Chloroplast gene sequence for the large subunit of ribulose bisphosphatecarboxylase of maize

EVOLUTIONARY ANALYSIS OF THE LARGE SUBUNIT OF CARBOXYLASE (rbcL) NUCLEOTIDE SEQUENCE AMONG THE GRASSES (GRAMINEAE)

The full nucleotide sequences of the chloroplast encoded large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) are available for nine grass species and partial sequence data for one species. Relative rate tests of the "molecular clock" hypothesis suggest that rbcL evolved more rapidly in the lineage leading to Zea than in those leading to the other species. The estimated overall substitution rate for rbcL among these grasses is about 5 times 10^-10 substitutions per site per year, or about one-half the synonymous rate. The nine full sequences were analyzed by the UPGMA, Wagner parsimony, maximum likelihood, and Fitch-Margoliash methods. The latter three methods produced trees with the same topology. This topology largely agrees with current taxonomic evidence regarding the relationships among these grasses. UPGMA produced a topology that conflicts more substantially with available taxonomic evidence. Statistical comparison of the three alternative topologies for the subfamilies Panicoideae, Pooideae and Bambusoideae failed to support one of these topologies over the others, reflecting the taxonomic ambiguities surrounding the relationships among these taxa. Phylogenetic analyses based on the partial sequences of all 10 species gave conflicting results with regard to the relationship between Hordeum and Triticum, both members of the tribe Triticeae. This indicates that rbcL sequences contain too little information to resolve relationships among genera within this tribe. Overall, the results suggest that rbcL sequence data can provide some new information concerning grass phylogeny, but that the amount of available data from this gene is too small to differentiate statistically among alternative topologies for the grasses. Conflicting results from parsimony, maximum likelihood, and Fitch-Margoliash methods proved useful in exploring the validity of assumptions underlying these methods.

Genista anglica (Fabaceae): One very diverse species or one species complex?

Genista anglica represents a widely distributed group of shrubs in the Iberian Peninsula, as well as in the North of the Moroccan Mountains, the South of Italy and in most oceanic territories of Western Europe, with its northern limit in Sweden. Up to five different species within the group have been described in these territories: Genista ancistrocarpa, G. acutifolia, G. brutia and G. silana, as well as G. anglica sensu stricto. The diversity of Genista anglica sensu lato as well as the phylogenetic patterns that have generated this diversity have been analyzed through the use of nuclear (ITS, ETS) and chloroplastic (trnL, trnL-F, rbcL, matK) DNA sequences. Our results show that the group probably originated in the West of the Iberian Peninsula and subsequently spread to the rest of the European oceanic territories. Additionally, the results support the idea that the presence of a group of plants in the South of Italy, where G. brutia and G. silana were previously described, has been the consequence of the introduction of seeds collected in the Northwest of the Iberian Peninsula. Our results also indicate that, in contrast to some authors, the populations from the West of the Iberian Peninsula are not isolated and, consequently, they should be grouped into one species with high diversity, therefore differentiation into different taxa is no longer adequate.

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

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

Nucleotide sequence of the gene for pre-apocytochrome f in the spinach plastid chromosome

We have characterized a cloned fragment of the spinach plastid chromosome encoding the gene for apocytochrome f. Northern blot analysis and hybrid selection translation discloses that the gene is expressed. From the nucleotide sequence, we deduce that the protein contains 285 amino acids and an amino-terminal signal sequence of 35 amino acid residues. The calculated molecular mass of pre-apocytochrome f is 35.3 kd. The clustering of hydrophobic residues indicates that the processed protein (31.3 kd) possesses only a single anchoring transmembrane domain close to the C terminus, and that 75% of the polypeptide chain including the heme-binding site protrudes into the thylakoid lumen. This topology resembles that reported for beef heart mitochondrial cytochrome c1.

Phylogeny and systematics of Micranthes (Saxifragaceae): an appraisal in European territories

Recent phylogenetic studies have shown that Saxifraga, as currently understood, must be divided into two genera: Saxifraga L. sensu stricto and Micranthes Haw. To better understand the evolutionary history of these two genera, we performed phylogenetic analyses inferred from the nuclear ribosomal sequences from the internal transcribed spacer and the sequences of the plastid DNA (rbcL). Our molecular data confirmed the monophyly of the genus Micranthes and the consistency of the existing systematic treatments based on morphological criteria. Moreover, Micranthes species native from the Iberian Peninsula (i.e. M. clusii, M. lepismigena and M. stellaris) should be included into Micranthes sect. Arabisa.

Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco

BACKGROUND

One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories.

RESULTS

We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time.

CONCLUSION

Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.

Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective

Historic discoveries and key observations related to Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase), from 1947 to 2006, are presented. Currently, around 200 papers describing Rubisco research are published each year and the literature contains more than 5000 manuscripts on the subject. While trying to ensure that all the major events over this period are recorded, this analysis will inevitably be incomplete and will reflect the areas of particular interest to the authors.

