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

The genes of both subunits of ribulose-1,5-bisphosphate carboxylase constitute an operon on the plastome of a red alga

Plastid (pt) DNA from the red alga Porphyridium aerugineum was purified by CsCl gradient centrifugation. An EcoRI library of the ptDNA was screened with a gene probe specific for the gene encoding the large subunit (LSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco EC 4.1.1.39) from spinach. A 5.8 kb EcoRI clone containing the LSU gene (rbcL) was isolated and the DNA sequence of the Porphyridium rbcL gene and its flanking regions was determined. An open reading frame was found 130 bp downstream from the rbcL gene that shows homology to genes coding for the small subunit of Rubisco (rbcS) from higher plants and cyanobacteria. Both genes (rbcL + rbcS) are cotranscribed. Comparison of rbcL and rbcS sequences from Porphyridium, higher plants and cyanobacteria seems to reveal a remarkable evolutionary distance between the plastids of the red algae (rhodoplasts), chloroplasts and cyanobacteria.

N-terminal sequencing of low-molecular-mass components in cyanobacterial photosystem II core complex. Two components correspond to unidentified open reading frames of plant chloroplast DNA

We recently reported the presence of several low-molecular-mass protein components in the PS II O2-evolving core complex from the thermophilic cyanobacterium, Synechococcus vulcanus [(1989) FEBS Lett. 244, 391-396]. Here we have characterized the three components (4.1, 4.7, 5 kDa) of the same cyanobacterial core complex by N-terminal sequencing. There were two components in the 4.7 kDa region, both having a blocked N-terminus. One has a sequence highly homologous to open reading frame 34 of plant chloroplast DNA (tentatively designated psbM), while the other has a sequence partially homologous to open reading frame 43 of chloroplast DNA (designated psbN), although neither of the two gene products has yet been confirmed in chloroplasts. The cyanobacterial 4.1 kDa protein partially corresponds to the 4.1 kDa nuclear-encoded core component of higher plant PS II. The cyanobacterial 5 kDa component, however, shows a sequence that is unrelated to any other known proteins.

Identification of photosystem I components from the cyanobacterium, Synechococcus vulcanus by N-terminal sequencing

The photosystem I core complex isolated from a thermophilic cyanobacterium, Synechococcus vulcanus, is composed of eight low-molecular-mass proteins of 18, 14, 12, 9.5, 9, 6.5, 5 and 4.1 kDa in addition to the PS I chlorophyll protein. N-terminal amino acid sequences of all these components were determined and compared with those of higher plants. Clearly, the 9.5 kDa component corresponds to the protein which carries the non-heme iron-sulfur centers A and B. This protein is so poorly visualized by staining that it has probably been overlooked in gel electrophoresis analyses. The 18, 14, 12 and 9 kDa components show appreciable homology with respective subunits of higher plant PS I. In contrast, the 6.5, 5 and 4.1 kDa components do not correspond to any known proteins except that the sequence of the 4.1 kDa component matches an unidentified open reading frame (ORF) 42 (liverwort) or ORF44 (tobacco) of chloroplast DNA.

Nucleotide sequences of cDNA clones encoding the entire precursor polypeptide for subunit VI and of the plastome-encoded gene for subunit VII of the photosystem I reaction center from spinach

Recombinant phage which encode the entire precursor polypeptide for subunit VI of the photosystem I reaction center have been selected from a lambda gt11 cDNA expression library made from polyadenylated RNA of spinach seedlings. The sequence predicts a precursor polypeptide of 144 amino acids (Mr = 15.3 kDa), a mature protein of 95 residues (Mr = 10.4 kDa) that lacks methionine, histidine and cysteine, and a transit peptide of 49 residues (Mr = 4.9 kDa). The corresponding gene(s) is (are) designated psaH. The gene for subunit VII, psaC, has been located in the small single-copy region of the spinach plastid chromosome using a synthetic oligonucleotide and a heterologous hybridization probe. It is part of a polycistronic transcription unit that is constitutively expressed and processed. Putative processing products include a monocistronic RNA for psaC. The polypeptide chain of 18 (deduced) amino acids is highly conserved and strikingly resembles bacterial-type ferredoxins. It harbours cysteine residues that appear to be involved in the ligation of the two 4Fe4S centres A and B in photosystem I. None of the two subunits appears to be membrane-spanning, and subunit VI, as subunit VII, is located at the reducing (stromal) side of the reaction center. All available information on the major subunits of photosystem I from spinach has been combined into a (revised) topographic model. Evidence that the innermost - plastome-encoded - core of photosystem I represents an old bacterial heritage in present day chloroplasts is discussed.

