Nucleotide sequence of the gene for the P680 chlorophyll alpha apoprotein of the photosystem II reaction center from spinach

Characterization of a cyanobacterial iron stress-induced gene similar to psbC

Recently we have reported that the flavodoxin gene from the cyanobacterium Anacystis nidulans R2 is transcribed as part of an iron stress-induced operon containing multiple mRNA species (D. E. Laudenbach, M. E. Reith, and N. A. Straus, J. Bacteriol. 170: 258-265, 1988). Here we report that nucleotide sequence analyses of DNA located immediately upstream of the flavodoxin gene revealed an open reading frame of 1,026 bases (designated isiA; iron stress inducible) with a deduced amino acid sequence showing similarity to that of the psbC polypeptide of higher plants and cyanobacteria. Assuming proteolytic cleavage of the initial methionine residue, the open reading frame encodes a 341-amino-acid polypeptide with a molecular mass of 36,824 daltons. Amino acid sequence comparisons with known psbC polypeptides from spinach and A. nidulans R2 showed extensive similarity, especially in the proposed membrane-spanning regions. Mung bean nuclease mapping and primer extension experiments have localized a transcriptional start site to a position 19 bases upstream from the first methionine codon of the isiA gene product. The upstream region contains an Escherichia coli-like -10 sequence but lacks the typical -35 consensus sequence. Approximately 15, 25, and 150 bases upstream from the isiA transcription start site are 17 base sequences which resemble the operator sequences of iron-regulated genes of E. coli.

Nicotiana chloroplast genes for components of the photosynthetic apparatus

In order to understand more fully chloroplast genetic systems, we have determined the complete nucleotide sequence (155, 844 bp) of tobacco (Nicotiana tabacum var. Bright Yellow 4) chloroplast DNA. It contains two copies of an identical 25,339 bp inverted repeat, which are separated by 86, 684 bp and 18,482 bp single-copy regions. The genes for 4 different rRNAs, 30 different tRNAs, 44 different proteins and 9 other predicted protein-coding genes have been located. Fifteen different genes contain introns.Twenty-two genes for components of the photosynthetic apparatus have so far been identified. Most of the genes (except the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase) code for thylakoid membrane proteins. Twenty of them are located in the large single-copy region and one gene for a 9-kd polypeptide of photosystem I is located in the small single-copy region. The gene for the 32-kd protein of photosystem II as well as the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase have strong promoters and are transcribed monocistronically while the other genes are transcribed polycistronically. We have found that the predicted amino acid sequences of six DNA sequences resemble those of components of the respiratory-chain NADH dehydrogenase from human mitochondria. As these six sequences are highly transcribed in tobacco chloroplasts, they are probably genes for components of a chloroplast NADH dehydrogenase. These observations suggest the existence of a respiratory-chain in the chloroplast of higher plants.

Structure and organization of Marchantia polymorpha chloroplast genome. III. Gene organization of the large single copy region from rbcL to trnI(CAU)

The nucleotide sequence (25,320 base-pairs) of a part of the large single-copy region of chloroplast DNA from the liverwort Marchantia polymorpha was determined. This region encodes putative genes for four tRNAs, isoleucine tRNA(CAU), arginine tRNA(CCG), proline tRNA(UGG) and tryptophan tRNA(CCA); eight photosynthetic polypeptides, the large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL), 51,000 Mr photosystem II chlorophyll alpha apoprotein (psbB), apocytochrome b-559 polypeptides (psbE and psbF), 10,000 Mr phosphoprotein (psbH), cytochrome f preprotein (petA), cytochrome b6 polypeptide (petB), and cytochrome b6/f complex subunit 4 polypeptide (petD); 13 ribosomal proteins (L2, L14, L16, L20, L22, L23, L33, S3, S8, S11, S12, S18 and S19); initiation factor 1 (infA); ribosome-associating polypeptide (secX); and alpha subunit of RNA polymerase (rpoA). Functionally related genes were located in several clusters in this region of the genome. There were two ribosomal protein gene clusters: rpl23-rpl2-rps19-rpl22-rps3-rpl16-+ ++rpl14-rps8-infA-secX-rps11-rpoA, with a gene arrangement similar to that of the Escherichia coli S10-spc-alpha operons, and the rps12'-rpl20-rps18-rpl33 cluster. There were gene clusters encoding photosynthesis components such as the psbB-psbH-petB-petD and the psbE-psbF clusters. Thirteen open reading frames, ranging in length from 31 to 434 amino acid residues, remain to be identified.

