The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression

Characterization of genes that encode subunits of cucumber PS I complex by N-terminal sequencing

N-terminal amino acid sequencing was carried out to characterize the genes of the cucumber PS I complex (PSI-100) that contains eight polypeptides and catalyzes the light-dependent transfer of electrons from plastocyanin to ferredoxin. The genes of all subunits except the 17.5 kDa polypeptide in PSI-100 have been identified. These are psaA/psaB (65/63 kDa), psaD (20 kDa), psaE (19.5 kDa), psaF (18.5 kDa), psaH (7.6 kDa), and psaC (5.8 kDa). The 17.5 kDa polypeptide is a new protein and is designated tentatively as the gene product of psaM. N-terminal amino-acid sequencing indicated the presence of two polypeptides in the 7.6 kDa band. One of these is the gene product of psaH and is essential for the activity of the PS I complex, and the other one is as yet unrecognized and largely depleted in the PSI-100 complex. Gene products of psaG, psaI, and psaK, which have been proposed as the components of PS I complex, are not involved in the PSI-100 complex, but are involved in the PS I complex (PSI-200), which contains 120 chlorophyll per reaction center chlorophyll (P700) and light-harvesting chlorophyll a/b protein complexes. Three polypeptides (26,23 and 22.5 kDa) are not involved in the PSI-100 and are assigned as the apo-protein of light-harvesting chlorophyll a/b protein complexes.

RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution

The gene coxII, normally present in the mitochondrion, was functionally transferred to the nucleus during flowering plant evolution. coxII transfer is estimated to have occurred between 60 and 200 million years ago, whereas loss of coxII from the mitochondrion occurred much more recently, being restricted to a single genus of legumes. Most legumes have coxII in both the nucleus and the mitochondrion; however, no evidence is found for simultaneous coxII expression in both compartments. The nuclear coxII sequence more closely resembles edited mitochondrial coxII transcripts than the genes encoding these RNAs. Hence, gene transfer appears to have involved reverse transcription of an edited RNA intermediate. The nuclear gene contains an intron at the junction of the transit peptide sequence and the mature protein-coding sequence; exon shuffling may have played a role in assembling a functional coxII gene in the nucleus.

Identities of four low-molecular-mass subunits of the photosystem I complex from Anabaena variabilis ATCC 29413. Evidence for the presence of the psaI gene product in a cyanobacterial complex

Photosystem I (PSI) complex of Anabaena variabilis ATCC 29413 consists of at least 11 subunits, 9 of which are resolved by high resolution gel electrophoresis. N-terminal amino acid sequences of the four subunits with molecular masses of 6.8, 5.2, 4.8 and 3.5 kDa were determined. Based on the sequence homology, the 3.5 kDa subunit was revealed to correspond to PSI-I (the gene product of psaI), which had so far been detected only in higher plant PSI complexes. The 6.8 kDa protein and 4.8 kDa protein were identified as gene products of psaK and psaJ, respectively. The 5.2 kDa protein was homologous to a 4.8 kDa subunit of PSI of the thermophilic cyanobacterium Synechococcus vulcanus, suggesting that this protein is a component of PSI in cyanobacteria.

Intercistronic group III introns in polycistronic ribosomal protein operons of chloroplasts

A novel ribosomal protein operon in the Euglena gracilis chloroplast genome was characterized. It encodes the genes for ribosomal proteins S4 and S11 (rps4 and rps11). The coding region of the rps11 gene is interrupted by two introns of 107 and 100 bp. The introns belong to a distinct class known as group III introns. The major transcript from this operon was characterized as a fully spliced dicistronic rps4-rps11 mRNA by RNA blot analysis, primer extension sequencing, and cDNA cloning and sequencing. An additional 95 nucleotide (nt) group III intron was identified in the 123 nt rps4-rps11 intercistronic region. The identification of the intercistronic intron between the rps4 and rps11 genes was unexpected. Other RNA transcripts from regions of the genome that could potentially contain intercistronic introns were re-examined and two other intercistronic, group III introns were found. These are located in a large ribosomal protein operon between the genes for the ribosomal proteins L23 and L2, and between L14 and L5. There are at least 50 group III introns in the E. gracilis chloroplast genome. All but 6 are found in genes encoding protein components of the transcriptional and translational apparatus. The distribution of group III introns and the unusual location of intercistronic group III introns may reflect some aspect of gene expression, or provide some insight into the mechanism of their splicing.

Mutation proximal to the tRNA binding region of the Nicotiana plastid 16S rRNA confers resistance to spectinomycin

Nicotiana tabacum lines carrying maternally inherited resistance to spectinomycin were obtained by selection for green callus in cultures bleached by spectinomycin. Two levels of resistance was found. SPC1 and SPC2 seedlings are resistant to high levels (500 micrograms/ml), SPC23 seedlings are resistant to low levels (50 micrograms/ml) of spectinomycin. Lines SPC2 and SPC23 are derivatives of the SR1 streptomycin-resistant plastome mutant. Spectinomycin resistance is due to mutations in the plastid 16S ribosomal RNA: SPC1, an A to C change at position 1138; SPC2, a C to U change at position 1139; SPC23, a G to A change at position 1333. Mutations similar to those in the SPC1 and SPC2 lines have been previously described, and disrupt a conserved 16S ribosomal RNA stem structure. The mutation in the SPC23 line is the first reported case of a mutation close to the region of the 16S rRNA involved in the formation of the initiation complex. The new mutants provide markers for selecting plastid transformants.

