Review

Ribosomopathies: There’s strength in numbers

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Science  03 Nov 2017:
Vol. 358, Issue 6363, eaan2755
DOI: 10.1126/science.aan2755

Molecular mechanisms behind ribosomopathies

Ribosomopathies are t issuespecific disorders that result from mutations in ribosomal proteins or ribosome biogenesis factors. Such disorders include Diamond-Blackfan anemia, isolated congenital asplenia, and Treacher Collins syndrome. Mills and Green review the underlying mechanisms of tissue-specific defects in these and related disorders. Because ribosomes are central to all cellular life, it is puzzling why mutations in components of the ribosome disproportionately affect certain tissues. The authors suggest that ribosome homeostasis is an overarching and simplifying principle that governs the sensitivity of specific cells and tissue types to mutation in components of the translational machinery.

Science, this issue p. eaan2755

Structured Abstract

BACKGROUND

Ribosomopathies are a heterogeneous group of human disorders that are in some cases known, and in other cases suspected, to result from ribosome dysfunction. This group broadly comprises two categories: (i) disorders caused by single-copy mutations in specific ribosomal proteins, and (ii) disorders associated with defects in ribosome biogenesis factors. The phenotypic patterns among different ribosomopathies in both categories are divergent but do tend to share some overlapping features. These include effects on bone marrow–derived cell lineages and skeletal tissues. These common tissue specificities of the different ribosomopathies are challenging to reconcile with the ubiquitous requirement for ribosomes in all cells.

ADVANCES

Several models have been advanced to explain how the dysfunction of the protein synthesis machinery is so variably expressed at the phenotypic level. An increasing number of studies in models of distinct ribosomopathies have revealed that “ribosomal stress” signals converge on the p53 signaling pathway in affected cells and tissues. In these models, a key consequence of ribosome dysfunction is cell- and tissue type–restricted activation of p53-dependent cell cycle arrest and apoptosis. However, the specific translational events upstream of p53 activation that lead to some cells being affected, with others being spared, are unknown.

We review evidence relating to two hypotheses that have been proposed to explain such tissue-specific effects of ribosome dysfunction. One hypothesis is that ribosome dysfunction (or deficiency) can affect global and messenger RNA (mRNA)–specific translational control, and that certain specific cells or tissues may be more vulnerable to ribosome dysfunction. A critical feature of this view is that mRNAs are variably dependent on cellular ribosome concentration, with more poorly initiated mRNAs being typically more sensitive to perturbations in ribosome concentration or function. Several recent studies suggest that the sensitivities of certain tissues to ribosomopathies, including reticuloctyes and platelets, may be related to differences in core processes of translation in these cells related to ribosome recycling and rescue. Perturbations in these processes will have a great impact on ribosome homeostasis and thus on broad aspects of gene expression. Related studies in the brain have revealed disease phenotypes in genetic backgrounds with deficiencies in ribosome rescue and in a specific neuronal transfer RNA. Together, these molecular insights provide a new perspective on ribosomopathies and their tissue specificities, while also raising a number of important questions to pursue.

The other hypothesis is that ribosomes from different tissues may have different compositions of core or more loosely associated proteins and posttranslational modifications, and that this heterogeneity could be critical to the translation of specific mRNAs. This is referred to as the “specialized” ribosome hypothesis. We argue that while such heterogeneity in ribosome composition likely exists in different tissues, such complex explanations may not be needed to explain the differences in gene expression that result from losses of specific ribosomal proteins. It is simpler to hypothesize that differences in mRNA-specific rates of initiation and changes in ribosome concentration can adequately explain much (if not all) of the diversity of gene expression changes in different tissues as a result of ribosomal mutations.

OUTLOOK

A cohesive mechanistic model connecting dysfunction of the ribosome to the specific phenotypic consequences observed in ribosomopathies remains a challenging goal. For example, it is inherently difficult to assess the function of particular ribosomes in a cell, and thus to differentiate among various models to explain the impacts of ribosome deficiencies on gene expression. Further biochemical analyses of the fundamental processes underlying the cellular response to protein synthesis dysfunction, refinements in cellular and animal models of ribosomopathies, and greater dialogue between clinical and basic scientists will all be important to extend our current understanding.

Ribosome concentration drives mRNA-specific effects on translation.

The translation rate varies as a function of cellular ribosome concentration and mRNA-specific initiation rates (heat map, left); a scatterplot model of ribosome footprinting data (right) shows how ribosome deficiency would be predicted to have varying effects on different mRNAs. The black, gray, and orange boxes define groups of mRNAs of similar initiation efficiencies as they respond to changes in ribosome concentration (as represented by the same colors at right).