Protein composition of the photosystem II core complex in genetically engineered mutants of the cyanobacterium Synechocystis sp. PCC 6803

The presence of four photosystem II proteins, CP47, CP43, D1 and D2, was monitored in mutants of Synechocystis sp. PCC 6803 that have modified or inactivated genes for CP47, CP43, or D2. It was observed that: (1) thylakoids from mutants without a functional gene encoding CP47 are also depleted in D1 and D2; (2) inactivation of the gene for CP43 leads to decreased but significant levels of CP47, D1 and D2; (3) deletion of part of both genes encoding D2, together with deletion of part of the CP43-encoding gene causes a complete loss of CP47 and D1; (4) thylakoids from a site-directed mutant in which the His-214 residue of D2 has been replaced by asparagine do not contain detectable photosystem II core proteins. However, in another site-directed mutant, in which His-197 has been replaced by tyrosine, some CP47 as well as breakdown products of CP43, but no D1 and D2, can be detected. These data could indicate a central function of CP47 and D2 in stable assembly of the photosystem II complex. CP43, however, is somewhat less critical for formation of the core complex, although CP43 is required for a physiologically functional photosystem II unit. A possible model for the assembly of the photosystem II core complex is proposed.

Protein composition of the photosystem II core complex in genetically engineered mutants of the cyanobacterium Synechocystis sp. PCC 6803

The presence of four photosystem II proteins, CP47, CP43, D1 and D2, was monitored in mutants of Synechocystis sp. PCC 6803 that have modified or inactivated genes for CP47, CP43, or D2. It was observed that: (1) thylakoids from mutants without a functional gene encoding CP47 are also depleted in D1 and D2; (2) inactivation of the gene for CP43 leads to decreased but significant levels of CP47, D1 and D2; (3) deletion of part of both genes encoding D2, together with deletion of part of the CP43-encoding gene causes a complete loss of CP47 and D1; (4) thylakoids from a site-directed mutant in which the His-214 residue of D2 has been replaced by asparagine do not contain detectable photosystem II core proteins. However, in another site-directed mutant, in which His-197 has been replaced by tyrosine, some CP47 as well as breakdown products of CP43, but no D1 and D2, can be detected. These data could indicate a central function of CP47 and D2 in stable assembly of the photosystem II complex. CP43, however, is somewhat less critical for formation of the core complex, although CP43 is required for a physiologically functional photosystem II unit. A possible model for the assembly of the photosystem II core complex is proposed.

Nucleotide sequence of psbC, the gene encoding the CP-43 chlorophyll a-binding protein of Photosystem II, in the cyanobacterium Synechocystis 6803

The nucleotide sequence for the Photosystem II gene psbC has been determined for the cyanobacterium Synechocystis 6803. The gene overlaps the last 50 bases of the psbD gene, and both genes are transcribed in the same direction, but read in different frames. This arrangement is identical to that found in all chloroplast genomes for which psbC has been sequenced. The Synechocystis nucleotide sequence is 70% homologous to the tobacco gene and the predicted amino acid sequence shows 85% homology. A possible alternative translation start site for psbC has been conserved between seven plant sequences and the cyanobacterial sequence. The hydropathy plot for the cyanobacterial protein is very similar to plots determined for six plant species. Pairs of histidines that may play a role in binding chlorophyll are conserved between the cyanobacterial and plant amino acid sequences.

