Comparative Analysis of the Ubiquitin-proteasome system in Homo sapiens and Saccharomyces cerevisiae

The UPS (ubiquitin-proteasome system) is the most important degradation pathway for intracellular proteins in the eukaryotic cell. In a first step, the protein to degrade (substrate) is tagged covalently with a Ubiquitin chain via an enzyme cascade. Subsequently, the Ubiquitin chain is recognized by the proteasome and the substrate is proteolytically cleaved. Ubiquitin has several homologues, which can be conjugated to proteins posttranslationally, e.g. SUMO or NEDD8. The enzymes used for activation and conjugation of the Ubiquitin homologues are completely analogous to the ones used in the UPS. A hallmark of the UPS is that most proteins involved belong to only a few protein families, which are characterized by common functional homology domains. Several of these homology domains are found in the modification systems of Ubiquitin homologues, but these systems appear to have specific homology domains on their own as well. Homology domains may be described as mathematical models in terms of domain descriptors (profile). These profiles together with appropriate search algorithms can be applied to screen a given protein sequence for the occurrence of the corresponding homology domains. As the homology domains involved in the UPS are almost exclusively found in proteins of this and analogous systems, profiles corresponding to these homology domains seem to be an appropriate means to catalogue proteins of the UPS of a given species. In this work catalogues of proteins with a known or putative role in the UPS or analogous systems were set up for human and Saccharomyces cerevisiae (here referred to as 'yeast') based on relevant homology domains and their corresponding profiles. In combination with phylogenetic methods the evolutionary relationships between the UPS components of these two organisms were analyzed and, if possible, orthologous relationships were derived. Using the highly sensitive profile technique and including genomic databases, several new proteins were identified that have not been associated with the UPS so far. Additionally, several unexpected relationships were revealed between proteins of the UPS. For example, the postulated yeast orthologue of the antizyme of the ornithine decarboxylase could be revealed, which may be important for the experimental analysis of Ubiquitin independent protein degradation by the proteasome. Another example is human ataxin-3, in which a homology domain was found with similarity to the catalytic site of deubiquitylating enzymes. As ataxin-3 is mutated in patients with a spinocerebellar ataxia 3 (SCA3), this discovery might have implications for the elucidation of the SCA3 disease mechanism. Furthermore, predictions on the structure of the 'lid' of the 19S regulatory particle could be formulated. A comparison of the UPS-relevant protein repertoires of yeast and human allowed conclusions on the evolutionary origin of UPS components. Especially protein families with an established or putative role in substrate recognition/ubiquitylation or in the reverse process of deubiquitylation exhibited a strong diversification in human. Simultaneously, elementary functions of the UPS are carried out by almost identical protein sets in both yeast and human. Despite the extensively expanded protein families in human, not all yeast proteins associated with the UPS could be assigned to human orthologues. This finding might indicate specific processes within the yeast UPS. To summarize, the similarities of both yeast and human UPS are significant and underline the role of S. Cerevisiae as a model organism used in analyzing the UPS

Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes

BACKGROUND: The 'lid' subcomplex of the 26S proteasome and the COP9 signalosome (CSN complex) share a common architecture consisting of six subunits harbouring a so-called PCI domain (proteasome, CSN, eIF3) at their C-terminus, plus two subunits containing MPN domains (Mpr1/Pad1 N-terminal). The translation initiation complex eIF3 also contains PCI- and MPN-domain proteins, but seems to deviate from the 6+2 stoichiometry. Initially, the PCI domain was defined as the region of detectable sequence similarity between the components mentioned above. RESULTS: During an exhaustive bioinformatical analysis of proteasome components, we detected multiple instances of tetratrico-peptide repeats (TPR) in the N-terminal region of most PCI proteins, suggesting that their homology is not restricted to the PCI domain. We also detected a previously unrecognized PCI domain in the eIF3 component eIF3k, a protein whose 3D-structure has been determined recently. By using profile-guided alignment techniques, we show that the structural elements found in eIF3k are most likely conserved in all PCI proteins, resulting in a structural model for the canonical PCI domain. CONCLUSION: Our model predicts that the homology domain PCI is not a true domain in the structural sense but rather consists of two subdomains: a C-terminal 'winged helix' domain with a key role in PCI:PCI interaction, preceded by a helical repeat region. The TPR-like repeats detected in the N-terminal region of PCI proteins most likely form an uninterrupted extension of the repeats found within the PCI domain boundaries. This model allows an interpretation of several puzzling experimental results

Single photons on demand from 3D photonic band-gap structures

We describe a practical implementation of a (semi-deterministic) photon gun based on stimulated Raman adiabatic passage pumping and the strong enhancement of the photonic density of states in a photonic band-gap material. We show that this device allows {\em deterministic} and {\em unidirectional} production of single photons with a high repetition rate of the order of 100kHz. We also discuss specific 3D photonic microstructure architectures in which our model can be realized and the feasibility of implementing such a device using ${Er}^{3+}$ ions that produce single photons at the telecommunication wavelength of $1.55 \mu$m.Comment: 4 pages, 4 EPS figure

