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Molecular and Cellular Biology, April 2004, p. 3295-3306, Vol. 24, No. 8
0270-7306/04/$08.00+0     DOI: 10.1128/MCB.24.8.3295-3306.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Mutations Linked to Leukoencephalopathy with Vanishing White Matter Impair the Function of the Eukaryotic Initiation Factor 2B Complex in Diverse Ways

Wei Li,^1, Xuemin Wang,^1, Marjo S. van der Knaap,² and Christopher G. Proud^1,*

Division of Molecular Physiology, Faculty of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom,¹ Department of Child Neurology, Free University Medical Center, Amsterdam, The Netherlands²

Received 8 September 2003/ Returned for modification 14 November 2003/ Accepted 14 January 2004

Top Abstract Introduction Materials and Methods Results Discussion References

 
Leukoencephalopathy with vanishing white matter (VWM) is a severe inherited human neurodegenerative disorder that is caused by mutations in the genes for the subunits of eukaryotic initiation factor 2B (eIF2B), a heteropentameric guanine nucleotide exchange factor that regulates both global and mRNA-specific translation. Marked variability is evident in the clinical severity and time course of VWM in patients. Here we have studied the effects of VWM mutations on the function of human eIF2B. All the mutations tested cause partial loss of activity. Frameshift mutations in genes for eIF2B or eIF2Bß lead to truncated polypeptides that fail to form complexes with the other subunits and are effectively null mutations. Certain point mutations also impair the ability of eIF2Bß or - to form eIF2B holocomplexes and also diminish the intrinsic nucleotide exchange activity of eIF2B. A point mutation in the catalytic domain of eIF2B impairs its ability to bind the substrate, while two mutations in eIF2Bß actually enhance eIF2 binding. We provide evidence that expression of VWM mutant eIF2B may enhance the translation of specific mRNAs. The variability of the clinical phenotype in VWM may reflect the multiple ways in which VWM mutations affect eIF2B function.

Top Abstract Introduction Materials and Methods Results Discussion References

 
Leukoencephalopathy with vanishing white matter (VWM) is a severe inherited neurodegenerative disease (35). This condition is also known as childhood ataxia with diffuse central nervous system hypomyelination (34). Clinically, this condition is characterized by progressive ataxia, spasticity, and variable optic atrophy, as well as seizures. Mental decline, if seen, is usually mild. More rapid deterioration is associated with minor head injury or fever, and the latter often results in coma. Death occurs after a variable time period, from several years up to decades. In magnetic resonance imaging, a diagnostic pattern with diffuse abnormality of cerebral white matter is observed (35, 36). Over time, the abnormal white matter vanishes to be replaced by cerebrospinal fluid or tissue water. There is considerable phenotypic variation. For example, the so-called "Cree" leukoencephalopathy seen in North American Indians is especially severe, leading to very early onset of neurological deterioration (3 to 9 months) and death before 21 months (8). Recent work has revealed additional serious forms of VWM that involve very early onset and early death (7, 8). In some cases, the ovaries are also affected (35).

VWM shows autosomal recessive inheritance. Linkage analysis initially assigned a VWM locus to a 5-centimorgan interval on chromosome 3q27 (21). Subsequent work showed that that mutations in the gene for the subunit of the translation factor eukaryotic initiation factor 2B (eIF2B) were associated with VWM. These included several point or frameshift mutations within this gene. In some patients, linkage analysis did not point to a role for the eIF2B (or EIF2B5) gene. In several of them, VWM was found to be associated with mutations in the ß subunit of eIF2B, a heteropentamer (22). Subsequent work showed that mutations in any eIF2B gene can cause VWM (37). All VWM patients have now been found to have mutations in one or other of the genes for the subunits of eIF2B. Affected individuals carry two mutated copies of a given eIF2B gene; i.e., inheritance shows an autosomal recessive pattern. The particularly severe Cree form of this disease is linked to a point mutation (R195H) in eIF2B (8), and a second severe form is linked to a different point mutation in the same gene (7).

eIF2B is a guanine nucleotide exchange factor that plays a key role in the initiation of mRNA translation and in its control (28). It promotes GDP/GTP exchange on initiation factor eIF2. In its GTP-bound state, eIF2 recruits the initiator Met-tRNA to the 40S subunit during translation initiation. Since it is the anticodon of this tRNA that recognizes the start codon in the mRNA, active eIF2 is required for all normal translation initiation events. eIF2B activity can be regulated in a number of ways. The best documented of these is the phosphorylation of the subunit of eIF2 at Ser51 (4), which converts it from a substrate of eIF2B into a potent competitive inhibitor (30). Phosphorylation of eIF2 is increased under a wide range of cellular stress conditions and can be catalyzed by several different protein kinases (3). Since active eIF2.GTP is required for all translation initiation events, inhibition of eIF2B activity causes a decrease in general protein synthesis. However, reduced eIF2B activity actually enhances the translation of certain mRNAs by virtue of the presence of upstream open reading frames (uORFs) in their 5' untranslated regions (UTRs). Examples include the mRNAs for the transcription regulators GCN4 in (16) and ATF4 in mammals (13). Since these proteins modulate transcription of multiple genes, decreased eIF2B activity may also affect the expression of many genes.

