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

An ancient group I intron shared by eubacteria and chloroplasts

Introns have been found in the genomes of all major groups of organisms except eubacteria. The presence of introns in chloroplasts and mitochondria, both of which are of eubacterial origin, has been interpreted as evidence either for the recent acquisition of introns by organelles or for the loss of introns from their eubacterial progenitors. The gene for the leucine transfer RNA with a UAA anticodon [tRNALeu (UAA)] from five diverse cyanobacteria and several major groups of chloroplasts contains a single group I intron. The intron is conserved in secondary structure and primary sequence, and occupies the same position, within the UAA anticodon. The homology of the intron across chloroplasts and cyanobacteria implies that it was present in their common ancestor and that it has been maintained in their genomes for at least 1 billion years.

Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria

A self-splicing group I intron has been found in the gene for a leucine transfer RNA in two species of Anabaena, a filamentous nitrogen-fixing cyanobacterium. The intron is similar to one that is found at the identical position in the same transfer RNA gene of chloroplasts of land plants. Because cyanobacteria were the progenitors of chloroplasts, it is likely that group I introns predated the endosymbiotic association of these eubacteria with eukaryotic cells.

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.

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 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.

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.

A chimeric gene containing the 5' portion of atp6 is associated with cytoplasmic male-sterility of rice

Three ATPase subunit 6 (atp6) genes of rice mitochondria were isolated, one from normal and two from cms-Bo male-sterile cytoplasms, in order to determine whether the extra atp6 gene in cms-Bo rice plays a role in cytoplasmic male-sterility (CMS). The nucleotide sequences of all three genes were determined and analysis showed a chimeric atp6 gene (urf-rmc) as well as a normal atp6 gene in cms-Bo cytoplasm, but only the normal atp6 gene in normal cytoplasm. The urf-rmc gene is completely homologous to the normal atp6 gene from at least position -426 in the 5' flanking region to position +511 downstream from the initiation codon ATG: however, the following downstream sequence shows no homology with the normal rice atp6 gene, or any other reported sequence. Introduction of the restorer of fertility gene altered transcription of the urf-rmc gene but not the atp6 gene, indicating participation of the chimeric gene in the expression of CMS. Southern blot analysis showed that the urf-rmc gene was generated by an intramolecular recombination event in mitochondrial DNA, and the homologous recombination point between the atp6 gene and the opposite ancestral sequence was identified as 5'-TTCCCTC-3'.

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.

Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates

Several known trans-splicing RNA structures were used to define a canonical trans-splicing structure which was then used to perform a computer search of the EMBL nucleotide database. In addition to most known trans-splicing structures, many putative new trans-splicing sites were detected. These were found in a broad range of organisms including the vertebrates. Control experiments indicate that the search predicts known false positives at a rate of only 20%. Trans-splicing may therefore be a very wide-spread phenomenon.

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.

Chloroplast DNA diversity in wild and cultivated species of rice (Genus Oryza, section Oryza). Cladistic-mutation and genetic-distance analysis

Using a novel nonaqueous procedure, chloroplast DNA was isolated from 318 individual adult rice plants, representing 247 accessions and the breadth of the diversity in section Oryza of genus Oryza. Among them, 32 different cpDNA restriction patterns were distinguished using the restriction endonucleases EcoRI and AvaI, and they were further characterized by restriction with BamHI, HindIII, SmaI, PstI, and BstEII enzymes. The differences in the electrophoretic band patterns were parsimoniously interpreted as being the result of 110 mutations, including 47 restriction site mutations. The relationships between band patterns were studied by a cladistic analysis based on shared mutations and by the computation of genetic distances based on shared bands. The deduced relationships were compared with earlier taxonomical studies. The maternal parents for BC genome allotetraploids were deduced. Within species, cpDNA diversity was found larger in those species with an evolutionary history of recent introgression and/or allotetraploidization. Occasional paternal inheritance and recombination of cpDNA in rice was suggested.

A repeated chromosomal DNA sequence is amplified as a circular extrachromosomal molecule in rice (Oryza sativa L.)