The intron of a plastid gene from a green alga contains an open reading frame for a reverse transcriptase-like enzyme

Plastid (pt) and mitochondrial (mt) DNA were isolated from the unicellular green alga KS3/2, which is presumed to be a species of the genera Ankistrodesmus or Monoraphidium. The DNA species are characterized by their different densities (pt, 1.685 g/ml; mt, 1.695 g/ml), individual restriction patterns, and their respective sizes of 130 and 47 kb. Using an intronic sequence from fungal mitochondria as a hybridization probe, intron sequences from mtDNA and from ptDNA were identified. DNA sequencing of the cloned ptDNA intron revealed that the plastid gene for subunit IV of the cytochrome b6/f petD complex is interrupted by a group II intron of unusual length (3533 bp). This was confirmed by transcript analysis. The intron encodes an open reading frame (ORF) which shows significant homology with reverse transcriptase genes from various genetic elements. This discovery is unique for plastomes and indicates that introns, retrotransposons, insertion elements and retroviruses may have a common evolutionary origin.

Mitochondrial DNA of Chlamydomonas reinhardtii: the ND4 gene encoding a subunit of NADH dehydrogenase

The ND4 gene encoding a subunit of respiratory NADH dehydrogenase has been identified on the linear 15.8 kb mitochondrial DNA of Chlamydomonas reinhardtii. The gene maps downstream of ND5. The 1,332 bp nucleotide sequence presented is the first complete reported ND4 sequence from a photoautotrophic organism. The deduced protein of 443 amino acid residues shows 34%, 29% and 27% homology to the protein sequences of Aspergillus amstelodami, Drosophila yakuba and mouse, respectively. ND4 is the fifth and last mitochondrial gene of the NADH dehydrogenase complex on the 15.8 kb mitochondrial genome of C. reinhardtii.

Electrophoretic and immunological comparisons of chloroplast and prokaryotic ribosomal proteins reveal that certain families of large subunit proteins are evolutionarily conserved

Antibodies to individual chloroplast ribosomal (r-)proteins of Chlamydomonas reinhardtii synthesized in either the chloroplast or the cytoplasm were used to examine the relatedness of Chlamydomonas r-proteins to r-proteins from the spinach (Spinacia oleracea) chloroplast, Escherichia coli, and the cyanobacterium Anabaena 7120. In addition, 35S-labeled chloroplast r-proteins from large and small subunits of C. reinhardtii were co-electrophoresed on 2-D gels with unlabeled r-proteins from similar subunits of spinach chloroplasts, E. coli, and Anabaena to compare their size and net charge. Comigrating protein pairs were not always immunologically related, whereas immunologically related r-protein pairs often did not comigrate but differed only slightly in charge and molecular weight. In contrast, when 35S-labeled chloroplast r-proteins from large and small subunits of a closely related species C. smithii were coelectrophoresed with unlabeled C. reinhardtii chloroplast r-proteins, only one pair of proteins from each subunit showed a net displacement in mobility. Analysis of immunoblots of one-dimensional SDS and two-dimensional urea/SDS gels of large and small subunit r-proteins from these species revealed more antigenic conservation among the four species of large subunit r-proteins than small subunit r-proteins. Anabaena r-proteins showed the greatest immunological similarity to C. reinhardtii chloroplast r-proteins. In general, antisera made against chloroplast-synthesized r-proteins in C. reinhardtii showed much higher levels of cross-reactivity with r-proteins from Anabaena, spinach, and E. coli than did antisera to cytoplasmically synthesized r-proteins. All spinach r-proteins that cross-reacted with antisera to chloroplast-synthesized r-proteins of C. reinhardtii are known to be made in the chloroplast (Dorne et al. 1984b). Four E. coli r-proteins encoded by the S10 operon (L2, S3, L16, and L23) were found to be conserved immunologically among the four species. Two of the large subunit r-proteins, L2 and L16, are essential for peptidyltransferase activity. The third (L23) and two other E. coli large subunit r-proteins (L5 and L27) that have immunological equivalents among the four species are functionally related to but not essential for peptidyltransferase activity.

Organization and nucleotide sequence of a transcriptional unit of Methanococcus vannielii comprising genes for protein synthesis elongation factors and ribosomal proteins

By a chromosome walking strategy the DNA region from Methanococcus vannielii flanking the genes for protein synthesis elongation factor (EF) 1 alpha and EF-2 was cloned and sequenced. A gene organization of 5' - beta' - open reading frame (ORF) 1 - ORF2 - S12 - S7 - EF-2 - EF-1 alpha - S10 - ORF3 - ORF4 - 3' was found where beta', S12, S7, S10, EF-2, and EF-1 alpha represent gene products with sequences similar to the beta' subunit of RNA polymerase, ribosomal proteins S12, S7, and S10, and EF-G and EF-Tu from Escherichia coli, respectively. ORF1-4 represent gene products with no known eubacterial counterparts. Northern blot analysis of transcripts and nuclease S1 mapping showed that transcription initiates between beta' and ORF1 and terminates at the 3' side of the S10 gene and that the genes from ORF1 to S10 are cotranscribed. Apart from the presence of two additional ORFs, ORF1 and ORF2, and of the gene for S10, this organization is identical to that of the eubacterial "streptomycin operon." ORF1 displays sequence similarity to rat liver ribosomal protein L30 and may represent one of the "additional" ribosomal proteins of Methanococcus. The sequenced part of the beta' gene and the EF-2 and EF-1 alpha gene products from Methanococcus are more similar to their eukaryotic than to their eubacterial counterparts. It appears, therefore, that the genetic organization of the translational components resembles the situation in eubacteria, whereas their primary structures are more eukaryotic in nature.