eIF2B is composed of five nonidentical subunits, through (16). Of these, eIF2B displays catalytic activity when expressed alone, and the minimal catalytic region of the yeast ortholog was recently delineated (9). The corresponding region of the mammalian protein contains the site that is phosphorylated by glycogen synthase kinase 3 and that inactivates eIF2B (39). The other subunits do not possess a region homologous to this catalytic segment and appear not to be involved in catalysis. However, eIF2B shows similarity to the N-terminal part of eIF2B and forms a binary complex with eIF2B in yeast, which is referred to as the catalytic subcomplex (25). The other three subunits, , ß and , also show mutual sequence similarity and form a trimeric subcomplex in yeast. Evidence from careful genetic studies with yeast indicates that these subunits play a key role in sensitizing the eIF2B holocomplex to inhibition by eIF2[P] (20, 24, 40). Indeed, recombinant eIF2 can bind to the ß subcomplex, which has been termed the regulatory subcomplex (25). Although eIF2B itself can mediate guanine nucleotide exchange, its activity is greatly enhanced by its association with the other subunits (6, 10).

VWM is the first example of an inherited human disease caused by mutations in a component of the basal translational machinery. A clear priority is now to establish how mutations in eIF2B lead to VWM and the other lesions associated with this condition. It will also be important to understand why they give rise primarily to a neurological disease and why its severity and age of onset are so variable. Here, as an essential first step, we have studied how they affect the integrity and function of the eIF2B complex. Our data show that all the VWM mutations tested cause partial loss of activity of human eIF2B. However, the magnitude of the effect differs between mutations. Most interestingly, the basis of the decreased activity differs between mutations, prompting the possibility that the variable phenotype of the condition may reflect the distinct ways in which different mutations affect the eIF2B complex.

Top Abstract Introduction Materials and Methods Results Discussion References

 
Materials. Chemicals and biochemicals were obtained as described previously (40). Antibodies to eIF2B subunits were obtained from Santa Cruz, apart from the anti-eIF2B antibody which was described in reference 38. Anti-myc was from Sigma. Antihemagglutinin (anti-HA) was from Boehringer Mannheim, and anti-eIF4A has been described previously (23). Antibodies to phosphorylated eIF2 were from Cell Signaling Technology, and anti-eIF2 is a monoclonal kindly provided by the late E. C. Henshaw.

Construction of expression vectors. Full-length eIF2B cDNAs were obtained from the IMAGE consortium or were generated by reverse transcriptase PCR (RT-PCR) (Table 1). VWM mutations were made by PCR-based technology (for further information, see Table 2). These mutant cDNAs or the wild-type (WT) cDNA were cloned into an expression vector with N-terminal hexahistidine (His₆) and myc tags. As the C terminus of eIF2B contains the catalytic domain (9) and the extreme C-terminal tip interacts with eIF2 (1), we reasoned that N-terminal tags were less unlikely to interfere with the function of the eIF2B complex than were C-terminal ones. All DNAs were confirmed by sequencing. A mutant lacking 47 residues within the catalytic domain (9) (CAT) was created as a negative control for activity studies. Mouse ATF4 uORF was amplified from pATF4luc (a kind gift from David Ron, New York, N.Y.) and was inserted into the NheI-BamHI site of pEGFP-N1 (Clontech). Sequences encoding an HA tag were introduced into the PCR primer to facilitate detection by immunoblotting.

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TABLE 1. Sources of cDNAs and WT human eIF2B constructs

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TABLE 2. Primers used for mutagenesis

Analysis of eIF2B complexes and activity. For analysis of eIF2B expression, lysates were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting, as described earlier (27). To isolate complexes containing the recombinant His-myc-tagged eIF2B subunits, lysates were purified on Ni-nitrilotriacetic acid (NTA)-agarose (Qiagen). Typically 300 µg of protein was used for this type of analysis. The bound material was analyzed by SDS-PAGE-Western blotting as described above. To measure eIF2B activity, complexes were isolated in the same way and GDP/GTP exchange activity was determined by using our standard assay with complexes containing purified human eIF2 and [³H]GDP as substrate. Since the levels of expression of WT or mutant eIF2Bß/ could vary significantly within a given experiment, we first assessed the amount of the purified complexes by SDS-PAGE-immunoblotting for myc and then adjusted the amounts of material for the assay accordingly to ensure that similar amounts of recombinant eIF2B were used in all assays.

Cell culture, transfection, treatment, and lysis. Human embryonic kidney 293 (HEK 293) cells were grown and lysed exactly as described earlier (40). Cells were transfected by using the calcium phosphate precipitation method as described in reference 11. Unless otherwise stated, cells were lysed about 48 h after transfection. For studies on the ATF-linked report, HEK 293 cells (in 10-cm-diameter dishes) were transfected with pEGFP or pATF4-EGFP plus the eIF2Bß construct under study (or empty vector as a control) as indicated. Twenty-four hours after transfection, the media were changed to Dulbecco's modified Eagle's medium without methionine. Four-and-a-half microliters of [³⁵S]methionine was then added. Sixteen hours later, cells were lysed and lysates were used for immunopreciptation (IP) with anti-GFP antibody (Roche). One quarter of the sample was loaded in each lane. For Northern blot analyses, 48 h after transfection, one dish of cells for each combination of vectors was collected for RNA isolation with Trizon (Invitrogen). One quarter of the total RNA isolated was loaded per lane in a 1.4% formaldehyde-agarose gel. Northern blot hybridization with probes for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and GFP were done as described by Sambrook et al. (31). Films were developed after 6 h (GFP) or 2 days (GAPDH) exposure at -80°C.

