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

Characterization of a chloroplast mutation in the psaA2 gene of Chlamydomonas reinhardtii

The synthesis of polypeptides related to the CPI chlorophyll-protein complex of photosystem I has been studied by pulse-labeling experiments in twenty chloroplast mutants of Chlamydomonas reinhardtii. Three mutations of the same locus (Girard-Bascou 1987) result in the absence of these CPI-related polypeptides. Among these mutations one, (FUD26) leads to the synthesis of a new polypeptide presumed to be a truncated CPI apoprotein. The molecular characterization of this mutation in the psaA2 gene has been achieved by DNA sequencing the 3' end of this gene. The FUD26 mutation is a 4 base pair deletion resulting in frameshift and premature termination of the protein.

Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7

Analysis of the nucleotide sequence of the genetic locus for yeast mitochondrial RNA polymerase (RPO41) reveals a continuous open reading frame with the coding potential for a polypeptide of 1351 amino acids, a size consistent with the electrophoretic mobility of this enzymatic activity. The transcription product from this gene spans the singular reading frame. In vivo transcript abundance reflects codon usage and growth under stringent conditions for mitochondrial biogenesis and function results in a several fold higher level of gene expression than growth under glucose repression. A comparison of the yeast mitochondrial RNA polymerase amino acid sequence to those of E. coli RNA polymerase subunits failed to demonstrate any regions of homology. Interestingly, the mitochondrial enzyme is highly homologous to the DNA-directed RNA polymerases of bacteriophages T3 and T7, especially in regions most highly conserved between the T3 and T7 enzymes themselves.

Rapid splicing and stepwise processing of a transcript from the psbB operon in tobacco chloroplasts: determination of the intron sites in petB and petD

Expression of the psbB gene cluster in tobacco chloroplasts has been studied. This cluster contains the genes for the 51 kDa chlorophyll a apoprotein (psbB) and the 10 kDa phosphoprotein (psbH) of the photosystem II, and cytochrome b6 (petB) and subunit IV (petD) of the cytochrome b/f complex in this order. Northern blot hybridization and reverse transcription analyses have revealed that petB and petD contain single introns and the psbB gene cluster is transcribed as a single polycistronic unit. The primary transcript seems to be spliced very rapidly and then processed into several small RNA species. The exact splice sites have been located by cDNA sequencing. The transcriptional initiation site of the psbB operon has been determined by S1 mapping with in vitro capped chloroplast RNA. The stepwise processing of chloroplast RNA precursors is discussed.

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

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

Physical map and gene localization on sunflower (Helianthus annuus) chloroplast DNA: evidence for an inversion of a 23.5-kbp segment in the large single copy region

As a first step in the study of chloroplast genome variability in the genus Helianthus, a physical restriction map of sunflower (Helianthus annuus) chloroplast DNA (cpDNA) has been constructed using restriction endonucleases BamH I, Hind III, Pst I, Pvu II and Sac. I. Sunflower circular DNA contains an inverted repeat structure with the two copies (23 kbp each) separated by a large (86 kbp) and a small (20 kbp) single copy region. Its total length is therefore about 152 kbp. Sunflower cpDNA is essentially colinear with that of tobacco with the exception of an inversion of a 23.5-kbp segment in the large single copy region. Gene localization on the sunflower cpDNA and comparison of the gene map with that from tobacco chloroplasts have revealed that the endpoints of the inversion are located between the trnT and trnE genes on the one hand, and between the trnG and trnS genes on the other hand.Analysis of BamH I restriction fragment patterns of H. annuus, H. occidentalis ssp. plantagineus, H. grossesseratus, H. decapetalus, H. giganteus, H. maximiliani and H. tuberosus cpDNAs suggests that structural variations are present in the genus Helianthus.

Functional in vivo verification in E. coli of promoter activities from the rDNA/tDNA(Val)(GAC) leader region of Zea mays chloroplasts

Restriction fragments containing upstream sequences of the rRNA operon from Zea mays chloroplasts were tested for promoter activity in vivo by insertion into an E. coli promoter-probe vector. The expression of this vector's reporter gene, which codes for alkaline phosphatase, was stimulated more than 1,500-fold upon linkage with the chloroplast rRNA promoter. Site specific mutagenesis of the invariant T of the -10 sequence of this promoter reduced the expression of the reporter gene to 2% of the wild type. This indicates that the chloroplast rRNA promoter, which directs transcriptional initiation 117 bp upstream of the 16S rRNA gene, is also active in the bacterial system. A restriction fragment further upstream containing the gene for tRNA(Val) (GAC) also showed strong promoter activity (29% as compared with the rRNA promoter). This promoter activity probably reflects the chloroplast promoter directing the synthesis of the tRNA(Val) (GAC) primary transcript. Surprisingly, this restriction fragment also displayed promoter activity (13% compared with the rRNA promoter) in reverse orientation.

