LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins

Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.

Bursting translation on single mRNAs in live cells

Stochasticity has emerged as a mechanism of gene regulation. Much of this so-called "noise" has been attributed to bursting transcription. Although bursting transcription has been studied extensively, the role of stochasticity in translation has not been fully investigated due to the lack of enabling imaging technology. In this study, we developed techniques to track single mRNAs and their translation in live cells for hours, allowing the measurement of previously uncharacterized translation dynamics. We applied genetic and pharmacological perturbations to control translation kinetics and found that, like transcription, translation is not a constitutive process but instead cycles between inactive and active states, or "bursts." However, unlike transcription, which is largely frequency-modulated, complex structures in the 5'-untranslated region alter burst amplitudes. Bursting frequency can be controlled through cap-proximal sequences and trans-acting factors such as eIF4F. We coupled single-molecule imaging with stochastic modeling to quantitatively determine the kinetic parameters of translational bursting.

Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant

The mitochondrial phospholipid cardiolipin (CL) promotes bioenergetics via oxidative phosphorylation (OXPHOS). Three tightly bound CLs are evolutionarily conserved in the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) which resides in the inner mitochondrial membrane and exchanges ADP and ATP to enable OXPHOS. Here, we investigated the role of these buried CLs in the carrier using yeast Aac2 as a model. We introduced negatively charged mutations into each CL-binding site of Aac2 to disrupt the CL interactions via electrostatic repulsion. While all mutations disturbing the CL-protein interaction destabilized Aac2 monomeric structure, transport activity was impaired in a pocket-specific manner. Finally, we determined that a disease-associated missense mutation in one CL-binding site in ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.

Translational control of stem cell function

Stem cells are characterized by their ability to self-renew and differentiate into many different cell types. Research has focused primarily on how these processes are regulated at a transcriptional level. However, recent studies have indicated that stem cell behaviour is strongly coupled to the regulation of protein synthesis by the ribosome. In this Review, we discuss how different translation mechanisms control the function of adult and embryonic stem cells. Stem cells are characterized by low global translation rates despite high levels of ribosome biogenesis. The maintenance of pluripotency, the commitment to a specific cell fate and the switch to cell differentiation depend on the tight regulation of protein synthesis and ribosome biogenesis. Translation regulatory mechanisms that impact on stem cell function include mTOR signalling, ribosome levels, and mRNA and tRNA features and amounts. Understanding these mechanisms important for stem cell self-renewal and differentiation may also guide our understanding of cancer grade and metastasis.

The Distinguished Teaching Society at the Johns Hopkins University School of Medicine: A Student-Led Initiative to Recognize Clinical Educators

PROBLEM

Some focus on recognizing excellence in clinical teaching has been lost with the increasing emphasis placed on clinical efficiency and value. Clinical teaching awards and academies of educators aim to address this problem. In 2015, medical student leaders at the Johns Hopkins University School of Medicine created the Distinguished Teaching Society (DTS), a student-driven program to recognize the best clinical educators.

APPROACH

Medical students designed a comprehensive scoring rubric focusing on 3 domains: feedback and evaluation, role model behavior, and teaching process. A student committee solicits student nominations providing narratives endorsing faculty or house staff for potential inclusion in the DTS. Using the rubric, student judges score each deidentified narrative nomination, as well as an application from finalists and comments about finalists submitted by the student body. Inductees are recognized at an annual ceremony.

OUTCOMES

From academic years 2015-2016 to 2018-2019, students nominated 254 unique candidates, and 82 nominees (32%) were inducted into the DTS. The majority of inductees were faculty and male. In 2017-2018 and 2018-2019, nearly half of inductees were female, and less than 10% of inductees self-reported as underrepresented in medicine and/or LGBTQ+. The Department of Internal Medicine had the greatest departmental representation. There were no statistically significant differences in the proportional representation within the nomination and inductee cohorts by gender, rank, and department. Several process changes were made in response to student feedback and to increase nominee and inductee diversity.

NEXT STEPS

Next steps include adding a diversity and inclusion chair to the student committee and collecting survey data on student and DTS inductee opinions on how to improve learner-teacher engagement and the clinical learning environment. Future activities may include educational workshops, panel discussions, mentorship programs, and networking events. Other medical schools may find value in considering similar structures.

EDF1 coordinates cellular responses to ribosome collisions

Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.

Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion

The gut microbiota metabolizes drugs and alters their efficacy and toxicity. Diet alters drugs, the metabolism of the microbiota, and the host. However, whether diet-triggered metabolic changes in the microbiota can alter drug responses in the host has been largely unexplored. Here we show that dietary thymidine and serine enhance 5-fluoro 2'deoxyuridine (FUdR) toxicity in C. elegans through different microbial mechanisms. Thymidine promotes microbial conversion of the prodrug FUdR into toxic 5-fluorouridine-5'-monophosphate (FUMP), leading to enhanced host death associated with mitochondrial RNA and DNA depletion, and lethal activation of autophagy. By contrast, serine does not alter FUdR metabolism. Instead, serine alters E. coli's 1C-metabolism, reduces the provision of nucleotides to the host, and exacerbates DNA toxicity and host death without mitochondrial RNA or DNA depletion; moreover, autophagy promotes survival in this condition. This work implies that diet-microbe interactions can alter the host response to drugs without altering the drug or the host.

