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Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences

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https://www.readbyqxmd.com/read/30397107/the-role-of-3-end-uridylation-in-rna-metabolism-and-cellular-physiology
#1
REVIEW
Dagmar Zigáčková, Štěpánka Vaňáčová
Most eukaryotic RNAs are posttranscriptionally modified. The majority of modifications promote RNA maturation, others may regulate function and stability. The 3' terminal non-templated oligouridylation is a widespread modification affecting many cellular RNAs at some stage of their life cycle. It has diverse roles in RNA metabolism. The most prevalent is the regulation of stability and quality control. On the cellular and organismal level, it plays a critical role in a number of pathways, such as cell cycle regulation, cell death, development or viral infection...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397106/role-of-oligouridylation-in-normal-metabolism-and-regulated-degradation-of-mammalian-histone-mrnas
#2
Stacie A Meaux, Christopher E Holmquist, William F Marzluff
Metazoan replication-dependent histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Histone mRNAs are present in large amounts only in S-phase cells, and their levels are coordinately regulated with the rate of DNA replication. In mammals, the stemloop at the 3' end of histone mRNA is bound to stemloop binding protein, a protein required for both synthesis and degradation of histone mRNA, and an exonuclease, 3'hExo (ERI1). Histone mRNAs are rapidly degraded when DNA synthesis is inhibited in S-phase cells and at the end of S-phase...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397105/the-multitasking-polya-tail-nuclear-rna-maturation-degradation-and-export
#3
REVIEW
Agnieszka Tudek, Marta Lloret-Llinares, Torben Heick Jensen
A polyA (pA) tail is an essential modification added to the 3' ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae , human cells and, when relevant, the fission yeast Schizosaccharomyces pombe Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3'-end trimming or complete decay of non-coding RNAs...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397104/fidelity-in-rna-based-recognition-of-transposable-elements
#4
REVIEW
Ilaria Ugolini, Mario Halic
Genomes are under constant threat of invasion by transposable elements and other genomic parasites. How can host genomes recognize these elements and target them for degradation? This requires a system that is highly adaptable, and at the same time highly specific. Current data suggest that perturbation of transcription patterns by transposon insertions could be detected by the RNAi surveillance pathway. Multiple transposon insertions might generate sufficient amounts of primal small RNAs to initiate generation of secondary small RNAs and silencing...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397103/mrnas-biotinylated-within-the-5-cap-and-protected-against-decapping-new-tools-to-capture-rna-protein-complexes
#5
Sylwia Bednarek, Vanesa Madan, Pawel J Sikorski, Ralf Bartenschlager, Joanna Kowalska, Jacek Jemielity
The 5'-terminus of eukaryotic mRNAs comprises a 7-methylguanosine cap linked to the first transcribed nucleotide via a 5'-5' triphosphate bond. This cap structure facilitates numerous interactions with molecules participating in mRNA processing, turnover and RNA translation. Here, we report the synthesis and biochemical properties of a set of biotin-labelled cap analogues modified within the triphosphate bridge and increasing mRNA stability while retaining biological activity. Successful co-transcriptional incorporation of the cap analogues allowed for the quantification of cap-dependent translation efficiency, capping efficiency and the susceptibility to decapping by Dcp2...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397102/rna-polyadenylation-and-its-consequences-in-prokaryotes
#6
REVIEW
Eliane Hajnsdorf, Vladimir R Kaberdin
Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in Escherichia coli more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that E. coli poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397101/mrna-decapping-finding-the-right-structures
#7
REVIEW
Clément Charenton, Marc Graille
In eukaryotes, the elimination of the m7 GpppN mRNA cap, a process known as decapping, is a critical, largely irreversible and highly regulated step of mRNA decay that withdraws the targeted mRNAs from the pool of translatable templates. The decapping reaction is catalysed by a multi-protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor, a holoenzyme that is poorly active on its own and needs several accessory proteins (Lsm1-7 complex, Pat1, Edc1-2, Edc3 and/or EDC4) to be fully efficient...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397100/rna-uridylation-and-decay-in-plants
#8
REVIEW
Caroline de Almeida, Hélène Scheer, Anthony Gobert, Veronica Fileccia, Federico Martinelli, Hélène Zuber, Dominique Gagliardi