Two promoters within the psbK-psbI-trnG gene cluster in tobacco chloroplast DNA

Transcription of the 2.6 kbp psbK-psbI-trnG cluster in tobacco chloroplasts has been studied. This cluster contains, in linear sequence, the genes encoding two low-molecular-mass polypeptides, K and I, of photosystem II (psbK and psbI, respectively), and tRNA(Gly) (UCC) (trnG). Northern blot hybridization revealed that the largest transcript (2.6 kb) hybridizes to psbK, psbI and trnG, but not to the following trnR-UCU. Ten other transcripts ranging from 0.1 to 1.3 kb were also detected. Three of these transcripts overlap the divergent transcript arising from trnS-GCU located on the opposite DNA strand. S1 mapping and primer extension experiments showed that these multiple transcripts comprise eight distinct 5' ends. By in vitro capping assays two of them were determined to be transcriptional initiation sites; one is located 163 bp upstream of psbK and the other is 6 bp upstream of trnG. The 3' ends of transcripts were determined by S1 mapping; one lies between psbI and trnG and the other is at the end of trnG. The presence of dual promoters of trnG is discussed.

RNA-protein interactions at transcript 3' ends and evidence for trnK-psbA cotranscription in mustard chloroplasts

In vitro transcripts from the 3' flanking regions of mustard chloroplast genes were tested for protein binding in a chloroplast extract. Efficient and sequence-specific RNA-protein interaction was detected with transcripts of the genes trnK, rps16 and trnH, but not with the 3' terminal region of trnQ RNA. The transacting component required for specific complex formation is probably a single 54 kDa polypeptide. The protein-binding region of the rps16 3' terminal region was mapped and compared with that of the trnK transcript determined previously. Both regions reveal a conserved 7-mer UUUAUCU followed by a stretch of U residues. Deletion of the trnK 3' U cluster resulted in more than 80% reduction in the binding activity, and after deletion of both the U stretch and the 7-mer motif no binding at all was detectable. RNase protection experiments indicate that the protein-binding regions of both the rps16 and trnK transcripts correlate with the positions of in vivo 3' ends, suggesting an essential role for the 54 kDa binding protein in RNA 3' end formation. In the case of the trnK gene, evidence was obtained for read-through transcripts that extend into the psbA coding region, thus pointing to the possibility of trnK-psbA cotranscription.

An essential gene of Escherichia coli that has sequence similarity to a chloroplast gene of unknown function

The dedB gene of Escherichia coli has sequence similarity to the zfpA gene of the chloroplast chromosome. The functions of dedB and zfpA are unknown. We constructed derivatives of temperature-sensitive polA strains into whose chromosomes a plasmid containing the disrupted dedB gene was integrated by homologous recombination. These strains contained normal and disrupted dedB genes in their chromosomes. We then selected plasmid-segregated strains and found no cells containing the disrupted dedB gene, indicating that disruption of the dedB gene was lethal in polA strains of E. coli.

Characterization and primary structure of proteins L28, L33 and L34 from Bacillus stearothermophilus ribosomes

The complete amino acid sequences of 3 proteins from the 50S subunit of Bacillus stearothermophilus ribosomes were determined by N-terminal sequence analysis and by sequencing of overlapping fragments obtained from enzymatic digestions and chemical cleavages. The proteins BstL28, BstL33 and BstL34, named according to the equivalent proteins in Escherichia coli ribosomes, consist of 60, 49, and 44 amino acid residues and have calculated molecular masses of 6811.0, 5908.6, and 5253.9 Da, respectively. They are highly basic with a content of positively charged residues ranging between 29% for L33 and 45% for L34. The 3 proteins were positioned in the 2-dimensional map of B stearothermophilus 50S ribosomal proteins. The electrophoretic mobilities confirm sizes and net charges deduced from the sequences.

The chloroplast genome of the gymnosperm Pinus contorta: a physical map and a complete collection of overlapping clones

Overlapping restriction fragments of chloroplast DNA from the conifer Pinus contorta were cloned. Out of a total of 49 clones, 33 comprise the minimum set required to represent the entire genome. Using the purified inserts of these clones as probes in filter hybridizations, all sites for the three restriction enzymes KpnI, HpaI and SacI in the P. contorta chloroplast genome were mapped. Heterologous filter hybridizations and sequence analysis of some of the P. contorta clones were used to determine the position of 15 genes on the restriction map. The size of the genome, which lacks an inverted repeat organization, was found to be approximately 121 kilobase pairs (kbp). Unusual features of this genome are a duplication of the psbA gene and the presence of two genes, gidA and frxC, which are not found in angiosperms. The genome appeared essentially colinear with that of Pinus radiata, for which a map has previously been published. Two different restriction fragment length polymorphisms were found to be produced by variable numbers of copies of 124 bp- and 150 bp-long, tandemly repeated elements.

A divergent plastid genome in Conopholis americana, an achlorophyllous parasitic plant

We have used heterologous probes to investigate the degree of sequence conservation in the plastid genome of Conopholis americana, a totally achlorophyllous angiosperm which exists as a root parasite on red oaks. Although Conopholis is completely nonphotosynthetic, it retains a plastid genome in which certain regions, including that which contains the ribosomal RNA genes, are highly conserved. Other regions, including those containing the genes for numerous photosynthesis proteins, are either absent or highly divergent. We also find that the 16S and 23S ribosomal genes of the Conopholis plastid are transcribed and processed, implying a potentially functional genetic apparatus. These results are in agreement with findings reported recently for a related root parasite, Epifagus virginiana (dePamphilis and Palmer, 1990). Furthermore, the plastid genome is maintained in high copy number in fruit tissue, whereas mature seeds have an approximately 10-fold lower copy number.