Abstract

Ribosomopathies are a group of human disorders most commonly caused by ribosomal protein haploinsufficiency or defects in ribosome biogenesis. These conditions manifest themselves as physiological defects in specific cell and tissue types. We review current molecular models to explain ribosomopathies and attempt to reconcile the tissue specificity of these disorders with the ubiquitous requirement for ribosomes in all cells. Ribosomopathies as a group are diverse in their origins and clinical manifestations; we use the well-described Diamond-Blackfan anemia (DBA) as a specific example to highlight some common features. We discuss ribosome homeostasis as an overarching principle that governs the sensitivity of specific cells and tissue types to ribosomal protein mutations. Mathematical models and experimental insights rationalize how even subtle shifts in the availability of ribosomes, such as those created by ribosome haploinsufficiency, can drive messenger RNA–specific effects on protein expression. We discuss recently identified roles played by ribosome rescue and recycling factors in regulating ribosome homeostasis.

Ribosomopathies are inherited or sporadic disorders caused by haploinsufficiency of genes encoding key factors in ribosome biogenesis or ribosome structural proteins (1). Such mutations often lead to tissue-specific developmental phenotypes, and the mechanisms underlying such tissue specificity have drawn considerable attention in light of the ubiquitous requirement for ribosomes in all cells. The list of conditions thought to involve or to result from “ribosomal stress” is extensive and varied. Examples include Diamond-Blackfan anemia (DBA) (2), Shwachman-Diamond syndrome (3), Treacher Collins syndrome (4), chromosome 5q syndrome (5), North American Indian childhood cirrhosis (6), and isolated congenital asplenia (7). These conditions constitute a heterogeneous group of clinical phenotypes that are linked by their common root in ribosomal dysfunction. The variability in clinical features associated with these conditions has been reviewed (1, 8).

Here, we focus on DBA as a specific example of a condition in which ribosome dysfunction clearly plays a critical role in causing a phenotype. Approximately 60% of cases of DBA are caused by heterozygous mutations in one of 12 ribosomal proteins (RPs): uL5, eL15, uL24, eL31, eL42, uL18, eS7, eS10, eS17, eS19, eS24, or eS26 (9). As would be expected, numerous studies in human cells and model systems have found that RP gene mutations lead to defects in ribosome assembly and reduce cellular ribosome abundance. In most cases, mutations in loci encoding RPs reduce transcription from the affected allele (allele silencing), and this typically results in reduced levels of the affected protein. However, increased transcription from the remaining wild-type allele (i.e., allelic compensation) can restore normal or near-normal levels of the affected RP in some instances. Such allelic compensation may provide one possible mechanism for the noted incomplete penetrance of these disorders. In some cases, mutated RPs may be assembled into ribosome particles, leading to impaired translational fidelity and the possibility of dominant negative effects. These effects can also be directly linked to the phenotypic consequences of RP mutations.

In certain model systems, such as Drosophila melanogaster, reduced overall protein synthesis has been shown to be a clear, cell-autonomous driver of the effects of >60 distinct RP loci mutations that all lead to a recognizable common pattern of phenotypes (10). Referred to as the minute syndrome, dominant RP mutations in flies cause developmental delay, small body size, and thin bristles. This phenotype results from the relatively high protein synthesis requirements of developing Drosophila embryos and, in particular, the rapidly proliferating cells that give rise to each bristle organ. Only a single non-RP minute loci has been identified and it encodes eIF2-α, a key translational initiation factor, providing additional evidence for a direct role of diminished protein synthesis in causing the minute phenotype (10).

In mammals, it is likely that the pathogenic effects of RP mutations are similarly shaped by a combination of mechanisms. In the case of DBA, for example, despite the presence of a mutated RP allele in all cells, the resulting clinical manifestations are typically limited to impairments in erythropoiesis and skeletal development. Across and even among kindreds, these tissue-specific effects occur with incomplete penetrance and a high degree of variable expressivity (including possible lethality) (11). RP mutations in mice yield similar diversity in physiological outcome (12). In seeming contrast, mutations in the RP uS2 that lead to human congenital asplenia have been noted to be fully penetrant, at least in the few kindreds reported thus far (7). It is possible that, as with DBA, the phenotypic variance among different kindreds with uS2 mutations will expand as more families with uS2 mutations are discovered. Indeed, the incomplete penetrance and variable expressivity of most RP mutations suggests an important contribution of modifier loci to RP mutant phenotypes. Together, these data underscore the difficulty of understanding the cause(s) of ribosomal mutant phenotypes.