Visualization of antibody binding to the photosynthetic membrane: the transmembrane orientation of cytochrome b-559

We have used immuno-gold labeling and electron microscopy to study the topography of thylakoid membrane polypeptides. Thylakoid vesicles formed by passage through a French press were adsorbed onto a plastic film supported by an electron microscope grid and processed for single or double immuno-gold labeling. After shadowing with platinum, the inside-out and right-side-out vesicles were identified by their distinctive morphologies. Right-side-out vesicles were labeled by a monoclonal antibody recognizing an epitope located in the trypsin-cleaved, N-terminal portion of the LHC II apoprotein, and by an antibody to CF1. A monoclonal antibody to the alpha-subunit of cytochrome b-559 reacted with a synthetic tridecapeptide corresponding to the C-terminal portion of the polypeptide. Both this antibody and a polyclonal antibody to the synthetic peptide labeled inside-out vesicles exclusively, indicating that the polypeptide C-terminus was exposed on the lumenal (exoplasmic) surface of the membrane.

Distribution of restriction site polymorphism within the chloroplast genome of the genus Glycine, subgenus Soja

Restriction fragment length polymorphisms (RFLPs) have been used to detect intragenic sequence diversity in Glycine subgenus soja chloroplast DNA. The distribution of these RFLPs allow Glycine max and G. soja accessions to be grouped according to cytoplasmic genetic relatedness. DNA clones from mung bean chloroplast DNA were used to locate the RFLPs to specific regions of the chloroplast genome. In the course of the experiments, several previously unobserved RFLPs were also identified. At least six molecular changes were detected, including both restriction site loss or gain and insertion/deletion events. Three of the fragment polymorphisms detected are due to changes in the juncture region between one inverted repeat region and the large single-copy region. Probes detecting polymorphisms in three representative soybean genotypes were used to screen additional cultivars and Plant Introductions. The distribution of RFLP patterns in these accessions were consistent with the patterns of previously described cytoplasmic groupings, with the exception of one accession, which formed a new plastome group.

The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals

The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp. Predicted genes have been identified along with open reading frames (ORFs) conserved between rice and the previously sequenced chloroplast genomes, a dicot, tobacco (Nicotiana tabacum), and a liverwort (Marchantia polymorpha). The same complement of 30 tRNA and 4 rRNA genes has been conserved between rice and tobacco. Most ORFs extensively conserved between N. tabacum and M. polymorpha are also conserved intact in rice. However, several such ORFs are entirely absent in rice, or present only in severely truncated form. Structural changes are also apparent in the genome relative to tobacco. The inverted repeats, characteristic of chloroplast genome structure, have expanded outward to include several genes present only once per genome in tobacco and liverwort and the large single copy region has undergone a series of inversions which predate the divergence of the cereals. A chimeric tRNA pseudogene overlaps an apparent endpoint of the largest inversion, and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.

An Examination of the Plastid DNA of Hypohaploid Nicotiana plumbaginifolia Plants

DNA was extracted from different morphological types of hypohaploid Nicotiana plumbaginifolia plants. The cellular levels of chloroplast DNA (expressed as percent of total DNA) were found to be approximately two- to threefold higher in two albino hypohaploids than in a green hypohaploid. The level of chloroplast DNA in the green hypohaploid was not significantly different from either in vitro or in vivo grown haploid N. plumbaginifolia plants. Molecular hybridization with DNA probes for the large subunit of ribulose bisphosphate carboxylase from spinach and with Pvull fragments representing the entire Nicotiana tabacum chloroplast genome revealed no gross qualitative differences in the chloroplast DNAs of hypohaploid plants. Based on these observations we have concluded that the lack of chloroplast function observed in the albino forms of hypohaploid N. plumbaginifolia plants is not due to changes in the chloroplast genome.

An unusual region of Paramecium mitochondrial DNA containing chloroplast-like genes

Based on DNA and amino acid comparisons with known genes and their products, a region of the Paramecium aurelia mitochondrial (mt) genome has been found to encode the following gene products: (1) photosystem II protein G (psbG); (2) a large open reading frame (ORF400) which is also found encoded in the chloroplast (cp) DNA of tobacco (as ORF393) and liverwort (as ORF392), and in the kinetoplast maxicircle DNA of Leishmania tarentolae (as ORFs 3 and 4); (3) ribosomal protein L2 (rpl2); (4) ribosomal protein S12 (rps12); (5) ribosomal protein S14 (rps14); and (6) NADH dehydrogenase subunit 2 (ndh2). All of these genes have been found in cp DNA, but the psbG gene has never been identified in a mt genome, and ribosomal protein genes have never been located in an animal or protozoan mitochondrion. The ndh2 gene has been found in both mitochondria and plastids. The Paramecium genes are among the most divergent of those sequenced to date. Two of the genes are encoded on the strand of DNA complementary to that encoding all other known Paramecium mt genes. No gene contains an identifiable intron. The rps12 and psbG genes are probably overlapping. It is not yet known whether these genes are transcribed or have functional gene products. The presence of these genes in the mt genome raises interesting questions concerning their evolutionary origin.

