Pupylation as a signal for proteasomal degradation in bacteria.

Posttranslational modifications in the form of covalently attached proteins like ubiquitin (Ub), were long considered an exclusive feature of eukaryotic organisms. The discovery of pupylation, the modification of lysine residues with a prokaryotic, ubiquitin-like protein (Pup), demonstrated that certain bacteria use a tagging pathway functionally related to ubiquitination in order to target proteins for proteasomal degradation. However, functional analogies do not translate into structural or mechanistic relatedness. Bacterial Pup, unlike eukaryotic Ub, does not adopt a ß-grasp fold, but is intrinsically disordered. Furthermore, isopeptide bond formation in the pupylation process is carried out by enzymes evolutionary descendent from glutamine synthetases. While in eukaryotes, the proteasome is the main energy-dependent protein degradation machine, bacterial proteasomes exist in addition to other architecturally related degradation complexes, and their specific role along with the role of pupylation is still poorly understood. In Mycobacterium tuberculosis (Mtb), the Pup-proteasome system contributes to pathogenicity by supporting the bacterium's persistence within host macrophages. Here, we describe the mechanism and structural framework of pupylation and the targeting of pupylated proteins to the proteasome complex. Particular attention is given to the comparison of the bacterial Pup-proteasome system and the eukaryotic ubiquitin-proteasome system. Furthermore, the involvement of pupylation and proteasomal degradation in Mtb pathogenesis is discussed together with efforts to establish the Pup-proteasome system as a drug target. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.

The mycobacterial Mpa-proteasome unfolds and degrades pupylated substrates by engaging Pup's N-terminus.

Mycobacterium tuberculosis, along with other actinobacteria, harbours proteasomes in addition to members of the general bacterial repertoire of degradation complexes. In analogy to ubiquitination in eukaryotes, substrates are tagged for proteasomal degradation with prokaryotic ubiquitin-like protein (Pup) that is recognized by the N-terminal coiled-coil domain of the ATPase Mpa (also called ARC). Here, we reconstitute the entire mycobacterial proteasome degradation system for pupylated substrates and establish its mechanistic features with respect to substrate recruitment, unfolding and degradation. We show that the Mpa-proteasome complex unfolds and degrades Pup-tagged proteins and that this activity requires physical interaction of the ATPase with the proteasome. Furthermore, we establish the N-terminal region of Pup as the structural element required for engagement of pupylated substrates into the Mpa pore. In this process, Mpa pulls on Pup to initiate unfolding of substrate proteins and to drag them toward the proteasome chamber. Unlike the eukaryotic ubiquitin, Pup is not recycled but degraded with the substrate. This assigns a dual function to Pup as both the Mpa recognition element as well as the threading determinant.

Activity of the mycobacterial proteasomal ATPase Mpa is reversibly regulated by pupylation.

Pupylation is a bacterial post-translational modification of target proteins on lysine residues with prokaryotic ubiquitin-like protein Pup. Pup-tagged substrates are recognized by a proteasome-interacting ATPase termed Mpa in Mycobacterium tuberculosis. Mpa unfolds pupylated substrates and threads them into the proteasome core particle for degradation. Interestingly, Mpa itself is also a pupylation target. Here, we show that the Pup ligase PafA predominantly produces monopupylated Mpa modified homogeneously on a single lysine residue within its C-terminal region. We demonstrate that this modification renders Mpa functionally inactive. Pupylated Mpa can no longer support Pup-mediated proteasomal degradation due to its inability to associate with the proteasome core. Mpa is further inactivated by rapid Pup- and ATPase-driven deoligomerization of the hexameric Mpa ring. We show that pupylation of Mpa is chemically and functionally reversible. Mpa regains its enzymatic activity upon depupylation by the depupylase Dop, affording a rapid and reversible activity control over Mpa function.

Dop functions as a depupylase in the prokaryotic ubiquitin-like modification pathway.

