Genomic organization, sequence analysis and expression of all five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from tomato

The small subunit of Rubisco and its potential as an engineering target

Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.

WHIRLY1 maintains leaf photosynthetic capacity in tomato by regulating the expression of RbcS1 under chilling stress

Rubisco, which consists of eight large subunits (RBCLs) and eight small subunits (RBCSs), is a major photosynthetic enzyme that is sensitive to chilling stress. However, it is largely unclear how plants maintain high Rubisco content under low temperature conditions. Here, we report that tomato WHIRLY1 (SlWHY1) positively regulates the Rubisco level under chilling stress by directly binding to the promoter region of SlRbcS1, resulting in the activation of SlRbcS1 expression. SlRbcS1-overexpressing lines had higher Rubisco contents and were more resistant to chilling stress compared with the wild type. Quantitative real-time PCR analyses showed that, among the five RbcS genes, only SlRbcS1 expression is up-regulated by chilling treatment. These results indicate that SlWHIRLY1 specifically enhances the levels of SlRbcS1 and confers tolerance to chilling stress. The amino acid sequence of SlRBCS1 shows 92.67% identity with those of another two RBCS proteins and three residues are specifically found in SlRBCS1. However, mutation of these residues to alanine in SlRBCS1 does not influence its function during cold adaptation. Thus, we conclude that high levels of Rubisco, but not the specific residues in SlRBCS1, play important roles in tolerance to chilling stress in tomato.

Duplication history and molecular evolution of the rbcS multigene family in angiosperms

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the main enzyme determining the rate of photosynthesis. The small subunit of the protein, encoded by the rbcS gene, has been shown to influence the catalytic efficiency, CO2 specificity, assembly, activity, and stability of RuBisCO. However, the evolution of the rbcS gene remains poorly studied. We inferred the phylogenetic tree of the rbcS gene in angiosperms using the nucleotide sequences and found that it is composed of two lineages that may have existed before the divergence of land plants. Although almost all species sampled carry at least one copy of lineage 1, genes of lineage 2 were lost in most angiosperm species. We found the specific residues that have undergone positive selection during the evolution of the rbcS gene. We detected intensive coevolution between each rbcS gene copy and the rbcL gene encoding the large subunit of RuBisCO. We tested the role played by each rbcS gene copy on the stability of the RuBisCO protein through homology modelling. Our results showed that this evolutionary constraint could limit the level of divergence seen in the rbcS gene, which leads to the similarity among the rbcS gene copies of lineage 1 within species.

A Graft Mimic Strategy for Verticillium Resistance in Tomato

Grafting vegetables for disease resistance has increased greatly in popularity over the past 10 years. Verticillium wilt of tomato is commonly controlled through grafting of commercial varieties on resistant rootstocks expressing the Ve1 R-gene. To mimic the grafted plant, proteomic analyses in tomato were used to identify a suitable root-specific promoter (TMVi), which was used to express the Ve1-allele in susceptible Craigella (Cs) tomato plants. The results indicate that when infected with Verticillim dahliae, race 1, the transformed plants are comparable to resistant cultivars (Cr) or grafted plants.

Silencing SlAGL6, a tomato AGAMOUS-LIKE6 lineage gene, generates fused sepal and green petal

Silencing SlAGL6 in tomato leads to fused sepal and green petal by influencing the expression of A-, B-class genes. AGAMOUS-LIKE6 (AGL6) lineage is an important clade MADS-box transcription factor and plays essential roles in various developmental programs especially in flower meristem and floral organ development. Here, we isolated a tomato AGL6 lineage gene SlAGL6 and successfully obtained several RNA interference (RNAi) lines. Silencing SlAGL6 led to abnormal fused sepals and light green petals with smaller size. The total chlorophyll content in transgenic petals increased and the morphology of epidermis cells altered. Further analysis showed that A-class gene MACROCALYX (MC) participating in sepal development and a NAC-domain gene GOBLET involving in boundary establishment were down-regulated in transgenic lines. In transgenic petals, two chlorophyll synthesis genes, Golden2-like1 (SlGLK1) and Golden2-like2 (SlGLK2), two photosystem-related genes, ribulose bisphosphate carboxylase small chain 3B (SlrbcS3B) and chlorophyll a/b-binding protein 7 (SlCab-7) were induced and three B-class genes TM6, TAP3 and SlGLO1 were repressed. These results suggest that SlAGL6 involves in tomato sepal and petal development.

The MADS-box gene SlMBP11 regulates plant architecture and affects reproductive development in tomato plants

MADS-domain proteins are important transcription factors that are involved in many biological processes of plants. In the present study, SlMBP11, a member of the AGL15 subfamily, was cloned in tomato plants (Solanum lycopersicon M.). SlMBP11 is ubiquitously expressed in all of the tissues we examined, whereas the SlMBP11 transcription levels were significantly higher in reproductive tissues than in vegetative tissues. Plants exhibiting increased SlMBP11 levels displayed reduced plant height, leaf size, and internode length as well as a loss of dominance in young seedlings, highly branched growth from each leaf axil, and increased number of nodes and leaves. Moreover, overexpression lines also exhibited reproductive phenotypes, such as those having a shorter style and split ovary, leading to polycarpous fruits, while the wild type showed normal floral organization. In addition, delayed perianth senescence was observed in transgenic tomatoes. These phenotypes were further confirmed by analyzing the morphological, anatomical and molecular features of lines exhibiting overexpression. These results suggest that SlMBP11 plays an important role in regulating plant architecture and reproductive development in tomato plants. These findings add a new class of transcription factors to the group of genes controlling axillary bud growth and illuminate a previously uncharacterized function of MADS-box genes in tomato plants.

