Identifying intrinsic and extrinsic determinants that regulate internal initiation of translation mediated by the FMR1 5' leader
© Dobson et al; licensee BioMed Central Ltd. 2008
Received: 21 December 2007
Accepted: 15 October 2008
Published: 15 October 2008
Regulating synthesis of the Fragile X gene (FMR1) product, FMRP alters neural plasticity potentially through its role in the microRNA pathway. Cap-dependent translation of the FMR1 mRNA, a process requiring ribosomal scanning through the 5' leader, is likely impeded by the extensive secondary structure generated by the high guanosine/cytosine nucleotide content including the CGG triplet nucleotide repeats in the 5' leader. An alternative mechanism to initiate translation – internal initiation often utilizes secondary structure to recruit the translational machinery. Consequently, studies were undertaken to confirm and extend a previous observation that the FMR1 5' leader contains an internal ribosomal entry site (IRES).
Cellular transfection of a dicistronic DNA construct containing the FMR1 5' leader inserted into the intercistronic region yielded significant translation of the second cistron, but the FMR1 5' leader was also found to contain a cryptic promoter possibly confounding interpretation of these results. However, transfection of dicistronic and monocistronic RNA ex vivo or in vitro confirmed that the FMR1 5' leader contains an IRES. Moreover, inhibiting cap-dependent translation ex vivo did not affect the expression level of endogenous FMRP indicating a role for IRES-dependent translation of FMR1 mRNA. Analysis of the FMR1 5' leader revealed that the CGG repeats and the 5' end of the leader were vital for internal initiation. Functionally, exposure to potassium chloride or intracellular acidification and addition of polyinosinic:polycytidylic acid as mimics of neural activity and double stranded RNA, respectively, differentially affected FMR1 IRES activity.
Our results indicate that multiple stimuli influence IRES-dependent translation of the FMR1 mRNA and suggest a functional role for the CGG nucleotide repeats.
The mRNA and protein generated from the FMR1 gene in neurons is localized to dendrites [1, 2]. The FMR1 protein, FMRP is synthesized in response to neural activity and its function as an RNA binding protein influences the translational level of other dendritically localized mRNAs [3–6]. FMRP is also part of the RISC complex [7, 8], a set of proteins that interact with micro-RNAs or short interfering RNAs to inhibit translation and or degrade the RNA, respectively.
Regulating the synthesis of FMRP is important for cellular function. FMRP over-expression leads to a defect in dendritic architecture, synaptic differentiation, and abnormal behaviors in mice and flies [9, 10]. Alternatively, the absence of FMRP in Fragile X Syndrome (FXS) leads to alterations in synaptic plasticity resulting in mental retardation . FXS develops from an expansion of the CGG nucleotide repeats in the 5' leader of the FMR1 gene [12–14]. Normal individuals carry from 5 – 50 repeats while those with FXS carry over 200 repeats. The expansion increases methylation of the gene inhibiting transcription. In some cases transcription of the gene occurs [15, 16], but translation of the mRNA is inhibited by the presence of the CGG repeat expansion . The CGG repeats are evolutionarily conserved in mammals suggesting that the repeats have some function aside from inhibiting transcription and translation .
During post-transcriptional gene processing, a 7-methyl guanosine (termed the cap structure) is positioned at the 5' end of an mRNA . All mRNAs can potentially be translated by the eukaryotic initiation factor (eIF) 4E binding to the cap structure and recruiting the remainder of the translational machinery including the ribosome . On the other hand, a subset of mRNAs initiate translation in a cap-independent manner through internal ribosomal entry sites (IRESes) situated in the 5' leader and in some cases in the open reading frame [21, 22]. IRES-dependent translation is thought to be utilized when cap-dependent translation is inhibited. This occurs during normal physiological processes including mitosis, but also in response to stressful events such as apoptosis [23–25]. It may also be a primary translational mechanism that can be regulated independently of pathways affecting cap-dependent translation. In the nervous system, numerous dendritically localized mRNAs contain IRESes including those coding for the alpha subunit of CAMKII, activity-related cytoskeletal protein, and the neurotrophin receptor TrkB [26, 27]. The high preponderance of dendritically localized mRNAs containing IRESes suggests that IRES-dependent translation is an important protein synthesis mechanism in dendrites.