Molecular cloning of a pea H1 histone cDNA

A pea (Pisum sativum, var. Little Marvel) H1 histone cDNA has been isolated from a lambda gt11 expression vector library. This cDNA has been sequenced and shown to represent the entire protein-coding region of the mRNA. The deduced protein sequence is 265 amino acids long (28018 Da) and contains 70 lysines and 3 arginines. The structure of the encoded protein is comparable to animal lysine-rich histones. The central region, which has an amino acid composition similar to that found in the globular domains of animal lysine-rich histones, is flanked by an amino-terminal region rich in lysine, glutamic acid and proline and by a carboxyl-terminal region rich in lysine, alanine, valine and proline. Despite the structural similarities, the protein has little sequence homology with animal lysine-rich histones. This H1 protein is unusual because 12 of the first 40 amino acids are glutamic acid.

Characterization of the TrnD, TrnK, PsaA locus of Euglena gracilis chloroplast DNA

The EcoRI fragment Eco J' of Euglena gracilis chloroplast DNA has previously been identified as a tRNA coding locus. The nucleotide sequence of a 2.3-kb region of the Eco J' fragment known to contain the tRNA genes has been determined. This locus was found to contain two tRNA genes, trnD-GTC and trnK-TTT. Separated from the trnK locus by a 43-bp spacer is an open reading frame of 398 codons. The open reading frame is 73-75% homologous to the amino-terminal coding regions of the spinach and maize genes for the P700 chlorophyll a apoprotein of photosystem I. It has been identified as exon I of an intron-containing psaA gene. The exon is followed by an intron of at least 214 bp that has features characteristic of other Euglena chloroplast introns. Major chloroplast RNA transcripts of sizes 5.5, 4.7, and 2.3 kb hybridize to a psaA-specific probe. The gene for a second photosystem I P700 apoprotein, psaB, has been located on an adjacent EcoRI fragment, Eco C.

Homology in the region containing a tRNA(Trp) gene and a (complete or partial) tRNA(Pro) gene in wheat mitochondrial and chloroplast genomes

We have used bean mitochondrial (mt) and chloroplast (cp) tRNA(Trp) as probes to locate the corresponding genes on the mt and cp genomes of wheat and we have determined the nucleotide sequences of the wheat mt and cp tRNA(Trp) genes and of the flanking regions. Sequence comparisons show that the wheat mt and cp tRNA(Trp) genes are 97% homologous. On the wheat cp DNA, a tRNA(UGGPro) gene was found 139 bp upstream of the cp tRNA(Trp) gene. On the wheat mt DNA, a sequence of 23 nucleotides completely homologous with the 3' end of this cp tRNA(Pro) gene was found 136 bp upstream of the mt tRNA(Trp) gene, but there is only 38% homology between cp and mt wheat genomes in the intergenic regions. The overall organization of this region in the chloroplast genome (a tRNA(Trp) gene separated by about 140 bp from a tRNA(Pro) gene) is also found in the mitochondrial genome, suggesting that this mitochondrial fragment might have originated from a chloroplast DNA insertion. A comparison of the genes and of the intergenic regions located between the tRNA(Trp) gene and the tRNA(Pro) (or partial tRNA(Pro)) gene shows that there is an almost complete conservation of these sequences in the mitochondrial DNA of wheat and maize, whereas wheat mt and cp intergenic regions show more sequence divergence. Wheat mt tRNA(Trp) gene is encoded by the main mt genome (accounted for by the master chromosome) but, in the case of maize mitochondria, this gene was found to be encoded by the 2.3 kb linear plasmid, indicating that this plasmid is not dispensable in maize mitochondria.

