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

A complex twintron is excised as four individual introns

Twintrons are introns-within-introns excised by sequential splicing reactions. A new type of complex twintron comprised of four individual group III introns has been characterized. The external intron is interrupted by an internal intron containing two additional introns. This 434 nt complex twintron within a Euglena gracilis chloroplast ribosomal protein gene is excised by four sequential splicing reactions. Two of the splicing reactions utilize multiple 5'- and/or 3'-splice sites. These findings are evidence that introns with multiple active splice sites can be formed by the repeated insertion of introns into existing introns.

Occurrence and transcription of genes for nad1, nad3, nad4L, and nad6, coding for NADH dehydrogenase subunits 1, 3, 4L, and 6, in liverwort mitochondria

The genes encoding subunits 1, 3, 4L, and 6 of NADH dehydrogenase (nad1, nad3, nad4L, nad6) in the mitochondrial genome of a liverwort, Marchantia polymorpha, were characterized by comparing homologies of the amino-acid sequences of the subunits with those of other organisms. The nad3 and nad4L genes are split by single and double group II introns, respectively. The 5'-half portion of the nad6 gene was repeated at an identity of 89% to form a reading frame consisting of 100 amino-acid residues. The Northern hybridization analysis showed that all four genes are transcribed in the liverwort mitochondria.

A plant mitochondrial gene encodes a protein involved in cytochrome c biogenesis

Analysis of a transcribed region in the mitochondrial genome of Oenothera revealed an open reading frame (ORF) of 577 codons (orf577) that is also conserved in carrot, here encoding a protein of 579 amino acids (orf579). RNA editing alters the mRNA sequence of orf577 in Oenothera with 46 C to U transitions, many of which improve sequence similarity with the homologous Marchantia gene orf509. The deduced polypeptides show significant similarity with the ccl1-encoded protein involved in cytochrome c biogenesis in the photosynthetic bacterium Rhodobacter capsulatus. A highly conserved domain is also found in plastid ORFs, suggesting that these bacterial, chloroplast and mitochondrial genes encode polypeptides with analogous functions in assembly and maturation of cytochromes c.

Redox control of gene expression and the function of chloroplast genomes - an hypothesis

Two-component regulatory systems that respond to changes in redox potential have recently been discovered in bacteria. 'Redox sensors' are defined as electron carriers which initiate control of gene expression upon oxidation or reduction. 'Redox response regulators' are defined as DNA-binding proteins which modify gene expression as a result of the action of redox sensors. Redox sensors and redox response regulators may comprise a mechanism for feedback control of redox potential in photosynthetic electron transport chains, thereby protecting plants, algae and photosynthetic bacteria from damage caused by electrochemistry operating on inappropriate electron donors and acceptors. Chloroplast redox sensors and redox response regulators, themselves encoded in the nucleus, may place chloroplast gene expression under redox regulatory control. This may account for the persistence, in evolution, of chloroplast genomes, and for the constancy of the sub-set of chloroplast proteins encoded and synthesised in situ. These and other predictions are discussed.

Cloning and expression of a high-molecular-mass major antigen of Helicobacter pylori: evidence of linkage to cytotoxin production

A high-molecular-mass (120- to 128-kDa) Helicobacter pylori antigen has been associated with peptic ulcer disease. We created a bank of 40,000 random chromosomal fragments of H. pylori 84-183 by using lambda ZapII. Screening of this bank in Escherichia coli XL1-Blue with absorbed serum from an H. pylori-infected person permitted the isolation and purification of a clone with a 3.5-kb insert. Subcloning of this insert (pMC3) permitted the expression of a recombinant H. pylori protein that had a mass of approximately 96 kDa and that was recognized by the human serum. Sera that were obtained from H. pylori-infected persons and that recognized the native 120- to 128-kDa H. pylori antigen recognized the recombinant 96-kDa pMC3 protein to a significantly greater extent than did sera that did not recognize the native H. pylori antigen. All 19 H. pylori isolates producing the 120- to 128-kDa antigen hybridized with pMC3; none of 13 nonproducers did so (P < 0.001). Because all 15 isolates producing the vacuolating cytotoxin hybridized with pMC3, we called the gene cagA (cytotoxin-associated gene). Sequence analysis of pMC3 identified an open reading frame of 859 amino acids, without a termination codon. Parallel screening of a lambda gt11 library with human serum revealed positive plaques with identical 0.6-kb inserts and sequences matching the sequence of the downstream region of pMC3. To clone the full-length gene, we used the 0.6-kb fragment as a probe and isolated a clone with a 2.7-kb insert from the lambda ZapII genomic library. Nucleotide sequencing of this insert (pYB 2) revealed a 785-bp sequence that overlapped the downstream region of pMC3. Translation of the complete nucleotide sequence of cagA revealed an open reading frame of 1,181 amino acids yielding a protein of 131,517 daltons. There was no significant homology with any previously reported protein sequence. These findings indicate the cloning and characterization of a high-molecular-mass H. pylori antigen potentially associated with virulence and with cytotoxin production.

