Chloroplast Genome Of Higher Plants Research Articles

Identification and analysis of RNA editing sites of chloroplast genes in foxtail millet [<italic>Setaria italica</italic> (L.) P. Beauv.

<p id="C3">RNA editing is one of the post-transcriptional regulation mechanisms of gene expression in the chloroplast genomes of higher plants, which affects the chloroplast development and leads to albino phenotype or yellow phenotype of plant leaves. In this study, chlorophyll content was measured with a UV spectrophotometer at seeding stage among Changnong 35, E752, and E1005, and chloroplast structure of leaves was observed with a transmission electron microscopy; the online tool Prep-CP was used to predict the RNA editing sites of chloroplast genes; RNA editing site was verified by PCR, RT-PCR, and sequencing method, and the editing sites were compared and analyzed between foxtail millet and other monocotyledon. Furthermore, the relative expression patterns of <italic>rpoB</italic> and PEP-transcription-dependent photosynthetic pathway related genes (<italic>ndhG</italic>,<italic> psaA</italic>,<italic> psbA</italic>, and<italic> rbcL</italic>) were analyzed by qRT-PCR at different developmental stages, and the secondary structure of rpoB protein before and after editing was analyzed by bioinformatics. The results showed that chlorophyll content of E752 and E1005 were significantly lower and their chloroplasts were abnormal compared with Changnong 35. A total of 20 RNA editing sites of 10 chloroplast genes were identified, among which all were C to U conversion; the number of editing sites among chloroplast genes was varied, and <italic>ndhB</italic> had the most editing sites with the number of 6. Among the 20 editing sites, 19 editing sites were highly conserved in the evolution of species, however <italic>rpoC1-2753</italic> was a unique editing site in foxtail millet. The editing efficiency of<italic> rpoB-467</italic>, <italic>rpoB-545</italic>, and<italic> rpoB-</italic>560 was distinctly different from those of the other editing sites among Changnong 35, E752, and E1005, leading to the expression level change of <italic>ropB</italic>, which might further affect the expression levels changes of <italic>ndhG</italic>,<italic> psaA</italic>,<italic> psbA</italic>, and<italic> rbcL</italic>. Bioinformatics analysis revealed that secondary structure of rpoB protein was changed due to the RNA editing of <italic>rpoB-467</italic> and <italic>rpoB-560</italic>. Our results laid a foundation for the molecular mechanism analysis of chloroplast RNA editing in chloroplast development of foxtail millet.

Molecular evolution of the plastid genome during diversification of the cotton genus

Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and one tetraploid genomic group, namely AD. To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome duringdiversification, chloroplast genomes (cpDNA) from 6 D-genome and 2 G-genome species of Gossypium (G. armourianum D2-1, G. harknessii D2-2, G. davidsonii D3-d, G. klotzschianum D3-k, G. aridum D4, G. trilobum D8, and G. australe G2, G. nelsonii G3) were newly reported here. In combination with the 26 previously released cpDNA sequences, we performed comparative phylogenetic analyses of 34 Gossypium chloroplast genomes that collectively represent most of the diversity in the genus. Gossypium chloroplasts span a small range in size that is mostly attributable to indels that occur in the large single copy (LSC) region of the genome. Phylogenetic analysis using a concatenation of all genes provides robust support for six major Gossypium clades, largely supporting earlier inferences but also revealing new information on intrageneric relationships. Using Theobroma cacao as an outgroup, diversification of the genus was dated, yielding results that are in accord with previous estimates of divergence times, but also offering new perspectives on the basal, early radiation of all major clades within the genus as well as gaps in the record indicative of extinctions. Like most higher-plant chloroplast genomes, all cotton species exhibit a conserved quadripartite structure, i.e., two large inverted repeats (IR) containing most of the ribosomal RNA genes, and two unique regions, LSC (large single sequence) and SSC (small single sequence). Within Gossypium, the IR-single copy region junctions are both variable and homoplasious among species. Two genes, accD and psaJ, exhibited greater rates of synonymous and non-synonymous substitutions than did other genes. Most genes exhibited Ka/Ks ratios suggestive of neutral evolution, with 8 exceptions distributed among one to several species. This research provides an overview of the molecular evolution of a single, large non-recombining molecular during the diversification of this important genus.

