Expression of the C4 Me1 Gene from Flaveria bidentis Requires an Interaction between 5[prime] and 3[prime] Sequences

Plant terminators: the unsung heroes of gene expression

To be properly expressed, genes need to be accompanied by a terminator, a region downstream of the coding sequence that contains the information necessary for the maturation of the mRNA 3' end. The main event in this process is the addition of a poly(A) tail at the 3' end of the new transcript, a critical step in mRNA biology that has important consequences for the expression of genes. Here, we review the mechanism leading to cleavage and polyadenylation of newly transcribed mRNAs and how this process can affect the final levels of gene expression. We give special attention to an aspect often overlooked, the effect that different terminators can have on the expression of genes. We also discuss some exciting findings connecting the choice of terminator to the biogenesis of small RNAs, which are a central part of one of the most important mechanisms of regulation of gene expression in plants.

Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops

As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.

Dynamic changes of genome sizes and gradual gain of cell-specific distribution of C4 enzymes during C4 evolution in genus Flaveria

C₄ plants are believed to have evolved from C₃ plants through various C₃ -C₄ intermediate stages in which a photorespiration-dependent CO₂ concentration system known as C₂ photosynthesis operates. Genes involved in the C₄ cycle were thought to be recruited from orthologs present in C₃ species and developed cell-specific expression during C₄ evolution. To understand the process of establishing C₄ photosynthesis, we performed whole-genome sequencing and investigated expression and mesophyll- or bundle-sheath-cell-specific localization of phosphoenolpyruvate carboxylase (PEPC), NADP-malic enzyme (NADP-ME), pyruvate, orthophosphate dikinase (PPDK) in C₃ , C₃ -C₄ intermediate, C₄ -like, and C₄ Flaveria species. While genome sizes vary greatly, the number of predicted protein-coding genes was similar among C₃ , C₃ -C₄ intermediate, C₄ -like, and C₄ Flaveria species. Cell-specific localization of the PEPC, NADP-ME, and PPDK transcripts was insignificant or weak in C₃ -C₄ intermediate species, whereas these transcripts were expressed cell-type specific in C₄ -like species. These results showed that elevation of gene expression and cell-specific control of pre-existing C₄ cycle genes in C₃ species was involved in C₄ evolution. Gene expression was gradually enhanced during C₄ evolution, whereas cell-specific control was gained independently of quantitative transcriptional activation during evolution from C₃ -C₄ intermediate to C₄ photosynthesis in genus Flaveria.

Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression

Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.

C3 cotyledons are followed by C4 leaves: intra-individual transcriptome analysis of Salsola soda (Chenopodiaceae)

Some species of Salsoleae (Chenopodiaceae) convert from C₃ photosynthesis during the seedling stage to the C₄ pathway in adult leaves. This unique developmental transition of photosynthetic pathways offers the exceptional opportunity to follow the development of the derived C₄ syndrome from the C₃ condition within individual plants, avoiding phylogenetic noise. Here we investigate Salsola soda, a little-studied species from tribe Salsoleae, using an ontogenetic approach. Anatomical sections, carbon isotope (δ¹³C) values, transcriptome analysis by means of mRNA sequencing, and protein levels of the key C₄ enzyme phosphoenolpyruvate carboxylase (PEPC) were examined from seed to adult plant stages. Despite a previous report, our results based on δ¹³C values, anatomy and transcriptomics clearly indicate a C₃ phase during the cotyledon stage. During this stage, the entire transcriptional repertoire of the C₄ NADP-malic enzyme type is detected at low levels compared to a significant increase in true leaves. In contrast, abundance of transcripts encoding most of the major photorespiratory enzymes is not significantly decreased in leaves compared to cotyledons. PEPC polypeptide was detected only in leaves, correlating with increased PEPC transcript abundance from the cotyledon to leaf stage.

Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation

Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution.