Chloroplast transformation in plants: polyethylene glycol (PEG) treatment of protoplasts is an alternative to biolistic delivery systems

Nicotiana plumbaginifolia protoplasts were directly transformed by PEG treatment with a cloned 16S rRNA gene isolated from a double antibiotic-resistant Nicotiana tabacum plastid mutant. Putative plastid transformants were selected in cell culture by their spectinomycin resistance and identified by their unselected streptomycin resistance. Alternatively, cell lines were selected in the presence of both antibiotics. The cell line (and its regenerated plants) selected solely for spectinomycin resistance demonstrated an extensive segregation of streptomycin resistance in subsequent tests, while the double-selected line showed stable resistance for both antibiotics. The resistance markers were inherited maternally. In the putative plastid transformants the origin of the resistance mutations was identified by the absence of an AatII site, missing in the donor N. tabacum plastid gene (spectinomycin resistance site) but present in that of wild-type N. plumbaginifolia, and a sequence analysis of the particular nucleotide changes in both resistance sites. Restriction enzyme analysis of total plastid DNA (ptDNA), and the recloning and full sequencing of the fragment introduced, investigated in one of the plastid transformants, showed no DNA rearrangements accompanied with the integration process. Sequence analysis indicated a targeted, homologous integration of the DNA fragment introduced but an unexpectedly complete homology of the parental ptDNA sequences in this region prevented the location of borders. Although the frequency of plastid transformant colonies (2 x 10(-5)) should still be improved, this method for stable chloroplast DNA transformation is comparable with or more efficient than the particle bombardment techniques.

bchFNBH bacteriochlorophyll synthesis genes of Rhodobacter capsulatus and identification of the third subunit of light-independent protochlorophyllide reductase in bacteria and plants

We present the nucleotide and deduced amino acid sequences of four contiguous bacteriochlorophyll synthesis genes from Rhodobacter capsulatus. Three of these genes code for enzymes which catalyze reactions common to the chlorophyll synthesis pathway and therefore are likely to be found in plants and cyanobacteria as well. The pigments accumulated in strains with physically mapped transposon insertion mutations are analyzed by absorbance and fluorescence spectroscopy, allowing us to assign the genes as bchF, bchN, bchB, and bchH, in that order. bchF encodes a bacteriochlorophyll alpha-specific enzyme that adds water across the 2-vinyl group. The other three genes are required for portions of the pathway that are shared with chlorophyll synthesis, and they were expected to be common to both pathways. bchN and bchB are required for protochlorophyllide reduction in the dark (along with bchL), a reaction that has been observed in all major groups of photosynthetic organisms except angiosperms, where only the light-dependent reaction has been clearly established. The purple bacterial and plant enzymes show 35% identity between the amino acids coded by bchN and chlN (gidA) and 49% identity between the amino acids coded by bchL and chlL (frxC). Furthermore, bchB is 33% identical to ORF513 from the Marchantia polymorpha chloroplast. We present arguments in favor of the probable role of ORF513 (chlB) in protochlorophyllide reduction in the dark. The further similarities of all three subunits of protochlorophyllide reductase and the three subunits of chlorin reductase in bacteriochlorophyll synthesis suggest that the two reductase systems are derived from a common ancestor.

Physical map of chloroplast DNA in sugi, Cryptomeria japonica

To investigate the evolution of conifer species, we constructed a physical map of the chloroplast DNA of sugi, Cryptomeria japonica, with four restriction endonucleases, PstI, SalI, SacI and XhoI. The chloroplast genome of C. japonica was found to be a circular molecule with a total size of approximately 133 kb. This molecule lacked an inverted repeat. Twenty genes were localized on the physical map of C. japonica cpDNA by Southern hybridization. The chloroplast genome structure of C. japonica showed considerable rearrangements of the standard genome type found in vascular plants and differed markedly from that of tobacco. The difference was explicable by one deletion and five inversions. The chloroplast genome of C. japonica differed too from that of the genus Pinus which also lacks one of the inverted repeats. The results indicate that the conifer group originated monophyletically from an ancient lineage, and diverged independently after loss of an inverted repeat structure.

Cotranscriptional expression of mitochondrial genes for subunits of NADH dehydrogenase, nad5, nad4, nad2, in Marchantia polymorpha

Three genes for the subunits of the NADH dehydrogenase (nad5, nad4, and nad2) are tandemly clustered on the liverwort mitochondrial genome. Their gene products showed high levels of amino acid sequence identity with the corresponding subunits from higher plant mitochondria (82.8-84.4%), and significant levels of identity with those from liverwort chloroplast (32.0-33.5%). Podospora anserina mitochondria (21.4-45.9%), and human mitochondria (18.4-27.9%). In addition, these three subunits from liverwort mitochondria have conserved amino acid residues in their central regions. The gene nad5 is interrupted by a 672 bp group I intron, while genes nad4 and nad2 are interrupted by group II introns of 899 bp and 1418 bp, respectively. Northern blot analysis using exon-intron specific probes indicated that these three genes are transcribed as a single precursor mRNA of 9.6 kb in length and are processed into mature mRNA molecules in liverwort mitochondria. Several regions of this nad gene cluster are repeated in the liverwort mitochondrial genome.

