degrading it from one terminus. it has been suggested that long loops on these proteins' surfaces serve as the proteasomal substrates and enter the central cavity, while the majority of the protein remains outside. similar effects have been observed in yeast proteins; this mechanism of selective degradation is known as regulated ubiquitin/proteasome dependent processing (rup). ubiquitin-independent degradation although most proteasomal substrates must be ubiquitinated before being degraded, there are some exceptions to this general rule, especially when the proteasome plays a normal role in the post-translational processing of the protein. the proteasomal activation of nf-κb by processing p105 into p50 via internal proteolysis is one major example. some proteins that are hypothesized to be unstable due to intrinsically unstructured regions, are degraded in a ubiquitin-independent manner. the most well-known example of a ubiquitin-independent proteasome substrate is the enzyme ornithine decarboxylase. ubiquitin-independent mechanisms targeting key cell cycle regulators such as p53 have also been reported, although p53 is also subject to ubiquitin-dependent degradation. finally, structurally abnormal, misfolded, or highly oxidized proteins are also subject to ubiquitin-independent and 19s-independent degradation under conditions of cellular stress. evolution the assembled complex of hslv (blue) and hslu (red) from e. coli. this complex of heat shock proteins is thought to resemble the ancestor of the modern proteasome. the 20s proteasome is both ubiquitous and essential in eukaryotes and archaea. the bacterial order actinomycetales, also share homologs of the 20s proteasome, whereas most bacteria possess heat shock genes hslv and hslu, whose gene products are a multimeric protease arranged in a two-layered ring and an atpase. the hslv protein has been hypothesized to resemble the likely ancestor of the 20s proteasome. in general, hslv is not essential in bacteria, and not all bacteria possess it, whereas some protists possess both the 20s and the hslv systems. many bacteria also possess other homologs of the proteasome and an associated atpase, most notably clpp and clpx. this redundancy explains why the hsluv system is not essential. sequence analysis suggests that the catalytic β subunits diverged earlier in evolution than the predominantly structural α subunits. in bacteria that express a 20s proteasome, the β subunits have high sequence identity to archaeal and eukaryotic β subunits, whereas the α sequence identity is much lower. the presence of 20s proteasomes in bacteria may result from lateral gene transfer, while the diversification of subunits among eukaryotes is ascribed to multiple gene duplication events. cell cycle control cell cycle progression is controlled by ordered action of cyclin-dependent kinases (cdks), activated by specific cyclins that demarcate phases of the cell cycle. mitotic cyclins, which persist in the cell for only a few minutes, have one of the shortest life spans of all intracellular proteins. after a cdk-cyclin complex has performed its function, the associated cyclin is polyubiquitinated and destroyed by the proteasome, which provides directionality for the cell cycle. in particular, exit from mitosis requires the proteasome-dependent dissociation of the regulatory component cyclin b from the mitosis promoting factor complex. in vertebrate cells, "slippage" through the mitotic checkpoint leading to premature m phase exit can occur despite the delay of this exit by the spindle checkpoint. earlier cell cycle checkpoints such as post-restriction point check between g1 phase and s phase similarly involve proteasomal degradation of cyclin a, whose ubiquitination is promoted by the anaphase promoting complex (apc), an e3 ubiquitin ligase. the apc and the skp1/cul1/f-box protein complex (scf complex) are the two key regulators of cyclin degradation and checkpoint control; the scf itself is regulated by the apc via ubiquitination of the adaptor protein, skp2, which prevents scf activity before the g1-s transition. individual components of the 19s particle have their own regulatory roles. gankyrin, a recently identified oncoprotein, is one of the 19s subcomponents that also tightly binds the cyclin-dependent kinase cdk4 and plays a key role in recognizing ubiquitinated p53, via its affinity for the ubiquitin ligase mdm2. gankyrin is anti-apoptotic and has been shown to be overexpressed in some tumor cell types such as hepatocellular carcinoma. like eukaryotes, some archaea also use the proteasome to control cell cycle, specifically by controlling escrt-iii-mediated cell division. regulation of plant growth in plants, signaling