Spinach chloroplast rpoBC genes encode three subunits of the chloroplast RNA polymerase

Sequence analysis of a 12,400 base-pair region of the spinach chloroplast genome indicates the presence of three genes encoding subunits of the chloroplast RNA polymerase. These genes are analogous to the rpoBC operon of Escherichia coli, with some significant differences. The first gene, termed rpoB, encodes a 121,000 Mr homologue of the bacterial beta subunit. The second and third genes, termed rpoC1 and rpoC2, encode 78,000 and 154,000 Mr proteins homologous to the N and C-terminal portions, respectively, of the bacterial beta' subunit. RNA mapping analysis indicates that the three genes are cotranscribed, and that a single intron occurs in the rpoC1 gene. No splicing occurs within the rpoC2 gene or between rpoC1 and rpoC2. Furthermore, the data indicate the possibility of an alternative splice acceptor site for the rpoC1 intron that would give rise to a 71,000 Mr gene product. Thus, with the inclusion of the alpha subunit encoded by rpoA at a separate locus, the chloroplast genome is predicted to encode four subunits (respectively called alpha, beta, beta', beta") equivalent to the three subunits of the core enzyme of the E. coli RNA polymerase.     

Evolution of the chloroplast genome

We discuss the suggestion that differences in the nucleotide composition between plastid and nuclear genomes may provide a selective advantage in the transposition of genes from plastid to nucleus. We show that in the adenine, thymine (AT)-rich genome of Borrelia burgdorferi several genes have an AT-content lower than the average for the genome as a whole. However, genes whose plant homologues have moved from plastid to nucleus are no less AT-rich than genes whose plant homologues have remained in the plastid, indicating that both classes of gene are able to support a high AT-content. We describe the anomalous organization of dinoflagellate plastid genes. These are located on small circles of 2-3 kbp, in contrast to the usual plastid genome organization of a single large circle of 100-200 kbp. Most circles contain a single gene. Some circles contain two genes and some contain none. Dinoflagellate plastids have retained far fewer genes than other plastids. We discuss a similarity between the dinoflagellate minicircles and the bacterial integron system.     

Genetic engineering of the chloroplast

Transformation of the plastid genome has a number of inherent advantages for the engineering of gene expression in plants. These advantages include: 10-50 times higher transgene expression levels; the absence of gene silencing and position effect variation; the ability to express polycistronic messages from a single promoter; uniparental plastid gene inheritance in most crop plants that prevents pollen transmission of foreign DNA; integration via a homologous recombination process that facilitates targeted gene replacement and precise transgene control; and sequestration of foreign proteins in the organelle which prevents adverse interactions with the cytoplasmic environment. It is now 12 years since the first conclusive demonstration of stable introduction of cloned DNA into the Chlamydomonas chloroplast by the Boynton and Gillham laboratory, and 10 years since the laboratory of Pal Maliga successfully extended these approaches to tobacco. Since then, technical developments in plastid transformation and advances in our understanding of the rules of plastid gene expression have facilitated tremendous progress towards the goal of establishing the chloroplast as a feasible platform for genetic modification of plants.     

Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes.

The entire nucleotide sequences of the rice, tobacco and liverwort chloroplast genomes have been determined. We compared all the chloroplast genes, open reading frames and spacer regions in the plastid genomes of these three species in order to elucidate general structural features of the chloroplast genome. Analyses of homology, GC content and codon usage of the genes enabled us to classify them into two groups: photosynthesis genes and genetic system genes. Based on comparisons of homology, GC content and codon usage, unidentified ORFs can also be assigned to each of these groups such that it is possible to speculate about the functions of products which may be produced by these ORFs. The spacer regions and intron sequences were compared and found to have no obvious homology between rice and liverwort or between tobacco and liverwort.     

Evolution of the chloroplast division machinery

Chloroplasts are photosynthetic organelles derived from endosymbiotic cyanobacteria during evolution. Dramatic changes occurred during the process of the formation and evolution of chloroplasts, including the large-scale gene transfer from chloroplast to nucleus. However, there are still many essential characters remaining. For the chloroplast division machinery, FtsZ proteins, Ftn2, SulA and part of the division site positioning system—MinD and MinE are still conserved. New or at least partially new proteins, such as FtsZ family proteins FtsZ1 and ARC3, ARC6H, ARC5, PDV1, PDV2 and MCD1, were introduced for the division of chloroplasts during evolution. Some bacterial cell division proteins, such as FtsA, MreB, Ftn6, FtsW and FtsI, probably lost their function or were gradually lost. Thus, the chloroplast division machinery is a dynamically evolving structure with both conservation and innovation.     

Evolution of the chloroplast division machinery

Chloroplasts are photosynthetic organelles derived from endosymbiotic cyanobacteria during evolution.Dramatic changes occurred during the process of the formation and evolution of chloroplasts,including the large-scale gene transfer from chloroplast to nucleus.However,there are still many essential characters remaining.For the chloroplast division machinery,FtsZ proteins,Ftn2,SulA and part of the division site positioning system- MinD and MinE are still conserved.New or at least partially new proteins,such as FtsZ family proteins FtsZl and ARC3,ARC6H,ARC5,PDV1,PDV2 and MCD1,were introduced for the division of chloroplasts during evolution.Some bacterial cell division proteins,such as FtsA,MreB,Ftn6,FtsW and Ftsl,probably lost their function or were gradually lost.Thus,the chloroplast division machinery is a dynamically evolving structure with both conservation and innovation.     

