Induction of the Mdm2 gene and protein by kinase signaling pathways is repressed by the pVHL tumor suppressor.

The tumor suppressor von Hippel-Lindau, pVHL, is a multifaceted protein. One function is to dock to the hypoxia-inducible transcription factor (HIF) and recruit a larger protein complex that destabilizes HIF via ubiquitination, preventing angiogenesis and tumor development. pVHL also binds to the tumor suppressor p53 to activate specific p53 target genes. The oncogene Mdm2 impairs the formation of the p53-pVHL complex and activation of downstream genes by conjugating nedd8 to pVHL. While Mdm2 can impact p53 and pVHL, how pVHL may impact Mdm2 is unclear. Like p53 somatic mutations, point mutations are evident in pVHL that are common in renal clear cell carcinomas (RCC). In patients with RCC, Mdm2 levels are elevated, and we examined whether there was a relationship between Mdm2 and pVHL. TCGA and DepMap analysis revealed that mdm2 gene expression was elevated in RCC with vhl point mutations or copy number loss. In pVHL reconstituted or deleted isogenetically match RCC or MEF cell lines, Mdm2 was decreased in the presence of pVHL. Furthermore, through analysis using genetic and pharmacological approaches, we show that pVHL represses Mdm2 gene expression by blocking the MAPK-Ets signaling pathway and blocks Akt-mediated phosphorylation and stabilization of Mdm2. Mdm2 inhibition results in an increase in the p53-p21 pathway to impede cell growth. This finding shows how pVHL can indirectly impact the function of Mdm2 by regulating signaling pathways to restrict cell growth.

A novel N4,N4-dimethylcytidine in the archaeal ribosome enhances hyperthermophily.

Ribosome structure and activity are challenged at high temperatures, often demanding modifications to ribosomal RNAs (rRNAs) to retain translation fidelity. LC-MS/MS, bisulfite-sequencing, and high-resolution cryo-EM structures of the archaeal ribosome identified an RNA modification, N4,N4-dimethylcytidine (m42C), at the universally conserved C918 in the 16S rRNA helix 31 loop. Here, we characterize and structurally resolve a class of RNA methyltransferase that generates m42C whose function is critical for hyperthermophilic growth. m42C is synthesized by the activity of a unique family of RNA methyltransferase containing a Rossman-fold that targets only intact ribosomes. The phylogenetic distribution of the newly identified m42C synthase family implies that m42C is biologically relevant in each domain. Resistance of m42C to bisulfite-driven deamination suggests that efforts to capture m5C profiles via bisulfite sequencing are also capturing m42C.

ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles.

Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.

Human RNase 4 improves mRNA sequence characterization by LC-MS/MS.

With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography-mass spectrometry (LC-MS/MS) permits direct assessment of the mRNA primary sequence and modifications thereof without conversion to cDNA or amplification. It relies upon digestion of mRNA with site-specific endoribonucleases to generate pools of short oligonucleotides that are then amenable to MS-based sequence analysis. Here, we showed that the uridine-specific human endoribonuclease hRNase 4 improves mRNA sequence coverage, in comparison with the benchmark enzyme RNase T1, by producing a larger population of uniquely mappable cleavage products. We deployed hRNase 4 to characterize mRNAs fully substituted with 1-methylpseudouridine (m1Ψ) or 5-methoxyuridine (mo5U), as well as mRNAs selectively depleted of uridine-two key strategies to reduce synthetic mRNA immunogenicity. Lastly, we demonstrated that hRNase 4 enables direct assessment of the 5' cap incorporation into in vitro transcribed mRNA. Collectively, this study highlights the power of hRNase 4 to interrogate mRNA sequence, identity, and modifications by LC-MS/MS.

Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs.