Although these many syndromes genetically implicate ribosomes and translation as critical, the mechanism(s) through which these mutations lead to disease manifestations remain a matter of debate. As might be anticipated, a majority of studies of RP mutants have documented at least modest reductions in overall protein synthesis (13). Thus, one obvious possibility is that impaired translation of global or specific mRNAs in certain tissues drives the specific ribosomopathy phenotype (8, 1417). Alternatively, the perturbed activity of “specialized” ribosomes, or ribosomes of heterogeneous structural composition within cells or across tissues, has also been proposed to be critical to the manifestations of RP mutant phenotypes (18). Other studies have suggested that the effects of RP mutations occur independently of effects on protein synthesis per se, and are instead attributable to aberrant p53 activation triggered by either an imbalance of ribosomal subunits or excess free RPs in the cytosol (19). The loss of specific functions of a RP not directly related to its role in translation within the ribosome (i.e., extraribosomal functions) has also been proposed to be critical in mediating the effects of RP mutations (20).

Here, we discuss these broad, primary mechanisms that may account for the tissue-specific effects of RP mutations and how they are supported by current literature. In particular, we focus on p53-dependent cell cycle arrest, global translational dysfunction, and impaired action of “specialized” ribosomes. We emphasize that these categories are not mutually exclusive. Each model is reviewed with the goal of highlighting unanswered questions and areas of future research. The role of extraribosomal functions is mentioned only briefly because it has been reviewed thoroughly (20).

Lineage-specific p53-dependent cell cycle arrest

Stoichiometric imbalance of specific RPs in the cytosol can trigger p53 activation. Activation of p53 leads to cell cycle arrest and apoptosis (21). Unincorporated uL18 or uL5 directly binds and inhibits the E3 ubiquitin ligase protein mouse double minute 2 (Mdm2; HDM2 in humans), which constitutively degrades p53 in the cell (22, 23). The view that p53 activation is an important consequence of ribosome mutations is supported by the finding that mutations in Mdm2 that block the binding of uL18 or uL5 prevent p53-dependent erythropoietic dysfunction in the context of eS19 deficiency (24). Remarkably, deletion of TP53 rescues many of the tissue-specific phenotypes caused by RP mutations or by biogenesis factor mutations in general (2530). This has led to the prevalent view that the diverse tissue manifestations of RP mutations are a direct result of p53-dependent cell cycle arrest and apoptosis (Fig. 1). Although any cell with reduced levels of a particular RP would presumably have excess unincorporated uL18 or uL5, it has been proposed that particular cell lineages with high protein synthesis requirements are more sensitive to such derangements (31). Thus, p53 activation is a critical mediator of cellular dysfunction in the context of impaired ribosome production.

Fig. 1 A current model for tissue-specific phenotypes of ribosomal protein mutations.

A ribosomal protein (RP) mutation may lead to allele silencing and reduced transcriptional output. Subsequently, reduced RP levels may limit or perturb ribosome assembly, causing impaired ribosome biogenesis. Alternatively, allele silencing may cause increased transcription from a second allele that restores normal or near-normal levels of the affected RP transcript (allelic compensation). When ribosome biogenesis is impaired, free cytosolic L5 (uL5) or L11 (uL18) directly binds and inhibits the E3 ligase mouse double minute 2 protein (Mdm2; HDM2 in humans), which stabilizes p53 (TP53) signaling, cell cycle arrest, and apoptosis. In this model, cells that require higher levels of protein synthesis (orange incline) are more sensitive to impairments in ribosome biogenesis. Ub, ubiquitin.

However, the mechanism(s) underlying tissue-specific differences in sensitivity to RP mutations are not understood. One possibility is that different cell types have different thresholds for p53 activation in response to ubiquitous ribosomal stress (e.g., reduced RP levels in all cells). Alternatively, the majority of cells may adequately compensate for modestly reduced RP levels (32), and in certain tissues, failure of such compensatory mechanisms triggers p53 activation and arrest (13). Another prevalent view is that cells that require high levels of protein synthesis (and therefore ribosomes), such as erythroid progenitors, are more sensitive to modest changes in RP levels (Fig. 1) (31).