Evolution of trnF(GAA) pseudogenes in cruciferous plants

In several studies we used the 5′-trnL(UAA)-trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions, gene diversity calculations and phylogenetic analyses among the genera Arabidopsis and Boechera. Despite the fact that extensive gene duplications are rare within the chloroplast genome of higher plants, within several genera of the Brassicaceae the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with 1-12 tandemly repeated copies in close 5′-proximity of the functional gene. A recent re-examination and additional analysis of trnL(UAA)-trnF(GAA) regions from numerous cruciferous taxa not only reveal extensive trnF gene duplications, but also favour the hypothesis that in cruciferous taxa at least four independent phylogenetic lineages are characterized by these pseudogenes. Among these lineages there is one major clade of taxa carrying pseudogenes indicating an ancient split in crucifer evolution. In two case studies, Boechera and Arabidopsis, intra- and inter-molecular recombinations have been shown to be the reason for the reciprocal exchange of several similar motifs. However, functional constraints might favour two to three or five to six copies as shown for Arabidopsis and Boechera. Herein, we compare the occurrence and distribution of pseudogene copy number in the framework of a comprehensive survey of cpDNA haplotype variation in Boechera, the former genus Cardaminopsis and Arabidopsis thaliana and comment on the value of such kind of mutations in phylogenetic and evolutionary reconstructions.

Two RNA editing sites with cis-acting elements of moderate sequence identity are recognized by an identical site-recognition protein in tobacco chloroplasts

The chloroplast genome of higher plants contains 20–40 C-to-U RNA editing sites, whose number and locations are diversified among plant species. Biochemical analyses using in vitro RNA editing systems with chloroplast extracts have suggested that there is one-to-one recognition between proteinous site recognition factors and their respective RNA editing sites, but their rigidness and generality are still unsettled. In this study, we addressed this question with the aid of an in vitro RNA editing system from tobacco chloroplast extracts and with UV-crosslinking experiments. We found that the ndhB-9 and ndhF-1 editing sites of tobacco chloroplast transcripts are both bound by the site-specific trans-acting factors of 95 kDa. Cross-competition experiments between ndhB-9 and ndhF-1 RNAs demonstrated that the 95 kDa proteins specifically binding to the ndhB-9 and ndhF-1 sites are the identical protein. The binding regions of the 95 kDa protein on the ndhB-9 and ndhF-1 transcripts showed 60% identity in nucleotide sequence. This is the first biochemical demonstration that a site recognition factor of chloroplast RNA editing recognizes plural sites. On the basis of this finding, we discuss how plant organellar RNA editing sites have diverged during evolution.

Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus

Gene transfer events from organelle genomes (mitochondria and chloroplasts in plants) to the nuclear genome are important processes in the evolution of the eukaryotic cell. It is highly likely that the gene transfer event is still an ongoing process in higher plant mitochondria and chloroplasts. The number and order of genes encoded in the chloroplast genome of higher plants are highly conserved. Recently, several exceptional cases of gene loss from the chloroplast genome have been discovered as the number of complete chloroplast genome sequences has increased. The Populus chloroplast genome has lost the rpl32 gene, while the corresponding the chloroplast rpl32 (cp rpl32) gene has been identified in the nuclear genome. Nuclear genes transferred from the chloroplast genome need to gain a sequence that encodes a transit peptide. Here, we revealed that the nuclear cp rpl32 gene has acquired the exon sequence, which is highly homologous to a transit peptide derived from the chloroplast Cu–Zn superoxide dismutase (cp sod-1) gene. The cp rpl32 gene has acquired the sequence that encodes not only for the transit peptide, but also for the conserved N-terminal portion of the mature SOD protein from the cp sod-1 gene, suggesting the occurrence of DNA sequence duplication. Unlike cp SOD-1, cp RPL32 did not show biased localization in the chloroplasts. This difference may be caused by mutations accumulated in the sequence of the SOD domain on the cp rpl32 gene. We provide new insight into the fate of the inherent sequence derived from a transit peptide.

