USP15 regulates dynamic protein-protein interactions of the spliceosome through deubiquitination of PRP31.

Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified with K63-linked ubiquitin chains by the PRP19 complex and deubiquitinated by USP15 and its substrate targeting factor SART3. USP15SART3 makes a complex with USP4 and this ternary complex serves as a platform to deubiquitinate PRP31 and PRP3. The ubiquitination and deubiquitination status of PRP31 regulates its interaction with the U5 snRNP component PRP8, which is required for the efficient splicing of chromosome segregation related genes, probably by stabilizing the U4/U6.U5 tri-snRNP complex. Collectively, our data suggest that USP15 plays a key role in the regulation of dynamic protein-protein interactions of the spliceosome

Crystal structure of PilF: functional implication in the type 4 pilus biogenesis in Pseudomonas aeruginosa

PilF is a requisite protein involved in the type 4 pilus biogenesis system from the Gram-negative human pathogenic bacteria, Pseudomonas aeruginosa. We determined the PilF structure at a 2.2A resolution; this includes six tandem tetratrico peptide repeat (TPR) units forming right-handed superhelix. PilF structure was similar to the heat shock protein organizing protein, which interacts with the C-terminal peptide of Hsp90 and Hsp70 via a concave Asn ladder in the inner groove of TPR superhelix. After simulated screening, the C-terminal pentapeptides of PilG, PilU, PilY, and PilZ proved to be a likely candidate binding to PilF, which are ones of 25 necessary components involved in the type 4 pilus biogenesis system. We proposed that PilF would be critical as a bridgehead in protein-protein interaction and thereby, PilF may bind a necessary molecule in type 4 pilus biogenesis system such as PilG, PilU, PilY, and PilZ

Regulation of Deubiquitinating Enzymes by Post-Translational Modifications

Ubiquitination and deubiquitination play a critical role in all aspects of cellular processes, and the enzymes involved are tightly regulated by multiple factors including posttranslational modifications like most other proteins. Dysfunction or misregulation of these enzymes could have dramatic physiological consequences, sometimes leading to diseases. Therefore, it is important to have a clear understanding of these regulatory processes. Here, we have reviewed the posttranslational modifications of deubiquitinating enzymes and their consequences on the catalytic activity, stability, abundance, localization, and interaction with the partner proteins

Pseudopolymorphs of LB30870, a Direct Thrombin Inhibitor: One-Dimensional Solvent Channel Structures Explain Reversible Hydration/Dehydration

Three different hydrates of LB30870, a new direct thrombin inhibitor, were identified during the screening of solid form, and their interconversion relationship and relative thermodynamic stabilities were investigated. Form I (hexahydrate) changes to Form II (dihydrate) or Form III (tetrahydrate) by dehydration, while Form II becomes Form I by hydration, and both Form II and Form III change to Form I in the aqueous slurry. Single crystals obtained from two different crystallization conditions, wet or air-dried, were found to be isostructural with a difference in the solvent channels, and based on the simulated and experimental powder X-ray diffraction patterns, the air-dried crystals are assigned as Form I and Form III, respectively. In all crystal structures, LB30870 is in a folded conformation forced by the presence of strong hydrogen bonds by two structural water molecules. The solvent channel formed can hold up to six additional hydration water sites per each LB30870, and the one-dimensional solvent channel facilitates the interconversion among the hydrates and rapid conversion to Form I in water. Although all hydrate forms would not differ in oral bioavailability as Form I predominates in the aqueous phase, considering the stable water content at 40-75% relative humidity Form III would be the most suitable for further development

MicroRNA-101-3p Suppresses Cancer Cell Growth by Inhibiting the USP47-Induced Deubiquitination of RPL11

MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that regulate a countless number of genes in the cell, and the aberrant expression of miRNA can lead to cancer. Here, we demonstrate that miR-101-3p regulates the RPL11–MDM2–p53 pathway by targeting ubiquitin-specific peptidase 47 (USP47), consequently inhibiting cancer cell proliferation. We confirm that miR-101-3p directly binds to the 3′-UTR region of the USP47 gene and inhibits USP47 expression. In addition, the overexpression of miR-101-3p suppresses cell proliferation in a p53-dependent manner. MiR-101-3p promotes interaction between RPL11 and MDM2 by inducing the translocation of RPL11 from the nucleolus to the nucleoplasm, thus preventing the MDM2-mediated proteasomal degradation of p53. However, these phenomena are restored by the overexpression of USP47, but not by its catalytically inactive form. Indeed, miR-101-3p regulates RPL11 localization and its interaction with MDM2 by inhibiting the USP47-induced deubiquitination of RPL11. Finally, the expression of miR-101-3p is downregulated in lung cancer patients, and the patients with low miR-101-3p expression exhibit a lower survival rate, indicating that miR-101-3p is associated with tumorigenesis. Together, our findings suggest that miR-101-3p functions as a tumor suppressor by targeting USP47 and could be a potential therapeutic target for cancers

Crystallization and preliminary X-ray crystallographic analysis of the probable tRNA-modification GTPase (TrmE) from Staphylococcus aureus

In this study, the TrmE protein from the pathogenic bacterium S. aureus was overexpressed and crystallized (space group I23, unit-cell parameters a = b = c = 229.47 Å, α = β = γ = 90°). Diffraction data were collected to 2.9 Å resolution using synchrotron radiation