Post-translational modification of proteins with prokaryotic ubiquitin-like protein (Pup) is the bacterial equivalent of ubiquitination in eukaryotes. Mycobacterial pupylation is a two-step process in which the carboxy-terminal glutamine of Pup is first deamidated by Dop (deamidase of Pup) before ligation of the generated γ-carboxylate to substrate lysines by the Pup ligase PafA. In this study, we identify a new feature of the pupylation system by demonstrating that Dop also acts as a depupylase in the Pup proteasome system in vivo and in vitro. Dop removes Pup from substrates by specific cleavage of the isopeptide bond. Depupylation can be enhanced by the unfolding activity of the mycobacterial proteasomal ATPase Mpa.

Deletion of dop in Mycobacterium smegmatis abolishes pupylation of protein substrates in vivo.

Proteasome-bearing bacteria make use of a ubiquitin-like modification pathway to target proteins for proteasomal turnover. In a process termed pupylation, proteasomal substrates are covalently modified with the small protein Pup that serves as a degradation signal. Pup is attached to substrate proteins by action of PafA. Prior to its attachment, Pup needs to undergo deamidation at its C-terminal residue, converting glutamine to glutamate. This step is catalysed in vitro by Dop. In order to characterize Dop activity in vivo, we generated a dop deletion mutant in Mycobacterium smegmatis. In the Deltadop strain, pupylation is severely impaired and the steady-state levels of two known proteasomal substrates are drastically increased. Pupylation can be re-established by complementing the mutant with either DopWt or a Pup variant carrying a glutamate at its ultimate C-terminal position (PupGGE). Our data show that Pup is deamidated by Dop in vivo and that likely Dop alone is responsible for this activity. Furthermore, we demonstrate that a putative N-terminal ATP-binding motif is crucial for catalysis, as a single point mutation (E10A) in this motif abolishes Dop activity both in vivo and in vitro.

Tafasitamab combined with idelalisib or venetoclax in patients with CLL previously treated with a BTK inhibitor.

Patients with relapsed/refractory chronic lymphocytic leukemia (R/R CLL) whose treatment failed with a Bruton's tyrosine kinase inhibitor have poor outcomes. We investigated tafasitamab plus idelalisib (cohort A) or venetoclax (cohort B) in this patient population in a phase II study (NCT02639910). In total, 24 patients were enrolled (cohort A: n = 11, median time on study, 7.4 months; cohort B: n = 13, median time on study, 15.6 months). The most common treatment-emergent adverse event (TEAE) in cohort A was anemia (63.6%) and in cohort B was infusion-related reaction (53.8%). The most common severe TEAE was neutropenia (cohort A: 45.5%; cohort B: 46.2%). The best overall response rate was 90.9% (cohort A) and 76.9% (cohort B). Undetectable minimal residual disease in peripheral blood was achieved in 2/8 patients (cohort A) and 6/7 patients (cohort B). Overall, these results suggest that anti-CD19 antibody-based combinations may be important in the treatment of patients with CLL.

Studying chaperone-proteases using a real-time approach based on FRET.

Chaperone-proteases are responsible for the processive breakdown of proteins in eukaryotic, archaeal and bacterial cells. They are composed of a cylinder-shaped protease lined on the interior with proteolytic sites and of ATPase rings that bind to the apical sides of the protease to control substrate entry. We present a real-time FRET-based method for probing the reaction cycle of chaperone-proteases, which consists of substrate unfolding, translocation into the protease and degradation. Using this system we show that the two alternative bacterial ClpAP and ClpXP complexes share the same mechanism: after initial tag recognition, fast unfolding of substrate occurs coinciding with threading through the chaperone. Subsequent slow substrate translocation into the protease chamber leads to formation of a transient compact substrate intermediate presumably close to the chaperone-protease interface. Our data for ClpX and ClpA support the mechanical unfolding mode of action proposed for these chaperones. The general applicability of the designed FRET system is demonstrated here using in addition an archaeal PAN-proteasome complex as model for the more complex eukaryotic proteasome.