The secY-rpmJ region of the spc ribosomal protein operon in Escherichia coli: structural alterations affecting secY expression

A unique feature of the spc ribosomal protein operon is that its region distal to the promoter contains a gene (secY) for an integral membrane protein, followed by an open reading frame termed X which has recently been proposed to encode a new ribosomal protein (protein B). We now show that the open reading frame X indeed directs the synthesis of a protein with electrophoretic mobilities similar to the B protein, and this supports the proposal that X may be more appropriately called rpmJ. Insertion of a plasmid sequence into the secY-rpmJ boundary of the chromosome caused a reduced expression of secY probably by destabilizing the secY part of the message. The results of complementation experiments suggested that a normal level of expression of rpmJ is not required for growth or protein secretion.

The 18-kD protein that binds to the chloroplast DNA replicative origin is an iron-sulfur protein related to a subunit of NADH dehydrogenase

From a high-salt extract of the purified thylakoid membrane, an 18-kD protein was detected. This protein was translated by the chloroplast ribosomes and could form a stable DNA-protein complex with a cloned chloroplast DNA replicative origin [Nie, Z.Q., Chang, D.Y., and Wu, M. (1987) Mol. Gen. Genet. 209, 265-269]. In this paper, the 18-kD protein is linked to frxB, a chloroplast-encoded, ferredoxin-type, iron-sulfur protein, by N-terminal microsequencing of the purified protein and computer analysis. The identification is further supported empirically by the fact that the electron paramagnetic resonance spectra of the protein indicate the presence of iron-sulfur clusters. A polyclonal antibody raised against a synthetic pentadecameric peptide with amino acid sequence corresponds to the highly conserved region of the frxB protein and reacts strongly and specifically with the 18-kD protein band in protein gel blot analyses. The 18-kD iron-sulfur protein is found to be related to a subunit of the respiratory chain NADH dehydrogenase by its cross-reaction with a polyclonal antibody raised against highly purified NADH-ubiquinone oxidoreductase, a key enzyme of the respiratory chain. These data are consistent with chlororespiration, and, thus, possible implication of chlororespiration in regulating the initiation of chloroplast DNA replication is discussed.

The plastid rpoA gene encoding a protein homologous to the bacterial RNA polymerase alpha subunit is expressed in pea chloroplasts

The gene rpoA, encoding a protein homologous to the alpha subunit of RNA polymerase from Escherichia coli has been located in pea chloroplast DNA downstream of the petD gene for subunit IV of the cytochrome b-f complex. Nucleotide sequence analysis has revealed that rpoA encodes a polypeptide of 334 amino acid residues with a molecular weight of 38916. Northern blot analysis has shown that rpoA is co-transcribed with the gene for ribosomal protein S11. A lacZ-rpoA gene-fusion has been constructed and expressed in E. coli. Antibodies raised against the fusion protein have been employed to demonstrate the synthesis of the rpoA gene product in isolated pea chloroplasts. Western blot analysis using these antibodies and antibodies against the RNA polymerase core enzyme from the cyanobacterium, Anabaena 7120, has revealed the presence of the gene product in a crude RNA polymerase preparation from pea chloroplasts.

A contiguous sequence in spinach nuclear DNA is homologous to three separated sequences in chloroplast DNA

A 3.4-kbp nuclear (n) DNA sequence has greater than 99% sequence homology to three segments of the chloroplast (cp) genes rps2, psbD/C, and psaA respectively. Each of these cpDNA segments is less than 3 kbp in length and appears to be integrated, at least in part, into several (>5) different sites flanked by unique sequences in the nuclear genome. Some of these sites contain longer homologies to the particular genes, while others are only homologous to smaller parts of the cp genes. Both the cpDNA fragments found in the nuclear genome and their flanking nDNA sequences are invested with short repeated A-T rich sequences but, apart from a hexanucleotide sequence and a palindromic sequence identified near each recombination point, there is no obvious structure that can suggest a mechanism of DNA transfer from the chloroplast to the nucleus in spinach.

A novel site for streptomycin resistance in the "530 loop" of chloroplast 16S ribosomal RNA

The chloroplast gene for 16S rRNA was cloned from two maternally inherited streptomycin-resistant mutants ofNicotiana differing in degree of resistance at the whole plant and isolated chloroplast level. A single-nucleotide change in the 16S rRNA gene was detected for each mutant: a C to T transition at nucleotide 860 (Escherichia coli coordinate C912) which is an often mutated site, and a novel transition of C to T at nucleotide 472 (E. coli coordinate C525). The novel mutation is located in the phylogenetically conserved "530 loop".