The mystery of oxygen evolution: analysis of structure and function of photosystem II, the water-plastoquinone oxido-reductase

Photosystem II (PS II) of thylakoid membrane of photosynthetic organisms has drawn attention of researchers over the years because it is the only system on Earth that provides us with oxygen that we breathe. In the recent past, structure of PS II has been the focus of research in plant science. The report of X-ray crystallographic structure of PS II complex by the research groups of James Barber and So Iwata in UK is a milestone in the area of research in photosynthesis. It follows the pioneering and elegant work from the laboratories of Horst Witt and W. Saenger in Germany, and J. Shen in Japan. It is time to analyze the historic events during the long journey made by the researchers to arrive at this point. This review makes an attempt to critically review the growth of the advancement of concepts and knowledge on the photosystem in the background of technological development. We conclude the review with perspectives on research and technology that should reveal the complete story of PS II of thylakoid in the future.

Protective role of exogenous polyamines on salinity-stressed rice (Oryza sativa) plants

Salt-tolerant Pokkali rice plants accumulate higher polyamines (PAs) such as spermidine (Spd) and spermine (Spm) in response to salinity stress, while the sensitive cultivarM-1-48 is unable to maintain high titres of these PAs under similar conditions. The effects of the triamine Spd and the tetramine Spm on physiological and biochemical changes in 12-day-old rice seedlings were investigated during salinity stress to determine whether they could protect the sensitive plants from stress effects. At physiological concentrations Spd and Spm significantly prevented the leakage of electrolytes and amino acids from roots and shoots induced by salinity stress. To different degrees they also prevented chlorophyll loss, inhibition of photochemical reactions of photosynthesis as well as downregulation of chloroplast-encoded genes like psbA, psbB, psbE and rbcL, indicating a positive correlation between salt tolerance and accumulation of higher PAs in rice. The inhibitory effect of salinity stress and its reversal by exogenous PAs were more pronounced in the salt-sensitiveM-1-48 plants than in the tolerant Pokkali plants.

RbcS suppressor mutations improve the thermal stability and CO2/O2 specificity of rbcL- mutant ribulose-1,5-bisphosphate carboxylase/oxygenase

In the green alga Chlamydomonas reinhardtii, a Leu(290)-to-Phe (L290F) substitution in the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco), which is coded by the chloroplast rbcL gene, was previously found to be suppressed by second-site Ala(222)-to-Thr and Val(262)-to-Leu substitutions. These substitutions complement the photosynthesis deficiency of the L290F mutant by restoring the decreased thermal stability, catalytic efficiency, and CO(2)/O(2) specificity of the mutant enzyme back to wild-type values. Because residues 222, 262, and 290 interact with the loop between beta strands A and B of the Rubisco small subunit, which is coded by RbcS1 and RbcS2 nuclear genes, it seemed possible that substitutions in this loop might also suppress L290F. A mutation in a nuclear gene, Rbc-1, was previously found to suppress the biochemical defects of the L290F enzyme at a posttranslational step, but the nature of this gene and its product remains unknown. In the present study, three nuclear-gene suppressors were found to be linked to each other but not to the Rbc-1 locus. DNA sequencing revealed that the RbcS2 genes of these suppressor strains have mutations that cause either Asn(54)-to-Ser or Ala(57)-to-Val substitutions in the small-subunit betaA/betaB loop. When present in otherwise wild-type cells, with or without the resident RbcS1 gene, the mutant small subunits improve the thermal stability of wild-type Rubisco. These results indicate that the betaA/betaB loop, which is unique to eukaryotic Rubisco, contributes to holoenzyme thermal stability, catalytic efficiency, and CO(2)/O(2) specificity. The small subunit may be a fruitful target for engineering improved Rubisco.

An examination of hybridization between the cattail species typha latifolia and typha angustifolia using random amplified polymorphic DNA and chloroplast DNA markers

Typha glauca represents a significant portion of the biomass of the wetlands surrounding the Great Lakes, USA. It is generally accepted to be a form of hybrid between T. latifolia and T. angustifolia, which itself appears to be an exotic introduction from Europe. Based on morphological and isozyme data, conflicting theories have been proposed for the hybrid nature of T. glauca: it has been described as a hybrid swarm, a distinct hybrid species and an F1 hybrid. Therefore, we developed random amplified polymorphic DNA (RAPD) and chloroplast DNA markers, specific to the parental species, to assess hybrids. Ten RAPD primers gave 17 fragments specific to T. angustifolia and 13 fragments specific to T. latifolia. All of the interspecific hybrids contained each of the species-specific markers, indicating an F1 hybrid status. Furthermore, all hybrids tested contained the T. angustifolia chloroplast haplotype, which is consistent with differential interspecific crossing success found previously. Additional confirmation of an F1 hybrid status was gained by examining seedlings from T. glauca. These progeny were expected to be advanced-generation hybrids, as opposed to the F1 hybrid parent. Analysis of the seedlings revealed segregating marker patterns consistent with patterns observed in experimental advanced-generation hybrids, although these advanced hybrids do not appear to be a significant part of mature stands. Our data do not provide support for extensive gene flow between T. latifolia and T. angustifolia. However, our results suggest that hybridization between the native and introduced Typha species has impacted the native population through the spread of the F1 hybrid, T. glauca.

