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Table of Contents for this page:

  • Current Issue
  • Advanced Online Publications Articles

  • Current Issue of Nature Structural and Molecular Biology

    Nature Structural aamp; Molecular Biology - Issue - nature.com science feeds

  • Climbing to the peak of nascent-chain knowledge

  • During protein synthesis, the growing nascent polypeptide chain acts as a positive or negative regulator of the rate of peptide-bond formation and ribosomal fidelity, and influences the efficiency of downstream protein-folding and targeting events. At a recent international meeting held on the banks of Lake Kawaguchi in Japan, scientists and students investigating diverse aspects of nascent-chain biology met to discuss their latest findings in the scenic presence of Mount Fuji.

  • Retrotransposons jump into alternative-splicing regulation via a long noncoding RNA

  • A conserved long noncoding RNA expressed at the 5S rDNA ribosomal locus has acquired a novel function in alternative-splicing regulation in primates, owing to the insertion of a mobile Alu element. This discovery opens new perspectives regarding the roles of transposable elements in expanding the human transcriptome and may be applied as a biotechnology tool to drive gene-specific changes in alternative splicing.

  • mRNA decapping in 3D

  • The degradation of mRNAs involves removal of the 5′ protective cap via a decapping-enzyme complex, in a largely irreversible process that commits the transcript for destruction. Understanding how the decapping reaction is catalyzed and regulated are major goals in the field. New data suggest how the chemistry of decapping is controlled and orchestrated within the cell.

  • The membrane strikes back: phosphoinositide binding regulates Skywalker function

  • Drosophila Skywalker regulates the GTPase Rab35, thereby controlling the turnover of synaptic-vesicle proteins. A new crystal structure of the TBC domain of Skywalker reveals an unexpected phosphoinositide-binding pocket, which is critical for synaptic function and is disrupted in DOORS syndrome–causing mutations in the human Skywalker homolog TBC1D24.

  • Regulation of CED-3 caspase localization and activation by C. elegans nuclear-membrane protein NPP-14

  • Perinuclear localization of CED-3 zymogen in C. elegans germ cells and interaction with nuclear-pore protein NPP-14 inhibit autocatalytic activation of CED-3, a central event in apoptosis.

  • Skywalker-TBC1D24 has a lipid-binding pocket mutated in epilepsy and required for synaptic function

  • Structural, biochemical and functional analyses elucidate the mechanisms by which mutations in the TBC1D24 gene interfere with protein function, thus causing early-onset epilepsy and DOORS syndrome.

  • Substrate-translocating loops regulate mechanochemical coupling and power production in AAA+ protease ClpXP

  • Single-molecule spectroscopy reveals the complete mechanochemical cycle of the AAA+ protease ClpXP: ADP release and ATP binding occur during the dwell phase, whereas ATP hydrolysis and Pi release occur during the burst phase.

  • Structure of the active form of Dcp1–Dcp2 decapping enzyme bound to m7GDP and its Edc3 activator

  • The crystal structure of the Kluyveromyces lactis decapping enzyme complex Dcp1–Dcp2 is solved in the presence of activator Edc3 and reaction product m7GDP, revealing an active conformation of the enzyme.

  • Structural basis of mRNA-cap recognition by Dcp1–Dcp2

  • The structure of the S. pombe Dcp2–Dcp1 decapping enzyme complex with human activator PNRC2 and tight-binding cap analog reveals a new conformation and, along with kinetics analyses, provides insight into substrate recognition and mechanisms of activators.

  • E4 ligase–specific ubiquitination hubs coordinate DNA double-strand-break repair and apoptosis

  • The E4 ligase UFD-2 is required for apoptosis induced by DNA damage in C. elegans, and for the resolution of RAD-51 foci during homologous recombination-dependent repair, thus coordinating these two cellular processes.

  • Dual interaction of the Hsp70 J-protein cochaperone Zuotin with the 40S and 60S ribosomal subunits

  • Structural and cross-linking analyses provide deeper insight into Zuo1's dual interactions with the ribosomal 60S and 40S subunits and indicate how Zuo1 may coordinate cotranslational protein folding and translation.

  • Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing

  • A primate-specific insertion of an Alu element in 5S-OT, a lncRNA transcribed from 5S rRNA loci, allows 5S-OT to regulate alternative splicing via RNA-RNA pairing and recruitment of the splicing factor U2AF65.

  • Importance of cycle timing for the function of the molecular chaperone Hsp90

  • Analyses of Hsp90 mutants show no correlation between the speed of ATP turnover and chaperone activity in vivo, indicating that timing of conformational transitions, rather than cycle speed, is essential for Hsp90 function.

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    Nature -Advance Online Publications

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    Nature Structural aamp; Molecular Biology - AOP - nature.com science feeds

  • Reciprocal regulation of carbon monoxide metabolism and the circadian clock

  • Genetic and biochemical assays reveal that carbon monoxide produced by heme catabolism influences circadian rhythm in mammals by altering the activity of transcription factor CLOCK–BMAL1 at clock-gene targets.

  • Position effects influence HIV latency reversal

  • Barcoded HIV ensembles (B-HIVE) provides a new approach to map HIV integration sites and to determine how genomic context influences proviral transcription activity and response to latency-reversing agents.

  • Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

  • Large-scale sequencing approaches reveal that the genetic code of Euplotes ciliates supports widespread ribosomal frameshifting at stop codons, and that additional mechanisms are required for efficient translation termination.

  • Oxidative guanine base damage regulates human telomerase activity

  • Opposing effects of 8-oxodGTP on telomerase activity– promoting elongation by destabilizing G4 structures or inhibiting elongation by acting as a chain terminator – explain the differential sensitivity of cells with short telomeres to oxidative stress.

  • Large-scale ATP-independent nucleosome unfolding by a histone chaperone

  • spFRET microscopy analysis reveals how FACT reversibly uncoils DNA from nucleosomes during remodeling, thus modulating DNA accessibility in vitro and in vivo.

  • RNA-binding protein CPEB1 remodels host and viral RNA landscapes

  • The RNA-binding protein CPEB1 drives post-transcriptional changes in the host transcriptome and poly(A)-tail lengthening of viral RNAs, processes essential for productive HCMV infection.

  • Ribosome-stalk biogenesis is coupled with recruitment of nuclear-export factor to the nascent 60S subunit

  • The ribosome-assembly factor Mrt4 prevents untimely recruitment of the RNA-export receptor Mex67–Mtr2 to the nascent 60S ribosomal subunit, thereby ensuring appropriately timed nuclear export.

  • Staggered ATP binding mechanism of eukaryotic chaperonin TRiC (CCT) revealed through high-resolution cryo-EM

  • Cryo-EM analyses of yeast TRiC (CCT) reveal conformational changes induced by ATP binding and a staggered mode of nucleotide binding to the different subunits.

  • The ribosome-engaged landscape of alternative splicing

  • Comparative analysis of RNA-seq and ribosome profiling data shows that a major fraction of exon-skipping events in transcripts with medium-to-high abundance are engaged by ribosomes and therefore are likely to be translated.

  • Integrative classification of human coding and noncoding genes through RNA metabolism profiles

  • Quantitative assessment of transcription, splicing, degradation, localization and translation of coding and noncoding genes allows classification of RNAs on the basis of their metabolism and may aid in inference of lncRNA function.

  • Cotranscriptional folding of a riboswitch at nucleotide resolution

  • Applying SHAPE-seq to analyze cotranscriptional folding of the B. cereus crcB fluoride riboswitch at nucleotide resolution shows that the folding pathway undergoes a ligand-dependent bifurcation that influences terminator formation via coordinated structural transitions.
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