Our goals were to confirm a previous study that the FMR1 5' leader mediates internal initiation of translation , identify regions in the FMR1 5' leader critical for IRES activity, and to determine if FMR1 IRES activity is affected by cellular processes in which FMRP participates. Initially, we re-examined the FMR1 5' leader for IRES activity and found that it contained a cryptic promoter, compelling the use of RNA constructs. Translation assays using RNA both in vitro and ex vivo demonstrated that the FMR1 5' leader does contain an IRES and that IRES-dependent translation may be an important mechanism for the synthesis of FMRP in vivo. A dissection of the 5' leader showed that the 5' 45 nucleotides (nt) as well as the CGG repeats are important for internal initiation. Finally, multiple cellular stimuli including exposure to KCl and intracellular acidification as models for neural activity and exposure to polyinosinic:polycytidylic acid as a model for the presence of double stranded RNA resulted in alterations of FMR1 IRES activity.
The FMR1 5' leader directs expression of the second cistron in a dicistronic DNA construct
The FMR1 5' leader contains a cryptic promoter
In addition to internal initiation, increased levels of Photinus luciferase protein can be generated from the dicistronic luciferase constructs through cryptic splicing or cryptic promoter activity. For example, the presence of a cryptic promoter in the 5' leader will lead to the production of a monocistronic Photinus luciferase mRNA [31, 32] and artificially increase the P:R ratio. To determine if cryptic promoter activity was present in the FMR1 5' leader, the dicistronic luciferase constructs with or without the SV40 promoter and intron were transfected into C6 cells. Photinus luciferase activity from the promoterless constructs containing the pRF MCS, β-globin 5' leader, and EMCV IRES was very low, less than 1% of the Photinus luciferase activity obtained from the constructs with the intact promoter. This result confirms previous studies indicating that these leaders do not contain a cryptic promoter [26, 33]. However, the promoterless construct containing the FMR1 5' leader generated approximately 15% of the 'total' Photinus luciferase activity. After subtracting the minor contribution of the cryptic promoter to the translation of the second cistron, the data still suggests that the FMR1 5' leader has an IRES, but it does temper this conclusion.
The FMR1 5' leader exhibits IRES activity from a dicistronic RNA
Translation of a monocistronic mRNA in vitro and ex vivo indicates a key role for IRES-dependent translation mediated by the FMR1 5' leader
The dicistronic luciferase assay is useful to identify sequences that can internally initiate translation, but it does not indicate the role of an IRES in a monocistronic mRNA, the context in which the IRES is normally found in cellular mRNA. Consequently, two approaches were utilized to determine whether the FMR1 IRES is a major contributor to the translation of a monocistronic capped mRNA. Initially, in vitro transcribed monocistronic mRNA containing the Photinus luciferase open reading frame (ORF) and the β-globin or FMR1 5' leader was translated in rabbit reticulocyte lysate. The overall level of Photinus luciferase synthesis was reduced by approximately 40% when the FMR1 5' leader was present. This result is not surprising since cap-dependent translation of a short unstructured 5' leader (β-globin) is very efficient. Increasing concentrations of cap analog were added to the lysate to compete with the cap structure for eIF-4E and inhibit cap-dependent translation. Translation of the mRNA containing the β-globin 5' leader decreased as the concentration of cap analog increased (Fig. 2B). This result demonstrates that the β-globin mRNA is being translated in a cap-dependent manner. On the other hand, translation of the mRNA containing the FMR1 5' leader was only moderately affected (Fig. 2B); translation of the Photinus luciferase cistron decreased by only 15% at the highest concentration of cap analog. This result not only indicates that the mRNA containing the FMR1 5' leader is being translated in a cap-independent manner, but that it may be the major mechanism for its translation.