Pre-Anthesis Reserve Utilization for Protein and Carbohydrate Synthesis in Grains of Wheat

We assessed the contribution of pre-anthesis reserve C to protein and carbohydrate deposition in grains of wheat (Triticum aestivum L.) using a new approach comprised of steady-state (13)C/(12)C labeling and separation of the protein and carbohydrate fractions of mature grains. Experiments were performed with two spring wheat cultivars (Kadett and Star) grown with differential N fertilizer supply over 2 years. Pre-anthesis reserves contributed between 30% and 47% of the C in protein and 8% to 27% of the C in carbohydrates of grains. Partitioning of pre-anthesis C among the grain fractions was strongly dependent on the C/N (w/w) ratio in mobilized pre-anthesis biomass (r(2) = 0.92). There appeared to be no significant exchange of pre-anthesis C between amino acids and carbohydrates during redistribution. The mean apparent efficiency of mobilized carbohydrate-C use in grain filling (ME(CHO), estimated as the mass of pre-anthesis C deposited in grain carbohydrates per gram of pre-anthesis C mobilized from carbohydrates in vegetative plant parts) was 0.72, whereas that of protein-C (ME(P)) was 0.56. However, ME(P) and ME(CHO) varied among treatments. ME(CHO) increased with increasing contributions of water-soluble carbohydrates to total pre-anthesis carbohydrate mobilization. ME(P) decreased with increasing residence time of protein in vegetative biomass. Possible causes for variability of ME(P) and ME(CHO) are discussed.

Subfamily divergence in the multigene family of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcS) in Triticeae and its relatives

To investigate genetic mechanisms acting on multigene family in plants, we analyzed sequence variation in the rbcS gene of 13 species of Triticeae and one species each of related tribes (Bromeae and Aveneae). A total of 36 rbcS genes were analyzed. Based on dimorphism in the length of intron, the rbcSs of investigated species were classified into two subfamilies A and B. The difference in intron length was caused by an indel of about 200 bp in the middle of the intron. The two subfamilies of rbcS were present in the three tribes, indicating that the divergence of rbcS subfamilies occurred before the split of these tribes. Generally, variation between the two subfamilies of rbcS was larger than that within subfamily, but these two measures were about the same at the tribe level. This result suggested that divergence of the subfamilies of rbcS occurred at about the same time of tribe diversification. The level of nucleotide variation in the exon region between subfamilies was reduced in the Triticeae, but clear change was not detected in the intron sequence. This result suggested that the exon sequences between subfamilies of rbcS were homogenized without affecting the intron sequence in the Triticeae lineage.

Future prospects for genetic manipulation of Rubisco

Recent advances in the development of techniques for the manipulation of gene structure in vitro and genetic transformation of plants have brought the goal of directed genetic modification of RuBP carboxylase-oxygenase (Rubisco) within grasp. Genes from both prokaryotic and eukaryotic species have been cloned, sequenced and expressed in Escherichia coli , and in several instances this has resulted in the production of large quantities of fully functional enzyme. Several specifically-modified enzymes have been produced by site-directed mutagenesis of a cloned gene and the effects of the mutations evaluated following expression of the modified genes in E. coli . Thus, there are no major technical barriers to the creation and analysis of modified enzymes. A number of new opportunities now exist to explore the structural basis of naturally occurring differences in kinetic constants of the enzymes from diverse taxonomic sources. The recent report of chloroplast transformation mediated by the Ti plasmid has also raised the possibility that, if useful natural variation can be identified, genes for both the large and small subunits of the enzyme may eventually be transferred between species. However, the opportunities for rational application of mutagenesis in vitro in the creation of useful or informative variants of the enzyme is currently limited by lack of information about tertiary structure and the role of specific residues in catalysis.

Molecular characterization of transketolase (EC 2.2.1.1) active in the Calvin cycle of spinach chloroplasts

A cDNA encoding the Calvin cycle enzyme transketolase (TKL; EC 2.2.1.1) was isolated from Sorghum bicolor via subtractive differential hybridization, and used to isolate several full-length cDNA clones for this enzyme from spinach. Functional identity of the encoded mature subunit was shown by an 8.6-fold increase of TKL activity upon induction of Escherichia coli cells that overexpress the spinach TKL subunit under the control of the bacteriophage T7 promoter. Chloroplast localization of the cloned enzyme is shown by processing of the in vitro synthesized precursor upon uptake by isolated chloroplasts. Southern blot-analysis suggests that TKL is encoded by a single gene in the spinach genome. TKL proteins of both higher-plant chloroplasts and the cytosol of non-photosynthetic eukaryotes are found to be unexpectedly similar to eubacterial homologues, suggesting a possible eubacterial origin of these nuclear genes. Chloroplast TKL is the last of the demonstrably chloroplast-localized Calvin cycle enzymes to have been cloned and thus completes the isolation of gene probes for all enzymes of the pathway in higher plants.