Nucleotide sequences of the continuous and separated petA, petB and petD chloroplast genes in Chlamydomonas reinhardtii

We have mapped and sequenced the petA (cytf), petB (cytb6) and petD (subunit IV) genes on the chloroplast genome of Chlamydomonas reinhardtii. At variance with the pet genes in higher plant chloroplasts, the petB and petD genes are continuous, not adjacent and not located next to the psbB gene. The corresponding polypeptide sequences are highly conserved when compared with their counterparts from other sources but have a few features specific of algal cytb6/f complexes. In particular the transit sequence of cytf displays unique characteristics when compared with those previously described for cytf in higher plants.

Differential accumulation of plastid transcripts encoding photosystem II components in the mesophyll and bundle-sheath cells of monocotyledonous NADP-malic enzyme-type C4 plants

As a first step in understanding the differential expression of the plastid-encoded photosystem II (PSII) genes in mesophyll and bundle-sheath cells, we have used RNA blotting techniques to investigate the transcript patterns of these genes in three NADP-malic enzymetype C4 species: Zea mays L., Sorghum bicolor (L.) Moench and Pennisetum americanum (L.) Leeke. Our comparison showed that in all three species the relative levels of transcripts encoding PSII proteins were diminished in bundle-sheath cells. No major differences, either in abundance or in the processing pathways, could be detected for transcripts encoding subunits of the PSI and ATP-synthase complexes. The transcript profiles of the psbB and psbD/C transcription units were particularly striking. These operons were of heterogeneous composition, i.e. they encode PSII subunits as well as proteins or RNAs which are involved in different functional entities. The transcript patterns of the psbB and psbD/C transcription units were complex and characterized by multiple, partially overlapping RNAs. Our analysis showed that the relative levels of the oligocistronic PSII transcripts derived from these transcription units with the exception of psbH were selectively reduced in bundlesheath cells. In contrast, RNAs carrying the non-PSII components were present in similar quantities in the two cell types. The data demonstrate that segmental RNAs within one single transcription unit can accumulate to different degrees. Regulatory mechanisms which may explain this expression behaviour are discussed.

Pea chloroplast DNA primase: characterization and role in initiation of replication

A DNA primase activity was isolated from pea chloroplasts and examined for its role in replication. The DNA primase activity was separated from the majority of the chloroplast RNA polymerase activity by linear salt gradient elution from a DEAE-cellulose column, and the two enzyme activities were separately purified through heparin-Sepharose columns. The primase activity was not inhibited by tagetitoxin, a specific inhibitor of chloroplast RNA polymerase, or by polyclonal antibodies prepared against purified pea chloroplast RNA polymerase, while the RNA polymerase activity was inhibited completely by either tagetitoxin or the polyclonal antibodies. The DNA primase activity was capable of priming DNA replication on single-stranded templates including poly(dT), poly(dC), M13mp19, and M13mp19 + 2.1, which contains the AT-rich pea chloroplast origin of replication. The RNA polymerase fraction was incapable of supporting incorporation of 3H-TTP in in vitro replication reactions using any of these single-stranded DNA templates. Glycerol gradient analysis indicated that the pea chloroplast DNA primase (115-120 kDa) separated from the pea chloroplast DNA polymerase (90 kDa), but is much smaller than chloroplast RNA polymerase. Because of these differences in size, template specificity, sensitivity to inhibitors, and elution characteristics, it is clear that the pea chloroplast DNA primase is an distinct enzyme form RNA polymerase. In vitro replication activity using the DNA primase fraction required all four rNTPs for optimum activity. The chloroplast DNA primase was capable of priming DNA replication activity on any single-stranded M13 template, but shows a strong preference for M13mp19 + 2.1. Primers synthesized using M13mp19 + 2.1 are resistant to DNase I, and range in size from 4 to about 60 nucleotides.

Evolutionary relationships among eubacteria, cyanobacteria, and chloroplasts: evidence from the rpoC1 gene of Anabaena sp. strain PCC 7120

RNA polymerases of cyanobacteria contain a novel core subunit, gamma, which is absent from the RNA polymerases of other eubacteria. The genes encoding the three largest subunits of RNA polymerase, including gamma, have been isolated from the cyanobacterium Anabaena sp. strain PCC 7120. The genes are linked in the order rpoB, rpoC1, rpoC2 and encode the beta, gamma, and beta' subunits, respectively. These genes are analogous to the rpoBC operon of Escherichia coli, but the functions of rpoC have been split in Anabaena between two genes, rpoC1 and rpoC2. The DNA sequence of the rpoC1 gene was determined and shows that the gamma subunit corresponds to the amino-terminal half of the E. coli beta' subunit. The gamma protein contains several conserved domains found in the largest subunits of all bacterial and eukaryotic RNA polymerases, including a potential zinc finger motif. The spliced rpoC1 gene from spinach chloroplast DNA was expressed in E. coli and shown to encode a protein immunologically related to Anabaena gamma. The similarities in the RNA polymerase gene products and gene organizations between cyanobacteria and chloroplasts support the cyanobacterial origin of chloroplasts and a divergent evolutionary pathway among eubacteria.