The redox state of SECIS binding protein 2 controls its localization and selenocysteine incorporation function.

Selenoproteins are central controllers of cellular redox homeostasis. Incorporation of selenocysteine (Sec) into selenoproteins employs a unique mechanism to decode the UGA stop codon. The process requires the Sec insertion sequence (SECIS) element, tRNASec, and protein factors including the SECIS binding protein 2 (SBP2). Here, we report the characterization of motifs within SBP2 that regulate its subcellular localization and function. We show that SBP2 shuttles between the nucleus and the cytoplasm via intrinsic, functional nuclear localization signal and nuclear export signal motifs and that its nuclear export is dependent on the CRM1 pathway. Oxidative stress induces nuclear accumulation of SBP2 via oxidation of cysteine residues within a redox-sensitive cysteine-rich domain. These modifications are efficiently reversed in vitro by human thioredoxin and glutaredoxin, suggesting that these antioxidant systems might regulate redox status of SBP2 in vivo. Depletion of SBP2 in cell lines using small interfering RNA results in a decrease in Sec incorporation, providing direct evidence for its requirement for selenoprotein synthesis. Furthermore, Sec incorporation is reduced substantially after treatment of cells with agents that cause oxidative stress, suggesting that nuclear sequestration of SBP2 under such conditions may represent a mechanism to regulate the expression of selenoproteins.

Shock-tube study of the thermal decomposition of CH3CHO and CH3CHO + H reaction.

The thermal decomposition of acetaldehyde, CH3CHO + M --> CH3 + HCO + M (eq 1), and the reaction CH3CHO + H --> products (eq 6) have been studied behind reflected shock waves with argon as the bath gas and using H-atom resonance absorption spectrometry as the detection technique. To suppress consecutive bimolecular reactions, the initial concentrations were kept low (approximately 10(13) cm(-3)). Reaction was investigated at temperatures ranging from 1250 to 1650 K at pressures between 1 and 5 bar. The rate coefficients were determined from the initial slope of the hydrogen profile via k1 = [CH3CHO]0(-1) x d[H]/dt, and the temperature dependences observed can be expressed by the following Arrhenius equations: k1(T, 1.4 bar) = 2.9 x 10(14) exp(-38 120 K/T) s(-1), k1(T, 2.9 bar) = 2.8 x 10(14) exp(-37 170 K/T) s(-1), and k1(T, 4.5 bar) = 1.1 x 10(14) exp(-35 150 K/T) s(-1). Reaction was studied with C2H5I as the H-atom precursor under pseudo-first-order conditions with respect to CH3CHO in the temperature range 1040-1240 K at a pressure of 1.4 bar. For the temperature dependence of the rate coefficient the following Arrhenius equation was obtained: k6(T) = 2.6 x 10(-10) exp(-3470 K/T) cm(3) s(-1). Combining our results with low-temperature data published by other authors, we recommend the following expression for the temperature range 300-2000 K: k6(T) = 6.6 x 10(-18) (T/K) (2.15) exp(-800 K/T) cm(3) s(-1). The uncertainties of the rate coefficients k1 and k6 were estimated to be +/-30%.

Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes.

Energy-dependent protein degradation is carried out by bipartite assemblies of conserved architecture. A chaperone ring comprising ATPase domains of the AAA+ -type caps both ends of a hollow protease cylinder, thereby controlling access to the active sites. Hydrolysis of ATP is translated into a force that unfolds substrates and translocates them into the protease. Several recent advances reveal how the modular composition and cellular localization of these complexes contribute to their fine-tuned regulation. Crystal structures of the ubiquitin receptor Rpn13 as well as ClpS, the bacterial determinant of N-end rule degradation, in complex with their respective substrates demonstrate principles of substrate recognition by chaperone-proteases. Mechanistic studies show that polyubiquitin tags can act in trans to target nonubiquitinated substrates for degradation.

Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes.

In analogy to ubiquitin in eukaryotes, the bacterial protein Pup is attached to lysine residues of substrate proteins, thereby targeting them for proteasomal degradation. It has been proposed that, before its attachment, Pup is modified by deamidation of its C-terminal glutamine to glutamate. Here we have identified Dop (locus tag Rv2112) as the specific deamidase of Pup in Mycobacterium tuberculosis. Deamidation requires ATP as a cofactor but not its hydrolysis. Furthermore, we provide experimental evidence that PafA (locus tag Rv2097) ligates deamidated Pup to the proteasomal substrate proteins FabD and PanB. This formation of an isopeptide bond requires hydrolysis of ATP to ADP, suggesting that deamidated Pup is activated for conjugation via phosphorylation of its C-terminal glutamate. By combining these enzymes, we have reconstituted the complete bacterial ubiquitin-like modification pathway in vitro, consisting of deamidation and ligation steps catalyzed by Pup deamidase (Dop) and Pup ligase (PafA).

A distinct structural region of the prokaryotic ubiquitin-like protein (Pup) is recognized by the N-terminal domain of the proteasomal ATPase Mpa.

The mycobacterial ubiquitin-like protein Pup is coupled to proteins, thereby rendering them as substrates for proteasome-mediated degradation. The Pup-tagged proteins are recruited by the proteasomal ATPase Mpa (also called ARC). Using a combination of biochemical and NMR methods, we characterize the structural determinants of Pup and its interaction with Mpa, demonstrating that Pup adopts a range of extended conformations with a short helical stretch in its C-terminal portion. We show that the N-terminal coiled-coil domain of Mpa makes extensive contacts along the central region of Pup leaving its N-terminus unconstrained and available for other functional interactions.

On the thermal unimolecular decomposition of the cyclohexoxy radical--an experimental and theoretical study.

The kinetics of the thermal unimolecular decomposition of the cyclohexoxy radical (c-C(6)H(11)O) was experimentally studied, and the results were analyzed in terms of statistical rate theory with molecular and transition state data from quantum chemical calculations. Laser flash photolysis of cyclohexylnitrite at 351 nm was used to produce c-C(6)H(11)O radicals, and their concentration was monitored by laser-induced fluorescence after excitation at 356.2 or 365.2 nm. The experiments were performed at temperatures ranging from 293 to 341 K and pressures between 5 and 55 bar with helium as the bath gas. Over the whole temperature range, biexponential profiles were observed, which is an indication of a consecutive reaction with a pre-equilibrium. From our quantum chemical calculations, it follows that this pre-equilibrium corresponds to the reversible ring-opening via beta-C-C bond fission to form the 6-oxo-1-hexyl radical (l-C(6)H(11)O), c-C(6)H(11)O <--> l-C(6)H(11)O (1,-1). The following temperature-dependent rate coefficients were deduced with an estimated uncertainty of +/-30%: k(1)(T) = 3.80 x 10(13) exp(-50.1 kJ mol(-1)/RT) s(-1) and k(-1)(T) = 3.02 x 10(8) exp(-23.8 kJ mol(-1)/RT) s(-1); a pressure dependence was not observed. In our theoretical analysis, the different conformers of c-C(6)H(11)O were explicitly taken into account, and the C-C torsional motions in l-C(6)H(11)O were treated as hindered internal rotators using a recently suggested approach. This explicit consideration of the hindered internal rotators significantly improved the agreement between the experimentally determined rate coefficients and the results from the quantum chemical computations.

An intrinsic degradation tag on the ClpA C-terminus regulates the balance of ClpAP complexes with different substrate specificity.

