The spatial/temporal expression of genes is the results of precise regulation networks that involve the interaction between DNA motifs and their cognate transcription factors. Therefore, it is expected that the MdACS1 promoter presents defined regions able to drive its specific expression mainly in fruit at ripening stage. Moreover the completely absence of MdACS1-2 allele transcript suggests that some of the identified differences between the two MdACS1 alleles could be responsible for the loss of its transcriptional activity.
A common strategy to identify important regions in promoters is the analysis of the promoter and its progressive deletion fragments in an in vivo system. For this reason we prepared promoter deletion constructs for both MdACS1 alleles, taking into account the four regions identified in the promoter on the basis of similarity analysis, and analyzed them by Agrobacterium-mediated transient transformation of lettuce and apple tissues.
The transient transformation with full promoter sequences of both the MdACS1 alleles (C6 and C7 constructs) confirmed the results of our qPCR expression analysis in apple fruit. The C6 construct containing 1639 bp of the 5’ flanking region of MdACS1-1 allele was able to induce GUS expression in infected lettuce leaves at level similar to that of the CaMV35S promoter. This result confirmed that this promoter fragment is fully functioning and able to drive transcription of MdACS1-1 allele, whose transcript was effectively detected in apple fruit by qPCR. The reporter expression was detected not only in lettuce but also in the apple flesh at levels similar to that of the CaMV35S. Despite the limited repeatability observed in apple system, this result is very important because suggests that our promoter is functioning in its native contest as well as in an heterologous ones and that the expression in the two systems is comparable.
qPCR analysis for MdACS1-1 allele showed a predominantly expression of this allele in ripe fruit while very low expression was found in skin of immature fruit, cotyledon and leaf. However when tested by transient expression assay, the chimeric C6::GUS fusion construct allowed gene expression in both apple fruits and lettuce leaves at comparable level. This discrepancy could be imputable to the use of an heterologous system but we cannot exclude also that the promoter sequence used in our studies, whose length was arbitrarily chosen, doesn’t contain regulatory region for the modulation of expression in different tissues. Yin et al. (2009) for example found that a TCCAAAA motif is necessary for fruit-specific expression in watermelon by inhibiting gene expression in leaves.
The C7 construct, representing 1790 bp of the MdACS1-2 promoter region, wasn’t able to activate transcription of GUSPlus reporter gene as expected on the basis of our real time PCR results in which the expression of the MdACS1-2 allele was never observed.
When 667 bp and 654 bp (the forth regions) were eliminated starting from the 5’ end of C7 and C6 constructs, to generate respectively constructs C5 and C4, a change in the GUS expression was observed for both promoters. The level of expression decreased dramatically in C4 infected tissue in respect of that transformed with C6 suggesting that these 654 bp should contain enhancer elements. Similar results are reported in literature in which a particularly high efficiency was obtained when the promoter fragment changed from about 1 Kb to about 2 kb and plant 5' fragment of about 3 Kb showed a strength higher than that of the constitutive CaMV35S promoter (Spolaore et al. 2003). So we could not excluded that in the 5’ flanking region upstream the C6 and C7 fragments, that we didn’t consider in our promoter analysis, are present more regulatory elements. Moreover we didn’t considered in the design of our promoter fragments the 3’ UTR region, but it is known that in this un-transcribed region can be located further regulatory elements able to control transcriptional activity.
An important role of the forth region in the control of MdACS1 transcription was suggested from the activation of the MdACS1-2 promoter with its elimination from the C7 construct. Indeed, lettuce leaves infected with this shorter construct (C5) showed GUS activity unlike that inoculated with C7. The level of expression was similar to that obtained with the corresponding construct C4 of the MdACS1-1 allele. C4 and C5 constructs were designed comprising the most variable promoter region (the third) between the two alleles. This region included the SINE element in the C5 construct and the 24 bp insertion in the C4 region. The comparable GUS activity obtained with the two constructs (C4 and C5) and the re-activation of MdACS1-2 promoter with C5 construct both suggest that the SINE element could not be alone responsible for the loss of promoter activity as was hypothesized by Harada et al. (2000). At the same time these results suggested a role of the forth region of C7 fragments in the loss of transcriptional activation.
Reducing further the sequence of the two promoters didn’t change the level of GUS expression as observed in lettuce leaves transformed with C2 and C3 constructs (comprising only the first and the second promoter region) that showed blue staining areas comparable to that induced by C5 and C4 constructs. Only a slightly lower GUS activity was found in experiments with the shortest C1 fragment demonstrating that this 225 bp are sufficient for accurate onset of transcription. Our findings are in agreement with that reported in other studies in which GUS activity just above the background started to be detected with
promoter fragment of about 200bp (Spolaore et al. 2003, E. Silfverberg-Dilworth et. al 2005). However many studies on plant promoters report a modulation in GUS strength with promoter fragments of different sizes (Spolaore et al., 2003; Yamagata et al., 2002; Yin et al., 2009) and it is also known that cis-acting element with positive or negative function are usually localized in a region of almost 1000 bp in plant promoters. So, some variability in the induction of GUS staining between our deletion constructs was expected. Without a quantitative analysis however it is not possible to distinguish clearly if the similar GUS staining results observed in tissues infected with C1-C2-C3-C4-C5 constructs correspond effectively to similar GUS activity or if significant, even though rare, differences occur. It could also be hypothesized that the heterologous lettuce system lack specific apple transcription factors able to interact with these promoter regions. When C1-C2-C3-C4-C5 constructs were used in transient transformation of apple fruit however we didn’t found any GUS expression. Since the transient transformation in lettuce confirmed that they are functioning, and so no mistakes in construct preparation were done, the absence of reporter expression in fruit could be due to an inefficient transformation rate in apple system that make difficult to detect the reporter gene activity driven by promoter fragments with very low strength. Indeed, also in lettuce the activity of this deletion constructs was very low in respect of that of the longest promoter construct C6 that was the only one that showed GUS staining in apple. We also didn’t prepared promoter fragment shorter than C1, so we can not ruled out if the observed GUS expression in tissues infected with this construct is effectively the basal level generated only by the binding of the RNA polymerase complex or if C1 include already some binding sites for proteins that interact with this complex and enhance transcription. All the evidences suggested to investigate more in detail the almost 600 bp in the distal region of promoters that seem to be responsible both for the highest expression found in the MdACS1-1 promoter and for the loss of functionality of the MdACS1-2 promoter.