bluuebunny/crossref_metadata_2025_split huggingface dataset:
M1A within cytoplasmic mRNAs at single nucleotide resolution: A reconciled transcriptome-wide map
Authors: Schwartz Schraga 
Published: April 2018

AbstractFollowing synthesis, RNA can be modified with over 100 chemically distinct modifications, and in recent years it was shown that processing, localization, stability and translation of mRNAs can be impacted by an increasing number of these modifications. A modification that recently gained attention is N1-methyladenosine (m1A), which is present across all three domains of life. Recently, two studies - one of them ours - developed conceptually similar approaches to map m1A in a transcriptome-wide manner and at single nucleotide resolution. Surprisingly, the two studies diverged quite substantially in terms of their estimates of the abundance, whereabouts and stoichiometry of this modification within internal sites in cytosolic mRNAs: One study reported it to be a very rare modification, present at very low stoichiometries, and invariably catalyzed by TRMT6/61A. The other found it to be present at >470 sites, in dozens of which at relatively high levels, and in the vast majority of cases these sites were highly unlikely to be substrates of TRMT6/61A, suggesting that additional methyltransferases are active on cytosolic mRNAs. Here we aim to reconcile the contradictions between the two studies, primarily by reanalyzing and re-annotating the set of sites identified in the latter study. We find that the vast majority of sites detected in this study originate from duplications, misannotations, mismapping, SNPs, sequencing errors, and a set of sites originating from the very first transcribed base (‘TSS sites’). We raise concerns as to whether the TSS sites truly reflect m1A originating from the first transcribed base. We find that only 53 of the sites detected in this study likely reflect bona-fide internal modifications of cytoplasmically encoded mRNA molecules. The vast majority of these are likely to be TRMT6/TRMT61A substrates, and are typically modified at low to undetectable levels. We conclude that within cytosolic mRNAs, m1A is a rare internal modification where it is typically catalyzed at ultra-low stoichiometries via TRMT6/TRMT61A. Our findings offer a clear and consistent view on the abundance and whereabouts of this modification, and lays out key directions for future studies in the field.
Functional recruitment of dynamin requires multimeric interactions for efficient endocytosis
Authors: Rosendale Morgane , Van Thi Nhu Ngoc , Grillo-Bosch Dolors , Sposini Silvia , Claverie Léa , Gauthereau Isabel , Claverol Stéphane , Choquet Daniel , Sainlos Matthieu , Perrais David 
Published: April 2018

AbstractDuring clathrin mediated endocytosis (CME), membrane scission is achieved by the concerted action of dynamin and its interacting partners. Essential interactions occur between the proline/arginine-rich domain of dynamin (dynPRD) and the Src-homology domain 3 (SH3) of various proteins including amphiphysins. Here we show that multiple SH3 domains must bind simultaneously to dynPRD through three adjacent motifs for dynamin’s efficient recruitment and function. First, we show in dynamin triple knock-out cells that mutant dynamins modified in a single motif, including the central amphiphysin SH3 (amphSH3) binding motif, are partially capable of rescuing CME. However, mutating two motifs largely prevents that ability. To support this observation, we designed divalent dynPRD-derived peptides. These ligands bind multimers of amphSH3 with >100-fold higher affinity than monovalent onesin vitro. Accordingly, dialyzing living cells with these divalent peptides through a patch-clamp pipette blocks CME 2 to 3 times more effectively than with monovalent ones. Finally, the frequency of endocytic events decreases with competing peptides or hypomorphic rescue mutants but the kinetics of dynamin recruitment is unaffected. This suggests that PRD-SH3 interactions act upstream of dynamin accumulation at the neck of nascent vesicles. We conclude from these data that dynamin drives vesicle scissionviamultivalent interactionsin vivo.
DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis
Authors: Nassrallah Amr , Rougée Martin , Bourbousse Clara , Drevensek Stéphanie , Fonseca Sandra , Iniesto Elisa , Ait-Mohamed Ouardia , Deton-Cabanillas Anne-Flore , Zabulonb Gerald , Ahmed Ikhlak , Stroebel David , Masson Vanessa , Lombard Bérangère , Eeckhout Dominique , Gevaert Kris , Loew Damarys , Genovesio Auguste , Breyton Cécile , de Jaeger Geert , Bowler Chris , Rubio Vicente , Barneche Fredy 
Published: April 2018