The chloroplast transcription apparatus from mustard (Sinapis alba L.). Evidence for three different transcription factors which resemble bacterial sigma factors

A chloroplast protein fraction with sigma-like activity [Bülow, S. & Link, G. (1988) Plant Mol. Biol. 10, 349-357], was further purified and characterized. Chromatography on heparin-Sepharose, DEAE-Sepharose and Sephacryl S-300 led to the separation of three sigma-like factors (SLF) polypeptides with Mr 67,000 (SLF67), 52,000 (SLF52) and 29,000 (SLF29). None of these polypeptides bind to DNA itself, but each one confers enhanced binding and transcriptional activity when added to Escherichia coli RNA-polymerase core enzyme and DNA fragments carrying a chloroplast promoter. SLF67, SLF52, and SLF29 differ in their ionic-strength requirements for activity. They each mediate the binding to promoters of the chloroplast genes psbA, trnQ, and rps16, with different efficiencies. It is suggested that chloroplast transcription in vivo might be controlled at least in part by these functionally distinct factors.

Analysis of the spc ribosomal protein operon of Thermus aquaticus

The gene region of Thermus aquaticus corresponding to the distal portion of the S10 operon and to the 5'-portion of the Escherichia coli spc operon was cloned, using the E. coli gene for the ribosomal protein L5 as hybridization probe. The gene arrangement was found to be identical to E. coli, i.e. S17, L14, L24, L5, S14, S8 and L6. Stop and start regions of contiguous cistrons overlap, except for the S14-S8 intergenic region, whose size (67 bases) even exceeds the corresponding spacer regions in E. coli and Bacillus subtilis. A G + C content of 94% in third positions of codons was found in the ribosomal protein genes of T. aquaticus analyzed here. The stop codon of gene S17 (the last gene of the S10 operon in E. coli) and the start codon of gene L14 (the first gene of the spc operon in E. coli) overlap in T. aquaticus, thus leaving no space to accommodate an intergenic promoter preceding spc-operon-encoded genes in T. aquaticus. A possible promoter, localized within the S17 coding region, yielded only weak resistance (20 micrograms/ml) to chloramphenicol in E. coli and therefore could be largely excluded as the main promoter for spc-operon-encoded genes. We failed to detect a structure resembling the protein S8 translational repressor site, located at the beginning of the L5 gene in E. coli, in the corresponding region or any other region in the cloned T. aquaticus spc DNA.

Trans splicing in Oenothera mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences

The complete NADH dehydrogenase subunit 1 (nad1) ORF in Oenothera mitochondria is encoded by five exons. These exons are located in three distant locations of the mitochondrial genome. One genomic region encodes exon a, the second encodes exons b and c, and the third specifies exons d and e. Cis-splicing group II introns separate exons b and c and d and e, while trans-splicing reactions are required to link exons a and b and c and d. The two parts of the group II intron sequences involved in these trans-splicing events can be aligned in domain IV. Exon sequences and the maturase-related ORF in intron d/e are edited by numerous C to U alterations in the mRNA. Two RNA editing events in the trans-splicing intron a/b improve conservation of the secondary structure in the stem of domain VI. RNA editing in intron sequences may thus be required for the trans-splicing reaction.

Changes in Chloroplast mRNA Stability during Leaf Development

During spinach leaf development, chloroplast-encoded mRNAs accumulate to different steady-state levels. Their relative transcription rates alone, however, cannot account for the changes in mRNA amount. In this study, we examined the importance of mRNA stability for the regulation of plastid mRNA accumulation using an in vivo system to measure mRNA decay in intact leaves by inhibiting transcription with actinomycin D. Decay of psbA and rbcL mRNAs was assayed in young and mature leaves. The psbA mRNA half-life was increased more than twofold in mature leaves compared with young leaves, whereas rbcL mRNA decayed with a similar relative half-life at both leaf developmental stages. The direct in vivo measurements demonstrated that differential mRNA stability in higher plant plastids can account for differences in mRNA accumulation during leaf development. The role of polysome association in mRNA decay was also investigated. Using organelle-specific translation inhibitors that force mRNAs into a polysome-bound state or deplete mRNAs of ribosomes, we measured mRNA decay in vivo in either state. The results showed that rbcL and psbA mRNAs are less stable when bound to polysomes relative to the polysome-depleted mRNAs and that their stabilities are differentially affected by binding to polysomes. The results suggested that ribosome binding and/or translation of the psbA and rbcL mRNAs may function to modulate the rate of their decay in chloroplasts.

Pea chloroplast genes encoding a 4 kDa polypeptide of photosystem I and a putative enzyme of C1 metabolism

The nucleotide sequence of 3.2 kbp of pea chloroplast DNA located upstream from the petA gene for cytochrome f, and previously reported to contain the gene for a photosystem I polypeptide, has been determined. Three open reading frames of 587, 40 and 157 codons have been identified. Orf40 encodes a highly conserved, hydrophobic, membrane-spanning polypeptide, and is identified as the gene psaI for the 4 kDa subunit of photosystem I. Orf587 is an extended version of the gene zfpA previously identified as encoding a conserved putative zinc-finger protein. The product of orf587 shows extensive homology to an unidentified open reading frame cotranscribed with a gene for folate metabolism in Escherichia coli and local homology to a region of the beta subunit of rat mitochondrial propionyl-CoA carboxylase. It is suggested that the product of orf587 is an enzyme of C1 metabolism and is unlikely to be a regulatory DNA-binding protein. Orf157 potentially encodes an unidentified basic protein, but the protein sequence is not conserved in other plants.