by auxins, or phytohormones that order the direction and tropism of plant growth, induces the targeting of a class of transcription factor repressors known as aux/iaa proteins for proteasomal degradation. these proteins are ubiquitinated by scftir1, or scf in complex with the auxin receptor tir1. degradation of aux/iaa proteins derepresses transcription factors in the auxin-response factor (arf) family and induces arf-directed gene expression. the cellular consequences of arf activation depend on the plant type and developmental stage, but are involved in directing growth in roots and leaf veins. the specific response to arf derepression is thought to be mediated by specificity in the pairing of individual arf and aux/iaa proteins. apoptosis both internal and external signals can lead to the induction of apoptosis, or programmed cell death. the resulting deconstruction of cellular components is primarily carried out by specialized proteases known as caspases, but the proteasome also plays important and diverse roles in the apoptotic process. the involvement of the proteasome in this process is indicated by both the increase in protein ubiquitination, and of e1, e2, and e3 enzymes that is observed well in advance of apoptosis. during apoptosis, proteasomes localized to the nucleus have also been observed to translocate to outer membrane blebs characteristic of apoptosis. proteasome inhibition has different effects on apoptosis induction in different cell types. in general, the proteasome is not required for apoptosis, although inhibiting it is pro-apoptotic in most cell types that have been studied. apoptosis is mediated through disrupting the regulated degradation of pro-growth cell cycle proteins. however, some cell lines — in particular, primary cultures of quiescent and differentiated cells such as thymocytes and neurons — are prevented from undergoing apoptosis on exposure to proteasome inhibitors. the mechanism for this effect is not clear, but is hypothesized to be specific to cells in quiescent states, or to result from the differential activity of the pro-apoptotic kinase jnk. the ability of proteasome inhibitors to induce apoptosis in rapidly dividing cells has been exploited in several recently developed chemotherapy agents such as bortezomib and salinosporamide a. response to cellular stress in response to cellular stresses – such as infection, heat shock, or oxidative damage – heat shock proteins that identify misfolded or unfolded proteins and target them for proteasomal degradation are expressed. both hsp27 and hsp90—chaperone proteins have been implicated in increasing the activity of the ubiquitin-proteasome system, though they are not direct participants in the process. hsp70, on the other hand, binds exposed hydrophobic patches on the surface of misfolded proteins and recruits e3 ubiquitin ligases such as chip to tag the proteins for proteasomal degradation. the chip protein (carboxyl terminus of hsp70-interacting protein) is itself regulated via inhibition of interactions between the e3 enzyme chip and its e2 binding partner. similar mechanisms exist to promote the degradation of oxidatively damaged proteins via the proteasome system. in particular, proteasomes localized to the nucleus are regulated by parp and actively degrade inappropriately oxidized histones. oxidized proteins, which often form large amorphous aggregates in the cell, can be degraded directly by the 20s core particle without the 19s regulatory cap and do not require atp hydrolysis or tagging with ubiquitin. however, high levels of oxidative damage increases the degree of cross-linking between protein fragments, rendering the aggregates resistant to proteolysis. larger numbers and sizes of such highly oxidized aggregates are associated with aging. dysregulation of the ubiquitin proteasome system may contribute to several neural diseases. it may lead to brain tumors such as astrocytomas. in some of the late-onset neurodegenerative diseases that share aggregation of misfolded proteins as a common feature, such as parkinson's disease and alzheimer's disease, large insoluble aggregates of misfolded proteins can form and then result in neurotoxicity, through mechanisms that are not yet well understood. decreased proteasome activity has been suggested as a cause of aggregation and lewy body formation in parkinson's. this hypothesis is supported by the observation that yeast models of parkinson's are more susceptible to toxicity from α-synuclein, the major protein component of lewy bodies, under conditions of low proteasome activity. impaired proteasomal activity may underlie cognitive disorders such as the autism spectrum disorders, and muscle and nerve