The phosphorylated RNA polymerase II CTD interacting factor 1 (PCIF1) is a methyltransferase that adds a methyl group to the N6-position of 2'O-methyladenosine (Am), generating N6, 2'O-dimethyladenosine (m6Am) when Am is the cap-proximal nucleotide. In addition, PCIF1 has ancillary methylation activities on internal adenosines (both A and Am), although with much lower catalytic efficiency relative to that of its preferred cap substrate. The PCIF1 preference for 2'O-methylated Am over unmodified A nucleosides is due mainly to increased binding affinity for Am. Importantly, it was recently reported that PCIF1 can methylate viral RNA. Although some viral RNA can be translated in the absence of a cap, it is unclear what roles PCIF1 modifications may play in the functionality of viral RNAs. Here we show, using in vitro assays of binding and methyltransfer, that PCIF1 binds an uncapped 5'-Am oligonucleotide with approximately the same affinity as that of a cap analog (KM = 0.4 versus 0.3 µM). In addition, PCIF1 methylates the uncapped 5'-Am with activity decreased by only fivefold to sixfold compared with its preferred capped substrate. We finally discuss the relationship between PCIF1-catalyzed RNA methylation, shown here to have broader substrate specificity than previously appreciated, and that of the RNA demethylase fat mass and obesity-associated protein (FTO), which demonstrates PCIF1-opposing activities on capped RNAs.

EPIC: software toolkit for elution profile-based inference of protein complexes.

Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectrometry analysis (chromatographic fractionation-mass spectrometry, CF-MS), but the resulting data are challenging to process and interpret. Here, we describe EPIC (elution profile-based inference of complexes), a software toolkit for automated scoring of large-scale CF-MS data to define high-confidence multi-component macromolecules from diverse biological specimens. As a case study, we used EPIC to map the global interactome of Caenorhabditis elegans, defining 612 putative worm protein complexes linked to diverse biological processes. These included novel subunits and assemblies unique to nematodes that we validated using orthogonal methods. The open source EPIC software is freely available as a Jupyter notebook packaged in a Docker container (https://hub.docker.com/r/baderlab/bio-epic/).

Enhanced expression and purification of nucleotide-specific ribonucleases MC1 and Cusativin.

Combinations of ribonucleases (RNases) are commonly used to digest RNA into oligoribonucleotide fragments prior to liquid chromatography-mass spectrometry (LC-MS) analysis. The distribution of the RNase target sequences or nucleobase sites within an RNA molecule is critical for achieving a high mapping coverage. Cusativin and MC1 are nucleotide-specific endoribonucleases encoded in the cucumber and bitter melon genomes, respectively. Their high specificity for cytidine (Cusativin) and uridine (MC1) make them ideal molecular biology tools for RNA modification mapping. However, heterogenous recombinant expression of either enzyme has been challenging because of their high toxicity to expression hosts and the requirement of posttranslational modifications. Here, we present two highly efficient and time-saving protocols that overcome these hurdles and enhance the expression and purification of these RNases. We first purified MC1 and Cusativin from bacteria by expressing and shuttling both enzymes to the periplasm as MBP-fusion proteins in T7 Express lysY/IqE. coli strain at low temperature. The RNases were enriched using amylose affinity chromatography, followed by a subsequent purification via a C-terminal 6xHIS tag. This fast, two-step purification allows for the purification of highly active recombinant RNases significantly surpassing yields reported in previous studies. In addition, we expressed and purified a Cusativin-CBD fusion enzyme in P. pastoris using chitin magnetic beads. Both Cusativin variants exhibited a similar sequence preference, suggesting that neither posttranslational modifications nor the epitope-tags have a substantial effect on the sequence specificity of the enzyme.

TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes.

While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here, we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the efficient nuclear export of mRNAs and lncRNAs that are generated from short transcripts that tend to have few introns, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from short transcripts accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.

K3Mo2O5.6F3.4 and K3V2O3.3F5.7 - exploring transition metal cation valence and anion distribution in oxyfluorides.

Oxyfluorides come in many different structures and are highly adaptable in composition, not least because of their mixed-anionic nature. Slight changes, unless specifically looked for, can easily go unnoticed. In this paper, we present two oxyfluorides, K3Mo2O5.6F3.4 and K3V2O3.3F5.7, synthesized under high-pressure/high-temperature conditions, and demonstrate the importance of careful analysis of composition, oxidation state and O/F anion distribution for an accurate description of oxyfluorides. Their crystal structures were determined by single-crystal X-ray diffraction and the transition metal cation valences analyzed by X-ray photoelectron spectroscopy (XPS). The O/F anion ratio was calculated using the principle of charge neutrality and the local distribution within the crystallographic framework was studied using bond valence (BV) and charge distribution (CHARDI) calculations. Madelung Part of Lattice Energy (MAPLE) calculations and magnetic measurements provide insight into phase stability and corroborate the mixed-valent nature of the compounds.