For thermal treatment of cells, dishes were transferred from the incubator (37°C) to a water bath at the desired temperature (usually 41°C) for 2 h. A water bath was used to ensure that cells quickly reached the new temperature.

Top Abstract Introduction Materials and Methods Results Discussion References

 
Choice of VWM mutants for investigation in this study. Our aim was to gain insight into the effects of VWM mutations on the function of human eIF2B complexes. We therefore overexpressed WT or mutant human eIF2B subunits in HEK 293 cells, as His₆- and/or myc-tagged proteins. We chose HEK 293 cells because they are highly transfectable human cells and because it has already been shown that eIF2B expressed in them is incorporated into functional eIF2B complexes (39). Many VWM mutations occur in eIF2B, and we chose several for analysis. These were the frameshift mutant 792delTinsACA, which truncates eIF2B at residue F264, and the point mutations T91A, R113H, R315G, R339P, W628R (22), and R195H (8) (Table 3). They were chosen as they give rise to VWM when present in a simple homozygous fashion (T91A, R113H, R195H, and R315G) and/or involve a substantial amino acid change and may thus also have marked effects on eIF2B itself (R339P and W628R). We also wished to study the effects of mutations in another subunit of eIF2B. eIF2Bß is a component of the regulatory, rather than the catalytic, subcomplex. We therefore chose a frameshift mutant in eIF2Bß, which is predicted to yield a severely truncated polypeptide, and the point mutants E213G (homozygous) and V316D (major change) (reference 22 and Table 3).

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TABLE 3. Mutations of eIF2B studied in this reporta

Requirements for the formation of mammalian eIF2B holocomplexes. Studies with eIF2B are complicated because it is a heteropentamer. To assess and interpret possible effects of VWM mutations on formation of eIF2B complexes, it was first important to understand the assembly of WT human eIF2B. To do this, we expressed His-myc-tagged WT eIF2B or eIF2Bß together with one or more of the other myc-tagged subunits. The His-myc-tagged polypeptide was then isolated on Ni-NTA-agarose, and the bound material was analyzed for other myc-tagged eIF2B subunits. When His-myc-tagged eIF2B was expressed with each of the other subunits singly, only eIF2B bound to eIF2B, suggesting that, as in yeast (25), the and subunits form a binary subcomplex (Fig. 1A). eIF2B, -ß, or - could not form ternary complexes with eIF2B (Fig. 1B). Without eIF2B, eIF2B was unable to bind even the combination of eIF2B, -ß, and - (Fig. 1B). Indeed, the only four-subunit combination that forms stable complexes is that of ß, , , and (Fig. 1B), consistent with the findings that eIF2B lacking eIF2B can be generated in insect cells (6) or isolated from mammalian cells (5).

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FIG. 1. Formation of eIF2B complexes in HEK 293 cells. HEK 293 cells were transfected with constructs encoding His-myc-tagged human eIF2B or -ß as indicated, together with vectors encoding myc-tagged versions of the other subunits, as indicated. Samples of cell lysate were either analyzed directly by SDS-PAGE and immunoblotting with anti-myc (lysate) or were first subjected to chromatography on Ni-NTA-agarose prior to this type of analysis (pull-down). Positions of the tagged eIF2B subunits are shown. *, a band that cross-reacts nonspecifically with the anti-myc antibody; all, cells were cotransfected with cDNAs for all four of the other eIF2B subunits. The weak signals in, e.g., the lanes for with His-myc-eIF2Bß in panel C may reflect some "bridging" of the recombinant subunits by the endogenous eIF2B subunits. Panel D presents a cartoon summarizing the data, showing which complexes between eIF2B subunits can form in mammalian cells, i.e., eIF2B, eIF2Bß, and eIF2Bß.

His-myc-eIF2Bß was unable to associate with any of the other individual subunits (Fig. 1A). We did not detect an eIF2Bß complex, suggesting that association with eIF2B may be needed for stable interaction between the mammalian , ß, and subunits (in contrast with the situation for yeast eIF2B (reference 40 and Fig. 1C). These data are the first detailed information on the assembly of mammalian eIF2B. Figure 1D is a summary cartoon showing which complexes can form.

Certain VWM mutations affect the ability of eIF2B subunits to form holocomplexes. To study whether VWM mutations affected assembly of eIF2B complexes, HEK 293 cells were transfected with vectors for VWM/WT eIF2B subunits, either with the cDNA for a single subunit (Fig. 2) or with the cDNAs for all five (Fig. 3). The missense mutants expressed as polypeptides of sizes similar to that of the WT protein (Fig. 2A). As expected, the constructs mimicking the frameshift mutants gave small polypeptides (Fig. 2B).

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FIG. 2. Formation of complexes containing a VWM mutant version of eIF2Bß or . HEK 293 cells were transfected with vectors for WT or selected VWM mutants of the ß or subunits of eIF2B, as fusions with His and myc tags, or with the empty vector (Vec). (A and B) Samples of cell lysate were analyzed by SDS-PAGE and Western blotting by using anti-myc. (C and D) Samples of cell lysate were subjected to chromatography on Ni-NTA-agarose prior to immunoblot analysis of the bound material with anti-myc, -eIF2B, and -eIF2B as well as anti-eIF2Bß (C) or -eIF2B (D). and ß in panels B and D indicate the frameshift mutants, the positions of the truncated polypeptides that they encode being indicated by diagonal arrows. Positions of the other, endogenous eIF2B subunits are also shown. Weak signals for the anti-eIF2Bß and antisera in panels C and D, respectively, mean that their signals are shown for longer exposures as insert panels. The asterisk indicates a nonspecific detection by anti-myc of a protein that binds nonspecifically to Ni-NTA-agarose. (E) Cells were transfected with vectors for myc/His-eIF2B or -ß. Lysates were subjected to IP with anti-eIF2B, and precipitates were analyzed by SDS-PAGE and immunoblotting with anti-eIF2B (left side) or anti-eIF2Bß (right side).

