Evolution of the C4 phosphoenolpyruvate carboxylase promoter of the C4 species Flaveria trinervia: the role of the proximal promoter region.

BACKGROUND: The key enzymes of photosynthetic carbon assimilation in C4 plants have evolved independently several times from C3 isoforms that were present in the C3 ancestral species. The C4 isoform of phosphoenolpyruvate carboxylase (PEPC), the primary CO2-fixing enzyme of the C4 cycle, is specifically expressed at high levels in mesophyll cells of the leaves of C4 species. We are interested in understanding the molecular changes that are responsible for the evolution of this C4-characteristic PEPC expression pattern, and we are using the genus Flaveria (Asteraceae) as a model system. It is known that cis-regulatory sequences for mesophyll-specific expression of the ppcA1 gene of F. trinervia (C4) are located within a distal promoter region (DR).
RESULTS: In this study we focus on the proximal region (PR) of the ppcA1 promoter of F. trinervia and present an analysis of its function in establishing a C4-specific expression pattern. We demonstrate that the PR harbours cis-regulatory determinants which account for high levels of PEPC expression in the leaf. Our results further suggest that an intron in the 5' untranslated leader region of the PR is not essential for the control of ppcA1 gene expression.
CONCLUSION: The allocation of cis-regulatory elements for enhanced expression levels to the proximal region of the ppcA1 promoter provides further insight into the regulation of PEPC expression in C4 leaves.

Background

About 90% of terrestrial plant species, including major crops such as rice, soybean, barley and wheat, assimilate CO2 via the C3 pathway of photosynthesis. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as the primary CO2-fixing enzyme of C3 photosynthesis, but its ability to use O2 as a substrate instead of CO2 results in the energy-wasting process of photorespiration. The photosynthetic C4 cycle represents an addition to the C3 pathway which acts as a pump that accumulates CO2 at the site of Rubisco so that the oxygenase activity of the enzyme is inhibited and photorespiration is largely suppressed. C4 plants therefore achieve higher photosynthetic capacities and better water- and nitrogen-use efficiencies when compared with C3 species [1].

C4 photosynthesis is characterized by the coordinated division of labour between two morphologically distinct cell types, the mesophyll and the bundle-sheath cells. The correct functioning of the C4 cycle depends upon the strict compartmentalization of the CO2 assimilatory enzymes into either mesophyll or bundle-sheath cells [2]. Phosphoenolpyruvate carboxylase (PEPC), which serves as the actual CO2 pump of the C4 pathway, is specifically expressed in the mesophyll cells of C4 leaves. This enzyme is not an unique feature of C4 species; other PEPC isoforms with different catalytic and regulatory properties are found in both photosynthetic and non-photosynthetic tissues of all plants where they participate in a variety of metabolic processes, e.g. replenishment of citric acid cycle intermediates and regulation of guard cell movement [3].

The polyphyletic origin of C4 photosynthesis suggests that the photosynthetic C4 isoforms of PEPC have evolved independently several times from non-photosynthetic C3 isozymes [4]. During the evolution of C4 PEPC genes from ancestral C3 genes, changes in expression strength and organ- and cell-specific expression patterns must have occurred. While C4 PEPC genes are highly expressed in the mesophyll cells of the leaf, the C3 isoform genes are only moderately transcribed in all plant organs [5-8].

To investigate the molecular evolution of a C4 PEPC gene we are using the genus Flaveria (Asteraceae) as a model system. This genus includes C4 and C3 as well as C3–C4 intermediate species [9,10] and thus provides an excellent system for studying the evolution of the C4 photosynthetic pathway [11]. Previous studies on the ppcA1 gene of F. trinervia, encoding the C4 isoform of PEPC, revealed that the strong mesophyll-specific expression is largely regulated at the transcriptional level and that the available 2188 bp (with reference to the AUG start codon of the ppcA1 reading frame) of the 5' flanking sequences contain all the essential cis-regulatory elements for high and mesophyll-specific expression [12]. Two parts of the ppcA1 promoter of F. trinervia, a proximal region (PR) up to -570 in combination with a distal region (DR) from -1566 to -2141, are sufficient to direct a high mesophyll-specific expression of a β-glucuronidase (GUS) reporter gene in transgenic F. bidentis (C4) plants [13]. The orthologous, 2538 bp comprising ppcA1 promoter of the C3 species F. pringlei displays only weak activity in all interior leaf tissues in transgenic F. bidentis, but fusion of the C4-DR to this C3 PEPC promoter leads to a confinement of GUS expression to the mesophyll [13]. Analysis of the C4-DR revealed that the 41-bp module MEM1 (mesophyll expression module 1) is responsible for the C4-characteristic spatial expression pattern of the ppcA1 gene of F. trinervia. Furthermore, it was shown that a high level of expression in the mesophyll requires an interaction of the C4-DR with the C4-PR. This suggests that quantity elements for an elevated expression of the C4 PEPC gene are located within the PR of the 5' flanking sequences [13].

