Proteasome
Proteasomes are essential protein complexes responsible for the degradation of proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases. Proteasomes are found inside all eukaryotes and archaea, and in some bacteria.
In eukaryotes, proteasomes are located both in the nucleus and in the cytoplasm. The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of gene expression, and responses to oxidative stress. The importance of proteolytic degradation inside cells and the role of ubiquitin in proteolytic pathways was acknowledged in the award of the 2004 Nobel Prize in Chemistry to Aaron Ciechanover, Avram Hershko and Irwin Rose.
The core 20S proteasome is a cylindrical, compartmental protein complex of four stacked rings forming a central pore. Each ring is composed of seven individual proteins. The inner two rings are made of seven β subunits that contain three to seven protease active sites, within the central chamber of the complex. Access to these proteases is gated on the top of the 20S, and access is regulated by several large protein complexes, including the 19S Regulatory Particle forming the 26S Proteasome. In eukaryotes, proteins that are tagged with Ubiquitin are targeted to the 26S proteasome and is the penultimate step of the Ubiquitin Proteasome System. Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins.
Proteins that are destined for degradation by the 26S proteasome require two main elements: 1) the attachment of a small protein called ubiquitin and 2) an unstructured region of about 25 amino acids. Proteins that lack this unstructured region can have another motor, cdc48 in yeast or P97 in humans, generate this unstructured region by a unique mechanism where ubiquitin is unfolded by cdc48 and its cofactors Npl4/Ufd1. The tagging of a target protein by ubiquitin is catalyzed by cascade of enzymes consisting of the Ubiquitin-activating enzyme, Ubiquitin-conjugating enzyme, and ubiquitin ligases. Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein in an ATP dependent manner. The degradation process by the proteasome yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins.
Discovery
Before the discovery of the ubiquitin–proteasome system, protein degradation in cells was thought to rely mainly on lysosomes, membrane-bound organelles with acidic and protease-filled interiors that can degrade and then recycle exogenous proteins and aged or damaged organelles. However, work by Joseph Etlinger and Alfred L. Goldberg in 1977 on ATP-dependent protein degradation in reticulocytes, which lack lysosomes, suggested the presence of a second intracellular degradation mechanism. This was shown in 1978 to be composed of several distinct protein chains, a novelty among proteases at the time. Later work on modification of histones led to the identification of an unexpected covalent modification of the histone protein by a bond between a lysine side chain of the histone and the C-terminal glycine residue of ubiquitin, a protein that had no known function. It was then discovered that a previously identified protein associated with proteolytic degradation, known as ATP-dependent proteolysis factor 1, was the same protein as ubiquitin. The proteolytic activities of this system were isolated as a multi-protein complex originally called the multi-catalytic proteinase complex by Sherwin Wilk and Marion Orlowski. Later, the ATP-dependent proteolytic complex that was responsible for ubiquitin-dependent protein degradation was discovered and was called the 26S proteasome.Much of the early work leading up to the discovery of the ubiquitin proteasome system occurred in the late 1970s and early 1980s at the Technion in the laboratory of Avram Hershko, where Aaron Ciechanover worked as a graduate student. Hershko's year-long sabbatical in the laboratory of Irwin Rose at the Fox Chase Cancer Center provided key conceptual insights, though Rose later downplayed his role in the discovery. The three shared the 2004 Nobel Prize in Chemistry for their work in discovering this system.
Although electron microscopy data revealing the stacked-ring structure of the proteasome became available in the mid-1980s, the first structure of the proteasome core particle was not solved by X-ray crystallography until 1994. Groundbreaking work on cryo-EM by Wolfgang Baumeister's group revealed the overall architecture of the 26S proteasome and enabled biochemical experiments to provide a general mechanism for ubiquitin dependent degradation. In 2018, the first structure of the yeast 26S proteasome followed by the first atomic structures of the human 26S proteasome holoenzyme in complex with a polyubiquitylated protein substrate were solved by cryogenic electron microscopy, confirming the mechanisms by which the substrate is recognized, deubiquitylated, unfolded and degraded by the 26S proteasome. Detailed biochemistry has provided a general mechanism for ubiquitin-dependent degradation by the proteasome: binding of a substrate to the proteasome, engagement of an unstructured region to the AAA motor accompanied by a major conformational change of the proteasome, translocation dependent de-ubiquitination by Rpn11, followed by unfolding and proteolysis by the 20S core particle.