The extensive m5C epitranscriptome of Thermococcus kodakarensis is generated by a suite of RNA methyltransferases that support thermophily.

RNAs are often modified to invoke new activities. While many modifications are limited in frequency, restricted to non-coding RNAs, or present only in select organisms, 5-methylcytidine (m5C) is abundant across diverse RNAs and fitness-relevant across Domains of life, but the synthesis and impacts of m5C have yet to be fully investigated. Here, we map m5C in the model hyperthermophile, Thermococcus kodakarensis. We demonstrate that m5C is ~25x more abundant in T. kodakarensis than human cells, and the m5C epitranscriptome includes ~10% of unique transcripts. T. kodakarensis rRNAs harbor tenfold more m5C compared to Eukarya or Bacteria. We identify at least five RNA m5C methyltransferases (R5CMTs), and strains deleted for individual R5CMTs lack site-specific m5C modifications that limit hyperthermophilic growth. We show that m5C is likely generated through partial redundancy in target sites among R5CMTs. The complexity of the m5C epitranscriptome in T. kodakarensis argues that m5C supports life in the extremes.

Atmospheric production of glycolaldehyde under hazy prebiotic conditions.

The early Earth's atmosphere, with extremely low levels of molecular oxygen and an appreciable abiotic flux of methane, could have been a source of organic compounds necessary for prebiotic chemistry. Here, we investigate the formation of a key RNA precursor, glycolaldehyde (2-hydroxyacetaldehyde, or GA) using a 1-dimensional photochemical model. Maximum atmospheric production of GA occurs when the CH4:CO2 ratio is close to 0.02. The total atmospheric production rate of GA remains small, only 1 × 10(7) mol yr(-1). Somewhat greater amounts of GA production, up to 2 × 10(8) mol yr(-1), could have been provided by the formose reaction or by direct delivery from space. Even with these additional production mechanisms, open ocean GA concentrations would have remained at or below ~1 µM, much smaller than the 1-2 M concentrations required for prebiotic synthesis routes like those proposed by Powner et al. (Nature 459:239-242, 2009). Additional production or concentration mechanisms for GA, or alternative formation mechanisms for RNA, are needed, if this was indeed how life originated on the early Earth.

Selective Characterization of mRNA 5' End-Capping by DNA Probe-Directed Enrichment with Site-Specific Endoribonucleases.

The N7-methyl guanosine cap structure is an essential 5' end modification of eukaryotic mRNA. It plays a critical role in many aspects of the life cycle of mRNA, including nuclear export, stability, and translation. Equipping synthetic transcripts with a 5' cap is paramount to the development of effective mRNA vaccines and therapeutics. Here, we report a simple and flexible workflow to selectively isolate and analyze structural features of the 5' end of an mRNA by means of DNA probe-directed enrichment with site-specific single-strand endoribonucleases. Specifically, we showed that the RNA cleavage by site-specific RNases can be effectively steered by a complementary DNA probe to recognition sites downstream of the probe-hybridized region, utilizing a flexible range of DNA probe designs. We applied this approach using human RNase 4 to isolate well-defined cleavage products from the 5' end of diverse uridylated and N1-methylpseudouridylated mRNA 5' end transcript sequences. hRNase 4 increases the precision of the RNA cleavage, reducing product heterogeneity while providing comparable estimates of capped products and their intermediaries relative to the widely used RNase H. Collectively, we demonstrated that this workflow ensures well-defined and predictable 5' end cleavage products suitable for analysis and relative quantitation of synthetic mRNA 5' cap structures by UHPLC-MS/MS.

The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1.

The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or 'PUS' enzymes include those that rely on guide RNA molecules and others that function as 'stand-alone' enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.

Simultaneous Nail and Skin Clearance in Ixekizumab Head-to-Head Trials for Moderate-to-Severe Psoriasis and Psoriatic Arthritis.

