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

Occurrence of oligopurine.oligopyrimidine tracts in eukaryotic and prokaryotic genes

A program to analyse the length and frequency distribution of specific base tracts in genomic sequences is described. The frequency of oligopurine.oligopyrimidine tracts (R.Y. tracts) in a data base of 163 transcribed genes is analysed and compared. The complete genomes of SV40 virus, N. tobacum chloroplast, yeast 2 micron plasmid, bacteriophage lambda, plasmid pBR322 and the E. coli lac operon are also analyzed. A highly significant overrepresentation of oligopurine and oligopyrimidine tracts is observed in all eukaryotic genes examined, as well as in the chloroplast genome. The overrepresentation is evident in all gene subregions of the chloroplast, in the following order: intergenic regions, 3' downstream and 5' upstream (promoter), 5' and 3' untranslated, introns and coding regions. In genes coding for basic proteins, oligopurine rather than oligopyrimidine tracts are found on the coding stand. In prokaryotic genes only the longest R.Y. tracts (greater than or equal to 12) are found in excess, and are concentrated near regulatory regions. While a structural role for R.Y. tracts is most likely in intergenic regions, a functional role, as initiation sites for strand separation, is proposed for regulatory gene regions.

Evolution of RNA polymerases and branching patterns of the three major groups of Archaebacteria

The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses. It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree. The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage. This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases. It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half of RNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints. In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited. In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method. It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues.

Chloroplast ribosomal protein L32 is encoded in the chloroplast genome

The 50 S subunit of chloroplast ribosomes was prepared from tobacco leaves. The proteins were fractionated and the N-terminal amino acid sequence of a 14 kDa protein was determined. This sequence matches the N-terminal sequence deduced from ORF55 located between ndhF and trnL on the small single-copy region of tobacco chloroplast DNA. The deduced protein shows homology to E. coli and B. stearothermophilus L32 proteins, and it has been named as CL32 and ORF55 as rpl32. The tobacco chloroplast genome therefore contains 21 different ribosomal protein genes.

Optimization of delivery of foreign DNA into higher-plant chloroplasts

We report here an efficient and highly reproducible delivery system, using an improved biolistic transformation device, that facilitates transient expression of beta-glucuronidase (GUS) in chloroplasts of cultured tobacco suspension cells. Cultured tobacco cells collected on filter papers were bombarded with tungsten particles coated with pUC118 or pBI101.3 (negative controls), pBI505 (positive nuclear control) or a chloroplast expression vector (pHD203-GUS), and were assayed for GUS activity. No GUS activity was detected in cells bombarded with pUC118 or pBI101.3. Cells bombarded with pBI505 showed high levels of expression with blue color being distributed evenly throughout the whole cytosol of the transformants. pHD203-GUS was expressed exclusively in chloroplasts. We base this conclusion on: i) the procaryotic nature of the promoter used in the chloroplast expression vector; ii) delayed GUS staining; iii) localization of blue color within subcellular compartments corresponding to plastids in both shape and size; and iv) confirmation of organelle-specific expression of pHD203-GUS using PEG-mediated protoplast transformation. Chloroplast transformation efficiencies increased dramatically (about 200-fold) using an improved helium-driven biolistic device, as compared to the more commonly used gun powder charge-driven device. Using GUS as a reporter gene and the improved biolistic device, optimal bombardment conditions were established, consistently producing several hundred transient chloroplast transformants per Petri plate. Chloroplast transformation efficiency was found to be increased further (20-fold) with supplemental osmoticum (0.55 M sorbitol and 0.55 M mannitol) in the bombardment and incubation medium. This system provides a highly effective mechanism for introducing and expressing plasmid DNA within higher-plant chloroplasts, and the fact that GUS functions as an effective marker gene now makes many genetic studies possible which were not possible before.

Genes for ribosomal proteins are retained on the 73 kb DNA from Astasia longa that resembles Euglena chloroplast DNA

The nucleotide sequence of a 6.7 kb segment of the circular 73 kb DNA from Astasia longa has been determined. We identified genes for a tRNA-Ile (CAU), a tRNA-Phe (GAA), a tRNA-Cys (GCA) and the ribosomal proteins CS8, CL36, CS14 and CS2, that are normally encoded by plastid genomes. In addition, a gene for the chloroplast ribosomal protein CL5 was found that is not encoded by the plastome in either higher plants or a liverwort, but has recently been identified in Euglena chloroplast DNA. Transcripts of these protein genes, and of an unidentified open reading frame (ORF50), were detected. These results support our previous suggestion that the 73 kb DNA from Astasia is a truncated form of plastid DNA. The 73 kb DNA resembles the chloroplast DNA of Euglena gracilis but contains, almost exclusively, genes for a plastid-type translational (and presumably transcriptional) apparatus.

