The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis.

Cancer initiates as a consequence of genomic mutations and its subsequent progression relies in part on increased production of ribosomes to maintain high levels of protein synthesis for unchecked cell growth. Recently, cytidine deaminases have been uncovered as sources of mutagenesis in cancer. In an attempt to form a connection between these 2 cancer driving processes, we interrogated the cytidine deaminase family of proteins for potential roles in human ribosome biogenesis. We identified and validated APOBEC3A and APOBEC4 as novel ribosome biogenesis factors through our laboratory's established screening platform for the discovery of regulators of nucleolar function in MCF10A cells. Through siRNA depletion experiments, we highlight APOBEC3A's requirement in making ribosomes and specific role within the processing and maturation steps that form the large subunit 5.8S and 28S ribosomal (r)RNAs. We demonstrate that a subset of APOBEC3A resides within the nucleolus and associates with critical ribosome biogenesis factors. Mechanistic insight was revealed by transient overexpression of both wild-type and a catalytically dead mutated APOBEC3A, which both increase cell growth and protein synthesis. Through an innovative nuclear RNA sequencing methodology, we identify only modest predicted APOBEC3A C-to-U target sites on the pre-rRNA and pre-mRNAs. Our work reveals a potential direct role for APOBEC3A in ribosome biogenesis likely independent of its editing function. More broadly, we found an additional function of APOBEC3A in cancer pathology through its function in ribosome biogenesis, expanding its relevance as a target for cancer therapeutics.

Palaeoclimate evidence of vulnerable permafrost during times of low sea ice.

Climate change in the Arctic is occurring rapidly, and projections suggest the complete loss of summer sea ice by the middle of this century1. The sensitivity of permanently frozen ground (permafrost) in the Northern Hemisphere to warming is less clear, and its long-term trends are harder to monitor than those of sea ice. Here we use palaeoclimate data to show that Siberian permafrost is robust to warming when Arctic sea ice is present, but vulnerable when it is absent. Uranium-lead chronology of carbonate deposits (speleothems) in a Siberian cave located at the southern edge of continuous permafrost reveals periods in which the overlying ground was not permanently frozen. The speleothem record starts 1.5 million years ago (Ma), a time when greater equator-to-pole heat transport led to a warmer Northern Hemisphere2. The growth of the speleothems indicates that permafrost at the cave site was absent at that time, becoming more frequent from about 1.35 Ma, as the Northern Hemisphere cooled, and permanent after about 0.4 Ma. This history mirrors that of year-round sea ice in the Arctic Ocean, which was largely absent before about 0.4 Ma (ref. 3), but continuously present since that date. The robustness of permafrost when sea ice is present, as well as the increased permafrost vulnerability when sea ice is absent, can be explained by changes in both heat and moisture transport. Reduced sea ice may contribute to warming of Arctic air4-6, which can lead to warming far inland7. Open Arctic waters also increase the source of moisture and increase autumn snowfall over Siberia, insulating the ground from low winter temperatures8-10. These processes explain the relationship between an ice-free Arctic and permafrost thawing before 0.4 Ma. If these processes continue during modern climate change, future loss of summer Arctic sea ice will accelerate the thawing of Siberian permafrost.

Discovery of novel microRNA mimic repressors of ribosome biogenesis.

While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.

Signal transduction at GPCRs: Allosteric activation of the ERK MAPK by ß-arrestin.

ß-arrestins are multivalent adaptor proteins that bind active phosphorylated G protein-coupled receptors (GPCRs) to inhibit G protein signaling, mediate receptor internalization, and initiate alternative signaling events. ß-arrestins link agonist-stimulated GPCRs to downstream signaling partners, such as the c-Raf-MEK1-ERK1/2 cascade leading to ERK1/2 activation. ß-arrestins have been thought to transduce signals solely via passive scaffolding by facilitating the assembly of multiprotein signaling complexes. Recently, however, ß-arrestin 1 and 2 were shown to activate two downstream signaling effectors, c-Src and c-Raf, allosterically. Over the last two decades, ERK1/2 have been the most intensely studied signaling proteins scaffolded by ß-arrestins. Here, we demonstrate that ß-arrestins play an active role in allosterically modulating ERK kinase activity in vitro and within intact cells. Specifically, we show that ß-arrestins and their GPCR-mediated active states allosterically enhance ERK2 autophosphorylation and phosphorylation of a downstream ERK2 substrate, and we elucidate the mechanism by which ß-arrestins do so. Furthermore, we find that allosteric stimulation of dually phosphorylated ERK2 by active-state ß-arrestin 2 is more robust than by active-state ß-arrestin 1, highlighting differential capacities of ß-arrestin isoforms to regulate effector signaling pathways downstream of GPCRs. In summary, our study provides strong evidence for a new paradigm in which ß-arrestins function as active "catalytic" scaffolds to allosterically unlock the enzymatic activity of signaling components downstream of GPCR activation.

The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22.

The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae.

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.

The spiral wave frequency effect in atrial fibrillation.