Directed mutagenesis of chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase. Loop 6 substitutions complement for structural stability but decrease catalytic efficiency

The structure of active-site loop 6 plays a role in determining the CO2/O2 specificity of chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39). Rubisco from the green alga Chlamydomonas reinhardtii differs from higher plant Rubisco within the loop 6 region, and the C. reinhardtii enzyme has a CO2/O2 specificity 25% lower than that of higher plant enzymes. To examine whether differences in sequence may account for differences in catalytic efficiency, we focused on a conserved pair of residues that are in van der Waals contact at the base of loop 6. C. reinhardtii Rubisco contains Leu-326 and Met-349, whereas higher plant enzymes contain Ile-326 and Leu-349. By employing in vitro mutagenesis and chloroplast transformation, L326I and M349L substitutions were created within the Rubisco large subunit of C. reinhardtii. M349L had little effect, but L326I destabilized the holoenzyme in vivo and in vitro. When present together, the M349L substitution partially alleviated the instability resulting from the L326I substitution, but caused a 21% decrease in CO2/O2 specificity and a 74% decrease in the Vmax of carboxylation. Interactions between loop 6 and other structural regions are likely to be responsible for both holoenzyme stability and catalytic efficiency in higher plant Rubisco enzymes.

The chloroplast genome

The chloroplast genome consists of homogeneous circular DNA molecules. To date, the entire nucleotide sequences (120-190 kbp) of chloroplast genomes have been determined from eight plant species. The chloroplast genomes of land plants and green algae contain about 110 different genes, which can be classified into two main groups: genes involved in gene expression and those related to photosynthesis. The red alga Porphyra chloroplast genome has 70 additional genes, one-third of which are related to biosynthesis of amino acids and other low molecular mass compounds. Chloroplast genes contain at least three structurally distinct promoters and transcribe two or more classes of RNA polymerase. Two chloroplast genes, rps12 of land plants and psaA of Chlamydomonas, are divided into two to three pieces and scattered over the genome. Each portion is transcribed separately, and two to three separate transcripts are joined together to yield a functional mRNA by trans-splicing. RNA editing (C to U base changes) occurs in some of the chloroplast transcripts. Most edited codons are functionally significant, creating start and stop codons and changing codons to retain conserved amino acids.

Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae

To study the phylogenetics of sugarcane (Saccharum officinarum L.) and its relatives we sequenced four loci on cytoplasmic genomes (two chloroplast and two mitochondrial) and analyzed mitochondrial RFLPs generated using probes for COXI, COXII, COXIII, Cob, 18S+5S, 26S, ATPase 6, ATPase 9, and ATPase α (D'Hont et al. 1993). Approximately 650 bp of DNA in the intergenic spacer region between rbcL and atpB and approximately 150 bp from the chloroplast 16S rDNA through the intergenic spacer region tRNA(val) gene were sequenced. In the mitochondrial genome, part of the 18S rRNA gene and approximately 150 bp from the 18S gene 3' end, through an intergenic spacer region, to the 5S rRNA gene were sequenced. No polymorphisms were observed between maize, sorghum, and 'Saccharum complex' members for the mitochondrial 18S internal region or for the intergenic tRNA(val) chloroplast locus. Two polymorphisms (insertion-deletion events, indels) were observed within the 18S-5S mitochondrial locus, which separated the accessions into three groups: one containing all of the Erianthus, Eccoilopus, Imperata, Sorghum, and 1 Miscanthus species; a second containing Saccharum species, Narenga porphyrocoma, Sclerostachya fusca, and 1 presumably hybrid Miscanthus sp. from New Guinea; and a third containing maize. Eighteen accessions were sequenced for the intergenic region between rbcL and atpB, which was the most polymorphic of the regions studied and contained 52 site mutations and 52 indels, across all taxa. Within the Saccharum complex, at most 7 site mutations and 16 indels were informative. The maternal lineage of Erianthus/Eccoilopus was nearly as divergent from the remaining Saccharum complex members as it was from sorghum, in agreement with a previous study. Sequences from the rbcL-atpB spacer were aligned with GENBANK sequences for wheat, rice, barley, and maize, which were used as outgroups in phylogenetic analyses. To determine whether limited intra-complex variability was caused by under sampling of taxa, we used seven restriction enzymes to digest the PCR-amplified rbcL-atpB spacer of an additional 36 accessions within the Saccharum complex. This analysis revealed ten restriction sites (none informative) and eight length variants (four informative). The small amount of variation present in the organellar DNAs of this polyploid complex suggests that either the complex is very young or that rates of evolution between the Saccharum complex and outgroup taxa are different. Other phylogenetic information will be required to resolve systematic relationships within the complex. Finally, no variation was observed in commercial sugarcane varieties, implying a world-wide cytoplasmic monoculture for this crop.