Expression of the wheat chloroplast gene for CF0 subunit IV of ATP synthase

The nucleotide sequence of the wheat chloroplast atp I gene encoding CF0 subunit IV of ATP synthase has been determined. The gene encodes a polypeptide of 247 amino acid residues with high sequence similarity to subunit IV from other plant chloroplasts and from cyanobacteria. The polypeptide shows sequence homology to the C-terminus of the F0 alpha subunit of Escherichia coli ATP synthase and subunit 6 of mitochondrial ATP synthase. The atp I gene is co-transcribed with the atp H, atp F and atp A genes for other subunits of ATP synthase in wheat. A gene-fusion of most of the atp I coding region with cro'-lacI'-lacZ' has been constructed in pEX2 and the fusion-protein has been used to raise antibodies in rabbits. The antibodies react with a polypeptide of 17 kDa in wheat thylakoid membranes indicating that the wheat atp I gene is expressed at the protein level. A model for the organisation of the polypeptide in the thylakoid membrane with four membrane-spanning segments is proposed.

DNA polymerase activity of tomato fruit chromoplasts

DNA polymerase activity was measured in chromoplasts of ripening tomato fruits. Plastids isolated from young leaves or mature red fruits showed similar DNA polymerase activities. The same enzyme species was present in either chloroplasts or chromoplasts as judged by pH and temperature profiles, sensitivities towards different inhibitors and relative molecular mass (Mr 88 kDa). The activities analyzed showed the typical behaviour of plastid-type polymerases. The results presented here suggest that chromoplast maintain their DNA synthesis potential in fruit tissue at chloroplast levels. Consequently, the sharp decrease of the plastid chromosome transcription observed at the onset of fruit ripening could not be due to limitations in the availability of template molecules. Other mechanisms must be involved in the inhibition of chromoplast RNA synthesis.

Nuclear mutation restores the reduced CO2/O2 specificity of ribulosebisphosphate carboxylase/oxygenase in a temperature-conditional chloroplast mutant of Chlamydomonas reinhardtii

The Chlamydomonas reinhardtii temperature-sensitive mutant 68-4PP results from a mutation within the chloroplast gene that encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. When grown at the permissive temperature (25 degrees C), the mutant has a reduced level of holoenzyme protein, and the purified enzyme has a lower CO2/O2 specificity than the wild-type enzyme. At the nonpermissive temperature (35 degrees C), the holoenzyme level is greatly reduced, and the mutant is unable to grow photosynthetically. When photosynthesis-competent revertants of 68-4PP were selected at 35 degrees C, a nuclear mutation was identified that suppresses the temperature-sensitive phenotype by enhancing both the activity and amount of the mutant enzyme. More significantly, the reduced CO2/O2 specificity of the 68-4PP enzyme is restored to the wild-type value. However, the nuclear suppressor mutation alone does not produce a phenotype different from wild type, and the CO2/O2 specificity of the suppressor strain's enzyme is normal. We have cloned and completely sequenced the two small-subunit genes from the suppressor strain, but no mutation has been found. These results suggest that some other nuclear-encoded protein is able to influence the structure of the holoenzyme, which in turn influences the CO2/O2 specificity factor.