Comparative study on the chloroplast, mitochondrial and nuclear genome differentiation in two cultivated rice species, Oryza sativa and O. glaberrima, by RFLP analyses

Restriction fragment length polymorphisms of chloroplast (ct), mitochondrial (mt) and nuclear DNA were investigated using eight cultivars of Oryza sativa and two cultivars of O. glaberrima. Relative variability in the nuclear and cytoplasmic genomes was estimated by a common measure, genetic distance. Based on the average genetic distances among ten cultivars for each genome, the evolutionary variabilities of the mitochondrial and nuclear genomes were found to be almost the same, whereas the variability of the chloroplast genome was less than half that of the other two genomes. Cluster analyses on ct and mt DNA variations revealed that chloroplast and mitochondrial genomes were conservative within a taxon and that their differentiations were well-paralleled with respect to each other. For nuclear DNA variation, an array of different degrees of differentiation was observed in O. sativa, in contrast with little variation in O. glaberrima. As a whole, differentiation between O. sativa and O. glaberrima was clearly observed in all three genomes. In O. sativa, no notable difference was found between the cultivars 'Japonica' and 'Javanica', whereas a large differentiation was noticed between 'Japonica' (including 'Javanica') and 'Indica'. In all three genomes, the average genetic distances within 'Indica' were much larger than those within 'Japonica' (including 'Javanica'), and almost similar between 'Japonica' (including 'Javanica') and 'Indica'. These facts indicate that differentiation in O. sativa was due mainly to 'Indica'.

A transcription map of the chloroplast genome from rice (Oryza sativa)

The complete nucleotide sequence (134,525 bp) of the chloroplast genome from rice (Oryza sativa L.) contains four rRNA genes, 30 tRNA genes, and over 100 genes that encode proteins. However, expression of only a few of these genes, namely psbA, rbcL, and atpB/E, has been detected. We constructed the complete transcription map of rice chloroplast DNA by Northern hybridization of total RNA from rice seedlings, using subclones from a clone bank of rice chloroplast DNA as probes. Approximately 90% of the chloroplast genome was transcribed, as detected by a non-radioactive hybridization system. Most of the genes on the chloroplast DNA are organized as clusters and are co-transcribed as long primary transcripts. We identified 16 polycistronic transcripts from the rice chloroplast genome. Furthermore, the genes for components of photosystems I and II, the gene for the large subunit of RuBisCO, the genes for ATPase, the genes for components of the cytochrome complex, and the rRNA genes were expressed at the highest levels.

Structural alterations of the chloroplast genome found in grasses are not common in monocots

The distribution of structural rearrangements of the chloroplast genome found in grass cpDNA in comparison to that of tobacco was systematically checked in the cpDNAs of representative monocots. The physical map of lily cpDNA, which shares a key position in the diversity of monocotyledonous plants, was constructed to assess whether three inversions found in grass cpDNA are common in monocots. Specific probes for the detection of (1) intron loss in the rpoC1 gene, (2) insertional sequence gain in rpoC2, (3) deletion of ORF2280 in the inverted repeats, (4) non-reciprocal translocation of rpl23, and (5) rearrangements of ORF512, were hybridized to cpDNAs of lily, onion, spiderwort, two turf grasses, and wheat. The existence of intervening sequences in the rpoC1 and rpoC2 genes was also confirmed by PCR analysis. All markers used in the study revealed that structural rearrangements of the chloroplast genome were restricted to grasses, indicating that drastic structural alterations of the chloroplast genome had occurred in the ancestor(s) of grasses. These results also suggest that structural analysis of the chloroplast genome is applicable to the phylogenetic reconstruction of related plants.

Nucleotide sequence of maize chloroplast rpl32: completing the apparent set of plastid ribosomal protein genes and their tentative operon organization

By sequencing the rpl32 gene, we have characterized the apparent complete set of the RP genes in Zea mays plastid genome. Key data for these 21 genes (total of 26 gene copies) and the proteins encoded by them are presented, and the operon organization is discussed on the basis of available transcription data. A nomenclature for the inferred 13 operons is suggested.

