The plastid is a semiautonomous organelle essential in photosynthesis and other 
metabolic activities of plants and algae. Plastid DNA is organized into the 
nucleoid with various proteins and RNA, and the nucleoid is subject to dynamic 
changes during the development of plant cells. Characterization of the major 
DNA-binding proteins of nucleoids revealed essential differences in the two 
lineages of photosynthetic eukaryotes, namely nucleoids of green plants contain 
sulfite reductase as a major DNA-binding protein that represses the genomic 
activity, whereas the prokaryotic DNA-binding protein HU is abundant in plastid 
nucleoids of the rhodophyte lineage. In addition, current knowledge on 
DNA-binding proteins, as well as the replication and transcription systems of 
plastids, is reviewed from comparative and evolutionary points of view. A 
revised hypothesis on the discontinuous evolution of plastid genomic machinery 
is presented: despite the cyanobacterial origin of plastids, the genomic 
machinery of the plastid genome is fundamentally different from its counterpart 
in cyanobacteria.