To determine the role of the FMR1 IRES within a cell, cap-dependent translation was inhibited ex-vivo. The 4E-Binding Protein 1 (4E-BP1) binds and sequesters eIF-4E preventing cap-dependent translation , but phosphorylation of 4E-BP1 decreases its affinity to eIF-4E. Consequently, C6 cells were transfected with a construct coding for a mutant of 4E-BP1 (4E-BPmut) with the two key phosphorylation sites mutated (Thr – 37 – Ala/Thr – 46 – Ala) or a control plasmid . Monocistronic constructs containing the β-globin, EMCV, or FMR1 5' leader were co-transfected. In the presence of over-expressed 4E-BPmut, the level of Photinus luciferase activity derived from the mRNA containing the β-globin 5' leader decreased by 72% (Fig. 2C). However, translation from the mRNAs containing the FMR1 or EMCV 5' leader only decreased by 19% and 27%, respectively (Fig. 2C). Since 81% of the luciferase activity remains when cap-dependent translation is inhibited, it indicates that IRES-dependent translation may be the primary mechanism for translation of the FMR1 mRNA in vivo.
Endogenous FMRP expression is unaffected by reducing cap-dependent translation
In addition to inhibiting cap-dependent translation, blocking mTOR activity can alter other cellular pathways and indirectly alter translation. To more directly examine whether IRES-dependent translation is utilized for the synthesis of endogenous FMRP, cap-dependent translation was inhibited by knocking-down expression of eIF-4E. C6 cells were exposed to a pool of siRNA (Dharmacon) directed against the eIF-4E mRNA or a nonsense siRNA for 72 hr. Quantitation of Western blots showed that eIF-4E expression was reduced by > 70% (Fig. 3B, C). The level of the transcription factor JunB whose mRNA is translated in a cap-dependent manner was also reduced by > 75%. However, FMRP expression was decreased by only 12% (Fig. 3B, C). The observations that FMRP expression is maintained despite reduced levels of eIF-4E or mTOR activity (detailed above) indicates that IRES-dependent translation is likely a important contributor to the synthesis of FMRP.
Multiple regions in the 5' leader contribute to FMR1 IRES activity
Changes in intracellular pH regulate the FMR1 IRES
To determine the regulatory elements in the FMR1 IRES, C6 cells were exposed to 500 μM ameloride for 24 hrs to block the Na+/H+ antiporter. Intracellular acidification inhibits neural activity and is a model of an inactive neuron . The P:R ratio from the dicistronic mRNA containing the full-length 5' leader dramatically decreased in the presence of ameloride (Fig. 4A). However, only subtle differences in the P:R ratio were observed from truncations of the 3' 208 nt. The minimal level of IRES activity remained in the shorter leaders. This result implies that a decrease in intracellular pH inhibits FMR1 IRES activity and this effect is mediated by repressing the IRES-promoting region located at the 5' end of the 5' leader.
The CGG repeats contribute to FMR1 IRES activity
The basal level of IRES activity exhibited in the 5' leader containing the 3' 120 nt was not affected by changes in intracellular pH. An additional truncation deleting the CGG repeats abolished all IRES activity. To further characterize the role of the CGG repeats in the FMR1 IRES, the repeats were internally deleted within the full-length 5' leader. Transfection of the dicistronic mRNA containing the FMR1 5' leader with the CGG repeats deleted exhibited an approximately 50% decrease in the P:R ratio compared to the full-length 5' leader (Fig. 4B). This result demonstrates the importance of the CGG repeats for internal initiation mediated by the FMR1 5' leader.
FMR1 IRES activity is affected by KCl and polyinosinic:polycytidylic acid
To examine whether KCl also affects FMRP expression, Western blots were performed from lysates obtained from the treated and untreated cells. Changes in endogenous FMRP levels mirrored that observed from FMRP IRES (Fig. 5B, C). An increase of 58% was seen after a 30 min KCl treatment, whereas a 150 min treatment led to a 40% decrease in FMRP expression.