Cellular differentiation in the process of generation of the eukaryotic cell

Primitive atmosphere of the earth did not contain oxygen gas (O2) when the proto-cells were generated successfully as the result of chemical evolution and then evolved. Therefore, they first had acquired anaerobic energy metabolism, fermentation. The cellular metabolisms have often been formed by reorganizing to combine or recombinate between pre-existing metabolisms and newly born bioreactions. Photosynthetic metabolism in eukaryotic chloroplast consists of an electron-transfer photosystem and a fermentative reductive pentose phosphate cycle. On the other hand, O2-respiration of eukaryotic mitochondrion is made of Embden-Meyerhof (EM) pathway and tricarboxylic acid cycle, which originate from a connection of fermentative metabolisms, and an electron-transfer respiratory chain, which has been derived from the photosystem. These metabolisms already are completed in some evolved prokaryotes, for example the cyanobacterium Chlorogloea fritschii and aerobic photosynthetic bacteria Rhodospirillum rubrum and Erythrobacter sp. Therefore, it can be reasonably presumed that the eukaryotic chloroplast and mitochondrion have once been formed as the result of metabolic (and genetic) differentiations in most evolved cyanobacterium. Symbiotic theory has explained the origin of eukaryotic cell as that in which the mitochondrion and chloroplast have been derived from endosymbionts of aerobic bacterium and cyanobacterium, respectively, and has mentioned as one of the most potent supportive evidences that amino acid sequences of the photosynthetic and O2 -respiratory enzymes show similarities to corresponding prokaryotic enzymes. However, as will be shown in this discussion, many examples have shown currently that prokaryotic sequences of informative molecules are conserved well not only in those of the mitochondrial and chloroplast molecules but also in the nuclear molecules. In fact, the similarities in sequence of informative molecules are preserved well among the organisms not only in phylogenetically close relationships but also under highly selective pressure, that is under a physiological constraint for the species in their habitats. Therefore, the similarities in amino acid sequences of proteins between the prokaryotes and the organelles are not necessarily direct evidence for their phylogenetical closeness: it gives still less evidence for a symbiotic relationship between the prokaryotes and the organelles. The metabolic compartmentalization of the membranes is an important tendency in cellular evolution to guarantee high specificity and rate of the metabolisms. It is suggested from the data that the intracellular membranes are not static but undergo dynamic turnover. Furthermore, these facts strongly support the Membrane Evolution Theory which was proposed by one of the authors in 1975.

The chloroplast psbK operon from mustard (Sinapis alba L.): multiple transcripts during seedling development and evidence for divergent overlapping transcription

The mustard chloroplasts genes psbK and psbI are co-transcribed, giving rise to precursor transcripts of several size classes, which are processed to the monocistronic mature RNAs. The psbK and psbI coding regions are flanked by the two tRNA genes trnS-GCU and trnQ-UUG on the opposite DNA strand. Transcript mapping indicates that the (primary) psbK-psbI transcript overlaps the complete trnS-GCU and trnQ-UUG transcripts. The transcription start site of the psbK operon appears to overlap that of the rps16 gene. During seedling development, the psbK and psbI precursors and mature transcripts all become detectable between 30 and 48 h after sowing and then remain at constant levels without much difference either in light or in darkness.

The cytochrome oxidase subunit III gene in sunflower mitochondria is cotranscribed with an open reading frame conserved in higher plants

The gene encoding subunit III of cytochrome oxidase (COXIII) has been identified in the sunflower mitochondrial genome. The COXIII coding region is located 570 bp downstream of a 477 bp open reading frame (ORFB). Sequence comparisons and hybridization experiments show that ORFB sequences are conserved in other plant mitochondrial genomes. Nucleotide and amino acid sequence comparisons suggest that RNA editing is required in sunflower mitochondria to synthesize a functional COXIII polypeptide.

The cyanelle S10 spc ribosomal protein gene operon from Cyanophora paradoxa

In Cyanophora paradoxa photosynthetic organelles termed cyanelles perform the functions of chloroplasts in higher plants, while the structural and biochemical characteristics of the cyanelle are essentially cyanobacterial. Our interest in studying the evolutionary relationship between cyanelles and chloroplasts led us to focus on cyanelle-encoded genes of the translational apparatus, specifically genes equivalent to those of the bacterial S10 and spc operons. The structure of a large ribosomal protein gene cluster from cyanelle DNA was characterized and compared with that from plastids and bacteria. Sequences of the following cyanelle genes encompassing 4.8 kb are reported here: 5'-rpl22-rps3-rpl16-rps17-rpl14-rpl5-rps8-rpl6-rpl18- rps5-3'. Cyanelles contain five more ribosomal protein genes than do higher plant chloroplasts and four more genes than Euglena gracilis plastids in the S10/spc region of this gene cluster. The gene encoding rpl36 is absent, in contrast to the case in other plastid DNAs. These genes, including the previously characterized genes rpl3, rpl2 and rps19, are transcribed as a primary transcript of approximately 7500 nucleotides. The occurrence of transcripts smaller than this presumptive primary transcript suggests that it is processed into defined segments. Transcription terminates 3' of rps5 where a 40 bp hairpin with one mismatch (-42.2 kcal) may be folded. Immediately downstream of rps5 an open reading frame, ORF492, is contained on a separate transcript. A comparison of gene content, operon structure and deduced amino acid sequence of the genes in the S10 and spc operons from different organisms supports the notion that cyanelles are intermediary between known plastids and cyanobacteria.

