The selective degradation of many short-lived proteins in eukaryotic cells is carried out by the ubiquitin system. In this pathway, proteins are targeted for degradation by covalent ligation to ubiquitin, a highly conserved small protein. Ubiquitin-mediated degradation of regulatory proteins plays important roles in the control of numerous processes, including cell-cycle progression, signal transduction, transcriptional regulation, receptor down-regulation, and endocytosis. The ubiquitin system has been implicated in the immune response, development, and programmed cell death. Abnormalities in ubiquitin-mediated processes have been shown to cause pathological conditions, including malignant transformation. In this review we discuss recent information on functions and mechanisms of the ubiquitin system. Since the selectivity of protein degradation is determined mainly at the stage of ligation to ubiquitin, special attention is focused on what we know, and would like to know, about the mode of action of ubiquitin-protein ligation systems and about signals in proteins recognized by these systems.

The Ubiquitin System

Between the 1960s and 1980s, most life scientists focused their attention on studies of nucleic acids and the translation of the coded information. Protein degradation was a neglected area, conside...

The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction

▪ Abstract The conjugation of ubiquitin to other cellular proteins regulates a broad range of eukaryotic cell functions. The high efficiency and exquisite selectivity of ubiquitination reactions reflect the properties of enzymes known as ubiquitin-protein ligases or E3s. An E3 recognizes its substrates based on the presence of a specific ubiquitination signal, and catalyzes the formation of an isopeptide bond between a substrate (or ubiquitin) lysine residue and the C terminus of ubiquitin. Although a great deal is known about the molecular basis of E3 specificity, much less is known about molecular mechanisms of catalysis by E3s. Recent findings reveal that all known E3s utilize one of just two catalytic domains—a HECT domain or a RING finger—and crystal structures have provided the first detailed views of an active site of each type. The new findings shed light on many aspects of E3 structure, function, and mechanism, but also emphasize that key features of E3 catalysis remain to be elucidated.

Mechanisms underlying ubiquitination.

E3 ligases confer specificity to ubiquitination by recognizing target substrates and mediating transfer of ubiquitin from an E2 ubiquitinconjugating enzyme to substrate. The activity of most E3s is specified by a RING domain, which binds to an E2∼ubiquitin thioester and activates discharge of its ubiquitin cargo. E2-E3 complexes can either monoubiquitinate a substrate lysine or synthesize polyubiquitin chains assembled via different lysine residues of ubiquitin. These modifications can have diverse effects on the substrate, ranging from proteasome-dependent proteolysis to modulation of protein function, structure, assembly, and/or localization. Not surprisingly, RING E3mediated ubiquitination can be regulated in a number of ways. RING-based E3s are specified by over 600 human genes, surpassing the 518 protein kinase genes. Accordingly, RING E3s have been linked to the control of many cellular processes and to multiple human diseases. Despite their critical importance, our knowledge of the physiological partners, biological functions, substrates, and mechanism of action for most RING E3s remains at a rudimentary stage.

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RING Domain E3 Ubiquitin Ligases

Basic Medical Research Award. The ubiquitin system.

Abstract The degradation of denatured globin in reticulocyte lysates is markedly stimulated by ATP. This system has now been resolved into two components, designated fractions I and II, in the order of their elution from DEAE-cellulose. Fraction II has a neutral protease activity but is stimulated only slightly by ATP, whereas fraction I has no proteolytic activity but restores ATP-dependent proteolysis when combined with fraction II. The active principle of fraction I is remarkably heat-stable, but it is non-dialysable, precipitable with ammonium sulfate and it is destroyed by treatment with proteolytic enzymes. In gel filtration on Sephadex-G-75, it behaves as a single component with a molecular weight of approximately 9,000.

A heat-stable polypeptide component of an ATP-Dependent Proteolytic System from reticullocytes

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Abstract
The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. The N-end rule pathway is one proteolytic pathway of the ubiquitin system. The recognition component of this pathway, called N-recognin or E3, binds to a destabilizing N-terminal residue of a substrate protein and participates in the formation of a substrate-linked multiubiquitin chain. We report the cloning of the mouse and human Ubr1 cDNAs and genes that encode a mammalian N-recognin called E3α. Mouse UBR1p (E3α) is a 1,757-residue (200-kDa) protein that contains regions of sequence similarity to the 225-kDa Ubr1p of the yeast Saccharomyces cerevisiae. Mouse and human UBR1p have apparent homologs in other eukaryotes as well, thus defining a distinct family of proteins, the UBR family. The residues essential for substrate recognition by the yeast Ubr1p are conserved in the mouse UBR1p. The regions of similarity among the UBR family members include a putative zinc finger and RING-H2 finger, another zinc-binding domain. Ubr1 is located in the middle of mouse chromosome 2 and in the syntenic 15q15-q21.1 region of human chromosome 15. Mouse Ubr1 spans ≈120 kilobases of genomic DNA and contains ≈50 exons. Ubr1 is ubiquitously expressed in adults, with skeletal muscle and heart being the sites of highest expression. In mouse embryos, the Ubr1 expression is highest in the branchial arches and in the tail and limb buds. The cloning of Ubr1 makes possible the construction of Ubr1-lacking mouse strains, a prerequisite for the functional understanding of the mammalian N-end rule pathway.

https://www.pnas.org/content/pnas/95/14/7898.full.pdf

The mouse and human genes encoding the recognition component of the N-end rule pathway.

It has been often stated that until recently the ubiquitin system was thought to be mainly a ‘garbage disposal’ for the removal of abnormal or damaged proteins. This statement is certainly not true for those who have been interested in the selective and regulated degradation of proteins in cells. The dynamic turnover of cellular proteins was discovered in the pioneering studies of Rudolf Schoenheimer in the 1930s, when he first used isotopically labeled compounds for biological studies 1 . Between 1960 and1970 it became evident that protein degradation in animal cells is highly selective, and is important in the control of specific enzyme concentrations 2 . The molecular mechanisms responsible for this process, however, remained unknown. Some imaginative models have been proposed to account for the selectivity of protein degradation, such as one suggesting that all cellular proteins are rapidly engulfed into the lysosome, but only short-lived proteins are degraded in the lysosome, whereas long-lived proteins escape back to the cytosol 3 . I became interested in the mechanisms of intracellular protein breakdown when I was a post-doctoral fellow in the laboratory of Gordon Tomkins 30 years ago (1969‐1971). At that time, the main subject in that laboratory was the mechanism by which corticosteroid hormones cause the increased synthesis of the enzyme tyrosine aminotransferase. I found this subject a bit crowded, so I chose to study a different process that also regulates tyrosine aminotransferase concentration: the degradation of this enzyme. I found that the degradation of tyrosine aminotransferase in cultured hepatoma cells is completely arrested by inhibitors of cellular energy production, such as fluoride or azide 4 . These results confirmed and extended the previous observations of Simpson on the energy dependence of the release of amino acids from liver slices 5

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Avram Hershko

Papers

A heat-stable polypeptide component of an ATP-Dependent Proteolytic System from reticullocytes

The mouse and human genes encoding the recognition component of the N-end rule pathway.

Ubiquitin-mediated protein degradation: The early days The ubiquitin system