An Untranslated cis-Element Regulates the Accumulation of Multiple C4 Enzymes in Gynandropsis gynandra Mesophyll Cells

C4 photosynthesis is a complex phenotype that allows more efficient carbon capture than the ancestral C3 pathway. In leaves of C4 species, hundreds of transcripts increase in abundance compared with C3 relatives and become restricted to mesophyll (M) or bundle sheath (BS) cells. However, no mechanism has been reported that regulates the compartmentation of multiple enzymes in M or BS cells. We examined mechanisms regulating CARBONIC ANHYDRASE4 (CA4) in C4 Gynandropsis gynandra. Increased abundance is directed by both the promoter region and introns of the G. gynandra gene. A nine-nucleotide motif located in the 5' untranslated region (UTR) is required for preferential accumulation of GUS in M cells. This element is present and functional in three additional 5' UTRs and six 3' UTRs where it determines accumulation of two isoforms of CA and pyruvate,orthophosphate dikinase in M cells. Although the GgCA4 5' UTR is sufficient to direct GUS accumulation in M cells, transcripts encoding GUS are abundant in both M and BS. Mutating the GgCA4 5' UTR abolishes enrichment of protein in M cells without affecting transcript abundance. The work identifies a mechanism that directs cell-preferential accumulation of multiple enzymes required for C4 photosynthesis.

Getting the most out of natural variation in C4 photosynthesis

C4 photosynthesis is a complex trait that has a high degree of natural variation, involving anatomical and biochemical changes relative to the ancestral C3 state. It has evolved at least 66 times across a variety of lineages and the evolutionary route from C3 to C4 is likely conserved but not necessarily genetically identical. As such, a variety of C4 species are needed to identify what is fundamental to the C4 evolutionary process in a global context. In order to identify the genetic components of C4 form and function, a number of species are used as genetic models. These include Zea mays (maize), Sorghum bicolor (sorghum), Setaria viridis (Setaria), Flaveria bidentis, and Cleome gynandra. Each of these species has different benefits and challenges associated with its use as a model organism. Here, we propose that RNA profiling of a large sampling of C4, C3-C4, and C3 species, from as many lineages as possible, will allow identification of candidate genes necessary and sufficient to confer C4 anatomy and/or biochemistry. Furthermore, C4 model species will play a critical role in the functional characterization of these candidate genes and identification of their regulatory elements, by providing a platform for transformation and through the use of gene expression profiles in mesophyll and bundle sheath cells and along the leaf developmental gradient. Efforts should be made to sequence the genomes of F. bidentis and C. gynandra and to develop congeneric C3 species as genetic models for comparative studies. In combination, such resources would facilitate discovery of common and unique C4 regulatory mechanisms across genera.

Evolution of the C4 photosynthetic pathway: events at the cellular and molecular levels

The biochemistry and leaf anatomy of plants using C4 photosynthesis promote the concentration of atmospheric CO2 in leaf tissue that leads to improvements in growth and yield of C4 plants over C3 species in hot, dry, high light, and/or saline environments. C4 plants like maize and sugarcane are significant food, fodder, and bioenergy crops. The C4 photosynthetic pathway is an excellent example of convergent evolution, having evolved in multiple independent lineages of land plants from ancestors employing C3 photosynthesis. In addition to C3 and C4 species, some plant lineages contain closely related C3-C4 intermediate species that demonstrate leaf anatomical, biochemical, and physiological characteristics between those of C3 plants and species using C4 photosynthesis. These groups of plants have been extremely useful in dissecting the modifications to leaf anatomy and molecular biology, which led to the evolution of C4 photosynthesis. It is now clear that great variation exists in C4 leaf anatomy, and diverse molecular mechanisms underlie C4 biochemistry and physiology. However, all these different paths have led to the same destination-the expression of a C4 CO2 concentrating mechanism. Further identification of C4 leaf anatomical traits and molecular biological components, and understanding how they are controlled and assembled will not only allow for additional insights into evolutionary convergence, but also contribute to sustainable food and bioenergy production strategies.

Antisense reduction of NADP-malic enzyme in Flaveria bidentis reduces flow of CO2 through the C4 cycle