An argument against this latter view is that the broad heterogeneity of tissues affected by RP mutations is not well correlated with empirical determinations of tissue protein synthesis rates (3335). Experiments infusing radioactive amino acids into animals and analyzing uptake into protein revealed that, in addition to blood, the liver, gastrointestinal tract, muscle, and skin have the highest protein synthesis rates in the body. Yet most of these tissues are not classically affected by RP mutations, with some exceptions (27, 36). In addition to large protein synthesis requirements, other features of translational dysfunction must be involved in determining which cells are sensitive to RP mutations and the resulting aberrant p53 activation.

Other data also suggest that additional factors, together with p53, are important in determining the heterogeneous effects of RP mutations. For example, deletion of p53 in zebrafish models of DBA fails to rescue defects in erythropoiesis, which suggests that there are p53-independent effects of RP mutations (37, 38). In humans, deficiency of uL18 or uL5 causes defects in erythropoiesis (and DBA) (9); this finding suggests that other signatures besides excess cytosolic uL18 or uL5 are capable of triggering p53 activation in response to RP mutations. The observation that there are p53-dependent and p53-independent effects of RP haploinsufficiency implies a role for translational dysfunction in the pathogenesis of ribosomopathies, in addition to the well-documented effects of aberrant p53 activation.

Translational dysfunction: The specialized ribosome hypothesis

Ribosome assembly involves the orchestrated action of hundreds of different factors, resulting in the production of functioning ribosomal particles that, in mammals, contain 80 RPs and four ribosomal RNAs (rRNAs) (39). However, the ultimate definition of what constitutes a ribosome versus what is merely associated with the ribosome depends on experimental conditions. A reasonable delineation of the core RPs includes those proteins that are required for activity (in some standard assay) and that are found associated with the ribosome (under a set of standard conditions) (40). We anticipate that the identification of noncore ribosome-associated proteins will ultimately reveal new and interesting modes of ribosome regulation (41).

Ribosome heterogeneity refers to the idea that within individual cells or across tissues, ribosomal composition varies over time or under different conditions. The “specialized” ribosome hypothesis refers to the idea that the translation of certain mRNAs requires (or is stimulated by) certain structural variations of the ribosome. The loss of such “specialized” ribosomes has been proposed to mediate the tissue specificity that results from deficiencies in some RPs such as eL38 and uS2 (7, 18) or ribosomal posttranslational modifications (42). Evidence supporting ribosome heterogeneity (and its regulation) is abundant in bacteria and yeast (43). Such ribosome variants have been reported to result from the incorporation of RP paralogs (44), posttranslational modifications (42, 4547), and ribosome-associated factors (41, 48, 49). Moreover, certain RPs may be variably associated with ribosomal complexes (50, 51). Many RPs appear to be differentially expressed across tissues (18), although such effects may be much more subtle than originally thought (52).

Although such heterogeneity is intriguing, the possibility that tissue-specific consequences of RP haploinsufficiency are mediated by loss or dysfunction of such ribosome variants also requires appraisal. In the case of mice harboring a mutated copy of the eL38 gene (called Tail-short or Ts mutants because of their characteristically short tails), the animals display reduced body size, delayed development, skeletal malformations, and impaired fetal erythropoiesis (12, 5356). Complicating the analyses of Ts mice, their phenotypes are seen to vary considerably, even among inbred animals, ranging from silent to lethal (12). Such variability in features appears to be typical for RP mutant phenotypes in humans, mice, and Drosophila, which all exhibit marked incomplete penetrance and broadly variable expressivity (10, 11, 13).

A key observation made about Ts mice is that eL38 haploinsufficiency is associated with relatively selective impairment in translation of Hox mRNAs in mouse embryos (18, 57). One possibility is that eL38 is found on all ribosomes (in all cells) but is specifically required for the translation of Hox mRNAs. This interpretation predicts that when eL38 levels are reduced (as in Ts mice), general translation will be unaffected while Hox translation will be impaired. HOXA5 protein levels were unaffected in mice with mutations in other RPs (eL29, eL24, eS19, or uS20), although these mutations do cause a range of skeletal malformations (18). Like other ribosome protein mutant phenotypes, eL38 mutant mice, broadly speaking, exhibit a spectrum of skeletal and hematopoietic defects (11, 5860) supporting a more generalized mechanism that accounts for the effects of L38 mutations on Hox translation rather than specialized dependence on eL38 function. Thus, although the heterogeneity of a molecular machine as complex as the ribosome will be adapted by the cell for complex regulation, it is not clear that such explanations are required to explain the phenotypes of the Ts mouse strains. Given the variable penetrance of these mutations and the strong dependence of RP mutant phenotypes on genetic background, it will be important to analyze large numbers of inbred mice harboring mutations in different RPs to look systematically for commonalities and differences in their phenotypes.