Evolution of the trnF(GAA) Gene in Arabidopsis Relatives and the Brassicaceae Family: Monophyletic Origin and Subsequent Diversification of a Plastidic Pseudogene

Recently, we used the 5'-trnL(UAA)-trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions and phylogenetic analysis among the genera Arabidopsis, Boechera, Rorippa, Nasturtium, and Cardamine. Despite the fact that extensive gene duplications are rare among the chloroplast genome of higher plants, within these taxa the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with one to eight tandemly repeated copies in close 5' proximity of the functional gene. Interestingly, even in Arabidopsis thaliana we found six putative pseudogenic copies of the functional trnF gene within the 5'-intergenic trnL-trnF spacer. A reexamination of trnL(UAA)-trnF(GAA) regions from numerous published phylogenetic studies among halimolobine, cardaminoid, and other cruciferous taxa revealed not only extensive trnF gene duplications but also favor the hypothesis about a single origin of trnF pseudogene formation during evolution of the Brassicaceae family 16-21 MYA. Conserved sequence motifs from this tandemly repeated region are codistributed nonrandomly throughout the plastome, and we found some similarities with a DNA sequence duplication in the rps7 gene and its adjacent spacer. Our results demonstrate the potential evolutionary dynamics of a plastidic region generally regarded as highly conserved and probably cotranscribed and, as shown here for several genera among cruciferous plants, greatly characterized by parallel gains and losses of duplicated trnF copies.

Molecular evolution of insertions and deletion in the chloroplast genome of silene.

Insertions, deletions, and inversions in the chloroplast genome of higher plants have been shown to be extremely useful for resolving phylogenetic relationships both between closely related taxa and among more basal lineages. Introns and intergenic spacers from the chloroplast genome are now increasingly used for phylogenetic and population genetic studies of populations from a single species, and it is therefore interesting to know whether indels can provide useful data and hence increase the power of intraspecific studies. Here, we show that indels in three cpDNA intergenic spacers and one cpDNA intron for two species of Silene evolve at slightly higher rates than base pair substitutions. Repeat indels appear to have the highest rate of evolution and are thus more prone to homoplasy. We show that coded indel data have high information content for phylogenetic analysis, and indels thus provide useful information to infer phylogenetic relationships at the intraspecific level.

Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit.