RNA uridylation consists of the untemplated addition of uridines at the 3' extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algae Chlamydomonas reinhardtii and the flowering plant Arabidopsis thaliana Plant TUTases target a variety of RNA substrates, differing in size and function...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397099/terminal-nucleotidyl-transferases-tents-in-mammalian-rna-metabolism
#9
REVIEW
Zbigniew Warkocki, Vladyslava Liudkovska, Olga Gewartowska, Seweryn Mroczek, Andrzej Dziembowski
In eukaryotes, almost all RNA species are processed at their 3' ends and most mRNAs are polyadenylated in the nucleus by canonical poly(A) polymerases. In recent years, several terminal nucleotidyl transferases (TENTs) including non-canonical poly(A) polymerases (ncPAPs) and terminal uridyl transferases (TUTases) have been discovered. In contrast to canonical polymerases, TENTs' functions are more diverse; some, especially TUTases, induce RNA decay while others, such as cytoplasmic ncPAPs, activate translationally dormant deadenylated mRNAs...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397098/human-rna-cap1-methyltransferase-cmtr1-cooperates-with-rna-helicase-dhx15-to-modify-rnas-with-highly-structured-5-termini
#10
Diana Toczydlowska-Socha, Magdalena M Zielinska, Malgorzata Kurkowska, Astha, Catarina F Almeida, Filip Stefaniak, Elzbieta Purta, Janusz M Bujnicki
The 5'-cap structure, characteristic for RNA polymerase II-transcribed RNAs, plays important roles in RNA metabolism. In humans, RNA cap formation includes post-transcriptional modification of the first transcribed nucleotide by RNA cap1 methyltransferase (CMTr1). Here, we report that CMTr1 activity is hindered towards RNA substrates with highly structured 5' termini. We found that CMTr1 binds ATP-dependent RNA DHX15 helicase and that this interaction, mediated by the G-patch domain of CMTr1, has an advantageous effect on CMTr1 activity towards highly structured RNA substrates...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30397097/5-and-3-modifications-controlling-rna-degradation-from-safeguards-to-executioners
#11
Dominique Gagliardi, Andrzej Dziembowski
RNA degradation is a key process in the regulation of gene expression. In all organisms, RNA degradation participates in controlling coding and non-coding RNA levels in response to developmental and environmental cues. RNA degradation is also crucial for the elimination of defective RNAs. Those defective RNAs are mostly produced by 'mistakes' made by the RNA processing machinery during the maturation of functional transcripts from their precursors. The constant control of RNA quality prevents potential deleterious effects caused by the accumulation of aberrant non-coding transcripts or by the translation of defective messenger RNAs (mRNAs)...
November 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348880/effects-of-large-herbivores-on-tundra-vegetation-in-a-changing-climate-and-implications-for-rewilding
#12
REVIEW
Johan Olofsson, Eric Post
In contrast to that of the Pleistocene epoch, between approximately 2.6 million and 10 000 years before present, the extant community of large herbivores in Arctic tundra is species-poor predominantly due to human extinctions. We here discuss how this species-poor herbivore guild influences tundra ecosystems, especially in relation to the rapidly changing climate. We show that present herbivore assemblages have large effects on tundra ecosystem composition and function and suggest that the effect on thermophilic species expected to invade the tundra in a warmer climate is especially strong, and that herbivores slow ecosystem responses to climate change...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348879/estimating-interaction-credit-for-trophic-rewilding-in-tropical-forests
#13
Emma-Liina Marjakangas, Luísa Genes, Mathias M Pires, Fernando A S Fernandez, Renato A F de Lima, Alexandre A de Oliveira, Otso Ovaskainen, Alexandra S Pires, Paulo I Prado, Mauro Galetti
Trophic rewilding has been suggested as a restoration tool to restore ecological interactions and reverse defaunation and its cascading effects on ecosystem functioning. One of the ecological processes that has been jeopardized by defaunation is animal-mediated seed dispersal. Here, we propose an approach that combines joint species distribution models with occurrence data and species interaction records to quantify the potential to restore seed-dispersal interactions through rewilding and apply it to the Atlantic Forest, a global biodiversity hotspot...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348878/governing-with-nature-a-european-perspective-on-putting-rewilding-principles-into-practice
#14
P Jepson, F Schepers, W Helmer