The plasmid pE10 is a pBR322-derived plasmid carrying a 4.5 kb rice (Oryza sativa L.) repeated DNA sequence. The cloned sequence has been shown to be amplified in cultured rice cells. The analysis of practically intact chromosomal rice DNA molecules by pulsed field gel electrophoresis has now shown that the amplification is associated with the appearance of extrachromosomal molecules. In fact, pE10 hybridizes exclusively with unfractionated DNA from leaf protoplasts, while it recognizes predominantly an extrachromosomal DNA molecule (ECD) of about 45 kb and its multiples in the case of protoplasts from cultured cells. Insensitivity to the action of the exonuclease Bal31 suggests that the molecule is circular. Analysis of restriction endonuclease products with both standard horizontal and pulsed field gel electrophoresis suggest that the extrachromosomal DNA, and its chromosomal counterpart, is composed of tandemly repeated units of about 7 kb. Thus, the smaller extrachromosomal circle should contain 6-7 repeats, while the sequence cloned in pE10 is a subset of this repeat. The extrachromosomal DNA represents about 1% of total rice DNA and its level of amplification is not affected by the different phases of growth in culture.

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.

Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding trnK(UUU), rps16, trnQ(UUG), psbK, psbI, and trnS(GCU)

A 6.25 kbp barley plastid DNA region located between psbA and psbD-psbC were sequenced and RNAs produced from this DNA were analyzed. TrnK(UUU), rps16 and trnQ(UUG) were located upstream of psbA. These genes were transcribed from the same DNA strand as psbA and multiple RNAs hybridized to them. TrnK and rsp16 contained introns; a 504 amino acid open reading frame (ORF504) was located within the trnK intron. Between trnQ and psbD-psbC was a 2.24 kbp region encoding psbK, psbI and trnS(GCU). PsbK and psbI are encoded on the same DNA strand as psbD-psbC whereas trnS(GCU) is transcribed from the opposite strand. Two large RNAs accumulate in barley etioplasts which contain psbK, psbI, anti-sense trnS(GCU) and psbD-psbC sequences. Other RNAs encode psbK and psbI only, or psbK only. The divergent trnS(GCU) located upstream of psbD-psbC and a second divergent trnS(UGA) located downstream of psbD-psbC were both expressed. Furthermore, RNA complementary to psbK and psbI mRNA was detected, suggesting that transcription from divergent overlapping transcription units may modulate expression from this DNA region.

Nucleotide sequence of the maize chloroplast rpo B/C1/C2 operon: comparison between the derived protein primary structures from various organisms with respect to functional domains

The genes (rpo B/C1/C2) coding for the beta, beta', beta" subunits of maize (Zea mays) chloroplast RNA polymerase have been located on the plastome and their nucleotide sequences established. The operon is part of a large inversion with respect to the tobacco and spinach chloroplast genomes and is flanked by the genes trnC and rps2. Notable features of the nucleotide sequence are the loss of an intron in rpoC1 and an insertion of approximately 450 bp in rpoC2 compared to the dicotyledons tobacco, spinach and liverwort. The derived amino acid sequence of this additional monocotyledon specific sequence is characterized by acidic heptameric repeat units containing stretches of glutamic acid, tyrosines and leucines with regular spacing. Other structural motifs, such as a nucleotide binding domain in the beta subunit and a zinc finger in the beta' subunit, are compared at the amino acid level throughout the RNA polymerase subunits with the enzymes from other organisms in order to identify functionally important conserved regions.

Rice chloroplast RNA polymerase genes: the absence of an intron in rpoC1 and the presence of an extra sequence in rpoC2

The chloroplast genome contains sequences homologous to the Escherichia coli rpoA, rpoB and rpoC genes. The chloroplast rpoC gene is divided into rpoC1 and rpoC2, of which rpoC1 contains an intron. Comparison of the rice rpo genes with those from tobacco, spinach and liverwort revealed unique features of the rice genes; the lack of an intron in rpoC1 and the presence of an extra sequence of 381 bp in rpoC2. The intron in rpoC1 is thus optional, and possible intron boundary sites in split rpoC1 genes can be estimated by comparison with rice rpoC1. The extra sequence is located in the middle of rpoC2 and has repeated structures. The amino acid sequence deduced from this sequence is extremely hydrophilic and anionic. The origin and function of this sequence are discussed.

The complete DNA sequence of the mitochondrial genome of Podospora anserina

The complete 94,192 bp sequence of the mitochondrial genome from race s of Podospora anserina is presented (1 kb = 10(3) base pairs). Three regions unique to race A are also presented bringing the size of this genome to 100,314 bp. Race s contains 31 group I introns (33 in race A) and 2 group II introns (3 in race A). Analysis shows that the group I introns can be categorized according to families both with regard to secondary structure and their open reading frames. All identified genes are transcribed from the same strand. Except for the lack of ATPase 9, the Podospora genome contains the same genes as its fungal counterparts, N. crassa and A. nidulans. About 20% of the genome has not yet been identified. DNA sequence studies of several excision-amplification plasmids demonstrate a common feature to be the presence of short repeated sequences at both termini with a prevalence of GGCGCAAGCTC.