Six ribosomal proteins are specific to higher plant chloroplast ribosomes [Subramanian, A.R. (1993) Trends Biochem. Sci.18, 177-180]. Three of them have been fully characterized [Yamaguchi, K., von Knoblauch, K. & Subramanian, A. R. (2000) J. Biol. Chem. 275, 28455-28465; Yamaguchi, K. & Subramanian, A. R. (2000) J. Biol. Chem. 275, 28466-28482]. The remaining three plastid-specific ribosomal proteins (PSRPs), all on the small subunit, have now been characterized (2D PAGE, HPLC, N-terminal/internal peptide sequencing, electrospray ionization MS, cloning/ sequencing of precursor cDNAs). PSRP-3 exists in two forms (alpha/beta, N-terminus free and blocked by post-translational modification), whereas PSRP-2 and PSRP-4 appear, from MS data, to be unmodified. PSRP-2 contains two RNA-binding domains which occur in mRNA processing/stabilizing proteins (e.g. U1A snRNP, poly(A)-binding proteins), suggesting a possible role for it in the recruiting of stored chloroplast mRNAs for active protein synthesis. PSRP-3 is the higher plant orthologue of a hypothetical protein (ycf65 gene product), first reported in the chloroplast genome of a red alga. The ycf65 gene is absent from the chloroplast genomes of higher plants. Therefore, we suggest that Psrp-3/ycf65, encoding an evolutionarily conserved chloroplast ribosomal protein, represents an example of organelle-to-nucleus gene transfer in chloroplast evolution. PSRP-4 shows strong homology with Thx, a small basic ribosomal protein of Thermus thermophilus 30S subunit (with a specific structural role in the subunit crystallographic structure), but its orthologues are absent from Escherichia coli and the photosynthetic bacterium Synechocystis. We would therefore suggest that PSRP-4 is an example of gene capture (via horizontal gene transfer) during chloro-ribosome emergence. Orthologues of all six PSRPs are identifiable in the complete genome sequence of Arabidopsis thaliana and in the higher plant expressed sequence tag database. All six PSRPs are nucleus-encoded. The cytosolic precursors of PSRP-2, PSRP-3, and PSRP-4 have average targeting peptides (62, 58, and 54 residues long), and the mature proteins are of 196, 121, and 47 residues length (molar masses, 21.7, 13.8 and 5.2 kDa), respectively. Functions of the PSRPs as active participants in translational regulation, the key feature of chloroplast protein synthesis, are discussed and a model is proposed.

The Arabidopsis chloroplast ribosomal protein L21 is encoded by a nuclear gene of mitochondrial origin

Many chloroplast genes of cyanobacterial origin have been transferred to the nucleus during evolution and their products are re-addressed to chloroplasts. The RPL21 gene encoding the plastid r-protein L21 has been lost in higher plant chloroplast genomes after the divergence from bryophytes. Based on phylogenetic analysis and intron conservation, we now provide evidence that in Arabidopsis a nuclear RPL21c gene of mitochondrial origin has replaced the chloroplast gene. The control of expression of this gene has been adapted to the needs of chloroplast development by the acquisition of plastid-specific regulatory promoter cis-elements.

Enslaved bacteria as new hope for plant biotechnologists.

The most distinguishing feature of the plant cell is a DNA-containing organelle that sets plants apart from all other organisms: the chloroplast. Compelling evidence supports an endosymbiotic origin for chloroplasts. According to this theory, chloroplasts are descendants of formerly free-living cyanobacterial ancestors which entered an endosymbiotic relationship with a pre-eukaryotic cell and were ultimately integrated into the metabolism of the host cell. Chloroplasts retain many prokaryotic features and their gene expression system still closely resembles that of their eubacterial ancestors. During the past decade, our knowledge about chloroplast biology has benefited immensely from a most remarkable methodological breakthrough: the development of transformation technologies for chloroplast genomes. Moreover, recent advances in the manipulation of higher plant chloroplast genomes have created unprecedented opportunities for the genetic engineering of plants and promise to overcome many of the problems associated with conventional transgenic technologies. This review describes the state of the art in genetic engineering of higher plant chloroplast genomes and highlights the tremendous potential of these technologies for the biotechnology of the future.

Physiological Function of a Respiratory Complex, NAD(P)H Dehydrogenase in Chloroplasts. Dissection by Chloroplast Reverse Genetics.

The chloroplast genome of higher plants contains eleven ndh genes encoding homologs of mitochondrial complex I subunits. The enigmatic occurrence of the respiratory complex in chloroplasts suggests the possibility that NAD (P) H dehydrogenase catalyzes cyclic electron flow around photosystem I and/or chlororespiratory electron flow, as it does in cyanobacteria. Establishment of a chloroplast transformation technique in tobacco facilitated the reverse genetic approach. Although some conclusions are still matters of controversy, it is sure that the gene product, NDH, functions to donate electrons to plastoquinone. Although NDH is dispensable under mild growth conditions, ndhB disruptant is more sensitive to high light stress, suggesting that NDH functions in minor compensation for the electron flow to cope with changes in environmental conditions. Here, we review the physiological function of NDH in chloroplasts, including important subjects that are still unclear.

