Expression in E. coli of maize and wheat chloroplast genes for large subunit of ribulose bisphosphate carboxylase

Plastid sigma factors: Their individual functions and regulation in transcription

Sigma factors are the predominant factors involved in transcription regulation in bacteria. These factors can recruit the core RNA polymerase to promoters with specific DNA sequences and initiate gene transcription. The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. Although all plastid sigma factors contain sequences conserved in bacterial sigma factors, a considerable number of distinct traits have been acquired during evolution. The present review summarises recent advances concerning the regulation of the structure, function and activity of plastid sigma factors since their discovery nearly 40 years ago. We highlight the specialised roles and overlapping redundant functions of plastid sigma factors according to their promoter selectivity. We also focus on the mechanisms that modulate the activity of sigma factors to optimise plastid function in response to developmental cues and environmental signals. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

Recent advances in the study of chloroplast gene expression and its evolution

Chloroplasts are semiautonomous organelles which possess their own genome and gene expression system. However, extant chloroplasts contain only limited coding information, and are dependent on a large number of nucleus-encoded proteins. During plant evolution, chloroplasts have lost most of the prokaryotic DNA-binding proteins and transcription regulators that were present in the original endosymbiont. Thus, chloroplasts have a unique hybrid transcription system composed of the remaining prokaryotic components, such as a prokaryotic RNA polymerase as well as nucleus-encoded eukaryotic components. Recent proteomic and transcriptomic analyses have provided insights into chloroplast transcription systems and their evolution. Here, we review chloroplast-specific transcription systems, focusing on the multiple RNA polymerases, eukaryotic transcription regulators in chloroplasts, chloroplast promoters, and the dynamics of chloroplast nucleoids.

The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase

Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Although genomes of mitochondria and plastids are very small compared to those of their bacterial ancestors, the transcription machineries of these organelles are of surprising complexity. With respect to the number of different RNA polymerases per organelle, the extremes are represented on one hand by chloroplasts of eudicots which use one bacterial-type RNA polymerase and two phage-type RNA polymerases to transcribe their genes, and on the other hand by Physcomitrella possessing three mitochondrial RNA polymerases of the phage type. Transcription of genes/operons is often driven by multiple promoters in both organelles. This review describes the principle components of the transcription machineries (RNA polymerases, transcription factors, promoters) and the division of labor between the different RNA polymerases. While regulation of transcription in mitochondria seems to be only of limited importance, the plastid genes of higher plants respond to exogenous and endogenous cues rather individually by altering their transcriptional activities.

Isolation and sequence of the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase from the cyanobacterium Anabaena 7120

Cloned DNA probes containing genes coding for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcA) of corn and of Chlamydomonas were used to identify, by heterologous hybridization, DNA fragments from Anabaena 7120 carrying the corresponding gene sequence. The same probes were used to isolate, from a recombinant lambda library, a 17-kilobase-pair EcoRI Anabaena DNA fragment containing the coding sequence for the rbcA gene. The entire coding sequence, as well as 210 base pairs of 5' flanking region and 210 base pairs of 3' flanking region, was determined. Comparison of the nucleotide and amino acid sequences with those of corn, spinach, Chlamydomonas, and Synechococcus rbcA genes revealed homology of 71-77% at the nucleotide level and 80-85% at the amino acid level. Conservation of sequence is lost immediately outside the coding region on either side. Codon usage in the Anabaena rbcA gene is not significantly different from that in the Anabaena genes for nitrogenase reductase and nitrogenase beta subunit.

Location and nucleotide sequence of the gene for the proton-translocating subunit of wheat chloroplast ATP synthase

The proton-translocating subunit of wheat chloroplast ATP synthase is encoded by a chloroplast gene that has been accurately mapped and whose nucleotide sequence has been determined. The predicted sequence of 81 amino acids has been confirmed in part by determination of the sequence of the first 40 amino acids from the NH(2) terminus of the protein, and it shows 100% homology with the known amino acid sequence of the spinach protein but no more than 35% homology with the amino acid sequences of bacterial and mitochondrial proteins. The gene shows no deviation from the "universal" genetic code and is not split. A potential ribosome binding site is located 12 nucleotides upstream from the initiation codon, but sequences homologous to prokaryotic promotors and transcription terminators are not apparent.

Isolation and characterization of a gene for a major light-harvesting polypeptide from Cyanophora paradoxa

Antibodies raised against mixtures of phycobilisome polypeptides from the eukaryotic alga Cyanidium caldarium were used in an immunological screen to detect expression of phycobiliprotein genes in an Escherichia coli library containing segments of plastid (chloroplast, cyanelle) DNA from another eukaryotic alga, Cyanophora paradoxa. The four candidate clones obtained were mapped by restriction analysis and found to be overlapping. The clone with the smallest insert (1.4 kilobases) was partially sequenced and a coding region similar to the carboxyl terminus of the phycobiliprotein subunit beta-phycocyanin was found. The coding region for the beta-phycocyanin gene in C. paradoxa has been mapped to the small single copy region on the cyanelle genome, and its orientation has been determined. A short probe unique to a conserved chromophore binding site shared by at least two phycobiliprotein subunits has now been generated from the carboxyl terminus of the beta-phycocyanin gene. This probe may be useful in identifying specific phycobiliprotein subunit genes, beta-phycocyanin, beta-phycoerythrocyanin, and possibly beta-phycoerythrin, in other eukaryotic algae and in prokaryotic cyanobacteria.