The sweet potato RbcS gene (IbRbcS1) promoter confers high-level and green tissue-specific expression of the GUS reporter gene in transgenic Arabidopsis

Sweet potato is an important crop because of its high yield and biomass production. We herein investigated the potential of the promoter activity of a small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RbcS) from sweet potato (Ipomoea batatas) in order to develop the high expression system of exogenous DNA in Arabidopsis. We isolated two different cDNAs (IbRbcS1 and IbRbcS2) encoding RbcS from sweet potato. Their predicted amino acid sequences were well conserved with the mature RbcS protein of other plants. The tissue-specific expression patterns of these two genes revealed that expression of IbRbcS1 was specific to green tissue, whereas that of IbRbcS2 was non-photosynthetic tissues such as roots and tubers. These results suggested that IbRbcS1 was predominantly expressed in the green tissue-specific of sweet potato over IbRbcS2. Therefore, the IbRbcS1 promoter was transformed into Arabidopsis along with β-glucuronidase (GUS) as a reporter gene. GUS staining and semi-quantitative RT-PCR showed that the IbRbcS1 promoter conferred the expression of the GUS reporter gene in green tissue-specific and light-inducible manners. Furthermore, qPCR showed that the expression levels of GUS reporter gene in IbRbcS1 pro:GUS were same as those in CaMV 35S pro:GUS plants. These results suggest that the IbRbcS1 promoter is a potentially strong foreign gene expression system for genetic transformation in plants.

Hybrid Rubisco of tomato large subunits and tobacco small subunits is functional in tobacco plants

Biogenesis of functional ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in plants requires specific assembly in the chloroplast of the imported, cytosol-synthesized small subunits (SS) with the chloroplast-made large subunits (LS). Accumulating evidence indicates that chloroplasts (plastids) generally have a low tolerance for assembling foreign or modified Rubisco. To explore Rubisco engineering, we created two lines of transplastomic tobacco plants whose rbcL gene was replaced by tomato-derived rbcL: plant LLS2 with Rubisco composed of tobacco SS and Q437R LS and plant LLS4 with a hybrid Rubisco of tobacco SS and tomato LS (representing four substitutions of Y226F, A230T, S279T and Q437R from tobacco LS). Plant LLS2 exhibited similar phenotypes as the wild type. Plant LLS4 showed lower chlorophyll and Rubisco levels particularly in young emerging leaves, lower photosynthesis rates and biomass during early stages of development, but was able to reach reproductive maturity and somewhat wild type-like phenotype under ambient CO₂ condition. In vitro assays detected similar carboxylase activity and RuBP affinity in LLS2 and LLS4 plants as in wild type. Our studies demonstrated that tomato LS was sufficiently assembled with tobacco SS into functional Rubisco. The hybrid Rubisco of tomato LS and tobacco SS can drive photosynthesis that supports photoautotrophic growth and reproduction of tobacco plants under ambient CO₂ and light conditions. We discuss the effect of these residue substitutions on Rubisco activity and the possible attribution of chlorophyll deficiency to the in planta photosynthesis performance in the hybrid Rubisco plants.

Cloning and characterization of ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) cDNA from green microalga Ankistrodesmus convolutus

An initial study on gene cloning and characterization of unicellular green microalga Ankistrodesmus convolutus was carried out to isolate and characterize the full-length cDNA of ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) as a first step towards elucidating the structure of A. convolutus RbcS gene. The full-length of A. convolutus RbcS cDNA (AcRbcS) contained 28 bp of 5' untranslated region (UTR), 225 bp of 3' non-coding region, and an open reading frame of 165 amino acids consisting of a chloroplast transit peptide with 24 amino acids and a mature protein of 141 amino acids. The amino acid sequence has high identity to those of other green algae RbcS genes. The AcRbcS contained a few conserved domains including protein kinase C phosphorylation site, tyrosine kinase phosphorylation site and N-myristoylation sites. The AcRbcS was successfully expressed in Escherichia coli and a ~21 kDa of anticipated protein band was observed on SDS-PAGE. From the phylogenetic analysis of RbcS protein sequences, it was found that the RbcS of A. convolutus has closer genetic relationship with green microalgae species compared to those of green seaweed and green macroalgae species. Southern hybridization analysis revealed that the AcRbcS is a member of a small multigene family comprising of two to six members in A. convolutus genome. Under different illumination conditions, RT-PCR analysis showed that AcRbcS transcription was reduced in the dark, and drastically recovered in the light condition. Results presented in this paper established a good foundation for further study on the photosynthetic process of A. convolutus and other green algae species where little information is known on Rubisco small subunit.

Over-expression of LeNCED1 in tomato (Solanum lycopersicum L.) with the rbcS3C promoter allows recovery of lines that accumulate very high levels of abscisic acid and exhibit severe phenotypes

Previous work where 9-cis-epoxycarotenoid dioxygenase (NCED) was over-expressed using the constitutive Gelvin Superpromoter resulted in mild increases in abscisic acid (ABA) accumulation, accompanied by stomatal closure and increased water-use efficiency (WUE), but with apparently little impact on long-term biomass production. However, one of the negative effects of the over-expression of NCED using constitutive promoters in tomato was increased seed dormancy. Here we report the use of the rbcS3C promoter, from a gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), to drive LeNCED1 transgene expression in tomato in a light-responsive and circadian manner. In comparison to the constitutive promoter, the rbcS3C promoter allowed the generation of transgenic plants with much higher levels of ABA accumulation in leaves and sap, but the effect on seed dormancy was diminished. These plants displayed the expected reductions in stomatal conductance and CO(2) assimilation, but they also exhibited a severe set of symptoms that included perturbed cotyledon release from the testa, increased photobleaching in young seedlings, substantially reduced chlorophyll and carotenoid content, interveinal leaf flooding, and greatly reduced growth. These symptoms illustrate adverse consequences of long-term, very high ABA accumulation. Only more moderate increases in ABA biosynthesis are likely to be useful in the context of agriculture. Implications are discussed for the design of transgenic 'high ABA' plants that exhibit increased WUE but have minimal negative phenotypic effects.

Heterologous expression of glycosyl hydrolases in planta: a new departure for biofuels

The concept of expressing non-plant glycosyl hydrolase genes in plant tissue is nearly two decades old, yet relatively little work in this field has been reported. However, resurgent interest in technologies aimed at enabling processes that convert biomass to sugars and fuels has turned attention toward this intuitive solution. There are several challenges facing researchers in this field, including the development of better and more specifically targeted delivery systems for hydrolytic genes, the successful folding and post-translational modification of heterologous proteins and the development of cost-effective process strategies utilizing these transformed plants. The integration of these concepts, from the improvement of biomass production and conversion characteristics to the heterologous production of glycosyl hydrolases in a high yielding bioenergy crop, holds considerable promise for improving the lignocellulosic conversion of biomass to ethanol and subsequently to fuels.