A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms

Short runs of mononucleotide repeats are present in chloroplast genomes of higher plants. In soybean, rice, and pine, PCR (polymerase chain reaction) with flanking primers has shown that the numbers of A or T residues in such repeats are variable among closely related taxa. Here we describe a set of primers for studying mononucleotide repeat variation in chloroplast DNA of angiosperms where database information is limited. A total of 39 (A)n and (T)n repeats (n > or = 10) were identified in the tobacco chloroplast genome, and DNA sequences encompassing these 39 regions were aligned with orthologous DNA sequences in the databases. Consensus primer pairs were constructed and used to amplify total genomic DNA from a hierarchical set of angiosperms. All 10 primer pairs generated PCR products from members of the Solanaceae, and 8 of the 10 were also functional in most other angiosperm species. Levels of interspecific polymorphism within the genera Nicotiana, Lycopersicon (both Solanaceae), and Actinidia (Actinidiaceae) proved to be high, while intraspecific variation in Nicotiana tabacum, Lycopersicon esculentum, and Actinidia chinensis was limited. Sequence analysis of PCR products from three primer pairs revealed variable numbers of A, G, and T residues in mononucleotide arrays as the major cause of polymorphism in Actinidia. Our results suggest that universal primers targeted to mononucleotide repeats may serve as general tools to study chloroplast variation in angiosperms.

Analysis of a hotspot for deletion formation within the intron of the chloroplast trnI gene.

The chloroplast genomes of higher plants encode several tRNA genes that contain highly conserved type II introns. Using primers specific to conserved 5' and 3' regions within the introns of the genes trnA (tRNA-ala) and trnI (tRNA-ile) we have PCR amplified parts of these introns from 36 plant species representing a wide range of plant families. Deletions were found in the introns of both tRNA genes. Fourteen species had detectable deletions within the intron of trnI and four species within the intron of trnA. The occurrence of these deletions among the various plant families suggests that the events leading to the formation of these deletions occurred independently many times during the evolution of higher plants. Analysis of the amplified PCR products from the trnI intron suggests that these independent deletions may not be random but appear to fall into two size classes. Several members of each class were cloned and sequenced and the end points of the deletions were mapped. The 3' ends of all deletions studied terminate within the same short region. The 5' ends of the deletions map to two different regions, giving rise to the two size classes. These two 5' deletion endpoint regions show some sequence similarity. Only two of the identified deletions contain directly repeated sequences at the deletion endpoints, a feature associated with homologous recombination. Our results suggest that within the trnI intron, there are preferred sites or "hotspots" for deletion formation involving a novel imprecise recombination mechanism. The significance of these sequences and possible mechanisms for deletion formation are discussed.

The Gene Locus of the Proton-translocating NADH : Ubiquinone Oxidoreductase in Escherichia coli: Organization of the 14 Genes and Relationship Between the Derived Proteins and Subunits of Mitochondrial Complex I

The gene locus nuo of the proton-translocating NADH : ubiquinone oxidoreductase in Escherichia coli was identified by means of a DNA probe made by the polymerase chain reaction. The primers used for the reaction were derived from consensus sequences of the NAD(H)-binding subunit of mitochondrial NADH : ubiquinone oxidoreductase and the NAD +-reducing hydrogenase of Alcaligenes eutrophus. The nuo locus lies between minutes 49·2 and 49·6 on the E. coli chromosome and contains a cluster of 14 genes. They are bordered upstream by a sequence resembling sigma 70-dependent promoters and downstream by a sequence resembling rho-independent terminators. All 14 proteins derived from the nuo -genes are related to subunits of mitochondrial NADH : ubiquinone oxidoreductase, among which all subunits presumed to bind the substrates and to harbour the redox groups are found, as well as all seven mitochondrially encoded subunits. The E. coli enzyme seems to represent the minimal form of a proton-translocating NADH : ubiquinone oxidoreductase. The gene order in the nuo locus is conserved in comparison with other bacterial genomes and the chloroplast genome of higher plants. To some extent, the gene order correlates with the topological arrangement of the encoded subunits. The conception of modular evolution of NADH : ubiquinone oxidoreductase is further supported by the arrangement of the nuo-genes.