Translational coupling of the maize chloroplast atpB and atpE genes

The genes for the beta and epsilon subunits of maize chloroplast ATP synthase are encoded by the organelle genome, are cotranscribed, and have overlapping translation initiation and termination codons. To determine whether the atpB and atpE genes are translationally coupled, they were transformed into Escherichia coli on a multicopy plasmid. Synthesis of full-length beta and epsilon polypeptides demonstrated correct initiation of translation by the bacterial ribosomes. To assay for translational coupling, the promoter-distal atpE gene was fused to lacZ, resulting in the synthesis of an active hybrid beta-galactosidase. A frameshift mutation was introduced into the promoter-proximal atpB gene, and its effect on the transcription and translation of the atpE::lacZ fusion was measured. The mutation resulted in a 1000- to 2000-fold reduction in beta-galactosidase activity, but only a 2-fold decrease in LacZ mRNA synthesis rates or galactoside transacetylase levels. Similar results were obtained when the atpB/atpE::lacZ fusion and the atpB frameshift mutation were introduced into the photosynthetic cyanobacterium Synechocystis sp. PCC6803. We show that >99% of atpE translation depends on successful translation of atpB and, thus, conclude that the two genes are translationally coupled.

Correction of chlorophyll deficiency in alloplasmic male sterile Brassica juncea through recombination between chloroplast genomes

Brassica juncea cv. Pusa Bold carrying B. oxyrrhina cytoplasm (oxy cytoplasm) was male sterile and chlorotic under field conditions at low temperature (Prakash & Chopra, 1990). Leaf protoplasts of the chlorotic male sterile alloplasmic line (2n = 36) were fused with hypocotyl protoplasts of green male fertile, B. juncea cv. RLM-198 (2n = 36) using polyethylene glycol. Of the 1043 plants regenerated from 10 fusion experiments, 123 had ‘gigas’ features and were identified as presumptive fusion products. Among field-grown population, one plant was dark green even at low temperatures and male sterile. It possessed 72 chromosomes which formed 36 bivalents at late diakinesis of meiosis-I. This plant was back-crossed to B. juncea cv. Pusa Bold (the maintainer line) for three successive generations. One male sterile, normal green BC3 progeny plant with 2n = 36 was analyzed for organelle constitution. Probing its total DNA with the mitochondrial gene for cytochrome oxidase subunit I revealed that it possessed mitochondria of B. oxyrrhina. Southern hybridization pattern with the gene for ribulose bisphosphate carboxylase oxygenase-large subunit (rbcL) revealed that the chloroplast genome of the chlorophyll deficiencycorrected plant had characteristics of both B. juncea and B. oxyrrhina. The deficiency correction has been attributed to recombination between chloroplast genomes of the two species.

Expression of plastid-encoded photosynthetic genes during chloroplast or chromoplast differentiation in Cucurbitae pepo L. fruits

The objective of the study was to determine the patterns of expression of two photosynthetic genes rbcL and psbA, during chloroplast and chromoplast differentiation in fruit tissues of three Cucurbitae pepo L. cultivars: Early Prolific, Foodhook Zucchini and Bicolor Gourds. In two Early Prolific isogenic lines, YYBB and YYB+B+, the steady-state amounts of rbcL and psbA transcripts increased with fruit development upto 14 days post-pollination. The YYB+B+ line in which chloroplast differentiates into chromoplast at about pollination, did not show significantly higher amounts of both transcripts compared to YYBB, in which chromoplast develops early prior to pollination. In the Bicolor Gourds, in which the chromoplast and chloroplast containing tissues lie in juxtaposition on the same fruit, showed little differences in rbcL and psbA transcripts between the two tissues, if any the chromoplast containing tissue contained more of both transcripts than the chloroplast containing tissue. In Fordhook Zucchini fruits, where the chloroplast containing tissue developed early prior to pollination and was maintained, the steady-state amounts of rbcL transcripts increased to a maximum at 3 days post-pollination and levelled at 14 and 21 days post-pollination. In contrast, in Fordhook Zucchini fruits, the psbA transcript increased gradually up to 21 days post-pollination. In Fordhook Zucchini, the apparent ratios of psbA transcripts versus rbcL transcripts ranged from 2.5 to 3.9, at day 3 to 21 post-pollination, while in Bicolor Gourds were 2.9 and 4.5 at days 14 and 21 post-pollination. The two photosynthetic genes, psbA and rbcL were developmentally regulated and differentially expressed. However, their expression in chloroplast containing fruit tissues was not higher than in the chromoplast containing fruit tissues.

Organellar RNA polymerases of higher plants

The nuclear genome of the model plant Arabidopsis thaliana contains a small gene family consisting of three genes encoding RNA polymerases of the single-subunit bacteriophage type. There is evidence that similar gene families also exist in other plants. Two of these RNA polymerases are putative mitochondrial enzymes, whereas the third one may represent the nuclear-encoded RNA polymerase (NEP) active in plastids. In addition, plastid genes are transcribed from another, entirely different multisubunit eubacterial-type RNA polymerase, the core subunits of which are encoded by plastid genes [plastid-encoded RNA polymerase (PEP)]. This core enzyme is complemented by one of several nuclear-encoded sigma-like factors. The development of photosynthetically active chloroplasts requires both PEP and NEP. Most NEP promoters show certain similarities to mitochondrial promoters in that they include the sequence motif 5'-YRTA-3' near the transcription initiation site. PEP promoters are similar to bacterial promoters of the -10/-35 sigma 70 type.