Adaptive response to salt involving carbohydrate metabolism in leaves of a salt-sensitive tomato cultivar

A salt-sensitive genotype of Solanum lycopersicum cv. Volgogradskij was submitted to a 6-day treatment with high salt (100, 200 mM NaCl), allowed to recover for 6 days and then submitted to a second period of salt stress in order to study changes in carbohydrate metabolism related to salt adaptation. The ion, soluble sugar and starch contents, as well as sucrose biosynthetic and sugar mobilizing enzyme activities and transcript levels were determined during the salt stress/recovery/stress cycle. Sodium ions were found to accumulate preferentially in old leaves. Young leaves accumulated lower levels of sodium ions but maintained control levels of potassium ions. Hexoses accumulated to higher levels and starch was better maintained in young compared to old leaves during the two salt treatments. Sucrose accumulated dramatically only in old leaves during the initial salt treatment. Sugar accumulation was not related to decreases in the activities of sugar mobilizing enzymes, acid (EC 3.2.1.25) and neutral (EC 3.2.1.26) invertases, sucrose synthase (EC 2.4.1.13) and hexokinase (EC 2.7.1.1). The activity of the biosynthetic enzyme sucrose phosphate synthase (EC 2.3.1.14) was linked to changes in sucrose levels but not with transcript levels. These results point to the importance of post-transcriptional regulation. Transcriptional regulation could nevertheless be seen in the down-regulation of ribulose bisphosphate carboxylase small subunit (EC 4.1.1.39) in old compared to young leaves, but this was not related to sugar levels.

Contribution of fructose-1,6-bisphosphatase and sedoheptulose-1,7-bisphosphatase to the photosynthetic rate and carbon flow in the Calvin cycle in transgenic plants

To clarify the contributions of fructose-1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) separately to the carbon flux in the Calvin cycle, we generated transgenic tobacco plants expressing cyanobacterial FBPase-II in chloroplasts (TpF) or Chlamydomonas SBPase in chloroplasts (TpS). In TpF-11 plants with 2.3-fold higher FBPase activity and in TpS-11 and TpS-10 plants with 1.6- and 4.3-fold higher SBPase activity in chloroplasts compared with the wild-type plants, the amount of final dry matter was approximately 1.3-, 1.5- and 1.5-fold higher, respectively, than that of the wild-type plants. At 1,500 micromol m(-2) s(-1), the photosynthetic activities of TpF-11, TpS-11 and TpS-10 were 1.15-, 1.27- and 1.23-fold higher, respectively, than that of the wild-type plants. The in vivo activation state of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the level of ribulose-1,5-bisphosphate (RuBP) in TpF-11, TpS-10 and TpS-11 were significantly higher than those in the wild-type plants. However, the transgenic plant TpF-9 which had a 1.7-fold higher level of FBPase activity showed the same phenotype as the wild-type plant, except for the increase of starch content in the source leaves. TpS-11 and TpS-10 plants with 1.6- and 4.3-fold higher SBPase activity, respectively, showed an increase in the photosynthetic CO(2) fixation, growth rate, RuBP contents and Rubisco activation state, while TpS-2 plants with 1.3-fold higher SBPase showed the same phenotype as the wild-type plants. These data indicated that the enhancement of either a >1.7-fold increase of FBPase or a 1.3-fold increase of SBPase in the chloroplasts had a marked positive effect on photosynthesis, that SBPase is the most important factor for the RuBP regeneration in the Calvin cycle and that FBPase contributes to the partitioning of the fixed carbon for RuBP regeneration or starch synthesis.

Optimization of Acidothermus cellulolyticus endoglucanase (E1) production in transgenic tobacco plants by transcriptional, post-transcription and post-translational modification

An attempt was made to obtain a high-level production of intact Acidothermus cellulolyticus endoglucanase (E1) in transgenic tobacco plants. The E1 expression was examined under the control of the constitutive and strong Mac promoter or light-inducible tomato Rubisco small sub-unit (RbcS-3C) promoter with its original or Alfalfa Mosaic Virus (AMV) RNA4 5'-untranslated leader (UTL) and targeted to different sub-cellular compartments via transit peptides. The transit peptides included native E1, endoplasmic reticulum, vacuole, apoplast, and chloroplast. E1 expression and its stability in transgenic plants were determined via E1 activity, protein immunoblotting, and RNA gel-blotting analyses. Effects of sub-cellular compartments on E1 production and its stability were determined in transgenic tobacco plants carrying one of six transgene expression vectors, where the E1 was under the control of Mac promoter, mannopine synthase transcription terminator, and one of the five transit peptides. Transgenic tobacco plants with an apoplastic transit peptide had the highest average E1 activity and protein accumulation, which was about 0.25% of total leaf soluble proteins estimated via E1 specific activity and protein gel blots. Intercellular fluid analyses confirmed that E1 signal peptide functioned properly in tobacco cells to secret E1 protein into the apoplast. By replacing RbcS-3C UTL with AMV RNA4 UTL E1 production was enhanced more than twofold, while it was less effective than the mannopine synthase UTL. It was observed that RbcS-3C promoter was more favorable for E1 expression in transgenic plants than the Mac promoter. E1 activity in dried tobacco seeds stored one year at room temperature was 45% higher than that observed immediately after harvesting, suggesting that E1 protein can be stored at room temperature for a long period. E1 stability in different sub-cellular compartments and the optimal combination of promoter, 5'-UTL, and sub-cellular compartmentation for heterologous protein production in transgenic plants are discussed.