NADH:ubiquinone oxidoreductase from bovine heart mitochondria A fourth nuclear encoded subunit with a homologue encoded in chloroplast genomes

The amino acid sequence has been determined of the precursor of a nuclear encoded 20 kDa subunit of complex I from bovine heart mitochondria. The sequence of the mature protein is related to a protein of uncertain function, hitherto known as psbG, encoded in the chloroplast genomes of higher plants. Open reading frames encoding homologues of psbG have also been detected in bacteria and in the mitochondrial genome of Paramecium tetraurelia. The chloroplast psbG gene is found between ndhC and ndhJ, which encode homologues of ND3, a hydrophobic subunit of complex I encoded in the bovine mitochondrial genome, and of the nuclear encoded 30 kDa subunit of complex 1. This 20 kDa protein is the eleventh out of the forty or more subunits of bovine complex I with a chloroplast encoded homologue, and its sequence provides further support for the presence in chloroplasts of a multisubunit enzyme related to complex I that could be involved in chlororespiration. The strict conservation of three cysteines suggests that the subunit might be an iron-sulphur protein.

Nucleotide sequence of the frxC, petB and trnL genes in the chloroplast genome of Chlamydomonas reinhardtii.

The nucleotide sequence of a 4262 bp DNA fragment was determined from the chloroplast genome of the green alga Chlamydomonas reinhardtii (wild-type, CC125, see [1]). Sequence analysis revealed two protein-encoding genes (frxC and petB) and one tRNA gene (trnL) (Fig. 1). In addition, the intergenic sequences predict three stable stem-loop structures possibly involved in regulating the accumulation of the gene transcripts. This DNA fragment is located upstream of a ribosomal protein gene cluster starting with the rpl23 gene (unpublished data), and is within the 7.6 kb Eco9 DNA fragment [1] which is equivalent to the R20 DNA fragment named by Rochaix [2]. The only frxC gene reported previously has been found in the chloroplast genome of the liverwort Marchantia polymorpha [4]. The putative protein product predicted from this gene shows significant sequence similarity to the ntf/-/ gene product of nitrogen-fixing bacteria, and appears to be an iron (Fe)-binding protein with conserved cysteine residues. It was not certain whether the frxC gene is a functional and typical chloroplast gene, because chloroplasts are not known to possess NifH activities, and because the frxC gene is not present in chloroplast genomes of higher plants examined [ e.g. 5 ]. Our finding of the frxC gene in the chloroplast genome of a green alga (Fig. 1), together with the previous finding of this gene in liverwort [4], suggests that the frxC gene is a common chloroplast gene which has been retained in chloroplasts of green algae and lower plants but transferred to the nucleus in higher plants. Amino acid sequence comparisons among the two chloroplast FrxC proteins and the three types of NifH proteins [6] revealed extensive sequence similarities (Fig. 2). The FrxC protein sequence of C. reinhardtii is 88~o identical to that of liverwort. This high degree of structural conservation, comparable to that of many photosynthetic complex proteins, suggests conserved cellular functions of the frxC genes. Sequence identities between the C. reinhardtii FrxC protein and the NifH proteins range from 32~o to 35~o, suggesting that these proteins are evolutionarily related. The FrxC sequence is about equally similar to each of the three types of NifH proteins, suggesting that the frxC gene diverged from an ancestral mf/-/gene that subsequently gave rise to the three contemporary types of n/fH genes [6]. Amino

