Spinach chloroplast mRNA for a 32 000 dalton polypeptide: size and localization on the physical map of the chloroplast DNA

Chloroplast DNA from the fern Osmunda cinnamomea: physical organization, gene localization and comparison to angiosperm

Chloroplast DNA from the fern Osmunda einnamomea was isolated by a sucrose gradient procedure utilizing PEG to stabilize chloroplasts. Analysis with the restriction endonucleases PvuII, Sacl and BstEII indicates a chloroplast genome size of 144 kb. A physical map of the fragments produced by these three enzymes was constructed by filter hybridizations using purified PvuII fragments as hybridization probes. The Osmunda chloroplast genome is circular and contains an inverted repeat 8-13 kb in size.Gene probes from tobacco, corn and spinach were used to map the positions of six genes on the Osmunda chloroplast chromosome. The 16S and 23S ribosomal RNAs are encoded by duplicate genes which lie within the inverted repeat. Genes for the large subunit of ribulose-1,5-bisphosphate carboxylase, a photosystem II polypeptide, and the alpha and beta subunits of chloroplast coupling factor are located in three different segments of the large single copy region.The Osmunda chloroplast genome is remarkably similar in size, conformation, physical organization, and map positions of known genes, to chloroplast DNA from a number of angiosperms. The major difference between chloroplast DNA from this fern and angiosperms is that the inverted repeat is smaller in Osmunda (8-13 kb) than in angiosperms (22-25 kb).

Chloroplast DNAs of Spinacia, Petunia and Spirodela have a similar gene organization

We have located the positions of the genes coding for the α, β and ε subunits of the ATPase complex on Spirodela oligorhiza chloroplast DNA by means of heterologous hybridization with Spinacia cpDNA fragments.The overall cpDNA sequence organization of Petunia hybrida and Spirodela was compared. We hybridized well-characterized, cloned Spirodela cpDNA fragments with size fractionated Petunia cpDNA digested by Sall. It appears that the monocotyledonous Spirodela and the dicotyledonous Petunia cpDNA share a common sequence organization around their entire circumference. These observations, together with data reported in the literature, indicate a strikingly similar genetic organization of the chloroplast genome in widely divergent plants.

Regulation of protein metabolism: Coupling of photosynthetic electron transport to in vivo degradation of the rapidly metabolized 32-kilodalton protein of the chloroplast membranes

In Spirodela oligorrhiza, mature chloroplasts copiously synthesize and degrade a 32-kilodalton membrane protein. The rates of synthesis and degradation are controlled by light intensity, the protein being unstable in the light and stable in the dark. Light-driven synthesis, but not degradation, is dependent on ATP. Degradation is blocked by herbicides inhibiting photosystem II electron transport, such as diuron and atrazine. Thus, both anabolism and catabolism of the 32-kilodalton protein are photoregulated, with degradation coupled to electron transport rather than phosphorylation.

Molecular Basis of Herbicide Resistance in Amaranthus hybridus

Resistance of different species of weeds to s-triazines, a commonly used class of herbicides, has been shown to involve a change in the binding affinity of the herbicide to a chloroplast polypeptide of 32,000 daltons. A single amino acid difference in this 32,000-dalton protein appears to be responsible for resistance to the herbicide in Amaranthus hybridus.

Translation of mRNAs for subunits of chloroplast coupling factor 1 in spinach

The chloroplast coupling factor 1 consists of five nonidentical subunits, three of which (alpha, beta, and epsilon subunits) have been shown in several laboratories to be synthesized within chloroplasts. The site of synthesis of the remaining two (gamma and delta subunits) was investigated by analyzing products directed by spinach leaf RNAs in wheat germ and reticulocyte translation systems in vitro. It was found that poly(A)(+) RNA directs the synthesis of two distinct polypeptides, one of which is immunochemically related to the gamma subunit but is 4,000 daltons larger. The other shares antigenic sites with the delta subunit but is 8,000 daltons larger. When wheat germ or reticulocyte translation systems were programmed with RNAs from purified chloroplasts, the only products related to CF(1) that we could detect were a putative precursor of beta, 2,000 daltons larger than the mature subunit, and some smaller polypeptides, which appear to be incomplete translation products of beta. From these results it appears likely that the gamma and delta subunits are synthesized in the cytoplasm as larger precursors and that beta is synthesized within the chloroplast as a precursor.