An antisense construct targeting the C(4) isoform of NADP-malic enzyme (ME), the primary enzyme decarboxylating malate in bundle sheath cells to supply CO(2) to Rubisco, was used to transform the dicot Flaveria bidentis. Transgenic plants (α-NADP-ME) exhibited a 34% to 75% reduction in NADP-ME activity relative to the wild type with no visible growth phenotype. We characterized the effect of reducing NADP-ME on photosynthesis by measuring in vitro photosynthetic enzyme activity, gas exchange, and real-time carbon isotope discrimination (Δ). In α-NADP-ME plants with less than 40% of wild-type NADP-ME activity, CO(2) assimilation rates at high intercellular CO(2) were significantly reduced, whereas the in vitro activities of both phosphoenolpyruvate carboxylase and Rubisco were increased. Δ measured concurrently with gas exchange in these plants showed a lower Δ and thus a lower calculated leakiness of CO(2) (the ratio of CO(2) leak rate from the bundle sheath to the rate of CO(2) supply). Comparative measurements on antisense Rubisco small subunit F. bidentis plants showed the opposite effect of increased Δ and leakiness. We use these measurements to estimate the C(4) cycle rate, bundle sheath leak rate, and bundle sheath CO(2) concentration. The comparison of α-NADP-ME and antisense Rubisco small subunit demonstrates that the coordination of the C(3) and C(4) cycles that exist during environmental perturbations by light and CO(2) can be disrupted through transgenic manipulations. Furthermore, our results suggest that the efficiency of the C(4) pathway could potentially be improved through a reduction in C(4) cycle activity or increased C(3) cycle activity.

Molecular evolution of genes recruited into C₄ photosynthesis

The C₄ pathway is found in 62 lineages of land plants. We assess evidence for parallel versus convergent evolution of C₄ photosynthesis from three approaches: (i) studies of specific genes and cis-elements controlling their expression; (ii) phylogenetic analyses of mRNAs and inferred amino acid sequences; and (iii) analysis of C₃ and C₄ genomes and transcriptomes. Evidence suggests that although convergent evolution is common, parallel evolution can underlie both changes to gene expression and amino acid sequence. cis-elements that direct cell specificity in C₄ leaves are present in C₃ orthologues of genes recruited into C₄, probably facilitating this parallel evolution. From this, and genomic data, we propose that gene duplication followed by neofunctionalisation is not necessarily important in the evolution of C₄ biochemistry.

Lessons from engineering a single-cell C(4) photosynthetic pathway into rice

The transfer of C(4) plant traits into C(3) plants has long been a strategy for improving the photosynthetic performance of C(3) plants. The introduction of a pathway mimicking the C(4) photosynthetic pathway into the mesophyll cells of C(3) plants was only a realistic approach when transgenic technology was sufficiently well developed and widely adopted. Here an attempt to introduce a single-cell C(4)-like pathway in which CO(2) capture and release occur in the mesophyll cell, such as the one found in the aquatic plant Hydrilla verticillata (L.f.) Royle, into rice (Oryza sativa L.) is described. Four enzymes involved in this pathway were successfully overproduced in the transgenic rice leaves, and 12 different sets of transgenic rice that overproduce these enzymes independently or in combination were produced and analysed. Although none of these transformants has yet shown dramatic improvements in photosynthesis, these studies nonetheless have important implications for the evolution of C(4) photosynthetic genes and their metabolic regulation, and have shed light on the unique aspects of rice physiology and metabolism. This article summarizes the lessons learned during these attempts to engineer single-cell C(4) rice.

The molecular evolution of β-carbonic anhydrase in Flaveria

Limited information exists regarding molecular events that occurred during the evolution of C(4) plants from their C(3) ancestors. The enzyme β-carbonic anhydrase (CA; EC 4.2.1.1), which catalyses the reversible hydration of CO(2), is present in multiple forms in C(3) and C(4) plants, and has given insights into the molecular evolution of the C(4) pathway in the genus Flaveria. cDNAs encoding three distinct isoforms of β-CA, CA1-CA3, have been isolated and examined from Flaveria C(3) and C(4) congeners. Sequence data, expression analyses of CA orthologues, and chloroplast import assays with radiolabelled CA precursor proteins from the C(3) species F. pringlei Gandoger and the C(4) species F. bidentis (L.) Kuntze have shown that both contain chloroplastic and cytosolic forms of the enzyme, and the potential roles of these isoforms are discussed. The data also identified CA3 as the cytosolic isoform important in C(4) photosynthesis and indicate that the C(4) CA3 gene evolved as a result of gene duplication and neofunctionalization, which involved mutations in coding and non-coding regions of the ancestral C(3) CA3 gene. Comparisons of the deduced CA3 amino acid sequences from Flaveria C(3), C(4), and photosynthetic intermediate species showed that all the C(3)-C(4) intermediates investigated and F. brownii, a C(4)-like species, have a C(3)-type CA3, while F. vaginata, another C(4)-like species, contains a C(4)-type CA3. These observations correlate with the photosynthetic physiologies of the intermediates, suggesting that the molecular evolution of C(4) photosynthesis in Flaveria may have resulted from a temporally dependent, stepwise modification of protein-encoding genes and their regulatory elements.