Codon reading properties of an unmodified transfer RNA

We have previously shown that the Mycoplasma mycoides glycine tRNA (anticodon UCC) effectively reads the codons GGU and GGC in violation of the classic codon reading rules. We have attempted to elucidate what structural elements in this tRNA molecule confer this translational property and in the course of this investigation T7 RNA polymerase transcription of the corresponding gene was used to produce a tRNA devoid of modified nucleosides. Using an in vitro translation system the ability of this tRNA to read the 4 glycine codons (GGU, GGC, and GGG) was tested and it was shown to be as efficient as its normal, fully modified counterpart in the reading of all four codons. This result demonstrates that a tRNA devoid of modified nucleosides is able to efficiently sustain protein synthesis in vitro and, furthermore, that the normal modification pattern of the Mycoplasma glycine tRNA is not essential for the ability of this tRNA to read the glycine codons GGU and GGC effectively.

Stem-loop structures at the 3' end of tobacco Rubisco large subunit mRNA

There are two inverted repeat nucleotide (nt) sequences, each capable of forming a stem-loop structure (sls) at the 3' end of the tobacco Rubisco large subunit mRNA (rbcL). The smaller sls is followed by a larger sls. The in vivo functions of the 3' sls of the rbcL mRNA were characterized using the Escherichia coli system. S 1 mapping of the rbcL transcripts synthesized in E. coli revealed that the 3' end of a major transcript in the bacterial cell is almost identical to the 3' end of authentic chloroplast (cp) rbcL mRNA. This native 3' end is located 4 nt downstream from the larger sls for the cp mRNA and 6 nt for the bacterial transcript, respectively. Deletion experiments show that the larger sls is essential for producing the native 3' end of rbcL mRNA in E. coli. The sls do not function as an efficient transcription terminator but can stabilize upstream mRNA segments in vivo.

The ndhH genes of gramminean plastomes are linked with the junctions between small single copy and inverted repeat regions

The junctions JSA and JSB between the two inverted repeat regions IRA and IRB and the small single copy region of the maize chloroplast DNA have been identified by DNA sequencing. The JSA junction coincides with the initiation codon of the ndhH gene which is encoded by the adjacent region of the small single copy region. A comparison with the plastomes of rice, rye, tobacco and liverwort shows that linkage of this junction with the ndhH gene is specific for gramminean species. The amino acid sequences deduced from the ndhH genes show conserved histidine and cysteine residues which are likely to form a metal-binding domain.

Three distinct ribonucleoproteins from tobacco chloroplasts: each contains a unique amino terminal acidic domain and two ribonucleoprotein consensus motifs

Chloroplasts contain their own genetic system. Eighteen different split genes have been found among approximately 130 chloroplast genes from higher plants. However, little is known about the chloroplast splicing system. Mammalian heterogeneous nuclear ribonucleoproteins (hnRNP proteins) have been shown to be involved in splicing. We applied a purification procedure developed for HeLa cell hnRNP proteins, which uses a single-stranded DNA (ssDNA) affinity column, directly to the tobacco chloroplast lysate to isolate their chloroplast counterparts. Four proteins (mol. wt approximately 30 kd) bound strongly to the column. The amino-terminal sequences of three of them were determined and their cDNA clones were isolated from a tobacco leaf cDNA library. Sequence analysis of these clones revealed that all three proteins contain two ribonucleoprotein consensus sequences (RNP-CS), confirming their ribonucleoprotein (RNP) nature. The presence of putative transit peptides in their predicted protein sequences, and an in vitro import experiment confirmed they are located in the chloroplast. This is the first report of organellar proteins containing RNP-CS. In addition, these three chloroplast proteins have a very acidic amino-terminal domain, a novel feature among RNP proteins identified so far. They are expressed both in leaves and roots; their mRNA levels showed different light modulation in mature leaves. The three proteins might be involved in splicing and/or processing of chloroplast RNAs.

The nucleotide sequence of abutilon mosaic virus reveals prokaryotic as well as eukaryotic features

The complete nucleotide sequence of abutilon mosaic virus (West Indian isolate, AbMVa) is presented. The resulting genomic structure resembles that of other geminiviruses which are transmitted by the whitefly Bemisia tabaci: AbMV possesses a bipartite circular genome with bidirectional orientation of the open reading frames (ORF). Both components have a common region of 180 bases with 99% homology while the rest of their sequence is distinct. Eukaryotic regulatory transcription elements precede most ORFs and polyadenylation signals are present at the end of most ORFs. However, two ORFs show features of prokaryotic genes. This chimaeric genome organisation is discussed with reference to the finding that AbMV DNA is present in plastids as well as in the nucleus of infected cells.