SummaryDE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a plant deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.
The Atomic Structure of the Microtubule-Nucleating γ-Tubulin Small Complex and its Implications for Regulation
Authors: Brilot Axel F. , Agard David A. 
Published: April 2018

AbstractThe microtubule cytoskeleton is essential in mediating a number of critical cellular processes, affecting cell shape, transport, organelle organization, and chromosomal segregation during mitosis. Microtubule network dynamics are controlled by many factors including the efficiency and localization of the nucleation machinery. Microtubule nucleation is dependent on the universally conserved γ-tubulin small complex (γTuSC), a 300 kDa heterotetramer composed of two copies of γ-tubulin and one each of accessory proteins GCP2 and GCP3. In yeast, nucleation is mediated by a heptameric ring of γTuSC, which presents 13 γ-tubulins to form a template for microtubule nucleation.We have obtained single-particle structures of the γTuSC as a monomer and dimer at resolutions of 3.6-4.6Å, allowing us to build an atomic model for this important complex. By comparison with a crystal structure of isolated γ-tubulin, it is clear that γ-tubulin is activated upon assembly into the γTuSC, in a manner analogous to the bent to straight transition in αβ-tubulin upon assembly into the microtubule lattice. Our structures allow us to map phosphorylation sites, revealing several at key interfaces, highly suggestive of their role in regulating spindle pole body attachment and assembly into rings. When combined with previous lower resolution structures of helical assemblies, we observe that additional conformational changes occur during ring assembly and activation.
Identification of novel genes including rpmF and yjjQ critical for Type II persister formation in Escherichia coli
Authors: Liu Shuang , Wu Nan , Zhang Shanshan , Zhang Yumeng , Zhang Wenhong , Zhang Ying 
Published: April 2018

AbstractPersister cells, which are characterized by inactive metabolism and tolerance to antibiotics or stresses, pose a significant challenge to the treatment of many persistent infections. Although multiple genes have been reported to be involved in persister formation through transposon mutant library screens, how persisters are formed during the natural process of persister formation as the culture transitions from log phase to stationary phase is unclear. Here, using E. coli as a model, we performed a comprehensive transcriptome analysis of gene expression profiles of successive cultures of an E. coli culture at different critical time points, starting from persister-free S1-nonexistence phase (3h) to persister appearing S2-emergence phase (4h), and persister abundant stage S3-abundance phase (5h). The differentially expressed genes (≥2-fold) in persister appearing stage (S1 to S2 transition) and persister abundant stage (S1 to S3) were compared, and 51 and 29 genes were identified to be up-regulated, respectively. Importantly, 13 genes (gnsA, gnsB, ybfA, yjjQ, ymdF, yhdU, csgD, yncN, rpmF, ydcX, yohJ, ssrA, rbsD) overlap in both persister S2-emergence phase and S3-abundance phase, including a member of the trans-translation pathway (ssrA) as well as an orphan toxin (ydcX), which are two well-known persister genes while the remaining 11 novel genes (gnsA, gnsB, ybfA, yjjQ, ymdF, yhdU, csgD, yncN, rpmF, yohJ, rbsD) have not been reported previously. Persister levels of 7 constructed knockout mutants (ΔgnsA, ΔybfA, ΔyjjQ, ΔyhdU, ΔcsgD, ΔyohJ and ΔrpmF) and 10 overexpression strains (gnsA, gnsB, ybfA, yjjQ, ymdF, yhdU, csgD, rpmF, yohJ, rbsD) in E. coli uropathogenic strain UTI89 were determined upon treatment with different cidal antibiotics (ampicillin, levofloxacin and gentamicin). Additionally, ranking of these overlapping genes according to their impact on persister levels were also performed. Two genes (rpmF encoding 50S ribosomal subunit protein L32, and yjjQ encoding a putative LuxR-type transcription factor) showed the most obvious phenotype on persister levels in both knockout and overexpression studies, which suggests they are broad and key factors for persister formation. While previous studies cannot distinguish if a given persister gene is involved in persister formation or persister survival, our findings clearly identify novel persister forming genes and pathways involving a ribosome protein and a LuxR type transcription factor during the bona fide persister formation process and may have implications for developing improved treatment of persistent infections.
Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly
Authors: Lyon Andrew , Zelter Alex , Viswanath Shruthi , Maxwell Alison , Johnson Richard , Yabut King Clyde B. , MacCoss Michael , Davis Trisha N. , Muller Eric , Sali Andrej , Agard David A. 
Published: April 2018