The promoter-terminator of chrysanthemum rbcS1 directs very high expression levels in plants

Transgenic plants are increasingly used as production platforms for various proteins, yet protein expression levels in the range of the most abundant plant protein, ribulose-1,5-bisphosphate carboxylase have not yet been achieved by nuclear transformation. Suitable gene regulatory 5' and 3' elements are crucial to obtain adequate expression. In this study an abundantly transcribed member (rbcS1) of the ribulose-1,5-bisphosphate carboxylase small-subunit gene family of chrysanthemum (Chrysanthemum morifolium Ramat.) was cloned. The promoter of rbcS1 was found to be homologous to promoters of highly expressed rbcS gene members of the plant families Asteraceae, Fabaceae and Solanaceae. The regulatory 5' and 3' non-translated regions of rbcS1 were engineered to drive heterologous expression of various genes. In chrysanthemum, the homologous rbcS1 cassette resulted in a beta-glucuronidase (gusA) accumulation of, at maximum, 0.88% of total soluble protein (population mean 0.17%). In tobacco (Nicotiana tabacum L.), the gusA expression reached 10% of total soluble protein. The population mean of 2.7% was found to be 7- to 8-fold higher than for the commonly used cauliflower mosaic virus (CaMV) 35S promoter (population mean 0.34%). RbcS1-driven expression of sea anemone equistatin in potato (Solanum tuberosum L.), and potato cystatin in tomato (Lycopersicon esculentum Mill.) yielded maximum levels of 3-7% of total soluble protein. The results demonstrate, that the compact 2-kb rbcS1 expression cassette provides a novel nuclear transformation vector that generates plants with expression levels of up to 10% of total protein.

Overexpression of a cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase in tobacco enhances photosynthesis and growth

Transgenic tobacco plants expressing a cyanobacterial fructose-1,6/sedoheptulose-1,7-bisphosphatase targeted to chloroplasts show enhanced photosynthetic efficiency and growth characteristics under atmospheric conditions (360 p.p.m. CO2). Compared with wild-type tobacco, final dry matter and photosynthetic CO2 fixation of the transgenic plants were 1.5-fold and 1.24-fold higher, respectively. Transgenic tobacco also showed a 1.2-fold increase in initial activity of ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco) compared with wild-type plants. Levels of intermediates in the Calvin cycle and the accumulation of carbohydrates were also higher than those in wild-type plants. This is the first report in which expression of a single plastid-targeted enzyme has been shown to improve carbon fixation and growth in transgenic plants.

Expression of Acidothermus cellulolyticus endoglucanase E1 in transgenic tobacco: biochemical characteristics and physiological effects

The expression of the Acidothermus cellulolyticus endoglucanase E1 gene in transgenic tobacco (Nicotiana tabacum) was examined in this study, where E1 coding sequence was transcribed under the control of a leaf specific Rubisco small subunit promoter (tomato RbcS-3C). Targeting the E1 protein to the chloroplast was established using a chloroplast transit peptide of Rubisco small subunit protein (tomato RbcS-2A) and confirmed by immunocytochemistry. The E1 produced in transgenic tobacco plants was found to be biologically active, and to accumulate in leaves at levels of up to 1.35% of total soluble protein. Optimum temperature and pH for E1 enzyme activity in leaf extracts were 81 degrees C and 5.25, respectively. E1 activity remained constant on a gram fresh leaf weight basis, but dramatically increased on a total leaf soluble protein basis as leaves aged, or when leaf discs were dehydrated. E1 protein in old leaves, or after 5 h dehydration, was partially degraded although E1 activity remained constant. Transgenic plants exhibited normal growth and developmental characteristics with photosynthetic rates similar to those of untransformed SR1 tobacco plants. Results from these biochemical and physiological analyses suggest that the chloroplast is a suitable cellular compartment for accumulation of the hydrolytic E1 enzyme.

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.

EVOLUTION OF LIGHT-REGULATED PLANT PROMOTERS

In this review, we address the phylogenetic and structural relationships between light-responsive promoter regions from a range of plant genes, that could explain both their common dependence on specific photoreceptor-associated transduction pathways and their functional versatility. The well-known multipartite light-responsive elements (LREs) of flowering plants share sequences very similar to motifs in the promoters of orthologous genes from conifers, ferns, and mosses, whose genes are expressed in absence of light. Therefore, composite LREs have apparently evolved from cis-regulatory units involved in other promoter functions, a notion with significant implications to our understanding of the structural and functional organization of angiosperm LREs.

Inhibition of ascorbate peroxidase under oxidative stress in tobacco having bacterial catalase in chloroplasts

To analyze the potential of the active oxygen-scavenging system of chloroplasts, we introduced Escherichia coli catalase into tobacco chloroplasts. Photosynthesis of transgenic plants was tolerant to high irradiance under drought conditions, while the wild plants suffered severe damage in photosynthesis under the same conditions. Irrespective of responses to the stress, ascorbate peroxidase was completely inactivated both in the transgenic and wild-type plants. These findings are contrary to the established idea that the ascorbate peroxidase-mediated antioxidative system protects chloroplasts from oxidative stress.

The tomato RBCS3A promoter requires integration into the chromatin for correct organ-specific regulation

In tomato, the RBCS1, RBCS2 and RBCS3A genes, encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, are expressed in leaves and light-grown seedlings, but only RBCS1 and RBCS2 are expressed in developing tomato fruits. The activities of the three promoters have been compared in transgenic plants and after transient transformation. Fruit-specific repression of the RBCS3A promoter was observed in transgenic plants, but not after ballistic transient transformation, indicating that chromatin integration is necessary for its correct organ-specific regulation. In addition, matrix attachment regions have been identified in the RBCS1, RBCS2 and RBCS3A promoters. This is the second case in plants of absence of correct regulation of a plasmid-borne plant promoter and correlating potential nuclear matrix attachment of the gene.

