Detection of O-propargyl-puromycin with SUMO and ubiquitin by click chemistry at PML-nuclear bodies during abortive proteasome activities

All these screens that we've done: how functional genetic screens have informed our understanding of ribosome biogenesis

Ribosome biogenesis is the complex and essential process that ultimately leads to the synthesis of cellular proteins. Understanding each step of this essential process is imperative to increase our understanding of basic biology, but also more critically, to provide novel therapeutic avenues for genetic and developmental diseases such as ribosomopathies and cancers which can arise when this process is impaired. In recent years, significant advances in technology have made identifying and characterizing novel human regulators of ribosome biogenesis via high-content, high-throughput screens. Additionally, screening platforms have been used to discover novel therapeutics for cancer. These screens have uncovered a wealth of knowledge regarding novel proteins involved in human ribosome biogenesis, from the regulation of the transcription of the ribosomal RNA to global protein synthesis. Specifically, comparing the discovered proteins in these screens showed interesting connections between large ribosomal subunit (LSU) maturation factors and earlier steps in ribosome biogenesis, as well as overall nucleolar integrity. In this review, a discussion of the current standing of screens for human ribosome biogenesis factors through the lens of comparing the datasets and discussing the biological implications of the areas of overlap will be combined with a look toward other technologies and how they can be adapted to discover more factors involved in ribosome synthesis, and answer other outstanding questions in the field.

Promyelocytic leukemia nuclear body-like structures can assemble in mouse oocytes

Promyelocytic leukemia (PML) nuclear bodies (PML-NBs), a class of membrane-less cellular organelles, participate in various biological activities. PML-NBs are known as the core-shell-type nuclear body, harboring ‘client’ proteins in their core. Although multiple membrane-less organelles work in the oocyte nucleus, PML-NBs have been predicted to be absent from oocytes. Here, we show that some well-known PML clients (but not endogenous PML) co-localized with small ubiquitin-related modifier (SUMO) protein in the nucleolus and peri-centromeric heterochromatin of maturing oocytes. In oocytes devoid of PML-NBs, endogenous PML protein localized in the vicinity of chromatin. During and after meiotic resumption, PML co-localized with SUMO gathering around chromosomes. To examine the benefit of the PML-NB-free intranuclear milieu in oocytes, we deliberately assembled PML-NBs by microinjecting human PML-encoding plasmids into oocytes. Under conditions of limited SUMO availability, assembled PML-NBs tended to cluster. Upon proteotoxic stress, SUMO delocalized from peri-centromeric heterochromatin and co-localized with SC35 (a marker of nuclear speckles)-positive large compartments, which was disturbed by pre-assembled PML-NBs. These observations suggest that the PML-NB-free intranuclear environment helps reserve SUMO for emergent responses by redirecting the flux of SUMO otherwise needed to maintain PML-NB dynamics.

Summary: PML-NB-free intranuclear environment in the oocyte helps reserve SUMO for emergent responses by redirecting the flux of SUMO otherwise needed to maintain PML-NB dynamics.

A chemical screen for modulators of mRNA translation identifies a distinct mechanism of toxicity for sphingosine kinase inhibitors

We here conducted an image-based chemical screen to evaluate how medically approved drugs, as well as drugs that are currently under development, influence overall translation levels. None of the compounds up-regulated translation, which could be due to the screen being performed in cancer cells grown in full media where translation is already present at very high levels. Regarding translation down-regulators, and consistent with current knowledge, inhibitors of the mechanistic target of rapamycin (mTOR) signaling pathway were the most represented class. In addition, we identified that inhibitors of sphingosine kinases (SPHKs) also reduce mRNA translation levels independently of mTOR. Mechanistically, this is explained by an effect of the compounds on the membranes of the endoplasmic reticulum (ER), which activates the integrated stress response (ISR) and contributes to the toxicity of SPHK inhibitors. Surprisingly, the toxicity and activation of the ISR triggered by 2 independent SPHK inhibitors, SKI-II and ABC294640, the latter in clinical trials, are also observed in cells lacking SPHK1 and SPHK2. In summary, our study provides a useful resource on the effects of medically used drugs on translation, identified compounds capable of reducing translation independently of mTOR and has revealed that the cytotoxic properties of SPHK inhibitors being developed as anticancer agents are independent of SPHKs.

The science of puromycin: From studies of ribosome function to applications in biotechnology

Puromycin is a naturally occurring aminonucleoside antibiotic that inhibits protein synthesis by ribosome-catalyzed incorporation into the C-terminus of elongating nascent chains, blocking further extension and resulting in premature termination of translation. It is most commonly known as a selection marker for cell lines genetically engineered to express a resistance transgene, but its additional uses as a probe for protein synthesis have proven invaluable across a wide variety of model systems, ranging from purified ribosomes and cell-free translation to intact cultured cells and whole animals. Puromycin is comprised of a nucleoside covalently bound to an amino acid, mimicking the 3′ end of aminoacylated tRNAs that participate in delivery of amino acids to elongating ribosomes. Both moieties can tolerate some chemical substitutions and modifications without significant loss of activity, generating a diverse toolbox of puromycin-based reagents with added functionality, such as biotin for affinity purification or fluorophores for fluorescent microscopy detection. These reagents, as well as anti-puromycin antibodies, have played a pivotal role in advancing our understanding of the regulation and dysregulation of protein synthesis in normal and pathological processes, including immune response and neurological function. This manuscript reviews the current state of puromycin-based research, including structure and mechanism of action, relevant derivatives, use in advanced methodologies and some of the major insights generated using such techniques both in the lab and the clinic.

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.