Identification of functional open reading frames in chloroplast genomes

We have used a rapid computer dot-matrix comparison method to identify all DNA regions which have been evolutionarily conserved between the completely sequenced chloroplast genomes of tobacco and a liverwort. Analysis of these regions reveals 74 homologous open reading frames (ORFs) which have been conserved as to length and amino acid sequence; these ORFs also have an excess of nucleotide substitutions at silent sites of codons. Since the nonfunctional parts of these genomes have become saturated with mutations and show no sequence similarity whatsoever, the homologous ORFs are almost certainly functional. A further four pairs of ORFs show homology limited to only a short part of their putative gene products. Amino acid sequence identities range between 50 and 99%; some chloroplast proteins are seen to be among the most slowly evolving of all known proteins. A search of the nucleotide and amino acid sequence databanks has revealed several previously unidentified genes in chloroplast sequences from other species, but no new homologies to prokaryotic genes.

Maize chloroplast genes ndhD, ndhE, and psaC. Sequences, transcripts and transcript pools

We present the nucleotide sequence and derived amino-acid sequence of three genes located in the small single copy region of the maize plastid chromosome. Two genes have some homology to respiratory NADH dehydrogenase subunits. They have been observed in Marchantia and tobacco and are designated ndhD and ndhE. The maize genes code for polypeptides of 58 and 11.3 kilodaltons respectively. The gene psaC is found upstream of ndhD; it encodes an 8.7-kilodalton iron-sulfur protein of PSI. The genes ndhD and psaC are cotranscribed in maize, and give rise to an RNA of 2.1 kilobases. The pool of RNAs from this transcription unit increases about three-fold within the first 10 hours of illumination of dark-grown maize seedlings. On the other hand, ndhE is transcribed independently.

Differential Expression in Bundle Sheath and Mesophyll Cells of Maize of Genes for Photosystem II Components Encoded by the Plastid Genome

We have explored the cell-specific expression of plastid genes encoding five photosystem II proteins (PSII-A, -B, -C, -D and cytochrome (Cyt) b-559 encoded by plastid genes psbA, B, C, D and E plus F, respectively) and one encoding the photosystem I protein PSI-A1 in bundle sheath and mesophyll cells (BSC and MC) at different stages of photoregulated development in leaves of dark-grown maize seedlings. Two types of cell-specific mRNA ccumulation patterns have been discerned. First is the PSII-A type: the mRNA is present in small but about equal amounts in both cell types in etiolated leaves; then, upon illumination, the level of mRNA increases progressively and remains high in MC but not BSC of green leaves. Second is the Cyt b-559 type: MC of etiolated leaves have about twice as much of this mRNA as do BSC; about a twofold to threefold transient increase is induced by light in MC but not in BSC. The genes for the PSII-C and -D proteins are complementary to a sizable family of transcripts over a large range of sizes; the patterns of changes in pools of some of these transcripts are of the PSII-A type and others are of the Cyt b-559 type. The DNA region encoding the PSII-B protein also hybridizes to multiple transcripts; among them is a prominent 2.2 kilobase transcript that follows the Cyt b-559 accumulation pattern. In contrast, the pattern of PSI-A1 mRNA accumulation is the same in both cell types. Accumulation of the PSII-B and -D proteins is light-dependent and coordinate. Both are much more abundant in MC than in BSC. PSII-A is detectable in MC of etiolated leaves and increases during photoregulated chloroplast maturation in both cell types, however, to a much greater extent in MC. We conclude that the expression of each of these plastidencoded photosystem II genes in BSC and MC is photoregulated differently; both transcript abundance and translation are regulated.

Gene organization and newly identified groups of genes of the chloroplast genome from a liverwort, Marchantia polymorpha

The complete nucleotide sequence of chloroplast DNA from a liverwort, Marchantia polymorpha has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. Other genes involved in photosynthesis, respiratory electron transport, and membrane-associated transport in chloroplasts were predicted by the amino acid sequence homology and secondary structure of gene products. Thirty-three open reading frames in the liverwort chloroplast genome remain unidentified. However, most of these open reading frames are also conserved in the chloroplast genomes of two species, a liverwort, Marchantia polymorpha, and tobacco, Nicotiana tabacum, indicating their active functions in chloroplasts.

Physical map and protein gene map of cyanelle DNA from the second known isolate of Cyanophora paradoxa (Kies-strain)

A restriction map of the cyanelle DNA from a different isolate of Cyanophora paradoxa (Kies-strain) was established. The positions of 18 protein genes and the rRNA genes have been located and compared to the positions of these genes from the first isolate of C. paradoxa (Pringsheim-strain). The gene arrangement is absolutely conserved in both cyanelle DNAs. The differences in size (ca. 9 kb) and the unrelatedness in the restriction patterns could be explained by numerous small insertions into intergenic regions of the cyanelle chromosomes.