Best practice procedures for the establishment of a C(4) cycle in transgenic C(3) plants

C(4) plants established a mechanism for the concentration of CO(2) in the vicinity of ribulose-1,5-bisphosphate carboxylase/oxygenase in order to saturate the enzyme with substrate and substantially to reduce the alternative fixation of O(2) that results in energy losses. Transfer of the C(4) mechanism to C(3) plants has been repeatedly tested, but none of the approaches so far resulted in transgenic plants with enhanced photosynthesis or growth. Instead, often deleterious effects were observed. A true C(4) cycle requires the co-ordinated activity of multiple enzymes in different cell types and in response to diverse environmental and metabolic stimuli. This review summarizes our current knowledge about the most appropriate regulatory elements and coding sequences for the establishment of C(4) protein activities in C(3) plants. In addition, technological breakthroughs for the efficient transfer of the numerous genes probably required to transform a C(3) plant into a C(4) plant will be discussed.

Regulatory mechanisms underlying C4 photosynthesis

C4 photosynthesis is an adaptation that evolved to alleviate the detrimental effects of photorespiration as a result of the gradual decline in atmospheric carbon dioxide levels. In most C4 plants, two cell types, bundle sheath and mesophyll, cooperate in carbon fixation, and, in so doing, are able to alleviate photorespiratory losses. Although much of the biochemistry is well characterized, little is known about the genetic mechanisms underlying the cell-type specificity driving C4 . However, several studies have shown that regulation acts at multiple levels, including transcriptional, post-transcriptional, post-translational and epigenetic. One example of such a regulatory mechanism is the cell-specific accumulation of major photorespiratory transcripts/proteins in bundle sheath cells, where ribulose-1,5-bisphosphate carboxylase/oxygenase is localized. Although many of the genes are expressed in the bundle sheath, some are expressed in both cell types, implicating post-transcriptional control mechanisms. Recently, ultra-high-throughput sequencing techniques and sophisticated mass spectrometry instrumentation have provided new opportunities to further our understanding of C4 regulation. Computational pipelines are being developed to accommodate the mass of data associated with these techniques. Finally, we discuss a readily transformable C4 grass--Setaria viridis--that has great potential to serve as a model for the genetic dissection of C4 photosynthesis in the grasses.

The regulation of gene expression required for C4 photosynthesis

C(4) photosynthesis is normally associated with the compartmentation of photosynthesis between mesophyll (M) and bundle sheath (BS) cells. The mechanisms regulating the differential accumulation of photosynthesis proteins in these specialized cells are fundamental to our understanding of how C(4) photosynthesis operates. Cell-specific accumulation of proteins in M or BS can be mediated by posttranscriptional processes and translational efficiency as well as by differences in transcription. Individual genes are likely regulated at multiple levels. Although cis-elements have been associated with cell-specific expression in C(4) leaves, there has been little progress in identifying trans-factors. When C(4) photosynthesis genes from C(4) species are placed in closely related C(3) species, they are often expressed in a manner faithful to the C(4) cycle. Next-generation sequencing and comprehensive analysis of the extent to which genes from C(4) species are expressed in M or BS cells of C(3) plants should provide insight into how the C(4) pathway is regulated and evolved.

The gene for the P-subunit of glycine decarboxylase from the C4 species Flaveria trinervia: analysis of transcriptional control in transgenic Flaveria bidentis (C4) and Arabidopsis (C3)

