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Annual Plant Reviews (2009) 36, 182–210 doi: 10.1111/b.9781405181891.2009.00008.x Chapter 8 CHLOROPLASTS Mamoru Sugita1 and Setsuyuki Aoki2 1Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan 2 Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan Abstract: In Physcomitrella patens, chloronemal and leaf cells contain numerous large round chloroplasts while caulonemal cells contain fewer and smaller spindle- shaped chloroplasts. Unlike seed plants, plastid differentiation is not usually ob- served in P. patens and the gametophytes always contain chloroplasts that develop even in the dark. The P. patens plastid genome (122 890 bp) possesses at least 118 genes. The most interesting feature is that the rpoA gene encoding the subunit of the plastid-encoded plastid RNA polymerase (PEP) is absent from the plastid genome of P. patens. Instead, two nuclear counterparts encode the subunits of PEP enzyme and modulate transcription of the plastid genes. Whether P. patens chloroplasts contain a second RNA polymerase, the nuclear-encoded plastid RNA polymerase (NEP), continues to be debated. Here, we provide biochemical evi- dence supporting the existence of NEP activity in P. patens. Plastid transformation, which has been achieved in P. patens, allows further investigation of the regulation of plastid gene expression and over-production of foreign polypeptides in the moss chloroplasts. Molecular techniques with the complete genome informatics open a way to study the molecular basis of plastid division and movement, chloroplast import, or circadian rhythm in P. patens. Keywords: chloroplast movement; circadian rhythm; plastid division; plastid DNA; plastid transformation; rpoA Abbreviations: BLRP blue-light responsive promoter GFP green fluorescent protein IR inverted repeat LSC l