Protecting the proteome: Eukaryotic cotranslational quality control pathways.

The correct decoding of messenger RNAs (mRNAs) into proteins is an essential cellular task. The translational process is monitored by several quality control (QC) mechanisms that recognize defective translation complexes in which ribosomes are stalled on substrate mRNAs. Stalled translation complexes occur when defects in the mRNA template, the translation machinery, or the nascent polypeptide arrest the ribosome during translation elongation or termination. These QC events promote the disassembly of the stalled translation complex and the recycling and/or degradation of the individual mRNA, ribosomal, and/or nascent polypeptide components, thereby clearing the cell of improper translation products and defective components of the translation machinery

Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches.

Previous genetic and biochemical studies from Saccharomyces cerevisiae have identified a critical ribosome-associated quality control complex (RQC) that facilitates resolution of stalled ribosomal complexes. While components of the mammalian RQC have been examined in vitro, a systematic characterization of RQC protein interactions in mammalian cells has yet to be described. Here we utilize both proximity-labeling proteomic approaches, BioID and APEX, and traditional affinity-based strategies to both identify interacting proteins of mammalian RQC members and putative substrates for the RQC resident E3 ligase, Ltn1. Surprisingly, validation studies revealed that a subset of substrates are ubiquitylated by Ltn1 in a regulatory manner that does not result in subsequent substrate degradation. We demonstrate that Ltn1 catalyzes the regulatory ubiquitylation of ribosomal protein S6 kinase 1 and 2 (RPS6KA1, RPS6KA3). Further, loss of Ltn1 function results in hyperactivation of RSK1/2 signaling without impacting RSK1/2 protein turnover. These results suggest that Ltn1-mediated RSK1/2 ubiquitylation is inhibitory and establishes a new role for Ltn1 in regulating mitogen-activated kinase signaling via regulatory RSK1/2 ubiquitylation. Taken together, our results suggest that mammalian RQC interactions are difficult to observe and may be more transient than the homologous complex in S. cerevisiae and that Ltn1 has RQC-independent functions

Bombardier Enables Delivery of Short-Form Bomanins in the Drosophila Toll Response.

Toll mediates a robust and effective innate immune response across vertebrates and invertebrates. In Drosophila melanogaster, activation of Toll by systemic infection drives the accumulation of a rich repertoire of immune effectors in hemolymph, including the recently characterized Bomanins, as well as the classical antimicrobial peptides (AMPs). Here we report the functional characterization of a Toll-induced hemolymph protein encoded by the bombardier (CG18067) gene. Using the CRISPR/Cas9 system to generate a precise deletion of the bombardier transcriptional unit, we found that Bombardier is required for Toll-mediated defense against fungi and Gram-positive bacteria. Assaying cell-free hemolymph, we found that the Bomanin-dependent candidacidal activity is also dependent on Bombardier, but is independent of the antifungal AMPs Drosomycin and Metchnikowin. Using mass spectrometry, we demonstrated that deletion of bombardier results in the specific absence of short-form Bomanins from hemolymph. In addition, flies lacking Bombardier exhibited a defect in pathogen tolerance that we trace to an aberrant condition triggered by Toll activation. These results lead us to a model in which the presence of Bombardier in wild-type flies enables the proper folding, secretion, or intermolecular associations of short-form Bomanins, and the absence of Bombardier disrupts one or more of these steps, resulting in defects in both immune resistance and tolerance

Differential Sialylation Modulates Voltage-gated Na+ Channel Gating throughout the Developing Myocardium

Voltage-gated sodium channel function from neonatal and adult rat cardiomyocytes was measured and compared. Channels from neonatal ventricles required an ∼10 mV greater depolarization for voltage-dependent gating events than did channels from neonatal atria and adult atria and ventricles. We questioned whether such gating shifts were due to developmental and/or chamber-dependent changes in channel-associated functional sialic acids. Thus, all gating characteristics for channels from neonatal atria and adult atria and ventricles shifted significantly to more depolarized potentials after removal of surface sialic acids. Desialylation of channels from neonatal ventricles did not affect channel gating. After removal of the complete surface N-glycosylation structures, gating of channels from neonatal atria and adult atria and ventricles shifted to depolarized potentials nearly identical to those measured for channels from neonatal ventricles. Gating of channels from neonatal ventricles were unaffected by such deglycosylation. Immunoblot gel shift analyses indicated that voltage-gated sodium channel α subunits from neonatal atria and adult atria and ventricles are more heavily sialylated than α subunits from neonatal ventricles. The data are consistent with approximately 15 more sialic acid residues attached to each α subunit from neonatal atria and adult atria and ventricles. The data indicate that differential sialylation of myocyte voltage-gated sodium channel α subunits is responsible for much of the developmental and chamber-specific remodeling of channel gating observed here. Further, cardiac excitability is likely impacted by these sialic acid–dependent gating effects, such as modulation of the rate of recovery from inactivation. A novel mechanism is described by which cardiac voltage-gated sodium channel gating and subsequently cardiac rhythms are modulated by changes in channel-associated sialic acids

Site-specific identification and quantitation of endogenous SUMO modifications under native conditions.