Differential transcription of plastome-encoded genes in the mesophyll and bundle-sheath chloroplasts of the monocotyledonous NADP-malic enzyme-type C4 plants maize and Sorghum

The transcription of plastome-encoded genes in mesophyll and bundle-sheath chloroplasts of the monocotyledonous NADP-malic enzyme-type C4 species Zea mays L. (maize) and Sorghum bicolor (L.) Moench. was investigated. RNA accumulation and transcription were assayed starting from isolated mesophyll and bundle-sheath chloroplasts and using quantitative northern and run-on transcription analysis. Determination of the mesophyll to bundle-sheath ratios of transcript abundance in maize and Sorghum chloroplasts showed that the mRNAs of the plastome-encoded photosystem II genes analysed (psbA, psbB, psbD, psbH and psbE/F) varied from 2.5- to 4.0-fold (maize) and 3.1- to 5.2-fold (Sorghum), respectively. The rbcL transcript, in contrast, was more abundant in bundle-sheath chloroplasts of both species, about 3-fold in maize and more than 10-fold in Sorghum. On the other hand, transcripts of genes encoding the 16S ribosomal RNA (r16) and subunits of photosystem I (psaA) and the cytochrome b/f complex (petB, petA) accumulated to similar levels in both types of chloroplasts. Determination of absolute transcript levels for rbcL and psbA in chloroplasts from maize and Sorghum demonstrated that for both genes, the mesophyll to bundle-sheath differences in transcript abundance were more pronounced in Sorghum. Measurements of the transcriptional activities of rbcL and psbA showed that the transcription rate of rbcL is higher in bundle-sheath chloroplasts while psbA is more actively transcribed in mesophyll chloroplasts. The differences in the transcription rates between the two chloroplast types were again more pronounced in Sorghum, thus reflecting the differences between maize and Sorghum in the relative levels of the rbcL and psbA transcripts. However, although transcription rate and mRNA abundance are correlated, they did not exactly match one another. This indicates additional regulation of transcript abundance at the level of RNA stability.

Construction and characterisation of a yeast artificial chromosome library containing five haploid sugarbeet (Beta vulgaris L.) genome equivalents

A yeast artificial chromosome (YAC) genomic library of Beta vulgaris was constructed in the pYAC4 vector. High-molecular-weight DNA was prepared from agarose-embedded leaf protoplasts from a triploid cultivar. The library was found to contain 33,500 clones in an ordered array of microtiter plates. Mean size of the inserts was estimated to be 135 kb, and the library should therefore represent the equivalent of five haploid genomes. The library was characterised for the presence of highly repetitive, chloroplast and single-copy sequences. In order to isolate single-copy sequences, 18 pools of DNA, each from 1920 individual YAC clones, were prepared for rapid screening of the library by the polymerase chain reaction. The results of these screenings showed that the number of isolated clones was at or near the frequency expected.

Chromosome assignment of four photosynthesis-related genes and their variability in wheat species

Copy numbers of four photosynthesis-related genes, PhyA, Ppc, RbcS and Lhcb1 (*)1, in wheat genomes were estimated by slot-blot analysis, and these genes were assigned to the chromosome arms of common wheat by Southern hybridization of DNA from an aneuploid series of the cultivar Chinese Spring. The copy number of PhyA was estimated to be one locus per haploid genome, and this gene was assigned to chromosomes 4AL, 4BS and 4DS. The Ppc gene showed a low copy number of small multigenes, and was located on the short arm of homoeologous group 3 chromosomes and the long arm of chromosomes of homoeologous group 7. RbcS consisted of a multigene family, with approximately 100 copies in the common wheat genome, and was located on the short arm of group 2 chromosomes and the long arm of group 5 chromosomes. Lhcb1 (*)1 also consisted of a multigene family with about 50 copies in common wheat. Only a limited number of restriction fragments (approximately 15%) were used to determine the locations of members of this family on the long arm of group 1 chromosomes owing to the multiplicity of DNA bands. The variability of hybridized bands with the four genes was less in polyploids, but was more in the case of multigene families. RFLP analysis of polyploid wheats and their presumed ancestors was carried out with probes of the oat PhyA gene, the maize Ppc gene, the wheat RbcS gene and the wheat Lhcb1 (*)1 gene. The RFLP patterns of common wheat most closely resembled those of T. Dicoccum (Emmer wheat), T. urartu (A genome), Ae. speltoides (S genome) and Ae. squarrosa (D genome). Diversification of genes in the wheat complex appear to have occurred mainly at the diploid level. Based on RFLP patterns, B and S genomes were clustered into two major groups. The fragment numbers per genome were reduced in proportion to the increase of ploidy level for all four genes, suggesting that some mechanism(s) might operate to restrict, and so keep to a minimum, the gene numbers in the polyploid genomes. However, the RbcS genes, located on 2BS, were more conserved (double dosage), indicating that the above mechanism(s) does not operate equally on individual genes.