Translational dysfunction: The ribosome concentration hypothesis

There is broad agreement that reduced RP expression leads to aberrant ribosome assembly and reduced ribosome levels. In most cases, global protein synthesis is modestly reduced, raising a critical question: How is the translation of specific mRNAs perturbed by relatively modest changes in ribosome availability? An illustrative example comes from the discovery that inherited mutations in GATA1—an important erythroid transcription factor rather than a RP—can cause DBA (14, 61). This discovery led to a critical experiment that helped to shed light on how RP haploinsufficiency could lead to DBA: Engineered increases in GATA1 protein levels were shown to overcome the effects of heterozygous RP mutations in DBA patient cells (14). The authors argued that the GATA1 mRNA is poorly translated as the result of a highly structured 5′ untranslated region (5′UTR), and so GATA1 protein production is particularly sensitive to the reduced ribosome concentration that results from RP mutations. Together, these observations suggest that reduced RP levels in DBA cells exert a pathogenic effect by impairing the translation of GATA1 (and likely that of other similarly structured mRNAs).

Quantitative changes in ribosome availability have long been predicted to drive mRNA-specific effects on protein synthesis because of the nonlinear relationship between initiation rate and available ribosome concentration (62) (Fig. 2). This classic view indicates that the effective protein synthesis rate for each mRNA in the cell is proportional to the product mRki (where m is the individual mRNA expression level, R is the cellular ribosome concentration, and ki is an mRNA-specific rate constant) and another term that involves the specific mRNA length and density of ribosomes over the transcript. Specifically, the relationship between protein synthesis rate and available ribosome concentration can be described by the equationEmbedded Image(62), where Q is the protein synthesis rate, ke is the termination rate, and L is the number of codons occupied by one ribosome. Figure 2 shows the physiologic range of Q according to estimates of based on mass spectrometry data (63), with the range of ki estimated on the basis of the empiric range defined in a reporter screen (64), L set to 10 codons (the average length of a ribosome footprint), and ke arbitrarily set to 1.0.

Fig. 2 Ribosome concentration drives mRNA-specific translation.

(A) Heat map showing the protein synthesis rate per mRNA (see text for details). The effects of reduced ribosome availability on three different mRNA populations are shown: (i) Reduced ribosome availability can increase translational output because, for mRNAs with very high initiation rates, inhibitory ribosome crowding during elongation is relieved by reduced ribosome density. (ii) The translation of mRNAs with modest initiation rates may undergo little change with reduced ribosome availability. (iii) The translation of certain mRNAs with low initiation rates ki, such as those with highly structured 5′UTRs, uORFs, IRES elements, multiple upstream start sites, or poor initiation contexts, will likely be impaired by reduced ribosome availability. RPH, RP haploinsufficiency. (B) The effects of changing ribosome concentrations on translational output of different mRNAs with varying ki values, or a dominant negative effect of ribosomes containing mutated RPs.

Analysis of this equation reveals that translation of mRNAs with high initiation rates (e.g., mRNAs encoding RPs or hemoglobin) can be efficient even at low concentrations of ribosomes. Conversely, this same analysis reveals that mRNAs with low initiation rates (e.g., those encoding hormones, transcription factors, certain Hox proteins, and GATA1) will be poor substrates for translation when ribosome availability is limited. Thus, the sensitivity of specific cells to RP mutations could result from selective reduction in the translation of particular mRNAs with inherently low translational efficiencies (15).

Global analyses of gene expression have supported this model of translation (6567). These analyses highlight the fact that as transcripts become filled with ribosomes, reaching their theoretical maximum ribosome occupancy, further increases in ribosome availability do not lead to more translation, but rather to less (68). On the basis of such models, optimal translation efficiency is expected to occur at about one-half of maximal ribosome density, as in traffic flow, because ribosome “crowding” interferes with translation elongation (Fig. 2A, blue mRNAs). In yeast under active growing conditions, experimental data show that the average ribosome density on the typical mRNA is only about one-sixth of its theoretical maximal value (65), validating the view that translation initiation is rate-limiting under these standard conditions. From such modeling, it is apparent that changes in cellular ribosome concentration will increase or decrease the expression of specific proteins, depending on the mRNA-specific translation initiation rate ki. Thus, biologic contexts in which cellular ribosome availability undergoes changes may play an underappreciated role in driving cellular translational programs (69).