Cloning and characterization of RNA polymerase core subunits of Chlamydia trachomatis by using the polymerase chain reaction

Taking advantage of sequence conservation of portions of the alpha, beta, and beta' subunits of RNA polymerase of bacteria and plant chloroplasts, we have designed degenerate oligonucleotides corresponding to these domains and used these synthetic DNA sequences as primers in a polymerase chain reaction to amplify DNA sequences from the chlamydial genome. The polymerase chain reaction products were used as a probe to recover the genomic fragments encoding the beta subunit and the 5' portion of the beta' subunit from a library of cloned murine Chlamydia trachomatis DNA. Similar attempts to recover the alpha subunit were unsuccessful. Sequence analysis demonstrated that the beta subunit of RNA polymerase was located between genes encoding the L7/L12 ribosomal protein and the beta' subunit of RNA polymerase; this organization is reminiscent of the rpoBC operon of Escherichia coli. The C. trachomatis beta subunit overproduced in E. coli was used as an antigen in rabbits to make a polyclonal antibody to this subunit. Although this polyclonal antibody specifically immunoprecipitated the beta subunit from Chlamydia-infected cells, it did not immunoprecipitate core or holoenzyme. Immunoblots with this antibody demonstrated that the beta subunit appeared early in infection.

Primary structure and expression of a nuclear-coded subunit of complex I homologous to proteins specified by the chloroplast genome

A 31-kDa subunit of complex I from Neurospora crassa, of nuclear origin, was cloned. The precursor polypeptide (33 kDa) could be efficiently expressed in an in vitro system for transcription and translation. The processing of the precursor to the mature protein was also obtained in vitro. An open reading frame coding for a precursor protein of 283 amino acids (32247 Da) was found by DNA sequencing. The predicted primary structure shows significant homology with proteins made in chloroplast. This supports the hypothesis that an enzyme similar to respiratory chain NADH dehydrogenase might exist in these organelles.

Two evolutionarily divergent genes encode a cytoplasmic ribosomal protein of Arabidopsis thaliana

Two clones of Arabidopsis thaliana possessing high sequence identity to the yeast gene encoding ribosomal (r) protein L3 were isolated by heterologous DNA hybridization. The coding regions of these two clones have approx. 63% amino acid (aa) sequence identity to the yeast L3 r-protein and 85% aa sequence identity to each other. Both genes are expressed in shoots. The presence of two divergent genes in A. thaliana raises the possibility that the gene products participate in the formation of functionally distinct ribosomes.

The MURF3 gene of T. brucei contains multiple domains of extensive editing and is homologous to a subunit of NADH dehydrogenase

Mitochondrial MURF3 transcripts of T. brucei are extensively edited by the addition and deletion of uridines. The editing creates potential initiation and termination codons and a continuous open reading frame. The predicted amino acid sequence has homology to a subunit of NADH dehydrogenase (ND7). ND7 is independently edited in two distinct domains, suggesting two editing initiation sites. Editing in the two domains is differentially regulated: the 5' domain is edited in both bloodstream and procyclic forms but the 3' domain is completely edited only in the bloodstream form. Two potential guide RNA (gRNA) coding sequences were identified in the same minicircle. One is complementary to edited sequence in the 5' domain, the other to edited sequence in the 3' domain.

A ferredoxin-type iron-sulfur protein gene, frx B, is expressed in the chloroplasts of tobacco and spinach

Previously, a ferredoxin-type iron-sulfur protein, frx B protein, was identified in a high-salt extract of the purified thylakoid membrane of Chlamydomonas reinhardtii, a unicellular green alga. Polyclonal antibody was raised against a synthetic pentadecameric peptide with an amino acid sequence corresponding to the highly conserved region of the putative frx B proteins of 3 land plants. In this report, protein(s) reacting strongly and specifically with this antibody was detected in the equivalent high-salt extract prepared from purified chloroplast of spinach and tobacco. One strong reaction polypeptide band from tobacco chloroplast was purified from SDS-polyacrylamide gel and subjected to endoproteinase lys C digestion. The resulting polypeptides were separated by reversed-phase chromatography. N-terminal sequencing of 3 purified polypeptides revealed that the protein is encoded by the 'frxB gene' identified from DNA sequence analysis.