Nucleotide sequence of the gene for the M(r) 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of M(r) 38,950

The gene for the so-called M(r) 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is approximately 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of M(r) 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of M(r) 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA.

Light-dependent accumulation and localization of photosystem II proteins in maize

We have raised antibodies against several major components of photosystem II. These antisera, which are directed against the apoproteins of two chlorophyll-binding proteins (CPa-1 and CPa-2), the apoprotein of light-harvesting complex II and the 33-kDa extrinsic protein of the oxygen-evolving complex, were used to examine the light regulation of photosystem II assembly in maize. The principal findings of this study are as follows. The 33-kDa protein is present in dark-grown maize and the content increases 5-10-fold upon illumination. The level of the protein is mediated at least in part by phytochrome and is independent of the accumulation of chlorophyll. In contrast, none of the three chlorophyll-binding proteins examined was detectable in leaves of maize grown in darkness or under other light regimes where chlorophyll does not accumulate. Even in the absence of photosystem II assembly, the 33-kDa protein is properly transported across the thylakoid into the lumen. However, the protein does not attach in the normal way to the inner surface of the membrane under these conditions.

Nuclear and mitochondrial DNA have sequence homology with a chloroplast gene

A PstI 7.7 kbp fragment from chloroplast (ct) DNA of spinach shows homology to an EcoRI 8.3 kbp fragment of mitochondrial (mt) DNA and in turn, both are homologous to a number of common regions of nuclear (n) DNA. The common area of homology between the chloroplast and mitochondrial fragments is between a KpnI 1.8 segment internal to the PstI sites in the ctDNA and an EcoRI/BamHI 2.9 kbp fragment at one end of the mitochondrial 8.3 kbp fragment. The KpnI 1.8 kbp ctDNA fragment is within a structural gene for the P700 chlorophyll a apoprotein. Further analysis of this KpnI 1.8 kbp fragment confined the homologous region in mtDNA to a ct 0.8 kbp HpaII fragment. These smaller pieces of the organellar genomes share homologies with nuclear DNA as well as displaying unique hybridization sites. The observations reported here demonstrate that there is a common or closely related sequence in all three genetic compartments of the cell.

In vitro expression of chloroplast genes in lysates of higher plant chloroplasts

A DNA-dependent in vitro-coupled transcription-translation system has been prepared from lysates of isolated chloroplasts. These lysates are comparable to those of Escherichia coli in transcriptional and translational fidelity and efficiency in response to a given template DNA. When Nicotiana tabacum chloroplast DNA is used as template with chloroplast lysates (N. tabacum or spinach) or E. coli lysates, NaDodSO4 gel analysis reveals similar polypeptide patterns that are distinct from the patterns obtained with E. coli DNA. Genes in recombinant plasmids containing chloroplast DNA are also expressed in these in vitro systems. DNA . RNA hybridization experiments show that transcripts are synthesized from most of the chloroplast genome. Newly synthesized large subunit of ribulosebisphosphate carboxylase/oxygenate and a transcript of the large subunit gene (rbcL) are observed in chloroplast lysates using as template chloroplast DNA or cloned fragments of tobacco chloroplast DNA that contain the large subunit gene. Results suggest that differential expression of chloroplast genes occurs in vitro. By using cloned chloroplast DNA templates in this homologous system, it is possible to identify and map structural genes for chloroplast proteins.

Localization of the gene for apocytochromeb-559 on the plastid chromosome of spinach

The gene for cytochromeb-559, associated with the photosystem II reaction center, has been located on the spinach plastid chromosome by cell-free coupled transcription-translation and RNA-programmed hybrid selection translation using appropriate recombinant DNAs, RNA fractions, and monospecific antisera. The gene is located in the large single-copy segment of the plastid chromosome between the genes for cytochomef and the P680 chlorophylla apoprotein of photosystem II and transcribed in the opposite direction relative to these genes. The 10 kd protein is decoded from a bicistronic 1.0 kb mRNA and is apparently not made as a precursor in cell-free rabbit reticulocyte andE. coli lysates.