Duplication of the psbA gene in the chloroplast genome of two Pinus species

The psbA gene, encoding the D1 protein of photosystem II, was found to be duplicated in the chloroplast genome of two pine species, Pinus contorta and P. banksiana. Analysis of cloned overlapping restriction fragments of P. contorta chloroplast DNA showed that the two psbA genes have the same orientation and are separated by approximately 3.3 kb. The nucleotide sequences of the coding and the upstream regions of the two psbA copies were found to be identical, whereas the downstream sequences diverged from a point 20 bp 3' of the stop codons. Downstream of the gene copy designated psbAII, a dyad symmetry which allows the formation of a strong mRNA hairpin structure, and a trnH gene were found. No such elements, which are characteristic of psbA downstream regions, were found 3' of psbAI. This suggests that psbAII is the ancestral gene copy in P. contorta. Upon comparison with psbA from other plants, the pine 353-codon sequence appeared almost as distant from the angiosperm as from the liverwort counterpart. As compared to tobacco, 14 substitutions in the predicted amino acid sequence were found, most of which were located in the terminal regions of the protein.

The chloroplast gene for ribosomal protein CL23 is functional in tobacco

Chloroplast rpl23 loci potentially coding for a polypeptide homologous to the E. coli L23 ribosomal protein are frame-shifted in spinach and several other plants, indicating that these loci are pseudogenes. In tobacco, rpl23 constitutes a continuous open reading frame of 93 codons and its transcript initiates at least 66 bp upstream from the initiation codon. The N-terminal amino acid sequence of a 13 kDa protein from the 50 S subunit of tobacco chloroplast ribosomes matches that derived from the tobacco rpl23 locus. This shows that rpl23 is a functional gene in tobacco.

Cloning in M13 phage or how to use biology at its best

A short historical account of the development of the M13mp phage vectors and of the pUC plasmids is presented. Moreover, a complete list of all the M13mp and pUC vectors is compiled.

Cloning, characterization, and physical location of the rplY gene which encodes ribosomal protein L25 in Escherichia coli K12

The rplY gene of Escherichia coli K12 encoding ribosomal protein L25 was cloned from the ordered clone bank and located at coordinate 2,291 kb on the physical map of E. coli. Determination of the nucleotide sequence indicated that the coding region contains 285 nucleotide pairs including a translational initiator and terminator. The amino acid sequence of the protein deduced from the nucleotide sequence matched completely the sequence determined for ribosomal protein L25. The coding region was found to be preceded by a typical promoter-like sequence and was followed by a DNA region capable of forming a secondary structure characteristic of a transcriptional terminator. Thus, the gene was concluded to constitute a transcriptional unit (operon). A preliminary analysis by Northern blot supported this conclusion. The codon usage pattern of the rplY gene is characteristic of the ribosomal protein genes in E. coli.

Expression of a higher plant psbA gene in Synechocystis 6803 yields a functional hybrid photosystem II reaction center complex

The psbA gene codes for the D1 polypeptide of the photosystem II reaction center complex and is found in all photosynthetic organisms that carry out oxygenic photosynthesis. Here we describe the construction and characterization of a strain of the cyanobacterium Synechocystis sp PCC 6803 in which the three endogenous psbA genes are replaced by a single psbA gene from the chloroplast genome of the higher plant Poa annua. The resulting chimeric strain, KWPAS, grows photoautotrophically with a doubling time of 26 hours compared with 20 hours for wild-type Synechocystis 6803. The mutant oxidizes water to oxygen at light-saturated rates comparable with wild type, despite differences in 15% of the primary structure of D1 between these species. RNA gel blot analysis indicates the presence in KWPAS of a psbA transcript of approximately 1.25 kilobases, consistent with the chloroplast promoter also acting as a promoter in Synechocystis. By using antibodies specific for the carboxyl-terminal extension of the D1 polypeptide of higher plants, we showed that the D1 polypeptide synthesized by KWPAS is post-translationally modified at the carboxyl terminus, probably through processing. A detailed biophysical analysis of the chimeric photosystem II complex indicated that the rates of forward electron transfer are similar to wild type. The rates of charge recombination between the donor and acceptor sides of the reaction center are, however, accelerated by as much as a factor of nine (QA- to S2) and are the most likely explanation for the lower rate of photoautotrophic growth in the mutant. We conclude that the psbA gene from a higher plant can be expressed in cyanobacteria and its product processed and assembled into a functional chimeric photosystem II reaction center.

Unusual organization of a ribosomal protein operon in the plastid genome of Cryptomonas phi: evolutionary considerations

The region of the plastid genome containing the genes for ribosomal proteins S12 and S7 and the elongation factor Tu (corresponding to three of the four str operon genes of Escherichia coli) was investigated in the unicellular marine alga Cryptomonas. Sequence analysis shows the gene organization to be rps12-60 bp spacer-rps7-68 bp spacer-tufA. No introns are present in any of the genes. Comparisons of the deduced amino acid sequence of these genes with homologues from other organisms show rps12 to be very highly conserved, except at the amino terminus, and rps7 and tufA to be less well-conserved. Transcript analysis suggests that these genes are co-transcribed along with several up and/or down-stream genes. The evolutionary significance of this unique gene organization is discussed.

