PerspectiveCell Biology

New developments for protein quality control

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Science  04 Aug 2017:
Vol. 357, Issue 6350, pp. 450-451
DOI: 10.1126/science.aao1896

The cellular proteome is maintained by a dynamic balance between protein synthesis and degradation, known as proteostasis. An imperative of successful proteostasis is the detection and removal of misfolded proteins by quality control pathways. Proteins that result from translation errors, misfolding, or age-induced or chemical damage, as well as orphan proteins (which result from inappropriate stoichiometry of multiprotein complexes), are all subject to a variety of degradative pathways to limit their cellular accumulation, which can be toxic (1). One of the striking features of degradative quality control is the juxtaposition of high specificity for misfolded versions of normal proteins with the very broad range of substrates that can be accommodated by each pathway. On pages 472 and 471 of this issue, Yanagitani et al. (2) and Nguyen et al. (3), respectively, show that a newly discovered quality control pathway is used to bring about the sweeping changes in proteome content that are observed in the differentiation of relatively “cellular” reticulocytes to the highly specialized hemoglobin-rich red blood cells (erythrocytes) (4, 5).

Degrading orphan proteins

UBE2O is a unique enzyme that functions as both an E2 ubiquitin-conjugating enzyme and an E3 ubiquitin ligase to target orphan proteins through multi-monoubiquitylation for degradation by the proteasome. This differs from the classic ubiquitin-proteasome degradation pathway that uses E1, E2, and E3 enzymes to polyubiquitylate substrates.

GRAPHIC: K. SUTLIFF/SCIENCE

Nguyen et al. aimed to decipher the mechanisms underlying the dramatic degradative remodeling that occurs during the differentiation of reticulocytes (the precursors of red blood cells) (3). This remodeling includes the removal of ribosomes and various other reticulocyte proteins, resulting in a highly specialized and simplified proteome comprising 98% hemoglobin, tailor-made for carrying oxygen. Their starting point was the identification of an autosomal recessive null allele of the gene encoding UBE2O, which resulted in anemia in mice. Interestingly, UBE2O is an E2 ubiquitin-conjugating enzyme—which usually adds ubiquitin to target proteins—that is overexpressed during erythroid differentiation. Using reticulocytes that do not express UBE2O (ube2O-/-), they found that orphan α-globin (which is a subunit of hemoglobin) is targeted for multimonoubiquitylation by UBE2O, leading to degradation by the proteasome.

These authors also identify ribosomal proteins (which usually form large multiprotein complexes that generate proteins) as major substrates of UBE2O. Ex vivo culture of wild-type and ube2O-/- reticulocytes confirmed that ribosome elimination, a hallmark of late stages of reticulocyte differentiation to form red blood cells, is due to the activities of both UBE2O and the proteasome. This activity of UBE2O thus results in degradation of the preexisting proteins in reticulocytes and down-regulation of protein production (which is mediated by ribosomes) that is observed in red blood cells. Furthermore, overexpression of UBE2O is sufficient to drive ribosome degradation in non-erythroid cells. In vitro biochemical data support a substrate recognition capacity for UBE2O, a property that is usually displayed by E3 ubiquitin ligases (see the figure). This work clearly showed the importance of this single enzyme in the destruction of a variety of proteins, and the breadth-with-specificity exhibited by UBE2O seems similar to the features of a quality control pathway.

The connection of UBE2O to quality control was established by Yanagitani et al. In their quest to understand the mechanisms underlying such pathways, the authors designed a cell-free assay for the ubiquitylation of an artificial substrate, corresponding to a transmembrane protein interrupted by three arginine residues. This substrate was not targeted by any of a number of previously described quality control machineries. Instead, UBE2O was identified as both necessary and sufficient for the recognition and ubiquitylation of the artificial substrate as well as other misfolded proteins [in the presence of E1 enzyme, ubiquitin, and adenosine triphosphate (ATP)]. This remarkable E2 ubiquitin-conjugating enzyme appeared to be the specificity-promoting E3 ligase as well. Further in vitro studies showed that conserved domains of UBE2O display a broad ability to recognize hydrophobic patches in proteins, thus leading to their multi-monoubiquitylation. Like Nguyen et al., they found that orphan a-globin is ubiquitylated by UBE2O. They also demonstrate that newly generated ribosomal proteins either are imported in the nucleus to be incorporated into ribosomal subunits, or are recognized and ubiquitylated by UBE2O for degradation.

Both studies show that UBE2O is a uniquely talented E2 enzyme that is capable of autonomously ubiquitylating a wide range of substrates to promote their degradation by the proteasome. The widely found “signal” in target proteins for UBE2O-mediated multi-monoubiquitylation consists of adjacent sequences of basic and hydrophobic amino acids, which are overrepresented in unassociated interaction surfaces that are typical of orphan subunits. Interestingly, such orphans are unstable in the first hours of their life and are stabilized with age (6). In this respect, UBE2O, despite its clear homology to E2 ubiquitin-conjugating enzymes, belongs to a group of quality control ubiquitin E3 ligases that function without adaptor or chaperone proteins to select their targets (7). In fact, physiological or artificial overexpression of UBE2O led to vast proteome remodeling. Whether such a property is shared by other quality control factors, and whether quality control is more generally used in proteome remodeling and differentiation pathways, are important avenues of future investigation.

Further understanding of UBE2O and other quality control pathways might open new therapeutic avenues to alter proteomes to improve cellular health, such as removal of a-globin aggregates that are observed in the blood disorder β-thalassemia, which features reduced hemoglobin expression. Learning how the cell alters these pathways, and possibly how we can do the same, could have remarkable basic and translational potential (8, 9).

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