Investigation of different combinations of derivatization, separation methods and electrospray ionization mass spectrometry for standard oligosaccharides and glycans from ovalbumin

Derivatization procedures using 1-phenyl-3-methyl-5-pyrazolone (PMP) and 2-aminonaphthalene trisulfone (ANTS) were selected among a number of well known methods for labelling carbohydrates. PMP derivatives were selected owing to our laboratory's previous high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) experience with these, whereas the ANTS-labelled compounds were prepared for fluorophore-assisted carbohydrate electrophoresis (FACE) separation. ANTS-oligosaccharide standards were characterized to study their ionization patterns. Reversed-phase and normal-phase HPLC systems were coupled on-line with ESI-MS. Each necessitated its own mobile phase system which, in turn, imposed some important changes in the ionization conditions used and/or on the ionization patterns and spectra obtained. Following characterization of the intact glycoprotein ovalbumin with ESI-MS, its glycans were detached using the enzyme PNGase-F. The glycans were subjected to PMP and ANTS derivatization. It was very difficult to separate ANTS derivatives by reversed-phase HPLC owing to lack of retention, and normal-phase HPLC offered reasonable retention with limited separation. PMP compounds overall yielded better normal- and reversed-phase separations and improved sensitivity over the ANTS-labelled sugars, for which negative mode ESI had to be used. The combination of ESI of intact ovalbumin and ESI of PMP-glycans gave rise to the detection of over 20 different glycoforms, excluding the possible presence of structural isomers for each sugar composition detected.

Effect of 1-phenyl-3-methyl-5-pyrazolone labeling on the fragmentation behavior of asialo and sialylated N-linked glycans under electrospray ionization conditions

The advantages of labeling free N-linked oligosaccharides with 1-phenyl-3-methyl-5-pyrazolone (PMP), for high performance liquid chromatography (HPLC) and electrospray ionization mass spectrometry (ESI-MS) are discussed. The study focuses on some asialo and sialylated sugars, and compares the HPLC and ESI-MS behaviors of the PMP-labeled substances vs. the native compounds. It is pointed out that native free N-linked carbohydrates have very low affinities for the C18 reversed phases commonly used in HPLC. Native asialo oligosaccharides yield good ESI-MS sensitivity, although they are very susceptible to in-source collision-induced dissociation (CID), and the fragments are produced from any of the branches of the molecules, i.e. do not give specific structural information. Native N-linked standards bearing one sialic acid residue yield a 10-fold loss of ESI-MS sensitivity vs. asialo compounds, and native sugars with two sialic acid moieties were not detectable. The PMP labeling of asialo and sialylated sugars yielded higher affinities for HPLC C18 columns and, even at the early stages of method development, it was possible to separate three PMP-labeled standards to a useful extent. In ESI-MS, PMP-asialo sugars did not yield a significant increase in sensitivity vs. the native species; however, fragmentation produced by in-source CID was more directed as all predominant fragment ions contained the bis-PMP label. This feature is particularly useful when structural determination of an unknown sugar is required. PMP-sialylated sugars gave rise to very clean and informative ESI mass spectra. The monosialo sugar yielded a 100-fold sensitivity improvement vs. its native analog and, in the case of the disialylated compound, a 100% improvement was obtained in the positive mode. Most fragment ions were informative and contained the reducing end on the molecules, thus facilitating spectral interpretation. The combination of PMP derivatization with on-line HPLC/ESI-MS is a promising method for the analysis of asialo and sialylated carbohydrate mixtures.

Isolation and characterization of two putative full-length Drosophila U4 small nuclear RNA genes

U4 RNA is one of the abundant small nuclear RNAs implicated in the processing of the 3' -ends of premessenger RNAs (Berget, S. (1984) Nature 309, 179-182). Two potential U4 RNA genes were isolated from a Drosophila genomic DNA library and characterized. These genes, which were from different loci, had transcription and processing signals common to Drosophila U1 and U2 small nuclear RNA genes. One U4 gene locus also contained a downstream 5'-truncated U4 pseudogene. This is the first report in which putative full-length genes for U4 small nuclear RNA were isolated and characterized.

U4 small nuclear RNA pseudogenes from rat genome have common truncated 3'-ends

Four U4 RNA pseudogenes were isolated and characterized from a rat genomic bank. The four pseudogenes contained sequences completely homologous to U4 RNA from nucleotides 1 to 67 and had common truncated 3'-ends. Three of the four pseudogenes were flanked by 14 to 18 nucleotide-long direct repeats. The structural features of these four U4 RNA pseudogenes are consistent with the hypothesis that these pseudogenes arose by RNA self-primed complementary DNA synthesis and integration into the genome (Van Arsdell et al., Cell 26:11-17, 1981).

A new moderately repetitive rat DNA sequence detected by a cloned 4.5 SI DNA

4.5 SI RNA is an abundant, noncapped, small nuclear RNA found in rodent cells. The 4.5 SI RNA is 98 or 99 nucleotides long and contains no modified nucleotides; it is synthesized by RNA polymerase III, is partly hydrogen-bonded to poly(A+) hnRNA, and was the first small nuclear RNA to be purified and sequenced (Busch, H., Reddy, R., Ruthblum, L., and Choi, Y. C. (1982) Annu. Rev. Biochem. 51, 617-654). In studies on the structure and organization of genes coding for this abundant RNA, it was found that this RNA is homologous to an apparently novel family of repetitive sequences. Two clones were characterized; one clone showed that its sequence is identical to the RNA in the first 92 residues and differed only in the last six nucleotides. In addition, the 3'-end of the sequence contained an A,T-rich region, and the sequence was flanked by a 15-nucleotide long direct repeat of AAAATATAGACACTG. The second clone characterized contained nucleotide sequences 1-57 corresponding to the RNA and was flanked by a 15-nucleotide long direct repeat. The structural features of these two DNAs are consistent with RNA-mediated DNA synthesis and integration of this DNA into the genome at random sites. It is estimated that there are about 10,000 copies of this family of sequences in the haploid rat genome.