Spreading depolarization and angiographic spasm are separate mediators of delayed infarcts

In DISCHARGE-1, a recent Phase III diagnostic trial in aneurysmal subarachnoid haemorrhage patients, spreading depolarization variables were found to be an independent real-time biomarker of delayed cerebral ischaemia. We here investigated based on prospectively collected data from DISCHARGE-1 whether delayed infarcts in the anterior, middle, or posterior cerebral artery territories correlate with (i) extravascular blood volumes; (ii) predefined spreading depolarization variables, or proximal vasospasm assessed by either (iii) digital subtraction angiography or (iv) transcranial Doppler-sonography; and whether spreading depolarizations and/or vasospasm are mediators between extravascular blood and delayed infarcts. Relationships between variable groups were analysed using Spearman correlations in 136 patients. Thereafter, principal component analyses were performed for each variable group. Obtained components were included in path models with a priori defined structure. In the first path model, we only included spreading depolarization variables, as our primary interest was to investigate spreading depolarizations. Standardised path coefficients were 0.22 for the path from extravascular bloodcomponent to depolarizationcomponent (P = 0.010); and 0.44 for the path from depolarizationcomponent to the first principal component of delayed infarct volume (P < 0.001); but only 0.07 for the direct path from bloodcomponent to delayed infarctcomponent (P = 0.36). Thus, the role of spreading depolarizations as a mediator between blood and delayed infarcts was confirmed. In the principal component analysis of extravascular blood volume, intraventricular haemorrhage was not represented in the first component. Therefore, based on the correlation analyses, we also constructed another path model with bloodcomponent without intraventricular haemorrhage as first and intraventricular haemorrhage as second extrinsic variable. We found two paths, one from (subarachnoid) bloodcomponent to delayed infarctcomponent with depolarizationcomponent as mediator (path coefficients from bloodcomponent to depolarizationcomponent = 0.23, P = 0.03; path coefficients from depolarizationcomponent to delayed infarctcomponent = 0.29, P = 0.002), and one from intraventricular haemorrhage to delayed infarctcomponent with angiographic vasospasmcomponent as mediator variable (path coefficients from intraventricular haemorrhage to vasospasmcomponent = 0.24, P = 0.03; path coefficients from vasospasmcomponent to delayed infarctcomponent = 0.35, P < 0.001). Human autopsy studies shaped the hypothesis that blood clots on the cortex surface suffice to cause delayed infarcts beneath the clots. Experimentally, clot-released factors induce cortical spreading depolarizations that trigger (i) neuronal cytotoxic oedema and (ii) spreading ischaemia. The statistical mediator role of spreading depolarization variables between subarachnoid blood volume and delayed infarct volume supports this pathogenetic concept. We did not find that angiographic vasospasm triggers spreading depolarizations, but angiographic vasospasm contributed to delayed infarct volume. This could possibly result from enhancement of spreading depolarization-induced spreading ischaemia by reduced upstream blood supply.Peer Reviewe

Search for gravitational-lensing signatures in the full third observing run of the LIGO-Virgo network

Gravitational lensing by massive objects along the line of sight to the source causes distortions of gravitational wave-signals; such distortions may reveal information about fundamental physics, cosmology and astrophysics. In this work, we have extended the search for lensing signatures to all binary black hole events from the third observing run of the LIGO--Virgo network. We search for repeated signals from strong lensing by 1) performing targeted searches for subthreshold signals, 2) calculating the degree of overlap amongst the intrinsic parameters and sky location of pairs of signals, 3) comparing the similarities of the spectrograms amongst pairs of signals, and 4) performing dual-signal Bayesian analysis that takes into account selection effects and astrophysical knowledge. We also search for distortions to the gravitational waveform caused by 1) frequency-independent phase shifts in strongly lensed images, and 2) frequency-dependent modulation of the amplitude and phase due to point masses. None of these searches yields significant evidence for lensing. Finally, we use the non-detection of gravitational-wave lensing to constrain the lensing rate based on the latest merger-rate estimates and the fraction of dark matter composed of compact objects

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M&gt;70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0&lt;e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

(A) shows the overall structure of eIF3k from the PDB-entry 1RZ4 26 with β-strands and α-helices represented as ribbons and cylinders, respectively

<p><b>Copyright information:</b></p><p>Taken from "Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes"</p><p>BMC Bioinformatics 2005;6():71-71.</p><p>Published online 24 Mar 2005</p><p>PMCID:PMC1274264.</p><p>Copyright © 2005 Scheel and Hofmann; licensee BioMed Central Ltd.</p> Regions of the structure with sequence similarity to canonical PCI domain are rendered in colour. Regions belonging to the WH subdomain are shown in green, while conserved structure elements of the helical hairpin regions are shown in dark blue. The connection between β-strand 2 and 3 is not resolved and thus missing in 1RZ4. Other regions (extreme N- and C- termini, connecting helices between hairpins, unstructured regions) are shown in grey. (B) Model of a PCI protein with three additional helical hairpins upstream of the PCI domain. Within the PCI domains, only regions that can be modelled on the eIF3k template are shown. The N-terminal extension is shown in light blue, the other colours are as in figure 3a