Complex RNA maturation in chloroplasts. The psbB operon from spinach

The psbB operon of the spinach plastid chromosome encodes the genes for the 51-kDa chlorophyll a apoprotein (psbB), the 10-kDa phosphoprotein (psbH), both associated with photosystem II, as well as cytochrome b6 (petB) and subunit IV (petD) of the cytochrome b/f complex in the order given. These genes are not expressed coordinately. The RNA pattern of this DNA region is complex and resolves into eighteen major RNA species. Using northern and S1 protection analysis we demonstrate (a) that all RNA species derive from one DNA strand and hybridize in an overlapping fashion; and (b) that they arise by processing rather than by multiple transcription initiation/termination. (c) The operon is bordered by a single prokaryote-like promotor in front of psbB, and by a putative factor-independent terminator with characteristic sequence elements following petD. The terminator appears to function bidirectionally. (d) At least four distinct modification activities operate on the putative primary transcript of 5650 nucleotides and on the processing intermediates, including a novel endonucleolytic activity cleaving within a characteristic hexanucleotide motif, 3'-exonucleolytic activity at discrete RNA ends, 5' shortage of mRNA (psbB), and excision of class II intervening sequences (petB and petD). (e) Kinetically, maturation of the primary transcript is largely a stochastic process. (f) Processing results ultimately in the formation of monocistronic mRNAs for each of the two photosystem II polypeptides and a bicistronic mRNA encoding both subunits of the cytochrome b/f complex. We postulate that these RNA species represent the translationally active components in the non-coordinate dark/light expression of these genes. (g) Light is without any noticeable effect on posttranscriptional modification. Under our conditions it appears to operate at a translational rather than a transcriptional or posttranscriptional level indicating that the biogenesis of thylakoid membranes is regulated at various levels.

The chlorophyll-protein complexes of higher plant photosynthetic membranes or Just what green band is that?

Higher plant thylakoid membranes can be fractionated into a bewildering array of macrocomplexes, chlorophyll-protein complexes and chlorophyll-proteins with various deteregents and separations techniques. The chemical nature of each of these entities depends on the particular methods used to obtain them. This review summarizes the current status of the biochemical identification and characterization of individual chlorophyll-proteins and chlorophyll-protein complexes, and attempts to clarify the relationships among them.

Primary structure of barley genes encoding quinone and chlorophyll a binding proteins of photosystem II

The psbA, psbD and psbC genes encoding the quinone binding D-1 and D-2 apoproteins and the 44 kD chlorophyll a-apoprotein 3 have been located in the chloroplast genome of barley. They are found on a 23 kbp SalI restriction endonuclease fragment in the large single copy region of the chloroplast DNA adjacent to the inverted repeat. As in other species the psbD and psbC genes have reading frames which overlap by 53 bp. They are transcribed in the same direction but translated with a frameshift of one nucleotide. Ten amino acid substitutions are found among the 18 N-terminal residues of the D-2 polypeptide if barley, spinach, tobacco, pea and the liverwort Marchantia are compared. Only 8 substitutions are present among the 335 other residues of the D-2 polypeptide. The amino acid residues located in the putative binding site for the special pair reaction center chlorophyll and the residues probably serving as ligands to non-heme iron in the D-1 and D-2 proteins of barley are strictly conserved when compared to those of purple bacteria and of other higher plants. Identity is also observed for the residues of importance in the binding of quinones.

Endosymbiotic origin and codon bias of the nuclear gene for chloroplast glyceraldehyde-3-phosphate dehydrogenase from maize

The nuclei of plant cells harbor genes for two types of glyceraldehyde-3-phosphate dehydrogenases (GAPDH) displaying a sequence divergence corresponding to the prokaryote/eukaryote separation. This strongly supports the endosymbiotic theory of chloroplast evolution and in particular the gene transfer hypothesis suggesting that the gene for the chloroplast enzyme, initially located in the genome of the endosymbiotic chloroplast progenitor, was transferred during the course of evolution into the nuclear genome of the endosymbiotic host. Codon usage in the gene for chloroplast GAPDH of maize is radically different from that employed by present-day chloroplasts and from that of the cytosolic (glycolytic) enzyme from the same cell. This reveals the presence of subcellular selective pressures which appear to be involved in the optimization of gene expression in the economically important graminaceous monocots.