Trans-splicing mutants of Chlamydomonas reinhardtii

In Chlamydomonas reinhardtii the three exons of the psaA gene are widely scattered on the chloroplast genome: exons 1 and 2 are in opposite orientations and distant from each other and from exon 3. The mature mRNA, encoding a core polypeptide of photosystem I, is thus probably assembled from separate precursors by splicing in trans. We have isolated and characterized a set of mutants that are deficient in the maturation of psaA mRNA. The mutants belong to 14 nuclear complementation groups and one chloroplast locus that are required for the assembly of psaA mRNA. The chloroplast locus, tscA, is remote from any of the exons and must encode a factor required in trans. The mutants all show one of only three phenotypes that correspond to defects in one or other or both of the joining reactions. These phenotypes, and those of double mutants, are consistent with the existence of two alternative splicing pathways.

Molecular evolution of plants as deduced from changes in free energy of 5S ribosomal RNAs

The nucleotide sequence of Pinus silvestyris 5S rRNA was determined using two independent methods and compared with other plant 5S rRNAs. It shows more than 90% sequence homology with gymnosperm 5S RNAs. The free energy (delta G) analysis of 5S rRNAs from gymnosperms, angiosperms and the other higher plants revealed that the free energy of this ribosomal RNA decreases with evolution.

An open reading frame encoding a putative haem-binding polypeptide is cotranscribed with the pea chloroplast gene for apocytochrome f

The nucleotide sequence of a 1 kbp region of pea chloroplast DNA upstream from the gene petA encoding apocytochrome f has been determined. An open reading frame of 231 codons (ORF231) encoding a putative membrane-spanning polypeptide is separated by 205 bp from the coding region of petA. The open reading frame is homologous to open reading frames located in a similar position with respect to petA in chloroplast DNA from Marchantia polymorpha, tobacco, rice, wheat and Vicia faba. The sequence around a conserved histidine residue in a putative membrane-spanning region of the polypeptide resembles sequences present in cytochrome b from chromaffin granules and neutrophil membranes, suggesting that the open reading frame may encode a haem-binding polypeptide, possibly a b-type cytochrome. Northern hybridisation analysis indicates the presence in pea chloroplasts of a complex pattern of transcripts containing ORF231. Large transcripts of 5.5 kb, 4.3 kb, 3.4 kb and 2.7 kb encode both ORF231 and apocytochrome f, indicating that ORF231 and petA are co-transcribed.

The 49 K subunit of NADH: ubiquinone reductase (complex I) from Neurospora crassa mitochondria: primary structure of the gene and the protein

The primary structure of the 49 K subunit of the respiratory chain NADH:ubiquinone reductase (complex I) from Neurospora crassa was determined by sequencing cDNA, genomic DNA and the N-terminus of the mature protein. The sequence lengths correlate to a molecular mass of 54,002 daltons for the preprotein and 49,239 daltons for the mature protein. The presequence consists of 42 amino acids of typical composition for sequences which target nuclear-encoded proteins into mitochondria. The mature protein consists of 436 amino acids and shows 64% similarity to a 49 K subunit of bovine heart NADH:ubiquinone reductase and 33% to a predicted translation product of an open reading frame in the chloroplast DNAs of Marchantia polymorpha and Nicotiana tabacum. Evidence for an iron-sulfur cluster in the subunit is discussed.

Complex RNA maturation pathway for a chloroplast ribosomal protein operon with an internal tRNA cistron

We have studied the expression of a large chloroplast ribosomal protein operon from Euglena gracilis that resembles the Escherichia coli S10 and spc ribosomal protein operons. We present evidence that 11 ribosomal protein genes, a tRNA gene, and a new locus, orf214/orf302, are expressed as a single transcription unit. The primary transcript also contains at least 15 group II and group III introns. Gene-specific probes for each ribosomal protein gene, orf214/orf302, and for trnl hybridized to a common pre-mRNA of an estimated size of 8.3 kilobases. This is the RNA size predicted for a full-length transcript of the entire operon after splicing of all 15 introns. Polycistronic ribosomal protein mRNAs accumulated primarily as spliced hepta-, hexa-, penta-, tetra-, tri-, and dicistronic mRNAs, which were presumed to arise by stepwise processing of the 8.3-kilobase pre-mRNA. A novel finding was the cotranscription of the trnl gene as an internal cistron within the ribosomal protein operon. Several combined mRNA/tRNA molecules, such as the pentacistronic rpl5-rps8-rpl36-trnl-rps14, were characterized. The occurrence of the orf214/orf302 is a unique feature of the Euglena operon, distinguishing it from all chloroplast and prokaryotic ribosomal protein operons characterized to date. The orf214/orf302 are not similar to any known genes but are cotranscribed with the ribosomal protein loci and encode stable RNA species of 2.4, 1.8, and 1.4 kilobases.

