Ubiquitin

Ubiquitin is a small regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms. Among other functions, it directs protein recycling.

Ubiquitin can be attached to proteins and label them for destruction. The ubiquitin tag directs proteins to the proteasome, which is a large protein complex in the cell that degrades and recycles unneeded proteins. This discovery won the Nobel Prize for chemistry in 2004.

Ubiquitin tags can also direct proteins to other locations in the cell, where they control other protein and cell mechanisms.

Identification
Ubiquitin (originally, ubiquitous immunopoietic polypeptide) was first identified in 1975 as an 8.5-kDa protein of unknown function expressed in all eukaryotic cells. The basic functions of ubiquitin and the components of the ubiquitination pathway were elucidated in the early 1980s in groundbreaking work performed at Fox Chase Cancer Center by Aaron Ciechanover, Avram Hershko, and Irwin Rose for which the Nobel Prize in Chemistry was awarded in 2004.

The ubiquitylation system was initially characterised as an ATP-dependent proteolytic system present in cellular extracts. A heat-stable polypeptide present in these extracts, ATP-dependent proteolysis factor 1 (APF-1), was found to become covalently attached to the model protein substrate lysozyme in an ATP- and Mg2+-dependent process. Multiple APF-1 molecules were linked to a single substrate molecule by an isopeptide linkage, and conjugates were found to be rapidly degraded with the release of free APF-1. Soon after APF-1-protein conjugation was characterised, APF-1 was identified as ubiquitin. The carboxyl group of the C-terminal glycine residue of ubiquitin (Gly76) was identified as the moiety conjugated to substrate lysine residues.

The protein
Ubiquitin is a small protein that exists in all eukaryotic cells. It performs its myriad functions through conjugation to a large range of target proteins. A variety of different modifications can occur. The ubiquitin protein itself consists of 76 amino acids and has a molecular mass of about 8.5 kDa. Key features include its C-terminal tail and the 7 lysine residues. It is highly conserved among eukaryotic species: Human and yeast ubiquitin share 96% sequence identity. The human ubiquitin sequence in one-letter code (lysine residues in bold):

Genes
Ubiquitin is encoded in mammals by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. The UBB and UBC genes code for polyubiquitin precursor proteins.

Origins
No ubiquitin and ubiquitination machinery are known to exist in prokaryotes. However, ubiquitin is believed to have descended from prokaryotic proteins similar to ThiS or MoaD. These prokaryotic proteins, despite having little sequence identity (ThiS has 14% identity to ubiquitin), share the same protein fold. These proteins also share sulfur chemistry with ubiquitin. MoaD, which is involved in molybdenum cofactor biosynthesis, interacts with MoeB, which acts like an E1 ubiquitin-activating enzyme for MoaD, strengthening the link between these prokaryotic proteins and the ubiquitin system. A similar system exists for ThiS, with its E1-like enzyme ThiF. It is also believed that the Saccharomyces cerevisiae protein Urm-1, a ubiquitin-related modifier, is a "molecular fossil" that connects the evolutionary relation with the prokaryotic ubiquitin-like molecules and ubiquitin.

Ubiquitination (ubiquitylation)


Ubiquitination is an enzymatic, protein post-translational modification (PTM) process in which the carboxylic acid of the terminal glycine from the di-glycine motif in the activated ubiquitin forms an amide bond to the epsilon amine of the lysine in the modified protein.

The process of marking a protein with ubiquitin (ubiquitylation or ubiquitination) consists of a series of steps:
 * 1) Activation of ubiquitin: Ubiquitin is activated in a two-step reaction by an E1 ubiquitin-activating enzyme in a process requiring ATP as an energy source. The initial step involves production of a ubiquitin-adenylate intermediate. The second step transfers ubiquitin to the E1 active site cysteine residue, with release of AMP. This step results in a thioester linkage between the C-terminal carboxyl group of ubiquitin and the E1 cysteine sulfhydryl group.
 * 2) Transfer of ubiquitin from E1 to the active site cysteine of a ubiquitin-conjugating enzyme E2 via a trans(thio)esterification reaction.  Mammalian genomes contain 30-40 UBCs.
 * 3) The final step of the ubiquitylation cascade creates an isopeptide bond between a lysine of the target protein and the C-terminal glycine of ubiquitin. In general, this step requires the activity of one of the hundreds of E3 ubiquitin-protein ligases (often termed simply ubiquitin ligase). E3 enzymes function as the substrate recognition modules of the system and are capable of interaction with both E2 and substrate.

In the ubiquitination cascade, E1 can bind with dozens of E2s, which can bind with hundreds of E3s in a hierarchical way. Other ubiquitin-like proteins (ULPs) are also modified via the E1–E2–E3 cascade.

E3
E3 enzymes possess one of two domains: Transfer can occur in two ways:
 * The HECT (Homologous to the E6-AP Carboxyl Terminus) domain
 * The RING (Really Interesting New Gene) domain (or the closely-related U-box domain)
 * Directly from E2, catalysed by RING domain E3s.
 * Via an E3 enzyme, catalysed by HECT domain E3s. In this case, a covalent E3-ubiquitin intermediate is formed before transfer of ubiquitin to the substrate protein.