AbstractMicrotubule (MT) nucleation in vivo is regulated by the γ-tubulin ring complex (γTuRC), an approximately 2-megadalton complex conserved from yeast to humans. In Saccharomyces cerevisiae, γTuRC assembly is a key point of regulation over the MT cytoskeleton. Budding yeast γTuRC is composed of seven γ-tubulin small complex (γTuSC) subassemblies which associate helically to form a template from which microtubules grow. This assembly process requires higher-order oligomers of the coiled-coil protein Spc110 to bind multiple γTuSCs, thereby stabilizing the otherwise low-affinity interface between γTuSCs. While Spc110 oligomerization is critical, its N-terminal domain (NTD) also plays a role that is poorly understood both functionally and structurally. In this work, we sought a mechanistic understanding of Spc110 NTD using a combination of structural and biochemical analyses. Through crosslinking-mass spectrometry (XL-MS), we determined that a segment of Spc110 coiled-coil is a major point of contact with γTuSC. We determined the structure of this coiled-coil segment by X-ray crystallography and used it in combination with our XL-MS dataset to generate an integrative structural model of the γTuSC-Spc110 complex. This structural model, in combination with biochemical analyses of Spc110 heterodimers lacking one NTD, suggests that the two NTDs within an Spc110 dimer act independently, one stabilizing association between Spc110 and γTuSC and the other stabilizing the interface between adjacent γTuSCs.
Cholesterol boundPlasmodium falciparumco-chaperone ‘PFA0660w’ complexes with major virulence factor ‘PfEMP1’ via chaperone ‘PfHsp70-x’
Authors: Behl Ankita , Kumar Vikash , Bisht Anjali , Panda Jiban J. , Hora Rachna , Mishra Prakash Chandra 
Published: April 2018

AbstractLethality ofPlasmodium falciparum(Pf) caused malaria results from ‘cytoadherence’, which is effected by exportedPlasmodium falciparumerythrocyte membrane protein 1 (PfEMP1) family. Several exported Pf proteins (exportome) including chaperones alongside cholesterol rich microdomains are crucial for PfEMP1 translocation to infected erythrocyte surface. An exported Hsp40 (heat shock protein 40) ‘PFA0660w’ functions as a co-chaperone of ‘PfHsp70-x’, and these co-localize to specialized intracellular mobile structures termed J-dots. Our studies attempt to understand the function of PFA0660w-PfHsp70-x chaperone pair using recombinant proteins. Biochemical assays reveal that N and C-terminal domains of PFA0660w and PfHsp70-x respectively are critical for their activity. We show the novel direct interaction of PfHsp70-x with the cytoplasmic tail of PfEMP1, and binding of PFA0660w with cholesterol. PFA0660w operates both as a chaperone and lipid binding molecule via its separate substrate and cholesterol binding sites. PfHsp70-x binds cholesterol linked PFA0660w and PfEMP1 simultaneouslyin vitroto form a complex. Collectively, our results and the past literature support the hypothesis that PFA0660w-PfHsp70-x chaperone pair assists PfEMP1 transport across the host erythrocyte through cholesterol containing ‘J-dots’. Since PFA0660w seems essential for parasite survival, characterization of its interaction with PfHsp70-x and J-dots may form the basis for development of future antimalarials.
NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning
Authors: Klausen Michael Schantz , Jespersen Martin Closter , Nielsen Henrik , Kjærgaard Jensen Kamilla , Jurtz Vanessa Isabell , Sønderby Casper Kaae , Sommer Morten Otto Alexander , Winther Ole , Nielsen Morten , Petersen Bent , Marcatili Paolo 
Published: April 2018