Intracellular coding sites of polypeptides associated with photosynthetic oxygen evolution of photosystem II

Three hydrophilic polypeptides of approximately 34, 23, and 16 kd located on the inner thylakoid surface are associated with the water-splitting activity of photosystem II. Stable transcripts for the three proteins were found only in cytosolic (polyadenylated) RNA, suggesting that they are encoded in nuclear genes. The immunologically reacting products synthesized in a rabbit reticulocyte cell-free translation system are larger in size than the authentic mature proteins by about 6-10 kd. These larger precursors are imported post-translationally into isolated, intact chloroplasts, and are processed to their mature forms during or after translocation. The imported proteins can be extracted from thylakoids by procedures used to isolate the three native proteins of the water-splitting complex, suggesting that they have assembled properly into their final destination, the inner thylakoid surface.

Sequence organization of a pea chloroplast DNA gene coding for a 34,500-dalton protein

A gene (PGII), which codes for a 34.5-kilodalton protein, has been isolated and cloned from pea chloroplast DNA. The production of its 1.2-kilobase mRNA is photodependent. The direction of transcription has been determined, the site of initiation of transcription has been found, and an in vitro protein product has been produced. The gene, including the 5' and 3'-flanking regions, has been sequenced. It shows ca. 95% homology to the photosystem II thylakoid membrane protein, photogene 32, from spinach and tobacco. There are no intervening sequences. The 5'-flanking region suggests similarities with Escherichia coli promoters. The 5'-flanking region is remarkably conserved among pea, spinach, and tobacco DNA.

Structure of the spinach chloroplast genes for the D2 and 44 kd reaction-centre proteins of photosystem II and for tRNASer (UGA)

We have determined the sequence of the spinach (Spinacia oleracea) chloroplast genes for the photosystem II proteins, D2 and the 44 kd reaction-centre, chlorophyll a-binding protein, and for tRNASer (UGA). The 3' end of the D2 gene overlaps the first 50 bp of the 5' end of the gene for the 44 kd protein. Northern RNA hybridization analysis indicates the two genes are cotranscribed into a single 3.5 kb RNA. The predicted molecular weight of the 353-residue D2 protein is 39536 and that of the 473-residue 44 kd protein is 51816. Both proteins are hydrophobic containing at least five possible membrane-spanning domains. D2 shows significant homology to the 32 kd herbicide-binding protein (Zurawski et al., (1982) Proc. Natl. Acad. Sci. USA 79, 7699-7703), and parts of the 44 kd protein show obvious similarities to parts of the 51 kd reaction-centre, chlorophyll a-binding protein of photosystem II (Morris and Herrmann (1984) Nucleic Acids Res. 12, 2837-2850). The gene for tRNASer (UGA) which is on the opposite strand to and transcribed towards the photosystem II genes is 72% homologous with the corresponding Escherichia coli tRNASer.

Sequence organization of a pea chloroplast DNA gene coding for a 34,500-dalton protein

A gene (PGII), which codes for a 34.5-kilodalton protein, has been isolated and cloned from pea chloroplast DNA. The production of its 1.2-kilobase mRNA is photodependent. The direction of transcription has been determined, the site of initiation of transcription has been found, and an in vitro protein product has been produced. The gene, including the 5' and 3'-flanking regions, has been sequenced. It shows ca. 95% homology to the photosystem II thylakoid membrane protein, photogene 32, from spinach and tobacco. There are no intervening sequences. The 5'-flanking region suggests similarities with Escherichia coli promoters. The 5'-flanking region is remarkably conserved among pea, spinach, and tobacco DNA.

Junctions of the large single copy region and the inverted repeats in Spinacia oleracea and Nicotiana debneyi chloroplast DNA: sequence of the genes for tRNAHis and the ribosomal proteins S19 and L2