A novel thioredoxin-like protein located in the chloroplast is induced by water deficit in Solanum tuberosum L. plants

By analysing two-dimensional patterns of chloroplastic proteins from Solanum tuberosum, the authors observed the accumulation of a 32-kDa polypeptide in the stroma of plants subjected to water deficit. N-terminus and internal peptides of the protein, named CDSP 32 for chloroplastic drought-induced stress protein, showed no obvious homology with known sequences. Using a serum raised against the protein N-terminus, a cDNA encoding CDSP 32 was cloned by screening an expression library. The deduced mature CDSP 32 protein is 243 amino acids long and displays typical features of thioredoxins in the C-terminal region (122 residues). In particular, CDSP 32 contains a CGPC motif corresponding to a thioredoxin active site and a number of amino acids conferring thioredoxin-type structure. The CDSP 32 C-terminal region was expressed as a fusion protein in Escherichia coli and was shown to possess thioredoxin activity based on reduction assay of insulin disulfide bridges. RNA blot analysis showed that CDSP 32 transcript does not accumulate upon mild water deficit conditions corresponding to leaf relative water contents (RWC) around 85%, but high levels of CDSP 32 transcripts were observed for more severe stress conditions (RWC around 70%). In vivo labelling and immunoprecipitation revealed a substantial increase in CDSP 32 synthesis upon similar stress conditions. Rewatering of wilted plants caused decreases in both transcript and protein abundances. In tomato wild-type plants and ABA-deficient mutants, a similar accumulation of a CDSP 32-related transcript was observed upon water deficit, most likely indicating no requirement for ABA in the regulation of CDSP 32 synthesis. Based on these results, it is proposed that CDSP 32 plays a role in preservation of the thiol: disulfide redox potential of chloroplastic proteins during water deficit.

Expression of bacterial Rubisco genes in Escherichia coli

The structural genes for three forms of Rubisco have been isolated from bacteria and introduced into various plasmids. Apart from details of the sequences which have been obtained from these constructs, they are now being exploited for mutagenesis to determine the identity and specific function of the individual amino acid residues that compose the active site. These methods have been applied to a plasmid that contains the structural gene for the simplest form of Rubisco from Rhodospirillum rubrum to obtain mutant enzymes with altered activity. The construct pRR2119 is also expressed to very high levels in Escherichia coli and enough recombinant protein of both the wild-type and m utant enzymes can be obtained for detailed physico-chemical studies. Other vectors have now been constructed, containing the genes of prokaryotic Rubisco that assemble into an active form I enzyme. The levels of expression are acceptable and the product is similar to the authentic enzyme. These constructs are now being used for mutagenesis in vitro to attempt to alter the relative rates of the oxygenase and carboxylase activities.

Expression of cyanobacterial and higher-plant ribulose 1,5-bisphosphate carboxylase genes in Escherichia coli

Expression strategies for the synthesis of higher-plant and cyanobacterial RuBP carboxylase genes in Escherichia coli have been developed to facilitate the study of the assembly pathway and properties of the enzyme’s large (L) and small (S) subunit proteins. The genes for the L and S subunits of the RuBP carboxylase of wheat and of a cyanobacterium, Synechococcus 6301 have been cloned into bacteriophage and plasmid vectors such that they are transcribed and translated in E. coli. To date no RuBP carboxylase activity has been detected in extracts prepared from E. coli cells synthesizing the wheat L and S subunits, although both gene products were present and soluble. Sucrose gradient analysis of cell extracts from E. coli synthesizing both L and S demonstrated that the soluble wheat L polypeptide was present as a large protein aggregate that contained no S subunits. With the cloned cyanobacterial genes, RuBP carboxylase activity could be recovered in E. coli cell extracts when the L and S gene products were synthesized from genes present on the same, or separate, replicons. Solubility and sedimentation studies of the cyanobacterial L subunits synthesized in the absence of S showed that the L subunit was soluble and present in E. coli as an L 8 structure. The E. coli extracts containing only the L subunit exhibited no detectable RuBP carboxylase activity. Infection of the E. coli cells containing L subunits with an M13 phage expressing the cyanobacterial S gene led to the assembly of functional RuBP carboxylase in these cells. This demonstrates the essential role of the S subunit in allowing the formation of an active enzyme.

Characterization of a novel drought-induced 34-kDa protein located in the thylakoids of Solanum tuberosum L. plants

Using two-dimensional electrophoresis and Coomassie Blue staining, the accumulation of a 34-kDa protein (named cdsp 34 for chloroplastic drought-induced stress protein) is shown in the thylakoids of Solanum tuberosum plants subjected to a progressive and reversible water deficit. In-vivo labeling experiments showed an increased synthesis of cdsp 34 from the early stages of drought stress (leaf relative water content around 85%) and throughout the constraint. Sequences of the N-terminal part and of four tryptic-digest peptides did not reveal significant homology between the cdsp 34 protein and other known proteins. Western blotting analysis, using a serum raised against the N-terminal part of cdsp 34, confirmed the accumulation of cdsp 34 in thylakoids upon drought stress. From immunoblot analysis of different chloroplastic subfractions, the cdsp 34 protein appears to be an extrinsic protein preferentially located in unstacked stroma thylakoids. Immunoprecipitation of in-vitro-translated products, as well as Southern analysis, showed that the cdsp 34 protein is nuclear encoded. After rewatering of water-stressed plants, the level of cdsp 34 synthesis was reduced, but remained substantially higher than in control plants. Western analysis showed the persistence of a high amount of cdsp 34 in rewatered plants for at least two weeks. Based on the abundance and on the location of cdsp 34 within thylakoids, a putative role for this novel chloroplastic protein is discussed in relation to the tolerance of the photosynthetic apparatus of higher plants to dehydration.