How likely is it that there are substantial variations in total ribosome content in different cells? Several analyses of RP expression levels from global mass spectrometry data have suggested that total tissue ribosome abundance may vary by a factor of 3 to 10 among different tissues (52, 63). A similar magnitude of variation in tissue-specific protein synthesis has been documented (3335) and is supported by a large-scale model of tissue-specific protein synthesis in animals (70). This model found that tissue ribosome concentrations would need to vary over a similar range (~600 to ~4700 nM) among different tissues in order to drive the variation in tissue-specific fractional protein synthesis rates determined by experimental data (70). Even though such analyses are limited to crude estimates of total ribosome abundance rather than the available ribosome concentration (which is more challenging to measure experimentally), they help to define a potential range of effective ribosome concentrations in vivo. One recent study found that diurnal changes in liver size were explained by a nuclear mechanism that modulates ribosome production, which suggests that ribosome concentration may vary markedly under different conditions (71). mRNA-specific features such as 5′UTR structure, upstream open reading frames (uORFs), and internal ribosome entry site (IRES) elements that influence the translation initiation rate can, in principle, exert a strong influence on specific gene expression as a consequence of even modest changes in ribosome concentration (69, 72, 73). Moreover, the translation of mRNAs with low initiation rates is likely to be most negatively affected by changes in ribosome concentration (Fig. 2A, orange mRNAs).

These ideas, in turn, may help to explain why alternative (i.e., inefficient) modes of translation initiation are often enhanced under conditions where overall translation is reduced, such as hypoxia (74), nutrient deprivation (75), and meiosis (76, 77). Under these conditions, the proportion of ribosomes engaged in translation is reduced and free ribosomes are therefore more abundant, disproportionately favoring the translation of specific mRNAs that are otherwise inefficiently translated (Fig. 2B, GATA1 and Hox mRNAs). As a corollary to this point, alternative start site usage is similarly increased during tumorigenesis (78), a condition characterized by prodigious ribosome synthesis. Given that the translation of specific mRNAs is expected to vary in response to shifts in cellular ribosome concentration, these results imply that regulators of ribosome availability could potentially have a large impact on mRNA-specific translational control.

Ribosome homeostasis is determined by synthesis, demand, and the translation cycle

The high energetic cost of ribosome synthesis—along with the need to produce coordinate amounts of RPs, processed rRNAs, and critical assembly factors—depends on the careful regulation of ribosome biogenesis (79). Whereas such mechanisms specify the total amount of ribosomes synthesized in a cell, ribosome homeostasis refers to the set of dynamic processes that govern the actual availability of cellular ribosomes to engage in protein synthesis (Fig. 3). Here, we focus on mechanisms that are involved in regulating ribosome availability in the cell. Processes involved in ribosome homeostasis are crucial during the synthesis of cellular proteins (including during the translation of noncoding RNAs) in which the bulk of cellular ribosomes are typically engaged (Fig. 3, orange arrows). Additionally, ribosomes that become stalled as a result of translation of problematic sequences must be “rescued” and returned to the available pool of ribosomes (Fig. 3, blue arrows). These dynamic processes are diverse and may act to maintain or constrain ribosome availability in the cell. Any circumstance in the cell that involves translation by ribosomes will necessarily draw on the cellular resources that affect ribosome homeostasis.

Fig. 3 Ribosome homeostasis and the translational cycle.

Ribosome homeostasis is maintained by ribosome synthesis (pink circuit), the normal translational cycle (orange circuit), and quality control processes (blue arrows) that retrieve or rescue translationally stalled ribosomes. During normal (i) and pervasive (ii) translation, ABCE1 and eRF1 separate 40S and 60S subunits, returning them to the available pool for translation. During nascent peptide–mediated ribosome pausing (iii), translation of rare codons or tRNA shortage (iv), or translation of truncated mRNAs (v), or after failure of ribosome recycling (vi), ribosomes must be rescued and returned to the available pool. This process usually involves the eRF1/3 homologs PELOTA/HBS1L as well as the canonical ribosome recycling factor ABCE1. (AAA)n, polyA tail; ncRNAs, noncoding RNAs.

During normal completion of protein synthesis, adenosine triphosphate–binding cassette subfamily E member 1 (ABCE1), working together with the canonical eukaryotic release factors 1 and 3, splits 80S ribosomes into 40S and 60S subunits, releasing them to the cytosol (80, 81). ABCE1 has an essential FeS cluster that is critically involved in movement within the ribosomal A-site region that drives subunit splitting (82). Because ABCE1 also binds to 48S “translation initiation” complexes after subunit splitting, it is thought to act as a crucial coordinator in eukaryotes among the processes of translation termination, recycling, and initiation (82). Depletion of ABCE1 in yeast and human cells is associated with the accumulation of unrecycled ribosomes in the 3′UTR, which may represent an important portion of total ribosomes (83, 84). These studies make clear that ABCE1 is a critical factor for maintaining ribosome homeostasis in the cell; their results complement modeling efforts that have arrived at similar conclusions about the likely critical role of ABCE1 in this process (69).