Selectable marker recycling in the chloroplast

The bacterial geneaadA is an important and widely used selectable marker for manipulation of the chloroplast genome through biolistic transformation. Because no other such marker is available, two strategies for recycling of theaadA cassette have been developed. One utilizes homologous recombination between two direct repeats flanking theaadA cassette to allow its loss under non-selective growth conditions. A second strategy is to perform co-transformation with a plasmid containing a modified, non-essential chloroplast gene and another plasmid in which theaadA cassette disrupts a chloroplast gene known to be essential for survival. Under selective growth conditions the first mutation can be transferred to all chloroplast DNA copies whereas theaadA insertion remains heteroplasmic. Loss of the selectable marker can be achieved subsequently by growing the cells on non-selective media. In both cases it is possible to reuse theaadA cassette for the stepwise disruption or mutagenesis of any gene in the same strain.     

Cellular content of chloroplast DNA and chloroplast ribosomal RNA genes in Euglena gracilis during chloroplast development.

The cellular content of chloroplast DNA in Euglena gracilis has been quantitatively determined. DNA was extracted from Euglena cells at various stages of chloroplast development and renatured in the presence of trace amounts of 3H-labeled chloroplast DNA. From the kinetics of renaturation of the 3H-labeled chloroplast DNA, compared with the kinetics of renaturation of excess nonradioactive chloroplast DNA, the fraction of cellular DNA represented by chloroplast DNA was calculated. The content of chloroplast DNA was found to increase from 4.9 to 14.6% of cellular DNA during light-induced chloroplast development. Correcting for the change in DNA mass per cell, the number of copies of chloroplast DNA is found to vary from 1400 to 2900 per cell. During this developmental transition, the cellular content of the chloroplast ribosomal RNA genes varies from 1900 to 5200 copies per cell. The ratio of the number of copies of rRNA genes to chloroplast genomes per cell remains in the range of 1-2 throughout chloroplast development, ruling out selective amplification of chloroplast rRNA genes as a means of regulation of rRNA gene expression. Direct measurement of the number of rRNA cistrons per 9.2 X 10(7) dalton genome yields a value of 1 or 2.     

The ultrastructure of the chloroplast lamellae

Summary The present study has shown that the thylakoid membrane consists of a central layer, probably lipid, covered on both sides with protein particles. The thickness of the middle layer reaches 40 Å, and the diameter of the attached globules 60 Å. The particles are partially embedded to a depth of about 20 Å in the central layer. If these globules are removed, the lipid layer appears perforated, indicating that the protein molecules are in direct contact through the lipid layer. On the outer side of the thylakoid membrane the particles are grouped in fours, forming a multienzyme complex of 120 Å diameter and 60 Å thickness. No such aggregates have been observed on the inner side.In frozen plastids a tripartite membrane at the periphery of a granum has a thickness of 120 Å, whereas the two membranes of adjacent thylakoids are together only 200 Å thick. This indicates that the particles attached to the two neighbouring membranes are interlocked and form a rigid layer.In comparison with the freeze-etched preparations the chemically fixed plastids show considerably thinner lamellae. They appear as unit membranes, consisting of a central layer 35 Å thick and two dense strata, each of 20 Å. This discrepancy cannot be explained simply by shrinkage in fixation and dehydration. It is proposed that fixation causes uncoiling of the protein molecules. In consequence, thin protein films are formed on each side of the lipid layer, and each appears as a dark band after osmium- or permanganate fixation. This new model of the thylakoid membrane is compared with other recent schemes.

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Zusammenfassung In der vorliegenden Untersuchung wird gezeigt, daß die Thylakoidmembran aus einer zentralen, wahrscheinlich lipidhaltigen Schicht besteht, die beidseitig mit Proteinpartikeln bedeckt ist. Die Dicke dieser Mittelschicht beträgt 40 Å und der Durchmesser der darauf liegenden Kügelchen 60 Å. Sowohl die innern wie die äußern Partikel sind ungefähr 20 Å tief in der zentralen Schicht eingebettet. Werden sie beim Herstellen des Gefrierabdruckes herausgerissen, so erscheint die Lipoidlamelle perforiert. Das zeigt, daß die Enzyme durch diese Schicht hindurch in direktem Kontakt stehen. Auf der Außenseite der Thylakoidmembran sind vier Partikel zu einem Multi-Enzym-Komplex von 120 Å Durchmesser und 60 Å Dicke vereinigt. Auf der Innenseite konnten solche Zusammenlagerungen nicht beobachtet werden. Die Dicke einer dreischichtigen Membran, wie sie z. B. an der Außenseite eines Granumstapels zu beobachten ist, beträgt 120 Å. Die Doppelmembranen benachbarter Thylakoide (200 Å dick) sind durch die auf der Oberfläche vorhandenen Partikel eng verzahnt.Ein Vergleich der Bilder von Plastiden nach der Gefrierätzung und nach einer gewöhnlichen Fixierung ergibt, daß die Lamellen durch die Fixierung und Entwässerung dünner werden. Sie zeigen die Struktur einer Einheitsmembran bestehend aus einer 35 Å dicken Zentralschicht und den beiden anliegenden 20 Å dicken osmiophilen Lamellen. Die unterschiedliche Lamellendicke (Gefriergetrocknet: 120 Å, fixiert: 75 Å) kann nicht nur auf die bei der Fixierung und Entwässerung eintretende Schrumpfung zurückgeführt werden. Es ist wahrscheinlich, daß die Fixierung eine Entknäuelung der Proteinmoleküle bewirkt. Der dadurch auf beiden Seiten der Lipidschicht gebildete, dünne Protein-film erscheint nach der Osmium-oder Permanganatfixierung als kontrastreiche 20 Å dicke Schicht. Dieses neue Modell der Thylakoidmembran wurde mit einigen neuen Strukturschemata verglichen.