Glycine decarboxylase (GDC) plays an important role in the photorespiratory metabolism of plants. GDC is composed of four subunits (P, H, L, and T) with the P-subunit (GLDP) serving as the actual decarboxylating unit. In C(3) plants, GDC can be found in all photosynthetic cells, whereas in leaves of C(3)-C(4) intermediate and C(4) species its occurrence is restricted to bundle-sheath cells. The specific expression of GLDP in bundle-sheath cells might have constituted a biochemical starting point for the evolution of C(4) photosynthesis. To understand the molecular mechanisms responsible for restricting GLDP expression to bundle-sheath cells, we performed a functional analysis of the GLDPA promoter from the C(4) species Flaveria trinervia. Expression of a promoter-reporter gene fusion in transgenic plants of the transformable C(4) species Flaveria bidentis (C(4)) showed that 1,571 bp of the GLDPA 5' flanking region contain all the necessary information for the specific expression in bundle-sheath cells and vascular bundles. Interestingly, we found that the GLDPA promoter of F. trinervia exhibits a C(4)-like spatial activity also in the C(3) plant Arabidopsis (Arabidopsis thaliana), indicating that a mechanism for bundle-sheath-specific expression is also present in this C(3) species. Using transgenic Arabidopsis, promoter deletion studies identified two regions in the GLDPA promoter, one conferring repression of gene expression in mesophyll cells and one functioning as a general transcriptional enhancer. Subsequent analyses in transgenic F. bidentis confirmed that these two segments fulfill the same function also in the C(4) context.

The evolution of C4 photosynthesis

C₄ photosynthesis is a series of anatomical and biochemical modifications that concentrate CO₂ around the carboxylating enzyme Rubisco, thereby increasing photosynthetic efficiency in conditions promoting high rates of photorespiration. The C₄ pathway independently evolved over 45 times in 19 families of angiosperms, and thus represents one of the most convergent of evolutionary phenomena. Most origins of C₄ photosynthesis occurred in the dicots, with at least 30 lineages. C₄ photosynthesis first arose in grasses, probably during the Oligocene epoch (24-35 million yr ago). The earliest C₄ dicots are likely members of the Chenopodiaceae dating back 15-21 million yr; however, most C₄ dicot lineages are estimated to have appeared relatively recently, perhaps less than 5 million yr ago. C₄ photosynthesis in the dicots originated in arid regions of low latitude, implicating combined effects of heat, drought and/or salinity as important conditions promoting C₄ evolution. Low atmospheric CO₂ is a significant contributing factor, because it is required for high rates of photorespiration. Consistently, the appearance of C₄ plants in the evolutionary record coincides with periods of increasing global aridification and declining atmospheric CO₂ . Gene duplication followed by neo- and nonfunctionalization are the leading mechanisms for creating C₄ genomes, with selection for carbon conservation traits under conditions promoting high photorespiration being the ultimate factor behind the origin of C₄ photosynthesis. Contents Summary 341 I. Introduction 342 II. What is C₄ photosynthesis? 343 III. Why did C₄ photosynthesis evolve? 347 IV. Evolutionary lineages of C₄ photosynthesis 348 V. Where did C₄ photosynthesis evolve? 350 VI. How did C₄ photosynthesis evolve? 352 VII. Molecular evolution of C₄ photosynthesis 361 VIII. When did C₄ photosynthesis evolve 362 IX. The rise of C₄ photosynthesis in relation to climate and CO₂ 363 X. Final thoughts: the future evolution of C₄ photosynthesis 365 Acknowledgements 365 References 365.

Distinct but conserved functions for two chloroplastic NADP-malic enzyme isoforms in C3 and C4 Flaveria species

In the most common C4 pathway for carbon fixation, an NADP-malic enzyme (NADP-ME) decarboxylates malate in the chloroplasts of bundle sheath cells. Isoforms of plastidic NADP-ME are encoded by two genes in all species of Flaveria, including C3, C3-C4 intermediate, and C4 types. However, only one of these genes, ChlMe1, encodes the enzyme that functions in the C4 pathway. We compared the expression patterns of the ChlMe1 and ChlMe2 genes in developing leaves of Flaveria pringlei (C3) and Flaveria trinervia (C4) and in transgenic Flaveria bidentis (C4). ChlMe1 expression in C4 species increases in leaves with high C4 pathway activity. In the C3 species F. pringlei, ChlMe1 expression is transient and limited to early leaf development. In contrast, ChlMe2 is expressed in C3 and C4 species concurrent with stages in chloroplast biogenesis. Because previous studies suggest that NADP-ME activities generally reflect the level of its mRNA abundance, we discuss possible roles of ChlMe1 and ChlMe2 based on these expression patterns.