This work describes the organization, at the nucleotide sequence level, of genes flanking the junctions of the large single copy regions and the inverted repeats of Spinacia oleracea (spinach) and Nicotiana debneyi chloroplast DNAs. In both genomes, trnH1, the gene for tRNA-His(GUG) is located at the extremity of the large single copy region 3' to psbA, the gene for the 35 kd Photosystem 2 protein. Both psbA and trnH1 are transcribed towards the inverted repeat. In spinach, the first 48 codons of rps19, the gene for the chloroplast ribosomal protein S19, lie in the inverted repeat and the last 44 codons lie in the large single copy region at the end opposite to that carrying trnH1. The gene for a protein homologous to the E. coli ribosomal protein L2, rp12, is in the inverted repeat immediately 5' to rps19 and, like rps19, is transcribed towards the large single copy region. In N. debneyi, but not in spinach, rp12 is interrupted by a 666 bp insertion. The gene for tRNA-lle(CAT), trnl1, is located in the inverted repeats of spinach and N. debneyi, 5' to rp12 and is transcribed in the same direction as rp12.

Chloroplast gene for Mr 32000 polypeptide of photosystem II in Euglena gracilis is interrupted by four introns with conserved boundary sequences

The gene for the Mr 32000 herbicide binding polypeptide of photosystem II has previously been mapped to the 5 kbp EcoRI fragment Eco I of Euglena gracilis chloroplast DNA. The nucleotide sequence of 3324 bp of Eco I, containing the psbA locus, has been determined. This locus encodes a polypeptide of 345 amino acids which is co-linear with, and has 86% derived amino acid sequence homology to sequences derived from four higher plants chloroplast psbA loci. The Euglena psbA gene contains four introns of size 435, 443, 434, and 617 bp. The four introns have conserved boundary sequences of the type previously described in the Euglena chloroplast gene (rbcL) for the large subunit of ribulose-1,5-bisphosphate carboxylase (Koller et al., Cell 36, 545-553, 1984).

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

The DNA sequence of 2210 nucleotides including the gene for the "51 kd" chlorophyll alpha-conjugated thylakoid membrane protein associated with the photosystem II reaction center of spinach has been determined. This protein is functionally identical with the P680 chlorophyll alpha apoprotein that catalyses the primary light-induced photochemical processes of photosystem II (Camm, E.L. and Green, B.R. (1983) Biochim. Biophys. Acta 724 291-293). The only large open reading frame in the sequence consists of 508 triplets encoding a protein of molecular mass of 56,246 kd. The deduced amino acid sequence shows clustering of hydrophobic residues into seven core regions which probably traverse the membrane, and a large hydrophilic domain of about 200 amino acids interspersed between span VI and VII. Potential transcription promotor and terminator signals flanking the structural gene show prokaryotic-like features. Seven discrete RNA species ranging in size from 2.0 to over 5.0 kilobases display complementarity to apoprotein coding sequences implying that the region can be polycistronically transcribed. The primary transcript includes information for at least two further genes coding for subunits of the cytochrome b/f complex.

Detection of multiple, unspliced precursor mRNA transcripts for the Mr 32,000 thylakoid membrane protein from Euglena gracilis chloroplasts

The psbA gene is the coding locus for a polypeptide of 32 kilodaltons that is involved in electron transport through photosystem II. The 4.9 kilobasepair (kbp) EcoRI restriction endonuclease fragment EcoI from the 145 kbp Euglena gracilis chloroplast DNA was shown to encode psbA. Five transcripts of size 3.1, 2.8, 2.3, 1.8, and 1.2 kilobases were detected by hybridization of psbA probes to nitrocellulose filter blots of electrophoretically separated RNAs. This same pattern was observed when the hybridization probe consisted of only exon sequences from this split gene. A synthetic, intron specific probe hybridized to all RNA precursors except the 1.2 kb mature RNA. These results and psbA DNA sequence data lead to the conclusion that the four higher molecular weight transcripts are unprocessed precursors of the 1.2 kilobase RNA, some of which contain unspliced intervening sequences. There is an increase in psbA transcripts during light induced maturation of the chloroplasts.

Structure of the chloroplast gene for the precursor of the Mr 32,000 photosystem II protein from mustard (Sinapis alba L.)

The nucleotide sequence of the mustard chloroplast gene for the precursor of the Mr 32,000 photosystem II protein is presented. A comparison with the corresponding genes from spinach and Nicotiana debneyi (14) reveals less than 5% nucleotide divergence in the coding region. The derived protein of mustard differs from the corresponding proteins by three amino acid positions at the C-terminus. We have defined the presumed transcription start and termination sites of the mustard gene. Upstream from the start site are sequences typical of a prokaryotic promoter and, also, a sequence that resembles the eukaryotic 'TATA' box. A search for intrastrand base pairing revealed stem-loop secondary structure at the transcription start and termination sites and in the region preceding the presumed promoter. This latter region is a 69-base-pair sequence element unique to the 5'flanking sequence of the mustard gene.