Localization and post-translational processing of the wound-induced leucine aminopeptidase proteins of tomato

Leucine aminopeptidase (LAP) is induced by wounding and bacterial pathogen infection in tomato. DNA blot analysis of XbaI-digested lambdalap genomic clones demonstrated that LapA1 and LapA2 cDNAs were encoded by two different LapA genes in the tomato genome. The coding and untranslated regions of LapA1 and LapA2 mRNAs shared more than 93% identity. The deduced amino acid sequences of LapA cDNA clones and in vitro translation of LapA1 mRNA indicated that LAP-A was synthesized as a 60-kDa precursor protein. The processing of a 60-kDa preLAP-A into the mature 55-kDa LAP-A was demonstrated in vivo by expression of the full-length LapA1 cDNA in insect cells. Sequencing of a single LAP-A form isolated from a two-dimensional polyacrylamide gel indicated that LAP-A proteins had two different N termini that were separated by two residues. The LAP-A presequence had features similar to chloroplast transit peptides. Comparison of LAP-A levels in chloroplast and total protein extracts from methyl jasmonate-treated leaves indicated that a small proportion of the LAP-A proteins was detected in the plastids. Inspection of the LAP-A presequence indicated the presence of a dibasic protease (Kex2/furin) processing site motif 6-8 residues upstream from the LAP-A N termini. Its potential role in LAP-A precursor biogenesis is discussed.

Repeated sequences from the Arabidopsis thaliana genome function as enhancers in transgenic tobacco

Sixteen segments of Arabidopsis thaliana DNA that function as enhancers in transgenic tobacco plants were isolated using the pROA97 enhancer cloning vehicle and library transformation of Nicotiana tabacum. The sequences were compared for AT content, homology, repeated motifs, and expression pattern in transgenic N. tabacum. The sequences were average with respect to the AT content of A. thaliana DNA. They could be placed into seven homology groups. Five of the sequences are single-copy sequences. The remaining eleven sequences represent two homology groups. Homology Group I contains seven sequences with minor differences. Homology Group II contains four sequences with minor differences. Two repeated motifs were identified (5'-CCTCT-3' and 5'-AAGGAT-3'). Both repeated motifs are found in other plant enhancers, and in the promoter region of the cauliflower mosaic virus 35S gene. In the 35S gene TATA region, the motifs can form two alternative stem-loop structures. The TATATAA sequence is located in the loop region of both stem-loop structures.

Genetic mapping of genes for twelve nuclear-encoded polypeptides associated with the thylakoid membranes in Beta vulgaris L

Thylakoid membranes of chloroplasts are composed of approx. 75 polypeptide species. Nearly 60% originate in nuclear genes, the remainder in plastid genes. In order to localize representatives of the nuclear-encoded gene complement in a eukaryotic plant genome (sugar beet, Beta vulgaris L.), we have investigated the RFLP patterns of 21 cDNAs from spinach that code for thylakoid proteins or proteins peripherally associated with thylakoid membranes. Differences in gene dosage were noted between both related species. Polymorphism was found for 12 cDNA loci in a segregating sugar beet F2 population. These loci were mapped along with genomic RFLP, isozyme, and morphological markers, and shown to be distributed in six of the nine sugar beet linkage groups. The lack of positional clustering even of genes that encode components of the same supramolecular membrane assembly is commensurate with phylogenetically independent gene translocations from the plastid (endosymbiont), and raises the question of the functional integration of various translocated genes into common signal transduction chains.

Telomere-homologous sequences occur near the centromeres of many tomato chromosomes

Several bacteriophage lambda clones containing interstitial telomere repeats (ITR) were isolated from a library of tomato genomic DNA by plaque hybridization with the cloned Arabidopsis thaliana telomere repeat. Restriction fragments lacking highly repetitive DNA were identified and used as probes to map 14 of the 20 lambda clones. All of these markers mapped near the centromere on eight of the twelve tomato chromosomes. The exact centromere location of chromosomes 7 and 9 has recently been determined, and all ITR clones that localize to these two chromosomes map to the marker clusters known to contain the centromere. High-resolution mapping of one of these markers showed cosegregation of the telomere repeat with the marker cluster closest to the centromere in over 9,000 meiotic products. We propose that the map location of interstitial telomere clones may reflect specific sequence interchanges between telomeric and centromeric regions and may provide an expedient means of localizing centromere positions.

Characterization and genetic mapping of simple repeat sequences in the tomato genome

Tomato genomic libraries were screened for the presence of simple sequence repeats (SSRs) with seventeen synthetic oligonucleotide probes, consisting of 2- to 5-basepair motifs repeated in tandem. GAn and GTn sequences were found to occur most frequently in the tomato genome (every 1.2 Mb), followed by ATTn and GCCn (every 1.4 Mb and 1.5 Mb, respectively). In contrast, only ATn and GAn microsatellites (n > 7) were found to be frequent in the GenBank database, suggesting that other motifs may be preferentially located away from genes. Polymorphism of microstellites was measured by PCR amplification of individual loci of by Southern hybridization, using a set of ten tomato cultivars. Surprisingly, only two of the nine microsatellite clones surveyed (five GTn, three GAn and one ATTn), showed length variation among these accessions. Polymorphism was also very limited between Lycopersicon esculentum and L. pennelli, two distant species. Southern analysis using the seventeen oligonucleotide probes identified GATAn and GAAAn as useful motifs for the detection of multiple polymorphic fragments among tomato cultivars. To determine the structure of microsatellite loci, a GAn probe was used for hybridization at low stringency on a small insert genomic library, and randomly selected clones were analyzed. GAn based motifs of increasing complexity were found, indicating that simple dinucleotide sequences may have evolved into larger tandem repeats such as minisatellites as a result of basepair substitution, replication slippage, and possibly unequal crossing-over. Finally, we genetically mapped loci corresponding to two amplified microsatellites, as well as nine large hypervariable fragments detected by Southern hybridization with a GATA8 probe. All loci are located around putative tomato centromeres. This may contribute to understanding of the structure of centromeric regions in tomato.