Cryo-Electron tomography has also provided unique insight into proteasomes within cells. Looking at neurons, proteasomes were found to be in the same ground-state and processing states as determined by cryo-EM. Interestingly, most proteasomes were in the ground state suggesting that they were ready to start working when a cell undergoes proteotoxic stress. In a separate study, when protein aggregates in the form of poly-Gly-Ala repeats are overexpressed, proteasome are captured stalled on these aggregates. Cryo-ET of green algae Chlamydomonas reinhardtii found that 26S proteasomes within the nucleus cluster around the Nuclear pore complex and are specifically attached to the membrane.
Structure and organization
The proteasome subcomponents are often referred to by their Svedberg sedimentation coefficient. The proteasome most exclusively used in mammals is the cytosolic 26S proteasome, which is about in molecular mass containing one 20S protein subcomplex and one 19S regulatory cap subcomplex. Doubly capped proteasomes are referred to as 30S proteasomes also exist in the cell. The 20S core is hollow and provides an enclosed cavity in which proteins are degraded; openings at the two ends of the core are gates that allow the target protein to enter. Each end of the core particle can associate with a 19S regulatory subunit that contains multiple ATPase active sites and ubiquitin binding sites; it is this structure that recognizes polyubiquitinated proteins and transfers them to the catalytic core.Several alternative caps can also bind the 20S core: 11S or Blm10 are also known to associate with the core and can bind either one or both sides. An alternative form of regulatory subunit called the 11S particle can associate with the core in essentially the same manner as the 19S particle; the 11S may play a role in degradation of foreign peptides such as those produced after infection by a virus. Archaea and bacteria also have proteasomes and have alternative caps that bind their cores. The following will discuss the structure and function of these subcomplexes.
20S core particle
The number and diversity of subunits contained in the 20S core particle depends on the organism; the number of distinct and specialized subunits is larger in multicellular than unicellular organisms and larger in eukaryotes than in prokaryotes. All 20S particles consist of four stacked heptameric ring structures that are themselves composed of two different types of subunits; α subunits are structural in nature, whereas β subunits are predominantly catalytic. The α subunits are pseudoenzymes homologous to β subunits. They are assembled with their N-termini adjacent to that of the β subunits. The outer two rings in the stack consist of seven α subunits each, which serve as docking domains for the regulatory particles and the alpha subunits N-termini form a gate that blocks unregulated access of substrates to the interior cavity. The inner two rings each consist of seven β subunits and in their N-termini contain the protease active sites that perform the proteolysis reactions. Three distinct catalytic activities were identified in the purified complex: chymotrypsin-like, trypsin-like and peptidylglutamyl-peptide hydrolyzing. The size of the proteasome is relatively conserved and is about 150 angstroms by 115 Å. The interior chamber is at most 53 Å wide, though the entrance can be as narrow as 13 Å, suggesting that substrate proteins must be at least partially unfolded to enter.In archaea such as Thermoplasma acidophilum, all the α and all the β subunits are identical, whereas eukaryotic proteasomes such as those in yeast contain seven distinct types of each subunit. In mammals, the β1, β2, and β5 subunits are catalytic; although they share a common mechanism, they have three distinct substrate specificities considered chymotrypsin-like, trypsin-like, and peptidyl-glutamyl peptide-hydrolyzing. Alternative β forms denoted β1i, β2i, and β5i can be expressed in hematopoietic cells in response to exposure to pro-inflammatory signals such as cytokines, in particular, interferon gamma. The proteasome assembled with these alternative subunits is known as the immunoproteasome, whose substrate specificity is altered relative to the normal proteasome.
Recently an alternative proteasome was identified in human cells that lack the α3 core subunit. These proteasomes instead form 20S core particles containing an additional α4 subunit in place of the missing α3 subunit. These alternative 'α4-α4' proteasomes have been known previously to exist in yeast. Although the precise function of these proteasome isoforms is still largely unknown, cells expressing these proteasomes show enhanced resistance to toxicity induced by metallic ions such as cadmium.
The peptides that are formed by the 20S core have recently been shown to act as important metabolites for both programmed cell death and for immunity. Molecular glues that target BRD4 for degradation, lead to 26S proteasome generated peptides that release Inhibitor of apoptosis leading to Apoptosis, suggesting that the peptides generated by the 26S act as secondary metabolites that drive major cell processes.