Role of the San1 ubiquitin ligase in the heat stress-induced degradation of nonnative Nup1 in the nuclear pore complex

The nuclear pore complex (NPC) mediates the selective exchange of macromolecules between the nucleus and the cytoplasm. Neurodegenerative diseases such as amyotrophic lateral sclerosis are characterized by mislocalization of nucleoporins (Nups), transport receptors, and Ras-related nuclear proteins into nucleoplasmic or cytosolic aggregates, underscoring the importance of precise assembly of the NPC. The assembly state of large protein complexes is strictly monitored by the protein quality control system. The ubiquitin-proteasome system may eliminate aberrant, misfolded, and/or orphan components; however, the involvement of the ubiquitin-proteasome system in the degradation of nonnative Nups in the NPC remains unclear. Here, we show that in Saccharomyces cerevisiae, although Nup1 (the FG-Nup component of the central core of the NPC) was stable, C-terminally green fluorescent protein-tagged Nup1, which had been incorporated into the NPC, was degraded by the proteasome especially under heat stress conditions. The degradation was dependent on the San1 ubiquitin ligase and Cdc48/p97, as well as its cofactor Doa1. We also demonstrate that San1 weakly but certainly contributes to the degradation of nontagged endogenous Nup1 in cells defective in NPC biogenesis by the deletion of NUP120. In addition, the overexpression of SAN1 exacerbated the growth defect phenotype of nup120Δ cells, which may be caused by excess degradation of defective Nups due to the deletion of NUP120. These biochemical and genetic data suggest that San1 is involved in the degradation of nonnative Nups generated by genetic mutation or when NPC biogenesis is impaired.

TEMPO-Assisted Free-Radical-Initiated Peptide Sequencing Mass Spectrometry for Ubiquitin Ions: An Insight on the Gas-Phase Conformations

TEMPO ((2,2,6,6-tetramethylpiperidine-1-yl)oxyl)-assisted free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) is applied to the top-down tandem mass spectrometry of guanidinated ubiquitin (UB(Gu)) ions, i.e., p-TEMPO-Bn-Sc-guanidinated ubiquitin (UBT(Gu)), to shed a light on gas-phase ubiquitin conformations. Thermal activation of UBT(Gu) ions produced protein backbone fragments of radical character, i.e., a-/x- and c-/z-type fragments. It is in contrast to the collision-induced dissociation (CID) results for UB(Gu), which dominantly showed the specific charge-remote CID fragments of b-/y-type at the C-terminal side of glutamic acid (E) and aspartic acid (D). The transfer of a radical "through space" was mainly observed for the +5 and +6 UBT(Gu) ions. This provides the information about folding/unfolding and structural proximity between the positions of the incipient benzyl radical site and fragmented sites. The analysis of FRIPS MS results for the +5 charge state ubiquitin ions shows that the +5 charge state ubiquitin ions bear a conformational resemblance to the native ubiquitin (X-ray crystallography structure), particularly in the central sequence region, whereas some deviations were observed in the unstable second structure region (β₂) close to the N-terminus. The ion mobility spectrometry results also corroborate the FRIPS MS results in terms of their conformations (or structures). The experimental results obtained in this study clearly demonstrate a potential of the TEMPO-assisted FRIPS MS as one of the methods for the elucidation of the overall gas-phase protein structures.

Cryo-LESA Mass Spectrometry-a Step Towards Truly Native Surface Sampling of Proteins

Liquid extraction surface analysis (LESA) is a powerful method for measuring proteins from surfaces. In this work, we present development and initial testing of a cryo-platform for LESA mass spectrometry of proteins. We explore the use of native sampling solutions for probing proteins directly from frozen surfaces. Our initial results from analysis of ubiquitin and hemoglobin standards showed that protein and protein complex refolding or unfolding occurs during the liquid solvent extraction stage of routine room temperature LESA. However, by employing the cryo-sampling method, the refolding or unfolding of protein ubiquitin can be dramatically reduced, while for the protein complex of hemoglobin, its native structures can be better preserved compared with room temperature sampling. This indicates that a truly native LESA sampling method of proteins is feasible. We also present detection of proteins directly from a frozen tissue section. Interestingly, slight conformational differences are observed from different regions of the frozen tissue surface. Further development of this strategy should be considered as a method for preserving, maintaining, and studying proteins in their native states, directly from tissue. Graphical Abstract.

Conditions for Analysis of Native Protein Structures Using Uniform Field Drift Tube Ion Mobility Mass Spectrometry and Characterization of Stable Calibrants for TWIM-MS

Determination of collisional cross sections (CCS) by travelling wave ion mobility mass spectrometry (TWIM-MS) requires calibration against standards for which the CCS has been measured previously by drift tube ion mobility mass spectrometry (DTIM-MS). The different extents of collisional activation in TWIM-MS and DTIM-MS can give rise to discrepancies in the CCS of calibrants across the two platforms. Furthermore, the conditions required to ionize and transmit large, folded proteins and assemblies may variably affect the structure of the calibrants and analytes. Stable hetero-oligomeric phospholipase A₂ (PDx) and its subunits were characterized as calibrants for TWIM-MS. Conditions for acquisition of native-like TWIM (Synapt G1 HDMS) and DTIM (Agilent 6560 IM-Q-TOF) mass spectra were optimized to ensure the spectra exhibited similar charge state distributions. CCS measurements (DTIM-MS) for ubiquitin, cytochrome c, holo-myoglobin, serum albumin and glutamate dehydrogenase were in good agreement with other recent results determined using this and other DTIM-MS instruments. PDx and its β and γ subunits were stable across a wide range of cone and trap voltages in TWIM-MS and were stable in the presence of organic solvents. The CCS of PDx and its subunits were determined by DTIM-MS and were used as calibrants in determination of CCS of native-like cytochrome c, holo-myoglobin, carbonic anhydrase, serum albumin and haemoglobin in TWIM-MS. The CCS values were in good agreement with those measured by DTIM-MS where available. These experiments demonstrate conditions for analysis of native-like proteins using a commercially available DTIM-MS instrument, characterize robust calibrants for TWIM-MS, and present CCS values determined by DTIM-MS and TWIM-MS for native proteins to add to the current literature database. Graphical Abstract ᅟ.