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FIG. 3. Formation of complexes containing VWM variants of eIF2Bß or -. HEK 293 cells were transfected with vectors for WT or selected VWM mutants of the ß or subunits of eIF2B, or the CAT mutant of eIF2B, as fusions with His and myc tags, and with vectors encoding myc-tagged version of the other four subunits. As a negative control, cells were transfected with empty vectors (indicated). Samples of cell lysate were analyzed directly by SDS-PAGE and Western blotting (A) or first subjected to chromatography on Ni-NTA-agarose prior to analysis by SDS-PAGE-immunoblotting (B). Blots were developed with anti-myc (A and B) and anti-eIF2 (B). Positions of the myc-tagged eIF2B subunits and of eIF2 are shown. and ß indicate the positions of the truncated polypeptides arising from the frameshift mutations. In the lower part of panel B, only the vectors for WT or mutant eIF2Bß were used (or empty vector as negative control). Samples of cell lysate were subjected to chromatography on Ni-NTA-agarose prior to analysis by SDS-PAGE and Western blotting with anti-eIF2(Ser51[P]). Equal expression of eIF2B subunits was confirmed by probing with anti-myc (data not shown). Where indicated, cells were pretreated with sodium arsenite (0.5 mM, 30 min) prior to lysis. Cells were also transfected with the empty vector, and similar pull-downs were performed to confirm that very little, if any, eIF2 was retained nonspecifically on the resin (B, upper and lower sections). (C and D) As done for panel B, vectors for the indicated His-myc-tagged eIF2B subunits were used together with myc-tagged versions of the other four WT subunits. Where indicated, cells also received DNA for the myc-tagged versions of eIF2B or ß. Data are immunoblots of material retained on Ni-NTA-agarose (except where indicated, "lysate"). In panel D, the two arrows for eIF2B indicate that the broad band seen for this subunit actually consists of a poorly resolved doublet of species, the lower one being the myc-tagged eIF2B and the upper one being the myc/His-tagged subunit. (E) HEK 293 cells were transfected with HA- and myc-tagged versions of eIF2B; those shown in lane 2 also received the vector for myc-eIF2B. Samples of lysates were subjected to IP with anti-HA followed by SDS-PAGE and immunoblotting, development being with anti-HA (upper section) or anti-myc (lower section).

Initially, we expressed the VWM mutant His-myc-tagged eIF2B subunits alone and used Ni-NTA-agarose to isolate them and study their ability to interact with the other, endogenous, subunits. A limitation here is that we are unable to detect eIF2B by using the available antisera. However, as shown above, eIF2B is not required for complex formation between the other four subunits. The ß, , and subunits were clearly detected in pull-downs from cells expressing WT His-myc-eIF2B and for each of the five point mutants of eIF2B tested (Fig. 2C). In contrast, the other subunits were not observed in pull-downs from cells expressing the eIF2B frameshift mutant, presumably because the truncated polypeptide lacks regions required for interaction with them. It also lacks the catalytic domain (9) and is thus functionally null. Lastly, the pull-downs for the T91A and CAT mutants consistently showed less of the other four subunits than were seen in pull-downs from WT eIF2B, suggesting that they have reduced ability to form eIF2B holocomplexes (Fig. 2C).

eIF2Bß(E213G) formed complexes with the other eIF2B subunits to almost the same extent as WT eIF2Bß (Fig. 2D). In contrast, only very weak signals were observed for the other subunits following affinity isolation of eIF2Bß(V316D) on NTA-agarose (Fig. 2D), indicating that it cannot efficiently form holocomplexes. The polypeptide that mimics the frameshift M203fs failed to interact with the other subunits, suggesting that the C terminus of eIF2Bß is needed for this. Thus, certain VWM mutations affect eIF2B function by impairing holocomplex formation. As complex formation greatly enhances eIF2B activity (10), this is likely to reduce markedly eIF2B activity in patients' cells.

To assess what proportion of total eIF2B complexes in the transiently transfected cells contain the recombinant subunit, we immunoprecipitated complexes with anti eIF2B and analyzed the precipitates through SDS-PAGE-immunoblotting by using anti-eIF2B or -ß. As seen in Fig. 2E, >50% and almost 80% of the complexes contain the recombinant eIF2B and -ß proteins, respectively.

The potencies of antisera for eIF2Bß, -, -, and - differ considerably, and there is no suitable antibody for eIF2B. We therefore also used an additional approach in which we coexpressed the eIF2B subunit under study with the other four polypeptides, each with a myc tag. All five subunits were fairly evenly expressed as assessed by immunoblotting of lysates with anti-myc (Fig. 3A). However, eIF2B(CAT) and the truncation mutants of eIF2B and -ß were expressed at lower levels, perhaps because they are less able to form complexes. When His-myc-tagged eIF2B missense mutant polypeptides were isolated on Ni-NTA-agarose, the other four myc-tagged subunits were readily detected in every case (Fig. 3B, top), showing that eIF2B is incorporated into these complexes.