Spinach chloroplast cpn21 co-chaperonin possesses two functional domains fused together in a toroidal structure and exhibits nucleotide-dependent binding to plastid chaperonin 60

Chloroplasts contain a 21-kDa co-chaperonin polypeptide (cpn21) formed by two GroES-like domains fused together in tandem. Expression of a double-domain spinach cpn21 in Escherichia coli groES mutant strains supports growth of bacteriophages lambda and T5, and will also suppress a temperature-sensitive growth phenotype of a groES619 strain. Each domain of cpn21 expressed separately can function independently to support bacteriophage lambda growth, and the N-terminal domain will additionally suppress the temperature-sensitive growth phenotype. These results indicate that chloroplast cpn21 has two functional domains, either of which can interact with GroEL in vivo to facilitate bacteriophage morphogenesis. Purified spinach cpn21 has a ring-like toroidal structure and forms a stable complex with E. coli GroEL in the presence of ADP and is functionally interchangeable with bacterial GroES in the chaperonin-facilitated refolding of denatured ribulose-1,5-bisphosphate carboxylase. Cpn21 also inhibits the ATPase activity of GroEL. Cpn21 binds with similar efficiency to both the alpha and beta subunits of spinach cpn60 in the presence of adenine nucleotides, with ATP being more effective than ADP. The tandemly fused domains of cpn21 evolved early and are present in a wide range of photosynthetic eukaryotes examined, indicating a high degree of conservation of this structure in chloroplasts.

Purified chaperonin 60 (groEL) interacts with the nonnative states of a multitude of Escherichia coli proteins

In vitro experiments employing the soluble proteins from Escherichia coli reveal that about half of them, in their unfolded or partially folded states, but not in their native states, can form stable binary complexes with chaperonin 60 (groEL). These complexes can be isolated by gel filtration chromatography and are efficiently discharged upon the addition of Mg.ATP. Binary complex formation is substantially reduced if chaperonin 60 is presaturated with Rubisco-I, the folding intermediate of Rubisco, but not with native Rubisco. Binary complex formation is also reduced if the transient species that interact with chaperonin 60 are permitted to progress to more stable states. This implies that the structural elements or motifs that are recognized by chaperonin 60 and that are responsible for binary complex formation are only present or accessible in the unfolded states of proteins or in certain intermediates along their respective folding pathways. Given the high-affinity binding that we have observed in the present study and the normal cellular abundance of chaperonin 60, we suspect that the folding of most proteins in E. coli does not occur in free solution spontaneously, but instead takes place while they are associated with molecular chaperones.

Survey of plastid RNA abundance during tomato fruit ripening: the amounts of RNA from the ORF 2280 region increase in chromoplasts

A comprehensive survey of the levels of plastid RNAs at progressive stages of tomato fruit ripening was conducted by hybridizing total RNA with labeled Pst I fragments that cover almost the entire tomato plastid genome and with gene-specific probes. Two different cultivars of tomato (Lycopersicon esculentum Mill.) were examined, Traveler 76 and Count II. One of the tomato probes, P7, revealed a pronounced increase in the amount of an 8.3 kb RNA in ripe fruit. The homologous region of the tobacco plastid genome contains several genes for ribosomal proteins and a large unidentified open reading frame (2280 codons). Little change was observed in the levels of many transcripts during ripening. However, in some cases (e.g. psbA and psbC/D) the amount of RNA decreased during ripening of Count II but showed little or no change in Traveler 76. The contrast between Traveler 76 and Count II tomatoes shows that the level of plastid transcripts can vary substantially during fruit ripening with no obvious effect on the chloroplast to chromoplast transition. The large RNA from the P7 region may encode a protein that functions predominantly in chromoplasts.

Restriction site and genetic map of Cucurbita pepo chloroplast DNA

A detailed restriction map of squash chloroplast DNA (cpDNA) was constructed with five restriction endonucleases, SalI, PvuII, BglI, SacII, and PstI. The cleavage sites were mapped by sequential digestion of cpDNA using low-gelling temperature agarose. The restriction map shows that squash cpDNA is an approximately 153 kilobase (kb) circle with a large inverted repeat sequence of 23.3 kb, separated by a large (83.7 kb) and a small (22.7 kb) single copy region. Genes for a number of chloroplast polypeptides were localized on the map by hybridizing the cpDNA restriction fragments to heterologous gene-specific probes from tobacco, pea, tomato, maize, and spinach chloroplasts. The gene locations and organization of squash cpDNA are highly conserved and similar to chloroplast genomes of tomato, pepper, and Ginkgo.

Transmission of organelles in triploid hybrids produced by gametosomatic fusions of two Nicotiana species

Gametosomatic hybrids produced by the fusion of microspore protoplasts of Nicotiana tabacum Km(+)Sr(+) with somatic cell protoplasts of N. rustica were analysed for their organelle composition. For the analysis of mitochondrial (mt)DNA, species-specific patterns were generated by Southern hybridization of restriction endonuclease digests of total DNA and mtDNA with four DNA probes of mitochondrial origin: cytochrome oxidase subunit I, cytochrome oxidase subunit II, 26s rDNA and 5s-18s rDNA. Of the 22 hybrids analyzed, some had parental-type pattern for some probes and novel-type for the others, indicating interaction between mtDNA of the two parent species. For chloroplast (cp)DNA analysis, species-specific patterns were generated by Southern hybridization of restriction endonuclease digests of total DNA with large subunits of ribulose bisphosphate carboxylase and cpDNA as probes. All the hybrids had N. rustica-specific patterns. Hybrids were not resistant to streptomycin, a trait encoded by the chloroplast genome of N. tabacum. In gametosomatic fusions of the two Nicotiana species, mitochondria but not the chloroplasts are transmitted from the parent contributing microspore protoplasts.

