UBIQUITONS: "UBIQUITIN AND UBIQUITIN-LIKE PROTEINS"

Ubiquitin-like proteins

Over recent years a number of proteins related to ubiquitin have been identified. These ubiquitin-like proteins fall into two separate classes, namely type I and type II. The type I proteins (UBLs) function as modifiers in a manner analogous to that of ubiquitin and exist either in a free form or attached covalently to other proteins by their C-termini.  Type II proteins bear domains that are related to ubiquitin but are otherwise unrelated in sequence to each other (termed ubiquitin-domain proteins or UDPs). In contrast to the ubiquitin-like modifiers the UDPs are not conjugated to other proteins. All currently known UBLs are related in sequence to ubiquitin to a greater or lesser extent. Whilst APG12, URM1 and FAT10 are expressed as mature proteins, all other UBLs (including ubiquitin) are expressed as inactive precursors made initially as fusions with C-terminal extensions. These tails, which prevent conjugation, can be either single amino acids or polypeptides.  The precursors are processed endoproteolytically by specific proteases, and the modifiers and their respective tails are released.   Type I (UBLs)   Fat10   Fub1    ISG15 (UCRP)   Nedd8   SUMO-1, -2, -3   Urm1   Ubl5   Ubiquitin    Apg12 Type II (UDPs)HHR23A/B Dsk2 Plic1/2 Bag1 Chap1/2 Parkin Elongin B Ubp6 Scythe The conjugation pathways for the UBLs elucidated to date closely resemble that for ubiquitin, although in some cases the E1 and E2 enzymes have yet to be identified.

FAT10 Encoded in the major histocompatibility complex class I locus and is synergistically inducible with interferon-gamma and tumor necrosis factor alpha1.  FAT10 expression causes apoptosis and is inducible with tumour necrosis factor alpha2 and it appears that FAT10 may modulate tumorigenesis through its interaction with the MAD2 spindle-assembly checkpoint protein3.  It has been demonstrated that FAT10 and its conjugates are rapidly degraded by the proteasome. Furthermore, a new interaction partner of FAT10, NEDD8 ultimate buster-1L (NUB1L), may function as a linker that targets FAT10 for degradation by the proteasome4. 1. Y.C. Liu et al. Proc. Natl. Acad. Sci. USA 1999 96 4313 2. S. Raasi et al. J. Biol. Chem. 2001 276 35334 3 .C.G. Lee et al. Oncogene 2003 22 2592 4. M.S. Hipp et al. J. Biol. Chem. 2004 279 16503

Fub1 Belongs to the ubiquitin-like protein group that is capable of forming conjugates to other proteins and shows amino acid sequence similarity to that of ubiquitin1.  Certain cloned cDNAs encode for a single ubiquitin-like (Fub1) protein fused in frame to S30, a protein of the small ribosomal subunit.  Purified ubiquicidin indicates that it is identical to S30 produced by post-translational processing of the fau protein2.  Fub1 may act as a substitute or inhibitor of ubiquitin, to which it is most closely related, or to the close ubiquitin-like relatives UCRP, FAT10, and/or NEDD83. 1. L. Michiels et al. Oncogene 1993 8 2537 2. P.S. Hiemstra et al. Leukoc. Biol. 1999 66 423 3. T.G. Rossman et al. Oncogene 2003 22 1817

ISG15 Originally identified as an interferon stimulated gene (ISG) whose expression is highly induced upon interferon treatment1.  ISG15 contains two ubiquitin homology domains in tandem and shows ~30% identity to ubiquitin.  ISG15 is conserved in dispersed regions and homology among the five identified mammalian proteins is around 47%. It is synthesized as a 17 kDa precursor form and processed to 15 kDa protein by a specific protease in order to expose di-glycine residues at the carboxyl terminus, which is critical for subsequent conjugation to target proteins2.  The ability of ISG15 to be conjugated to the other cellular proteins has been identified3.  UBE1L (ISG15-activating enzyme) and UBP43 (deISGylating enzyme), share a significant homology with counterparts of ubiquitin system4.  ISGylation may play important roles in viral or bacterial infection where protein ISGylation is highly induced5. 1. P.J. Farrell et al. Nature 1979 279 523 2. E. Knight Jr. et al. J. Biol. Chem. 1988 263 4520 3. K.R. Loeb et al. J. Biol. Chem. 1992 267 7806 4. K. Kok et al. Proc. Natl. Acad. Sci. USA 1993 90 6071 5. C.E. Samuel Clin. Microbiol. 2001 14 778