Using the yeast one-hybrid system, Windhövel and colleagues [14,15] identified four different proteins which bind to the PR of the ppcA1 promoter of F. trinervia, but not to the corresponding part of the ppcA1 promoter of F. pringlei. These proteins (named FtHB1 to FtHB4) belong to the class of zinc finger homeodomain proteins (ZF-HD). Two regions of the C4-PR specifically interact with the FtHB proteins in vitro: an intron sequence within the 5' untranslated leader region and a DNA fragment that is located upstream of the putative TATA-box. To the latter one, the FtHB proteins showed a much lower binding affinity [14]. Homeobox proteins are known to act as transcriptional regulators of eukaryotic gene expression [16-18], and the fact that the FtHB homeobox proteins interact specifically with the PR of the ppcA1 promoter of F. trinervia makes them prime candidates for transcription factors that are involved in the establishment of the C4-characteristic expression pattern of the C4 ppcA1 gene.

In this study we have investigated the role of the proximal promoter region of the ppcA1 gene of F. trinvervia with regard to its high and mesophyll-specific expression by transgenic analyses in the closely related C4 species F. bidentis. We demonstrate that the proximal promoter region of the ppcA1 gene contains cis-regulatory elements that determine promoter strength. Furthermore, we show that the deletion of an intron located in the 5' untranslated segment of ppcA1 does not alter promoter activity in transgenic F. bidentis.

Results and discussion

Experimental strategy

We are interested in elucidating the molecular events that are crucial for the evolution of the high and mesophyll-specific expression of the C4 phosphoenolpyruvate carboxylase gene (ppcA1) of the C4 plant F. trinervia. In this study we focus on the proximal promoter region (PR) of the ppcA1 gene with respect to its function in establishing the C4-characteristic expression pattern. We performed a comparative analysis of three different promoter-GUS fusion constructs (Fig. 1) in transgenic F. bidentis plants. F. bidentis is a close relative to F. trinervia, but in contrast to F. trinervia this C4 species is transformable by Agrobacterium tumefaciens mediated gene transfer [19] and was therefore chosen for these experiments.

Figure 1

Schematic presentation of the promoter-GUS fusion constructs used for the transformation of Flaveria bidentis (C4).

Construct ppcA-PRFt-DR(+)Ft served as a reference because it was already known from previous experiments that a combination of the distal (DR) and the proximal (PR) promoter regions was sufficient to direct a high and mesophyll specific expression of a GUS reporter gene in F. bidentis [13]. To find out if the PR of the C4 ppcA1 promoter contains quantity elements conferring high expression in the mesophyll cells we designed construct ppcA-PRFp-DR(+)Ft. Here, the C4-PR was exchanged for its counterpart from the orthologous ppcA1 gene of the C3 species F. pringlei. Deletion of the intron sequences in the 5' untranslated segment of promoter construct ppcA-PRFt-DR(+)Ft resulted in the formation of construct ppcA-PRFtΔIntron-DR(+)Ft. Thereby a putative binding site for the ZF-HD proteins FtHB1 to FtHB4 [14] was removed from the C4-PR. Hence, this chimeric promoter-GUS fusion could answer the question whether the intron-located putative binding site of the FtHB proteins is necessary for the establishment of the C4-specific ppcA1 expression pattern.

The proximal region of the ppcA1 promoter of F. trinervia harbours cis-regulatory elements for a high level of PEPC expression in the mesophyll

Gowik et al. [13] assumed that the PR of the ppcA1 promoter of F. trinervia comprises cis-regulatory determinants conferring high levels of expression in mesophyll cells of C4 leaves. To examine whether the PR actually harbours such quantity elements we analyzed the GUS expression patterns of constructs ppcA-PRFt-DR(+)Ft and ppcA-PRFp-DR(+)Ft (Fig. 1) in transgenic F. bidentis.