DNA sequencing of the seven remaining structural genes of the gene cluster encoding the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans

In our previous papers, seven structural genes (NQO1-7) of the energy-transducing NADH-quinone (Q) oxidoreductase of Paracoccus denitrificans were characterized [Xu, X., Matsuno-Yagi, A., & Yagi, T. (1991a) Biochemistry 30, 8678-8684; (1991b) Biochemistry 30, 6422-6428; (1992a) Biochemistry 31, 6925-6932; (1992b) Arch. Biochem. Biophys. 296, 40-48]. This paper reports the identification, cloning, and sequencing of seven additional structural genes in the same gene cluster (P. denitrificans enzyme complex). These seven genes, designated NQO8-14, are composed of 1038, 492, 603, 306, 2112, 1542, and 1500 base pairs, respectively. The polypeptides encoded by the NQO8-14 genes are homologous, respectively, to the ND1 product, the 23-kDa polypeptide, and the ND6, ND4L, ND5, ND4, and ND2 products of the bovine NADH-Q oxidoreductase. The order of the 14 structural genes of the Paracoccus energy-transducing NADH-Q oxidoreductase in the gene cluster is NQ07, NQO6, NQO5, NQO2, NQO1, NQO3, NQO8, NQO9, NQO10, NQO11, NQO12, NQO13, and NQO14. Downstream from the NQO14 gene an open reading frame (designated URF240) was detected which encodes a predicted polypeptide homologous to the biotin [acetyl-CoA-carboxylase] ligase of Escherichia coli. In addition, a putative terminal sequence motif was observed downstream of the NQO14 gene, suggesting that the structural gene NQO14 is the 3'-terminal gene of the Paracoccus NADH-Q oxidoreductase gene cluster. Nucleotide sequencing of the entire gene cluster revealed the presence of three unidentified reading frames: one between the NQO3 and NQO8 genes and other two between the NQO9 and NQO10 genes. These are designated URF4, URF5, and URF6 and are composed of 768, 393, and 405 base pairs, respectively. The possible functions of the putative proteins encoded by URF5 and URF6 are discussed.

Chloroplast envelope protein encoded by chloroplast genome

The gene product of an open reading frame of chloroplast genome, ORF 231 in pea, was immunochemically detected in chloroplast and etioplast envelopes. This is the first protein of a Chloroplast Envelope Membrane encoded by a chloroplast genome. It was named CEM A and the gene, cem A. CEM A is an acidic protein having an apparent molecular mass of 34 kDa on SDS-PAGE, and a minor component detected in the fractionated inner envelope.

Purification and characterization of ribonucleoproteins from pea chloroplasts

RNA-binding proteins are known to mediate the post-transcriptional regulation of genes in many organisms. Recently they have been found to be important in the expression of plastid genes. We have purified a group of three single-stranded nucleic-acid-specific acidic proteins (33, 30 and 28 kDa) from chloroplast extracts of pea (Pisum sativum L.), using single-stranded DNA affinity chromatography. All of them have acidic amino termini but the amino acid sequences are unique to each polypeptide, with partial similarities to the recently reported ribonucleoproteins from tobacco chloroplasts. The pea proteins are also antigenically distinct, as shown by Western blot analysis using polyclonal antisera for purified proteins. Further, from their large nucleic-acid-binding domains and the polynucleotide substrate affinities, they are predicted to belong to a family of pea plastid ribonucleoproteins. In vivo radiolabeling of proteins in the presence of translational inhibitors as well as in vitro translation of leaf tissue RNA suggest that these proteins are encoded in the nucleus. Antibody cross-reactivity experiments reveal that their genes are conserved during plastid evolution.

SecA is plastid-encoded in a red alga: implications for the evolution of plastid genomes and the thylakoid protein import apparatus

Partial sequence analysis of the plastid DNA (ptDNA) from a red alga, Antithamnion sp., revealed the presence of a homologue to the Escherichia coli secA gene as well as two open reading frames (ORF 510, ORF 179). In addition a sec Y homologue has been detected on the plastid genome by heterologous hybridization. None of these genes has been found in completely sequenced chlorophytic plastid genomes. SecA and secY gene copies were also detected in the ptDNA of a chromophytic alga, indicating that secA Y may be ubiquitous in rhodophytes and chromophytes. The significance of these findings for the evolution of plastid genomes and the thylakoid protein import mechanism is discussed.

RNA editing in plant mitochondria and chloroplasts

In the mitochondria and chloroplasts of flowering plants (angiosperms), transcripts of protein-coding genes are altered after synthesis so that their final primary nucleotide sequence differs from that of the corresponding DNA sequence. This posttranscriptional mRNA editing consists almost exclusively of C-to-U substitutions. Editing occurs predominantly within coding regions, mostly at isolated C residues, and usually at first or second positions of codons, thereby almost always changing the amino acid from that specified by the unedited codon. Editing may also create initiation and termination codons. The net effect of C-to-U RNA editing in plants is to make proteins encoded by plant organelles more similar in sequence to their nonplant homologs. In a few cases, a strong argument can be made that specific C-to-U editing events are essential for the production of functional plant mitochondrial proteins. Although the phenomenon of RNA editing in plants is now well documented, fundamental questions remain to be answered: What determines the specificity of editing? What is the biochemical mechanism (deamination, base exchange, or nucleotide replacement)? How did the system evolve? RNA editing in plants, as in other organisms, challenges our traditional notions of genetic information transfer.