A spiral wavefront (WF), generated by a cardiac rotor that drifts between surface electrodes during atrial fibrillation, exhibits frequency changes inconsistent with classical Doppler effect (CDE) phenomena. Recent clinical studies reveal three repeatedly observed events--1) side-dependent frequency changes across the path of the rotor, 2) one additional WF strike on the higher frequency side, and 3) a reversal of WF strike sequence--which constitute a diametrical property of spinning WF sources. A linear ray model is first used to reveal and develop the diametrical phenomena. Mathematical models of an Archimedean spiral and a spiral generated by the diffusion equation are developed and compared. Each formulation predicts the diametrical property that CDE does not capture and illuminates the occurrence of a strong side and weak side with respect to the rotor path. Whereas CDE exhibits higher and lower frequencies from approaching and receding sources of WFs, respectively, spiral rotors generate higher and lower frequencies on opposite sides of the migration path. This motivates the reconsideration of mapping and ablation strategies that have traditionally been based on identifying sites of the dominant frequency. While this research aims to characterize the path of a spiral rotor during atrial fibrillation accurately, the results are applicable in other fields of science and engineering in which rotating spiral waves occur.

Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing.

In eukaryotes, the nucleolus is the site of ribosome biosynthesis, an essential process in all cells. While human ribosome assembly is largely evolutionarily conserved, many of the regulatory details underlying its control and function have not yet been well-defined. The nucleolar protein RSL24D1 was originally identified as a factor important for 60S ribosomal subunit biogenesis. In addition, the PeBoW (BOP1-PES1-WDR12) complex has been well-defined as required for pre-28S rRNA processing and cell proliferation. In this study, we show that RSL24D1 depletion impairs both pre-ribosomal RNA (pre-rRNA) transcription and mature 28S rRNA production, leading to decreased protein synthesis and p53 stabilization in human cells. Surprisingly, each of the PeBoW complex members is also required for pre-rRNA transcription. We demonstrate that RSL24D1 and WDR12 co-immunoprecipitate with the RNA polymerase I subunit, RPA194, and regulate its steady state levels. These results uncover the dual role of RSL24D1 and the PeBoW complex in multiple steps of ribosome biogenesis, and provide evidence implicating large ribosomal subunit biogenesis factors in pre-rRNA transcription control.

Biomechanics of biting in loggerhead shrikes: jaw-closing force, velocity and an argument for power.

Differences in the physical and behavioral attributes of prey are likely to impose disparate demands of force and speed on the jaws of a predator. Because of biomechanical trade-offs between force and speed, this presents an interesting conundrum for predators of diverse prey types. Loggerhead shrikes (Lanius ludovicianus) are medium-sized (∼50 g) passeriform birds that dispatch and feed on a variety of arthropod and vertebrate prey, primarily using their beaks. We used high-speed video of shrikes biting a force transducer in lateral view to obtain corresponding measurements of bite force, upper and lower bill linear and angular displacements, and velocities. Our results show that upper bill depression (about the craniofacial hinge) is more highly correlated with bite force, whereas lower bill elevation is more highly correlated with jaw-closing velocity. These results suggest that the upper and lower jaws might play different roles for generating force and speed (respectively) in these and perhaps other birds as well. We hypothesize that a division of labor between the jaws may allow shrikes to capitalize on elements of force and speed without compromising performance. As expected on theoretical grounds, bite force trades-off against jaw-closing velocity during the act of biting, although peak bite force and jaw-closing velocity across individual shrikes show no clear signs of a force-velocity trade-off. As a result, shrikes appear to bite with jaw-closing velocities and forces that maximize biting power, which may be selectively advantageous for predators of diverse prey that require both jaw-closing force and speed.

Progression and perceptual responses to blood flow restriction resistance training among people with multiple sclerosis.

PURPOSE: Resistance exercise can attenuate muscular impairments associated with multiple sclerosis (MS), and blood flow restriction (BFR) may provide a viable alternative to prescribing heavy training loads. The purpose of this investigation was to examine the progression of upper and lower body low-load (30% of one-repetition maximum [1RM]) resistance training (RT) with BFR applied intermittently during the exercise intervals (RT + BFR) versus volume-matched heavy-load (65% of 1RM) RT. METHODS: Men and women with MS (n = 16) were randomly assigned to low-load RT + BFR (applied intermittently) or heavy-load RT and completed 12 weeks (2 × /week) of RT that consisted of bilateral chest press, seated row, shoulder press, leg press, leg extension, and leg curl exercises. Exercise load, tonnage, and rating of perceived exertion were assessed at baseline and every 6 weeks. RESULTS: Training load increased to a greater extent and sometimes earlier for RT + BFR (57.7-106.3%) than heavy-load RT (42.3-54.3%) during chest press, seated row, and leg curl exercises, while there were similar increases (63.5-101.1%) for shoulder press, leg extension, and leg press exercises. Exercise tonnage was greater across all exercises for RT + BFR than heavy-load RT, although tonnage only increased during the chest press (70.7-80.0%) and leg extension (89.1%) exercises. Perceptions of exertion (4.8-7.2 au) and compliance (97.9-99.0%) were similar for both interventions. CONCLUSION: The training-induced increases in load, high compliance, and moderate levels of exertion suggested that RT + BFR and heavy-load RT are viable interventions among people with MS. RT + BFR may be a preferred modality if heavy loads are not well tolerated and/or to promote early-phase training responses.