Additionally, during translation of mRNAs with problematic features, ribosomes may become stalled on rare codons (85), sticky nascent peptide motifs (86), stable mRNA structures (87), oxidized mRNAs (88), or truncated mRNAs (89). These circumstances, along with tRNA shortages (90), continued translation of histone mRNA degradation intermediates during mitosis (91), and unrecycled ribosomes, require the constant activity of quality control surveillance mechanisms to retrieve the stalled ribosomes. The primary surveillance system that is involved in these processes comprises the termination factor (eRF1/3) homologs PELOTA (DOM34 in yeast) and HBS1L (92). Together with ABCE1, these factors recycle or “rescue” ribosomes that become translationally stalled during the course of protein synthesis (i.e., not on normal stop codons). ABCE1 and PELOTA each exhibit ribosome splitting activity on their own, although this activity is most substantial when these proteins act together (80). Thus, this quality control system, together with the normal translation termination and recycling machinery, works continuously to maintain ribosome homeostasis.

Tissue-specific regulation of ribosome homeostasis

A recent study reported unusual regulation of the regulators of ribosome availability in the erythroid lineage, where deleterious effects of RP mutations are often manifested. More specifically, ABCE1 levels selectively decline in a model of terminal erythropoiesis (84), which leads to a global defect in ribosome recycling consistent with the accumulation of unrecycled 3′UTR ribosomes in primary reticulocytes. Erythropoietin treatment of erythroid progenitors from mouse fetal liver leads to a similar phenomenon (93). Furthermore, PELOTA and its cofactor HBS1L are strongly induced during erythroid differentiation, and this expression is required to restore the unrecycled 3′UTR ribosomes to the available pool for translation (84). The spike in PELOTA expression during differentiation in a model system is precisely coincident with the expression of hemoglobin during this critical period, and after this period of transient PELOTA induction, levels of the protein fall to undetectable levels as differentiation proceeds. Although the cause of reduced ABCE1 levels in these tissues is not known, impaired FeS cluster biogenesis during mitochondrial breakdown in erythropoiesis may be involved (9497).

These observations in erythroid differentiation are consistent with the previously documented synthetic interactions of the PELOTA homolog DOM34 and various RP genes in yeast (98). There, loss of PELOTA is thought to exacerbate the ribosome shortage caused by RP mutations. The idea that PELOTA activity is critical to ribosome homeostasis and the production of key proteins during differentiation is supported by the observation that transgenic overexpression of PELOTA (overwhelming the transient spike in expression caused by natural induction and subsequent decline) rescues the recycling defect associated with ABCE1 depletion, whereas combined loss of ABCE1 and PELOTA lead to reduced hemoglobin expression (84). Further, increased expression of PELOTA/HBS1L rescued the observed defects in hemoglobin expression that resulted from depletion of eS19, a model for DBA. These data are reminiscent of the effect of PELOTA DOM34 overexpression in yeast, which rescues growth defects associated with ribosomal mutations (98). These data argue that modulation of PELOTA/HBS1L expression levels could help to mitigate the impact of ribosome haploinsufficiency by increasing the proportion available for translation.

Curiously, the HBS1L-MYB region of the human genome is a quantitative trait locus (QTL) harboring many genomic variants that are strongly associated with multiple hematologic traits (99, 100). The role of MYB (a known hematopoietic transcription factor) in influencing these associations is well documented (101); in light of the molecular studies highlighting the role of PELOTA/HBS1L in erythroid cells and platelets (84), it remains an exciting possibility that these variants hint at an additional role for HBS1L (and ribosome rescue) in hematopoietic tissue homeostasis (102).