Small ubiquitin-like modifier (SUMO) modification regulates numerous cellular processes. Unlike ubiquitin, detection of endogenous SUMOylated proteins is limited by the lack of naturally occurring protease sites in the C-terminal tail of SUMO proteins. Proteome-wide detection of SUMOylation sites on target proteins typically requires ectopic expression of mutant SUMOs with introduced tryptic sites. Here, we report a method for proteome-wide, site-level detection of endogenous SUMOylation that uses α-lytic protease, WaLP. WaLP digestion of SUMOylated proteins generates peptides containing SUMO-remnant diglycyl-lysine (KGG) at the site of SUMO modification. Using previously developed immuno-affinity isolation of KGG-containing peptides followed by mass spectrometry, we identified 1209 unique endogenous SUMO modification sites. We also demonstrate the impact of proteasome inhibition on ubiquitin and SUMO-modified proteomes using parallel quantitation of ubiquitylated and SUMOylated peptides. This methodological advancement enables determination of endogenous SUMOylated proteins under completely native conditions

The Octarepeat Domain of the Prion Protein Binds Cu(II) with Three Distinct Coordination Modes at pH 7.4

The prion protein (PrP) binds Cu2+ in its N-terminal octarepeat domain. This unusual domain is comprised of four or more tandem repeats of the fundamental sequence PHGGGWGQ. Previous work from our laboratories demonstrates that at full copper occupancy, each HGGGW segment binds a single Cu2+. However, several recent studies suggest that low copper occupancy favors different coordination modes, possibly involving imidazoles from histidines in adjacent octapeptide segments. This is investigated here using a combination of X-band EPR, S-band EPR, and ESEEM, along with a library of modified peptides designed to favor different coordination interactions. At pH 7.4, three distinct coordination modes are identified. Each mode is fully characterized to reveal a series of copper-dependent octarepeat domain structures. Multiple His coordination is clearly identified at low copper stoichiometry. In addition, EPR detected copper−copper interactions at full occupancy suggest that the octarepeat domain partially collapses, perhaps stabilizing this specific binding mode and facilitating cooperative copper uptake. This work provides the first complete characterization of all dominant copper coordination modes at pH 7.4

Quantum-noise--randomized data-encryption for WDM fiber-optic networks

We demonstrate high-rate randomized data-encryption through optical fibers using the inherent quantum-measurement noise of coherent states of light. Specifically, we demonstrate 650Mbps data encryption through a 10Gbps data-bearing, in-line amplified 200km-long line. In our protocol, legitimate users (who share a short secret-key) communicate using an M-ry signal set while an attacker (who does not share the secret key) is forced to contend with the fundamental and irreducible quantum-measurement noise of coherent states. Implementations of our protocol using both polarization-encoded signal sets as well as polarization-insensitive phase-keyed signal sets are experimentally and theoretically evaluated. Different from the performance criteria for the cryptographic objective of key generation (quantum key-generation), one possible set of performance criteria for the cryptographic objective of data encryption is established and carefully considered.Comment: Version 2: Some errors have been corrected and arguments refined. To appear in Physical Review A. Version 3: Minor corrections to version

Biaxial Tensile Strain Enhances Electron Mobility of Monolayer Transition Metal Dichalcogenides

Strain engineering can modulate the material properties of two-dimensional (2D) semiconductors for electronic and optoelectronic applications. Recent theory and experiments have found that uniaxial tensile strain can improve the electron mobility of monolayer MoS$_2$, a 2D semiconductor, but the effects of biaxial strain on charge transport are not well-understood in 2D semiconductors. Here, we use biaxial tensile strain on flexible substrates to probe the electron mobility in monolayer WS$_2$ and MoS$_2$ transistors. This approach experimentally achieves ~2x higher on-state current and mobility with ~0.3% applied biaxial strain in WS$_2$, the highest mobility improvement at the lowest strain reported to date. We also examine the mechanisms behind this improvement through density functional theory simulations, concluding that the enhancement is primarily due to reduced intervalley electron-phonon scattering. These results underscore the role of strain engineering 2D semiconductors for flexible electronics, sensors, integrated circuits, and other optoelectronic applications.Comment: Corrected titl

Widespread initiation, reactivation, and acceleration of landslides in the northern California Coast Ranges due to extreme rainfall

Episodically to continuously active slow‐moving landslides are driven by precipitation. Climate change, which is altering both the frequency and magnitude of precipitation worldwide, is therefore predicted to have a major impact on landslides. Here we examine the behavior of hundreds of slow‐moving landslides in northern California in response to large changes in annual precipitation that occurred between 2016 and 2018. We quantify the landslide displacement using repeat‐pass radar interferometry and pixel offset tracking techniques on a novel dataset from the airborne NASA/JPL Uninhabited Aerial Vehicle Synthetic Aperture Radar. We found that 312 landslides were moving due to extreme rainfall during 2017, compared to 119 during 2016, which was the final year of a historic multi‐year drought. However, with a return to below‐average rainfall in 2018, only 146 landslides remained in motion. The increased number of landslides during 2017 was primarily accommodated by landslides that were smaller than the landslides that remained active between 2016 and 2018. Furthermore, by examining a subset of 51 landslides, we found that 49 had increased velocities during 2017 when compared to 2016. Our results show that slow‐moving landslides are sensitive to large changes in annual precipitation, particularly the smaller and thinner landslides that likely experience larger basal pore‐water pressure changes. Based on climate model predictions for the next century in California, which include increases in average annual precipitation and increases in the frequency of dry‐to‐wet extremes, we hypothesize that there will be an overall increase in landslide activity