Nucleotide sequence and homology comparison of two genes of the sulfate transport operon from the cyanobacterium Synechocystis sp. PCC 6803

The genome of Synechocystis sp. PCC 6803 contains an operon with homology to the sulfate permease of other prokaryotes. We used antibodies raised against cytoplasmic membrane protein to find three genes with strong homology to sbpA, orf81 and cysT genes of the cyanobacterium Synechococcus sp. PCC 7942, Escherichia coli, Salmonella typhimurium and Marchantia polymorpha. It is likely that the permease genes are expressed and the proteins are inserted into the cytoplasmic membrane.

Two amino-acid biosynthetic genes are encoded on the plastid genome of the red alga Porphyra umbilicalis

To isolate the gene encoding the amino-acid biosynthetic enzyme acetolactate synthase (ALS) from the red alga Porphyra umbilicalis, PCR experiments were carried out using P. umbilicalis DNA as the template and degenerate oligonucleotides representing conserved regions of ALS amino-acid sequences. Interestingly, the PCR product (0.9 kb) hybridized exclusively to the plastid DNA of this red alga. DNA sequencing of two contiguous EcoRI plastid DNA clones revealed a 590 amino-acid open reading frame with 55 to 61% identity to cyanobacterial ALS sequences. A second gene (argB) encoding another amino-acid biosynthetic enzyme, N-acetylglutamate kinase, was identified upstream of, and on the opposite strand to the gene encoding ALS (ilvB). This is the first molecular characterization of a gene for an arginine biosynthetic enzyme from any plant. In addition, two tRNA genes, trnT(GGU) and trnY(GUA), were detected downstream from ilvB while four tRNA genes, trnfM(CAU), trnA(GGC), trnA(GGC), trnS(-GCU) and trnD(GUC), were found downstream from argB. trnA(GGC) is not found in the chloroplast genomes of land plants.

A chloroplast DNA deletion located in RNA polymerase gene rpoC2 in CMS lines of sorghum

Fertile lines of sorghum (Sorghum bicolor) were shown to differ from cytoplasmic male sterile (CMS) lines by the presence of a 3.8 kb HindIII chloroplast DNA fragment in the former and a smaller (3.7 kb) fragment in the latter. DNA/DNA hybridization studies showed that these two fragments are homologous. Fertile plants from S. versicolor, S. almum, S. halepense, and Sorghastrum nutans (Yellow Indiangrass) also have the 3.8 kb fragment, and CMS lines studied containing A1, A2 and A3 cytoplasms have the 3.7 kb fragment. The size difference between the two fragments was localized to a 1.0 kb SacI-HindIII fragment by restriction mapping. A 165 bp deletion, which is flanked by a 51 bp tandem repeat, was identified in the CMS lines by sequencing the clones. Comparison of the two sequences with those from maize, rice, tobacco, spinach, pea, and liverwort revealed that the deleted sequence is located in the middle of the RNA polymerase beta" subunit encoded by the gene rpoC2. The amino acid sequence deleted in the CMS lines is in a monocot-specific region which contains two protein motifs that are characteristic of several transcriptional activation factors, namely, a leucine zipper motif and an acidic domain capable of forming an amphipathic alpha-helix. Further studies designed to determine whether or not the deletion is involved in CMS of sorghum are underway.

A beta-ketoacyl-acyl carrier protein synthase III gene (fabH) is encoded on the chloroplast genome of the red alga Porphyra umbilicalis

DNA sequencing of a region of the chloroplast genome of the red alga Porphyra umbilicalis revealed an open reading frame of 326 amino acids. Databank searches indicated that this ORF is 34% identical to an E. coli gene (fabH) encoding beta-ketoacyl-carrier protein synthase III. In addition, a leucine tRNA gene (trnL(GAG)) was detected just downstream. Neither of these genes are encoded on the chloroplast genomes of land plants.

Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice

The entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare) was identified using clone banks that cover the chloroplast and mitochondrial genomes. The mitochondrial fragments that were homologous to chloroplast DNA were mapped and sequenced. The nucleotide sequences around the termini of integrated chloroplast sequences in the rice mtDNA revealed no common sequences or structures that might enhance the transfer of DNA. Sixteen chloroplast sequences, ranging from 32 bases to 6.8 kb in length, were found to be dispersed throughout the rice mitochondrial genome. The total length of these sequences is equal to approximately 6% (22 kb) of the rice mitochondrial genome and to 19% of the chloroplast genome. The transfer of segments of chloroplast DNA seems to have occurred at different times, both before and after the divergence of rice and maize. The mitochondrial genome appears to have been rearranged after the transfer of chloroplast sequences as a result of recombination at these sequences. The rice mitochondrial DNA contains nine intact tRNA genes and three tRNA pseudogenes derived from the chloroplast genome.