Polypeptide composition of higher plant photosystem I complex. Identification of psaI, psaJ and psaK gene products

High resolution gel electrophoresis of the native photosystem I complex retaining light-harvesting chlorophyll complex revealed the presence of three low-molecular-mass proteins of 7, 4.1 and 3.9 kDa in spinach, and 6.8, 4.4 and 4.1 kDa in pea, in addition to the other well-characterized higher-molecular-mass components. Upon further detergent treatment to deplete light-harvesting chlorophyll complex, the 7 kDa and 4.1 kDa proteins were removed from the photosystem I core complex of spinach, while the 3.9 kDa protein was retained. N-terminal sequencing demonstrated that the 4.1 kDa proteins from both spinach and pea correspond to the gene product of ORF42/44 in chloroplast genome of liverwort and higher plants, which was previously hypothesized as a photosystem I gene (psaJ) based on sequence homology with the cyanobacterial photosystem I component of 4.1 kDa [(1989) FEBS Lett. 253, 257-263]. N-terminal sequence of the spinach 3.9 kDa and pea 4.4 kDa proteins fitted with chloroplast ORF36/40 (psaI) although no homologue has been found in cyanobacteria. The spinach 7 kDa and pea 6.8 kDa proteins correspond to the nuclear-encoded psaK product and significantly matched with the N-terminal sequence of the cyanobacterial 6.5 kDa subunit. The evolutional conservation of the psaJ and psaK seems to suggest their intrinsic role(s) in photosystem I.

Chloroplast DNA sequence from a miocene Magnolia species

DNA has been successfully extracted from several samples of preserved tissue, the oldest so far reported originating from a 13,000-year-old ground sloth. Both severe damage to the preserved DNA, primarily due to oxidation of the pyrimidines, has prevented the acquisition of sequence data from ancient samples except in a few cases. We report here the extraction of DNA from fossil leaf samples from the Miocene Clarkia deposit (17-20 Myr old), the amplification of an 820-base pair (bp) DNA fragment from the chloroplast gene rbcL from a fossil of the genus Magnolia, and its subsequent sequencing. The sequence was verified by comparison with published and unpublished rbcL sequences. These results extend our ability to analyse ancient DNA and may open new avenues into problems in palaeobotany, biogeography, and in the calibration of mutation rates.

The Euglena gracilis chloroplast rpoB gene. Novel gene organization and transcription of the RNA polymerase subunit operon

The rpoB gene coding for a beta-like subunit of the chloroplast DNA-dependent RNA polymerase has been located on the chloroplast genome of Euglena gracilis distal to the rrnC ribosomal RNA operon. We have determined 5760 base-pairs of DNA sequence, including 97 bp of the 5S rRNA gene, an intergenic spacer of 1264 bp, the rpoB gene of 4249 bp, 84 bp spacer and 67 bp of the rpoC1 gene. The rpoB gene is of the same polarity as the rRNA operons. The organization of the rpoB and rpoC genes resembles the E. coli rpoB-rpoC and higher plant chloroplast rpoB-rpoC1-rpoC2 operons. The Euglena rpoB gene (1082 codons) encodes a polypeptide with a predicted molecular weight of 124,288. The rpoB gene is interrupted by seven Group III introns of 93, 95, 94, 99, 101, 110 and 99 bp respectively and a Group II intron of 309 bp. All other known rpoB genes lack introns. All the exon-exon junctions were experimentally determined by cDNA cloning and sequencing or direct primer extension RNA sequencing. Transcripts from the rpoB locus were characterized by Northern hybridization. Fully-spliced, monocistronic rpoB mRNA, as well as rpoB-rpoC1 and rpoB1-rpoC1-rpoC2 mRNAs were identified.

The human genome project: past, present, and future

This article presents a short discussion of the development of the human genome program in the United States, a summary of the current status of the organization and administration of the National Institutes of Health component of the program, and some prospects for the future directions of the program and the applications of genome information.