The Caenorhabditis elegans heterochronic gene pathway controls stage-specific transcription of collagen genes

In Caenorhabditis elegans, the terminal differentiation of the hypodermal cells occurs at the larval-to-adult molt, and is characterized in part by the formation of a morphologically distinct adult cuticle. The timing of this event is controlled by a pathway of heterochronic genes that includes the relatively direct regulatory gene, lin-29, and upstream genes lin-4, lin-14 and lin-28. Using northern analysis to detect endogenous collagen mRNA levels and collagen/lacZ reporter constructs to monitor collagen transcriptional activity, we show that the stage-specific switch from larval cuticle to adult cuticle correlates with the transcriptional activation of adult-specific collagen genes and repression of larval-specific collagen genes. Heterochronic mutations that cause precocious formation of adult cuticle also cause precocious transcription of the adult-specific collagen genes, col-7 and col-19; heterochronic mutations that prevent the switch to adult cuticle cause continued expression of the larval collagen gene, col-17, in adults and prevent adult-specific activation of col-7 or col-19. A 235 bp segment of col-19 5′ sequences is sufficient to direct the adult-specific expression of a col-19/lacZ reporter gene in hypodermal cells. These findings indicate that the heterochronic gene pathway regulates the timing of hypodermal cell terminal differentiation by regulating larval- and adult-specific gene expression, perhaps by the direct action of lin-29.

Sequence of cassava ribulose-1,5-bisphosphate carboxylase small subunit precursor cDNA

The cDNA sequence of cassava ribulose-1,5-bisphosphate carboxylase small subunit rbcS precursor has been determined. The cassava rbcS precursor cDNA contains 266 nucleotides (nts) of 5' untranslated region, 546 nts of coding region, 280 nts of 3' untranslated region and a poly (A) tail of 70 nts. The 5' untranslated region is characterized by some unusual features which include two plausible open reading frames, several repeated sequences and a putative Shine-Dalgarno sequence. The predicted amino acid sequence shows that the precursor consists of a 59 amino acid transit peptide followed by the 123 amino acid rbcS sequence. Cassava rbcS shares 82% amino acid sequence identity with a rubber rbcS sequence.

Light activation of expression associated with the tomato rbcS promoter in transformed tobacco cell line BY-2

The promoter (2.3 kb) of ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS3B) from tomato was inserted into the upstream multi-cloning site of beta-glucuronidase (GUS) gene. The construction was introduced into the tobacco suspension cultured cell, BY-2. The transformed tobacco cell exhibited greater GUS activity (10-fold) under the light condition than the dark condition. The specific GUS activity increased with increasing culture time under the light condition. In fed-batch culture, high density culture was achieved, 47.6 g l-1 dry weight, which was 6.8-fold greater than the batch culture, whereas the GUS was produced 1.7-fold in specific activity compared with the batch culture. Growth of BY-2 and GUS gene expression during the culture were simulated by a kinetic model.

Characterization of a phenylalanine ammonia-lyase multigene family in Trifolium subterraneum

The enzyme phenylalanine ammonia-lyase (PAL) was found to be encoded by a small gene family in the legume Trifolium subterraneum (subterranean clover). At least three of the family members are tightly clustered within approx. 20 kb of DNA. Sequencing of one of the genes established that it possesses two exons, the position of the single intron being identical to that found for PAL genes from other plants. The PAL protein consists of 725 amino acids, as deduced from the nucleotide sequence.

The gene family encoding the ribulose-(1,5)-bisphosphate carboxylase/oxygenase (Rubisco) small subunit of potato

We determined the nucleotide sequences of five members of the rbcS gene family encoding the small subunit (SSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of potato. The genomic organization, structure and expression of the genes is compared to the features of the rbcS genes in tomato. Within the two species, Lycopersicon esculentum and Solanum tuberosum, both members of the Solanaceae, the rbcS genes share more interspecific sequence identity, especially in the 5'- and 3'-untranslated regions and the intron sequences, than within one species. However, the expression data of orthologous rbcS genes containing highly identical regulatory cis-acting elements were found to be different, suggesting that the simple finding of these motifs does not automatically imply similar transcriptional and/or post-transcriptional gene regulation.

Leucine aminopeptidase: an inducible component of the defense response in Lycopersicon esculentum (tomato)

A leucine aminopeptidase (EC 3.4.11.1) cDNA clone (DR57) that was induced in response to Pseudomonas syringae pv. tomato (P.s. tomato) infection was isolated using a subtractive hybridization-enriched cDNA probe. Genomic DNA blot analysis showed that the tomato genome had two leucine aminopeptidase genes. The levels of DR57 mRNAs after P.s. tomato infection and mechanical wounding were determined in two inbred tomato lines that exhibit susceptibility and resistance to P.s. tomato. DR57 mRNAs were detected 12 hours after infection and 4 hours after wounding. Furthermore, DR57 mRNAs were systemically induced in response to wounding. DR57 mRNAs were induced in leaves after Spodoptera littoralis feeding but were not detected in detached leaf controls. Possible roles for the DR57 leucine aminopeptidase in the defense reactions are discussed.

Characterization of tomato DNA clones with sequence similarity to human minisatellites 33.6 and 33.15

A tomato lambda genomic library was screened with the human minisatellites 33.6 and 33.15. Similar tomato sequences are estimated to occur on average every 4000 kb. In thirteen hybridizing clones characterized, the size of minisatellite arrays varied between 100 bp and 3 kb. The structure of the repetitive elements is complex as the human core sequence is interspersed with other elements. In three cases, sequences similar to the human minisatellites were part of a higher-order tandem repeat. The chromosomal position of these sequences was established by ascertaining linkage to previously mapped RFLP markers. In contrast to the human genome, no clustering of minisatellite loci was observed in tomato. The fingerprints generated by hybridizing tomato minisatellites to genomic DNA of a set of cultivars were, in two cases, more variable than those obtained with 33.6 or 33.15. Two of the characterized probes detected 4-8 alleles of a single locus, which displayed 10-15 times more polymorphism than random RFLP clones. Some minisatellites contain di- and tri-nucleotide microsatellite repeated motifs which may account for the high level of polymorphism detected with these clones.