Synthesis and Assembly of the Polypeptides of Photosystem I and II in Isolated Etiochloroplasts of Wheat

Synthesis and assembly of photosystems (PS) I and II polypeptides in etiochloroplasts isolated from greening wheat (Triticum aestivum L. cv Norin 61) seedlings were studied. The isolated etiochloroplasts synthesized PSI polypeptides of 66 and 15 kilodaltons, PSII polypeptides of 46 and 42 kilodaltons, and atrazine-binding 34 to 32 kilodalton polypeptide. Their assembly processes in the thylakoid membrane were studied by pulse-chase labeling with [(35)S]methionine, mild solubilization of the thylakoid membrane with Triton X-100, sucrose density gradient centrifugation, and polyacrylamide gel electrophoresis. The newly synthesized polypeptides of 66, 46, 42, 34, and 32 kilodaltons were first integrated into the complexes of 7.5, 5.9, 7.5, 6.3, and 7.5 Svedberg units, respectively, in 20 minutes. After the chase with excess amount of methionine for 100 min, they were found in complexes of 9.5, 9.1, 9.1, 9.1, and 9.1 Svedberg units, respectively. In this condition, stained polypeptides of PSI and PSII were found in the complexes of 11.1 and 10.3 Svedberg units, respectively. These results indicated that newly synthesized PSI or PSII polypeptides are integrated into intermediate complexes, but not complete complexes in the isolated etiochloroplasts. The relationship between the processing of the atrazine-binding 32 kilodalton polypeptide and its assembly into the PSII complex is also discussed.

Control of plastid gene expression during development: the limited role of transcriptional regulation

We have analyzed the transcriptional regulation of plastid genes during chloroplast development in illuminated spinach cotyledons and during leaf formation. The RNAs encoded by plastid genes accumulate with different kinetics during the developmental transitions. Using a novel plastid run-on transcription assay we demonstrate that the transcriptional regulation of a large, diverse group of chloroplast genes is of relatively minor importance for the control of their expression. The general transcriptional activity of the plastid genome increases after illumination and decreases during leaf development. This modulation of general transcriptional activity affects most plastid genes simultaneously and is not correlated with adjustments of the plastid DNA copy number. There are no major changes in the relative transcriptional activities of different genes, although their steady-state mRNA levels change dramatically. The analysis of ten specific plastid genes shows that their relative transcriptional activities are largely maintained throughout the developmental program. This limited transcriptional regulation suggests that plastid gene expression in higher plants is effectively controlled at the posttranscriptional level.

The maize plastid psbB-psbF-petB-petD gene cluster: spliced and unspliced petB and petD RNAs encode alternative products

The chloroplast psbB, psbF, petB, and petD genes are cotranscribed and give rise to many overlapping RNAs. The mechanism and significance of this mode of expression are of interest, particularly because the accumulation of the psb and pet gene products respond differently to both light and, in C4 species such as maize, developmental signals. We present an analysis of the maize psbB, psbF, petB, and petD genes and intergenic regions. The genes are organized similarly in maize (a C4 species) and in several C3 species. Functional class II-like introns interrupt the 5' ends of petB and petD. Both spliced and unspliced RNAs accumulate; these encode alternative forms of the petB and petD proteins, differing at their N-termini. Promoter-like elements between psbF and petB, and biased codon usage suggest that the differential regulation of the psb and pet genes might be achieved at both the transcriptional and translational levels.

Localization, sequence and expression of the gene coding for tRNA(Pro) (UGG) in plant mitochondria

The four Sal I fragments of wheat mitochondrial DNA containing the 18S and 5S ribosomal RNA genes were screened for the presence of tRNA genes. Upon sequencing, a tRNA(Pro) (UGG) gene was found in two of these four fragments. The localization of the corresponding gene on the maize mitochondrial genome was established. Transcriptional studies have shown that this gene is transcribed in wheat and maize mitochondria. The sequence of the corresponding tRNA(Pro) (UGG) of bean mitochondria was determined using in vitro post-labeling techniques.

