Subcellular Distribution and Dynamics of Active Proteasome Complexes Unraveled by a Workflow Combining in Vivo Complex Cross-Linking and Quantitative Proteomics

Through protein degradation, the proteasome plays fundamental roles in different cell compartments. Although the composition of the 20S catalytic core particle (CP) has been well documented, little is known about the composition and dynamics of the regulatory complexes that play a crucial role in its activity, or about how they associate with the CP in different cell compartments, different cell lines, and in response to external stimuli. Because of difficulties performing acceptable cell fractionation while maintaining complex integrity, it has been challenging to characterize proteasome complexes by proteomic approaches. Here, we report an integrated protocol, combining a cross-linking procedure on intact cells with cell fractionation, proteasome immuno-purification, and robust label-free quantitative proteomic analysis by mass spectrometry to determine the distribution and dynamics of cellular proteasome complexes in leukemic cells. Activity profiles of proteasomes were correlated fully with the composition of protein complexes and stoichiometry. Moreover, our results suggest that, at the subcellular level, proteasome function is regulated by dynamic interactions between the 20S CP and its regulatory proteins—which modulate proteasome activity, stability, localization, or substrate uptake—rather than by profound changes in 20S CP composition. Proteasome plasticity was observed both in the 20S CP and in its network of interactions following IFNγ stimulation. The fractionation protocol also revealed specific proteolytic activities and structural features of low-abundance microsomal proteasomes from U937 and KG1a cells. These could be linked to their important roles in the endoplasmic reticulum associated degradation pathway in leukemic cells.The proteasome is the proteolytic machinery of the ubiquitin-proteasome system (UPS)¹, the main pathway responsible for degradation of intracellular proteins. As the major cellular protease, the proteasome is a key player in eukaryotic protein homeostasis and dysregulation of the UPS has been involved in neurodegenerative diseases and cancers. Because of this, proteasomes have been identified as therapeutic targets, especially for some cancers (1). Therefore, understanding the structure and function relationship controlling proteasome activity is of major interest in biology.Mammalian proteasomes are composed of a central α7β7β7α7 barrel-shaped catalytic core particle (CP), the 20S proteasome, the structure of which has been determined (2). In cells, the 20S proteasome has been found as an isolated complex, and associated with one or two regulatory particles (RPs) of identical or different protein composition (3). Four RPs have been identified: 19S, PA28αβ, PA28γ, and PA200. The 26S proteasome is a particular complex in which the CP is capped by two 19S RPs, forming a 2.5 MDa complex. Because of a high level of heterogeneity and to the dynamics of the complex, the structure of the mammalian 26S proteasome has yet to be fully determined, but major progress has been made, resulting in a suggested spatial arrangement for the yeast 26S proteasome (4, 5). In the 19S complex, some specific subunits have specialized functions: poly-ubiquitinated (polyUb) substrate recognition, ATP-unfolding, and ubiquitin recycling. These allow ubiquitin-dependent protein degradation. In addition to the RPs, other proteasome interacting proteins (PIPs) bind proteasome complexes and affect their efficiency. These include Ecm29, which plays a role in yeast 26S proteasome assembly and stability (6–8).The CP degrades proteins through three main proteolytic activities, defined as trypsin-like (T-like), chymotrypsin-like (ChT-like), and peptidyl-glutamyl peptide hydrolyzing (PGPH). These activities are exerted by the three beta catalytic subunits, β2, β5, and β1, respectively. An alternative form of the 20S proteasome has been characterized, the immuno-proteasome, where the three standard catalytic subunits are replaced by the so called immuno-subunit counterparts (β2i, β5i, β1i), which can modulate its activity. The proportion of 20S immuno-proteasome varies in different cell types and is increased in cells stimulated by interferon γ (IFNγ) (9, 10). In addition, other 20S proteasome subtypes made up of a mixed assortment of standard catalytic and immuno-subunits were recently described (11). These intermediate 20S proteasome complexes exist in high proportions in many human organs, but also in human tumor cells and dendritic cells. By generating specific antigenic peptides, intermediate 20S proteasome complexes can trigger an immune response (11). Although changes in the CP composition modulate the relative contribution of the cleavage specificity of each catalytic site, overall proteasome activity is drastically increased by association between the CP and RPs.Cell imaging technologies or subcellular fractionation combined with protein blotting techniques have located proteasome complexes in several cellular compartments, mainly the cytosol, nucleus, and associated with the cytoplasmic face of the ER (12). Unlike these antibody-based techniques, quantitative proteomic approaches provide a global view of the cellular distribution of proteins in all their physiological forms (spliced, post-translationally modified, etc.) (13) and have revealed intracellular proteasome relocalization following DNA damage (14). Given the broad function of proteasomes, in quality control, antigenic peptide generation, or short-lived protein-tuned regulation, the cell is likely to adapt proteasome plasticity and dynamics to meet specific subcellular needs or to respond to stress or other stimuli. However, the precise intracellular subunit composition and distribution of proteasome complexes remains largely undetermined. This could be explained by the highly dynamic state of proteasome complexes, their heterogeneity and instability, which make them inherently difficult to study. To deal with this, efficient strategies are needed to purify and quantify fully assembled, active proteasome complexes in homogeneous cellular fractions. These strategies will help us to understand how cells adapt proteasome activity to their needs.In vivo formaldehyde cross-linking can be an efficient tool to study protein–protein interactions and cellular networks (15). It has recently been used to stabilize labile proteasome complexes, allowing the study of the proteasome network in yeast (16) and human cells (17) by quantitative proteomic analyses.In this article, we describe an integrated strategy combining in vivo cross-linking, efficient cell fractionation, affinity purification, and robust label-free quantitative proteomics. We have used this strategy to determine the intracellular distribution of fully assembled active proteasome complexes in human leukemic cells for the first time. Following IFNγ stimulation, our strategy also revealed recruitment of specific PIPs (known to participate in the UPS) to microsomal proteasome complexes. This suggests an important role for these complexes in the endoplasmic reticulum associated degradation (ERAD) pathway.