Clone bank of Nicotiana tabacum chloroplast DNA: mapping of the alpha, beta and epsilon subunits of the ATPase coupling factor, the large subunit of ribulosebisphosphate carboxylase, and the 32-kDal membrane protein

All of the PstI restriction fragments of the chloroplast DNA of Nicotiana tabacum have been cloned in the plasmid vector pBR322. The cloned fragment sizes range from 0.8 to 26 kb, are stable, and can be amplified by chloramphenicol with varying efficiencies. Using these clones we have detailed a PstI physical map of the tobacco chloroplast genome. Selected clones of SalI, BamHI and PstI fragments were used to localize the map positions of the alpha, beta, and epsilon subunits of the chloroplast ATPase coupling factor, the large subunit of ribulosediphosphate carboxylase and the 32-kDal membrane protein. The gene products of these clones were characterized by RNA transcript sizing, immunoprecipitation of maxicell-directed protein synthesis, and hybrid-arrested translation.

Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats

The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2.

Genes and transcripts for the P700 chlorophylla apoprotein and subunit 2 of the photosystem I reaction center complex from spinach thylakoid membranes

A photosystem I reaction center complex has been purified to homogeneity by a procedure involving partial solubilization of spinach thylakoid membranes, ion exchange chromatography and centrifugation in sucrose gradients. The complex contains 7 polypeptides: the P700 chlorophylla apoprotein with an apparent molecular weight of 67 kd, which at high resolution splits into two bands, and smaller polypeptides of 22 (subunit 2), 18.5, 18, 16, 12 and 10 kd.Stable transcripts for the P700 chlorophylla apojprotein and subunit 2 were found in plastid and cytosolic RNA, respectively. The apoprotein product obtained by translation in a mRNA-dependent cell-free rabbit reticulocyte lysate and also by DNA-programmed transcription-translation of cloned plastid DNA fragments inE. coli lysates was indistinguishable immunologically and electrophoretically from the authentic protein. However, the product immunologically related to subunit 2 was 4 kd larger than the mature compound indicating that this protein is encoded in the nucleus and synthesized as a precursor.The gene for the P700 chlorophylla apoprotein has been physically mapped on the spinach plastid chromosome by hybrid selection mapping and DNA-programmed cell-free transcription-translation using cloned restriction fragments of plastid DNA. There is one gene copy per chromosome and it is located centrally in the large single-copy region of the circular DNA molecule. This gene is uninterrupted and is transcribed in the same direction as that of the large subunit of ribulose bisphosphate carboxylase/oxygenase. Its transcript is approximately 4 kb longer than the 2 kbp structural gene.

Novel evolutionary variation in transcription and location of two chloroplast genes

We have found major evolutionary changes in the types of transcripts produced by specific chloroplast genes, in particular those encoding the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase and a photosystem II polypeptide (PII). Two distinct patterns of LS gene transcripts are revealed by hybridizing an LS gene probe to electrophoretically separated RNA from 19 angiosperms. Most species, including pea, contain the single transcript of approximately 1.6 kb previously observed in corn, spinach and mustard. However, in mung bean and other members of the legume genera Vigna and Phaseolus, the 1.6 kb transcript represents only a minor fraction of LS transcripts, and instead, two larger LS transcripts of approximately 2.4 and 2.6 kb predominate. The PII gene produces a single transcript in pea and most other species examined, while members of the related legume genera Vigna, Phaseolus and Glycine contain two additional transcripts which are smaller in size and probably represent specific RNA breakdown products. A single species, sweet pea (Lathyrus odoratus), contains a second PII transcript which is 0.2 kb larger than the approximately 1.2 kb transcript found in all species. The LS and PII genes map to the same 5 kb region in both pea and mung bean and are transcribed off the same DNA strand. In contrast, published studies indicate that the two genes are approximately 50 kb apart and are transcribed off opposite DNA strands in five other chloroplast genomes. These differences are probably the consequence of an approximately 50 kb inversion which distinguishes the pea and mung bean genomes from those of most other angiosperms (1).