Localization of a r-protein gene within the chloroplast DNA replication origin of Chlamydomonas

In our previous study of chloroplast (Cp) DNA replication in Chlamydomonas reinhardtii, one D-loop site with its flanking regions was cloned and sequenced. The D-loop site mapped by electron microscopy (EM) overlaps with an open reading frame (ORF) potentially coding for a polypeptide of 136 amino acids. In this report, the corresponding D-loop isolated from another species of Chlamydomonas was sequenced. An ORF was also detected. Sequence comparison indicated that most conserved sequences between these two cloned origins are located within the ORF. Amino acid sequences of these two ORFs are highly conserved. The corresponding sequence for this ORF in the tobacco Cp genome was located by a Southern blotting analysis. Since the complete sequence data of Cp DNAs from a liverwort and from tobacco have been determined in 2 Japanese laboratories recently, it has been possible for us to show that this ORF encodes a protein homologous to the Cp ribosomal protein (r-protein) L16, by sequence comparison.

Evidence for in vivo trans splicing of pre-mRNAs in tobacco chloroplasts

The rps12 gene codes for chloroplast ribosomal protein S12. In the tobacco chloroplast genome (156 kbp circular DNA), exons II and III of this gene are separated by an intron of 536 bases and are present in two copies in the inverted repeat region, while exon I is located in the large single copy region at a distance of 90 kb and 126 kb from the two copies of exons II and III. These three exons were artificially combined in cloned DNA fragments and hybridized with tobacco chloroplast RNA. Electron microscopic analysis of RNA-DNA hybrids showed that exon I is transcribed as part of a polycistronic RNA containing upstream and downstream sequences; the same is true for exons II and III. Exon I is shown to be transcribed separately from exons II and III. In the most abundant class of the hybridized RNA molecules, exon I was covalently linked to exon II. In these molecules the sequences downstream of exon I and upstream of exon II are not present. These data indicate that maturation of rps12 pre-mRNAs in chloroplasts of tobacco involves trans splicing.

Sequence studies on the soybean chloroplast 16S-23S rDNA spacer region : Comparison with other angiosperm sequences and proposal of a generalized RNA secondary structure model for the intergenic regions

The sequence of the ribosomal spacer region of soybean chloroplast DNA including the 3' end of the 16S rRNA gene, the tRNA(Ala) and tRNA(Ile) genes (but not their introns), the three intergenic regions and the 5' end of the 23S rRNA gene, has been determined. This sequence has been compared to corresponding regions of other angiosperm chloroplast DNAs. Secondary structure models are proposed for the entirety of the intergenic regions a, b and c and for the flanking rRNA regions. A model for a common secondary structure of the ribosomal spacer intergenic regions from chloroplasts of higher plants is proposed, which is supported by comparative evidence.

State 1/State 2 changes in higher plants and algae

Current ideas regarding the molecular basis of State 1/State 2 transitions in higher plants and green algae are mainly centered around the view that excitation energy distribution is controlled by phosphorylation of the light-harvesting complex of photosystem II (LHC-II). The evidence supporting this view is examined and the relationship of the transitions occurring in these systems to the corresponding transitions seen in red and blue-green algae is explored.

Plant molecular developmental genetics

Although a wide range of mutations in the nuclear genome also affect chloroplast biogenesis, their pleiotropic nature often limits their use in studying nuclear genes that regulate or facilitate chloroplast development. However, many mutations that cause a high-chlorophyll-fluorescent (hcf) phenotype exhibit limited pleiotrophy, causing the loss of functionally related sets of chloroplast polypeptides. Several hcf mutations are described that result in the loss of one specific protein complex from the thylakoid membrane. Chloroplast and cytosolic mRNAs coding for component polypeptides of the missing complex are unaffected in the mutants, suggesting that each mutation disrupts some process in the synthesis and assembly of the missing complex. Another hcf mutation causes both the loss of three protein complexes and grossly abnormal thylakoid membrane structures. The primary effect of this mutation might be in the assembly of thylakoid membranes or in the stable accumulation of the three protein complexes. Two other hcf mutations are more pleiotropic. Hcf*-38 causes a quantitative reduction of many chloroplast proteins and a reduction of some chloroplast RNAs, including several splicing intermediates. Hcf*-7 causes a major reduction of all chloroplast-encoded proteins examined. The range of pleiotropic effects of hcf mutations indicates that the mutations identify nuclear genes whose products are involved in a number of different steps in chloroplast development. Because some of the mutations described have been generated by transposon insertions, they can be cloned using the transposon to identify the mutant allele.