Similar data were obtained for WT and VWM mutant eIF2Bß (Fig. 3B). The data for the eIF2B(T91A) and eIF2Bß(V316D) mutants obtained here differ from those of Fig. 2, in which only single subunits were expressed and where both showed decreased ability to form eIF2B complexes. In the earlier experiments, the overexpressed subunit must compete with the corresponding endogenous polypeptide for binding to a small pool of the other four eIF2B polypeptides. It thus appears that eIF2B(T91A) and eIF2Bß(V316D) can indeed form complexes but fail to compete efficiently with the endogenous WT eIF2Bß.

To test this, we examined whether the mutant eIF2B proteins could compete with WT myc-tagged eIF2Bß and - to form holocomplexes. As expected, coexpression of WT myc-eIF2Bß with His-myc WT eIF2Bß or the E213G mutant reduced somewhat the amounts of the other subunits that bound to the His-myc-tagged polypeptide (Fig. 3C). However, coexpression of WT eIF2Bß almost completely blocked the association of the eIF2Bß(V316D) mutant with the other subunits.

In the case of eIF2B(T91A), we saw only a modest effect from expressing WT-myc eIF2B alongside the T91A-His-myc protein (Fig. 3D). Surprisingly, we also saw that, along with the His-myc-eIF2B polypeptide, the slightly smaller myc-tagged eIF2B polypeptide was also present in the pull-down, suggesting that eIF2B might dimerize, which could account for the small decrease in recovery of the T91A mutant. To confirm this, we coexpressed HA-tagged eIF2B with His-myc-eIF2B. After IP with anti-HA, His-myc-eIF2B was indeed clearly seen (Fig. 3E, lower part, lane 1). As described above, eIF2B interacts with eIF2B in eIF2B holocomplexes (2, 25). Parts of their sequences are homologous (2) and could be involved in the - interaction. Thus, one explanation is that, when eIF2B is expressed at high levels, it self dimerizes via the region resembling eIF2B. To test this, we overexpressed myc-eIF2B with both HA- and myc-tagged eIF2B: strikingly, only myc-eIF2B was now seen in the anti-HA IP (Fig. 3E, lower part, lane 2). Dimerization of eIF2B is thus likely an artifact of overexpression.

VWM mutations decrease the activity of eIF2. The major aim of this study was to assess whether, and how, VWM mutations affect the function of eIF2B. The above data show that most of the mutated subunits can efficiently form eIF2B complexes, at least when overexpressed with the four other subunits. We therefore assayed the activity of complexes containing recombinant WT or VWM mutant subunits after isolation from extracts of transfected cells by using NTA-resin and our standard assay with preformed eIF2-[³H]GDP complexes as substrate. Initially, we expressed a single WT and/or mutant eIF2B subunit and isolated complexes containing this polypeptide and endogenous subunits. Although eIF2B displays some activity on its own (6, 10), this is greatly enhanced by association with the other subunits (10), as verified by earlier studies with HEK 293 cells (39). Thus, although the pull-down material contains both free His-myc-eIF2B and complexes containing this polypeptide, the activity detected overwhelmingly reflects that of complexes. In all cases, complexes containing VWM mutants of eIF2B showed lower activity than WT complexes (Fig. 4A). The defect varied from mild for, e.g., eIF2B(R315G) to severe for the W628R mutation. No exchange activity was detected for NTA-pull-downs of the eIF2Bß or eIF2B truncation mutants, consistent with their inability to form eIF2B holocomplexes and with the absence from the eIF2B frameshift mutant of the C-terminal catalytic domain (9).

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FIG. 4. Effects of VWM mutations on the activity of eIF2B. HEK 293 cells were transfected with vectors for WT or selected VWM mutant versions of the ß or subunits of eIF2B, or the CAT mutant of eIF2B, as fusions with His and myc tags (A and B), and with vectors encoding myc-tagged version of the other four subunits (B). Samples of cell lysate were subjected to chromatography on Ni-NTA-agarose prior to analysis. Levels of expression were carefully assessed by SDS-PAGE and Western blot analysis (using anti-myc) of the bound material to normalize the amounts used in each assay. Appropriate amounts of this bound material were then assayed for GDP/GTP exchange activity by using eIF2-[3H]GDP complexes as the substrate. Data are shown as percentage of activity with corresponding WT subunit and are typical of between 4 and 10 experiments performed.

By using the above approach, we could not obtain accurate data for the eIF2B(T91A) and eIF2Bß(V316D) mutants as they do not efficiently form eIF2B holocomplexes. Thus, we tested the VWM mutant under study expressed together with the other four WT subunits, since they can form holocomplexes under this set of conditions (Fig. 3B, upper part). The eIF2B(T91A) and eIF2Bß(V316D) mutants still displayed low intrinsic GDP/GTP exchange activity, in addition to their defective abilities to form complexes (Fig. 4B). Since Western analysis of these pull-downs shows similar amounts of all five recombinant subunits (Fig. 3B, upper part), these data also accurately reflect the activities of other VWM mutant eIF2B complexes. The data in Fig. 1 rule out the occurrence of diverse complexes of differing subunit compositions.