ABSTRACTThe ability to predict local structural features of a protein from the primary sequence is of paramount importance for unravelling its function in absence of experimental structural information. Two main factors affect the utility of potential prediction tools: their accuracy must enable extraction of reliable structural information on the proteins of interest, and their runtime must be low to keep pace with sequencing data being generated at a constantly increasing speed.Here, we present an updated and extended version of the NetSurfP tool (http://www.cbs.dtu.dk/services/NetSurfP-2.0/), that can predict the most important local structural features with unprecedented accuracy and runtime. NetSurfP-2.0 is sequence-based and uses an architecture composed of convolutional and long short-term memory neural networks trained on solved protein structures. Using a single integrated model, NetSurfP-2.0 predicts solvent accessibility, secondary structure, structural disorder, and backbone dihedral angles for each residue of the input sequences.We assessed the accuracy of NetSurfP-2.0 on several independent test datasets and found it to consistently produce state-of-the-art predictions for each of its output features. We observe a correlation of 80% between predictions and experimental data for solvent accessibility, and a precision of 85% on secondary structure 3-class predictions. In addition to improved accuracy, the processing time has been optimized to allow predicting more than 1,000 proteins in less than 2 hours, and complete proteomes in less than 1 day.
Home ground advantage: selection against dispersers promotes local adaptation in wild Atlantic salmon
Authors: Mobley Kenyon B. , Granroth-Wilding Hanna , Ellmen Mikko , Vähä Juha-Pekka , Aykanat Tutku , Johnston Susan E. , Orell Panu , Erkinaro Jaakko , Primmer Craig R. 
Published: April 2018

AbstractA long-held, but poorly tested, assumption in natural populations is that individuals that disperse into new areas for reproduction are at a disadvantage compared to individuals that reproduce in their natal habitat, underpinning the eco-evolutionary processes of local adaptation and ecological speciation. Here, we capitalize on fine-scale population structure and natural dispersal events to compare the reproductive success of local and dispersing individuals captured on the same spawning ground in four consecutive parent-offspring cohorts of wild Atlantic salmon (Salmo salar). Parentage analysis conducted on adults and juvenile fish showed that local females and males had 9.6 and 2.9 times higher reproductive success than dispersers, respectively. Our results reveal how dispersal disadvantage in reproductive success may act in natural populations to drive population divergence and local adaptation over microgeographic spatial scales without clear morphological differences or physical barriers to gene flow.
Beyond the traditional simulation design for evaluating type 1 error rate: from ‘theoretical’ to ‘empirical’ null
Authors: Zhang Ting , Sun Lei 
Published: April 2018

AbstractWhen evaluating a newly developed statistical test, the first step is to check its type 1 error (TIE) control using simulations. This is often achieved by the standard simulation design S0 under the so-called ‘theoretical’ null of no association. In practice, whole-genome association analyses scan through a large number of genetic markers (Gs) for the ones associated with an outcome of interest (Y), where Y comes from an unknown alternative while the majority of Gs are not associated with Y, that is under the ‘empirical’ null. This reality can be better represented by two other simulation designs, where design S1.1 simulates Y from an alternative model based on G then evaluates its association with independently generated Gnew, while design S1.2 evaluates the association between permutated Yperm and G. More than a decade ago, Efron (2004) has noted the important distinction between the ‘theoretical’ and ‘empirical’ null in false discovery rate control. Using scale tests for variance heterogeneity and location tests of interaction effect as two examples, here we show that not all null simulation designs are equal. In examining the accuracy of a likelihood ratio test, while simulation design S0 shows the method has the correct T1E control, designs S1.1 and S1.2 suggest otherwise with empirical T1E values of 0.07 for the 0.05 nominal level. And the inflation becomes more severe at the tail and does not diminish as sample size increases. This is an important observation that calls for new practices for methods evaluation and interpretation of T1E control.
ADAM22 and ADAM23 modulate the targeting of the Kv1 channel-associated protein LGI1 to the axon initial segment
Authors: Hivert Bruno , Marien Laurène , Agbam Komlan Nassirou , Faivre-Sarrailh Catherine 
Published: April 2018

AbstractThe distribution of voltage-gated potassium channels Kv1 at the axon initial segment (AIS), along the axon and at presynaptic terminals influences intrinsic excitability and transmitter release. Kv1.1/1.2 subunits are associated with cell adhesion molecules (CAMs), including Caspr2 and LGI1 that are implicated in autoimmune and genetic neurological diseases with seizures. In particular, mutations in the LGI1 gene cause autosomal dominant lateral temporal lobe epilepsy (ADTLE). In the present study, we used rat hippocampal neurons in culture to assess whether interplay between distinct Kv1-associated CAMs contributes to targeting at the AIS. Strikingly, LGI1 was highly restricted to the AIS surface when transfected alone, whereas the missense mutant LGI1S473L associated with ADLTE was not. