A system for naming ribosomal proteins is described that the authors intend to use in the future. They urge others to adopt it. The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as 'new system' names.

SUMMARY Blood cell formation is classically thought to occur through a hierarchical differentiation process, although recent studies have shown that lineage commitment may occur earlier in hematopoietic stem and progenitor cells (HSPCs). The relevance to human blood diseases and the underlying regulation of these refined models remain poorly understood. By studying a genetic blood disorder, Diamond-Blackfan anemia (DBA), where the majority of mutations affect ribosomal proteins and the erythroid lineage is selectively perturbed, we are able to gain mechanistic insight into how lineage commitment is programmed normally and disrupted in disease. We show that in DBA, the pool of available ribosomes is limited, while ribosome composition remains constant. Surprisingly, this global reduction in ribosome levels more profoundly alters translation of a select subset of transcripts. We show how the reduced translation of select transcripts in HSPCs can impair erythroid lineage commitment, illuminating a regulatory role for ribosome levels in cellular differentiation.

The ubiquitin-related protein SUMO-1 is covalently attached to proteins by SUMO-1 ligases. We have performed a proteome-wide analysis of sumoylated substrate proteins in yeast. Employing the powerful affinity purification of Protein A-Smt3 (Smt3 is the yeast homologue of SUMO-1) from yeast lysates in combination with tandem liquid chromatography mass spectrometry, we have isolated potential Smt3-carrying substrate proteins involved in DNA replication and repair, chromatin remodeling, transcription activation, Pol-I, Pol-II, and Pol-III transcription, 5 pre-mRNA capping, 3 pre-mRNA processing, proteasome function, and tubulin folding. Employing tandem affinity purifications or a rapid biochemical assay referred to as "SUMO fingerprint," we showed that several subunits of RNA polymerases I, II, and III, members of the transcription repression and chromatin remodeling machineries previously not known to be sumoylated, are modified by SUMO-1. Thus, the identification of a broad range of SUMO-1 substrate proteins is expected to lead to further insight into the regulatory aspects of sumoylation.The ubiquitin-like protein SUMO-1 (Smt3 in yeast) is a 100-residue protein that is conjugated to substrate proteins by sequential thioester transfer reactions via specific E1 1 activating enzymes (Uba2/Aos1) and E2 (Ubc9) conjugating enzyme (1, 2). SUMO is conjugated to specific lysine residues on substrate proteins typically exhibiting consensus sites hKxE, where h is a hydrophobic amino acid (3, 4). Unlike ubiquitylation, sumoylation of target proteins does not lead to proteasomal degradation but can affect diverse functions of the protein, such as subcellular localization, protein/DNA interaction, or enzymatic activity (5, 6).Smt3 is highly conserved and essential in yeast. In addition, the conjugating and deconjugating machinery are conserved from yeast to humans and perform essential functions in yeast. The only yeast proteins known to be modified by Smt3 are the nonessential septins involved in cytokinesis and the essential Pol30, Top2, and Pds5 (7-9). A growing number of proteins that are modified by SUMO-1 in mammalian cells have been reported (6). Recent proteomic approaches in mammalian cells have identified new proteins that are subject to SUMO-1 and SUMO-2 modification (10 -12). The confirmation of sumoylation of target proteins in these approaches was limited by the need for protein specific antibodies.Previously, we have shown that the deconjugating enzyme Ulp1 is tethered to the nuclear pore channel via nuclear import receptors (13). The biological significance of such a tethering mechanism is poorly understood because of the lack of knowledge about its substrate proteins. Yeast has served as a powerful, rapid, genetic and in vivo biochemical model system to gain mechanistic insights into protein function in eukaryotes. Hence, we applied a proteomic approach in yeast to unravel the SUMO proteome. We have enriched sumoylated proteins from yeast cell lysates using the high affinity tag of Protein A (ProtA). In this...

Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation.