Maximizing Selective Cleavages at Aspartic Acid and Proline Residues for the Identification of Intact Proteins

A new approach for the identification of intact proteins has been developed that relies on the generation of relatively few abundant products from specific cleavage sites. This strategy is intended to complement standard approaches that seek to generate many fragments relatively non-selectively. Specifically, this strategy seeks to maximize selective cleavage at aspartic acid and proline residues via collisional activation of precursor ions formed via electrospray ionization (ESI) under denaturing conditions. A statistical analysis of the SWISS-PROT database was used to predict the number of arginine residues for a given intact protein mass and predict a m/z range where the protein carries a similar charge to the number of arginine residues thereby enhancing cleavage at aspartic acid residues by limiting proton mobility. Cleavage at aspartic acid residues is predicted to be most favorable in the m/z range of 1500-2500, a range higher than that normally generated by ESI at low pH. Gas-phase proton transfer ion/ion reactions are therefore used for precursor ion concentration from relatively high charge states followed by ion isolation and subsequent generation of precursor ions within the optimal m/z range via a second proton transfer reaction step. It is shown that the majority of product ion abundance is concentrated into cleavages C-terminal to aspartic acid residues and N-terminal to proline residues for ions generated by this process. Implementation of a scoring system that weights both ion fragment type and ion fragment area demonstrated identification of standard proteins, ranging in mass from 8.5 to 29.0 kDa. Graphical Abstract ᅟ.

Top-down analysis of novel synthetic branched proteins

A strategy for top-down analysis of branched proteins has been reported earlier, which relies on electron transfer dissociation assisted by collisional activation, and software designed for graphic interpretation of tandem mass spectra and adapted for branched proteins. In the present study, the strategy is applied to identify unknown and novel products of reactions in which rationally mutated proteoforms of Rub1 are used to probe the selectivity of E1 and E2 enzymes normally active in ubiquitination. To test and demonstrate this application, components and attachment sites of three branched dimers are deduced and the mutations are confirmed.

Optimization of identity operation in NMR spectroscopy via genetic algorithm: Application to the TEDOR experiment

Identity operation in the form of π pulses is widely used in NMR spectroscopy. For an isolated single spin system, a sequence of even number of π pulses performs an identity operation, leaving the spin state essentially unaltered. For multi-spin systems, trains of π pulses with appropriate phases and time delays modulate the spin Hamiltonian to perform operations such as decoupling and recoupling. However, experimental imperfections often jeopardize the outcome, leading to severe losses in sensitivity. Here, we demonstrate that a newly designed Genetic Algorithm (GA) is able to optimize a train of π pulses, resulting in a robust identity operation. As proof-of-concept, we optimized the recoupling sequence in the transferred-echo double-resonance (TEDOR) pulse sequence, a key experiment in biological magic angle spinning (MAS) solid-state NMR for measuring multiple carbon-nitrogen distances. The GA modified TEDOR (GMO-TEDOR) experiment with improved recoupling efficiency results in a net gain of sensitivity up to 28% as tested on a uniformly ¹³C, ¹⁵N labeled microcrystalline ubiquitin sample. The robust identity operation achieved via GA paves the way for the optimization of several other pulse sequences used for both solid- and liquid-state NMR used for decoupling, recoupling, and relaxation experiments.

Preparing to read the ubiquitin code: top-down analysis of unanchored ubiquitin tetramers

The characterization of polyubiquitin chains has been an analytical challenge for several decades. It has been shown that anchored and unanchored polyubiquitin chains with different isopeptide linkages and lengths exhibit a wide range of profoundly different cellular functions. However, structure function studies have been hindered by the difficulty of characterizing these complex chain structures. This report presents a broadly applicable workflow to characterize ubiquitin tetramers without the need for genetic mutations or reiterative immunoprecipitations. We use a top-down proteomic strategy that exploits ETciD activation on an orbitrap Fusion Lumos and manual interpretation aided by graphical interpretation of mass shifts to facilitate characterization of chain topography and lysine linkage sites. Our workflow differentiates all topological features of the numerous isomers of tetraubiquitin, which have molecular masses in excess of 34 000 Da and identifies linkage sites in these branched proteins. Copyright © 2016 John Wiley & Sons, Ltd.

Puromycin induces SUMO and ubiquitin redistribution upon proteasome inhibition

We have previously reported the co-localization of O-propargyl-puromycin (OP-Puro) with SUMO-2/3 and ubiquitin at promyelocytic leukemia-nuclear bodies (PML-NBs) in the presence of the proteasome inhibitor MG132, implying a role for the ubiquitin family in sequestering OP-puromycylated immature polypeptides to the nucleus during impaired proteasome activity. Here, we found that as expected puromycin induced SUMO-1/2/3 accumulation with ubiquitin at multiple nuclear foci in HeLa cells when co-exposed to MG132. Co-administration of puromycin and MG132 also facilitated redistribution of PML and the SUMO-targeted ubiquitin ligase RNF4 concurrently with SUMO-2/3. As removal of the drugs from the medium led to disappearance of the SUMO-2/3-ubiquitin nuclear foci, our findings indicated that nuclear assembly/disassembly of SUMO-2/3 and ubiquitin was pharmacologically manipulable, supporting our previous observation on OP-Puro, which predicted the ubiquitin family function in sequestrating aberrant proteins to the nucleus.

To What Extent is FAIMS Beneficial in the Analysis of Proteins?

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered.

Mitophagy programs: mechanisms and physiological implications of mitochondrial targeting by autophagy

Mitochondria are an essential source of ATP for cellular function, but when damaged, mitochondria generate a plethora of stress signals, which lead to cellular dysfunction and eventually programmed cell death. Thus, a major component of maintaining cellular homeostasis is the recognition and removal of dysfunctional mitochondria through autophagy-mediated degradation, i.e., mitophagy. Mitophagy further constitutes a developmental program, and undergoes a high degree of crosstalk with apoptosis. Reduced mitochondrial quality control is linked to disease pathogenesis, suggesting the importance of process elucidation as a clinical target. Recent work has revealed multiple mitophagy programs that operate independently or undergo crosstalk, and require modulated autophagy receptor activities at outer membranes of mitochondria. Here, we review these mitophagy programs, focusing on pathway mechanisms which recognize and target mitochondria for sequestration by autophagosomes, as well as mechanisms controlling pathway activities. Furthermore, we provide an introduction to the currently available methods for detecting mitophagy.

Western Blotting Inaccuracies with Unverified Antibodies: Need for a Western Blotting Minimal Reporting Standard (WBMRS)

Western blotting is a commonly used technique in biological research. A major problem with Western blotting is not the method itself, but the use of poor quality antibodies as well as the use of different experimental conditions that affect the linearity and sensitivity of the Western blot. Investigation of some conditions that are commonly used and often modified in Western blotting, as well as some commercial antibodies, showed that published articles often fail to report critical parameters needed to reproduce the results. These parameters include the amount of protein loaded, the blocking solution and conditions used, the amount of primary and secondary antibodies used, the antibody incubation solutions, the detection method and the quantification method utilized. In the present study, comparison of ubiquitinated proteins in rat heart and liver samples showed different results depending on the antibody utilized. Validation of five commercial ubiquitin antibodies using purified ubiquitinated proteins, ubiquitin chains and free ubiquitin showed that these antibodies differ in their ability to detect free ubiquitin or ubiquitinated proteins. Investigating proteins modified with interferon-stimulated gene 15 (ISG15) in young and old rat hearts using six commercially available antibodies showed that most antibodies gave different semi-quantitative results, suggesting large variability among antibodies. Evidence showing the importance of the Western blot buffer and the concentration of antibody used is presented. Hence there is a critical need for comprehensive reporting of experimental conditions to improve the accuracy and reproducibility of Western blot analysis. A Western blotting minimal reporting standard (WBMRS) is suggested to improve the reproducibility of Western blot analysis.

Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation

Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.

SPLIFF: A Single-Cell Method to Map Protein-Protein Interactions in Time and Space

Protein interactions occur at certain times and at specific cellular places. The past years have seen a massive accumulation of binary protein-protein interaction data. The rapid increase of this context-free information necessitates robust methods to monitor protein interactions with temporal and spatial resolution in single cells. We have developed a simple split-ubiquitin-based method (SPLIFF) that uses the ratio of two fluorescent reporters as a signal for protein-protein interactions. One protein of the pair of interest is attached to the linear fusion of mCherry, the C-terminal half of ubiquitin, and GFP (mCherry-Cub-GFP). The other potential binding partner is expressed as a C-terminal fusion to the N-terminal half of ubiquitin (Nub). Upon co-expression the interaction between the two proteins of interest induces the reassociation of Nub and Cub to the native-like ubiquitin. GFP is subsequently cleaved from the C-terminus of Cub and degraded whereas the red-fluorescent mCherry stays attached to the Cub-fusion protein. We first implemented this method in the model yeast Saccharomyces cerevisiae. One fusion protein is expressed in cells of the a-mating type and the complementary fusion protein in cells of the α-mating type. Upon mixing, both cell types fuse and the Nub- and Cub-fusion proteins are free to interact. The red and green fluorescence is monitored by two-channel fluorescence time-lapse microcopy. The moment of cell fusion defines the start of the analysis. The calculated ratio of green to red fluorescence allows mapping the spatiotemporal interaction profiles of the investigated proteins in single cells.

[The pathological TDP-43 protein expression in the central nervous system of motor neuron disease]

OBJECTIVE

To understand pathological TDP-43 features in the central nervous systems of patients with clinically and autopsy confirmed motor neuron disease (MND).

METHODS

The clinical and histopathological features of 4 cases with MND confirmed by autopsy were summarized; anti-ubiquitin (Ub) and anti-TDP-43 immunohistochemical staining were carried out on tissue of brains and spinal cords from 4 cases with MND and 3 control cases without history of neurological disorders.

RESULTS

These 4 cases presented with typical clinical and histologic features of MND. Ub-positive inclusions were observed in brain and spinal cord from 3 cases with the Ub-positive inclusions of skein- round- and lewy body- like structures. Strong TDP-43 pathological staining in brain and spinal cord was identified in 2 cases with MND presented as neuronal and glial cytoplasmic inclusions with various shapes. The TDP-43 positive inclusions were widely distributed in the motor cortex of brain and the anterior horn of spinal cord. TDP-43 weak staining in the spinal cord tissue was observed in 1 case with MND. No Ub- and TDP-43 positive inclusions were found in 3 control cases.

CONCLUSION

There is widespread pathological TDP-43 expression in the central nervous system of MND. TDP-43 positive inclusions in MND have relatively high specificity. It is worth further study on their formation mechanism.

In ESI-source H/D exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa: the role of the temperature of the desolvating capillary on H/D exchange

Transition of proteins from the solution to the gas phase during electrospray ionization remains a challenging problem despite the large amount of attention it has received during the past few decades. One of the major questions relates to the extent to which proteins in the gas phase retain their condensed phase structures. We have used in-electrospray source hydrogen/deuterium exchange to determine the number of deuterium incorporations as a function of protein mass, charge state and temperature of the desolvating capillary where the reaction occurs. All experiments were performed on a Thermo LTQ FT Ultra equipped with a 7-T superconducting magnet. Ions were generated by an IonMax Electrospray ion source operated in the positive ESI mode. Deuterium exchange was performed by introducing a droplet of D2 O beneath the ESI capillary. We systematically investigated gas phase hydrogen/deuterium (H/D) exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa. We observed that almost all proteins demonstrate similar exchange rates for all charge states and that these rates increase exponentially with the temperature of the desolvating capillary. We did not observe any clear correlation of the number of H/D exchanges with the value of the cross section for a corresponding charge state. We have demonstrated the possibility of performing in-ESI source H/D exchange of large proteins under atmospheric pressure. The simplicity of the experimental setup makes it a useful experimental technique that can be applied for the investigation of gas phase conformations of proteins.

[Expression of proteins related neurodegeneration in autopsy brains of the aged]

OBJECTIVE

To recognize relationship of protein related neurodegeneration abnormal aggregation in the aged brains with their cognitive and motor functions.

METHODS

Brain tissues from the consecutive autopsy cases of the aged from January 2005 to December 2006 in PLA General Hospital were carried out for immunohistochemical staining with beta amyloid, tau, α-synuclein and ubiquitin antibodies. The consortium to establish a registry for Alzheimer's disease (CERAD) was used to semi-quantitatively analyze Aβ positive core plaques density and Braak staging for tau positive neurofibrillary tangles (NFTs) and α-synuclein positive Lewy bodies. In addition, Aβ positive cerebral amyloid angiopathy (CAA), neuritic plaques and various ubiquitin positive structures were also observed. The relationship of these protein abnormal depositions in the aged brains with cognitive and motor functions were analyzed.

RESULTS

In brain tissues of 16 consecutive autopsy cases of the aged from 78 to 95 years, there were 13 cases with Aβ positive core plaques, their density was 2 cases with sparse, 2 cases with moderate and 9 cases with frequent, respectively, according to CREAD.Eight cases with Aβ positive CAA were found, including 6 cases of mild CAA and 2 cases of severe CAA. There were 12 cases with tau positive NFTs, including 6 cases with Braak stageI-II, 4 cases with stage III-IV and 2 cases with stage V-VI. There were 5 cases with frequent Aβ core plaques, meanwhile existing numerous tau/ubiquitin positive neuritic plaques and Braak stage IV-VI of tau positive NFTs, all of them presented cognitive dysfunction. Among 4 other cases with frequent Aβ core plaques, only one case coexisted α-synuclein positive Lewy bodies showed moderate cognitive impairment, remaining 3 cases did not present cognitive dysfunction. There were 4 cases with α-synuclein positive Lewy bodies in the brainstem, and all of these cases presented parkinsonian motor dysfunction. 13 cases with ubiquitin positive structures were found.

CONCLUSIONS

Beta amyloid protein positive deposit in the aged brain is an important marker of normal brain aging and cognitive impairment; frequent Aβ core plaques in the neocortex plus Braak IV and above tau positive NFTs are closely related to cognitive dysfunction of Alzheimer's disease; α-synuclein positive Lewy bodies in the brainstem is one of the important pathological markers of parkinsonian motor disorders; ubiquitin deposition involves the development of some characteristic structures of several neurodegenerative diseases.