The six genes of the Rubisco small subunit multigene family from Mesembryanthemum crystallinum, a facultative CAM plant

The nucleotide sequences of the entire gene family, comprising six genes, that encodes the Rubisco small subunit (rbcS) multigene family in Mesembryanthemum crystallinum (common ice plant), were determined. Five of the genes are arranged in a tandem array spanning 20 kb, while the sixth gene is not closely linked to this array. The mature small subunit coding regions are highly conserved and encode four distinct polypeptides of equal lengths with up to five amino acid differences distinguishing individual genes. The transit peptide coding regions are more divergent in both amino acid sequence and length, encoding five distinct peptide sequences that range from 55 to 61 amino acids in length. Each of the genes has two introns located at conserved sites within the mature peptide-coding regions. The first introns are diverse in sequence and length ranging from 122 bp to 1092 bp. Five of the six second introns are highly conserved in sequence and length. Two genes, rbcS-4 and rbcS-5, are identical at the nucleotide level starting from 121 bp upstream of the ATG initiation codon to 9 bp downstream of the stop codon including the sequences of both introns, indicating recent gene duplication and/or gene conversion. Functionally important regulatory elements identified in rbcS promoters of other species are absent from the upstream regions of all but one of the ice plant rbcS genes. Relative expression levels were determined for the rbcS genes and indicate that they are differentially expressed in leaves.

Complex duplications in maize lines

Rp1 is a disease resistance complex and is the terminal morphological marker on the short arm of maize chromosome 10. Several restriction fragment length polymorphisms (RFLPs), which map within 5 map units of Rp1, were examined to determine if they are also complex in structure. Two RFLP loci, which mapped distally to Rp1, BNL3.04 and PIO200075, existed in a single copy in all maize lines examined. These two loci cosegregated perfectly in 130 test cross progeny. Two RFLP loci that map proximally to Rp1 had unusual structures, which have not yet been reported for maize RFLPs; the loci were complex, with variable numbers of copies in different maize lines. One of the loci, NP1285, occasionally recombined in meiosis to yield changes in the number of copies of sequences homologous to the probe. The other proximal locus, detected by the probes NPI422, KSU3, and KSU4, was relatively stable in meiosis and no changes in the number of restriction fragments were observed. The similarity in map position between Rp1 and the complex RFLP loci indicate there may be genomic areas where variable numbers of repeated sequences are common. The structure of these complex loci may provide insight into the structure and evolution of Rp1.

Developmental and organ-specific changes in DNA-protein interactions in the tomato rbcS3B and rbcS3C promoter regions

Sites of DNA-protein interaction were mapped in the promoter regions of two of the five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS) in tomato. The two genes, designated rbcS3B and -3C, are actively transcribed in cotyledons of light-grown seedlings and in leaves, but are transcriptionally inactive cotyledons of dark-grown seedlings, in young and mature tomato fruit, and in roots. The combination and order of conserved DNA sequence elements in the promoter regions of the two genes are essentially identical, but differ considerably from that found in the promoters of the other three tomato rbcS genes, which show different transcription patterns. Nuclear extracts from cotyledons of 7-day-old tomato seedlings, and from leaves and young tomato fruit of mature plants defined multiple DNase I-protected sites in the promoter regions of both genes. The protection patterns were organ-specific, and encompassed previously identified conserved DNA sequence motifs as well as uncharacterized sequences. In contrast, nuclear extracts from mature tomato fruit and roots of 7-day-old seedlings failed to protect any of the promoter sequences, implying that DNA-binding proteins required for transcription of rbcS3B and -3C are inactive in these organs. These results are somewhat surprising since DNA-binding proteins from cotyledons of dark-grown seedlings and young fruit interact with the two promoters, although rbcS3B and -3C are not transcribed in these organs. The basis for transcriptional regulation of these two genes is discussed and the detailed pattern of DNase I protection in the promoter regions of the two genes is presented.

Developmental and organ-specific changes in DNA-protein interactions in the tomato rbcS1, rbcS2 and rbcS3A promoter regions

DNase I footprinting assays were used to map sites of DNA-protein interaction in the promoter regions of three of the five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS) in tomato. Organ-specific differences in DNase I protection patterns were observed using nuclear extracts derived from cotyledons, leaves, young fruit, mature fruit, and roots of tomato, implying that organ-specific transcription of these genes is controlled at the level of DNA-protein interaction. The three genes, designated rbcS1, -2 and -3A are similarly expressed in cotyledons of dark-grown seedlings, in immature tomato fruit, and in leaves under conditions of water stress. These three genes share at least three DNA sequence motifs, including the G-box sequence, which are apparently not present in the other two tomato rbcS genes. We find protection of one or more of these sequences in the aforementioned organs, indicating that the corresponding DNA-binding proteins could function in directing differential expression of the genes, although functional studies would be required to establish this point. While most of the DNase I protections encompass previously identified conserved sequence motifs and their flanking sequence, we also observe protection of additional sequences, many of which occur in the region of the transcription start site.

The Euglena gracilis rbcS gene contains introns with unusual borders

We have recently shown that, in Euglena gracilis, leader sequences are transferred by trans-splicing to the vast majority of cytoplasmic mRNAs. Trans-splicing is involved in the maturation of the rbcS transcript, which encodes eight small subunits of the ribulose 1,5 bisphosphate carboxylase/oxygenase. In this report, we show that the Euglena rbcS gene introns are different from introns found in plant rbcS genes. In addition these introns do not have the conserved 5' and 3' border sequences found in introns of eucaryotic nuclear-encoded pre-mRNAs, and they do not present any homology with self-splicing introns of groups I and II. Secondary structure analyses show that the 5' and 3' ends of Euglena introns can base-pair, suggesting that an unusual splicing mechanism exists in Euglena.

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.

Isolation and characterization of tomato cDNA and genomic clones encoding the ubiquitin gene ubi3

We report here the isolation and nucleotide sequence of tomato cDNA and genomic clones encoding a ubiquitin extension protein homologous to the yeast gene ubi3. Sites similar to upstream activating sites commonly found in the promoters of yeast ribosomal genes were observed in the tomato promoter. The tomato ubi3 promoter also contained elements found in the rbcS promoter from pea. The transcription initiation site was determined to occur 66 bp upstream of the initiating Met. RFLP mapping revealed that the gene was located on chromosome 1, 23 cM from marker TG301. A ubi3 gene-specific probe hybridized to a single 800 nt transcript. Expression was reduced in heat-shocked plants and plants kept in the dark. Expression was highest in young leaves and immature green fruit and lowest in mature leaves and petals. We isolated the original cDNA clone using an antibody prepared against chloroplast polypeptides. Immunological studies did not detect ubiquitin or ubiquitin extension proteins in the chloroplast. However, higher-molecular-weight chloroplast proteins were detected with ubiquitin antisera suggesting that ubiquitin conjugates are transported into the chloroplast.

