Chloroplast Gene Expression: How Plants Turn Their Plastids On Review

Wilhelm Gruissem Department of Botany University of California Berkeley, California 94720 Plant and animal cells are fundamentally very similar. Be- sides the organelles found in both cell types, however, plant cells contain a unique class of organelles, the plastids. Since the early discovery by Correns (1909) and Baur (1909) that mutations affecting plastid phenotypes in higher plants frequently exhibit non-Mendelian inheri- tance, research on the DNA of this organelle has now yielded the complete sequence of the plastid genomes from tobacco (Shinozaki et al., 1986) and liverwort (Oh- yama et al., 1986). Plastids exist in a number of different forms with different functions, but the green chloroplast was the first to be discovered, and is the best studied of all plastids. The diversity of plastid types is controlled by the developmental program of the plant, which indicates that there must be a significant flow of information be- tween two separate genetic compartments in the cell. The use of chloroplasts to study photosynthesis and the in- tricacy of photosynthetic complexes has yielded new infor- mation on controls of organelle gene expression and the communication of different genomes in eukaryotic cells. In developing plants, chloroplasts are derived from small proplastids, which are the undifferentiated plastids present in meristematic cells. During the development of chloroplasts in photosynthetic tissues, photosynthetic electron-transfer components are assembled into pho- tosystems I and II, cytochrome bsf, and ATP synthase complexes, each of which consists of up to 20 polypep- tides. Proplastids and chloroplasts can also differentiate into specialized plastid types that assume other functions in nonphotosynthetic plant organs of higher plants, such as amyloplasts in roots and tubers or chromoplasts in many flowers and fruits. Photosynthesis, together with other plastid functions, requires the products of several hundred genes, of which only about 120 are present in the approximately 150 kb chloroplast genome. All other plas- tid proteins are expressed from nuclear genes. The devel- opment and differentiation of photosynthetically compe- tent chloroplasts and other plastid types thus present a challenging opportunity: to decipher how plastid gene ex- pression is controlled temporally and spatially in different plant organs, and also in coordination with the expression of nuclear genes for chloroplast proteins. Initial efforts to analyze the controls of plastid gene expression have con- centrated on the transcription of genes for photosynthetic proteins and tRNAs. Recent progress appears to support a model that places a major emphasis on posttranscrip- tional and translational regulatory mechanisms. In con- trast, known nuclear genes for photosynthetic proteins ap- pear to be regulated primarily at the level of transcription. The purpose of this review is to discuss some of the cen- tral problems and ideas in the field of chloroplast gene ex- pression, not to provide a comprehensive review on all that is known. (For further information on chloroplast ge- nome structures, genes, and transcriptional and transla- tional components, readers should consult Whitfeld and Bottomley, 1983; Ellis, 1984; Sugiura, 1987; Umesono and Ozeki, 1987; Gruissem, 1989; Mullet, 1988; Bonham- Smith and Bourque, 1988.) Linkage of Genes in Many Chloroplast Transcription Units Is Conserved Compared with the small number of genes in animal, fun- gal and plant mitochondria, the chloroplast genome con- tains a substantially larger number of genes, encoding both genetic and photosynthetic functions. The genes identified thus far include a complete set of 30 tRNAs, four ribosomal RNAs (23S, 16S, 5S, and 4.5s) and 20 ribo- somal proteins. Twenty-two genes encode proteins for thylakoid membrane complexes (photosystem I, photosys- tern II, cytochrome bsf complex, and ATP synthase), and the sequences of six other open reading frames share similarities with the mitochondrial genes for the subunits of the human respiratory chain NADH dehydrogenase. Several of the remaining unidentified reading frames are conserved between diverse species, which suggests that they may also encode functional plastid polypeptides. Most plastid genes are organized into polycistronic tran- scription units reminiscent of bacterial operons. The se- quence analysis of the entire tobacco and liverwort chlo- roplast genomes (Shinozaki et al., 1986; Ohyama et al., 1986) together with the partial sequence and mapping data from other plant chloroplast genomes, has revealed that the arrangement of genes within these transcription units is highly conserved, although transcription are extensively rearranged in some plant species (reviewed by Palmer, 1985). Detailed mapping of chloroplast DNAs from pea and geranium, for example, has found that such rearrangements involve primarily inversions of large clus- ters of genes. Most, but not all, the genes linked in these clusters are cotranscribed. It has been possible, at least some cases, to trace the linkage of chloroplast gene sets to the cyanobacterial genome (Cozens et al., 1986) which is the putative ancestral genome of chloroplast genome. However, the conserved arrangement of genes in plant chloroplast genomes is not found algae, for which Chlamydomonas and Euglena are the best studied examples, possibly indicating different endosymbiotic events. Chloroplast RNA Polymerases and Promoter Regions The possibility that transcriptional regulation chlo- roplast genes could be a key control during chloroplast development in plants spurred early investigations into the transcriptional components of this organelle. Applica- tion of different schemes for preparing DNA-dependent RNA polymerase from chloroplasts led to the intriguing idea that chloroplasts of algae and plants may contain at least two different RNA polymerase activities distinguish-