Quantum mechanical NMR simulation algorithm for protein-size spin systems

Nuclear magnetic resonance spectroscopy is one of the few remaining areas of physical chemistry for which polynomially scaling quantum mechanical simulation methods have not so far been available. In this communication we adapt the restricted state space approximation to protein NMR spectroscopy and illustrate its performance by simulating common 2D and 3D liquid state NMR experiments (including accurate description of relaxation processes using Bloch-Redfield-Wangsness theory) on isotopically enriched human ubiquitin - a protein containing over a thousand nuclear spins forming an irregular polycyclic three-dimensional coupling lattice. The algorithm uses careful tailoring of the density operator space to only include nuclear spin states that are populated to a significant extent. The reduced state space is generated by analysing spin connectivity and decoherence properties: rapidly relaxing states as well as correlations between topologically remote spins are dropped from the basis set.

Enhancing the quality of protein conformation ensembles with relative populations

The function and dynamics of many proteins are best understood not from a single structure but from an ensemble. A high quality ensemble is necessary for accurately delineating protein dynamics. However, conformations in an ensemble are generally given equal weights. Few attempts were made to assign relative populations to the conformations, mainly due to the lack of right experimental data. Here we propose a method for assigning relative populations to ensembles using experimental residue dipolar couplings (RDC) as constraints, and show that relative populations can significantly enhance an ensemble's ability in representing the native states and dynamics. The method works by identifying conformation states within an ensemble and assigning appropriate relative populations to them. Each of these conformation states is represented by a sub-ensemble consisting of a subset of the conformations. Application to the ubiquitin X-ray ensemble clearly identifies two key conformation states, with relative populations in excellent agreement with previous work. We then apply the method to a reprotonated ERNST ensemble that is enhanced with a switched conformation, and show that as a result of population reweighting, not only the reproduction of RDCs is significantly improved, but common conformational features (particularly the dihedral angle distributions of ϕ 53 and ψ 52) also emerge for both the X-ray ensemble and the reprotonated ERNST ensemble.

Ubiquitination-induced fluorescence complementation (UiFC) for detection of K48 ubiquitin chains in vitro and in live cells

Proteins can be modified with eight homogenous ubiquitin chains linked by an isopeptide bond between the C-terminus of one ubiquitin and an amine from one of the seven lysines or the N-terminal methionine of the next ubiquitin. These topologically distinct ubiquitin chains signal for many essential cellular functions, such as protein degradation, cell cycle progression, DNA repair, and signal transduction. The lysine 48 (K48)-linked ubiquitin chain is one of the most abundant chains and a major proteasome-targeting signal in cells. Despite recent advancements in imaging linkage-specific polyubiquitin chains, no tool is available for imaging K48 chains in live cells. Here we report on a ubiquitination-induced fluorescence complementation (UiFC) assay for detecting K48 ubiquitin chains in vitro and in live cells. For this assay, two nonfluorescent fragments of a fluorescent protein were fused to the ubiquitin-interacting motifs (UIMs) of epsin1 protein. Upon simultaneous binding to a ubiquitin chain, the nonfluorescent fragments of the two fusion proteins are brought in close proximity to reconstitute fluorescence. When used in vitro, UiFC preferentially detected K48 ubiquitin chains with excellent signal-to-noise ratio. Time-lapse imaging revealed that UiFC is capable of monitoring increases in polyubiquitination induced by treatment with proteasome inhibitor, by agents that induce stress, and during mitophagy in live cells.

Separation of protein conformers by differential ion mobility in hydrogen-rich gases

Proteins in solution or the gas phase tend to exhibit multiple conformational families, each comprising distinct structures. Separation methods have generally failed to resolve these, with their convolution producing wide peaks. Here, we report full separation of >10 conformers for most ubiquitin charge states by the new approach of differential ion mobility spectrometry (field asymmetric waveform ion mobility spectrometry, FAIMS) employing H2/N2 gas mixtures with up to 85% H2. The resolving power (up to 400) is five times the highest previously achieved (using He/N2 buffers), greatly increasing the separation specificity. The peak widths match the narrowest obtained by FAIMS for any species under the same conditions and scale with the protein charge state (z) and ion residence time (t) as z(-1/2) and t(-1/2), as prescribed for instrumental (diffusional) broadening. This suggests resolution of specific geometries rather than broader ensembles.

High-resolution differential ion mobility spectrometry of a protein

Use of elevated electric fields and helium-rich gases has recently enabled differential ion mobility spectrometry (IMS) with a resolving power up to R ∼ 300. Here we applied that technique to a protein (ubiquitin), achieving R up to ∼80 and separating previously unresolved conformers. While still limited by conformational multiplicity, this resolution is some 4 times greater than that previously reported using either conventional (drift-tube or traveling-wave) or differential IMS. The capability for fine resolution of protein conformers may open new avenues for proteoform separations in top-down and intact-protein proteomics.

Immunofluorescence Reveals Ubiquitination of Retained Distal Cytoplasmic Droplets on Ejaculated Porcine Spermatozoa

The purpose of the present study was twofold: 1) to determine if antibodies raised against ubiquitin would recognize antigens associated with the porcine cytoplasmic droplet (CD), and 2) to determine if the same antibody would identify ubiquitinated substrates on the surface of morphologically abnormal boar spermatozoa. Permeabilization with the detergent Triton X-100 (0.05%) showed virtually all CDs to be ubiquitin positive. Distal droplets (DDs) retained in situ on boar spermatozoa were readily labeled following Triton permeabilization, whereas DDs present on nonpermeabilized cells were not. Negative control preparations lacked the ubiquitin staining on the DD. The use of microtubes for fixation and incubation provided clearer images as well as better sperm cell distribution and density than an initial slide-mounted technique. Immunoblotting indicated that larger amounts of ubiquitinated proteins were present in extracts from sperm cells from an ejaculate with an abnormally high percentage of retained DDs (52% DDs) compared to a morphologically normal sample (6% DDs). The primary antibody recognized both mono-ubiquitin of bovine origin (8.5 kd) and human ubiquitin conjugate (35 kd), as demonstrated by Western blot. Preabsorption of the anti-ubiquitin antibody with purified bovine ubiquitin was successful in preventing diaminobenzidine staining of sperm extract from the high DD ejaculate. The presence of antigens recognized by anti-ubiquitin antibodies in the boar sperm CD, coupled with the possibility that superfluous ubiquitin species are detrimental to embryonic development by targeting critical paternally contributed zygotic organelles, raises concerns that retained DDs may be more detrimental to fertility than previously suspected.

Protein analyses using differential ion mobility microchips with mass spectrometry

Differential ion mobility spectrometry (FAIMS) integrated with mass spectrometry (MS) is a powerful new tool for biological and environmental analyses. Large proteins occupy regions of FAIMS spectra distinct from peptides, lipids, or other medium-size biomolecules, likely because strong electric fields align huge dipoles common to macroions. Here we confirm this phenomenon in separations of proteins at extreme fields using FAIMS chips coupled to MS and demonstrate their use to detect even minor amounts of large proteins in complex matrixes of smaller proteins and peptides.