The 3' non-coding region of a C4 photosynthesis gene increases transgene expression when combined with heterologous promoters

The Me1 gene of the dicot Flaveria bidentis encodes NADP malic enzyme, which catalyses the decarboxylation reaction of C4 photosynthesis in bundle sheath cells. We have previously shown that the 3' non-coding region (Me1 3') controls quantitative expression of the gene. We wondered whether Me1 3' can increase expression when combined with heterologous promoters. We tested a highly expressed, constitutive promoter, the S4 promoter from subterranean clover stunt virus, and a highly expressed, leaf-specific promoter, the light-harvesting chlorophyll a/b-binding protein gene 3 (Lhcb3) promoter of Arabidopsis thaliana. Promoter-3'-end combinations were tested in transgenic C4 Flaveria plants and C3 tobacco. We found that Me1 3' increased expression of the gusA reporter gene several-fold in leaves of both species in combination with either of the promoters. In both cases Me1 3' does not alter the expression pattern for either promoter. We conclude that Me1 3' can be used as a transcription terminator to increase transgene expression in C3 dicot plants.

MOLECULAR ENGINEERING OF C4 PHOTOSYNTHESIS

The majority of terrestrial plants, including many important crops such as rice, wheat, soybean, and potato, are classified as C3 plants that assimilate atmospheric CO2 directly through the C3 photosynthetic pathway. C4 plants such as maize and sugarcane evolved from C3 plants, acquiring the C4 photosynthetic pathway to achieve high photosynthetic performance and high water- and nitrogen-use efficiencies. The recent application of recombinant DNA technology has made considerable progress in the molecular engineering of C4 photosynthesis over the past several years. It has deepened our understanding of the mechanism of C4 photosynthesis and provided valuable information as to the evolution of the C4 photosynthetic genes. It also has enabled us to express enzymes involved in the C4 pathway at high levels and in desired locations in the leaves of C3 plants for engineering of primary carbon metabolism.

Quantitative regulation of the Flaveria Me1 gene is controlled by the 3'-untranslated region and sequences near the amino terminus

The Me1 gene of Flaveria bidentis codes for the C4 isoform of NADP malic enzyme, which accumulates to a high-level only in bundle sheath cells. Previous experiments demonstrated that sequences at the 5' end of the gene control cell specificity whereas sequences at the 3' end are necessary for high-level expression. To localize quantitative regulator sequences, we have analysed a series of Me1 3' deletion constructs fused to the gusA reporter gene. We show that sequences within the 3'-untranslated region (3'-UTR) control quantitative levels of expression. Analysis of 5' promoter fusions demonstrated that high-level expression also requires sequences within the N-terminal coding region of the gene, suggesting possible interactions between the 3'-UTR and 5' coding regions. Cell-specific regulatory sequences are located in a different part of the 5' end of the gene, between 1023 bp upstream of the transcription start and the start of translation.

Effects of the polyubiquitin gene Ubi. U4 leader intron and first ubiquitin monomer on reporter gene expression in Nicotiana tabacum

We have previously shown by RNA gel blot analyses that the tobacco polyubiquitin-encoding gene Ubi.U4 is expressed in a complex pattern during plant development (Genschik et al., 1994). In order to study its tissue-specific expression, we cloned the fragment containing the -263 bp proximal promoter of the gene, the leader intron and the first ubiquitin monomer in front of the reporter GUS gene. Histochemical analyses for GUS activity during tobacco plant development revealed that the gene is expressed at variable amounts in many plant tissues with high levels in metabolically active and/or dividing cells and in the vascular tissues of the plant. We also analysed the expression pattern of constructs in which either the intron or the intron together with the first ubiquitin monomer were deleted. Our results indicate that the ubiquitin leader intron is not only a quantitative determinant of gene expression but may also influence the tissue-specific expression pattern.