In F. bidentis plants that had been transformed with promoter construct ppcA-PRFt-DR(+)Ft, GUS expression was exclusively detected in the mesophyll cells of the leaves (Fig. 2A). This observation shows that the DR and PR of the ppcA1 promoter together are sufficient for a high and mesophyll-specific expression of the linked GUS reporter gene and therefore confirms the results obtained by Gowik et al. [13]. Replacement of the C4-PR by the corresponding region from the ppcA1 promoter of F. pringlei (construct ppcA-PRFp-DR(+)Ft) did not cause any alteration in the cellular GUS expression pattern when compared to ppcA-PRFt-DR(+)Ft; GUS activity was still restricted to the mesophyll compartment (Fig. 2B). However, both chimeric promoters differed greatly in transcriptional strength. Quantitative GUS assays revealed that promoter activity was decreased by a factor of 15 when the C4-PR was substituted for the C3-PR (Fig. 2D). This clearly demonstrated that the C4-characteristic transcription-enhancing cis-regulatory elements must be located within the proximal region of the ppcA1 promoter of F. trinervia. The low expression level of construct ppcA-PRFp-DR(+)Ft could be the result of an absence of transcription-enhancing cis-regulatory elements in the C3-PR, but it might also be caused by problems in the interaction of the C4-DR and the C3-PR.

Figure 2

(A) to (C): Histochemical localization of GUS activity in leaf sections of transgenic F. bidentis plants transformed with constructs ppcA-PRFt-DR(+)Ft(A), ppcA-PRFp-DR(+)Ft (B) or ppcA-PRFtΔIntron-DR(+)Ft (C). Incubation times were 6 h (A, C) and 20 h (B). (D): GUS activities in leaves of transgenic F. bidentis plants. The numbers of independent transgenic plants tested (N) are indicated at the top of each column. Median values (black lines) of GUS activities are expressed in nanomoles of the reaction product 4-methylumbelliferone (MU) generated per milligram of protein per minute.

The intron in the C4-PR is not required for the establishment of a C4-specific expression pattern of the ppcA1 gene of F. trinervia

The 5' untranslated region of the ppcA1 gene of F. trinervia contains an intron between positions -209 and -40 (+1 refers to the starting point of translation). Introns are of prominent importance for the molecular evolution of eukaryotic genomes by facilitating the generation of new genes via exon-shuffling and by providing the possibility to create multiple proteins from a single gene via alternative splicing [20-22]. Furthermore, it has been shown that introns can affect many different stages of gene expression, including both transcriptional and post-transcriptional mechanisms [22-24].

Here, we wanted to investigate whether the first intron of the ppcA1 gene of F. trinervia is essential for establishing the C4-characteristic expression pattern. We therefore deleted the intron sequences from the C4-PR in construct ppcA-PRFp-DR(+)Ft, resulting in the formation of construct ppcA-PRFtΔIntron-DR(+)Ft (Fig. 1). The histochemical analysis of transgenic F. bidentis plants demonstrated that the ppcA-PRFtΔIntron-DR(+)Ftpromoter was exclusively active in the mesophyll cells of the leaves (Fig. 2C). The quantitative examination of GUS activity (Fig. 2D) also revealed no significant differences between ppcA-PRFtΔIntron-DR(+)Ft (6,5 nmol MU/(mg*min)) and ppcA-PRFt-DR(+)Ft (5,9 nmol MU/(mg*min)). These data suggest that the 5' located intron of ppcA1 does not contain any cis-regulatory elements that are essential for achieving high mesophyll-specific expression of a reporter gene. Accordingly, the specific binding of the FtHB proteins to this intron that was observed in vitro and in yeast one-hybrid experiments [14,15] has no in planta relevance concerning the regulation of ppcA1 expression in C4 leaves. However, our results do not necessarily indicate that the intron is completely dispensable for the regulation of ppcA1 gene expression. It is known that C4 gene transcription is modulated by various metabolites such as sugar hexoses [25-27], and we cannot exclude that the first intron of the ppcA1 gene of F. trinervia might be involved in the metabolic control of gene expression.

Comparison of proximal ppcA promoter sequences from different Flaveria species

As reported above, cis-regulatory elements for leaf-specific enhanced transcription of the ppcA1 gene of F. trinervia could be allocated to the PR of the 5' flanking sequences, but their exact nature and localization was still unclear. To identify potential cis-regulatory enhancing elements, a sequence comparison between the PR of the ppcA1 gene of F. trinervia and equivalent promoter sequences from other Flaveria species was performed (Fig. 3). This approach was chosen because it was already known from northern analyses of ppcA transcript levels in different Flaveria species that ppcA RNA amounts in leaves increase gradually from C3 to C4 species [28]. This is consistent with the important function of PEPC during C4 photosynthesis. The C4-like species F. brownii and F. vaginata exhibited ppcA RNA levels that were comparable to those of the C4 plants F. bidentis and F. trinervia, and even in F. pubescens, a C3–C4 intermediate with rather poorly developed C4-characteristic traits, ppcA transcript accumulation in the leaves was significantly higher than in the C3 species F. cronquistii and F. pringlei [28].

