Transcription in chloroplasts

Transcription in Chloroplasts
The Chloroplast genome differs from the nuclear genome in having a much smaller information content (10^-3 to 10^-4 fold less), but with 100-10,000 copies per cell, making upto 15% of the cellular DNA. There are about 120 plastid genes in the chloroplast genome, about 60 coding for plastid proteins, 30 coding for a part of photosynthetic apparatus (photosystem II or PSII, Cytochrome b6/f, photosystem I or PSI, ATP synthase and RUBISCO), and the remaining genes with unknown functions. (Many subunits of photosynthetic apparatus are coded by nuclear genes). It has been shown that in Chlamydomonas reinhardtii, most chloroplast genes are transcribed independently of each other as monocistronic transcripts, but chloroplast genomes of maize and other higher plants contain several polycistronic transcription units, a single unit encoding subunits of different photosynthetic complexes.

Further, it has also been shown in C. reinhardtii, that for the expression of each of the nearly 120 chloroplast genes, factors coded by 5-70 nuclear loci are required, so that more than 1000 nuclear genes (5-10% of the nuclear genome) are involved in the expression of these genes. These nuclear encoded factors may function at the level of transcription, RNA processing, RNA maturation, translation, or during the assembly of photosynthetic complexes. While differential transcription has been documented for several chloroplast genes, regulation is manly exercised at the post transcriptional level.

The mechanism of transcription for majority of chloroplasts genes resembles that in prokaryotes in several respects including the following : (i) Promoter sequences are found at -10 and -35 positions for all kinds of genes (rRNAs, tRNAs and mRNAs), so that same RNA polymerase is used for the transcription of these three classes of genes, (ii) Termination of transcription in plastid genes is facilitated by the formation of hairpin structures (like in prokaryotes) due to the presence of short inverted repeat sequences, (iii) Chloroplast mRNAs have neither a cap at the 5' end, nor a long poly A tail at their 3' end (as in prokaryotes). However, three classes of introns are found in chloroplast genes, which need to be spliced out during RNA processing (unlike prokaryotes; see Organization of Genetic Material 2.  Repetitive and Unique DNA Sequences and next main topic). There are also chloroplast genes (e.g. genes for large submit of RUBISCO and 32 kD protein of PSII) which lack introns ir higher plants, but have introns in chloroplasts of plants like Euglena.