Assembly of Rubisco from native subunits

Large subunits of ribulosebisphosphate carboxylase/oxygenase (Rubisco) (3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39) from prokaryotic sources can assemble into intact enzyme either in vitro or in Escherichia coli cells. Large subunits of higher plant Rubisco do not assemble into Rubisco in E. coli cells, nor is it possible to reconstitute higher plant Rubisco from its dissociated subunits in vitro. This behavior represents an obstacle to any practical attempts at engineering the higher plant enzyme, and it suggests that the in vivo assembly mechanism of higher plant Rubisco must be more complex than is commonly expected for oligomeric proteins of organelles. In pea chloroplasts, a binding protein interacts with newly synthesized large subunits, in quantities expected for an intermediate in the assembly process, as judged by Western blotting. Radiotracer-labeled large subunits which interact with this binding protein can be shown to assemble into Rubisco in reactions which lead to changes in the aggregation state of the binding protein. Antibody to this binding protein specifically inhibits the assembly of these subunits into Rubisco. Rubisco synthesis appears to be subject to many types of control: gene dosage, transcription rate, selective translation of message, post-translational degradation and threshold concentration effects have been observed in various organisms' synthesis of Rubisco. The biochemical mechanisms underlying most of these effects have not been elucidated. The post-translational assembly mechanism in particular appears to require further study.

In wheat ctDNA, segments of ribosomal protein genes are dispersed repeats, probably conserved by nonreciprocal recombination

Some dispersed repeated sequences and their flanking regions from wheat and maize ctDNAs have been characterized. Two sets of wheat ctDNA repeats were found to be the chloroplast ribosomal protein genes rpl2 and rpl23, plus nonfunctional segments of them, designated rpl2' and rpl23'. Pairwise comparisons were made between the wheat rpl23 and rpl23', and the maize rpl23' sequences. The precise patterns of homology suggest that the divergence of the wheat and maize nonfunctional (rpl23') sequences is being retarded by nonreciprocal recombination, biased by selection for individuals with functional (rpl23) sequences). The implied involvement of these sequences in mechanisms of homologous recombination, and therefore in the creation and spread of new ctDNA variants, is discussed.

Synthesis and assembly of bacterial and higher plant Rubisco subunits in Escherichia coli

The synthesis in Escherichia coli of both the large and small subunits of cereal ribulose bisphosphate carboxylase/oxygenase has been obtained using expression plasmids and bacteriophages. The level and order of synthesis of the large and small subunits were regulated using different promoters, resulting in different subunit pool sizes and ratios that could be controlled in attempts to optimize the conditions for assembly. Neither assembly nor enzyme activity were observed for the higher plant enzyme. In contrast, cyanobacterial large and small subunits can assemble to give an active holoenzyme in Escherichia coli. By the use of deletion plasmids, followed by infection with appropriate phages, it can be demonstrated that the small subunit is essential for catalysis. However, the small subunit is not required for the assembly of a large subunit octomer core in the case of the Synechococcus enzyme; self-assembly of the octomer will occur in an rbcS deletion strain. The cyanobacterial small subunits can be replaced by wheat small subunits to give an active enzyme in Escherichia coli. The hybrid cyanobacterial large/wheat small subunit enzyme has only about 10% of the level of activity of the wild-type enzyme, reflecting the incomplete saturation of the small subunit binding sites on the large subunit octomer, and possibly a mismatch in the subunit interactions of those small subunits that do bind, giving rise to a lower rate of turnover at the active sites.

Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms

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Using bacteria to analyze sequences involved in chloroplast gene expression

The expression of higher plant chloroplast genes in prokaryotic cells has been used to examine organelle sequences involved in promoter recognition by RNA polymerase, and protein translocation through membranes. The similarity in sequence structure between Escherichia coli promoters and the maize chloroplast atpB promoter has been investigated using deletion and single base pair substitution mutants. The atpB mutants were mainly isolated by a selection system in E. coli, and then used as templates for the analysis of transcription using chloroplast RNA polymerase. It was found that both the bacterial and chloroplast RNA polymerases behaved in a similar fashion with the wild-type and mutant promoters, indicating that the sequences involved in promoter recognition share a considerable degree of homology. Signal peptide recognition of pea cytochrome f has also been examined in E. coli. This signal peptide, which is probably responsible for insertion of the protein into the thylakoid membrane, is efficiently recognized in E. coli leading to the inner membrane insertion of petA::lacZ fusion proteins. This process requires the bacterial SecA protein and points to a general similarity in the mechanisms of protein translocation within chloroplasts and bacteria.