In genetic screens for ribosomal export mutants, we identified CFD1, NBP35 and NAR1 as factors involved in ribosome biogenesis. Notably, these components were recently reported to function in extramitochondrial iron-sulfur (Fe-S) cluster biosynthesis. In particular, Nar1 was implicated to generate the Fe-S clusters within Rli1, a potential substrate protein of unknown function. We tested whether the Fe-S protein Rli1 functions in ribosome formation. We report that rli1 mutants are impaired in prerRNA processing and defective in the export of both ribosomal subunits. In addition, Rli1p is associated with both pre-40S particles and mature 40S subunits, and with the eIF3 translation initiation factor complex. Our data reveal an unexpected link between ribosome biogenesis and the biosynthetic pathway of cytoplasmic Fe-S proteins.

Eukaryotic ribosome synthesis is a complex, energy-consuming process that takes place across the nucleolus, nucleoplasm and cytoplasm and requires more than 200 conserved assembly factors. Here, we discuss mechanisms by which the ribosome assembly and nucleocytoplasmic transport machineries collaborate to produce functional ribosomes. We also highlight recent cryo-EM studies that provided unprecedented snapshots of ribosomes during assembly and quality control.

In eukaryotic cells ribosomes are preassembled in the nucleus and exported to the cytoplasm where they undergo final maturation. This involves the release of trans-acting shuttling factors, transport factors, incorporation of the remaining ribosomal proteins and final rRNA processing steps. Recent work, especially on the large (60S) ribosomal subunit, has made it abundantly clear that the 60S subunit is exported from the nucleus in a functionally inactive state. Its arrival in the cytoplasm triggers events that that render it translationally competent. Here we focus on these cytoplasmic maturation events and speculate about why eukaryotic cells have evolved such an elaborate pathway of maturation. The biogenesis of ribosomal subunits -"state of the art"In all living cells, the ribosome is responsible for the final step of decoding genetic information into proteins. This universal "translating apparatus" comprises two subunits, each of which is a complex assemblage of RNA and proteins (Box 1). The two subunits display a distinct division of labour: the small 40S subunit (30S in prokaryotes) is responsible for decoding whereas the large 60S subunit (50S in prokaryotes) carries out the chemistry of polypeptide synthesis. Although structural analysis of prokaryotic ribosomes is providing detailed molecular insights into the mechanisms of ribosome function 1-3 , our knowledge of the in vivo assembly of ribosomes remains rudimentary. How do cells assemble such an intricate machine and ensure that it functions faithfully in the critical role of decoding a cell's genome? In this review we elaborate on the cytoplasmic maturation events that generate fully functional ribosomes and discuss why eukaryotic cells might have evolved these additional steps. BOX 1 Prokaryotic and eukaryotic ribosome biogenesisRibosomes are universally constructed from two subunits. In E. coli, the large (50S) subunit contains two rRNAs (23S and 5S) and 34 r-proteins and the small (30S) subunit contains one rRNA (16S) and 21 r-proteins. Eukaryotic ribosomes are more complex: the large (60S) subunit contains three rRNAs (25S, 5.8S, 5S) and 49 r-proteins whereas the small (40S) subunit contains a single rRNA (18S) and 33 r-proteins.

The assembly of large multimeric complexes in the crowded cytoplasm is challenging. Here we reveal a mechanism that ensures accurate production of the yeast proteasome, involving ribosome pausing and cotranslational assembly of Rpt1 and Rpt2. Interaction of nascent Rpt1 and Rpt2 then lifts ribosome pausing. We show that the N-terminal disordered domain of Rpt1 is required to ensure efficient ribosome pausing and association of nascent Rpt1 protein complexes into heavy particles, wherein the nascent protein complexes escape ribosome quality control.Immunofluorescence and in situ hybridization studies indicate that Rpt1-and Rpt2encoding mRNAs colocalize in these particles that contain and depend upon Not1, the scaffold of the Ccr4-Not complex. We refer to these particles as Not1-Containing Assemblysomes (NCA), as they are smaller and distinct from other RNA granules such as stress granules, GW-or P-bodies. Synthesis of Rpt1 with ribosome pausing and NCA induction is conserved from yeast to human cells.