Plastid Gene Expression Mechanisms in Higher Plants

Plastids in higher plants harbour a semi-autonomous genome that retains elements of its prokaryotic ancestry while relying extensively on nuclear-encoded factors. Transcription is carried out by two distinct RNA polymerases: a bacterial-type plastid-encoded RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP). These enzymes recognise different promoter classes, allowing sequential and overlapping expression of photosynthesis, housekeeping and developmental genes. Nascent transcripts undergo extensive processing, including intron splicing, RNA editing and precise end trimming, orchestrated by families of nucleus-encoded RNA-binding proteins such as pentatricopeptide repeat (PPR) and mTERF proteins. Concurrently, ribosomal RNA maturation and ribosome assembly occur within nucleoid regions, integrating transcript synthesis with translation machinery biogenesis. This tight coupling of transcriptional and post-transcriptional events underpins plastid differentiation from proplastids to specialised forms, and conveys retrograde signals that adjust nuclear gene expression in response to developmental and environmental cues. Understanding these mechanisms has profound implications for crop improvement, synthetic biology and resilience to abiotic stress.

Research from Nature Portfolio

No recent Nature Portfolio content available.

Plastid Gene Expression Mechanisms in Higher Plants publication trend

The graph below shows the total number of articles in plastid gene expression mechanisms in higher plants across all publications each year (not limited to Nature Index journals).

Technical terms

Plastome: The circular genome of a plastid encoding core genes for transcription, translation and photosynthetic function.

PEP: Plastid-encoded RNA polymerase, a multisubunit, bacterial-type enzyme that drives the bulk of chloroplast gene transcription.

NEP: Nuclear-encoded RNA polymerase, a single-subunit phage-type enzyme responsible for transcription of housekeeping genes and early plastid development.

Nucleoid: A specialised suborganellar compartment where plastid DNA, transcription machinery and RNA-processing factors coalesce.

PPR protein: Pentatricopeptide repeat protein, a sequence-specific RNA-binding factor that mediates splicing, editing and transcript stabilization in plastids.

References

1. The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids. Nucleic Acids Research (2024).
2. The plastid-encoded RNA polymerase of plant chloroplasts. Trends in Plant Science (2025).
3. Regulatory Shifts in Plastid Transcription Play a Key Role in Morphological Conversions of Plastids during Plant Development. Frontiers in Plant Science (2017).
4. Recent advances in the study of chloroplast gene expression and its evolution. Frontiers in Plant Science (2014).