The anaphase-promoting complex (APC) and the SCF complex (for Skp1-Cullin-F-box protein complex) are two examples of multi-subunit E3s involved in recognition and ubiquitination of specific target proteins for degradation by the proteasome.

Function and variety of ubiquitin modifications
Following addition of a single ubiquitin moiety to a protein substrate (monoubiquitination), further ubiquitin molecules can be added to the first, yielding a polyubiquitin chain. In addition, some substrates are modified by addition of ubiquitin molecules to multiple lysine residues in a process termed multiubiquitination. As discussed, ubiquitin possesses a total of 7 lysine residues. Historically the original type of ubiquitin chains identified were those linked via lysine 48. However, more recent work has uncovered a wide variety of linkages involving all possible lysine residues and in addition chains assembled on the N-terminus of a ubiquitin molecule ("linear chains"). Work published in 2007 has demonstrated the formation of branched ubiquitin chains containing multiple linkage types. "Atypical" (non-lysine 48-linked) ubiquitin chains have been discussed in a review by Ikeda & Dikic.

The ubiquitination system functions in a wide variety of cellular processes, including :
 * Antigen processing
 * Apoptosis
 * Biogenesis of organelles
 * Cell cycle and division
 * DNA transcription and repair
 * Differentiation and development
 * Immune response and inflammation
 * Neural and muscular degeneration
 * Morphogenesis of neural networks
 * Modulation of cell surface receptors, ion channels and the secretory pathway
 * Response to stress and extracellular modulators
 * Ribosome biogenesis
 * Viral infection

Lysine linked chains
The most studied polyubiquitin chains - lysine48-linked - target proteins for destruction, a process known as proteolysis. At least four ubiquitin molecules must be attached to lysine residues on the condemned protein in order for it to be recognised by the 26S. Lysine 63 linked chains direct the localization of proteins. Monoubiquitylation of proteins also targets the localization of proteins -proteasome. The proteasome is a complex, barrel-shaped structure with two chambers, within which proteolysis occurs. Proteins are rapidly degraded into small peptides (usually 3-24 amino acid residues in length). Ubiquitin molecules are cleaved off the protein immediately prior to destruction and are recycled for further use. Although the majority of proteasomal substrates are ubiquitinated, there are examples of non-ubiquitinated proteins targeted to the proteasome.

Monoubiquitination
Ubiquitin can also mark transmembrane proteins (for example, receptors) for removal from membranes and fulfill several signaling roles within the cell. Cell-surface transmembrane molecules that are tagged with ubiquitin are often monoubiquitinated, and this modification alters the subcellular localization of the protein, often targeting the protein for destruction in lysosomes.

Histones are usually monoubiquitinated and associated with signaling or structural marking.

Other chain types
Ubiquitin has seven lysine residues that may serve as points of polyubiquitylation, they are; K48, K63, K6, K11, K27, K29 and K33. These different linkages may define unique signals that are recognized by ubiquitin-binding proteins, which have Ubiquitin interacting motifs (UIMs) that bind to ubiquitin. It is thought that the different linkages are recognized by proteins that are specific for the unique topologies that are intrinsic to the linkage. One example, is the K63 linkage, which is known to be involved in DNA damage recognition of DNA double-strand breaks. The K63 linkage appears to be placed on the H2AX histone by the E2/E3 ligase pair, Ubc13-Mms2/RNF168. This K63 chain appears to recruit RAP80, which contains a UIM, and RAP80 then helps localize BRCA1. This pathway will eventually recruit the necessary proteins for Homologous Recombination Repair.

Genetic disorders
Some genetic disorders associated with ubiquitin are:


 * The gene that controls "ubiquitin-1", which is found in lesions associated with Alzheimer's and Parkinson's disease. Two transcript variants encoding different isoforms have been found for this gene. Higher levels of ubiquitin in the brain decreased malformation of the APP molecule, which plays a key role in triggering Alzheimer's disease. Conversly, lower levels of ubiquilin-1 in the brain were associated with increased malformation of APP.
 * The gene whose disruption causes Angelman syndrome, UBE3A, encodes a ubiquitin ligase (E3) enzyme termed E6-AP.
 * The gene disrupted in Von Hippel-Lindau syndrome encodes a ubiquitin E3 ligase termed the VHL tumor suppressor or VHL gene.
 * The gene disrupted in Liddle's Syndrome results in disregulation of an epithelial Na+ channel (ENaC) and causes hypertension.
 * Eight of the thirteen identified genes whose disruption causes Fanconi anemia encode proteins that form a large ubiquitin ligase (E3) complex.
 * Mutations of the Cullin7 E3 ubiquitin ligase are linked to 3-M syndrome, an autosomal-recessive growth retardation disorder

Frameshift mutant (UBB+1)
The ubiquitin B gene may be erroneously transcribed due to a monotonic nucleotide sequence in the coding region of the gene. As a result, a dinucleotide deletion occurs at the mRNA level causing a frameshift. When translated into protein, a dysfunctional ubiquitin that has lost its C-terminal glycine and has a peptide of 20 amino acids instead is generated. UBB+1 has shown to accumulate selectively in tauopathies and polyglutaminopathies.