Figure 3

Nucleotide sequence alignment of the proximal regions of ppcA promoters from F. trinervia (C4, ppcA-Ft), F. bidentis (C4, ppcA-Fb), F. vaginata (C4-like, ppcA-Fv), F. brownii (C4-like, ppcA-Fbr), F. pubescens (C3–C4, ppcA-Fpub), F. cronquistii (C3, ppcA-Fc) and F. pringlei (C3, ppcA-Fp). Identical positions in all ppcA sequences are marked by an asterisk. The intron sequences in the 5' untranslated leader regions are marked by grey nucleotides. The start site of the F. trinervia ppcA transcript is indicated by an arrow, the TATA-box by a yellow box, the putative MYB-binding site by a blue box, and the CCAAT-sequences by a green box. Fragments of the F. trinervia ppcA1 promoter that interact with the FtHB proteins in the yeast one-hybrid system [14, 15] are marked by red bars. The translational ATG start codon is indicated by green nucleotides.

Searching for known plant cis-regulatory DNA elements in the PLACE database [29] resulted in the identification of two distinct sequence motifs which might be involved in the regulation of ppcA expression levels (Fig. 3). Both of them, a putative MYB transcription factor binding site (GTTAGTT, [30]) and a CCAAT box [31], are present in all examined C3–C4, C4-like and C4 species, but are missing in the two C3 species (Fig. 3). Thus, these sequences are prime candidates for transcription-enhancing cis-regulatory elements. CCAAT boxes are common sequences that are found in the 5' untranslated regions of many eukaryotic genes [32]. They are able to regulate the initiation of transcription by an interaction of CCAAT-binding transcription factors with the basal transcription initiation complex [33]. There is no unifying expression pattern for plant genes containing putative CCAAT promoter elements, indicating that they may play a complex role in regulating plant gene transcription [32]. MYB proteins, on the other hand, comprise one of the largest families of transcription factors in plants, with almost 200 different MYB genes present in the Arabidopsis genome [34-36]. To test the physiological importance of the putative MYB and CCAAT binding sites (that are located within the PR of the ppcA1 promoter of F. trinervia) it will be crucial to inactivate these sequences in construct ppcA-PRFtΔIntron-DR(+)Ft by site-directed mutagenesis and to investigate whether this results in a decrease of reporter gene expression in the leaves of transgenic F. bidentis plants.

When searching for quantity elements in the PR of the ppcA1 promoter of F. trinervia, one should always keep in mind that high levels of reporter gene expression in the leaf mesophyll require the synergistic action of the distal and proximal promoter regions. The C4-PR alone exhibits very low transcriptional activity in all interior leaf cell types of transgenic F. bidentis [37], indicating that the cis-regulatory elements for enhanced expression are only functional when the C4-PR is combined with the cognate C4-DR. One may speculate that a strong expression of the ppcA1 gene in the mesophyll cells of F. trinervia depends on the interaction of trans-acting factors which bind to cis-regulatory elements within the PR with other transcription factors that are recruited to C4-specific cis-regulatory determinants in the DR. In the future, further dissection of the C4-PR of F. trinervia and expression analyses of additional DR-PR combinations from ppcA promoters of different Flaveria species in transgenic F. bidentis will be useful for uncovering the control of ppcA expression levels in C4 leaves.

Conclusion

In this study, we have demonstrated that the proximal region (-570 to -1) of the ppcA1 promoter of F. trinervia (C4) harbours cis-regulatory elements conferring high expression levels in leaf mesophyll cells of transgenic F. bidentis (C4). It was further demonstrated that the deletion of an intron in the 5' untranslated leader region does not affect the C4-specific ppcA1 expression pattern and strength, indicating that the previously isolated zinc finger-homeobox transcription factors that specifically interact with this intron in vitro are not involved in regulating ppcA1 expression levels. Sequence comparisons resulted in the identification of potential cis-regulatory elements in the proximal part of the ppcA1 promoter that might play a role in controlling ppcA1 expression quantity. Genetic manipulation of these sequences and subsequent analyses in transgenic F. bidentis will clarify whether they are able to direct high ppcA1 expression levels in C4 leaves.

