Phytochromes (phy) are key regulators of photosynthesis that act in the nucleus to orchestrate signalling pathways involved in co-ordinating plant growth and development in response to environmental cues, including light and temperature. Using publicly available transcriptomic datasets, this thesis identifies phys as master modulators for the control of nuclear genes involved in plastome gene expression mechanisms in response to red light, regulating genes involved in both the transcriptional and post-transcriptional signalling pathways. This thesis also identifies that the bZIP transcription factor HY5 may be a key transducer for phys in regulating these pathways.

Among the RNA-binding proteins families that conduct the post-transcriptional regulation of
the plastome are the chloroplast RNA-binding proteins (cpRNPs). Published research has shown that the cpRNPs are global modulators of plastome genes, and this thesis further identifies them as a part of an R-phyB-HY5-cpRNP signalling cascade. This thesis also shows that cpRNPs are essential to Rlight mediated greening responses in Arabidopsis thaliana and are involved in delivering light signals to the required chloroplast-encoded genes during de-etiolation. Through phyB and HY5, this thesis also shows that in addition to light quality signals, cpRNPs also integrate a diverse range of light intensity and temperature environmental signals to maintain photosynthesis.

The cpRNP family has previously been characterised as regulators of the plastome but this thesis shows that they are also involved in the nucleus. Reverse genetics studies identify reductions in photosynthesis-associated nuclear-encoded gene (PhANG) transcripts in cprnp mutants, making cpRNPs a part of the co-ordination of nuclear- and plastid-encoded genes pathways for tuning photosynthesis to environmental changes. The evidence gathered here also reveals that through the phyB-modulation of alternative transcriptional start sites (TSS), cpRNP isoforms are generated with alternative nuclear subcellular localisations. Furthermore, this thesis shows that cpRNP expression is linked to retrograde signals from the chloroplast through chemical retrograde signal activator treatments affecting both cpRNP subcellular localisation and transcript accumulation.

Finally, this thesis shows that the conservation of cpRNPs across higher plants makes them notable for the global efforts to generate new toolkits to maintain photosynthetic rates in crops under changing environments. This thesis describes a novel role for cpRNPs in plastid transition processes, using Solanum lycopersicum as a model crop to study chloroplast-to-chromoplast transitions.