A model for the evolution of the Vicia faba chloroplast genome

The Vicia faba chloroplast genome lacks inverted repeat sequences and contains only one set of ribosomal RNA genes. The genetic organization has been altered by inversions, relative to the typical arrangement of most higher plant chloroplast genomes. The Vicia faba plastid genome thus represents one of the more interesting results of chloroplast genomic evolution. The present study employs small DNA probes and Southern blot hybridizations to investigate the steps involved in the evolution of the Vicia faba chloroplast genome. The data from heterologous hybridizations between chloroplast DNA of Brassica napus (a conserved genome) and of Vicia faba led to three observations: 1) The inverted repeat segment closest to the psbA gene was deleted prior to the rearrangements. 2) A quarter of the ancestral small single copy region was lost during the deletion. 3) The genetic organization observed in Vicia faba resulted from three inversions after the deletion event. Our findings, combined with previous observations, helped devise a stepwise model for the evolution of the Vicia faba chloroplast genome. The area of the small single copy region absent from the Vicia faba chloroplast chromosome lacks in vivo transcription activity in Brassica napus.

Chloroplast genes encoding subunits of the H+-ATPase complex of Chlamydomonas reinhardtii are rearranged compared to higher plants: sequence of the atpE gene and location of the atpF and atpI genes

The chloroplast gene for the epsilon subunit (atpE) of the CF1/CF0 ATPase in the green alga Chlamydomonas reinhardtii has been localized and sequenced. In contrast to higher plants, the atpE gene does not lie at the 3' end of the beta subunit (atpB) gene in the chloroplast genome of C. reinhardtii, but is located at a position 92 kb away in the other single copy region. The uninterrupted open reading frame for the atpE gene is 423 bp, and the epsilon subunit exhibits 43% derived amino acid homology to that from spinach. Codon usage for the atpE gene follows the restricted pattern seen in other C. reinhardtii chloroplast genes.The genes for the CF0 subunits I (atpF) and IV (atpI) of the ATPase complex have also been mapped on the chloroplast genome of C. reinhardtii. The six chloroplast ATPase genes in C. reinhardtii are dispersed individually between the two single copy regions of the chloroplast genome, an organization strikingly different from the highly conserved arrangement in two operon-like units seen in chloroplast genomes of higher plants.

Molecular cloning and nucleotide sequence of the psaA and psaB genes of the cyanobacterium Synechococcus sp. PCC 7002

The psaA and psaB genes, which encode the P700 chlorophyll a apoproteins of the Photosystem I complex, have been cloned from the unicellular, transformable cyanobacterium Synechococcus sp. PCC 7002. The nucleotide sequence of these genes and of their flanking sequences have been determined by the chain termination method. As found in the chloroplast genomes of higher plants, the psaA gene lies 5' to the psaB gene; however, the cyanobacterial genes are separated by a greater distance (173 vs. 25-26 bp). The psaA gene is predicted to encode a polypeptide of 739 amino acid residues (81.7 kDa), and the psaB gene is predicted to encode a polypeptide of 733 residues (81.4 kDa). The cyanobacterial psa gene products are 76% to 81% identical to their higher plant homologues; moreover, because of conservative amino acid replacements, the cyanobacterial sequences are more than 95% homologous to those determined for higher plants. These results provide the basis for a genetic analysis of Photosystem I, and are discussed in relationship to structural and functional aspects of the Photosystem I complexes of both cyanobacteria and higher plants.

Ubiquity of the genes for components of a NADH dehydrogenase in higher plant chloroplast genomes

Sequences homologous to the six tobacco chloroplast genes, ndhA-F, which correspond to the genes for components of the human mitochondrial NADH dehydrogenase, have been identified in rice, sugar beet and broad bean chloroplast genomes. The locations of the six ndh sequences are essentially conserved among these chloroplast genomes. The results indicate that the ndh sequences are widespread in chloroplast genomes of higher plants.