A homologue of a nuclear-coded iron-sulfur protein subunit of bovine mitochondrial complex I is encoded in chloroplast genomes

The chloroplast genomes of Marchantia polymorpha, Nicotiana tabacum, and Oryza sativa contain open reading frames (ORFs or potential genes) encoding homologues of some of the subunits of mitochondrial NADH:ubiquinone oxidoreductase (complex I). Seven of these subunits (ND1-ND4, ND4L, ND5, and ND6) are products of the mitochondrial genome, and two others (the 49- and 30-kDa components of the iron-sulfur protein fraction) are nuclear gene products. These findings have been taken to indicate the presence in chloroplasts of an enzyme related to complex I, possibly an NAD(P)H:plastoquinone oxidoreductase, participating in chlororespiration. This view is reinforced by the present work in which we have shown that chloroplast genomes encode a homologue of the 23-kDa subunit, another nuclear-encoded component of bovine complex I. The 23-kDa subunit is in the hydrophobic protein fraction of the enzyme, the residuum after removal of the flavoprotein and iron-sulfur protein fractions. The sequence motif CysXXCysXXCysXXXCysPro, which provides ligands for tetranuclear iron-sulfur centers in ferredoxins, occurs twice in its polypeptide chain and is evidence of two associated 4Fe-4S clusters. This is the only iron-sulfur protein identified so far in the hydrophobic protein fraction of complex I, and so it is possible that one of these centers is that known as N-2, the donor of electrons to ubiquinone. The sequence of the 23-kDa subunit is closely related to potential proteins, which also contain the cysteine-rich sequence motifs, encoded in the frxB ORFs in chloroplast genomes.(ABSTRACT TRUNCATED AT 250 WORDS)

The role of coxI-associated repeated sequences in plant mitochondrial DNA rearrangements and radish cytoplasmic male sterility

The gene coxI, encoding subunit I of mitochondrial cytochrome c oxidase, has been characterized from the normal (fertile) and Ogura (male-sterile) cytoplasms of radish to determine if a previously identified mitochondrial DNA rearrangement, and its associated transcriptional differences, could play a role in Ogura cytoplasmic male sterility (CMS). The normal and Ogura loci are virtually identical for 2.8 kb, including a 527-codon open reading frame whose product is approximately 95% identical to other plant COXI polypeptides. A rearrangement 120 bp 5' to the coding region results in different 5' transcript termini for the two genes. A comparison of several crucifer mitochondrial DNAs indicates that this rearrangement also occurs in the normal radish cytoplasm and is, therefore, not involved in Ogura CMS. Sequences present at the coxI locus belong to at least two different dispersed repeat families, members of which are also associated with other rearranged genes in radish.

Fragments of plastid DNA in the nuclear genome of tomato: prevalence, chromosomal location, and possible mechanism of integration

We have undertaken a systematic search for plastid DNA sequences integrated in the tomato nuclear genome, using heterologous probes taken from intervals of a plastid DNA region spanning 58 kb. A total of two short integrates (202 and 141 nucleotides) were isolated and mapped to chromosomes 9 and 5, respectively. The nucleotide sequence of the integrates and that of the flanking regions were determined. The integration sites contain direct repeat elements similar in position (but not in length or sequence) to the direct repeats previously observed with another plastid integrate in the tomato nuclear genome. Based on these results, a model for the process of movement and integration of plastid sequences into the nuclear genome is discussed.

Differential expression of the psbB and psbH genes encoding the 47 kDa chlorophyll a-protein and the 10 kDa phosphoprotein of photosystem II during chloroplast development in wheat

The nucleotide sequence of a region of wheat chloroplast DNA containing the psbB gene for the 47 kDa chlorophyll a-binding protein of photosystem II has been determined. The gene encodes a polypeptide of 508 amino acid residues which is predicted to contain six hydrophobic membrane-spanning regions. The psbB gene is located 562 bp upstream of the psbH gene for the 10 kDa phosphoprotein of photosystem II. A small open reading frame of 38 codons is located between psbB and psbH, and on the opposite strand the psbN gene, encoding a photosystem II polypeptide of 43 amino acid residues, is located between orf38 and psbH. S1 nuclease mapping indicated that the 5' ends of transcripts were located 371 and 183 bp upstream of the psbB translation initiation codon. Predominant transcripts of 2.1 kb and 1.8 kb for psbB and 0.4 kb for psbH were present in RNA isolated from etiolated and greening wheat seedlings. Immunodecoration of Western blots indicated that the 47 kDa polypeptide was absent, or present in very low amounts, in dark-grown tissue and accumulated on greening, whereas the 10 kDa polypeptide was present in similar amounts in both dark-grown and greening seedlings. The 10 kDa polypeptide was phosphorylated in vitro by incubating wheat etioplast membranes with [gamma 32P] ATP.

A heptapeptide repeat contributes to the unusual length of chloroplast ribosomal protein S18. Nucleotide sequence and map position of the rpl33-rps18 gene cluster in maize

The rpl33-rps18 gene cluster of the maize chloroplast genome has been mapped and sequenced. The derived amino acid sequence of the S18 protein shows a 7-fold repeat of a hydrophilic heptapeptide domain, S K Q P F R K, in the N-terminal region. Such a sequence is absent in the E. coli S18 and in the chloroplast S18 of the lower plant liverwort. In tobacco and rice chloroplast S18 it is present 2 and 6 times, respectively. Thus a long N-terminal repeat (resembling in composition the large C-terminal heptapeptide repeat in the eukaryotic pol II) appears to be characteristic of monocot cereal S18.