Chloroplast ribosomal protein L12 is encoded in the nucleus: construction and identification of its cDNA clones and nucleotide sequence including the transit peptide

An architectural feature found in all classes of ribosomes is a thin, 10-nm-long protuberance in the large subunit, generated by multiple copies of r-protein L12. The primary structure of spinach chloroplast r-protein L12 is known [Bartsch, M., Kimura, M., & Subramanian, A. R. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6871-6875], but the location of its gene, whether in the organelle or in the nucleus, has not been determined. Therefore, we synthesized four oligodeoxynucleotides based on the amino acid sequence data and used them to probe a spinach cDNA library we constructed in lambda gt11 vector. cDNA inserts from four of the hybridizing recombinant clones were characterized and sequenced. The data showed that they are reverse transcripts of varying length, all derived from a single poly(A+) RNA species. The longest cDNA molecule is 900 base pairs (bp) long and includes a 5' noncoding sequence followed by two neighboring AUG codons both in the consensus, eukaryotic initiator context, a 56-codon-long transit peptide sequence (starting from the first AUG codon), the amino acid sequence of mature L12 protein, and a 238 bp long 3' downstream noncoding sequence including a polyadenylation signal and the start of the poly(A) tail. The transit peptide sequence has an unusual amino acid composition similar to that of other known chloroplast transit peptides. Northern blot analysis of the poly(A+) RNA isolated from spinach seedlings and probed with the cDNA insert revealed the occurrence of a strong, broad, 950-nucleotide-long band of the corresponding poly(A+)-containing mRNA species.(ABSTRACT TRUNCATED AT 250 WORDS)

Unusual characteristics of Codium fragile chloroplast DNA revealed by physical and gene mapping

A complete physical map of the Codium fragile chloroplast genome was constructed and the locations of a number of chloroplast genes were determined. Several features of this circular genome are unusual. At 89 kb in size, it is the smallest chloroplast genome known. Unlike most chloroplast genomes it lacks any large repeat elements. The 8 kb spacer region between the 16S and 23S rRNA genes is the largest such spacer characterized to date in chloroplast DNA. This spacer region is also unusual in that it contains the rps12 gene or at least a portion thereof. Three regions polymorphic for size are present in the Codium chloroplast genome. The psbA and psbC genes map closely to one of these regions, another region is in the spacer between the 16S and 23S rRNA genes and the third is very close to or possibly within the 16S rRNA gene. The gene order in the Codium genome bears no marked resemblance to either the "consensus" vascular plant order or to that of any green algal or bryophyte genome.

Cotranscription of the S10- and spc-like operons in spinach chloroplasts and identification of three of their gene products

The organisation and expression of the rpl22, rps3, rpl16 and rpl14 genes, which belong to the S10- and spc-like operons of spinach chloroplasts, have been studied. Northern experiments and nuclease S1 mapping show that the two operon-like groups of genes are cotranscribed. It is demonstrated that the intron-containing rpl16 gene is spliced in vivo. Based on amino acid composition and protein sequence data, the products of the rpl22, rpl16 and rpl14 genes are identified respectively as the spinach chloroplast ribosomal proteins CS-L13, CS-L24 and CS-L29. The rpl22 gene product is a 5S rRNA binding protein and therefore is distinguishable from the homologous Escherichia coli L22 ribosomal protein.

The complete amino acid sequence of ribosomal protein S18 from the moderate thermophile Bacillus stearothermophilus

The amino acid sequence of ribosomal protein S18 from Bacillus stearothermophilus has been completely determined by automated sequence analysis of the intact protein as well as of peptides derived from digestion with Staphylococcus aureus protease at pH 4.0 and cleavage with cyanogen bromide. The carboxy-terminal region was verified by both amino acid analyses of chymotryptic peptides and by mass spectrometry from the terminal region. The protein contains 77 amino acid residues and has an Mr of 8838. Comparison of this sequence with the sequences of the S18 proteins from tobacco and liverwort chloroplasts and E. coli shows a relatively high similarity, ranging from 42 to 55% identical residues with the B. stearothermophilus S18 protein. The regions of homology common to all four proteins consist of several positively charged sections spanning the entire length of the protein.

Two small open reading frames are co-transcribed with the pea chloroplast genes for the polypeptides of cytochrome b-559

The genes encoding the 9 kDa and 4 kDa polypeptides of cytochrome b-559 have been located in pea chloroplast DNA by coupled transcription-translation of cloned restriction fragments of chloroplast DNA in a cell-free extract of Escherichia coli and by nucleotide sequence analysis. The genes (psbE and psbF) are located approximately 1.0 kbp downstream of the gene for cytochrome f and are transcribed in the opposite direction, similar to the arrangement in the chloroplast genomes of other higher plants. Nucleotide sequence analysis of this region revealed four open reading frames encoding hydrophobic proteins of 83 (psbE), 39 (psbF), 38 and 40 amino acid residues, which are co-transcribed as a single major RNA of 1.1 kb. The 5' and 3' ends of this RNA have been located by primer extension and S1 nuclease mapping. The 5' end of the RNA is located 140 bp upstream of the initiating ATG codon of psbE and is preceded by typical chloroplast promoter sequences. The 3' end of the RNA is located approximately 515 bp downstream of the TAA stop codon of psbF close to a stable stem-loop structure.