Immunohistochemistry
Antibodies to ubiquitin are used in histology to identify abnormal accumulations of protein inside cells that are markers of disease. These accumulations are called inclusion bodies. Examples of such abnormal inclusions in cells are
 * Neurofibrillary tangles in Alzheimer's disease
 * Lewy body in Parkinson's disease
 * Pick bodies in Pick's disease
 * Inclusions in motor neuron disease and Huntington's Disease
 * Mallory bodies in alcoholic liver disease
 * Rosenthal fibers in astrocytes

Ubiquitin-like modifiers
Although ubiquitin is the most well understood post-translation modifier, there is a growing family of ubiquitin-like proteins (UBLs) that modify cellular targets in a pathway that is parallel to, but distinct from, that of ubiquitin. Known UBLs include: small ubiquitin-like modifier (SUMO), ubiquitin cross-reactive protein (UCRP, also known as interferon-stimulated gene-15 ISG15), ubiquitin-related modifier-1 (URM1), neuronal-precursor-cell-expressed developmentally downregulated protein-8 (NEDD8, also called Rub1 in S. cerevisiae), human leukocyte antigen F-associated (FAT10), autophagy-8 (ATG8) and -12 (ATG12), Fau ubiquitin-like protein (FUB1), MUB (membrane-anchored UBL), ubiquitin fold-modifier-1 (UFM1) and ubiquitin-like protein-5 (UBL5, which is but known as homologous to ubiquitin-1 [Hub1] in S. pombe). Whilst these proteins share only modest primary sequence identity with ubiquitin, they are closely related three-dimensionally. For example, SUMO shares only 18% sequence identity, but contain the same structural fold. This fold is called "ubiquitin fold" or sometimes called  ubiquiton fold. FAT10 and UCRP contain two. This compact globular beta-grasp fold is found in ubiquitin, UBLs, and proteins that comprise a ubiquitin-like domain e.g. the S. cerevisiae spindle pole body duplication protein, Dsk2, and NER protein, Rad23, both contain N-terminal ubiquitin domains.

These related molecules have novel functions and influence diverse biological processes. There is also cross-regulation between the various conjugation pathways since some proteins can become modified by more than one UBL, and sometimes even at the same lysine residue. For instance, SUMO modification often acts antagonistically to that of ubiquitination and serves to stabilize protein substrates. Proteins conjugated to UBLs are typically not targeted for degradation by the proteasome, but rather function in diverse regulatory activities. Attachment of UBLs might alter substrate conformation, affect the affinity for ligands or other interacting molecules, alter substrate localization and influence protein stability.

UBLs are structurally similar to ubiquitin and are processed, activated, conjugated and released from conjugates by enzymatic steps that are similar to the corresponding mechanisms for ubiquitin. UBLs are also translated with C-terminal extensions that are processed to expose the invariant C-terminal LRGG. These modifiers have their own specific E1 (activating), E2 (conjugating) and E3 (ligating) enzymes that conjugate the UBLs to intracellular targets. These conjugates can be reversed by UBL-specific isopeptidases that have similar mechanisms to that of the deubiquitinating enzymes.

Within some species, the recognition and destruction of sperm mitochondria through a mechanism involving ubiquitin is responsible for sperm mitochondria's disposal after fertilization occurs.

Human proteins containing ubiquitin domain
ANUBL1;   BAG1;      BAT3;      DDI1;      DDI2;      FAU;       HERPUD1;   HERPUD2; HOPS;     IKBKB;     ISG15;     LOC391257; MIDN;      NEDD8;     OASL;      PARK2; RAD23A;   RAD23B;    RPS27A;    SACS;      SF3A1;     SUMO1;     SUMO2;     SUMO3; SUMO4;    TMUB1;     TMUB2;     UBA52;     UBB;       UBC;       UBD;       UBFD1; UBL4;     UBL4A;     UBL4B;     UBL7;      UBLCP1;    UBQLN1;    UBQLN2;    UBQLN3; UBQLN4;   UBQLNL;    UBTD1;     UBTD2;     UHRF1;     UHRF2;

Academic

 * UniProt entry for ubiquitin
 * UbiPred &mdash; server for the prediction of ubiquitylation sites
 * Ubiquitin Web-page
 * 7.340 Ubiquitination: The Proteasome and Human Disease MIT OpenCourseWare. Notes from MIT course.

Commercial

 * Enzo Life Sciences : Ubiquitin and Proteasome Research Products
 * Boston Biochem : Ubiquitin and Ubiquitin-like Research Products
 * Progenra Inc. : Ubiquitin-based Biotechnology Corporation

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