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.

A model for the mechanism of chloride activation of oxygen evolution in photosystem II

A hypothesis is proposed to explain the function of Cl(-) in activating the oxygenevolving complex (OEC) of photosystem II (PS II), based on the results of recent (35)Cl-NMR studies. The putative mechanism involves Cl(-) binding to two types of sites. An intrinsic site is suggested to be composed of three histidyl residues (His 332 and His 337 from D1 and His 337 D2). It is proposed that Cl(-) binding to this site accelerates the abstraction of H(+) from water by raising the pKa's of the histidine imidazole groups. Cl(-) binding also stimulates the transfer of H(+) from this intrinsic site to a set of extrinsic sites on the 33 kD extrinsic polypeptide. The extrinsic Cl(-) binding sites are suggested to involve four protein domains that are linked together by salt-bridge contacts. Chloride and H(+) donated from the intrinsic site attack these intramolecular salt-bridges in a defined sequence, thereby exposing previously inaccessible Cl(-) and H(+) binding sites and stimulating the oxidation of water. This hypothesis also proposes a possible structure for the Mn active site within the D1/D2 complex. Specific amino-acid residues that are likely to participate as Mn lignads are identified on the lumenal portions of the D1 and D2 proteins that are different from those in the L and M subunits of photosynthetic bacteria; the choice of these residues is based on the metal coordination chemistry of these residues, their location within the polypeptide chain, the regularity of their spacing, and their conservation through evolution. The catalytic Mn-binding residues are suggested to be D-61, E-65, E-92, E-98, D-103; D-308, E-329, E-342 and E-333 in D1, and H-62, E-70, H-88, E-97, D-101; E-313, D-334, E-338 and E-345 in D2. Finally, this hypothesis identifies sites on both D2 and the 33 kD extrinsic polypeptide that might be involved in high- and low-affinity Ca(2+) binding.

Use of a monoclonal antibody in structural investigations of the 49-kDa polypeptide of photosystem II

A monoclonal antibody, FAC2, was isolated by immunization of mice with a Photosystem II core preparation followed by splenic fusion and standard monoclonal antibody screening and production techniques. This antibody recognizes the 49-kDa polypeptide of Photosystem II which is the apoprotein of CPal. The antigenic determinant recognized by this antibody lies on a cyanogen bromide fragment which appears as a doublet with an apparent molecular mass of 14.5 kDa. FAC2 was used to follow the effects of trypsin on the 49-kDa polypeptide in a membrane environment. Our results indicate that the extrinsic polypeptides of Photosystem II which are known to be involved in oxygen evolution protect the 49-kDa polypeptide from tryptic attack. Additionally, Photosystem II membranes which are treated with alkaline Tris exhibit a large increase in the ability to bind FAC2. This increase is not observed with membranes treated with calcium chloride or sodium chloride. These results indicate that the 49-kDa polypeptide may be at least structurally associated with the component(s) responsible for oxygen evolution.

Sequencing and modification of psbB, the gene encoding the CP-47 protein of Photosystem II, in the cyanobacterium Synechocystis 6803

The Photosystem II protein CP-47 has been hypothesized to be involved in binding the reaction center chlorophyll. The psbB gene, encoding this protein, was cloned from the genome of the cyanobacterium Synechocystis 6803, and sequenced. The DNA sequence is 68% homologous with that of the psbB gene from spinach, whereas the predicted amino acid sequence is 76% homologous. The hydropathy patterns of Synechocystis and spinach CP-47 are almost indistinguishable, indicating the same general CP-47 folding pattern in the thylakoid membrane in the two species. There are five pairs of histidine residues in CP-47 that are spaced by 13 or 14 amino acids and that are located in hydrophobic regions of the protein; these histidine residues may be involved in chlorophyll binding. Interruption of the psbB gene by a DNA fragment carrying a gene conferring kanamycin resistance results in a loss of Photosystem II activity. This indicates that an intact CP-47 is required for a functional Photosystem II complex, but does not necessarily indicate that this protein would house the reaction center.