Difference in the location inDasycladaceae of a DNA sequence homologous to theDrosophila per locus

The period (per) locus ofDrosophila melanogaster has a fundamental role on the expression of biological rhythms. A DNA sequence, which is homologous to a short region of theDrosophila per locus, has been found at different locations in various species of Dasycladaceae. InBatophora oerstedii, one of the phylogenetically oldest member of Dasycladaceae, a DNA sequence homologous to theDrosophila per locus was detected only in the chloroplast genome but not in the nuclear genome. In contrast, inAcetabularia cliftonii which in phylogeny branched off Batophora 350 million years ago, like in higher plants, theper locus homologous sequence is located in the nuclear rather than the chloroplast genome. The difference in the location of this sequence in phylogenetically separated species of the ancient unicellular and uninucleate green algae suggests gene translocation between the chloroplast genome and the nuclear genome during evolution.

Genes for the ribosomal proteins S12 and S7 and elongation factors EF-G and EF-Tu of the cyanobacterium, Anacystis nidulans: structural homology between 16S rRNA and S7 mRNA

A 6.5 kb region from the genome of the cyanobacterium, Anacystis nidulans 6301 was cloned using the tobacco chloroplast gene for ribosomal protein S12 as a probe. Sequence analysis revealed the presence of genes for ribosomal proteins S12 and S7 and elongation factors EF-G and EF-Tu in this DNA region. The arrangement is rps12 (124 codons) - 167 bp spacer - rps7 (156 codons) - 77 bp spacer - fus (694 codons) - 26 bp spacer - tufA (409 codons), which is similar to that of the Escherichia coli str operon. The deduced amino acid sequences of the A. nidulans S12 and EF-Tu show high homology (72%-82%) with the E. coli and chloroplast counterparts while those of the A. nidulans S7 and EF-G give low homology (51%-59%). Striking structural homology was found between the potential S7 binding region of 16S rRNA and the beginning of S7 mRNA, suggesting that feedback regulation of rps7 expression operates in A. nidulans.

Characterization of the ndhC-psbG-ORF157/159 operon of maize plastid DNA and of the cyanobacterium Synechocystis sp. PCC6803

The ndhC and ORF159 genes of the maize plastid DNA (ptDNA) were sequenced and maize ORF159 was used to screen a library of genomic DNA of the blue-green alga Synechocystis sp. PCC 6803. The cyanobacterial gene homologous to ORF159 (ORF157) was isolated and sequenced. In sequencing the region upstream of ORF157, reading frames with homology to the ndhC and psbG genes of maize ptDNA were identified. The ndhC and psbG genes overlap in the ptDNAs of maize, tobacco and Marchantia polymorpha, but are separated by a noncoding spacer in Synechocystis. Northern blot analysis showed that the ndhC, psbG and ORF157/159 genes are cotranscribed in maize and Synechocystis. The three genes occur in the same order in ptDNA of maize, tobacco, and M. polymorpha as in Synechocystis 6803. The amino acid sequences of the NDH-C, PSII-G and the ORF157/159 proteins deduced from the maize genes are 65%, 52% and 53% homologous to those of Synechocystis. However, the cyanobacterial and higher plant NDH-C protein sequences are only 23% homologous to the mitochondrial NDH-3 protein. Protein products of in vitro transcription/translation of the Synechocystis transcription unit had apparent molecular masses of 6 kDa (NDH-C), 25 kDa (PSII-G) and 22 kDa (ORF157) on lithium dodecyl sulfate (LDS) polyacrylamide gel electrophoresis. If these are components of an NADH dehydrogenase, cyanobacteria appear to resemble mitochondria more than they do Escherichia coli and Rhodopseudomonas capsulata with regard to this enzyme complex.

A new member of the CAB gene family: structure, expression and chromosomal location of Cab-8, the tomato gene encoding the Type III chlorophyll a/b-binding polypeptide of photosystem I

We have previously reported the isolation and characterization of tomato nuclear genes encoding two types of chlorophyll a/b-binding (CAB) polypeptides localized in photosystem (PS) I and two types of CAB polypeptides localized in PSII. Sequence comparisons shows that all these genes are related to each other and thus belong to a single gene family. Here we report the isolation and characterization of an additional member of the tomato CAB gene family, the single tomato nuclear gene, designated Cab-8, which encodes a third type of CAB polypeptide localized in PSI. The protein encoded by Cab-8 is 65% and 60% divergent from the PSI Type I and Type II CAB polypeptides, respectively. The latter two are 65% divergent from each other. Only some short regions of the polypeptides are strongly conserved. The Cab-8 locus maps to chromosome 10, 9 map units from Cab-7, the gene encoding the Type II PSI CAB polypeptide. The Cab-8 gene contains two introns; the first intron matches in position the single intron in the Type II PSII CAB genes and the second intron matches in position the second intron in the Type II PSI CAB gene. Like other CAB genes, Cab-8 is light-regulated and is highly expressed in the leaf and to a lesser extent in other green organs.