Large unidentified open reading frame in plastid DNA (ORF2280) is expressed in chloroplasts

The chloroplast DNA encodes genes for components of photosynthesis and the transcription-translation machinery; a number of unidentified open reading frames (ORFs) are also present. To determine whether a large ORF in the inverted repeat of chloroplast DNA of tobacco (ORF2280) encodes a chloroplast protein, a conserved region of the ORF was expressed in Escherichia coli. An antibody against the ORF protein was prepared using the purified fusion protein as an antigen. When incubated with proteins from the soluble fraction of tobacco, spinach and Oenothera chloroplasts, the antiserum detects relatively labile polypeptides, which have apparent molecular weights of 170 to 180 kDa. The ORF in tobacco and spinach is large enough to encode a protein of 240-250 kDa, thus it is possible that post-transcriptional or post-translational processing reduces the size of the expression product. Analysis of Oenothera chloroplasts representing four different plastome types revealed endonuclease restriction fragment length polymorphisms in chloroplast DNA indicative of insertion/deletion events in a region of the chloroplast DNA that shared significant sequence similarity with ORF2280. The ORF2280 antiserum was used to demonstrate that there are qualitative differences in the ORF proteins from different Oenothera plastome types.

Identification of editing positions in the ndhB transcript from maize chloroplasts reveals sequence similarities between editing sites of chloroplasts and plant mitochondria

A comparison of the nucleotide sequences from genomic DNA and cDNA of the ndhB gene from maize chloroplasts shows that the ndhB transcript is edited by C-to-U transitions at six positions which appear to exist as editing sites also in the chloroplast ndhB genes from rice and tobacco but not from liverwort. In order to identify possible sequence determinants necessary for editing, the sequences surrounding the newly identified ndhB and previously identified ndhA editing sites were compared with each other and with editing sites observed in plant mitochondrial transcripts. Among the chloroplast editing sites two closely positioned ndhB sites show similarity by sharing a common octanucleotide. The existence of the identical octanucleotide in the ndhJ gene whose transcript is not edited at the respective position, shows, however, that this octanucleotide is not sufficient to elicit the editing process. On the other hand, several of the chloroplast editing sites show sequence similarities with certain sets of consensus sequences reported earlier for editing sites of plant mitochondria. This supports the view that the editing processes of both plant organelles share common components and/or mechanistic steps and that the consensus sequences are part of the determinants necessary for editing.

Evolution of linear plasmids

Linear plasmids are genetic elements commonly found in yeast, filamentous fungi, and higher plants. In contrast to all other plasmids they possess terminal inverted repeats and terminal bound proteins and encode their own DNA and RNA polymerases. Here we present alignments of conserved amino acid sequences of both the DNA and RNA polymerases encoded by those linear plasmids for which DNA sequence data are available. Additionally these sequences are compared to a number of polymerases encoded by related viral and cellular entities. Phylogenetic trees have been established for both types of polymerases. These trees appear to exhibit very similar subgroupings, proving the accuracy of the method employed.

Evolutionary analysis of the plastid-encoded gene for the alpha subunit of the DNA-dependent RNA polymerase of Pyrenomonas salina (Cryptophyceae)

The nucleotide sequence of the gene coding for the plastid-encoded alpha subunit of DNA-dependent RNA polymerase from the cryptomonad alga Pyrenomonas salina was determined. The deduced amino-acid sequence, corresponding to a 35.2 kDa polypeptide, was compared to homologues from other organisms. Evolutionary relationships were analyzed in detail by the parsimony method together with bootstrap analysis. The deduced phylogenetic tree shows that the cryptomonad gene is the most ancient type of known plastid-encoded RNA polymerase.

Dynamical behavior of psb gene transcripts in greening wheat seedlings. I. Time course of accumulation of the pshA through psbN gene transcripts during light-induced greening

The time course of the accumulation of the transcripts from 13 psb genes encoding a major part of the proteins composing photosystem II during light-induced greening of dark-grown wheat seedlings was examined focusing on early stages of plastid development (0.5 h through 72 h). The 13 genes can be divided into three groups. (1) The psbA gene is transcribed as a single transcript of 1.3 kb in the dark-grown seedlings, but its level increases 5- to 7-fold in response to light due to selective increase in RNA stability as well as in transcription activity. (2) The psbE-F-L-J operon, psbM and psbN genes are transcribed as a single transcript of 1.1 kb, two transcripts of 0.5 and 0.7 kb and a single transcript of 0.3 kb, respectively, in the dark-grown seedlings. The levels of accumulation of every transcript remain unchanged or rather decrease during plastid development under illumination. (3) The psbK-I-D-C gene cluster and psbB-H operon exhibit fairly complicated northern hybridization patterns during the greening process. When a psbC or psbD gene probe was used for northern hybridization, five transcripts differing in length were detected in the etioplasts from 5-day old dark-grown seedlings. After 2 h illumination, two new transcripts of different length appeared. Light induction of new transcripts was also observed in the psbB-H operon.