Academic interest in rewilding is moving from commentary to discussion on future research agendas. The quality of rewilding research design will be enhanced if it is informed by knowledge of the rewilding practice. Here, we describe the conceptual origins and six case study examples of a mode of rewilding that emerged in the Dutch Delta and is being promoted and supported by Rewilding Europe, an umbrella organization established in 2011. The case experiences presented help position this version of rewilding in relation to the US 3C's version and point towards a rewilding action philosophy characterized by pragmatic realism and pioneer projects around which multiactor networks interested in policy innovation and change form...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348877/measuring-rewilding-progress
#15
Aurora Torres, Néstor Fernández, Sophus Zu Ermgassen, Wouter Helmer, Eloy Revilla, Deli Saavedra, Andrea Perino, Anne Mimet, José M Rey-Benayas, Nuria Selva, Frans Schepers, Jens-Christian Svenning, Henrique M Pereira
Rewilding is emerging as a promising restoration strategy to enhance the conservation status of biodiversity and promote self-regulating ecosystems while re-engaging people with nature. Overcoming the challenges in monitoring and reporting rewilding projects would improve its practical implementation and maximize its conservation and restoration outcomes. Here, we present a novel approach for measuring and monitoring progress in rewilding that focuses on the ecological attributes of rewilding. We devised a bi-dimensional framework for assessing the recovery of processes and their natural dynamics through (i) decreasing human forcing on ecological processes and (ii) increasing ecological integrity of ecosystems...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348876/trophic-rewilding-impact-on-ecosystems-under-global-change
#16
Elisabeth S Bakker, Jens-Christian Svenning
No abstract text is available yet for this article.
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348875/hope-and-caution-rewilding-to-mitigate-the-impacts-of-biological-invasions
#17
REVIEW
Tristan T Derham, Richard P Duncan, Christopher N Johnson, Menna E Jones
Rewilding is a novel approach to ecological restoration. Trophic rewilding in particular aims to reinstate ecological functions, especially trophic interactions, through the introduction of animals. We consider the potential for trophic rewilding to address biological invasions. In this broad review, we note some of the important conceptual and ethical foundations of rewilding, including a focus on ecosystem function rather than composition, reliance on animal agency, and an appeal to an ethic of coexistence...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348874/soil-biological-responses-to-and-feedbacks-on-trophic-rewilding
#18
REVIEW
W S Andriuzzi, D H Wall
Trophic rewilding-the (re)introduction of missing large herbivores and/or their predators-is increasingly proposed to restore biodiversity and biotic interactions, but its effects on soils have been largely neglected. The high diversity of soil organisms and the ecological functions they perform mean that the full impact of rewilding on ecosystems cannot be assessed considering only above-ground food webs. Here we outline current understanding on how animal species of rewilding interest affect soil structure, processes and communities, and how in turn soil biota may affect species above ground...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348873/using-species-distribution-modelling-to-determine-opportunities-for-trophic-rewilding-under-future-scenarios-of-climate-change
#19
Scott Jarvie, Jens-Christian Svenning
Trophic rewilding, the (re)introduction of species to promote self-regulating biodiverse ecosystems, is a future-oriented approach to ecological restoration. In the twenty-first century and beyond, human-mediated climate change looms as a major threat to global biodiversity and ecosystem function. A critical aspect in planning trophic rewilding projects is the selection of suitable sites that match the needs of the focal species under both current and future climates. Species distribution models (SDMs) are currently the main tools to derive spatially explicit predictions of environmental suitability for species, but the extent of their adoption for trophic rewilding projects has been limited...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/30348872/unintentional-rewilding-lessons-for-trophic-rewilding-from-other-forms-of-species-introductions
#20
Andrew J Tanentzap, Bethany R Smith
Trophic rewilding involves adding species into ecosystems to restore extinct, top-down interactions, but limited quantitative data have prevented a systematic attempt to quantify its outcomes. Here, we exploit species introductions that have occurred for purposes other than restoration to inform trophic rewilding. We compiled 51 studies with 158 different responses of lower trophic levels to a species introduction that restored an extinct interaction, whether it intended to do so or not. Unintentional introductions were compared with checklists of extinct animals to identify potential analogues...
October 22, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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