Methods

Construction of chimeric promoters

DNA manipulations and cloning were performed according to Sambrook and Russell [38]. The construction of the promoter-GUS fusion ppcA-PRFt-DR(+)Ft has been described in detail [13]. Plasmids ppcA-S-Fp[39] and ppcA-PRFt-DR(+)Ft served as the basis for the production of ppcA-PRFp-DR(+)Ft. The distal region (-2141 to -1566) of the ppcA1 promoter of F. trinervia was excised from ppcA-PRFt-DR(+)Ft by digestion with XbaI. Insertion of this promoter fragment into XbaI-cut ppcA-S-Fp resulted in the generation of construct ppcA-PRFp-DR(+)Ft.

For the production of construct ppcA-PRFtΔIntron-DR(+)Ft a part of the ppcA1 promoter from F. trinervia (-570 to -209) was amplified by PCR with primers S-Ft-F (5'-TGCTCTAGACCGGTGTTAATGATGG-3') and S-Ft-R (5'-CTGAATATTGGGTATG-CTCAG-3'). Plasmid ppcA-PRFt-DR(+)Ft was used as the template for this PCR reaction. The amplified promoter fragment was cut with XbaI. The outermost 3' region of the ppcA1 promoter (-39 to -1) was generated by annealing the two oligonucleotides S-Ft-3'-1 (5'-GGTTGGAGGGGAATTAAGTATTAAGCAAGGGTGTGAGTAC-3') and S-Ft-3'-2 (5'-CCGGGTACTCACACACCCTTGCTTAATACTTAATTCCCCTCCAACC-3'). Thereby a XmaI-compatible 5' overhang was created next to position -1. The ppcA-S-Ft promoter plasmid [39] was digested with XbaI and XmaI and the released ppcA1 promoter fragment was removed by agarose gel electrophoresis. The XbaI/XmaI-cut ppcA-S-Ft plasmid was ligated with the two ppcA1 promoter fragments (-570 to -209/-39 to -1) and the resulting plasmid was named ppcA-PRFtΔIntron. The distal region of the ppcA1 promoter of F. trinervia (-2141 to -1566) was removed from of ppcA-PRFt-DR(+)Ft by incubation with XbaI and inserted into XbaI-cut ppcA-PRFtΔIntron. The resulting plasmid was designated ppcA-PRFtΔIntron -DR(+)Ft.

Plant transformation

In all transformation experiments the Agrobacterium tumefaciens strain AGL1 was used [40]. The promoter-GUS constructs were introduced into AGL1 by electroporation. The transformation of Flaveria bidentis was performed as described by Chitty et al. [19]. The integration of the transgenes into the genome of regenerated F. bidentis plants was proved by PCR analyses.

Measurement of GUS activity and histochemical analysis

F. bidentis plants used for GUS analysis were 40 to 50 cm tall and before flower initiation. Fluorometrical quantification of GUS activity in the leaves was performed according to Jefferson et al. [41] and Kosugi et al. [42]. For histochemical analysis of GUS activity the leaves were cut manually with a razorblade and the sections were transferred to incubation buffer (100 mM Na2HPO4, pH 7.5, 10 mM EDTA, 50 mM K4 [Fe(CN)6], 50 mM K3 [Fe(CN)6], 0.1% (v/v) Triton X-100, 2 mM 5-bromo-4-chloro-3-indolyl-β-D-glucuronid acid). After brief vacuum infiltration the sections were incubated at 37°C for 6 to 20 hrs. After incubation chlorophyll was removed from the tissue by treatment with 70% ethanol.

Computer analyses

DNA sequence analyses were performed with MacMolly Tetra [43]. The sequence alignments were created with the program DIALIGN 2.2.1 [44]. Sequence data mentioned in this article can be found in GenBank under accession numbers X64143 (F. trinervia ppcA1), X64144 (F. pringlei ppcA1), AY297090 (F. vaginata ppcA1), AY297089 (F. cronquistii ppcA1), AY297087 (F. bidentis ppcA1), EF522173 (F. brownii ppcA1) and EF522174 (F. pubescens ppcA1).

Authors' contributions

SE carried out the histochemical and quantitative GUS assays, the cloning of construct ppcA-PRFtΔIntron-DR(+)Ft, the sequence alignments and wrote the manuscript. CZ produced construct ppcA-PRFp-DR(+)Ft. MK, US and MS performed the transformation of F. bidentis. PW coordinated the design of this study and participated in drafting the manuscript. All authors read and approved the final manuscript.