The role of the N-terminus of the large subunit of ribulose-bisphosphate carboxylase investigated by construction and expression of chimaeric genes

The genes for the large and small subunits of ribulose bisphosphate carboxylase/oxygenase (Rubisco) from Anacystis nidulans have been expressed in Escherichia coli under the control of the lac promoter to produce active enzyme. The enzyme can be purified from the cells to yield up to 200 mg Rubisco/l cultured bacteria, and is indistinguishable from the enzyme extracted from A. nidulans. In order to investigate the role of the N-terminus of the large subunit in catalysis, chimaeric genes were constructed where the DNA coding for the 12 N-terminal amino acids in A. nidulans was replaced by DNA encoding the equivalent, but poorly conserved, region of either the wheat or maize large subunit. These genes, in constructs also containing the gene for the A. nidulans small subunit, were expressed in E. coli and produced enzymes with similar catalytic properties to the wild-type Rubisco of A. nidulans. In contrast, when the N-terminal region of the large subunit was replaced by unrelated amino acids encoded by the pUC8 polylinker, enzyme activity of the expressed protein was reduced by 90% under standard assay conditions, due to an approximately tenfold rise in the Km for ribulose 1,5-bisphosphate. This confirms that the N-terminus of the large subunit has a function in catalysis, either directly in substrate binding or in maintaining the integrity of the active site.

Bacterial expression and isolation of Petunia hybrida 5-enol-pyruvylshikimate-3-phosphate synthase

5-enol-Pyruvylshikimate-3-phosphate synthase (EPSP synthase, EPSPS), an in vivo enzyme target of the herbicide glyphosate (N-phosphonomethyl glycine), was purified from a Petunia hybrida suspension culture line, MP4-G, by a small-scale high-performance chromatographic purification procedure. The cDNA encoding the mature petunia EPSPS (lacking the chloroplast transit sequence) was cloned into a plasmid, pMON342, for expression in Escherichia coli. This clone complemented the EPSPS deficiency of an E. coli aroA- mutant, and the plant enzyme constituted approximately 1% of the total extractable protein. Large-scale purification of the enzyme from E. coli cells resulted in a highly active protein which was homogeneous as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and amino terminal sequencing. Antibodies raised against the purified enzyme also reacted with the E. coli EPSPS in Western analyses. The availability of large quantities of the plant enzyme will significantly facilitate mechanistic investigations as well as a comparative study with EPSPS from bacteria and fungi.

Co-expression of both the maize large and wheat small subunit genes of ribulose-bisphosphate carboxylase in Escherichia coli

A cDNA clone for the precursor form of the small subunit of wheat ribulose-bisphosphate carboxylase has been modified to allow the expression in Escherichia coli of a mature form of small subunit that lacks the transit peptide. Synthesis of the protein is controlled by a lac promoter, and translation is initiated from a lacZ ribosome binding site, giving rise to a small subunit with several beta-galactosidase amino acids fused to its N-terminus. A plasmid has been constructed that enables both wheat small subunits and maize large subunits to be synthesized in the bacterial cell, but using different promoters to allow independent expression of the rbcS and rbcL genes. When the small subunit is synthesized in the absence of the large subunit, it is found in the soluble fraction but the polypeptide is unstable and has a half-life of less than 15 min. Its size on sucrose gradients indicates a monomeric or dimeric form. When large subunit synthesis is induced in cells containing the small subunit, both subunits are found predominantly in the insoluble fraction and are fully stable for more than 120 min, suggesting that aggregation of the subunits may occur. The two subunits do not assemble together to form an active holoenzyme in vivo, even when nascent large subunits ware synthesized in a pool of mature small subunits. This indicates that other factors may be required to mediate the assembly of the higher plant enzyme.

Functional in vivo verification in E. coli of promoter activities from the rDNA/tDNA(Val)(GAC) leader region of Zea mays chloroplasts

Restriction fragments containing upstream sequences of the rRNA operon from Zea mays chloroplasts were tested for promoter activity in vivo by insertion into an E. coli promoter-probe vector. The expression of this vector's reporter gene, which codes for alkaline phosphatase, was stimulated more than 1,500-fold upon linkage with the chloroplast rRNA promoter. Site specific mutagenesis of the invariant T of the -10 sequence of this promoter reduced the expression of the reporter gene to 2% of the wild type. This indicates that the chloroplast rRNA promoter, which directs transcriptional initiation 117 bp upstream of the 16S rRNA gene, is also active in the bacterial system. A restriction fragment further upstream containing the gene for tRNA(Val) (GAC) also showed strong promoter activity (29% as compared with the rRNA promoter). This promoter activity probably reflects the chloroplast promoter directing the synthesis of the tRNA(Val) (GAC) primary transcript. Surprisingly, this restriction fragment also displayed promoter activity (13% compared with the rRNA promoter) in reverse orientation.

Genes encoding the beta and epsilon subunits of the proton-translocating ATPase from Anabaena sp. strain PCC 7120

The genes encoding the beta (atpB) and epsilon (atpE) subunits of the ATPase from the cyanobacterium Anabaena sp. strain PCC 7120 were cloned, and their sequences were determined. atpB and atpE are each single-copy genes in the Anabaena genome. The two genes are separated by a 96-base-pair intergenic spacer and transcribed as a single mRNA of 2.3 kilobases that initiates approximately 200 base pairs upstream of the atpB coding region. The predicted translation product of atpB has 81 and 68% amino acid identity with the corresponding proteins from spinach chloroplasts and Escherichia coli, respectively. The atpE gene product is less conserved, with 41 and 33% amino acid identity with the corresponding proteins from spinach chloroplasts and E. coli, respectively. The organization of the Anabaena atpB and atpE genes relative to adjacent genes differs from that of both E. coli and chloroplasts.