ATP-dependent protein degradation in bacteria is carried out by barrel-shaped proteases architecturally related to the proteasome. In Escherichia coli, ClpP interacts with two alternative ATPases, ClpA or ClpX, to form active protease complexes. ClpAP and ClpXP show different but overlapping substrate specificities. ClpXP is considered the primary recipient of ssrA-tagged substrates while ClpAP in complex with ClpS processes N-end rule substrates. Notably, in its free form, but not in complex with ClpS, ClpAP also degrades ssrA-tagged substrates and its own chaperone component, ClpA. To reveal the mechanism of ClpAP-mediated ClpA degradation, termed autodegradation, and its possible role in regulating ClpAP levels, we dissected ClpA to show that the flexible C-terminus of the second AAA module serves as the degradation signal. We demonstrate that ClpA becomes largely resistant to autodegradation in the absence of its C-terminus and, conversely, transfer of the last 11 residues of ClpA to the C-terminus of green fluorescent protein (GFP) renders GFP a substrate of ClpAP. This autodegradation tag bears similarity to the ssrA-tag in its degradation behavior, displaying similar catalytic turnover rates when coupled to GFP but a twofold lower apparent affinity constant compared to ssrA-tagged GFP. We show that, in analogy to the prevention of ssrA-mediated recognition, the adaptor ClpS inhibits autodegradation by a specificity switch as opposed to direct masking of the degradation signal. Our results demonstrate that in the presence of ssrA-tagged substrates, ClpA autodegradation will be competitively reduced. This simple mechanism allows for dynamic reallocation of free ClpAP versus ClpAPS in response to the presence of ssrA-tagged substrates.

Reaction of hydrogen atoms with propyne at high temperatures: an experimental and theoretical study.

The kinetics of the reaction of hydrogen atoms with propyne (pC3H4) was experimentally studied in a shock tube at temperatures ranging from 1200 to 1400 K and pressures between 1.3 and 4.0 bar with Ar as the bath gas. The hydrogen atoms (initial mole fraction 0.5-2.0 ppm) were produced by pyrolysis of C2H5I and monitored by atomic resonance absorption spectrometry under pseudo-first-order conditions with respect to propyne (initial mole fraction 5-20 ppm). From the hydrogen atom time profiles, overall rate coefficients k(ov) identical with -([pC3H4][H])(-1) x d[H]/dt for the reaction H + pC3H4 --> products ( not equal H) were deduced; the following temperature dependence was obtained: kov = 1.2 x 10(-10) exp(-2270 K/T) cm(3) s(-1) with an estimated uncertainty of +/-20%. A pressure dependence was not observed. The results are analyzed in terms of statistical rate theory with molecular and transition state data from quantum chemical calculations. Geometries were optimized using density functional theory at the B3LYP/6-31G(d) level, and single-point energies were computed at the QCISD(T)/cc-pVTZ level of theory. It is confirmed that the reaction proceeds via an addition-elimination mechanism to yield C2H2 + CH3 and via a parallel direct abstraction to give C3H3 + H2. Furthermore, it is shown that a hydrogen atom catalyzed isomerization channel to allene (aC3H4), H + pC3H4 --> aC3H4 + H, is also important. Kinetic parameters to describe the channel branching of these reactions are deduced.

Reaction of OH + NO2: high pressure experiments and falloff analysis.

High pressure experiments on the OH + NO2 reaction are presented for 3 different temperatures. At 300 K, experiments in He (p = 2-500 bar) as well as in Ar (p = 2-4 bar) were performed. The rate constants obtained in Ar agree well with values which have been reported earlier by our group (Forster, R.; Frost, M.; Fulle, D.; Hamann, H. F.; Hippler, H.; Schlepegrell, A.; Troe, J. J. Chem. Phys. 1995, 103, 2949. Fulle, D.; Hamann, H. F.; Hippler, H.; Troe, J. J. Chem. Phys. 1998, 108, 5391). In contrast, the rate coefficients determined in He were found to be 15-25% lower than the values given in our earlier publications. Additionally, results for He as bath gas at elevated temperatures (T = 400 K, p = 3-150 bar; T = 600 K, p = 3-150 bar) are reported. The results obtained at elevated pressures are found to be in good agreement with existing literature data. The observed falloff behavior is analyzed in terms of the Troe formalism taking into account two reaction channels: one yielding HNO3 and one yielding HOONO. It is found that the extracted parameters are in agreement with rate constants for vibrational relaxation and isotopic scrambling as well as with experimentally determined branching ratios. Based on our analysis we determine falloff parameters to calculate the rate constant for atmospheric conditions.