In the present report we demonstrate that the FMR1 5' leader contains an IRES whose activity is dependent upon the 5' 45 nt as well as the CGG repeats in the 5' leader. Moreover, our studies indicate that internal initiation may be an important mechanism for the translation of the FMR1 mRNA. This conclusion is supported by the observation that synthesis of FMRP is maintained when cap-dependent translation is inhibited by knocking-down eIF-4E expression or rapamycin treatment. In addition, multiple stimuli differentially affect FMR1 IRES activity suggesting that similar processes are dynamically regulating FMR1 translation in the cell.
Our results show that the FMR1 5' leader contains a cryptic promoter, an observation that has been noted in other 5' leaders [31, 39]. The presence of elements influencing transcription is not surprising as transcriptional elements are located throughout a gene. While the FMR1 5' leader affects transcription when present as DNA, the same region promotes internal initiation as RNA as deduced from both in vitro and ex vivo experiments using monocistronic and dicistronic mRNA. RNA for these assays was produced from in vitro transcription and this process could yield a FMR1 5' leader with a secondary structure different than what occurs in the cell. Indeed, it is likely that proteins including IRES transactivating factors (ITAFs, see below) bind to the FMR1 5' leader and alter its structure in vivo. However, viral IRESes whose activity depends extensively upon secondary structure yield robust IRES activity from in vitro transcribed RNA [40, 41] and are suitable for structural analysis .
The CGG repeats, which are amplified in FXS, are evolutionarily conserved in mammals . We suggest that the CGG repeats are retained due to their ability to promote translation and specifically internal initiation of translation. This hypothesis is supported by evidence indicating that mRNA containing the normal number of CGG repeats translates at a higher level compared to mRNA absent of the repeats or containing a higher number of repeats . Moreover, we found that deleting the CGG repeats significantly decreased FMR1 IRES activity. The mechanism by which the repeats affect IRES activity is open to speculation. Secondary structure is important for viral IRESes and their ability to recruit canonical factors and the ribosome . Minor changes in the RNA structure can dramatically alter viral IRES activity [45, 46]. Since the 3' 120 nt are able to mediate internal initiation, the ribosome must bind somewhere in this region and the CGG repeats may create a structure conducive for ribosomal recruitment. On the other hand, it has been proposed that expansion of the CGG repeats (~50 – 200) in the Fragile X pre-mutation allele sequesters an RNA binding protein and indirectly affects the function of other mRNAs . Thus, the CGG repeats may bind an ITAF that directly recruits the translational machinery or may act as a molecular chaperone and alter the secondary structure, which in turn recruits the translational machinery.
Deletion of the 5' 45 nt (or more specifically the nt 18 – 45 from the 5' end) of the FMR1 5' leader yielded the largest decrease in IRES activity. This segment is also very conserved in mammals. In general, viral IRESes are greater than 200 nt in length and it would be of interest if a substantially smaller RNA segment of the FMR1 5' leader could internally initiate translation. This observation is not unprecedented as we have found that a region of 50 nt in the 5' leader of the amyloid precursor protein yields IRES activity (Beaudoin et al. submitted). However, the 5' deletion analysis as discussed above indicates that the ribosome binds further downstream. It is likely that the 5' 45 nt does not contain an IRES, but acts as an enhancer by affecting downstream RNA secondary structure, perhaps through protein binding. Of interest is a region of ten contiguous nt (nt 33 – 42 from the 5' end) of which nine are pyrimidines making this a potential binding site for the polypyrimidine binding protein PTB) and its neural homolog nPTB. PTB aside from its role in RNA splicing is an important ITAF for many eukaryotic IRESes .