Low-molecular-mass proteins in cyanobacterial photosystem II: identification of psbH and psbK gene products by N-terminal sequencing

The O2-evolving photosystem II core complex was isolated from a thermophilic cyanobacterium, Synechococcus vulcanus Copeland. Analysis by SDS-polyacrylamide gel electrophoresis revealed that the complex contained at least seven low-molecular-mass proteins in addition to the well characterized CP47 apoprotein, CP43 apoprotein, 33 kDa extrinsic protein, D1 protein, D2 protein and large subunit of cytochrome b-559. The separation of these low-molecular-mass proteins were very similar between cyanobacterial and higher plant PS II. N-terminal sequences of the 6.5 kDa and 3.9 kDa proteins of cyanobacterial core complex were determined after blotting to a polyvinylidene difluoride membrane. The sequence of the 6.5 kDa protein showed high homology with an internal sequence of plant psbH gene product, so-called 10 kDa phosphoprotein, but did not conserve the Thr residue which is specifically phosphorylated in plants. The sequence of the 3.9 kDa protein corresponded to the K protein of higher plants (mature form of psbK gene product). These results indicate that the products of both psbH and psbK genes are present in cyanobacterial PS II as well as being associated with the O2-evolving core complex.

The components of the plastid ribosome are not accumulated synchronously during the early development of spinach plants

The expression of components of the 70S plastid ribosome has been determined during the first 13 days of spinach plant development. Total cellular RNA and proteins were used to determine the relative steady-state levels of mRNA for ribosomal proteins (r-proteins) by dot blot hybridization and the relative amounts of proteins by immunodetection with specific antibodies. The 16S rRNA as well as mRNAs for 9 out of 11 proteins studied, including those for the 32 kDa polypeptide of photosystem II and the large subunit (LSU) of ribulose-1,5-bisphosphate carboxylase (Rubisco) show a marked increase at the beginning of the germination (day 5). At this time the plastid DNA content increases from 4% to 6% of total DNA content and so the plastome copy number can only in part account for the important increase in mRNA steady-state levels. Interestingly the transcripts of the rpl23 and rps19 genes show a different accumulation pattern, indicating either a differential gene transcription and/or an increased stability of the transcripts. In the western blot analysis a group of r-proteins can be detected in dry seeds or after 24 hours of imbibition while a second group of proteins accumulates after 3 to 5 days of development. The differential accumulation pattern of r-proteins and mRNA for r-proteins indicates that post-transcriptional control plays an important role in plastid r-protein synthesis.

A photosystem II polypeptide is encoded by an open reading frame co-transcribed with genes for cytochrome b-559 in wheat chloroplast DNA

The N-terminal amino acid sequence of a 3.2 kDa photosystem II polypeptide is shown to be identical to that of a polypeptide encoded by an open reading frame of 38 codons (orf38) in wheat chloroplast DNA. Orf38 is located just downstream of the psbE and psbF genes for the polypeptides of cytochrome b-559. Analysis of the transcription of this region of chloroplast DNA shows that psbE, psbF and orf38 are co-transcribed to give a 1.1 kb polycistronic transcript which also contains another open reading frame of 40 codons. The orf38 and orf40 products are hydrophobic polypeptides which are both predicted to span the thylakoid membrane once. Orf38 and orf40 are highly conserved, and map to similar locations adjacent to psbE and psbF, in all organisms from which this region of DNA has been sequenced. We propose that orf38 is named psbL.

psbA genes indicate common ancestry of prochlorophytes and chloroplasts

It has long been suspected that chloroplasts evolved after an endosymbiotic event involving a photosynthetic prokaryote, presumably a cyanobacterium, and a eukaryotic organism. Recent studies have provided strong evidence about the cyanobacterial nature of chloroplasts. Since the discovery of prochlorophytes, oxygen-evolving photosynthetic prokaryotes containing chlorophyll a and chlorophyll b and lacking phycobiliproteins, there has been speculation that these represent evolutionary intermediates between cyanobacteria and chloroplasts. Prochloron sp., the first described prochlorophyte, proved difficult to work with because it is an obligate symbiont of marine ascidians. Prochlorothrix hollandica, a recently isolated, freshwater filamentous prochlorophyte, is easily maintained in the laboratory. Overall pigment composition and thylakoid membrane structure of P. hollandica suggest it has intermediate characteristics between cyanobacteria and the chloroplasts of higher plants. The P. hollandica psbA genes, which encode the photosystem II thylakoid protein D1, were cloned and sequenced and the sequences compared to those reported for cyanobacteria, a green alga, a liverwort, and several higher plants. The two psbA genes present in P. hollandica encode an identical amino-acid sequence. As in all chloroplast psbA genes, there is a seven amino-acid gap near the C terminus of the derived protein relative to the protein predicted by cyanobacterial genes, suggesting that P. hollandica is part of the lineage that led to chloroplasts after a divergence from cyanobacteria. This hypothesis is also supported by phylogenetic analysis of derived D1 amino-acid sequences from psbA genes of thirteen taxa on the basis of parsimony.