Inhibition of ribulose bisphosphate carboxylase assembly by antibody to a binding protein

We have developed an assay to monitor in vitro the posttranslational assembly of the chloroplast protein, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Most of the newly synthesized 55-kD catalytic ("large") subunits of this enzyme occur in a 29S complex together with 60- and 61-kD "binding" proteins. When the 29S complex is incubated with ATP and MgCl2 it dissociates into subunits, and the formerly bound large subunits now sediment at 7S (still faster than expected for a monomer). Upon incubation at 24 degrees C, these large subunits assemble into RuBisCO. The minority of newly made large subunits which are not bound to the 29S complex also sediment at 7S. When endogenous ATP was removed by addition of hexokinase and glucose, the dissociation of the 29S complex was inhibited. Nevertheless, the 7S large subunits assembled into RuBisCO, and did so to a greater extent than in controls retaining endogenous ATP. Thus the 7S large subunits are also assembly competent, at least when ATP is removed. Apparently, in chloroplast extracts, ATP can have a dual effect on the assembly of RuBisCO: on the one hand, even at low concentrations it can inhibit incorporation of 7S large subunits RuBisCO; on the other hand, at higher concentrations it can lead to substantial buildup of the 7S large subunit pool by causing dissociation of the 29S complex, and stimulate overall assembly. At both high and zero concentrations of ATP, however, antibody to the binding protein inhibited the assembly of endogenous large subunits into RuBisCO. Thus it appears that all assembly-competent large subunits are associated with the binding protein, either in the 7S complex or in the 29S complex. The involvement of the binding protein in RuBisCO assembly may represent the first example of non-autonomous protein assembly in higher plants and may pose problems for the genetic engineering of RuBisCO from these organisms.

In vitro synthesis and processing of a maize chloroplast transcript encoded by the ribulose 1,5-bisphosphate carboxylase large subunit gene

The large subunit gene (rbcL) of ribulose 1,5-bisphosphate carboxylase was transcribed in vitro by using maize and pea chloroplast extracts and a cloned plastid DNA template containing 172 base pairs (bp) of the maize rbcL protein-coding region and 791 bp of upstream sequences. Three major in vitro RNA species were synthesized which correspond to in vivo maize rbcL RNAs with 5' termini positioned 300, 100 to 105, and 63 nucleotides upstream of the protein-coding region. A deletion of 109 bp, including the "-300" 5' end (the 5' end at position -300), depressed all rbcL transcription in vitro. A plasmid DNA containing this 109-bp fragment was sufficient to direct correct transcription initiation in vitro. A cloned template, containing 191 bp of plastid DNA which includes the -105 and -63 rbcL termini, did not support transcription in vitro. Exogenously added -300 RNA could be converted to the -63 transcript by maize chloroplast extract. These results established that the -300 RNA is the primary maize rbcL transcript, the -63 RNA is a processed form of the -300 transcript, and synthesis of the -105 RNA is dependent on the -300 region. The promoter for the maize rbcL gene is located within the 109 bp flanking the -300 site. Mutagenesis of the 109-bp chloroplast sequence 11 bp upstream of the -300 transcription initiation site reduced rbcL promoter activity in vitro.

Expression of a wheat alpha-amylase gene in Escherichia coli: recognition of the translational initiation site and the signal peptide

Transcription of a full-length cDNA clone of wheat alpha-amylase using a lac promoter in Escherichia coli results in synthesis of a precursor alpha-amylase polypeptide of the correct size, indicating that translation initiates correctly. Recognition of the plant translational initiation site by E. coli ribosomes is 15-20% as efficient as the ribosome-binding site of the beta-lactamase gene when it is fused to alpha-amylase. The alpha-amylase signal peptide is recognised in E. coli resulting in secretion of the enzyme into the periplasmic space; deletion of the signal peptide prevents secretion. Replacement of the alpha-amylase signal peptide with a beta-lactamase signal peptide also enables the bacterial cell to secrete the enzyme. The presence of the beta-lactamase and the alpha-amylase signal peptides in tandem results in secretion of the enzyme and removal of both signal peptides.

Synthesis of maize chloroplast ATP-synthase beta-subunit fusion proteins in Escherichia coli and binding to the inner membrane

The maize chloroplast gene for the beta subunit (atpB) of the chloroplast CF1 component of ATPase from maize, when fused to either the lacZ or ral genes in the vectors pMC1403 or pHUB4, is expressed in Escherichia coli as a fusion protein with beta-galactosidase or with bacteriophage lambda Ral sequences. Some of the fusion proteins are converted to a membrane-bound form, as determined by differential and sucrose-gradient centrifugation. The specificity of membrane binding has been examined using E. coli unc mutants that are defective in binding of the F1 ATPase component to the F0 receptor site on the membrane, and by the use of two different length maize atpB::lacZ gene fusions. We show that the first 365 N-terminal amino acids (aa) of the maize beta subunit are involved in binding to the E. coli inner membrane, and that this binding is probably mediated by the bacterial F0 receptor.

Antitermination is required for readthrough transcription of the maize rbcL gene by a bacteriophage promoter in Escherichia coli

Sequences upstream of the 5' end of the rbcL gene in maize chloroplast fragment Bam 9, have a polar effect on the expression of rbcL from an external upstream bacteriophage PL promoter in Escherichia coli. This polarity can be suppressed by the bacteriophage transcription antitermination protein N or Q. The requirement for transcription antitermination is abolished if DNA upstream of rbcL is removed by a deletion. We have also investigated the ability of RNA polymerase initiating transcription at PL in the presence of N to transcribe through the normal rbcL transcription terminator and into sequences beyond. RNA polymerase initiating at PL can traverse rbcL and its 5' and 3'-flanking regions in the presence of N.