Tobacco nuclear DNA contains long tracts of homology to chloroplast DNA

Long tracts of DNA with high sequence homology to chloroplast DNA were isolated from nuclear genomic libraries of Nicotiana tabacum. One lambda EMBL4 clone was characterised in detail and assigned to nuclear DNA. The majority of the 15.5-kb sequence is greater than 99% homologous with its chloroplast DNA counterpart, but a single base deletion causes premature termination of the reading frame of the psaA gene. One region of the clone contains a concentration of deleted regions, and these were used to identify and quantify the sequence in native nuclear DNA by polymerase chain reaction (PCR) methods. An estimated 15 copies of this specific region are present in a 1c tobacco nucleus.

Large ATP synthase operon of the red alga Antithamnion sp. resembles the corresponding operon in cyanobacteria

The large plastid ATP synthase operon of the multicellular red alga Antithamnion sp. was cloned and the sequence of six ATPase genes determined. The operon resembles more the one from cyanobacteria than the ATP synthase operon of the chloroplast genome. The gene order is atpI, H, G, F, D and A, coding for the ATPase subunits a, c, b', b, delta and alpha, respectively. In green plants, the genes atpG and atpD are located in the nucleus. Unlike the situation in three published cyanobacterial ATP synthase operons, atpC, coding for the gamma subunit, is not a part of the rhodoplast operon. A single 4.5 kb transcript was detected with atpG, F, D and A gene probes that could span the whole operon, but no transcript could be detected with atpI and atpH probes. The end of an open reading frame preceding the atp genes shows remarkable homology to elongation factor TS from Escherichia coli. Behind the ATPase cluster, two open reading frames were detected that are not homologous to any known chloroplast gene. One of them may code for a transport protein of unknown specificity. Gene arrangement and sequence comparisons support the hypothesis of a polyphyletic origin of rhodoplasts and chloroplasts.

Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes

The vestigial plastid genome of Epifagus virginiana (beechdrops), a nonphotosynthetic parasitic flowering plant, is functional but lacks six ribosomal protein and 13 tRNA genes found in the chloroplast DNAs of photosynthetic flowering plants. Import of nuclear gene products is hypothesized to compensate for many of these losses. Codon usage and amino acid usage patterns in Epifagus plastic genes have not been affected by the tRNA gene losses, though a small shift in the base composition of the whole genome (toward A+T-richness) is apparent. The ribosomal protein and tRNA genes that remain have had a high rate of molecular evolution, perhaps due to relaxation of constraints on the translational apparatus. Despite the compactness and extensive gene loss, one translational gene (infA, encoding initiation factor 1) that is a pseudogene in tobacco has been maintained intact in Epifagus.

Conformity of RNAs that interact with tetranucleotide loop binding proteins

A group of RNA binding proteins, termed tetraloop binding proteins, includes ribosomal protein S15 and protein SRP19 of signal recognition particle. They are primary RNA binding proteins, recognize RNA tetranucleotide loops with a GNAR consensus motif, and require a helical region located adjacent to the tetraloop. Closely related RNA structures that fit these criteria appear in helix 6 of SRP RNA, in helices 22 and 23A of 16 S ribosomal RNA, and, as a pseudoknot, in the regulatory region of the rpsO gene.

Structural analysis of length mutations in a hot-spot region of wheat chloroplast DNAs

The hot-spot region related to length mutations in the chloroplast genome of the wheat group was precisely analyzed at the DNA sequence level. This region, located downstream from the rbcL gene, was highly enriched in A + T, and contained a number of direct and inverted repeats. Many deletions/insertions were observed in the region. In most deletions/insertions of multiple nucleotides, short repeated sequences were found at the mutation points. Furthermore, a pair of short repeated sequences was also observed at the border of the translocated gene. A sequence homologous with ORF512 of tobacco cpDNA was truncated in cpDNAs of the wheat group and found only in the mitochondrial DNA of Ae. crassa, suggesting the inter-organellar translocation of this sequence. Mechanisms that could generate structural alterations of the chloroplast genome in the wheat group are discussed.

A homolog of Escherichia coli RecA protein in plastids of higher plants

Studies of chloroplast DNA variations, and several direct experimental observations, indicate the existence of recombination ability in algal and higher plant plastids. However, no studies have been done of the biochemical pathways involved. Using a part of a cyanobacterial recA gene as a probe in Southern blots, we have found homologous sequences in total DNA from Pisum sativum and Arabidopsis thaliana and in a cDNA library from Arabidopsis. A cDNA was cloned and sequenced, and its predicted amino acid sequence is 60.7% identical to that of the cyanobacterial RecA protein. This finding is consistent with our other results showing both DNA strand transfer activity and the existence of a protein of the predicted molecular mass crossreactive with antibodies to Escherichia coli RecA in the stroma of pea chloroplasts.