INTRODUCTION: The lifetime incidence of nail psoriasis in patients with psoriasis is 80-90%, with 23-27% of patients having nail psoriasis at any given time. Nail psoriasis is even more prevalent in patients with comorbid psoriatic arthritis. Complete psoriasis clearance, an achievable therapeutic goal, should ideally include the resolution of nail psoriasis. Here, we assessed simultaneous skin and nail clearance in patients with psoriasis across five head-to-head trials comparing ixekizumab with other biologics. METHODS: Data were assessed in patients with moderate-to-severe psoriasis (with or without psoriatic arthritis) with nail psoriasis at baseline from the IXORA-R, IXORA-S, UNCOVER-2, UNCOVER-3, and SPIRIT-H2H trials. Ixekizumab patients received IXEQ2W to week 12 and IXEQ4W beyond week 12. PASI 100 depicted complete skin clearance, and PGA-F 0 (IXORA-R) or NAPSI 0 (all other trials) depicted complete nail clearance. Treatment comparisons were evaluated using the Cochran-Mantel-Haenszel test. Non-responder imputation was used for missing data. RESULTS: Ixekizumab achieved significantly greater simultaneous skin and nail complete clearance than etanercept (UNCOVER-2: p < 0.001 and UNCOVER-3: p < 0.001) at week 12, demonstrating an efficacious and rapid response. Across all five head-to-head trials, ixekizumab achieved a high rate of simultaneous skin and nail clearance (range: 28.6-45.9% of patients) by week 24 that was maintained up to week 52 (range: 40.5-51.4% of patients). Ixekizumab achieved numerically greater simultaneous complete clearance than guselkumab at week 24 (p = 0.079), but statistically significant greater simultaneous clearance compared to ustekinumab (p < 0.001) and adalimumab (p = 0.006) at week 24 and week 52 (p < 0.001 and p = 0.007, respectively). CONCLUSION: In five head-to-head trials, ixekizumab-treated patients had higher rates of simultaneous complete skin and nail clearance compared to etanercept, guselkumab, ustekinumab, and adalimumab, thereby reinforcing ixekizumab's ability to achieve high levels of efficacy in multiple domains of psoriatic disease. TRIAL REGISTRATION: NCT01474512, NCT01597245, NCT01646177, NCT03573323, NCT02561806, and NCT03151551.

Mdm2-mediated neddylation of pVHL blocks the induction of antiangiogenic factors.

Mutations in the tumor suppressor TP53 are rare in renal cell carcinomas. p53 is a key factor for inducing antiangiogenic genes and RCC are highly vascularized, which suggests that p53 is inactive in these tumors. One regulator of p53 is the Mdm2 oncogene, which is correlated with high-grade, metastatic tumors. However, the sole activity of Mdm2 is not just to regulate p53, but it can also function independent of p53 to regulate the early stages of metastasis. Here, we report that the oncoprotein Mdm2 can bind directly to the tumor suppressor VHL, and conjugate nedd8 to VHL within a region that is important for the p53-VHL interaction. Nedd8 conjugated VHL is unable to bind to p53 thereby preventing the induction of antiangiogenic factors. These results highlight a previously unknown oncogenic function of Mdm2 during the progression of cancer to promote angiogenesis through the regulation of VHL. Thus, the Mdm2-VHL interaction represents a pathway that impacts tumor angiogenesis.

A Review of Possible Planetary Atmospheres in the TRAPPIST-1 System.

TRAPPIST-1 is a fantastic nearby (∼39.14 light years) planetary system made of at least seven transiting terrestrial-size, terrestrial-mass planets all receiving a moderate amount of irradiation. To date, this is the most observationally favourable system of potentially habitable planets known to exist. Since the announcement of the discovery of the TRAPPIST-1 planetary system in 2016, a growing number of techniques and approaches have been used and proposed to characterize its true nature. Here we have compiled a state-of-the-art overview of all the observational and theoretical constraints that have been obtained so far using these techniques and approaches. The goal is to get a better understanding of whether or not TRAPPIST-1 planets can have atmospheres, and if so, what they are made of. For this, we surveyed the literature on TRAPPIST-1 about topics as broad as irradiation environment, planet formation and migration, orbital stability, effects of tides and Transit Timing Variations, transit observations, stellar contamination, density measurements, and numerical climate and escape models. Each of these topics adds a brick to our understanding of the likely-or on the contrary unlikely-atmospheres of the seven known planets of the system. We show that (i) Hubble Space Telescope transit observations, (ii) bulk density measurements comparison with H2-rich planets mass-radius relationships, (iii) atmospheric escape modelling, and (iv) gas accretion modelling altogether offer solid evidence against the presence of hydrogen-dominated-cloud-free and cloudy-atmospheres around TRAPPIST-1 planets. This means that the planets are likely to have either (i) a high molecular weight atmosphere or (ii) no atmosphere at all. There are several key challenges ahead to characterize the bulk composition(s) of the atmospheres (if present) of TRAPPIST-1 planets. The main one so far is characterizing and correcting for the effects of stellar contamination. Fortunately, a new wave of observations with the James Webb Space Telescope and near-infrared high-resolution ground-based spectrographs on existing very large and forthcoming extremely large telescopes will bring significant advances in the coming decade.