Binding of pea cytochrome f to the inner membrane of Escherichia coli requires the bacterial secA gene product

Various sequences from the 5' end of the pea chloroplast gene for cytochrome f have been fused in the correct reading frame with lacZ, and the cellular location of the hybrid polypeptides in Escherichia coli has been examined. Hybrid polypeptides containing N-terminal parts of cytochrome f are located in the cytoplasmic membrane of E. coli. Membrane localization is most efficient when the intact signal sequence of cytochrome f is present at the N-terminal end of the fusion proteins. Fusion within the signal sequence, so that the processing site is absent, reduces the efficiency of membrane binding. Membrane insertion of fusion proteins containing signal sequences is prevented in a temperature-sensitive secA strain at the nonpermissive temperature and the hybrid proteins accumulate in the cytoplasm. This indicates that specific recognition of the chloroplast signal sequence occurs in the bacterial secretory pathway.

Expression of genes for subunits of plant-type RuBisCO from Chromatium and production of the enzymically active molecule in Escherichia coli

A DNA fragment containing genes for both large (A) and small (B) subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from a photosynthetic bacterium Chromatium vinosum was ligated with vectors for expressing unfused proteins and introduced into cells of Escherichia coli. The expressers of RuBisCO were screened on agar plates using the specific antibody raised against the native enzyme from Chromatium. The production of both subunits A and B in the expressers was demonstrated by an immunoblotting experiment. The amount of RuBisCO produced in the E. coli cells was as high as 15% of the total soluble protein after induction with isopropyl-beta-D-thiogalactoside. The specific activity of enzyme molecules produced in E. coli was nearly the same as that of the original Chromatium enzyme. On gel filtration high-performance liquid chromatography the two enzymes showed identical elution behavior, strongly indicating their similar quaternary structures.

Chloroplast promoters from higher plants

This survey compiles 60 chloroplast promoter sequences from higher plants published to date and compares them with these sequences from procaryotic systems. The current evidence demonstrates that structurally defined chloroplast promoters are, in most cases, functionally active in initiating gene expression in chloroplasts.

In vitro synthesis and processing of a maize chloroplast transcript encoded by the ribulose 1,5-bisphosphate carboxylase large subunit gene

The large subunit gene (rbcL) of ribulose 1,5-bisphosphate carboxylase was transcribed in vitro by using maize and pea chloroplast extracts and a cloned plastid DNA template containing 172 base pairs (bp) of the maize rbcL protein-coding region and 791 bp of upstream sequences. Three major in vitro RNA species were synthesized which correspond to in vivo maize rbcL RNAs with 5' termini positioned 300, 100 to 105, and 63 nucleotides upstream of the protein-coding region. A deletion of 109 bp, including the "-300" 5' end (the 5' end at position -300), depressed all rbcL transcription in vitro. A plasmid DNA containing this 109-bp fragment was sufficient to direct correct transcription initiation in vitro. A cloned template, containing 191 bp of plastid DNA which includes the -105 and -63 rbcL termini, did not support transcription in vitro. Exogenously added -300 RNA could be converted to the -63 transcript by maize chloroplast extract. These results established that the -300 RNA is the primary maize rbcL transcript, the -63 RNA is a processed form of the -300 transcript, and synthesis of the -105 RNA is dependent on the -300 region. The promoter for the maize rbcL gene is located within the 109 bp flanking the -300 site. Mutagenesis of the 109-bp chloroplast sequence 11 bp upstream of the -300 transcription initiation site reduced rbcL promoter activity in vitro.

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

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

Characterization of the mRNA transcripts of the maize, ribulose-1,5-bisphosphate carboxylase, large subunit gene

The analysis of RNA isolated from maize leaves indicates that there are two mRNA transcripts which are homologous to the chloroplast encoded gene for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL). The 5' end of the smaller transcript, 1.62 Kb in length, begins at a position which is 60 nucleotides upstream from the coding sequence of the gene, corresponding to the position mapped by earlier workers. The larger transcript, 1.86 Kb in length, has not been previously described and originates from a site on the gene which is 302 nucleotides upstream from the coding sequence. The increased size of the largerbcL mRNA transcript from maize, as compared to the transcripts from spinach and tobacco, results from the presence of a 130 nucleotide insert between the two maizerbcL gene mRNA start sites. The DNA sequence adjacent to the start site for the large mRNA transcript is shown to have greater than 90% homology to the DNA sequences adjacent to the mRNA start sites for the spinach and tobaccorbcL gene. Discounting the presence of the insert in the maizerbcL gene, the nucleotides upstream from the coding sequence in the maize, spinach and tobaccorbcL genes, all share approximately the same amount of homology to each other. This homology, along with other evidence, suggests that the large mRNA species are the primary transcripts and that the smaller RNA species are the result of post-transcriptional processing. The finding that spinach also contains two different mRNA transcripts for therbcL gene is consistent with this model.

Synthesis of a wheat storage protein subunit in Escherichia coli using novel expression vectors

Useful plasmid expression vectors have been constructed which allow the synthesis of beta-galactosidase (betaG) fusion polypeptides or of polypeptides specified by cDNA clones in Escherichia coli hosts. A foreign DNA fragment can be inserted in any one of the three reading frames at the unique EcoRI, BamHI or SmaI sites immediately after the initiation codon. The cloned foreign gene is under the control of the lac promoter. Using a cDNA clone that encodes part of a wheat storage protein [a high-Mr (HMW) glutenin subunit] synthesis of a glutenin-beta G fusion protein was demonstrated. Synthesis of the glutenin polypeptide, not fused to beta G, was achieved by replacing the lacZYA genes with a stop codon.