Some VWM mutations affect the binding of eIF2B to eIF2. Since neither of the truncation mutants forms complexes and both are thus effectively null mutations, we focused our studies on the point mutations, which all reduce eIF2B activity. One way in which they might do this is by altering the ability of eIF2B to bind eIF2. This involves multiple interactions. A lysine block in eIF2ß interacts with the extreme C terminus of eIF2B (1, 18, 19). The eIF2Bß subcomplex interacts with eIF2, especially when eIF2 is phosphorylated (20, 25). To study binding of eIF2B to eIF2, we analyzed Ni-NTA-agarose pull-downs from cells transfected with vectors for the His-myc-tagged WT-VWM mutant eIF2B or ß- and myc-tagged versions of the other four subunits for the presence of eIF2. In most cases, complexes containing VWM mutants showed binding to eIF2 similar to that shown by the WT complexes (Fig. 3B, upper part). However, in three cases marked differences were seen. Firstly, complexes containing eIF2B(W628R) bound markedly less eIF2. Secondly, both the eIF2Bß point mutations tested here actually increase the binding of eIF2. In other experiments, NTA-agarose pull-down experiments were performed and the bound material was analyzed for eIF2(S51[P]). The amount of eIF2(P) bound to complexes containing the VWM mutants of eIF2Bß was greater than for the WT complexes (consistent with the increased binding of total eIF2) (Fig. 3B). Treatment of cells with sodium arsenite, which enhances eIF2 phosphorylation, increased this binding to similar extents for the complexes containing WT and mutant eIF2B (Fig. 3B, lower part). It thus seems that the VWM point mutations do not affect association of eIF2B with eIF2(P), and it is thus unlikely that they abolish regulation of eIF2B by eIF2(P). This is consistent with the data for the effects of VWM mutations on the properties of yeast eIF2B (29).

The VWM mutations do not confer a temperature-sensitive phenotype. Clinically, the onset or deterioration of VWM symptoms in children is associated with febrile infection (12, 34-36). It has therefore been suggested that VWM mutant eIF2B complexes might show a temperature-sensitive phenotype. We used a range of approaches to test this. WT or VWM eIF2B polypeptides were expressed in HEK 293 cells, as detailed above. In some experiments, we subjected cells to thermal stress by incubating them at an elevated temperature, usually 41°C. Cells were lysed and samples were processed for analysis of formation of eIF2B complexes and an activity assay. Elevated temperatures did not generally affect the integrity of eIF2B complexes containing WT or VWM mutant eIF2B or -ß (Fig. 5A and B): amounts of other subunits copurifying with the myc-His-tagged eIF2B subunit under study were the same from lysates of cells kept at 37°C or were transferred for 2 h to a higher temperature. In some cases, the total amount of the tagged subunit fell at the higher temperature but not the amount of the other subunits copurifying with it. Effects were similar for the WT and VWM mutant polypeptides and likely reflect greater instability of the excess single subunits than of those that incorporated into complexes. In some experiments, eIF2B complexes containing eIF2B(T91A) did appear less stable than those containing WT eIF2B (Fig. 5C). It was also possible that the intrinsic activity of VWM eIF2B is thermosensitive. However, in multiple experiments, we saw no thermosensitivity of WT or VWM eIF2B at temperatures that ranged up to suprapathological values (44°C). This was true whether the elevated temperature was applied to the cells prior to isolation of eIF2B complexes, following their isolation but prior to assay or during the assay.

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FIG. 5. Analysis of potential thermosensitivity of eIF2B complexes containing WT or VWM mutant eIF2B subunits. HEK 293 cells were transfected with vectors for WT or selected VWM mutant versions of the (A and C) or ß (B) subunits of eIF2B, as fusions with His and myc tags. In some cases, cells were held at 41° for 2 h prior to lysis instead of at the normal temperature of 37°C. Samples of lysate were subjected to chromatography on Ni-NTA-agarose prior to analysis by SDS-PAGE and Western blotting with anti-myc for His-myc-eIF2B (A and C) and for His-myc-eIF2Bß (B) and anti- eIF2B and eIF2B. *, nonspecific detection by anti-myc of proteins that bind nonspecifically to Ni-NTA-agarose.

Functional consequences of VWM mutations for specific protein synthesis in vivo. It was important to assess the effects of VWM mutations on the function of eIF2B in vivo. However, even though free eIF2B has only low activity, overall eIF2B activity in cells expressing it will increase, obscuring any effects due to impaired activity due to VWM mutations. We therefore focused on eIF2Bß as it lacks intrinsic activity and 80% of eIF2B complexes in cells overexpressing eIF2Bß contain the recombinant subunit (Fig. 2E). The translation of certain mRNAs whose 5' UTRs contain multiple uORFs provides a sensitive readout for small decreases in eIF2B activity; e.g., the ATF4 mRNA is regulated in this way (13). We therefore used a vector encoding enhanced green fluorescent protein (EGFP) downstream of the ATF4 5' UTR to assess alterations in eIF2B activity in vivo. The EGFP was cloned behind the ATF4 5' UTR with an HA tag to facilitate detection (Fig. 6A). The control vector pEGFP yields an mRNA with a very short 5' UTR devoid of uORFs.