The 30-kilodalton subunit of bovine mitochondrial complex I is homologous to a protein coded in chloroplast DNA

In cattle, 7 of the 30 or more subunits of the respiratory enzyme NADH:ubiquinone reductase (complex I) are encoded in mitochondrial DNA, and potential genes (open reading frames, orfs) for related proteins are found in the chloroplast genomes of Marchantia polymorpha and Nicotiana tabacum. Homologues of the nuclear-coded 49- and 23-kDa subunits are also coded in chloroplast DNA, and these orfs are clustered with four of the homologues of the mammalian mitochondrial genes. These findings have been taken to indicate that chloroplasts contain a relative of complex I. The present work provides further support. The 30-kDa subunit of the bovine enzyme is a component of the iron-sulfur protein fraction. Partial protein sequences have been determined, and synthetic oligonucleotide mixtures based on them have been employed as hybridization probes to identify cognate cDNA clones from a bovine library. Their sequences encode the mitochondrial import precursor of the 30-kDa subunit. The mature protein of 228 amino acids contains a segment of 57 amino acids which is closely related to parts of proteins encoded in orfs 169 and 158 in the chloroplast genomes of M. polymorpha and N. tabacum. Moreover, the chloroplast orfs are found near homologues of the mammalian mitochondrial genes for subunit ND3. Therefore, the plant chloroplast genomes have at least two separate clusters of potential genes encoding homologues of subunits of mitochondrial complex I. The bovine 30-kDa subunit has no extensive sequences of hydrophobic amino acids that could be folded into membrane-spanning alpha-helices, and although it contains two cysteine residues, there is no clear evidence in the sequence that it is an iron-sulfur protein.

Repetitive sequence-mediated rearrangements in Chlorella ellipsoidea chloroplast DNA: completion of nucleotide sequence of the large inverted repeat

A 3454 base pair (bp) sequence of the large inverted repeat (IR) of chloroplast DNA (cpDNA) from the unicellular green alga Chlorella ellipsoidea has been determined. The sequence includes: (1) the boundaries between the IR and the large single copy (LSC) and the small single copy (SSC) regions, (2) the gene for psbA and (3) an approximately 1.0 kbp region between psbA and the rRNA genes which contains a variety of short dispersed repeats. The total size of the Chlorella IR was determined to be 15243 bp. The junction between the IR and the small single copy region is located close to the putative promoter of the rRNA operon (906 bp upstream of the -35 sequence on each IR). The junction between the IR and the large single copy region is also just upstream of the putative psbA promoter, 218 bp upstream from the ATG initiation codon. A few sets of unique sequences were found repeatedly around both junctions. Some of the sequences flanking the IR-LSC junction suggest a unidirectional and serial expansion of the IR within the genome. The psbA gene is located close to the LSC-side junction and codes for a protein of 352 amino acid residues. A highly conserved C-terminal Gly is absent Unlike the psbA of Chlamydomonas species, which contains 2-4 large introns, the gene of Chlorella has no introns.(ABSTRACT TRUNCATED AT 250 WORDS)

Large-scale deletions of rice plastid DNA in anther culture

Plastid DNA (ptDNA) in albino rice plants regenerated from pollen by anther culture was investigated by Southern blotting. Of the 20 albino plants investigated, 7 contained ptDNA that had suffered large-scale deletion. The size and location of the deletions differed among the plants. In all cases about 30 kbp of the region containing the PstI-2 fragment (15.7 kbp) had been retained. The deleted ptDNA molecules were retained in calluses derived from the roots of each albino plant.

Complete cloning of the chloroplast genome of safflower in lambda EMBL3 and mapping of 23S and 16S rRNA genes

A recombinant DNA library was constructed from partial BamHI or MboI digests of safflower (Carthamus tinctorius L.) chloroplast DNA, in the BamHI site of lambda EMBL3. Seventeen lambda recombinants, selected by chromosome walking, were found to contain overlapping fragments of the entire chloroplast genome. These clones were mapped using single and double digests of BamHI, EcoRI and HindIII. cDNAs synthesized from isolated 16S and 23S chloroplast rRNAs were used to map the ribosomal RNA genes relative to physical maps of the above restriction enzymes. The mapped positions of the rRNA genes for the safflower chloroplast DNA are in good agreement with previously published data for tobacco, spinach and several other higher plants.

Experience in shotgun sequencing a 134 kilobase pair DNA molecule

Until now, large DNA sequences have been obtained by cloning fragments of the target molecule into plasmid, cosmid or bacteriophage lambda vectors. The 134 kbp DNA sequence of channel catfish virus was determined with relative ease by shotgun cloning of random fragments of genomic DNA directly into a bacteriophage M13 vector, sequencing by dideoxynucleotide chain termination, and compilation of the data using Staden's database handling programs. Experience gained during this endeavour indicates that sequences substantially larger than 134 kbp may be obtained using this approach.

Structural organization and transcription of plant mitochondrial and chloroplast genomes

Experimental evidence is presented showing that the plant mitochondrial and chloroplast genomes are multipartite and, that besides a large circular genomic DNA, they contain subgenomic minicircular and plasmid-like molecules. It is demonstrated that plant mitochondrial and chloroplast DNAs are packaged into deoxynucleoprotein fibrils comprising nucleosome-like and nucleomere-like globules; the fibrils form loops and rosette-like structures with central proteinaceous components. A similar structure is characteristic of the subgenomic DNAs. The basic proteins involved in the formation of nucleosome-like globules are quite different from the nuclear histones, indeed the basic proteins from plant mitochondria and chloroplasts are also distinct. Some of the basic proteins share common antigens with the E. coli HU protein. The genetic code for the mitochondrial and chloroplast genes is universal. The only codon now thought to be different from the universal in the mitochondrial genome is corrected during post-transcriptional mRNA editing. There are two hexanucleotides in the promoters of the chloroplast genes homologous to the sequences in -10 and -35 regions of the prokaryotic genes promoters requisite for transcription. Promoter sequences of the plant mitochondria genes responsible for transcription regulation were not identified. Immunoelectronmicroscopic evidence suggest that mitochondrial and chloroplast RNA polymerases have antigens in common with the beta-subunit of E. coli RNA polymerase. It is shown that the mitochondrial genes are intensely transcribed in the dark and repressed by illumination. Electron microscopy demonstrated that about 70% of plant mitochondria contain numerous RNA polymerase molecules in the dark, but this percentage falls to 10-15% after light exposure.

