1,720,957 research outputs found
The many faces of ribosome translocation along the mRNA: reading frame maintenance, ribosome frameshifting and translational bypassing
Get PDFIn each round of translation elongation, the ribosome translocates along the mRNA by precisely one codon. Translocation is promoted by elongation factor G (EF-G) in bacteria (eEF2 in eukaryotes) and entails a number of precisely-timed large-scale structural rearrangements. As a rule, the movements of the ribosome, tRNAs, mRNA and EF-G are orchestrated to maintain the exact codon-wise step size. However, signals in the mRNA, as well as environmental cues, can change the timing and dynamics of the key rearrangements leading to recoding of the mRNA into production of trans-frame peptides from the same mRNA. In this review, we discuss recent advances on the mechanics of translocation and reading frame maintenance. Furthermore, we describe the mechanisms and biological relevance of non-canonical translocation pathways, such as hungry and programmed frameshifting and translational bypassing, and their link to disease and infection
Altered tRNA dynamics during translocation on slippery mRNA as determinant of spontaneous ribosome frameshifting
Get PDFWhen reading consecutive mRNA codons, ribosomes move by exactly one triplet at a time to synthesize a correct protein. Some mRNA tracks, called slippery sequences, are prone to ribosomal frameshifting, because the same tRNA can read both 0- and –1-frame codon. Using smFRET we show that during EF-G-catalyzed translocation on slippery sequences a fraction of ribosomes spontaneously switches from rapid, accurate translation to a slow, frameshifting-prone translocation mode where the movements of peptidyl- and deacylated tRNA become uncoupled. While deacylated tRNA translocates rapidly, pept-tRNA continues to fluctuate between chimeric and posttranslocation states, which slows down the re-locking of the small ribosomal subunit head domain. After rapid release of deacylated tRNA, pept-tRNA gains unconstrained access to the –1-frame triplet, resulting in slippage followed by recruitment of the –1-frame aa-tRNA into the A site. Our data show how altered choreography of tRNA and ribosome movements reduces the translation fidelity of ribosomes translocating in a slow mode
Modulation of translational decoding by m6A modification of mRNA
Get PDFN 6 -methyladenosine (m 6 A) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. m 6 A in the mRNA coding regions inhibits translation elongation. Here, we show how m 6 A modulates decoding in the bacterial translation system using a combination of rapid kinetics, smFRET and single-particle cryo-EM. We show that, while the modification does not impair the initial binding of aminoacyl-tRNA to the ribosome, in the presence of m 6 A fewer ribosomes complete the decoding process due to the lower stability of the complexes and enhanced tRNA drop-off. The mRNA codon adopts a π-stacked codon conformation that is remodeled upon aminoacyl-tRNA binding. m 6 A does not exclude canonical codon-anticodon geometry, but favors alternative more dynamic conformations that are rejected by the ribosome. These results highlight how modifications outside the Watson-Crick edge can still interfere with codon-anticodon base pairing and complex recognition by the ribosome, thereby modulating the translational efficiency of modified mRNAs
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Ribosome dynamics during spontaneous frameshifting
Get PDFDuring protein synthesis, the ribosome moves along the mRNA in steps of three nucleotides at a time to maintain the translational reading frame. However, on some mRNA sequences that are denoted as slippery, ribosomes may shift by one or several nucleotides to the 5’ direction in a process called spontaneous –1 frameshifting. The result is the production of aberrant peptides with a different length and amino acid sequence than the 0-frame peptide. Frameshifting is a major potential source of translation errors, which compromise the fitness of the cell. It is thus important to understand the molecular mechanism that leads to spontaneous frameshifting. In this study, we use single molecule Förster resonance energy transfer (smFRET) to investigate how the tRNAs move through the ribosome during translocation on slippery mRNA. We investigate the internal motions of the ribosome (i.e. ribosome dynamics) and the role of EF-G during translocation on slippery mRNA. Our results show that uncoupling the movements of the two tRNA that are displaced during translocation is a key determinant of spontaneous frameshifting. While the deacylated tRNA moves rapidly from the P to the E site and is released from the ribosome, the translocation of the peptidyl-tRNA from the A to the P site is slow and stalled between intermediate (chimeric, CHI) and posttranslocation states. Delayed translocation in a different stage of translocation, i.e. prior to the formation of chimeric states, does not contribute to frameshifting. During slow translocation of the peptidyl-tRNA, the SSU head domain is in the swiveled conformation, further facilitating the positional uncertainty of the peptidyl-tRNA. This allows sampling of the 0- and –1-frame codons, thus shifting the reading frame. We anticipate our work to be the starting point for further investigation of spontaneous frameshifting, the effect of frameshifted peptides in the cell in physiological and pathological conditions, the respective mechanism of frameshifting in eukaryotes, as well as the emergence of spontaneous frameshifting as a therapeutic target in human disease and infection.2022-10-2
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
- …