Solution additives that desalt protein ions in native mass spectrometry

The presence of many salts, such as sodium chloride, can adversely affect the performance of native electrospray ionization mass spectrometry for the analysis of proteins and protein complexes by reducing the overall molecular ion abundances and distributing signal for any given charge state into many cationized forms with various numbers of adducts attached. Several solution additives, such as ammonium bromide, ammonium iodide, and NaSbF(6), can significantly lower the extent of sodium ion adduction to the molecular ions of proteins and protein complexes. For ubiquitin, addition of 25 mM ammonium bromide or ammonium iodide into aqueous solutions also containing 1.0 mM NaCl results in a factor of 72 and 56 increase, respectively, in the relative abundances of the fully protonated molecular ions compared to when these additives are not present. The effectiveness of this method for reducing sodium ion adduction is related to the low proton affinity (PA) values of the anions. Anions with very low PA also have a propensity to adduct as an acid molecule, but these adducts can be readily dissociated from the molecular ions either by activation in the source or subsequently by collisional activation in the mass spectrometer. This method of reducing sodium ion adduction to proteins is simple and requires no experimental modifications, making it an attractive alternative to other methods for desalting proteins prior to mass spectrometry analysis.

A new calibrant for matrix-assisted laser desorption/ionization time-of-flight-time-of-flight post-source decay tandem mass spectrometry of non-digested proteins for top-down proteomic analysis

RATIONALE

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight-time-of-flight (TOF-TOF) post-source decay (PSD) tandem mass spectrometry (MS/MS) has seen increasing use for analysis of non-digested protein ions for top-down proteomic identification. However, there is no commonly accepted calibrant for this purpose beyond the use of peptide calibrants whose fragment ions span a lower mass-to-charge (m/z) range.

METHODS

We have used the PSD-generated fragment ions of disulfide-reduced/alkylated thioredoxin (AlkTrx) for TOF-TOF calibration in reflectron mode for the purpose of PSD-MS/MS analysis. The average m/z values of AlkTrx fragment ions were used for calibration. The quality of the calibration was assessed from the observed fragment ion mass error of MS/MS of the YahO protein from an unfractionated bacterial cell lysate of Escherichia coli O157:H7 as well as from MS/MS of bovine ubiquitin. The fragment ion mass errors of these two analytes were also used to assess instrument calibration using the monoisotopic fragment ions of [Glu(1)]-fibrinopeptide B (GluFib).

RESULTS

A general improvement in fragment ion mass accuracy was observed using the AlkTrx calibration compared to the GluFib calibration which resulted in a more significant top-down proteomic identification of these analyte proteins.

CONCLUSIONS

Our results suggest that AlkTrx may be useful as a calibrant for MALDI-TOF-TOF-PSD-MS/MS of small and modest-sized protein ions. The uniform fragmentation efficiency of YahO across its sequence suggests that it may be useful as a post-calibration standard to assess PSD-MS/MS instrument performance as well as establishing appropriate top-down proteomic fragment ion tolerances.

Characterization and biological function analysis of the trim3a gene from zebrafish (Danio rerio)

The biological significance of tripartite motif (TRIM) proteins is increasingly being appreciated due to their roles in a broad range of biological processes that associated with innate immunity. In this study, we have described the structural and functional analysis of TRIM3a from zebrafish. Annotation of domain architectures found that the TRIM3a fulfills the TRIM-NHL rule of domain composition with a Filamin/ABP280 domain and NHL repeats at its C-terminal region. In addition, the mRNA expression level of TRIM3a was the highest in brain, and with a relatively higher level in spleen, liver, and gill. A strong expression starting at 36 h post fertilization (hpf) was observed by real-time PCR and could be detected in brain by in situ hybridization, suggesting that TRIM3a protein might play an important role in brain development in zebrafish. Considering that TRIM3a has a RING finger domain, we expressed and purified the TRIM3a protein and performed ubiquitylation assays, our results showed that TRIM3a underwent self-polyubiquitylation in combination with E1, UbcH5c, biotin-ubiquitin in vitro. Meanwhile, TRIM3a-R without the RING domain was expressed and purified as well, in vitro ubiquitylation assays showed that the self-ubiquitylation of TRIM3a was dependent on its RING domain, suggesting that TRIM3a might function as a RING finger E3 ubiquitin ligase.

FLAMEnGO: a fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data

Building on a recent method by Matthews and co-workers [1], we developed a new and efficient algorithm to assign methyl resonances from sparse and ambiguous NMR data. The new algorithm (FLAMEnGO: Fuzzy Logic Assignment of MEthyl GrOups) uses Monte Carlo sampling in conjunction with fuzzy logic to obtain the assignment of methyl resonances at high fidelity. Furthermore, we demonstrate that the inclusion of paramagnetic relaxation enhancement (PRE) data in the assignment strategy increases the percentage of correct assignments with sparse NOE data. Using synthetic tests and experimental data we show that this new approach provides up to ∼80% correct assignments with only 30% of methyl-methyl NOE data. In the experimental case of ubiquitin, PRE data from two spin labeled sites improve the percentage of assigned methyl groups up to ∼91%. This new strategy promises to further expand methyl group NMR spectroscopy to very large macromolecular systems.

Homonuclear mixing sequences for perdeuterated proteins

We tested the performance of several (13)C homonuclear mixing sequences on perdeuterated microcrystalline ubiquitin. All sequences were applied without (1)H decoupling and at relatively low MAS frequencies. We found that RFDR gave the highest overall transfer efficiency and that DREAM performs surprisingly well under these conditions being twice as efficient in the aliphatic region of the spectrum than the other mixing sequences tested.

Acid hydrolysis of proteins in matrix assisted laser desorption ionization matrices

Sample preparation is crucial to the success of experiments in biological mass spectrometry. In proteomics, digestion of the proteins into peptides is a key step for "bottom-up" approaches. Often, the use of enzymes requires physiological conditions, producing peptides that must be extracted or further purified before mass analysis. Chemical cleavage reagents offer more flexibility and can be more compatible with downstream mass analysis. Expanding on prior work using acid hydrolysis, proteolysis with matrix-assisted laser desorption ionization (MALDI) matrices is presented. This sample preparation can be performed rapidly with a minimum of reagents and sample handling, but it must first be evaluated in terms of digestion efficiency, missed cleavages, and side reactions before implementation for in-gel digestion and in-solution digestion using minimal volumes of protein. Time courses of acid hydrolysis are shown for protein standards, illustrating the sensitivity of this type of sample preparation, minimization of side reactions, and performance for proteins in mixtures. To illustrate the potential for sensitive detection of a specific protein, MALDI matrix hydrolysis is used to digest a protein immunoprecipitated from cell lysate.