FMRP is synthesized in response to neural activity [2, 37] and in particular, a brief exposure to KCl stimulates FMR1 synthesis in neuronal dendrites . In our study, both internal initiation mediated by the FMR1 5' leader and FMRP expression were also regulated by the duration of KCl exposure; a short exposure increased and a longer exposure decreased FMR1 IRES activity and FMRP expression. Moreover, intracellular acidification associated with decreased neural activity also inhibited FMR1 IRES activity. These results suggest that neural activity of differing intensity or duration may produce distinct changes in IRES-dependent translation mediated by the FMR1 5' leader and that IRES-dependent translation is a mechanism contributing to the synthesis of FMRP in neurons. These results also indicate that a feedback mechanism exists that is dependent upon the duration of the calcium influx through voltage gated calcium channels stimulated by KCl. Indeed, extent and duration of intracellular calcium can regulate the translation of other mRNAs [50, 51].
FMRP is associated with the RISC complex [7, 8] and our results indicate that the presence of double stranded RNA stimulates IRES-dependent synthesis of FMRP. This result implicates a positive feedback mechanism regulating the synthesis of FMRP and the level of FMRP could regulate the activity or the targets of the RISC complex. However, the overall level of FMRP was not altered after poly I:C exposure. Poly I:C leads to phosphorylation of eIF-2α  and a subsequent decrease in cap-dependent translation . It is possible that the loss of any cap-dependent translation of the FMR1 mRNA is compensated by an increase in IRES-dependent translation, but the global level of FMRP is unaffected.
In summary, we demonstrated that the FMR1 5' leader contains an IRES, whose critical elements include the CGG repeats as well as the 5' end of the leader. Inhibiting cap-dependent translation in vitro and ex vivo resulted in only a small diminution in the translation of reporter mRNAs containing the FMR1 5' leader. Under similar conditions, endogenous FMRP expression was maintained. Multiple stimuli altered internal initiation of translation mediated by the FMR1 5' leader that in some cases mirrors that of FMRP synthesis in vivo. Taken together, our study indicates that IRES-dependent translation of the FMR1 mRNA may be a major contributor to the synthesis of FMRP in vivo.
The FMR1 5' leader was PCR amplified from a human brain cDNA library (Clontech) and inserted into the dual luciferase vector – pRF [54, 55] (a generous gift from Dr. Anne Willis, University of Leicester) with EcoRI and NcoI restriction endonuclease sites. The promoterless construct was created by digesting the dicistronic construct with SmaI and EcoRV and religating the construct. The monocistronic vector for the ex vivo experiments was created by digesting the RP vector with EcoRI and BamHI. The digest released the 5' leader, the Photinus luciferase gene, and the SV40 3' UTR, which were cloned into the pGL3 vector (Promega). The monocistronic vector for the in vitro experiments was created by inserting the above Photinus gene into the SK+ Bluescript vector (Stratagene) downstream of a T7 promoter.
Serial truncations were produced by PCR amplification with 5' and 3' primers containing EcoRI and NcoI endonuclease restriction sites, respectively. Deletion of the CGG repeats was accomplished by amplifying the region 3' to the repeats in the FMR1 5' leader and inserting it into the pRF construct with EcoRI and NcoI restriction sites on the 5' and 3' end, respectively. The 5' leader upstream of the CGG repeats was amplified and inserted upstream of the 3' FMR1 5' leader using EcoRI restriction sites. In experiments using a hypophosphorylated form of 4E-BP1 (containing Thr-37-Ala/Thr-46-Ala mutations), plasmids expressing this protein or the parent vector (both based on pACTAG-2) were co-transfected with the monocistronic constructs described above, using a 8-fold molar excess of the 4E-BP1 or control expression constructs . The 4E-BP1 double mutant and control expression plasmids were generously provided by Dr. Nahum Sonenberg (McGill University, Montreal).