MKRN2 Physically Interacts with GLE1 to Regulate mRNA Export and Zebrafish Retinal Development.

The mammalian mRNA nuclear export process is thought to terminate at the cytoplasmic face of the nuclear pore complex through ribonucleoprotein remodeling. We conduct a stringent affinity-purification mass-spectrometry-based screen of the physical interactions of human RNA-binding E3 ubiquitin ligases. The resulting protein-interaction network reveals interactions between the RNA-binding E3 ubiquitin ligase MKRN2 and GLE1, a DEAD-box helicase activator implicated in mRNA export termination. We assess MKRN2 epistasis with GLE1 in a zebrafish model. Morpholino-mediated knockdown or CRISPR/Cas9-based knockout of MKRN2 partially rescue retinal developmental defects seen upon GLE1 depletion, consistent with a functional association between GLE1 and MKRN2. Using ribonomic approaches, we show that MKRN2 binds selectively to the 3' UTR of a diverse subset of mRNAs and that nuclear export of MKRN2-associated mRNAs is enhanced upon knockdown of MKRN2. Taken together, we suggest that MKRN2 interacts with GLE1 to selectively regulate mRNA nuclear export and retinal development.

Author Correction: Mutant p53 drives clonal hematopoiesis through modulating epigenetic pathway.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An atypical presentation of acanthamoeba keratitis in a patient with keratoconus treated briefly with topical anesthetic.

OBJECTIVES: To present a case of biopsy proven acanthamoeba keratitis requiring penetrating keratoplasty in a patient with keratoconus whose clinical course was remarkable for its lack of ocular injection and pain. The absence of these key findings may have contributed to a delay in diagnosis and a delay in instituting antiamoebic therapy. METHODS: Case report. RESULTS: A 21-year-old woman who wore soft contact lenses for management of keratoconus presented with a painful suppurative corneal infiltrate and epithelial defect. The patient was initially seen in an emergency department where she was given a bottle of topical anesthetic drops (proparacaine) to use for pain. When she was seen by the authors 18 hr after presenting to the emergency department, the proparacaine was immediately discontinued, and she was treated with fortified antibiotic (vancomycin and tobramycin) eye drops and oral antiviral medications (famciclovir). Despite an initial improvement and complete resolution of ocular discomfort, the patient went on to develop a dense, peripheral stromal infiltrate that failed to improve despite intensive treatment. Confocal microscopy and corneal biopsy were definitive for acanthamoeba infection. The patient subsequently failed medical therapy and underwent large diameter penetrating keratoplasty. The patient has shown no evidence of acanthamoeba recurrence in the corneal graft. CONCLUSIONS: Keratoconic patients may have atypical presentations of acanthamoeba keratitis, which may delay diagnosis and institution of medical therapy. Even brief use of topical anesthetics may further complicate the clinical picture.

Matching the waveform and the temporal window in the creation of experimental signals.

When a periodic waveform with a discrete-harmonic spectrum is temporally windowed to make a signal, its spectrum becomes a continuous function of frequency. However, there are discrete-frequency representations for windowed signals such as the Fourier series representation of a periodically extended signal. This article introduces the concept of matching between the temporal window and the periodic waveform. Matching leads to a discrete-frequency representation in which the Fourier transform of the windowed signal preserves the amplitudes and phases of the waveform on the set of original waveform frequencies. Generating signals with matched window and waveform leads to important control of experiments.