Critical contributions to ribosome availability in other systems

Recently, GTPBP2—a distinct binding partner of PELOTA that shares homology with eRF3 and HBS1L—was found to be required to relieve ribosome stalling triggered by a specific tRNA shortage in the brains of Arg-tRNA mutant mice (90). Mutation of GTPBP2 leads to lethal neurodegeneration in mice (90), and related findings were recently reported in an associated human neuronal disease (103). These data reveal an important role for ribosome rescue in brain tissue. The specific requirement for GTPBP2 (rather than HBS1L) in the brain argues for nonredundant functions for PELOTA binding partners. The molecular features of ribosome-mRNA complexes that are differentially recognized by GTPBP2 or HBS1L are not known. Whether the fate of stalled ribosomes (and mRNAs) resolved by PELOTA-GTPBP2 or PELOTA-HBS1L differs is also not known, although PELOTA-HBS1L is known to be involved in the degradation of certain messages in yeast (104), mammalian cells (91), and platelets (105).

Another area of biology where ribosome rescue is emerging as an important process is during viral infection, where a majority of the cellular ribosome supply is engaged in producing viral proteins. Analysis of naturally occurring single-nucleotide polymorphisms in the PELOTA locus led to the identification of a critical role for PELOTA during viral infection in plants (106, 107). In this setting, PELOTA may be needed by the virus to maintain high levels of ribosomes to support viral protein synthesis. In contrast, during HIV replication, the interferon-induced host antiviral protein SLFN11 restricts viral replication by limiting access to the needed materials (in this case, tRNAs) for protein synthesis (108). Thus, it is easy to envision that future discoveries may disclose an even greater role for regulators of ribosome homeostasis, such as PELOTA, during states of increased ribosome demand.

A high demand for ribosomes may also be experienced in the mammalian epidermis, a rapidly proliferative tissue with high protein synthesis requirements. There, a conditional deletion of PELOTA in mouse epidermis leads to lethal skin barrier defects and (somewhat paradoxically) to hyperplasia and increased cellularity, although the mechanism underlying this transformation is unclear (109). Such a result is reminiscent of the predisposition to cancer observed in patients with congenital RP mutations (110, 111). New data support the idea that mutant RP alleles (either when inherited or somatically acquired) may lead to selection for compensatory mutations, such as those in p53, which then confer an increased risk for cancer (112, 113). Somatically acquired RP mutations are known to be extremely common in human cancer and are indeed frequently associated with p53 mutations (114, 115). It seems clear that conditions that perturb the balance of ribosome supply and demand—inherited, sporadic, or environmental—impose a substantial burden on cells to maintain cellular ribosome availability using multiple diverse mechanisms, including induction of ribosome rescue factors, acquisition of p53 mutations, or others not yet discovered.

Conclusions

The cellular consequences of inherited RP mutations primarily include translational dysfunction (both reduced global synthesis and impaired translation of specific mRNAs) and selective activation of p53-dependent cell cycle arrest. The tissue-specific effects of RP mutations are not likely to be broadly explained by the loss of specialized ribosomes, nor are they simply explained by increased translation rates in affected tissues. We argue instead that the tissue specificity resulting from inherited RP mutations may, at least in part, be governed by tissue-specific differences in the effectiveness of compensatory processes. Such processes likely include allelic compensation (which may restore normal or near-normal levels of the affected RP in certain tissues) or increased reliance on ribosome quality control processes (which may help to restore the available ribosome supply and avoid catastrophic ribosome shortage) (Fig. 4). In our view, p53 activation is likely to arise after such compensatory processes are overwhelmed, signaling irreversible dyshomeostasis and triggering cell cycle arrest and eventual apoptosis. One critical link in need of further exploration is how dysfunctional translation per se leads to activation of p53. Does this occur through the sensing of global ribosome levels, or because certain key mRNAs fail to be translated (e.g., GATA1 in hematopoietic cells)? We propose that the role of general translation factors such as ABCE1, and ribosome rescue proteins such as PELOTA and HBS1L, in calibrating ribosome availability is a critical link between disorders of ribosome supply and cellular sensitivities to RP mutations.

Fig. 4 A revised model for tissue-specific phenotypes of RP mutations.

RP mutations may cause allele silencing (leading to subunit imbalance), impaired ribosome biogenesis (leading to ribosome shortage), or defective ribosomes (if a mutant RP is assembled into a ribosome). Together such processes cause translational dysfunction, which involves reduced (or normal) global protein synthesis levels and failure to translate certain key mRNAs. In this model, the impact (or “weight”) of such dysfunction is balanced in most cells by compensatory processes (pink weights) such as allelic compensation and ribosome rescue (unaffected cells, left). In some cells, such balancing mechanisms are overwhelmed, signaling irreversible dyshomeostasis, p53 activation, and cell cycle arrest (affected cells, right).

References and Notes

  1. Acknowledgments: We thank J. Wangen for helpful comments and discussion. We apologize to those whose work could not be cited because of space limitations.
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