[Neuropathology of frontotemporal lobar degeneration with ubiquitinated inclusions]

Frontotemporal lobar degeneration (FTLD) has two pathological types: tau-positive and tau-negative. The most common tau-negative type is FTLD with ubiquitinated inclusions, which are composed of TAR DNA-binding protein-43 (TDP-43) (FTLD-TDP). FTLD-TDP can be subdivided into at least three main types based on the histological patterns of TDP-43-positive neuronal cytoplasmic inclusions (NCI), dystrophic neurites (DN), and neuronal intranuclear inclusions (NII). Type 1 is characterized by the predominance of long, thick DN in the cortices with numerous NCI in the hippocampus, amygdala, and basal ganglia, accompanied by the degeneration of the pyramidal tract in the spinal cord. Type 2 is characterized by numerous NCI in the cortices, associated with the involvement of lower motor neurons. TDP-43-positive skein-like inclusions and round inclusions identical to those observed in amyotrophic lateral sclerosis (ALS) patients are also seen in the lower motor neurons in type 2. Type 3 is characterized by both NCI and DN with variable NII. Lower motor neuron involvement is usually less prominent in types 1 and 3 than in type 2. These findings suggest that FTLD-TDP and ALS are at two ends of the same disease spectrum, i. e., TDP-43 proteinopathy.

[Neuropathological similarities and differences between frontotemporal lobar degeneration with ubiquitin inclusions and amyotrophic lateral sclerosis with dementia]

Findings of clinical, neuropathological and biochemical studies have supported the idea that frontotemporal lobar degeneration with ubiquitin inclusions (FTLD-U) and amyotrophic lateral sclerosis (ALS) are part of a neurological disease spectrum. This concept is now further strengthened by the recent discovery of a 43-kDa transactivating responsive sequence DNA-binding protein (TDP-43) as a key component of the underlying neuropathology of FTLD-U, ALS with dementia (ALS-D) and ALS. Here we describe the clinicopathological features of selected autopsy cases belonging to this disease spectrum, and discuss the neuropathological similarities and differences between FTLD-U and ALS-D, with special reference to the morphology, distribution and density of ubiquitin/TDP-43-positive abnormal structures, along with a review of the literature.

Immunohistochemical expression of ubiquitin and telomerase in cervical cancer

Ubiquitin and telomerase immunohistochemical expression patterns in cervical cancer were compared with normal cervical tissue samples. Eighty-one cervical cancer cases and 22 normal exo-endocervical tissue were examined with polyclonal antibody for ubiquitin and 44G12 clone for telomerase using tissue microarrays. The results were interpreted using a semiquantitative scale The average age of patients was 50.67 years. The most frequent histological types were moderately differentiated epidermoid carcinoma (43.5%), according to the degree of differentiation, and endocervical adenocarcinoma (42.1%). Immunohistochemical findings were as follows: 98.7% of cervical cancers showed immunoexpression for ubiquitin and 52.6% for telomerase. Statistically significant differences were found in tumor immunoreactivity when compared with control tissue (p < 0.0007) for both biomarkers. There was no significant difference in biomarker expression at different histological types of tumors, although telomerase was less expressed in endocervical adenocarcinoma. Our findings confirm that abnormal immunoexpression pattern of ubiquitin and telomerase is common in HPV-positive cervical cancer, indicating the existence of an intense degradation of proteins, subsequent cellular immortalization and maintenance of the malignant phenotype.

Data-dependent electron transfer dissociation of large peptides and medium size proteins in a QTOF instrument on a liquid chromatography timescale

Liquid chromatography (LC) electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) of protein digests is demonstrated in a hybrid quadrupole-hexapole orthogonal time-of-flight (OTOF) mass spectrometer. Analyte ions are selected in a mass-analyzing quadrupole, accumulated in the hexapole linear ETD reaction cell and mutually stored with ETD reagent anions. Product ions are collected in an ion cooler and then analyzed by an OTOF mass analyzer. The hexapole structure of the ETD reaction cell allows for a broad fragment ion mass range distribution and a high ion storage capacity. Analytically useful ETD OTOF-MS/MS spectra could be obtained at a rate of faster than 2 Hz. When used in conjunction with LC this high speed allows for several MS and MS/MS spectra to be obtained across each LC peak. An MS scan is used to select the precursor ions. With a 1 m flight tube and single reflection, resolutions of about 10 k and a mass accuracy of 5 ppm were achieved. When analyzing a 100 fmol solution of a tryptic digest of bovine serum albumin (BSA) by LC/ETD MS/MS, 27 unique peptides were identified with a summed Mascot score of 1316 using the Swiss Prot database. In addition, we explored the capability for analyzing small proteins with the present hybrid instrument. ETD MS/MS of intact ubiquitin ([M+12H](12+)) leads to the identification of the protein with a Mascot score of 264.

[Immunohistochemical study of nonspecific interstitial pneumonia and ubiquitin-positive pneumocytes in elderly patients]

AIM

The Ubiquitin (Ub)-proteasome system maintains cellular homeostasis through proteolysis, and Ub appears in the damaged cells of many organs. Nonspecific interstitial pneumonia (NSIP)in elderly patients was studied to clarify the relationship between Ub-positive cells, cellular damage, and resistance to therapy.

METHODS

Specimens of surgical lung biopsy with the NSIP pattern (NSIP/P) from 13 patients (mean age, 68 years old) were examined histologically and immunohistochemically. Pneumocytes examined under high-power microscopy were counted for eosinophilic inclusion bodies and Ub-positive cells. NSIP/P was histologically evaluated and cases were scored for erosion and intraluminal granulation tissue subtypes (polypoid, mural, or occluded) as lung injury markers. NSIP/P was subdivided into cellular NSIP and fibrosing NSIP according to the proportions of interstitial inflammation and fibrosis.

RESULTS

1) Six of 13 patients with NSIP/P had Ub-positive cells (Ub+ group), and all inclusions identified by light-microscope were positive for Ub. A greater number of Ub+ pneumocytes were found compared with the inclusions by light-microscope, and Ub immunostaining was useful for the detection of the inclusions. 2) Granulation tissue scores in the Ub+ group were significantly greater than in the Ub- group (p<0.05); there was no difference in granulation tissue subtypes between the groups. 3) Granulation tissue scores in fibrosing NSIP/P (including each subtype) were significantly greater than in cellular NSIP/P. 4) After a follow-up period, there was no correlation between Ub+ group and NSIP therapy resistance or between the granulation tissue subtypes and therapy resistance.

CONCLUSION

Some elderly patients with NSIP had inclusions, and these inclusions were Ub+. Pneumocyte injury might occur via the Ub-proteasome system pathway in elderly patients with NSIP/P, although there was no correlation between Ub+ pneumocytes and therapy resistance.

