Protein Genes
Whether or not most chloroplast protein genes are transcribed as parts of operons remains to be determined. It is known that rbcS and psbA produce very abundant monocistronic transcripts but these genes may be exceptions to the general rule. Transcript mapping studies indicate that the situation in other regions of the genome may be much more complex.

When Northern blots of electrophoretically separated RNA are probed by hybridization with small cloned fragments of chloroplast DNA, numerous RNA bands with homology to the probe are often seen. Some of the RNA molecules visual-sized in this way are quite large (for example, 4-8 kb), much larger than any one gene, and often many times the length of the probe.

In E. coli ATP genes are part of a well defined operon. Some remnants of such a structure may be imagined in the plastid genome where atpB and atpE are very close together. In fact, they actually overlap in many chloroplast genomes, with the sequence ATGA containing both the first codon of the atpE coding sequence (ATG) and the translation stop codon of atpB (TGH). The genes atpA and atpH are also found fairly close together (within 2 kb) but are located far away from atp8 and atpE.

Genes for the other components of the ATPase complex are not found in the chloroplast DNA; they are located in the nucleus. Examples of functionally related genes scattered in different locations in the plastid genome include those for chloroplast ribosomal proteins, proteins of the cytochrome b6/f complex, and proteins of the photosynthetic reaction centre.

This observation indicates that the mechanism for intron excision and splicing for chloroplast protein genes may be similar to that for nuclear mRNAs in that conserved intron boundary sequences seem to direct the splicing process. This mechanism differs from intron processing in tRNA genes; ergo, two different splicing mechanisms probably exist in the chloroplast.