NEDD8 Shares ~60% identity with ubiquitin at the amino acid level, that can be covalently conjugated (neddylation) to a limited number of cellular proteins in a fashion similar to that of ubiquitin.  The C-terminus of pro-NEDD8 is processed to expose glycine76 in the mature form.  This processing is required for conjugation to target proteins via a range of specific activating and conjugating enzymes1. Neddylation acts to regulate the function of ubiquitin-protein ligases (E3s) and organisms with lesions in the neddylation process exhibit severe growth defects2. Substrates for neddylation include the von Hippel-Lindau (VHL) tumour suppressor gene3 and the tumour suppressor and transcriptional regulator p534 amongst others. 1. L. Gong et al. J. Biol. Chem. 1999 274 12036 2. G. Perry et al. Cell Dev. Biol. 2004 15 221 3. N.H. Stickle et al. Mol. Cell Biol. 2004 24 3251 4. J.W. Harper Cell 2004 118 2

SUMO SUMO is present in all eukaryotic kingdoms and is highly conserved from yeast to humans1. Whereas invertebrates have only one SUMO gene, three members of the SUMO family have een described in vertebrates. SUMO-1 and the close homologuesSUMO-2 and SUMO-3, with some 50% homology between UMO-1 and SUMO-2/3. A fourth SUMO (SUMO-4) has been reported2, however, there is debate over its expression as a functional protein. The SUMO family members are expressed with short C-terminal extensions (the pro-forms), which are processed to expose the C-terminal glycine residue that is essential for conjugation to target proteins (the mature forms). An increasing number of SUMO substrates are being described including RanGAP1, SP100, PML and IκBα proteins3. Unlike ubiquitin, SUMO does not appear to target proteins for degradation, but seems to be involved in the modulation of protein-protein interactions. Although having only 18% amino acid sequence identity with ubiquitin, the overall structure closely resembles that of ubiquitin. Whereas the two C-terminal glycine residues required for isopeptide bond formation are conserved between the two molecules, Lys48 found in ubiquitin, and required to generate ubiquitin polymers, is substituted by Gln69 in SUMO-1 thereby providing an explanation of why SUMO-1 has not been observed to form polymers4. However, SUMO-2 and SUMO-3 sequences both contain the consensus SUMO-modification site, as a consequence of which the SUMO-activating and conjugating enzymes may catalyze the formation of polymeric chains of SUMO-2 and SUMO-3 on protein substrates5. 1. S. Müller et al. Nat. Rev. Mol. Cell Biol. 2001 2 202 2. K. Bohren et al. J. Biol. Chem 2004 279 27233 3. C. Kretz-Remy and R.M. Tanguay Biochem. Cell Biol. 1999 77 299 4. P. Bayer et al. Nat. Rev. Mol. Cell Biol. 1998 10 275 5. M.H. Tathman et al. J. Biol. Chem. 2001 276 35368

UBL5 Initially identified in a screen for highly expressed genes in human iris1. The gene encodes a protein of 73 amino acids with a molecular weight of 8.5 kDa.  Orthologs of UBL5 occur in every eukaryotic genome characterized to date, which suggests an important function for UBL5.  The amino acid sequence of UBL5 is identical to that of Beacon2, a protein reported to be involved in feeding behaviour and development of obesity and type 2 diabetes in the Israeli sand rat Psammomys obeseus, and it may also interact with the cyclin-like kinase CLK42.  The yeast ortholog of UBL5, HUB1, has recently been demonstrated to be an essential gene, whose loss results in cell cycle defects, inefficient pre-mRNA splicing, and incorrect sub-cellular targeting3.  Based on sequence homology and structure prediction algorithms it has been demonstrated that the protein structure of UBL5 is very similar to that of ubiquitin despite the low, approximately 25%, residue similarity4.  1. J.S. Friedmann et al. Genomics 2001 71 252 2. G.R. Collier et al. Diabetes 2000 49 1766 3. C.R. Wilkinson et al. Curr. Biol. 2004 14 2283 4. T. McNally et al. Prot. Sci. 2003 12 1562

Urm1 Acts as a post-translational protein modifier in Saccharomyces cerevisiae1. Simultaneous loss of Urm1p and Cla4p, a p21-activated kinase that functions in budding, is lethal, suggesting a role for the urmylation pathway in budding whilst additional results suggest an involvement in nutrient sensing2. The first in vivo target for the urmylation pathway has been identified as the antioxidant protein Ahp1p.  It has been suggested that the conjugation of Urm1p to Ahp1p could regulate the function of Ahp1p in antioxidant stress response in Saccharomyces cerevisiae3.   1. K. Furukawa et al. J. Biol. Chem. 2000 275 7462 2. A.S. Goehring et al. Mol. Biol. Cell 2003 14 4329 3. A.S. Goehring et al. Eukaryot. Cell 2003 2 930