The amino terminal region delimited by Met1 and Met 37 is an integral part of the 32 kDa herbicide binding protein

The 33.5 kDa precursor of the 32 kDa herbicide binding protein is encoded in the chloroplast by the psbA gene. Previous work on the gene and protein did not pinpoint the initiation site of translation in vivo. To resolve this issue, constructs containing full length, truncated or mutated psbA from Solanum nigrum were used as templates for in vitro transcription in an SP6-promoter directed system. The resulting RNAs were then translated in a reticulocyte lysate system. The SDS-PAGE and partial proteolysis patterns of the translation products demonstrate that constructs containing the first ATG codon (Met1) of the psbA open reading frame code for a full length precursor protein (33.5 kDa), irrespective of whether the second ATG codon (Met37) is replaced by site directed mutagenesis or not. However, a 5' deleted gene, lacking the codon for Met1 but containing the codon for Met37, codes for a truncated 29 kDa protein. It is concluded that the 33.5 kDa precursor protein and its 32 kDa maturation product initiate at Met1 of the psbA open reading frame.

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.

Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences

Protein coding sequences carry an additional message in the form of a universal three-base periodical pattern (G-non-G-N)n, which is expressed as a strong preference for guanines in the first positions of the codons in mRNA and lack of guanines in the second positions. This periodicity appears immediately after the initiation codon and is maintained along the mRNA as far as the termination triplet, where it disappears abruptly. Known cases of ribosome slippage during translation (leaky frameshifts, out-of-frame gene fusion) are analyzed. At the sites of the slippage the G-periodical pattern is found to be interrupted. It reappears downstream from the slippage sites, in a new frame that corresponds to the new translation frame. This suggests that the (G-non-G-N)n pattern in the mRNA may be responsible for monitoring the correct reading frame during translation. Several sites with complementary C-periodical structure are found in the Escherichia coli 16 S rRNA sequence. Only three of them are exposed to various interactions at the surface of the small ribosomal subunit: (517)gcCagCagCegC, (1395)caCacCgcC and (1531)auCacCucC. A model of a frame-monitoring mechanism is suggested based on the weak complementarity of G-periodical mRNA to the C-periodical sites in the ribosomal RNA. The model is strongly supported by the fact that the hypothetical frame-monitoring sites in the 16 S rRNA that are derived from the nucleotide sequence analysis are also the only sites known to be actually involved or implicated in rRNA-mRNA interactions.

The organization and sequence of the genes for ATP synthase subunits in the cyanobacterium Synechococcus 6301. Support for an endosymbiotic origin of chloroplasts

The nucleotide sequence has been determined of two regions of DNA cloned from the cyanobacterium Synechococcus 6301. The larger, 8890 base-pairs in length, contains a cluster of seven genes for subunits of ATP synthase. The order of the genes is a:c:b':b:delta:alpha:gamma, b' being a duplicated and diverged form of b. As in the Escherichia coli unc operon, the a gene is preceded by a gene for a small hydrophobic and basic protein. The hydrophobic profile of the potential gene product suggests that its secondary structure is similar to the uncI protein. The smaller DNA fragment, 4737 base-pairs in length, is separated from the larger by at least 15 X 10(3) base-pairs of DNA. It contains a cluster of two genes encoding ATP synthase subunits beta and epsilon. Both clusters of ATP synthase genes are preceded by sequences resembling the -10 (Pribnow) box of E. coli promoters and are followed by sequences able to form stable stem-loop structures that might serve to terminate transcription. These features and the small intergenic non-coding sequences suggest that the clusters are operons, for which the names atp1 and atp2 are proposed. The order of genes within the two clusters is very similar to the gene order in the E. coli unc operon. However, it is most closely related to the arrangement of genes for ATP synthetase subunits a:c:b:alpha and beta:epsilon in two clusters in pea chloroplast DNA. This close relationship between chloroplasts and the cyanobacterium is also evident from comparisons of the sequences of ATP synthase subunits; the Synechococcus proteins are much more closely related to chloroplast homologues than to those in other bacteria or in mitochondria. It is further supported by the cyanobacterial b and b' proteins which, in common with their chloroplast counterpart, subunit I, have extra amino-terminal extensions relative to the E. coli b protein. This extension is known to be removed by post-translational processing in the chloroplast, but its function is obscure. It also seems likely that the cyanobacterial and chloroplast ATP synthases have important similarities in subunit composition. For example, the presence of two related genes, b and b', in the cyanobacterium suggests that its ATP synthase is a complex of nine polypeptides, and that it may have single copies of related b and b' proteins rather than two copies of identical b subunits as found in the E. coli enzyme.4+off