Isolation and characterization of DNA-binding proteins from the cyanobacterium Synechococcus sp. PCC 7002 (Agmenellum quadruplicatum) and from spinach chloroplasts

Basic, low-molecular-weight DNA-binding proteins were isolated from the unicellular cyanobacterium Synechococcus sp. PCC 7002 (Agmenellum quadruplicatum) and from the chloroplasts of spinach (Spinacia oleacera). In Synechococcus, two major proteins which bind to double-strand DNA (10 and 16 kDa, respectively) were purified. The 10 kDa protein, named HAq, resembles strongly, in amino-acid composition, eubacterial HU-type proteins. The 16 kDa protein is slightly basic. Its characteristics are compared to those of E. coli protein H1 and 17K. In spinach chloroplasts, a major protein HC (10 kDa), which also binds to ds-DNA, was purified. As observed for known archaebacterial and mitochondrial DNA-binding proteins, its amino-acid composition differs significantly from those of eubacterial HU. The comparison of the amino-terminal sequence (27 residues) with other chloroplast peptidic sequences is discussed.

N-terminal sequencing of photosystem II low-molecular-mass proteins. 5 and 4.1 kDa components of the O2-evolving core complex from higher plants

High resolution gel electrophoresis in the low-molecular-mass region combined with electroblotting using polyvinylidene difluoride membranes enabled us to sequence the low-molecular-mass proteins of photosystem II membrane fragments from spinach and wheat. The determined N-terminal sequences, all showing considerable homology between the two plants, involved two newly determined sequences for the 4.1 kDa protein and one for the 5 kDa proteins. The sequence of the 4.1 kDa protein did not match any part of the chloroplast DNA sequence from tobacco or liverwort, suggesting that it is encoded by the nuclear genome. In contrast, the sequence of the 5 kDa protein matched ORF38, which is located just downstream of psbE and psbF in the chloroplast DNA and is assumed to be co-transcribed with them. These two components were associated with the O2-evolving core complex. Sequences of other low-molecular-mass proteins confirmed the previous identification as photosystem II components.

Structure and expression of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein gene rps16 reveals unusual transcriptional features and complex RNA maturation

The mustard chloroplast gene rps16 is split by an 887 bp group II (or III) intron. Three RNA 5' ends upstream of the rps16 coding region define both the transcription start site and two RNA processing sites. The DNA region preceding the start site contains a procaryotic-type "-10" promoter element, but not a typical "-35" element. One single RNA 3' end has been detected downstream from the rps16 coding region, but it is not in close proximity to any inverted repeat that might serve as a termination signal. Northern analysis has revealed several rps16 transcripts ranging in size from 1.6 kb to 0.5 kb. During seedling development, transcript levels show an initial increase and then remain constant without much difference between seedlings grown under light or in the dark.

Studies on Chlamydomonas chloroplast transformation: foreign DNA can be stably maintained in the chromosome

As shown originally by Boynton and co-workers (Boynton, J.E., Gillham, N.W., Harris, E.H., Hosler, J.P., Johnson, A.M., Jones, A.R., Randolph-Anderson, B.L., Robertson, D., Klein, T.M., Shark, K.B., and Sanford, J.C. [1988]. Science 240, 1534-1538), a nonphotosynthetic, acetate-requiring mutant strain of Chlamydomonas reinhardtii with a 2.5-kilobase pair deletion in the chloroplast Bam 10 restriction fragment region that removes the 3' half of the atpB gene and a portion of one inverted repeat can be transformed to photosynthetic competency following bombardment with microprojectiles coated with wild-type Bam 10 DNA. We have found that assorted other circular plasmids, single-strand DNA circles, or linear, duplex DNA molecules containing the wild-type atpB gene can also complement the same mutant. DNA gel blot hybridization analysis of all such transformants indicates that the complementing DNA has integrated into the chromosome at the atpB locus and suggests that a copy-correction mechanism operating between the inverted repeats maintains sequence identity in this region. Sequences from the intact inverted repeat may be recruited to restore the incomplete copy when exogenous DNA with only a portion of the deleted sequence is introduced. Furthermore, a foreign, unselected-for, chimeric gene flanked by chloroplast DNA sequences can be integrated and maintained stably in the chloroplast chromosome. The bacterial neomycin phosphotransferase structural gene fused to the maize chloroplast promoter for the large subunit gene of ribulose-1,5-biphosphate carboxylase (rbcL) has been integrated into the inverted repeat region of the Bam10 restriction fragment. RNA transcripts that hybridize to the introduced foreign gene have been identified.

Chloroplast and nuclear genomes of Chlamydomonas reinhardtii share homology with Escherichia coli genes for DNA replication, repair and transcription

Most of the cpDNA genes studied to date are genes encoding elements of the photosynthetic apparatus and translational machinery. Much less is known about genes encoding the polypeptides involved in transcription, cpDNA replication, recombination and repair. The similarities between bacterial and some cpDNA genes were exploited to identify some of these chloroplast genes using bacterial probes. Probes derived from the Escherichia coli genes dnaA, recA, uvrC, transcriptional factor rho, and rpoC were used to search for homologous DNA sequences in chloroplast and nuclear genomes of Chlamydomonas reinhardtii. Regions homologous to all of these genes were located on the cpDNA physical map by probing restriction fragments of cpDNA with plasmid fragments containing these genes. Probing nuclear DNA with bacterial gene probes revealed DNA fragments homologous to dnaA and rpoC genes.