In Vitro Translation
The Bluescript SK+ vector containing the 5' leaders upstream of the Photinus luciferase gene was linearized with BamHI and in vitro transcribed using mMessage Machine (Ambion) producing capped mRNA. The mRNA was extracted with phenol/chloroform and a sample was run on an agarose gel to ensure RNA integrity. 0.5 μg of the mRNA and 1.6 nM methionine was added to rabbit reticulocyte lysate (Speed Read, Novagen) and incubated for 1 hr at 30°C in the presence or absence of cap analog (Ambion). The sample was subsequently assayed for Photinus luciferase activity.
Cell Culture/Luciferase Assays
C6 cells were obtained from ATCC and cultured in DMEM, 10% fetal bovine serum and 2 mM L-glutamine. Polyinosinic:polycytidylic acid, ameloride, and KCl were obtained from Sigma. Cells were transfected with 2 μg of DNA using Fugene transfection reagent (Roche) or 4 μg of mRNA using the TransMessenger RNA transfection reagent (Qiagen) according to the manufacturer's directions. The RNA was in vitro transcribed using the mMessage Machine (Ambion) and purified as detailed above. After 24 hr (DNA transfections) or 7 hours (RNA transfections), the cells were lysed with 500 μl of lysis buffer (Promega). Forty μl of the supernatant were used for the luciferase assays using the Dual-Luciferase Reporter Assay System and analyzed in a Luminoskan luminometer. For the siRNA experiments, C6 cells were transfected with 10 pmol of rat siRNA targeted against eIF-4E (On-Target plus SMARTpool, cat# L-0088826-01, Dharmacon) or nonsense siRNA (Dharmacon) using INTERFERin siRNA transfection reagent (Polyplus-Transfection) as directed by the manufacturer. Cells were lysed with 200 μl of lysis buffer (Promega) including phosphatase (Pierce) and protease (Roche) inhibitors after 72 hours. The cell lysates were analyzed by Western blot.
Western blot analysis
Cells were harvested in cell lysis buffer (Promega) with protease (Roche) and phosphatase inhibitors (Pierce). The cell lysate was analyzed by Western blot by separating the proteins on a 12% SDS-polyacrylamide gel and transferred onto nitrocellulose. The membranes were blocked (Invitrogen) and probed with a monoclonal antibody (7G-1, 1:1000 dilution; Developmental Hybridoma Bank) or a polyclonal antibody (sc-28739, 1:200 dilution; Santa Cruz) directed against FMRP. Both antibodies mainly recognized a single band at approximately 80 kD in lysates from C6 cells and rat hippocampus (see Additional file 1). In addition monoclonal antibodies directed against phosphorylated p70 S6 kinase (9206,1:1000 dilution; Cell Signaling) and eIF-4E (610269; 1:500 dilution, BD Biosciences) or polyclonal antibodies directed against JunB (Ab31421, 1:500 dilution; Abcam), and GAPDH (sc-25778, 1:200 dilution; Santa Cruz) were used in 5% nonfat dried milk in a solution of PBS containing 0.1% Tween 20. The blots were then incubated with alkaline phosphatase-conjugated secondary antibodies (1:10,000 – 1:50,000 dilution; Invitrogen) for 1 hour. Immunoreactive bands were detected using chemiluminescence (Invitrogen) as per manufacturer's directions. Westerns blots were either from individual PAGE gels (Fig. 3A) or the nitrocellulose was restripped and reprobed (Figs. 3B, 5B, 6B). The Western blots were quantitated using ImageQuant software (Applied Biosystems).
List of Abbreviations
The abbreviations used are
FMR1 Fragile X gene
internal ribosomal entry site
4E-Binding Protein 1
mammalian target of rapamycin
short interfering RNA
- poly I:
C: polyinosinic:polycytidylic acid
R: Photinus Renilla :luciferase
We thank Dr. Geoff Owens for initial unpublished results. We also thank Olga Hartman for excellent technical assistance and the other members of the Krushel lab for their crucial assistance and helpful suggestions, and Dr. Jessica Tyler for critical comments on the manuscript. This work was supported by NIH grant AG028156.
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