Chlorophyll a/b binding (CAB) polypeptides of CP29, the internal chlorophyll a/b complex of PSII: characterization of the tomato gene encoding the 26 kDa (type I) polypeptide, and evidence for a second CP29 polypeptide

CP29, the core chlorophyll a/b (CAB) antenna complex of Photosystem II (PSII), has two nuclear-encoded polypeptides of approximately 26 and 28 kDa in tomato (Lycopersicon esculentum). Cab9, the gene for the Type I (26 kDa) CP29 polypeptide was cloned by immunoscreening a tomato leaf cDNA library. Its identity was confirmed by sequencing tryptic peptides from the mature protein. Cab9 is a single-copy gene with five introns, the highest number found in a CAB protein. In vitro transcription-translation gave a 31 kDa precursor which was cleaved to about 26 kDa after import into isolated tomato chloroplasts. The Cab9 polypeptide has the two highly conserved regions common to all CAB polypeptides, which define the members of this extended gene family. Outside of the conserved regions, it is only slightly more closely related to other PSII CABs than to PSI CABs. Sequence analysis of tryptic peptides from the Type II (28 kDa) CP29 polypeptide showed that it is also a member of the CAB family and is very similar or identical to the CP29 polypeptide previously isolated from spinach. All members of the CAB family have absolutely conserved His, Gln and Asn residues which could ligate the Mg atoms of the chlorophylls, and a number of conserved Asp. Glu, Lys and Arg residues which could form H-bonds to the polar groups on the porphyrin rings. The two conserved regions comprise the first and third predicted trans-membrane helices and the stroma-exposed segments preceding them.

Fragments of plastid DNA in the nuclear genome of tomato: prevalence, chromosomal location, and possible mechanism of integration

We have undertaken a systematic search for plastid DNA sequences integrated in the tomato nuclear genome, using heterologous probes taken from intervals of a plastid DNA region spanning 58 kb. A total of two short integrates (202 and 141 nucleotides) were isolated and mapped to chromosomes 9 and 5, respectively. The nucleotide sequence of the integrates and that of the flanking regions were determined. The integration sites contain direct repeat elements similar in position (but not in length or sequence) to the direct repeats previously observed with another plastid integrate in the tomato nuclear genome. Based on these results, a model for the process of movement and integration of plastid sequences into the nuclear genome is discussed.

Comparison of cloned genes provides evidence for intergenomic exchange of DNA in the evolution of a tobacco glucan endo-1,3-beta-glucosidase gene family

Two genes for prepro glucan endo-1,3-beta-glucosidase (1,3-beta-glucanase; 1,3-beta-D-glucan glucanohydrolase, EC 3.2.1.39) of tobacco were cloned and their sequences were compared with cDNA clones. Southern analysis indicates that the genomic clones represent genes derived from ancestral parents of tobacco similar to the present day species Nicotiana sylvestris and Nicotiana tomentosiformis, whereas the genes represented by two of the cDNA clones appear to be unique to tobacco. The coding sequences of the genomic clones and cDNA clones differed at less than 2.2% of the positions, indicating that the tobacco 1,3-beta-glucanase gene family is highly conserved. Alternating blocks of sequence in the cDNA clones were identical to the coding sequence of the two genomic clones. These results and an analysis of evolutionary distances for nucleotide substitution are consistent with the hypothesis that the evolution of the tobacco 1,3-beta-glucanase gene family has involved exchange of DNA between members of the tomentosiformis and sylvestris subgenomes by recombination or gene conversion.

Rapid isolation of a rice waxy sequence: a simple PCR method for the analysis of recombinant plasmids from intact Escherichia coli cells

Polymerase chain reaction (PCR) is an efficient method for obtaining a desired nt sequence if both required primers can hybridize to the target DNA molecule specifically. A rapid and simple PCR-based method for analyzing plasmids using intact cells was established. An attempt to target a rice waxy sequence by PCR using homologous primers was also carried out. In three cases, specific fragments were amplified and their nucleotide sequences were determined. However, the cloned rice waxy gene contained base substitution mutations. The cumulative frequency of mutation after 30 polymerization cycles was estimated to be one in 500 bp.

Molecular biology of the C3 photosynthetic carbon reduction cycle

In recent years the enzymes of the C3 photosynthetic carbon reduction (PCR) cycle have been studied using the techniques of molecular biology. In this review we discuss the primary protein sequences and structural predictions that have been made for a number of these enzymes, which, with the input of crystallographic analysis, gives the opportunity to understand the mechanisms of enzyme activity.The genome organisation and gene structure of the PCR enzymes is another area which has recently expanded, and we discuss the regulation of the genes encoding these enzymes and the complex interaction of various factors which influence their expression.

Structure and expression of tomato mitochondrial genes coding for tRNA(Cys) (GCA), tRNA(Asn) (GUU) and tRNA(Tyr) (GUA): a native tRNA(Cys) gene is present in dicot plants but absent in monocot plants

The nucleotide sequences of tRNA(Asn) (GUU) and tRNA(Tyr) (GUA) genes from tomato mitochondria and their flanking regions have been determined. The tomato mitochondrial tRNA(Asn) gene is located 2.1 kb downstream from the tRNA(Cys) gene reported previously (Izuchi and Sugita 1989) and shows a nearly complete identity with the corresponding chloroplast gene. The tRNA(Tyr) gene, which shows only 73% homology with the corresponding chloroplast gene, has to be considered a "native" mitochondrial tRNA gene and is 535 bp from the "chloroplast-like" tRNA(Asn) gene on the same strand. Northern hybridization analysis revealed that the three tRNA genes are transcribed in tomato mitochondria. Southern hybridization analysis of tomato, sugar beet. rice and wheat mitochondrial DNAs, with oligonucleotide probes for mitochondrial or chloroplast tRNA genes, demonstrated that the mitochondrial tRNA(Cys) gene found in tomato is present in dicot plants but not in monocots. On the other hand, a chloroplast-like tRNA(Cys) gene exists in monocot plants.