Sequence of the intercistronic region between the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit and coupling factor beta subunit gene

The nucleotide sequence of the region between the genes for the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase and the beta subunit of coupling factor from tobacco chloroplast DNA has been determined. The 5' ends of their mRNAs have been located on the DNA sequence using s1 nuclease mapping. The promoter sequences of these chloroplast genes have features in common with those of prokaryotes. E. coli RNA polymerase can recognize these sequences and start transcription at authentic initiation sites.

The subcellular localization of DNA components from Cyanophora paradoxa, a flagellate containing endosymbiotic cyanelles

Cyanophora paradoxa, a unicellular flagellate, contains cyanelles which are supposed to be cyanobacterial origin. DNA was isolated from subcellular fractions and separated according to density components in CsC1 density gradients. The main DNA component, comprising more than 90% of the total DNA, has a buoyant density of 1.724 g X cm-3. Several subsfractions in the range from 1.718 g X cm-3 to 1.735 g X cm-3 are contained in this component. This DNA of high complexity was considered to be host nuclear DNA. The DNA from the endosymbiotic cyanelles, which were isolated, treated with DNase, and purified by sucrose density gradient centrifugation exhibited a buoyant density of 1.692 g X cm-3 in one strain and 1.695 g X cm-3 in a second strain. Both cyanelle DNAs (cyDNA) have a complexity of approximately 126 X 10(3) base pairs and comprise about 5% of the total cellular DNA content. Two additional DNA components of low complexity were isolated from crude cyanelle pellets obtained without DNase treatment. The larger of these, approximately 48 X 10(3) base pairs in size, had a density of approximately 1.688 g X cm-3. The second component, about 15 X 10(3) base pairs in size, banded in the density range between 1.710 g X cm-3 and 1.720 g X cm-3. The latter is associated with nuclear DNA. The 48 X 10(3)-base-pair component was located in the cytosol and could be obtained after CsC1/ethidium bromide density gradient centrifugation at the position of covalently closed circular DNA. Both these components amounted to approximately 0.5-1% of total DNA. A further DNA component with a complexity of more than 150 X 10(3) base pairs, enriched in fractions where mitochondria are expected, was not characterized further. The density was intermediate between cyDNA and nuclear DNA (1.710-1.720 g X cm-3) and it amounted to 1-2% of the total DNA. Our results indicate that the DNA from cyanelles, believed to be endosymbiotic cyanobacteria, is not more complex than higher plant chloroplast DNAs.

Mapping of genes on the chloroplast DNA of Spirodela oligorhiza

With the use of spinach chloroplast RNAs as probes, we have mapped the rRNA genes and a number of protein genes on the chloroplast DNA (cpDNA) of the duckweed Spirodela oligorhiz. For a more precise mapping of these genes we had to extend the previously determined [14] restriction endonuclease map of the duckweed cpDNA with the cleavage sites for the restriction endonucleases Sma I and Bgl I. The physical map indicates that duckweed cpDNA contains two inverted repeat regions (18 Md) separated by two single copy regions with a size of 19 Md and 67 Md, respectively.By hybridization with spinach chloroplast rRNAs it could be shown that each of the two repeat units contains one set of rRNA genes in the order: 16S rRNA gene - spacer - 23S rRNA gene - 5S rRNA gene.A spinach chloroplast mRNA preparation (14S RNA), which is predominantly translated into a 32 Kilodalton (Kd) protein [9], hybridized strongly to a DNA fragment in the large single copy region, immediately outside one of the inverted repeats. With another mRNA preparation (18S), which mainly directs the in vitro synthesis of a 55 Kd protein [9], hybridization was observed with two DNA regions, located between 211° and 233° and between 137° and 170°, respectively. Finally, with a spinach chloroplast genomic probe for the large subunit of ribulose 1,5-bisphosphate carboxylase [17], hybridization was found with a DNA fragment located between 137° and 158° on the map.

Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost

We examined the arrangement of sequences common to seven angiosperm chloroplast genomes. The chloroplast DNAs of spinach, petunia and cucumber are essentially colinear. They share with the corn chloroplast genome a large inversion of approximately 50 kb relative to the genomes of three legumes--mung bean, pea and broad bean. There is one additional rearrangement, a second, smaller inversion within the 50 kb inversion, which is specific to the corn genome. These two changes are the only detectable rearrangements that have occurred during the evolution of the species examined (corn, spinach, petunia, cucumber and mung bean) whose chloroplast genomes contain a large inverted repeat sequence of 22-25 kb. In contrast, we find extensive sequence rearrangements in comparing the pea and broad bean genomes, both of which have deleted one entire segment of the inverted repeat, and also in comparing each of these to the mung bean genome. Thus there is a relatively stable arrangement of sequences in those genomes with the inverted repeat and a much more dynamic arrangement in those that have lost it. We discuss several explanations for this correlation, including the possibility that the inverted repeat may play a direct role in maintaining a conserved arrangement of chloroplast DNA sequences.

Physical and gene mapping of chloroplast DNA from Atriplex triangularis and Cucumis sativa

A rapid and simple method for constructing restriction maps of large DNAs (100-200 kb) is presented. The utility of this method is illustrated by mapping the Sal I, Sac I, and Hpa I sites of the 152 kb Atriplex triangularis chloroplast genome, and the Sal I and Pvu II sites of the 155 kb Cucumis sativa chloroplast genome. These two chloroplast DNAs are very similar in organization; both feature the near-universal chloroplast DNA inverted repeat sequence of 22-25 kb. The positions of four different genes have been localized on these chloroplast DNAs. In both genomes the 16S and 23S ribosomal RNAs are encoded by duplicate genes situated at one end of the inverted repeat, while genes for the large subunit of ribulose-1,5-bisphosphate carboxylase and a 32 kilodalton photosystem II polypeptide are separated by 55 kb of DNA within the large single copy region. The physical and genetic organization of these DNAs is compared to that of spinach chloroplast DNA.

Influence of the ionic environment on the in vitro transcription of the spinach plastid DNA by a selectively bound RNA-polymerase DNA complex

The in vitro transcription of chloroplast DNA (ctDNA) is studied using a DNA-protein complex isolated from spinach plastids. The RNA products are compared to the in vivo synthesized ctRNA by competition for hybridization. At least 80% of the in vitro RNA sequences are present in vivo. Modifications of ionic strength or introduction of heparin in the reaction medium has an important effect on transcriptional activity of the complex. Furthermore, the length of the RNA chains increases ionic strength and amount of heparin. The RNA products are analysed by Southern hybridizations to EcoRI cTDNA fragments. Changes in the ionic strength or in the amount of heparin modify heterogeneously the transcription of the various DNA regions. The quantitative distribution of transcripts among the ctDNA fragments is used as evidence for the selectivity of the transcription. The activity of the DNA-protein complex is much more resistant to high ionic strength than an heterologous transcription system using Escherichia coli RNA polymerase and ctDNA. This latter system transcribes less ctDNA fragments.

Homologies among ribosomal RNA and messenger RNA genes in chloroplasts, mitochondria and E. coli

Labelled chloroplast rRNAs from Spinacia oleracea were hybridized to restriction endonuclease digests of chloroplast DNA from Oenothera hookeri and Euglena gracilis, to mitochondrial DNA of Acanthamoeba castellanii, and to DNA of the E. coli rrn B operon in the transducing phage lambda rifd 18. The degree of homology is greatest for the 16S rRNA gene. Greater than 90% occurs between the two higher plant genes, 80% homology to the lower plant gene, 60%-70% homology to the bacterial gene, and 20% homology to the mitochondrial gene. The degree of hybridization varied considerably for the 23S and the 5S rRNA genes. Very high homology exists between the two higher plant genes, only about 50% homology for both the Euglena and bacterial genes, and no significant homology for the mitochondrial genes. These results show that any chloroplast (or E. coli) rRNA may be used as a probe to identify rRNA genes in other ctDNAs. Two RNA populations, each enriched for a different ctDNA-encoded mRNA, proved useful in the location of these genes on both higher plant ctDNAs. No significant hybridization was obtained using these probes to the Euglena ctDNA which seems to be too distantly related.