Chloroplast Genome


Chloroplasts contain a genome that is a relic of the endosymbiont that gave rise to the organelle. These genomes typically contain 100–200 genes and encode proteins important for photosynthesis and other chloroplast functions, although dinoflagellate algae have a greatly reduced and fragmented chloroplast genome. Many, but not all, nonphotosynthetic taxa retain a remnant chloroplast genome. In some organisms the chloroplast genome may be retained to allow redox‐mediated control of gene expression, whereas in others it may continue to exist because transfer of essential genes to the nucleus is no longer possible. Multiple ribonucleic acid (RNA) polymerases are involved in chloroplast transcription in land plants, and post‐transcriptional processing involving nuclear‐encoded RNA‐binding proteins also plays an important part in the expression of the chloroplast genome. Gene expression may be regulated at a number of levels, and redox poise in the organelle may be particularly important for this.

Key Concepts

  • Chloroplasts originated in the ancestor of plants and red and green algae by endosymbiotic acquisition of a cyanobacterium, and then spread to many other eukaryotic lineages.
  • There are other examples of stable acquisition of a cyanobacterium by a nonphotosynthetic host.
  • Chloroplast genomes are typically 100–200 kbp in size, and include a set of genes for proteins essential to photosynthesis. Other genes present in the ancestral symbiont have been lost or relocated to the nucleus.
  • Many nonphotosynthetic organisms retain remnant chloroplasts, with genomes, reflecting the fact that photosynthesis is not the only biochemical process that takes place in the chloroplast.
  • In many organisms, gene transfer from chloroplast to nucleus can still take place, at an unexpectedly high frequency.
  • Establishment of the chloroplast has resulted in the development of nuclear‐encoded RNA‐binding protein families and, in land plants, additional RNA polymerases that play a central role in chloroplast gene expression.
  • Post‐transcriptional RNA processing plays an important role in chloroplast gene expression.
  • In photosynthetic organisms, chloroplast gene expression is closely linked to the organelle's redox poise.
  • The chloroplast can also influence the expression of nuclear genes.

Keywords: plastid; endosymbiosis; organelle; cyanobacteria; PPR protein; CORR; retrograde signalling; endosymbiotic gene transfer

Figure 1. Organisation of a typical chloroplast genome. This example is from wheat, and shows the inverted repeated (IR) sequences, together with the small and large single copy regions. Genes for proteins that are encoded in essentially all conventional chloroplast genomes (Martin et al., ) are shown, as well as the genes for 16S and 23S rRNA. Genes for products with related functions are shown in similar colours. Genes on the inside of the molecule are transcribed clockwise; those on the outside are transcribed counter‐clockwise. The components of the trans‐spliced rps 12 gene are indicated by 5′ and 3′. Redrawn from Ogihara et al.2002.
Figure 2. Conserved gene order in cyanobacteria and chloroplasts. The figure shows the order of genes in part of a cluster from the cyanobacterium Synechocystis sp. PCC6803, the chloroplast genome of Nicotiana tabacum and the chloroplast genome of Porphyra purpurea. Where genes are not shown for the chloroplast, they are absent from it. Lines indicate (not to scale) spacer regions without additional genes. L and S indicate genes for polypeptides of the large and small subunits of the ribosome, respectively. TS indicates a gene for tRNA pseudouridine synthase. Other gene abbreviations are standard.
Figure 3. Origin of the nucleomorph. In stage 1, a photosynthetic bacterium is engulfed by a nonphotosynthetic eukaryotic host to generate a photosynthetic eukaryote (stage 2). This in turn is engulfed (stage 3) by another nonphotosynthetic eukaryote to generate a eukaryote with DNA in the chloroplast, the nucleus and the nucleomorph. Over time, the nucleomorph may be lost (stage 5). For simplicity, the mitochondrion and its genome are not shown.
Figure 4. Schematic representation of how cleavage and exonucleolytic degradation limited by PPR protein‐binding can generate overlapping final transcripts. (Under this model, not all transcripts are cleaved and degraded in both directions from all possible sites.)


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Further Reading

Allen JF (2015) Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression. Proceedings of the National Academy of Sciences of the United States of America 112: 10231–10238.

Barkan A and Small I (2014) Pentatricopeptide repeat proteins in plants. Annual Review of Plant Biology 65: 415–442.

Bock R (2014) Engineering chloroplasts for high‐level foreign protein expression. In: Maliga P (ed.) Methods in Molecular Biology, vol. 1132: Chloroplast Biotechnology, pp. 93–106, chap. 5. New York: Humana Press, Springer.

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Larkum AWD, Lockhart PJ and Howe CJ (2007) Shopping for plastids. Trends in Plant Science 12: 189–195.

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Pfannschmidt T, Blanvillain R, Merendino L, et al. (2014) Plastid RNA polymerases: orchestration of enzymes with different evolutionary origins controls chloroplast biogenesis during the plant life cycle. Journal of Experimental Botany 66: 6957–6973.

Stern DB, Goldschmidt‐Clermont M and Hanson MR (2010) Chloroplast RNA metabolism. Annual Review of Plant Biology 61: 121–155.

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Howe, Christopher J(Aug 2016) Chloroplast Genome. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0002016.pub3]