Nucleotide sequence and transcripts of the pea chloroplast gene encoding CFo subunit III of ATP synthase

The structure and expression of the pea chloroplast atpH gene, encoding ATP synthase CFo subunit III, have been investigated. The atpH gene is situated between the atpI and atpF genes for CFo subunits IV and I, and encodes a hydrophobic polypeptide of 81 amino acid residues which is very similar to subunit III from other species. Analysis of transcripts from the region of chloroplast DNA encoding ATP synthase subunits IV-III-I-alpha shows a complex pattern of transcription, with large transcripts potentially coding for several subunits and also smaller gene-specific transcripts. Two abundant transcripts of 660 nucleotides (nt) and 980 nt specific for atpH were identified. Primer extension and S1 nuclease protection mapping suggested that the 660-nt transcripts were produced by endonucleolytic processing at the sequence, 5'-UGGAAU.

Cloning and characterization of chloroplast ribosomal protein-encoding genes, rpl16 and rps3, of the marine macro-algae, Gracilaria tenuistipitata

In Gracilaria tenuistipitata, a highly differentiated multicellular member of the marine red algae, Rhodophyta, chloroplast (cp) DNA can be separated as a satellite band from the nuclear DNA in a CsCl gradient. Using a heterologous probe from Chlamydomonas, the ribosomal protein-encoding gene, rpl16, was located on a 4.5-kb EcoRI fragment of cp DNA. The fragment was cloned and a 1365-bp region around rpl16 was sequenced. The gene order around rpl16, 5' rpl22-rps3-rpl16, is identical to that detected in the chloroplast DNA of liverwort, tobacco and maize. Both the nucleotide sequence and the amino-acid sequence of rpl16 are more conserved than that of rps3. The rpl16 gene contains no intron, a feature which shows more similarity to the unicellular green algae, Chlamydomonas, than to other land plants. Sequences that may form a stable stem-loop structure were detected within the coding sequence of rpl16.

Linguistic measure of taxonomic and functional relatedness of nucleotide sequences

The frequencies of "words", oligonucleotides within nucleotide sequences, reflect the genetic information contained in the sequence "texts". Nucleotide sequences are characteristically represented by their contrast word vocabularies. Comparison of the sequences by correlating their contrast vocabularies is shown to reflect well the relatedness (unrelatedness) between the sequences. A single value, the linguistic similarity between the sequences, is suggested as a measure of sequence relatedness. Sequences as short as 1000 bases can be characterized and quantitatively related to other sequences by this technique. The linguistic sequence similarity value is used for analysis of taxonomically and functionally diverse nucleotide sequences. The similarity value is shown to be very sensitive to the relatedness of the source species, thus providing a convenient tool for taxonomic classification of species by their sequence vocabularies. Functionally diverse sequences appear distinct by their linguistic similarity values. This can be a basis for a quick screening technique for functional characterization of the sequences and for mapping functionally distinct regions in long sequences.

Sorting of precursor proteins between isolated spinach leaf mitochondria and chloroplasts

The precursors of the F1-ATPase beta-subunits from Nicotiana plumbaginifolia and Neurospora crassa were imported into isolated spinach (Spinacia oleracea L.) leaf mitochondria. Both F1 beta precursors were imported and processed to mature size products. No import of the mitochondrial precursor proteins into isolated intact spinach chloroplasts was seen. Moreover, the precursor of the 33 kDa protein of photosynthetic water-splitting enzyme was not imported into the leaf mitochondria. This study provides the first experimental report of in vitro import of precursor proteins into plant mitochondria isolated from photosynthetic tissue and enables studies of protein sorting between mitochondria and chloroplasts in a system which is homologous with respect to organelles. The results suggest a high organellar specificity in the plant cell for the cytoplasmically synthesized precursor proteins.

Organellar DNA replication in Nicotiana tabacum cultured cells

In the diploid vegetative plant cell, the nuclear DNA is present in two copies, whereas the chloroplast and mitochondria genomes are present in a higher and variable copy number. We have studied the replication of the nuclear, chloroplast and mitochondrial DNA in cultured Nicotiana tabacum cells using density and radioactive markers. Essentially all the 10,000 chloroplast genomes in a given cell replicate in one cell cycle as do all the mitochondrial DNA molecules. No measurable level of unreplicated organellar DNA molecules can be detected in these cells.