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FIG. 6. VWM mutants of eIF2Bß enhance expression of EGFP from a reporter construct containing the ATF4 5' UTR. (A) Diagram showing the reporter construct based on the 5' UTR of the ATF4 mRNA. The broad arrows indicate that the reporter vector gives rise to two translation products, one of which lacks the HA tag (lower, broken arrow) (see panels B, C, and E). (B to E) HEK 293 cells were transfected with vectors for WT eIF2Bß or the indicated VWM mutants or the empty vector (Vec), along with the reporter construct containing the 5' UTR of mouse ATF4 ahead of the coding region for HA-tagged EGFP. (C) The control reporter (pEGFP) was used in place of the ATF4-based vector where indicated. In panels B and C, samples were analyzed by SDS-PAGE and Western blotting by using the indicated antisera. (Anti-eIF4A was used as a loading control.) For panel B, where indicated, cells were treated with TnA (2.5 µg/ml) for 16 h prior to lysis. The two bands seen with anti-GFP for the ATF4-based vector in panel C reflect the fact that a second in-frame AUG within the HA-EGFP cistron gives rise to a product lacking the HA tag (only the upper band is recognized by anti-HA). This downstream start codon is likely the start codon for the EGFP itself. This phenomenon probably reflects continued ribosome movement beyond the ATF4 5' UTR leading up to acquisition by the ribosome of active eIF2, allowing use of the downstream start codon. (D) Samples of lysate were processed for Northern blot analysis. Shown are the autoradiography data obtained with probes for GAPDH (top) and GFP (bottom) and the stained gel showing the positions of the 18S and 28S rRNAs (middle: the top and middle panels serve as loading controls). The ATF4-EGFP mRNA is, as expected, larger than the EGFP one. (E) Cells were labeled with [35S]methionine (see Materials and Methods), and samples of cell lysate were analyzed by IP with anti-GFP, SDS-PAGE, and fluorography to detect the labeled HA-EGFP polypeptides (positions indicated by arrowheads). Again, two bands are seen here, for the reason described above.

As shown in Fig. 6B, treatment of HEK 293 cells with tunicamycin A (TnA) led to increased phosphorylation of eIF2 (due to activation of the eIF2 kinase PERK) (14). In cells transfected with empty vector or with vector for WT eIF2Bß, the level of expression of HA-tagged EGFP was low under control conditions and increased after treatment with TnA (Fig. 6B). This is as expected, since the TnA-induced increase in eIF2 phosphorylation inhibits eIF2B, promoting translation of the ATF4-HA-EGFP mRNA. WT eIF2Bß had little effect on the expression of HA-EGFP. In cells expressing either of the eIF2Bß mutants, increased basal expression of HA-EGFP was observed even without TnA treatment (Fig. 6B and C), consistent with the data showing that both mutations impair the activity of eIF2B. These findings also imply that, in VWM patients, these mutations may increase translation of mRNAs such as that for ATF4, potentially leading (as ATF4 is a transcription factor) to changes in the expression of multiple genes. No change in expression of EGFP from the control vector was seen (Fig. 6C), implying that there are no gross changes in protein synthesis (Fig. 2E). This is consistent with data from direct measurements of protein synthesis (our unpublished findings) and the fact that no growth defects have been reported for VWM patients with these mutations.

When cells expressing VWM mutants of eIF2Bß were treated with TnA, a further increase in HA-EGFP expression was seen. Given that a high proportion of eIF2B complexes in cells transfected with eIF2Bß cDNAs contain the recombinant subunit (Fig. 2E), the data suggest that the mutant complexes probably remain sensitive to inhibition by eIF2(P). Northern blot analysis revealed that mRNA expression was not altered by VWM eIF2B (Fig. 6D) and that increased rates of synthesis of EGFP were directly confirmed by [³⁵S]methionine labeling (Fig. 6E).

Further analysis revealed that expression of the VWM mutant eIF2Bß subunits, but not WT eIF2Bß, by itself increased the phosphorylation of eIF2 (Fig. 6B, see also Fig. 3B, lower part)). Thus, the elevated level of expression of EGFP from the ATF4-based reporter may stem both from increased eIF2 phosphorylation and the lower intrinsic activity of the eIF2B complexes containing the mutant eIF2Bß. The overall point remains the same, that expression of the WVM mutants activates translation of mRNAs containing uORFs. Since eIF2B binds phosphorylated eIF2 more tightly than it binds dephosphorylated eIF2 (30), this finding may explain why more eIF2 is found associated with eIF2B complexes containing the eIF2Bß mutants (Fig. 3B).

Top Abstract Introduction Materials and Methods Results Discussion References

 
The aim of this study was to examine the effects of VWM mutations in eIF2B genes on the properties of human eIF2B. This is the first key step to understanding the molecular and cellular pathology of this devastating condition. The data described here provide the first information on the effects on the human eIF2B complex of mutations that give rise to VWM in humans and reveal that all the VWM mutations tested in either the ß or subunit of eIF2B result in a partial loss of function. This is probably as expected, as VWM shows a recessive pattern of inheritance, and is in agreement with the data in reference 29 on the effects of VWM mutations on yeast eIF2B. A striking feature of our data is the diverse ways in which VWM mutations affect eIF2B.

The frameshift mutants give rise to severely truncated proteins that are expressed poorly in HEK 293 cells. They cannot form eIF2B holocomplexes and thus fail to give rise to productive eIF2B complexes. These mutations essentially give rise to a complete loss of function and therefore are null, but not interfering, mutants. It is therefore not surprising that these mutations occur only in a compound heterozygous manner, since simple homozygotes would lack functional eIF2B (22) (a situation that is almost certainly lethal). Patients with these mutations therefore rely on their second (point-mutated) copy of the relevant gene.