Extracellular HIV-1 Nef increases migration of monocytes.

Infiltration of human immunodeficiency virus type 1 (HIV-1)-infected and uninfected monocytes/macrophages in organs and tissues is a general phenomenon observed in progression of acquired immunodeficiency syndrome (AIDS). HIV-1 protein Nef is considered as a progression factor in AIDS, and is released from HIV-1-infected cells. Here, we show that extracellular Nef increases migration of monocytes. This effect is (i) concentration-dependent, (ii) reaches the order of magnitude of that induced by formyl-methyonyl-leucyl-proline (fMLP) or CC chemokine ligand 2 (CCL2)/monocyte chemotactic protein (MCP)-1, (iii) inhibited by anti-Nef monoclonal antibodies as well as by heating, and (iv) depends on a concentration gradient of Nef. Further, Nef does not elicit monocytic THP-1 cells to express chemokines such as CCL2, macrophage inhibitory protein-1alpha (CCL3) and macrophage inhibitory protein-1beta (CCL4). These data suggest that extracellular Nef may contribute to disease progression as well as HIV-1 spreading through affecting migration of monocytes.

Shock wave study on the thermal unimolecular decomposition of allyl radicals.

We present the first direct study on the thermal unimolecular decomposition of allyl radicals. Experiments have been performed behind shock waves, and the experimental conditions covered temperatures ranging from 1125 K up to 1570 K and pressures between 0.25 and 4.5 bar. Allyl radicals have been generated by thermal decomposition of allyl iodide, and H-atom resonance absorption spectroscopy has been used to monitor the reaction progress. A marked pressure dependence of the rate constant has been observed which is in agreement with the results from a master equation analysis. However, our experimental results as well as our Rice-Ramsperger-Kassel-Marcus calculations seem to contradict the results of Deyerl et al. (J. Chem. Phys. 1999, 110, 1450) who investigated the unimolecular decomposition of allyl radicals upon photoexcitation and tried to deduce specific rate constants for the unimolecular dissociation in the electronic ground state. At pressures around 1 bar we extracted the following rate equation: k(T) = 5.3 x 10(79)(T/K)(-19.29) exp[(-398.9 kJ/mol)/RT] s(-1). The uncertainty of the rate constant calculated from this equation is estimated to be 30%.

Control of dual-specificity phosphatase-1 expression in activated macrophages by IL-10.

Ligation of Toll-like receptors (TLR) on macrophages induces cytokines and mediators important for the control of pathogens. Macrophage activation has to be tightly controlled to prevent hyper-inflammation. Accordingly, the hallmarks of TLR-triggered signaling, nuclear translocation of NF-kappaB and phosphorylation of mitogen-activated protein kinases (MAPK), are transient events. We have mined microarray datasets for changes in the expression of phosphatases in resting and TLR-activated macrophages. Several members of the dual-specificity phosphatases (DUSP) were induced upon triggering TLR4 with LPS. Up-regulation of DUSP1 mRNA was transient after stimulation with LPS alone, but addition of the immunosuppressive cytokine IL-10 resulted in robust, continued DUSP1 expression. IL-10 also synergized with the anti-inflammatory glucocorticoid dexamethasone in the induction of DUSP1 mRNA expression in activated macrophages, as well as in the inhibition of IL-6 and IL-12 production. Increased expression of DUSP1 in IL-10-treated activated macrophages was correlated with a faster down-regulation of p38 MAPK activation. Thus, these data suggest an operational link between IL-10 and inhibition of p38 MAPK via sustained expression of DUSP1.