Dynamics of the history of photosynthesis research

A personal view of the history of progress in photosynthesis research beginning in the seventeenth century and ending in 1992 is presented in a chart form. The 350-year time span is divided arbitrarily into seven periods by the "development junctures", which are likened to bamboo joints. The tempo of progress is reflected in the duration of the periods, starting from over 200 years for Period I, which progressively shortens in subsequent periods. This brief introduction highlights some of the events to show the dynamic nature of the progress in photosynthesis research.

Construction of a Synechocystis PCC6803 mutant suitable for the study of variant hexadecameric ribulose bisphosphate carboxylase/oxygenase enzymes

The cyanobacterium Synechocystis PCC6803 was chosen as a target organism for construction of a suitable photosynthetic host to enable selection of variant plant-like ribulose bisphosphate carboxylase/oxygenase (Rubisco) enzymes. The DNA region containing the operon encoding Rubisco (rbc) was cloned, sequenced and used for the construction of a transformation vector bearing flanking sequences to the rbc genes. This vector was utilized for the construction of a cyanobacterial rbc null mutant in which the entire sequence comprising both rbc genes, was replaced by the Rhodospirillum rubrum rbcL gene linked to a chloramphenicol resistance gene. Chloramphenicol-resistant colonies, Syn6803 delta rbc, were detected within 8 days when grown under 5% CO2 in air. These transformants were unable to grow in air (0.03% CO2). Analysis of their genome and Rubisco protein confirmed the site of the mutation at the rbc locus, and indicated that the mutation had segregated throughout all of the chromosome copies, consequently producing only the bacterial type of the enzyme. In addition, no carboxysome structures could be detected in the new mutant. Successful restoration of the wild-type rbc locus, using vectors bearing the rbc operon flanked by additional sequences at both termini, could only be achieved upon incubating the transformed cells under 5% CO2 in air prior to their transferring to air. The yield of restored transformants was proportionally related to the length of those sequences flanking the rbc operon which participate in the homologous recombination. The Syn6803 delta rbc mutant is amenable for the introduction of in vitro mutagenized rbc genes into the rbc locus, aiming at the genetic modification of the hexadecameric type Rubisco.

A chloroplast DNA mutational hotspot and gene conversion in a noncoding region near rbcL in the grass family (Poaceae)

The noncoding DNA region of the chloroplast genome, flanked by the genes rbcL and psaI (ORF36), has been sequenced for seven species of the grass family (Poaceae). This region had previously been observed as a hotspot area for length mutations. Sequence comparison reveals that short duplications, probably resulting from slipped-strand mispairing, account for many small length differences between sequences but that major mutational hotspots are localized in three small areas, two of which show potential secondary structure. Mutation in one of these hotspots appears to be a result of more complex recombination events. All seven species contain a pseudogene for rpl23 and evidence is presented that this pseudogene is being maintained by gene conversion with the functional gene. Different transition/transversion biases and AT contents between the pseudogene and the surrounding noncoding sequences are noted. In the subfamily Panicoideae there is a deletion in which almost 1 kb of ancestral sequence, including the 3' end of the rpl23 pseudogene, has been replaced by a non-homologous 60-base sequence of unknown origin. Two other deletions of almost the same region have occurred in the grass family. The deleted noncoding region has mutational and compositional properties similar to the rbcL coding sequence and the rpl23 pseudogene. The three independent deletions, as well as the pattern of mutation in the localized hotspots, indicate that such noncoding DNA may be misleading for studies of phylogenetic inference.

Construction and characterisation of a yeast artificial chromosome library containing two haploid Beta vulgaris L. genome equivalents

We have constructed a yeast artificial chromosome (YAC) library using high-molecular-weight DNA prepared from agarose-embedded protoplasts of a sugar beet (Beta vulgaris L.) cell suspension line, Ar+. This library contains 15,000 clones with an average insert size of 140 kb. Based on a sugar beet haploid genome size of 1.1 x 10(3) Mb it should represent approximately two haploid genome equivalents. The library is organised as an ordered array in duplicate microtitre plates. High-density filters, each containing 864 YAC clones, have been screened in colony hybridisation experiments. In this way, sugar beet YAC clones have been identified containing chloroplast DNA, mitochondrial DNA and two satellite DNAs. Ten pools of DNA from 1500 individual YAC clones have also been prepared for rapid PCR screening of the library. Using this approach, in combination with colony hybridisation, we have been able to isolate sugar beet YAC clones containing a transcribed low-copy-number gene.

Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants

We subjected 35 rbcL nucleotide sequences from monocotyledonous taxa to maximum likelihood relative rate tests and estimated relative differences in rates of nucleotide substitution between groups of sequences without relying on knowledge of divergence times between taxa. Rate tests revealed that there is a hierarchy of substitution rate at the rbcL locus within the monocots. Among the taxa analyzed the grasses have the most rapid substitution rate; they are followed in rate by the Orchidales, the Liliales, the Bromeliales, and the Arecales. The overall substitution rate for the rbcL locus of grasses is over 5 times the substitution rate in the rbcL of the palms. The substitution rate at the third codon positions in the rbcL of the grasses is over 8 times the third position rate in the palms. The pattern of rate variation is consistent with the generation-time-effect hypothesis. Heterogenous rates of substitution have important implications for phylogenetic reconstruction.

Identification and chromosomal location of four subfamilies of the rubisco small subunit genes in common wheat

Three different 3' noncoding sequences of wheat rubisco small subunit (SSU) genes (RbcS) were used as probes to identify the gene members of different RbcS subfamilies in the common wheat cultivar Chinese Spring (CS). All genes of the wheat RbcS multigene family were previously assigned to the long arm of homoeologous group 5 and to the short arm of homoeologous group 2 chromosomes of cv CS. Extracted DNA from various aneuploids of these homoeologous groups was digested with four restriction enzymes and hybridized with three different 3' noncoding sequences of wheat SSU clones. All RbcS genes located on the long arm of homoeologous group 5 chromosomes were found to comprise a single subfamily, while those located on the short arm of group 2 comprised three subfamilies. Each of the ancestral diploid genomes A, B, and D has at least one representative gene in each subfamily, suggesting that the divergence into subfamilies preceded the differentiation into species. This divergence of the RbcS genes, which is presumably accompanied by a similar divergence in the 5' region, may lead to differential expression of various subfamilies in different tissues and in different developmental stages, in response to different environmental conditions. Moreover, members of one subfamily that belong to different genomes may have diverged also in the coding sequence and, consequently, code for distinguishable SSU. It is assumed that such utilization of the RbcS multigene family increases the adaptability and phenotypic plasticity of common wheat over its diploid progenitors.

Chromosomal location of genes for Rubisco small subunit and Rubisco-binding protein in common wheat

The genes coding for the Rubisco small subunit (SSU) and for the α-subunit of the Rubisco-binding protein were located to chromosome arms of common wheat. HindIII-digested total DNA from the hexaploid cultivar Chinese Spring and from ditelosomic and nullisomic-tetrasomic lines was probed with these two genes, whose chromosomal location was deduced from the disappearance of or from changes in the relative intensity of the relevant band(s). The Rubisco SSU pattern consisted of 14 bands, containing at least 21 different types of DNA fragments, which were allocated to two homoeologous groups: 15 to the short arm of group 2 chromosomes (4 to 2AS, 7 to 2BS, and 4 to 2DS) and 6 to the long arm of group 5 chromosomes (2 on each of arms 5AL, 5BL, and 5DL). The pattern of the Rubisco-binding protein consisted of three bands, each containing one type of fragment. These fragments were located to be on the short arm of group 2 chromosomes. The restriction fragment length polymorphism (RFLP) patterns of several hexaploid and tetraploid lines were highly conserved, whereas the patterns of several of their diploid progenitors were more variable. The variations found in the polyploid species were mainly confined to the B genome. The patterns of the diploids T. monococcum var. urartu and Ae. squarrosa were similar to those of the A and D genome, respectively, in polyploid wheats. The pattern of T. monococcum var. boeoticum was different from the patterns of the A genome, and the patterns of the diploids Ae. speltoides, Ae. longissima, and Ae. Searsii differed from that of the B genome.

Cell-specific accumulation of maize phosphoenolpyruvate carboxylase is correlated with demethylation at a specific site greater than 3 kb upstream of the gene

Development of the C4 photosynthetic pathway relies upon the cell-specific accumulation of photosynthetic enzymes. Although the molecular basis of this cell-specific gene expression is not known, regulation appears to be exerted at the level of transcript accumulation. We have investigated the relationship between gene expression patterns and DNA methylation for genes of two of the C4 photosynthetic enzymes, ribulose bisphosphate carboxylase (RuBPCase) and phosphoenolpyruvate carboxylase (PEPCase). We found no correlation between methylation state and gene expression for either the large subunit or a small subunit gene of RuBPCase. In contrast, demethylation of a specific site 5' to the PEPCase gene was correlated with the light-induced, cell-specific accumulation of PEPCase mRNA. This differentially methylated site is positioned at great distance (greater than 3 kb) from the start of transcription. This observation is made more interesting by the fact that the immediate 5' region of the gene, and some of the coding region, represents an unmethylated CpG island. Such islands are normally associated with constitutively expressed genes.