Nucleotide sequence of the second psbG gene in Synechocystis 6803. Possible implications for psbG function as a NAD(P)H dehydrogenase subunit gene

Nucleotide sequencing of the second Synechocystis 6803 psbG gene, psbG2 shows the predicted polypeptide to be 219 amino acids long. It is less similar to chloroplast psbG genes than is the Synechocystis psbG1 copy. Alignment with seven other psbG protein sequences, including that from the Paramecium mitochondrial genome reveals a central highly conserved region common to each. This is discussed as evidence supporting the proposal that the psbG polypeptide is a NAD(P)H dehydrogenase (complex I) subunit in cyanobacteria, chloroplasts and mitochondria.

Maize chloroplast RNA polymerase: the 180-, 120-, and 38-kilodalton polypeptides are encoded in chloroplast genes

Prominent polypeptides with apparent molecular masses of 180, 120, 85, and 38 kDa are found in an extensively purified preparation of maize chloroplast DNA-dependent RNA polymerase that retains the capacity to initiate transcription of the cloned chloroplast gene rbcL correctly and the requirement for a supercoiled DNA template for specific and active transcription. Amino-terminal amino acid sequences of the 180-, 120-, and 38-kDa polypeptides have been determined and found to correspond precisely to the sequences deduced from the 5' ends of the maize chloroplast rpoC2, rpoB, and rpoA genes, respectively. These experiments show that these chloroplast rpo genes encode the prominent polypeptides in the highly enriched maize chloroplast RNA polymerase preparation and support the conclusion that these polypeptides are functional components of the enzyme. The rpoB, rpoC1, and rpoC2 genes have been mapped on the maize chloroplast chromosome.

The nucleotide sequence of five ribosomal protein genes from the cyanelles of Cyanophora paradoxa: implications concerning the phylogenetic relationship between cyanelles and chloroplasts

The nucleotide sequences of the ribosomal protein genes rps18, rps19, rpl2, rpl33, and partial sequence of rpl22 from cyanelles, the photosynthetic organelles of the protist Cyanophora paradoxa, have been determined. These genes form two clusters oriented in opposite and divergent directions. One cluster contains the rpl33 and rps18 genes; the other contains the rpl2, rps19, and rpl22 genes, in that order. Phylogenetic trees were constructed from both the DNA sequences and the deduced protein sequences of cyanelles, Euglena gracilis and land plant chloroplasts, and Escherichia coli, using parsimony or maximum likelihood methods. In addition, a phylogenetic tree was built from a distance matrix comparing the number of nucleotide substitutions per site. The phylogeny inferred from all these methods suggests that cyanelles fall within the chloroplast line of evolution and that the evolutionary distances between cyanelles and land plant chloroplasts are shorter than between E. gracilis chloroplasts and land plant chloroplasts.

The cyanelle genome of Cyanophora paradoxa encodes ribosomal proteins not encoded by the chloroplasts genomes of higher plants

The rpl35, rpl20, rpl5, rps8, and a portion of the rpl6 genes of the cyanelle genome of Cyanophora paradoxa have been cloned, mapped and sequenced. Homologs of the rpl35, rpl5, and rpl6 genes are not found in the chloroplasts of higher plants. The rpl35 genes most likely form a dicistronic operon which is located upstream from the apcE-apcA-apcB locus of the cyanelle and which is divergently transcribed from this locus. The rpl5, rpl8, and rpl6 genes probably form a part of a larger cluster of genes encoding components of the cyanellar ribosomes. These genes are organized in a fashion similar to that observed in all procaryotes examined to date, with the exception that the rps14 gene is not found between the rpl5 and rps8 coding sequences. Hypotheses concerning the origins of cyanelles and chloroplasts are discussed.

Pseudogenes and short repeated sequences in the rice chloroplast genome

The rice chloroplast genome has been derived from a tobacco-like ancestral form by three major inversions. In the rice genome we have found six pseudogenes, psi trnG, psi trnI, psi 3'-rps 12a, psi trnT, psi trnE and psi trnfM/G, all located near inversion endpoints, as well as four short repeated sequences. A comparison of rice, wheat and tobacco sequences indicated that similar pseudogenes are present in wheat but not in tobacco, suggesting that the creation of these pseudogenes occurred before the divergence of rice and wheat. The region downstream of rbcL is a variable region and contains psi rpl23 in rice and wheat and another psi 3'-rps 12b further downstream in rice. This psi 3'-rps 12b shows a higher homology to the functional rps 12 than psi 3'-rps 12a, which suggests that it appeared more recently. The involvement of these pseudogenes in genome inversions and the creation of the pseudogenes and short repeated sequences are discussed.