Structure and expression of cytochrome f in an Oenothera plastome mutant

The chloroplast mutant pm7 is one of a number of mutants derived from the plastome mutator (pm) line of Oenothera hookeri, strain Johansen. Immunoblotting showed that this mutant accumulates a protein that is cross-antigenic with cytochrome f, but five kilodaltons larger than the mature wild-type protein. Since cytochrome f is known to be translated on plastid ribosomes as a precursor with an amino-terminal extension, it is proposed that the unprocessed cytochrome f precursor accumulates in pm7. In addition to this precursor-sized cytochrome f protein, some mature-sized cytochrome f was also found in the mutant plastids. The pm7 mutation is inherited in a non-Mendelian fashion; but no alterations in chloroplast DNA restriction patterns, or differences in DNA sequence in the region encoding cytochrome f, were found in a comparison of the wild-type and pm7 chloroplast DNAs. Although the mutant was capable of synthesizing heme, no covalently-bound heme, normally found associated with mature, functional, cytochrome f was detected in the mutant at sizes expected for the presumed precursor, or for mature cytochrome f. These results indicate that the aberrant accumulation of a precursor-sized cytochrome f in pm7 is not due to a lesion directly in the plastid gene encoding cytochrome f, petA, or to a deficiency in the ability of the mutant plastids to synthesize or accumulate heme.

Blocking of the initiation-to-elongation transition by a transdominant RNA polymerase mutation

RNA polymerase, the principal enzyme of gene expression, possesses structural features conserved in evolution. A substitution of an evolutionarily invariant amino acid (Lys1065----Arg) in the beta subunit of Escherichia coli RNA polymerase apparently disrupts its catalytic center. The mutant protein inhibited cell growth when expressed from an inducible promoter. The assembled holoenzyme carrying the mutant subunit formed stable promoter complexes that continuously synthesized promoter-specific dinucleotides but that did not enter the elongation step. The mutant polymerase inhibited transcription by blocking the access of the wild-type enzyme to promoters.

The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants

The relationship of green algae to land plants has greatly interested botanists for more than a century. In recent years, several characters, particularly ultrastructural ones, have been used to define a green algal group (Charophyceae) from which land plants are thought to have arisen. Here we provide the first molecular genetic evidence in support of the charophycean origin of land plants. Group II introns have previously been found in both the tRNAAla and tRNAIle genes of all land plant chloroplast DNAs examined, whereas all algae and eubacteria examined have uninterrupted genes. The distribution of these introns in Coleochaete, Nitella and Spirogyra, members of the Charophyceae, confirms that these taxa are part of the lineage that gave rise to land plants. Furthermore, the intron data place Coleochaete and Nitella closer to land plants than Spirogyra. These introns were most probably acquired by the chloroplast genome more than 400-500 million years ago, the time of land plant origin.

Photosystem I reaction-centre proteins contain leucine zipper motifs. A proposed role in dimer formation

The photosystem I (PS I) reaction-centre polypeptides, encoded by the psaA and psaB genes, are shown to contain several highly conserved leucine repeats, consisting of a leucine residue every seventh amino acid, similar to the leucine zipper motifs known to mediate DNA-binding polypeptide dimerisation. In each of the PSI reaction-centre subunits the leucine zipper motif precedes highly conserved cysteine residues which have been proposed to ligate the interpolypeptide [4Fe-4S] centre, Fx. We propose that PS I reaction-centre dimerisation and [4Fe-4S] centre formation are mediated through the leucine zipper.

Temporal and spatial pattern of plastid gene expression during crucifer seedling development and embryogenesis

Several genes which are located close together on mustard (Sinapis alba L.) chloroplast DNA have been found to differ in their temporal mode of expression throughout seedling development. One predominant expression program, exemplified by thepsbA gene, is characterized by an early (light-independent) rise in transcript levels, followed by subsequent further accumulation to levels which are much higher in the light than in darkness (development of 'competence' for photocontrol). Other genes located next to thepsb A gene show transient or constitutive modes of expression, with no light-dark difference in transcript levels throughout seedling development. The characteristics of light-responsive expression were shown for the nuclearrbcS gene family inBrassica napus L. andSinapis alba L. cotyledons. The spatial distribution ofrbcS andpsbA transcripts across sections of crucifer cotyledons appeared to be relatively uniform, but restricted to photosynthetically active cells. Finally, assessment of these transcripts in immature seeds and embryos ofCapsella bursa-pastoris has provided in-situ evidence for tissuespecific gene expression during early development.