{'fraction_non_alphanumeric': 0.02117486338797814, 'fraction_numerical': 0.0, 'mean_word_length': 5.656818181818182, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
Regulating Proteasomal Degradation in Mycobacteria: Pup-dependent and –independent Substrate Recruitment by Alternative Proteasome Assemblies

All organisms require an efficient mechanism to degrade proteins and make use of molecular degradation machines referred to as compartmentalizing chaperone-proteases. Of these large degradation complexes, the proteasome is an especially elaborate representative, which canonically occurs in eukaryotes and archaea, but also as an anomaly in the phylum of actinobacteria. A key requirement for proteasomal degradation is the modular association of the cylinder-shaped core particle (CP), whose inner walls are lined with the protease active sites, with one of a set of ring-shaped activation complexes. Proteasomal activators generally share an analogous binding mode mediated through a C-terminal binding motif. Aside from passive complexes that simply mediate access to the CP chamber, there exist proteasomal ATPase complexes (referred to here as regulatory particle, RP) in all three kingdoms, which share a common evolutionary origin and which participate in the bulk of proteasomal degradation of stably folded proteins. Those ATPases engage proteins that are marked for degradation and thread them into the proteolytic chamber of the CP under expense of energy (ATP hydrolysis). As the “marker” usually a post-translational modification of lysines with a small protein is employed, ubiquitination in eukaryotes and pupylation in Actinobacteria. Thus, pupylation and ubiquitination are functionally analogous. However, they do not share a common evolutionary origin and, therefore, differ with respect to their chemical and molecular mechanisms in protein modification. While ubiquitination passes through a threestage ligation cascade providing it with tagging specificity, only a single ligase (PafA) capable of modifying a large number of proteins is used in pupylation. Intriguingly, most enzymes involved in pupylation are themselves targets for pupylation, bearing the characteristic signature of an autoregulatory feedback loop. In the first part of this dissertation study, it is demonstrated in vitro that pupylation of the mycobacterial proteasomal ATPase (Mpa), the bacterial counterpart of the eukaryotic RP, leads to a reversible two step shut-down of the proteasomal degradation pathway in bacteria. In a first step, Pup ligated to Mpa acts as a sterical perturbation preventing complex formation between Mpa and the proteasome. In a second step, Mpa-mediated disassembly of pupylated Mpa ring complexes transfers them into a completely inactive low oligomeric or monomeric storage form. The process is shown to be reversible: depupylation by the depupylase Dop enables Mpa to reassemble spontaneously thus restoring its full activity. In the second part, the discovery of a previously unknown proteasomal activator is described which we named Bpa (bacterial protea-