponics with different regimes of N variants) and reproductive (pot soil) growth phases. During vegetative growth phase, compared with the wild-type, OsPHR3 mutants showed significant variations in the adventitious root development, influx rates of 15N-NO3− and 15N-NH4+, concentrations of total N, NO3− and NH4+ in different tissues, and the relative expression levels of OsNRT1.1a, OsNRT2.4, OsAMT1;1, OsNia1 and OsNia2. The effects of the mutation in OsPHR3 was also explicit on the seed-set and grain yield during growth in a pot soil. Although Pi deficiency affected total N and NO3− concentration, the lateral root development and the relative expression levels of some of the NO3− and NH4+ transporter genes, its availability did not exert any notable regulatory influences on the traits governing N homeostasis.ConclusionsOsPHR3 plays a pivotal role in regulating the homeostasis of N independent of Pi availability.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1462-7) contains supplementary material, which is available to authorized users.

Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5′ ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.