Chloroplast DNA inversions and the origin of the grass family (Poaceae)

The phylogenetic affinities of the grass family (Poaceae) have long been debated. The chloroplast genomes of at least some grasses have been known to possess three inversions relative to the typical gene arrangement found in most flowering plants. We have surveyed for the presence of these inversions in grasses and other monocots by polymerase chain reaction amplification with primers constructed from sequences flanking the inversion end points. Amplification phenotypes diagnostic for the largest inversion (28 kilobase pairs) were found in genera representing all grass subfamilies, and in the nongrass families Restionaceae, Ecdeiocoleaceae, and Joinvilleaceae, but not in any other monocots--notably, Flagellariaceae, Anarthriaceae, Cyperaceae, or Juncaceae. This finding is consistent with one of the two principal views of grass phylogeny in suggesting that Poaceae and Cyperaceae (sedges) are not closest relatives. A second (approximately 6 kilobases) inversion appears to occur in a subset of the families possessing the 28-kilobase inversion and links Joinvilleaceae and Poaceae, while the smallest inversion appears unique to grasses. These inversions thus provide a nested set of phylogenetic characters, indicating a hierarchy of relationships in the grasses and allies, with Joinvilleaceae identified as the likely sister group to the Poaceae.

Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes

The DNA sequence of 91.4 kilobases of the Escherichia coli K-12 genome, spanning the region between rrnC at 84.5 minutes and rrnA at 86.5 minutes on the genetic map (85 to 87 percent on the physical map), is described. Analysis of this sequence identified 82 potential coding regions (open reading frames) covering 84 percent of the sequenced interval. The arrangement of these open reading frames, together with the consensus promoter sequences and terminator-like sequences found by computer searches, made it possible to assign them to proposed transcriptional units. More than half the open reading frames correlated with known genes or functions suggested by similarity to other sequences. Those remaining encode still unidentified proteins. The sequenced region also contains several RNA genes and two types of repeated sequence elements were found. Intergenic regions include three "gray holes," 0.6 to 0.8 kilobases, with no recognizable functions.

The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains

The inner membranes of mitochondria contain three multi-subunit enzyme complexes that act successively to transfer electrons from NADH to oxygen, which is reduced to water (Fig. I). The first enzyme in the electron transfer chain, NADH:ubiquinone oxidoreductase (or complex I), is the subject of this review. It removes electrons from NADH and passes them via a series of enzyme-bound redox centres (FMN and Fe-S clusters) to the electron acceptor ubiquinone. For each pair of electrons transferred from NADH to ubiquinone it is usually considered that four protons are removed from the matrix (see section 4.1 for further discussion of this point).

Nuclear-encoded chloroplast ribosomal protein L27 of Nicotiana tabacum: cDNA sequence and analysis of mRNA and genes

A tobacco (Nicotiana tabacum cv. Petite Havana) leaf cDNA library was constructed in the expression vector lambda gt11. Immunological and nucleic acid hybridization screening yielded several cDNAs encoding an M(r) 19,641 precursor to an M(r) 14,420 mature protein which is homologous to Escherichia coli ribosomal protein L27. One cDNA (L27-1; 882 nucleotides long) contains 104 bp of 5'-noncoding sequence, 51 codons for a transit peptide, 128 codons for the predicted mature L27 polypeptide, and 241 bp of 3'-noncoding sequence, including the poly(A)29 tail. A beta-galactosidase-L27 fusion protein was bound to nitrocellulose filters, expressed, and used as an affinity matrix to purify monospecific antibody to L27 protein from an antiserum of rabbits immunized with 50S chloroplast ribosomal proteins. Using this monospecific antibody, protein L27 was identified among HPLC-purified tobacco chloroplast ribosome 50S subunit proteins. The predicted amino terminus of the mature L27 protein was confirmed by partial sequencing of the HPLC-purified L27 protein. The mature L27 protein has 66%, 61%, 56%, and 48% amino acid sequence identity with the L27-type ribosomal proteins of Bacillus subtilis, E. coli, Bacillus stearo-thermophilus, and yeast mitochondria (MRP7), respectively, in the homologous overlapping regions. The transit peptide of tobacco chloroplast ribosomal protein L27 has 41% amino acid sequence similarity with the MRP7 mitochondrial targeting sequence. Tobacco chloroplast L27 protein also has a 40 amino acid long carboxyl-terminal extension (compared to its bacterial counterparts) which is similar to the corresponding portion of yeast MRP7.(ABSTRACT TRUNCATED AT 250 WORDS)