Detection of ubiquitination in 2DE

Ubiquitination involves the tagging of proteins with one (mono-) or more (poly-) ubiquitin molecules. Primarily the role of ubiquitination involves mainly short-lived and regulatory proteins being tagged with a poly-ubiquitin tail, thus introducing a hydrophobic patch that allows the protein to be identified and degraded by the 26S proteasome. Transfer of ubiquitin to the lysine residue of a target protein is a multi-step ATP-dependent process. The functions of ubiquitination have been extended in recent years to all areas of biology, many of them proteasome independent. As a small fraction of any protein may potentially be ubiquitinated, this may explain the wide range and large number of proteins that have been identified as being tagged with ubiquitin in the literature. This chapter outlines a general method for an indication of ubiquitination levels and identification of ubiquitinated proteins by two-dimensional electrophoresis in combination with immunoblotting.

Rapid identification of differentiation markers from whole epithelial cells by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and statistical analysis

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) was applied to identify markers for cellular differentiation. The differentiation of a human colon epithelial carcinoma T84 cell line was monitored over a period of 28 days by transepithelial electrical resistance (TER) measurements, alkaline phosphatase (AP) assay, and MALDI-TOF mass spectral fingerprints combined with statistical analysis. MALDI-MS generated specific mass spectral fingerprints characteristic of cell differentiation. Twenty-two ions were selected as diagnostic signals of fully differentiated T84 cells. Ten protein ion signals, detected by MALDI-MS and validated by statistical analysis, were proposed as T84 cell differentiation markers. Among these signals, ubiquitin was identified as a T84 cell differentiation marker by nanospray liquid chromatography/tandem mass spectrometry (nanoLC/MS/MS). Moreover, depending on the concentration of the cells seeded on the growth support, it was possible to predict the timing of the exponential phase and of cellular differentiation by MALDI-MS-derived marker ions. MALDI-TOFMS was compared to other methods for the determination of cellular differentiation: TER measurements are rapid but yield limited information as to the cellular differentiation state. AP assays are more specific for the differentiation state but take more time. By contrast, MALDI-MS has been found to be a fast, sensitive and precise method for cell differentiation assessment and provides the opportunity for multiplexing and high throughput. Moreover, the consumable costs per assay are very low.

Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometry

We report a simple approach for determining ion score cutoffs that permit the confident identification of ubiquitinated proteins by tandem mass spectrometry (MS/MS). Initial experiments involving the analysis of gel bands containing multi-Ubiquitin chains with quadrupole time-of-flight and quadrupole ion trap mass spectrometers revealed that standard ion score cutoffs used for database searching were not sufficiently stringent. We also found that false positive and false negative rates (FPR and FNR) varied significantly depending on the cutoff scores used and that appropriate cutoffs could only be determined following a systematic evaluation of false positive rates. When standard cutoff scores were used for the analysis of complex mixtures of ubiquitinated proteins, unacceptably high FPR were observed. Finally, we found that FPR for ubiquitinated proteins are affected by the size of the protein database that is searched. These observations may be applicable for the study of other post-translational modifications.

Nuclear receptor and nuclear receptor target gene messenger ribonucleic acid levels at different sites of the gastrointestinal tract and in liver of healthy dogs

Nuclear receptors (NR) are ligand-activated transcription factors that regulate different metabolic pathways by influencing the expression of target genes. The current study examined mRNA abundance of NR and NR target genes at different sites of the gastrointestinal tract (GIT) and the liver of healthy dogs (Beagles; n = 11). Samples of GIT and liver were collected postmortem and homogenized, total RNA was extracted and reverse transcribed, and gene expression was quantified by real-time reverse-transcription PCR relative to the mean of 3 housekeeping genes (beta-actin, glyceraldehyde-3-phosphate dehydrogenase, and ubi-quitin). Differences were observed (P < or = 0.05) in the mRNA abundance among stomach (St), duodenum (Du), jejunum (Je), ileum (Il), and colon (Col) for NR [pregnane X receptor (Du, Je > Il, Col > St), peroxisome proliferator-associated receptor gamma (St, Du, Col > Je, Il), constitutive androstane receptor (Je, Du > Il, Col), and retinoid x receptor alpha (Du > Il)] and NR target genes [glutathione-S-transferase A3-3 (Du > Je > St, Il; St > Col), phenol-sulfating phenol sulfotransferase 1A1 (Du, Je > Il, St; Col > St), cytochrome P450 3A12 (Du, Je > St, Il, Col), multiple drug resistance gene 1 (Du, Je, Il, Col > St), multiple drug resistance-associated protein 2 (Je, Du > Il > St, Col), multiple drug resistance-associated protein 3 (Col > St > Il; Du > Je, Il; St > Il), NR corepressor 2 (St > Il, Col), and cytochrome P450 reductase (St, Du, Je > Il, Col)], but not for peroxisome proliferator-associated receptor alpha. Differences (P > 0.05) in mRNA abundance in the liver relative to the GIT were also observed. In conclusion, the presence of numerous differences in expression of NR and NR target genes in different parts of the GIT and in liver of healthy dogs may be associated with location-specific functions and regulation of GIT regions.

Fragmentation of multiply-charged intact protein ions using MALDI TOF-TOF mass spectrometry

Top down proteomics in a TOF-TOF instrument was further explored by examining the fragmentation of multiply charged precursors ions generated by matrix-assisted laser desorption ionization. Evaluation of sample preparation conditions allowed selection of solvent/matrix conditions and sample deposition methods to produce sufficiently abundant doubly and triply charged precursor ions for subsequent CID experiments. As previously reported, preferential cleavage was observed at sites C-terminal to acidic residues and N-terminal to proline residues for all ions examined. An increase in nonpreferential fragmentation as well as additional low mass product ions was observed in the spectra from multiply charged precursor ions providing increased sequence coverage. This enhanced fragmentation from multiply charged precursor ions became increasingly important with increasing protein molecular weight and facilitates protein identification using database searching algorithms. The useable mass range for MALDI TOF-TOF analysis of intact proteins has been expanded to 18.2 kDa using this approach.

Ubiquitin reduces contusion volume after controlled cortical impact injury in rats

Recent data suggest that ubiquitin has anti-inflammatory properties and therapeutic potential after severe trauma and brain injuries. However, direct evidence for its neuroprotective effects has not yet been provided. We hypothesized that ubiquitin treatment is neuroprotective, and thus reduces brain edema formation and cortical contusion volume after closed traumatic brain injuries. To test this hypothesis, a focal cortical contusion was induced using a controlled cortical impact (CCI) model in Sprague-Dawley rats. Animals (n = 27) were randomized to either 1.5 mg/kg ubiquitin or vehicle (placebo) intravenously within 5 min after CCI. Blood pressure, arterial blood gases (ABG) and intracranial pressure (ICP) were monitored. Ubiquitin serum and cerebrospinal fluid levels were measured by ELISA. Brain water content was quantified gravimetrically after 24 h and cerebral contusion volume was determined in triphenyltetrazolium-chloride stained brains after 7 days. All animals recovered to normal activity. ICP and cerebral perfusion pressures were normal at the end of the observation period. Ubiquitin serum and CSF levels at 24 h and 7 days after CCI were similar in both groups. With ubiquitin brain water content of the injured hemisphere was slightly lower (n = 6/group; 79.97 +/- 0.29% vs. 81.11 +/- 0.52%; p = 0.08). Cortical contusion volume was significantly lower with ubiquitin (n = 7-8/group; 32.88 +/- 2.1 mm(3) vs. 43.96 +/- 4.56 mm(3); p = 0.025). This study shows that ubiquitin treatment after brain injury has direct neuroprotective effects, as demonstrated by improved brain morphology 7 days after brain injury. In connection with its beneficial effects in our previous studies, these data suggest ubiquitin as a promising candidate protein therapeutic for the treatment of brain injuries.