Unusual structure of geranium chloroplast DNA: A triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families

Physical and gene mapping studies reveal that chloroplast DNA from geranium (Pelargonium hortorum) has sustained a number of extensive duplications and inversions, resulting in a genome arrangement radically unlike that of other plants. At 217 kilobases in size, the circular chromosome is about 50% larger than the typical land plant chloroplast genome and is by far the largest described to date, to our knowledge. Most of this extra size can be accounted for by a 76-kilobase inverted duplication, three times larger than the normal chloroplast DNA inverted repeat. This tripling has occurred primarily by spreading of the inverted repeat into regions that are single copy in all other chloroplast genomes. Consequently, 10 protein genes that are present only once in all other land plants are duplicated in geranium. At least six inversions, occurring in both the inverted repeat and large single-copy region, must be postulated to account for all of the gene order differences that distinguish the geranium genome from other chloroplast genomes. We report the existence in geranium of two families of short dispersed repeats and hypothesize that recombination between repeats may be the major cause of inversions in geranium chloroplast DNA.

Tetranitromethane modification of photosystem 2

Inhibition of photosystem 2 by the peptide-modification reagent, tetranitromethane, has been investigated with spinach digitonin particles. In the presence of tetranitromethane, (1) the initial fluoresence yield is suppressed with a concomitant elimination of the variable component of fluorescence; (2) the optical absorption transient at 820 nm, attributed to P680(+), is greatly attenuated; (3) diphenylcarbazide-supported photoreduction of dichlorophenol indophenol is abolished; and (4) electron spin resonance Signal 2f and Signal 2s are eliminated. These results are consistent with multiple sites of modification in photosystem 2 by tetranitromethane, and suggest further that this reagent can inhibit charge stabilization in the reaction center.

The gene for the Mr 10,000 phosphoprotein associated with photosystem II is part of the psbB operon of the spinach plastid chromosome

We present the nucleotide and derived amino acid sequence of the gene for the 10 kd phosphoprotein associated with photosystem II. This gene was identified by comparing the recently published first nine amino acid residues for the 10 kd phosphoprotein of spinach (Farchaus and Dilley 1986) with available sequence data from the spinach plastid chromosome. The gene, designated psbH, is part of an operon that encodes the 51 kd chlorophyll a apoprotein of the photosystem II reaction center (psbB), the phosphoprotein (73 codons), cytochrome b6 (petB) and subunit IV (petD) of the cytochrome b/f complex in the order given. Northern blot analysis revealed a complex in vivo RNA pattern for this DNA segment resulting from an extensive modification of a 5.6 kb long putative primary transcript which includes a monocistronic RNA species for the phosphoprotein of approximately 420 bases. The deduced amino acid sequence for the phosphoprotein indicates a polypeptide corresponding to a molecular weight of 7.8 kb. Secondary structure predictions place all potential phosphorylation sites on the stromal side of the membrane.