Chloroplast DNA evolution in potato (Solanum tuberosum L.)

A deletion specific to chloroplast (ct) DNA of potato (Solanum tuberosum ssp. tuberosum) was determined by comparative sequence analysis. The deletion was 241 bp in size, and was not flanked by direct repeats. Five small, open reading frames were found in the corresponding regions of ctDNAs from wild potato (S. tuberosum ssp. andigena) and tomato (Lycopersicon esculentum). Comparison of the sequences of 1.35-kbp HaeIII ctDNA fragments from potato, tomato, and tobacco (Nicotiana tabacum) revealed the following: the locations of the 5' ends of both rubisco large subunit (rbcL) and ATPase beta subunit (atpβ) mRNAs were probably the same as those of spinach (Spinacia oleracea); the promoter regions of the two genes were highly conserved among the four species; and the 5' untranslated regions diverged at high rates. A phylogenetic tree for the three potato cultivars, one tomato cultivar, and one tobacco cultivar has been constructed by the maximum parsimony method from DNA sequence data, demonstrating that the rate of nucleotide substitution in potato ctDNA is much slower than that in tomato ctDNA. This fact might be due to the differences in the method of propagation between the two crops.

Restriction fragment length polymorphism in plants and its implications

In the last decade RFLP analysis has evolved from an idea that seemed promising to a well-established tool that has led to fundamental advances in several fields. Construction of genetic maps has now become feasible in many organisms where it would previously have been impractical. Since genetic maps are of general utility for many sorts of biological research, they cannot fail to have a significant impact in the immediate future. As genetic maps become reconciled with physical maps in several plants, it will become possible to clone virtually any gene. For a plant breeder this will have the effect of broadening the gene pool available for plant improvement to include virtually all organisms, including animals and microorganisms. Much remains to be done, however. We need basic studies of the biochemistry, physiology, and genetics of plants and the insects and pathogens infesting them to be able to identify target genes for cloning. We need basic studies of transformation and gene expression to be able to have introduced genes expressed in transformed plants in the proper amounts and in the desired tissues. It must also be kept in mind that the best of our present technologies only suffice to clone and transform single genes. We will have to make another large jump in capabilities to be able to transfer QTL between plants. Since the most important agronomic traits are controlled by QTL, this effort will have to be undertaken. However, the future looks promising for plant breeding and RFLP analysis. The molecular genetic revolution now has every indication of being transferrable to practical problems such as plant breeding, and the first steps in this transferral have already occurred through the medium of RFLP analysis.

Chromoplast formation during tomato fruit ripening. No evidence for plastid DNA methylation

Ripening of tomato fruits involves differentiation of chloroplasts into non-photosynthetic chromoplasts. Plastid DNAs isolated either from green leaf chloroplasts or mature red fruit chromoplasts were compared by restriction endonuclease and DNA/DNA hybridization analyses. The same restriction and gene maps were obtained for both types of DNAs, illustrating the lack of major recombinational events during chromoplast formation. Several enzymes were used that discriminate the presence of methylated bases in their target sequences (Pst I, Pvu II, Sal I, Mbo I/Sau 3AI, Msp I/Hpa II, Bst NI/Eco RII). Plastid DNA fragments generated by these enzymes were hybridized against DNA probes encompassing about 85% of the tobacco chloroplast genome. These probes represented genes that follow very different expression behaviors in response to plastid development. Extensive restriction and hybridization analyses failed to reveal any difference between the chloroplast and chromoplast genomes, indicating that no developmentally related DNA methylation was detected by these methods. The results presented here do not support the hypothesis that selective DNA methylation of the chromoplast genome might play a major role in the transcriptional control of gene expression in these non-photosynthetic plastids.

Highly purified pea chloroplast RNA polymerase transcribes both rRNA and mRNA genes

Pea chloroplast RNA polymerase has been obtained with about 2000-fold purification using DEAE-cellulose and phosphocellulose chromatography. The purified enzyme contained ten prominent polypeptides of 150, 130, 115, 110, 95, 85, 75, 48, 44 and 39 kDa and four other minor polypeptides of 90, 34, 32 and 27 kDa. Purification of this enzyme using chloroplast 16S rDNA promoter affinity column chromatography also yielded an enzyme with similar polypeptides. Purified polyclonal antibodies against the purified chloroplast RNA polymerase were found to recognize most of the polypeptides of the enzyme in Western blot experiments. Primary mobility shift of the 16S rRNA gene and ribulose-1,5-bisphosphate carboxylase large subunit (rbc-L) gene promoters observed with the chloroplast RNA polymerase was abolished by these antibodies. The specific in vitro transcription of these rRNA and mRNA genes was also inhibited by these antibodies. The transcription of the rRNA and mRNA genes was also abolished by tagetitoxin, a specific inhibitor of chloroplast RNA polymerase. The chloroplast RNA polymerase was found to bind specifically to the chloroplast 16S rRNA gene promoter region as visualized in electron microscopy. The presence of the polypeptides of 130, 110, 75-95 and 48 kDa in the DNA-enzyme complex was confirmed by a novel approach using immunogold labeling with the respective antibodies. The polypeptides of this purified RNA polymerase were found to be localized in chloroplasts by an indirect immunofluorescence.