The gene for the 9 kd polypeptide, a possible apoprotein for the iron-sulfur centers A and B of the photosystem I complex, in tobacco chloroplast DNA

The gene for the 9 kd polypeptide (a possible apoprotein for the iron-sulfur centers A and B) of photosystem I has been located in the small single-copy region of tobacco chloroplast DNA. This gene (psaC) was identified by comparing the N-terminal amino acid sequence of the spinach 9 kd polypeptide with the entire sequence of tobacco chloroplast genome. The gene organization is ndhE (101 codons)--263 bp spacer--psaC (81 codons)--94 bp spacer--ndhD (509 codons). Northern blot hybridization revealed that psaC is transcribed in the chloroplasts. The deduced amino acid sequence and secondary structure are presented. The predicted polypeptide is rich in cysteine residues and contains a unique repeated sequence.

Primary structure of the reaction center from Rhodopseudomonas sphaeroides

The reaction center is a pigment-protein complex that mediates the initial photochemical steps of photosynthesis. The amino-terminal sequences of the L, M, and H subunits and the nucleotide and derived amino acid sequences of the L and M structural genes from Rhodopseudomonas sphaeroides have previously been determined. We report here the sequence of the H subunit, completing the primary structure determination of the reaction center from R. sphaeroides. The nucleotide sequence of the gene encoding the H subunit was determined by the dideoxy method after subcloning fragments into single-stranded M13 phage vectors. This information was used to derive the amino acid sequence of the corresponding polypeptide. The termini of the primary structure of the H subunit were established by means of the amino and carboxy terminal sequences of the polypeptide. The data showed that the H subunit is composed of 260 residues, corresponding to a molecular weight of 28,003. A molecular weight of 100,858 for the reaction center was calculated from the primary structures of the subunits and the cofactors. Examination of the genes encoding the reaction center shows that the codon usage is strongly biased towards codons ending in G and C. Hydropathy analysis of the H subunit sequence reveals one stretch of hydrophobic residues near the amino terminus; the L and M subunits contain five such stretches. From a comparison of the sequences of homologous proteins found in bacterial reaction centers and photosystem II of plants, an evolutionary tree was constructed. The analysis of evolutionary relationships showed that the L and M subunits of reaction centers and the D1 and D2 proteins of photosystem II are descended from a common ancestor, and that the rate of change in these proteins was much higher in the first billion years after the divergence of the reaction center and photosystem II than in the subsequent billion years represented by the divergence of the species containing these proteins.

Structures of tobacco chloroplast genes for tRNA(Ile) (CAU), tRNA (Leu) (CAA), tRNA (Cys) (GCA), tRNA (Ser) (UGA) and tRNA (Thr) (GGU): a compilation of tRNA genes from tobacco chloroplasts

The location and nucleotide sequences of tobacco chloroplast genes for tRNA(Ile) (CAU), tRNA(Leu) (CAA), tRNA(Cys) (GCA), tRNA(Ser) (UGA) and tRNA(Thr) (GGU) (trnI-CAU, trnL-CAA, trnC-GCA, trnS-UGA and trnT-GGU, respectively) have been determined. The trnI and trnL are located in the inverted repeat region. The trnC, trnS and trnT are present in the large single copy region. These five tRNA genes together with the 25 different tRNA genes previously published have been compiled and compared. These 30 tRNA genes corresponding to 20 amino acids are most likely to be all of the tRNA genes encoded in tobacco chloroplast genome.

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

The complete nucleotide sequence (155 844 bp) of tobacco (Nicotiana tabacum var. Bright Yellow 4) chloroplast DNA has been determined. It contains two copies of an identical 25 339 bp inverted repeat, which are separated by a 86 684 bp and a 18 482 bp single-copy region. The genes for 4 different rRNAs, 30 different tRNAs, 39 different proteins and 11 other predicted protein coding genes have been located. Among them, 15 genes contain introns. Blot hybridization revealed that all rRNA and tRNA genes and 27 protein genes so far analysed are transcribed in the chloroplast and that primary transcripts of the split genes hitherto examined are spliced. Five sequences coding for proteins homologous to components of the respiratory-chain NADH dehydrogenase from human mitochondria have been found. The 30 tRNAs predicted from their genes are sufficient to read all codons if the ;two out of three' and ;U:N wobble' mechanisms operate in the chloroplast. Two sequences which autonomously replicate in yeast have also been mapped. The sequence and expression analyses indicate both prokaryotic and eukaryotic features of the chloroplast genes.