Plastocyanin is encoded by an uninterrupted nuclear gene in spinach

Plastocyanin is a member of photosynthetic electron transport chains that transfers electrons from cytochrome f to the oxidized P700 chlorophyll a pigment of the photosystem I reaction center. We have isolated and characterized cDNA- and genomic clones from spinach (Spinacia oleracea) encoding the complete plastocyanin-precursor polypeptide. The amino acid sequence derived from the nucleotide sequence shows that the precursor consists of 168 amino acid residues including a transit sequence of 69 residues. The precursor polypeptide has a predicted Mr of 16,917, the mature protein of 10,413. The available data indicate that plastocyanin derives probably from a single-copy gene. The coding region contains no intron. The size of the mRNA as determined by S1 nuclease protection experiments is approximately 660 nucleotides, although analysis of different cDNA clones suggests that longer RNA species do exist, approaching the size of the mRNA (850 bases) estimated by Northern blot techniques.

Biogenesis of photosystem II complexes: transcriptional, translational, and posttranslational regulation

The integral membrane proteins of photosystem II (PS II) reaction center complexes are encoded by chloroplast genomes. These proteins are absent from thylakoids of PS II mutants of algae and vascular plants as a result of either chloroplast or nuclear gene mutations. To resolve the molecular basis for the concurrent absence of the PS II polypeptides, protein synthesis rates and mRNA levels were measured in mutants of Chlamydomonas reinhardtii that lack PS II. The analyses show that one nuclear gene product regulates the levels of transcripts from the chloroplast gene encoding the 51-kD chlorophyll a-binding polypeptide (polypeptide 5) but is not involved in the synthesis of other chloroplast mRNAs. Another nuclear product is specifically required for translation of mRNA encoding the 32-34-kD polypeptide, D1. The absence of either D1 or polypeptide 5 does not eliminate the synthesis and thylakoid insertion of two other integral membrane proteins of PS II, the chlorophyll a-binding polypeptide of 46 kD (polypeptide 6) and the 30-kD "D1-like" protein, D2. However, these two unassembled subunits cannot be properly processed and/or are degraded in the mutants even though they reside in the membrane. In addition, pulse labeling of the nuclear mutants and a chloroplast mutant that does not synthesize D1 mRNA indicates that synthesis of polypeptide 5 and D1 is coordinated at the translational level. A model is presented to explain how absence of one of the two proteins could lead to translational arrest of the other.

The light-dependent accumulation of the P700 chlorophyll a protein of the photosystem I reaction center in barley. Evidence for translational control

The light-dependent accumulation of the P700 chlorophyll a protein of the photosystem I reaction center has been studied in greening barley (Hordeum vulgare L.) seedlings. Immunoblot analysis of total cellular protein fractions and immunogold labelling of the P700 chlorophyll a protein in ultrathin sections of Lowicryl-embedded leaf tissue revealed that the concentration of this chlorophyll-binding protein in plastids of dark-grown barley seedlings is below the limit of detection. Upon illumination with white light, a rapid accumulation of this protein is induced. This light effect seems not to be regulated at the level of transcription. The gene for the P700 chlorophyll a protein has been mapped within the large single-copy region of the plastid DNA of barley. High levels of transcripts of this gene are present already in dark-grown seedlings and remain fairly constant throughout an extended illumination period. Polysomes were isolated from etioplasts and chloroplasts. The same high relative concentration of mRNA encoding the P700 chlorophyll a protein was present in both polysome fractions. This result suggests that the light-dependent accumulation of the P700 chlorophyll a protein during chloroplast formation in barley seedlings is regulated at the translational, or posttranslational, level.

Structure of a 3.2 kb region of pea chloroplast DNA containing the gene for the 44 kD photosystem II polypeptide

The gene for the 44 kD chlorophyll a-binding photosystem II polypeptide has been localized on the pea (Pisum sativum) chloroplast genome. The nucleotide sequence of the gene and its flanking regions has been analyzed. The gene codes for a polypeptide of 473 amino acid residues and is possibly cotranscribed with the gene for the D2 photosystem II polypeptide with which it has 50 bp in common. The amino acid sequences of the 44 kD polypeptides from pea, spinach and maize are approximately 95% homologous. Within the 1 kb fragment 3' to the 44 kD gene a 93 bp tRNA-Ser (UGA) gene and an open reading frame of 62 codons (ORF 62) were identified. Both show high homology to corresponding genes 3' to the 44 kD genes from spinach, maize and barley. The 44 kD gene and ORF 62 are encoded in the same strand, and have putative promoter sequences, ribosome binding sites and transcription termination signals.

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.