Binding of cell type-specific nuclear proteins to the 5'-flanking region of maize C4 phosphoenolpyruvate carboxylase gene confers its differential transcription in mesophyll cells

C4-type phosphenolpyruvate carboxylase (C4PEPC) acts as a primary carbon assimilatory enzyme in the C4 photosynthetic pathway. The maize C4PEPC gene (C4Ppc1) is specifically expressed in mesophyll cells (MC) of light-grown leaves, but the molecular mechanism responsible for its cell type-specific expression has not been characterized. In this study, we introduced a chimeric maize C4Ppc1 5'-flanking region/beta-glucuronidase (GUS) gene into maize plants by Agrobacterium-mediated transformation. Activity assay and histochemical staining showed that GUS is almost exclusively localized in leaf MC of transgenic maize plants. This observation suggests that the introduced 5' region of maize C4Ppc1 contains the necessary cis element(s) for its specific expression in MC. Next, we investigated whether the 5' region of the maize gene interacts with nuclear proteins in a cell type-specific manner. By gel shift assays with nuclear extracts prepared from MC or bundle sheath cells (BSC), cell type-specific DNA-protein interactions were detected: nuclear factors PEP(Ib) and PEP(Ic) are specific to MC whereas PEP(Ia) and PEP(IIa) are specific to BSC. Light alters the binding activity of these factors. These interactions were not detected in the assay with nuclear extract prepared from root, or competed out by oligonucleotides corresponding to the binding sites for the maize nuclear protein, PEP-I, which is known to bind specifically to the promoter region of C4Ppc1. The results suggest that novel cell type-specific positive and negative nuclear factors bind to the maize C4Ppc1 5'-flanking region and regulate its differential transcription in MC in a light-dependent manner.

Tissue-preferential expression of a rice alpha-tubulin gene, OsTubA1, mediated by the first intron

The genomic clone encoding an alpha-tubulin, OsTubA1, has been isolated from rice (Oryza sativa L.). The gene consists of four exons and three introns. RNA-blot analysis showed that the gene is strongly expressed in actively dividing tissues, including root tips, young leaves, and young flowers. Analysis of chimeric fusions between OsTubA1 and beta-glucuronidase (GUS) revealed that the intron 1 was required for high-level GUS expression in actively dividing tissues, corresponding with normal expression pattern of OsTubA1. Fusion constructs lacking the intron 1 showed more GUS staining in mature tissues rather than young tissues. When the intron 1 was placed at the distal region from 5'-upstream region or at the 3'-untranslated region, no enhancement of GUS expression was observed. Sequential deletions of the OsTubA1 intron 1 brought about a gradual reduction of GUS activity in calli. These results suggest that tissue-preferential expression of the OsTubA1 gene is mediated by the intron 1 and that it may be involved in a mechanism for an efficient RNA splicing that is position dependent.

Light induction of cell type differentiation and cell-type-specific gene expression in cotyledons of a C(4) plant, Flaveria trinervia

In Flaveria trinervia (Asteraceae) seedlings, light-induced signals are required for differentiation of cotyledon bundle sheath cells and mesophyll cells and for cell-type-specific expression of Rubisco small subunit genes (bundle sheath cell specific) and the genes that encode pyruvate orthophosphate dikinase and phosphoenolpyruvate carboxylase (mesophyll cell specific). Both cell type differentiation and cell-type-specific gene expression were complete by d 7 in light-grown seedlings, but were arrested beyond d 4 in dark-grown seedlings. Our results contrast with those found for another C(4) dicot, Amaranthus hypochondriacus, in which light was not required for either process. The differences between the two C(4) dicot species in cotyledon cell differentiation may arise from differences in embryonic and post-embryonic cotyledon development. Our results illustrate that a common C(4) photosynthetic mechanism can be established through different developmental pathways in different species, and provide evidence for independent evolutionary origins of C(4) photosynthetic mechanisms within dicotyledonous plants.

C4 GENE EXPRESSION

C4 plants, including maize, Flaveria, amaranth, sorghum, and an amphibious sedge Eleocharis vivipara, have been employed to elucidate the molecular mechanisms and signaling pathways that control C4 photosynthesis gene expression. Current evidence suggests that pre-existing genes were recruited for the C4 pathway after acquiring potent and surprisingly diverse regulatory elements. This review emphasizes recent advances in our understanding of the creation of C4 genes, the activities of the C4 gene promoters consisting of synergistic and combinatorial enhancers and silencers, the use of 5' and 3' untranslated regions for transcriptional and posttranscriptional regulations, and the function of novel transcription factors. The research has also revealed new insights into unique or universal mechanisms underlying cell-type specificity, coordinate nuclear-chloroplast actions, hormonal, metabolic, stress and light responses, and the control of enzymatic activities by phosphorylation and reductive processes.