Nucleotide sequence of the gene for the large subunit of Rubisco from Cyanophora paradoxa--phylogenetic implications

The gene (rbcL) for the large subunit (LSU) of Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Cyanophora paradoxa was cloned and the nucleotide sequence determined. Sequence homologies to rbcL genes from other sources clearly indicated a close phylogenetic relationship between the photosynthetic organelles of Cyanophora (cyanelles), green chloroplasts and cyanobacteria. Our data support the hypothesis that the cyanelles of Cyanophora may represent a closely related, but independent, side line to chloroplast evolution. Cyanelles and rhodoplasts or phaeoplasts seem not to be related.

Rubisco genes indicate a close phylogenetic relation between the plastids of Chromophyta and Rhodophyta

The genes for both subunits of Rubisco (rbcL, rbcS) are located on the plastome of the brown alga Ectocarpus siliculosus (Chromophyta, Phaeophyceae). The organization of these genes in the form of an operon was similar to that found in rhodoplasts, cyanobacteria and the plastids of Cryptomonas phi. Sequence analysis of the complete operon revealed a high degree of homology and great structural similarities to corresponding genes from two red algae. In contrast, sequence homology to Rubisco genes from chloroplasts and cyanobacteria was much lower. This clearly indicated a close phylogenetic relationship between the plastids of Rhodophyta and Chromophyta which seem to have evolved independently from the chloroplasts (polyphyletic origin). Our data suggest that the plastids of Chromophyta and Cryptophyta have originated from endosymbiotic unicellular red algae. Surprisingly, red and brown algal Rubiscos show a significantly higher degree of homology to that from a hydrogen bacterium than to those from cyanobacteria.

Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site

The X-ray structure of the quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase from spinach with CO2, Mg2+ and a reaction-intermediate analogue (CABP) has been determined and refined at 2.4 A resolution. Cyclic non-crystallographic symmetry averaging around the molecular 4-fold axis and phase combination were used to improve the initial multiple isomorphous replacement phases. A model composed of one large subunit and one small subunit was built in the resulting electron density map, which was of excellent quality. Application of the local symmetry gave an initial model of the L8S8 molecule with a crystallographic R-value of 0.43. Refinement of this initial model was performed by a combination of conventional least-squares energy refinement and molecular dynamics simulation using the XPLOR program. Three rounds of refinement, interspersed with manual rebuilding at the graphics display, resulted in a model containing all of the 123 amino acid residues in the small subunit, and 467 of the 475 residues in the large subunit. The R-value for this model is 0.24, with relatively small deviations from ideal stereochemistry. Subunit interactions in the L8S8 molecule have been analysed and are described. The interface areas between the subunits are extensive, and bury almost half of the accessible surface areas of both the large and the small subunit. A number of conserved interaction areas that may be of functional significance have been identified and are described, and biochemical and mutagenesis data are discussed in the structural framework of the model.

Evidence for a composite phylogenetic origin of the plastid genome of the brown alga Pylaiella littoralis (L.) Kjellm

The nucleotide sequence and the 5' flanking region of the rbcL gene coding for the large subunit of ribulose bisphosphate-1,5-carboxylase/oxygenase of Pylaiella littoralis, a brown alga, has been determined and the deduced amino-acid sequence has been compared to those of various photosynthetic and chemoautotrophic Eubacteria, of a red alga and of green plastids (Euglena gracilis, green algae and higher plants). Unlike the rbcL genes of green plastids which are more closely related to those of cyanobacteria, the P. littoralis rbcL gene is more closely related to that of a beta-purple bacterium, as was found for the rbcS gene of another chromophytic alga [Boczar et al., Proc Natl Acad Sci USA 86: 4996-4999, 1989]. Matrix data of homology between the rbcL gene of P. littoralis and the same gene of other organisms are presented. Based on our previous report, the gene coding for the 16S rRNA from P. littoralis is closely related to that of E. gracilis (Markowicz et al., Curr Genet 14: 599-608, 1988). We suggest that the large plastid DNA molecule of P. littoralis is a phylogenetically composite genome which probably resulted from mixed endosymbiosis events, or from a horizontal transfer of DNA.

Structure of the Rubisco operon from the unicellular red alga Cyanidium caldarium: evidence for a polyphyletic origin of the plastids

The genes for both subunits of ribulose-1,5-bisphosphate-carboxylase/oxygenase (Rubisco) were located on the plastid DNA (ptDNA) of the unicellular red alga Cyanidium caldarium. Both genes are organized together in an operon. The sequence homology of both genes to the corresponding genes from the unicellular red alga Porphyridium aerugineum is remarkably high, whereas homology to Rubisco genes from chloroplasts and two recent cyanobacteria is significantly lower. These data provide strong evidence for a polyphyletic origin of chloroplasts and rhodoplasts. In addition the genes for the small subunit of Rubisco (rbcS) from red algae show about 60% homology to rbcS genes from cryptophytes and chromophytes. Thus, homologies in the rbcS gene indicate a close phylogenetic relationship between rhodoplasts and the plastids of Chromophyta.