225 research outputs found

    A novel intermediate in transcription initiation by human mitochondrial RNA polymerase

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    The mitochondrial genome is transcribed by a single-subunit T7 phage-like RNA polymerase (mtRNAP),structurally unrelated to cellular RNAPs. In higher eukaryotes, mtRNAP requires two transcription factors for efficient initiation-TFAM, a major nucleoid protein, and TFB2M, a transient component of mtRNAP catalytic site. The mechanisms behind assembly of the mitochondrial transcription machinery and its regulation are poorly understood. We isolated and identified a previously unknown human mitochondrial transcription intermediate-a pre-initiation complex that includes mtRNAP, TFAM and promoter DNA. Using protein-protein cross-linking, we demonstrate that human TFAM binds to the N-terminal domain of mtRNAP, which results in bending of the promoter DNA around mtRNAP. The subsequent recruitment of TFB2M induces promoter melting and formation of an open initiation complex. Our data indicate that the pre-initiation complex is likely to be an important target for transcription regulation and provide basis for further structural, biochemical and biophysical studies of mitochondrial transcription

    Mechanisms of mitochondrial promoter recognition in humans and other mammalian species

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    Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for \u3e 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation

    Mechanism of Transcription Anti-termination in Human Mitochondria.

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    In human mitochondria, transcription termination events at a G-quadruplex region near the replication origin are thought to drive replication of mtDNA by generation of an RNA primer. This process is suppressed by a key regulator of mtDNA-the transcription factor TEFM. We determined the structure of an anti-termination complex in which TEFM is bound to transcribing mtRNAP. The structure reveals interactions of the dimeric pseudonuclease core of TEFM with mobile structural elements in mtRNAP and the nucleic acid components of the elongation complex (EC). Binding of TEFM to the DNA forms a downstream sliding clamp, providing high processivity to the EC. TEFM also binds near the RNA exit channel to prevent formation of the RNA G-quadruplex structure required for termination and thus synthesis of the replication primer. Our data provide insights into target specificity of TEFM and mechanisms by which it regulates the switch between transcription and replication of mtDNA

    New palynological data for Toarcian (Lower Jurassic) deep-marine sandstones of the Western Caucasus, southwestern Russia

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    Information on Jurassic palynomorphs from the Greater Caucasus is potentially of great importance, but its availability to the international research community is severely limited. New palynological data for Toarcian deposits of the Western Caucasus are recorded in the present paper. Particularly, dinoflagellate cysts are described for the first time from the Bagovskaja Formation; palynomorphs are found in sandstone levels within this unit. The most representative assemblage includes pollen (with predominant bisaccate pollen), spores (Cyathidites being commonest), and dinoflagellate cysts amongst which the predominant taxon is Nannoceratopsis spiculata. The dinocyst assemblage implies a late Toarcian age for the upper part of the Bagovskaja Formation. On the basis of these new palynostratigraphical results, the range of the formation is extended; previously, only the lower part had been dated on ammonite evidence

    Warming Trend in Antarctic Bottom Water in the Vema Channel in the South Atlantic

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    The excess heat absorbed from the atmosphere has increased the temperature in the upper layers of the ocean (<2,000 m). In the abyss, infrequently repeated ship sections, deep Argo float measurements, and sparse moored observations have found signs of warming in the Southwest Atlantic, possibly linked to changes in the Weddell Sea. We present a new moored temperature time series sampled near the bottom in the Vema Channel, from February 2019 to August 2020. Together with historical data, the combined record confirms the warming of the abyssal waters, with an increase of 0.059°C in potential temperature between January 1991 and August 2020, embedded within intense high-frequency variability. Moreover, the data suggest the possibility of an accelerated warming, with a change in the temperature trend from 0.0016°C yr−1, between the early 1990s and 2005, to 0.0026°C yr−1 afterwards

    Large expert-curated database for benchmarking document similarity detection in biomedical literature search

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    Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

    CTD data over a repeated section in the Vema Channel

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    We present a CTD dataset of repeated sections across the Vema Channel in the South Atlantic approximately along 31°12′ S between longitudes 39°18.0 W and 39°30.0′ W. The Vema Channel is a narrow conduit for Antarctic Bottom Water across the Rio Grande Rise. The measurements at CTD stations (Conductivity-Temperature-Depth) across the Vema Channel were started by German scientists in 1991. In 2002, Russian scientists took part in this work and have been establishing stations across this standard section until recently. The data were collected using the Sea-Bird Electronics SBE-19 profiler. The data are presented in tabular format. The data are available at http://dx.doi.org/10.17632/hh4hhn6ny8.1
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