Regulation of ferulate-5-hydroxylase expression in Arabidopsis in the context of sinapate ester biosynthesis

Sinapic acid is an intermediate in syringyl lignin biosynthesis in angiosperms, and in some taxa serves as a precursor for soluble secondary metabolites. The biosynthesis and accumulation of the sinapate esters sinapoylglucose, sinapoylmalate, and sinapoylcholine are developmentally regulated in Arabidopsis and other members of the Brassicaceae. The FAH1 locus of Arabidopsis encodes the enzyme ferulate-5-hydroxylase (F5H), which catalyzes the rate-limiting step in syringyl lignin biosynthesis and is required for the production of sinapate esters. Here we show that F5H expression parallels sinapate ester accumulation in developing siliques and seedlings, but is not rate limiting for their biosynthesis. RNA gel-blot analysis indicated that the tissue-specific and developmentally regulated expression of F5H mRNA is distinct from that of other phenylpropanoid genes. Efforts to identify constructs capable of complementing the sinapate ester-deficient phenotype of fah1 mutants demonstrated that F5H expression in leaves is dependent on sequences 3' of the F5H coding region. In contrast, the positive regulatory function of the downstream region is not required for F5H transcript or sinapoylcholine accumulation in embryos.

Evolution of C4 photosynthesis in flaveria species. Isoforms Of nadp-malic enzyme

NADP-malic enzyme (NADP-ME, EC 1.1.1.40), a key enzyme in C4 photosynthesis, provides CO2 to the bundle-sheath chloroplasts, where it is fixed by ribulose-1,5-bisphosphate carboxylase/oxygenase. We characterized the isoform pattern of NADP-ME in different photosynthetic species of Flaveria (C3, C3-C4 intermediate, C4-like, C4) based on sucrose density gradient centrifugation and isoelectric focusing of the native protein, western-blot analysis of the denatured protein, and in situ immunolocalization with antibody against the 62-kD C4 isoform of maize. A 72-kD isoform, present to varying degrees in all species examined, is predominant in leaves of C3 Flaveria spp. and is also present in stem and root tissue. By immunolabeling, NADP-ME was found to be mostly localized in the upper palisade mesophyll chloroplasts of C3 photosynthetic tissue. Two other isoforms of the enzyme, with molecular masses of 62 and 64 kD, occur in leaves of certain intermediates having C4 cycle activity. The 62-kD isoform, which is the predominant highly active form in the C4 species, is localized in bundle-sheath chloroplasts. Among Flaveria spp. there is a 72-kD constitutive form, a 64-kD form that may have appeared during evolution of C4 metabolism, and a 62-kD form that is necessary for the complete functioning of C4 photosynthesis.

Analysis of promoter activity for the gene encoding pyruvate orthophosphate dikinase in stably transformed C4 flaveria species

The C4 enzyme pyruvate orthophosphate dikinase is encoded by a single gene, Pdk, in the C4 plant Flaveria trinervia. This gene also encodes enzyme isoforms located in the chloroplast and in the cytosol that do not have a function in C4 photosynthesis. Our goal is to identify cis-acting DNA sequences that regulate the expression of the gene that is active in the C4 cycle. We fused 1.5 kb of a 5' flanking region from the Pdk gene, including the entire 5' untranslated region, to the uidA reporter gene and stably transformed the closely related C4 species Flaveria bidentis. beta-Glucuronidase (GUS) activity was detected at high levels in leaf mesophyll cells. GUS activity was detected at lower levels in bundle-sheath cells and stems and at very low levels in roots. This lower-level GUS expression was similar to the distribution of mRNA encoding the nonphotosynthetic form of the enzyme. We conclude that cis-acting DNA sequences controlling the expression of the C4 form in mesophyll cells and the chloroplast form in other cells and organs are co-located within the same 5' region of the Pdk gene.

Controlling gene expression in transgenics

The repertoire of cis-regulatory elements has increased to a level of sophistication that offers considerable spatial and temporal control over transgene expression. Recent advances made with transgenes have revealed that the control of their expression is also influenced by factors that range from transgene copy number and arrangement to nuclear architecture and chromosomal location. These factors must now be included with the standard considerations of transcriptional and translational enhancers of gene expression during transgene design.