Ribosomopathies: how a common root can cause a tree of pathologies

Abstract

Defects in ribosome biogenesis are associated with a group of diseases called the ribosomopathies, of which Diamond-Blackfan anemia (DBA) is the most studied. Ribosomes are composed of ribosomal proteins (RPs) and ribosomal RNA (rRNA). RPs and multiple other factors are necessary for the processing of pre-rRNA, the assembly of ribosomal subunits, their export to the cytoplasm and for the final assembly of subunits into a ribosome. Haploinsufficiency of certain RPs causes DBA, whereas mutations in other factors cause various other ribosomopathies. Despite the general nature of their underlying defects, the clinical manifestations of ribosomopathies differ. In DBA, for example, red blood cell pathology is especially evident. In addition, individuals with DBA often have malformations of limbs, the face and various organs, and also have an increased risk of cancer. Common features shared among human DBA and animal models have emerged, such as small body size, eye defects, duplication or overgrowth of ectoderm-derived structures, and hematopoietic defects. Phenotypes of ribosomopathies are mediated both by p53-dependent and -independent pathways. The current challenge is to identify differences in response to ribosomal stress that lead to specific tissue defects in various ribosomopathies. Here, we review recent findings in this field, with a particular focus on animal models, and discuss how, in some cases, the different phenotypes of ribosomopathies might arise from differences in the spatiotemporal expression of the affected genes.

Keywords: Diamond-Blackfan anemia; Ribosomal protein; Ribosome biogenesis; Ribosomopathy; p53; ΔNp63.

Fig. 1.

Duplicated digits and phalanges in mice heterozygous for Rpl24. Skeletal stain of newborn forelimbs (upper) and hindlimbs (lower). Mice heterozygous for a mutation in Rpl24 (Bst/+ phenotype) show preaxial polydactyly (0) and triphalangy of the first digit (1). Figure reproduced with permission (Oliver et al., 2004).

Fig. 2.

A simplified schematic of ribosome biogenesis in human cells. (A) 18S, 5.8S and 28S rRNAs are transcribed by Pol1 in the nucleolus as segments of a long precursor pre-rRNA, which also includes two externally transcribed spacers 5′ETS and 3′ETS and two internally transcribed spacers, ITS1 and ITS2 (B; Box 1). 5S rRNA is transcribed independently by PolIII in the nucleus. (B) Concomitant with transcription, the pre-rRNA assembles with accessory factors and a subset of ribosomal proteins (RPs: RPSs and RPLs). This facilitates the formation of a secondary structure necessary for the correct folding, modification and cleavage of pre-rRNA. (C) After removal of the 5′ETS and cleavage in the ITS1 site, pre-40S (which contains the 20S precursor of 18S rRNA) and pre-60S subunits are formed and continue to mature. 5S rRNA incorporates into pre-60S subunit. Subunits are then exported to the cytoplasm. (D) Once in the cytoplasm, small and large subunits undergo final maturation, which involves the removal of remaining accessory factors and incorporation of missing RPs. (E) A functional ribosome forms after transcribed mRNA binds to the 40S subunit, which triggers association of the 60S subunit with this complex. More than 200 accessory factors, which include helicases, nucleases, small nucleolar RNAs (snoRNAs; Box 1), chaperones and transporters, temporally associate with the maturing ribosomal subunits at various steps. In human cells, pre-rRNA processing is differentially affected by deficiency of various RPs. For example, deficiency of RPS24 or RPS7 prevents formation of the 20S precursor of 18S rRNA, whereas deficiency of RPS19 or RPS17 prevents conversion of the 20S precursor to a mature 18S rRNA.

Fig. 3.

Defects in ribosomal biogenesis activate p53 and other stress-response mechanisms. A schematic showing pre-rRNA transcription, and assembly of accessory factors and RPs on the nascent pre-rRNA. (A) Recent studies have suggested that problems with pre-rRNA processing can affect DNA transcription, leading to the activation of ATR-ATM-Chk1/2 signaling (which is responsible for the replication-stress and DNA-damage checkpoints) and p53 upregulation. In addition, deoxynucleoside triphosphate (dNTP) imbalance caused by RP deficiency might interfere with transcription and replication and contribute to ATR-ATM activation. (B) Problems with pre-RNA processing compromise ribosome biogenesis and lead to nucleolar disruption. The nucleolus is involved in maintaining low p53 levels by exporting it for degradation. Various stressors disrupt nucleolar organization, compromising p53 export and leading to p53 accumulation in the nucleus. Nucleolar disruption might also lead to the release of factors that activate p53 or cause cell cycle arrest by p53-independent mechanisms. (C) An alternative pathway of p53 activation is through free RPs that, in complex with 5S RNA, bind the p53 negative regulator MDM2, releasing p53 from its control. (D) Upregulation of MYC and RAS pro-survival factors in DBA patients and in animal models suggests that they might activate p14ARF, which, in complex with 5S RNA, also negatively regulates MDM2. Hypothetically, additional not-yet-identified nucleolar factors might also negatively interact with MDM2 and contribute to p53 upregulation. (E) p53 might also be activated by secondary changes in RP-deficient cells, such as increased levels of ROS or decreased levels of ATP, which activates AMPK, which, in turn, activates p53. p53 then translocates to the nucleus. (F) p53 activation leads to cell cycle arrest and to the induction of downstream pathways ranging from cellular repair to apoptotic mechanisms. (G) A p53-independent response might also originate from the cytoplasm owing to a decreased number and altered activity of ribosomes, which also can lead to cell cycle arrest. For example, decreased levels of cyclins or PIM1 caused by RP deficiency might inhibit cell cycle progression. Abbreviations: AMPK, AMP-activated protein kinase; ATM, ataxia telangiectasia mutated; ATR, ataxia telangiectasia and Rad3 related; Chk1/2, checkpoint kinase 1/2; MDM2, MDM2 oncogene, E3 ubiquitin protein ligase; MYC, avian myelocytomatosis viral oncogene homolog; p14ARF, alternate reading frame protein product of the CDKN2A, cyclin-dependent kinase inhibitor 2A; PIM, pim-1 oncogene; PolI, RNA polymerase I; RAS, rat sarcoma viral oncogene homolog; ROS, reactive oxygen species; 5S, rRNA. See Fig. 2 for a key.

Fig. 4.

Origin of developmental defects in RP-deficient zebrafish embryos. (A) ΔNp63 expression (black arrow, upper panels) in early zebrafish embryos defines the non-neural ectoderm field and overlaps with a marker of non-neural ectoderm, gata2 (black arrow, lower panels). In Rps19-deficient zebrafish [in which rps19 expression has been knocked down with a morpholino oligonucleotide (MO)], this field is expanded (right upper and lower panels). Staining with a probe for goosecoid (gsc), necessary for the formation of the dorsoventral axis of the embryo, marks the dorsal side (red arrow). Arrowheads point to the neural field. This is an in situ hybridization image at gastrulation, 80% epiboly (Box 1). Dorsal is to the right. wt, wild type. (B) Expression of pax2, which has a key role in the development of the CNS, eyes, urogenital tract and kidneys, is altered in Rps19-deficient zebrafish embryos. Arrows and arrowheads point, respectively, to forebrain and eye fields, which are contracted in Rps19-deficient embryos. This is an in situ hybridization image at 16 hpf. (C) Schematics showing how expansion of non-neural ectoderm in early zebrafish embryos leads to the contraction of the neural field, especially the area of the forebrain and eye. This research was originally published in Blood (Danilova et al., 2008b). ^© American Society of Hematology.