Residual water suppression by indirect covariance NMR

Residual water solvent signals in 2D NMR experiments adversely affect appearance and subsequent analysis of spectra. A method for water suppression that is based on indirect covariance processing is described. It produces a symmetric spectrum with a water signal that is substantially decreased or completely absent. The method, which can be combined with other water suppression schemes, is demonstrated for 2D TOCSY, NOESY, and ROESY spectra of the protein, ubiquitin in aqueous solution.

Targeted acquisition for real-time NMR spectroscopy

A target-oriented approach for the acquisition of information in biomolecular NMR spectroscopy is being developed. This approach combines concurrent data accumulation, processing, and monitoring of spectral quality. Real-time estimation of parameters allows acquisition to be stopped when results are complete and have a specified precision. The technique is based on multidimensional decomposition, which can process incomplete data. An incremental nonuniform sampling scheme ensures the optimization of resolution sensitivity. To validate this method, 3D HNCO spectra of three biomolecular systems (8 kDa ubiquitin, 22 kDa barstar-barnase complex, and 82 kDa malate synthase G) are processed incrementally at small acquisition time steps. The range of molecular sizes illustrates applicability in both sample- and sensitivity-limited regimes. In each case, the target was to acquire all backbone resonances in the spectra. For the three systems, the targets are achieved after 4.5 min, 1.6 h, and 22 h of acquisition time, respectively. A number of other targets that can be similarly monitored as a function of time are discussed.

In vitro production of Mallory bodies and intracellular hyaline bodies: the central role of sequestosome 1/p62

Mallory bodies (MBs) and intracellular hyaline bodies (IHBs) are characteristic hepatocellular inclusions. MBs are hallmarks of steatohepatitis, whereas IHBs have first been detected in hepatocellular carcinoma. MBs and IHBs contain ubiquitin and sequestosome 1/p62 (p62), a stress-inducible adapter protein with affinity to polyubiquitinated proteins. MBs differ from IHBs by their keratin content and morphology. In vitro transfections were undertaken to study under defined conditions MB and IHB formation, their pathogenesis, and relationship. CHO-K1, TIB73, and HeLa cells were transfected with keratin 8, keratin 18, ubiquitin, p62, and p62 lacking the ubiquitin binding domain (p62DeltaUBA) and analyzed by immunofluorescence, immunoelectron microscopy, and immunoblotting. Transfection of p62 complementary deoxyribonucleic acid (cDNA) alone led to cytoplasmic aggregates consisting of filaments mostly arranged in parallel arrays resembling amyloid and type 1 MBs. Transfection of p62 and ubiquitin resulted in globular cytoplasmic aggregates with indistinct fibrillar ultrastructure resembling IHBs. Cotransfection of p62, keratin 8, and ubiquitin was necessary to produce in vitro type 2 MBs-like aggregates consisting of randomly oriented 10- to 15-nm filaments. A similar result was obtained when keratin 8 was replaced by keratin 18. After cotransfection of p62DeltaUBA, keratin 8, and ubiquitin, keratin formed irregular aggregates with electron-dense granular-amorphous ultrastructure (resembling type 3 MBs), whereas p62DeltaUBA remained in diffuse cytoplasmic distribution.

CONCLUSION

Our studies show that in vitro development of classical type 2 MBs requires overexpression of keratin 8 (or keratin 18), ubiquitin, and p62 containing the ubiquitin binding domain, whereas IHBs result from overexpression of p62 together with ubiquitin without keratin involvement.

Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway

The ubiquitin proteasome system (UPS) comprises hundreds of different conjugation/deconjugation enzymes and multiple receptors that recognize ubiquitylated proteins. A formidable challenge to deciphering the biology of ubiquitin is to map the networks of substrates and ligands for components of the UPS. Several different receptors guide ubiquitylated substrates to the proteasome, and neither the basis for specificity nor the relative contribution of each pathway is known. To address how broad of a role the ubiquitin receptor Rpn10 (S5a) plays in turnover of proteasome substrates, we implemented a method to perform quantitative analysis of ubiquitin conjugates affinity-purified from experimentally perturbed and reference cultures of Saccharomyces cerevisiae that were differentially labeled with 14N and 15N isotopes. Shotgun mass spectrometry coupled with relative quantification using metabolic labeling and statistical analysis based on q values revealed ubiquitylated proteins that increased or decreased in level in response to a particular treatment. We first identified over 225 candidate UPS substrates that accumulated as ubiquitin conjugates upon proteasome inhibition. To determine which of these proteins were influenced by Rpn10, we evaluated the ubiquitin conjugate proteomes in cells lacking either the entire Rpn10 (rpn10delta) (or only its UIM (ubiquitin-interacting motif) polyubiquitin-binding domain (uimdelta)). Twenty-seven percent of the UPS substrates accumulated as ubiquitylated species in rpn10delta cells, whereas only one-fifth as many accumulated in uimdelta cells. These findings underscore a broad role for Rpn10 in turnover of ubiquitylated substrates but a relatively modest role for its ubiquitin-binding UIM domain. This approach illustrates the feasibility of systems-level quantitative analysis to map enzyme-substrate networks in the UPS.

Ubiquitin trafficking to the lysosome: keeping the house tidy and getting rid of unwanted guests

Bacterial killing by autophagic delivery to the lysosomal compartment has been shown for Mycobacteria, Streptococcus, Shigella, Legionella and Salmonella, indicating an important role for this conserved trafficking pathway for the control of intracellular bacterial pathogens.(1-5) In a recent study we found that solubilized lysosomes isolated from bone marrow-derived macrophages had potent antibacterial properties against M. tuberculosis and M. smegmatis that were associated with ubiquitin and ubiquitin-derived peptides. We propose that ubiquitinated proteins are delivered to the lysosomal compartment, where degradation by lysosomal proteinases generates ubiquitin-derived peptides with antimycobacterial properties. This surprising finding provokes a number of questions regarding the nature and trafficking of ubiquitin and ubiquitin-modified proteins in mammalian cells. We discuss the possible role(s) that the multivesicular body (MVB), the late endosome and the autophagosome may play in trafficking of ubiquitinated proteins to the lysosome.