All the missense mutations tested give rise to full-length polypeptides that can form eIF2B holocomplexes, although some show reduced abilities to do so. These are the eIF2B(T91A) mutant, which shows a modest impairment of complex formation, and the eIF2Bß(V316D) mutant, which shows a more severe deficit in complex formation. T91 is conserved in the known mammalian eIF2B sequences but is not found in sequences from other species. V316 may be a more critical residue, as this residue is also found at the corresponding positions in eIF2Bß sequences from other mammals and from Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana. This may explain the more drastic effect of a mutation at this position on eIF2B complex assembly. When coexpressed with the other four human polypeptides at high levels, both variants were able to form complexes, showing that they are not completely unable to interact with the other subunits but are merely less able to do so. Measurements of the GDP/GTP exchange activity of such complexes showed that they have lower activity than do complexes containing WT eIF2B. Our data for the eIF2Bß(V316D) mutant agree closely with those of the authors of reference 29, who found that the corresponding yeast mutation (V341D) also impaired complex formation and activity.

To try to explain the basis of the reduced activity of these VWM eIF2B complexes, we examined their ability to bind to eIF2, the substrate for eIF2B. Three mutations altered the binding of eIF2B to eIF2. The eIF2B(W628R) mutation markedly decreased the ability of the eIF2B complex to bind eIF2. The fact that this residue lies within the catalytic domain of eIF2B (9) may explain why it impairs substrate binding. It is important that this tryptophan residue is not one of the conserved tryptophans within the cluster of aromatic and acidic residues that constitute the eIF2ß binding site at the extreme C terminus of eIF2B (1). This decrease in substrate binding may explain the reduced nucleotide exchange activity of eIF2B complexes containing the eIF2B(W628R) mutant. Both the eIF2Bß missense mutants tested here showed increased binding to eIF2. This appears surprising since their activities are also lower than for the WT complex. However, their expression increases the level of phosphorylation of eIF2, and the increased binding may thus reflect the higher affinity of eIF2(P) for eIF2B than that of the nonphosphorylated factor (30). This would lead to inhibition of eIF2B activity. Thus, the observed effects of these eIF2Bß mutants on the ATF4-based reporter may reflect both the reduced activity of complexes containing them and the increased phosphorylation of eIF2 (Fig. 6). It is unclear why expression of mutant eIF2Bß increases basal eIF2 phosphorylation. The accumulation of (unfolded) mutant eIF2Bß may elicit a stress response leading to increased eIF2 phosphorylation, or the lower activity of the VWM mutant eIF2B complexes may lead to increased translation of stress genes (e.g., ATF4). It will be important to study whether eIF2 phosphorylation and stress protein expression are increased in cells from VWM. Our data provide no information to suggest that the VWM mutations affect the susceptibility of eIF2B to regulation by eIF2 phosphorylation.

Episodes of infection accompanied by fever cause deterioration of VWM patients, and it has been suggested (37) that VWM mutations might confer on the eIF2B complex a thermosensitive phenotype. However, in extensive studies that used a range of complementary approaches, we did not detect any general enhancement of the temperature sensitivity of VWM eIF2B. Like the WT complex, its activity was not affected by temperatures up to 44°C. Our data agree with those of Richardson et al. (29), who also found no evidence for thermosensitivity of yeast eIF2B complexes containing VWM mutant subunits. The link between VWM and pyrexia thus appears more complex than a simple model where eIF2B complexes containing VWM mutant subunits are thermosensitive: perhaps the already decreased eIF2B activity in brain tissue of VWM patients is further reduced due to the increased phosphorylation of eIF2 that occurs during pyrexia (reviewed in reference 32) or after traumatic brain injury (26). This may have marked effects either on total protein synthesis or, more likely, on the translation of specific mRNAs.

It is known from other studies that inhibition of eIF2B due to increased phosphorylation of its substrate eIF2 leads to upregulation of the translation of certain mRNAs, e.g., those for GCN4 in yeast (16) and ATF4 in mammals (13). eIF2 phosphorylation—and thus regulation of eIF2B activity—also appears to be important for the control of other transcription factors (15, 17, 33). As both proteins are transcriptional regulators, this effect could in principle affect the expression of multiple genes. Given that VWM mutations impair the activity of eIF2B, we asked whether expression of VWM mutant eIF2B had a similar effect. Using a reporter construct in which the ATF4 5' UTR was cloned upstream of the coding region for an HA-tagged version of EGFP, we showed that both the eIF2Bß point mutants do indeed enhance the expression of the reporter protein. Thus, one anticipates that the translation of mRNAs that are regulated in this way would be upregulated in VWM patients. Examples of such mRNAs are already known in mammals (e.g., ATF4), and others likely await discovery. If such mRNAs were expressed in a tissue-specific manner (e.g., in brain), this could explain why the phenotype of VWM is primarily neurological. Alternatively, it could be that overall protein synthesis in neuronal tissue is especially sensitive to perturbations in eIF2B activity.

Further progress requires cells (in particular, brain cells) that homozygously express VWM eIF2B, e.g., the generation of transgenic knock-in mice bearing VWM mutations. Work towards this goal is already under way.

 
This work was supported by the Wellcome Trust (grants 066330 and 067782).

We are grateful to David Ron for generously providing reagents.

 
* Corresponding author. Mailing address: Division of Molecular Physiology, Faculty of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom. Phone: 44 1382 344919. Fax: 44 1382 345507. E-mail: c.g.proud{at}dundee.ac.uk.

W.L. and X.W. should be considered joint first authors.

Top Abstract Introduction Materials and Methods Results Discussion References

 

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Molecular and Cellular Biology, April 2004, p. 3295-3306, Vol. 24, No. 8
0270-7306/04/$08.00+0     DOI: 10.1128/MCB.24.8.3295-3306.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

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