diseases such as inclusion body myopathy. role in the immune system the proteasome plays a straightforward but critical role in the function of the adaptive immune system. peptide antigens are displayed by the major histocompatibility complex class i (mhc) proteins on the surface of antigen-presenting cells. these peptides are products of proteasomal degradation of proteins originated by the invading pathogen. although constitutively expressed proteasomes can participate in this process, a specialized complex composed of proteins, whose expression is induced by interferon gamma, are the primary producers of peptides which are optimal in size and composition for mhc binding. these proteins whose expression increases during the immune response include the 11s regulatory particle, whose main known biological role is regulating the production of mhc ligands, and specialized β subunits called β1i, β2i, and β5i with altered substrate specificity. the complex formed with the specialized β subunits is known as the immunoproteasome. another β5i variant subunit, β5t, is expressed in the thymus, leading to a thymus-specific "thymoproteasome" whose function is as yet unclear. the strength of mhc class i ligand binding is dependent on the composition of the ligand c-terminus, as peptides bind by hydrogen bonding and by close contacts with a region called the "b pocket" on the mhc surface. many mhc class i alleles prefer hydrophobic c-terminal residues, and the immunoproteasome complex is more likely to generate hydrophobic c-termini. due to its role in generating the activated form of nf-κb, an anti-apoptotic and pro-inflammatory regulator of cytokine expression, proteasomal activity has been linked to inflammatory and autoimmune diseases. increased levels of proteasome activity correlate with disease activity and have been implicated in autoimmune diseases including systemic lupus erythematosus and rheumatoid arthritis. the proteasome is also involved in intracellular antibody-mediated proteolysis of antibody-bound virions. in this neutralisation pathway, trim21 (a protein of the tripartite motif family) binds with immunoglobulin g to direct the virion to the proteasome where it is degraded. proteasome inhibitors main article: proteasome inhibitor chemical structure of bortezomib (boronated form of mg132), a proteasome inhibitor used in chemotherapy that is particularly effective against multiple myeloma bortezomib bound to the core particle in a yeast proteasome. the bortezomib molecule is in the center colored by atom type (carbon = pink, nitrogen = blue, oxygen = red, boron = yellow), surrounded by the local protein surface. the blue patch is the catalytic threonine residue whose activity is blocked by the presence of bortezomib. proteasome inhibitors have effective anti-tumor activity in cell culture, inducing apoptosis by disrupting the regulated degradation of pro-growth cell cycle proteins. this approach of selectively inducing apoptosis in tumor cells has proven effective in animal models and human trials. lactacystin, a natural product synthesized by streptomyces bacteria, was the first non-peptidic proteasome inhibitor discovered and is widely used as a research tool in biochemistry and cell biology. lactacystin was licensed to myogenics/proscript, which was acquired by millennium pharmaceuticals, now part of takeda pharmaceuticals. lactacystin covalently modifies the amino-terminal threonine of catalytic β subunits of the proteasome, particularly the β5 subunit responsible for the proteasome's chymotrypsin-like activity. this discovery helped to establish the proteasome as a mechanistically novel class of protease: an amino-terminal threonine protease. bortezomib (boronated mg132), a molecule developed by millennium pharmaceuticals and marketed as velcade, is the first proteasome inhibitor to reach clinical use as a chemotherapy agent. bortezomib is used in the treatment of multiple myeloma. notably, multiple myeloma has been observed to result in increased proteasome-derived peptide levels in blood serum that decrease to normal levels in response to successful chemotherapy. studies in animals have indicated that bortezomib may also have clinically significant effects in pancreatic cancer. preclinical and early clinical studies have been started to examine bortezomib's effectiveness in treating other b-cell-related cancers, particularly some types of non-hodgkin's lymphoma. clinical results also seem to justify use of proteasome inhibitor combined with chemotherapy, for b-cell acute lymphoblastic leukemia proteasome inhibitors can kill some types of cultured leukemia cells that are resistant to glucocorticoids. the molecule ritonavir, marketed as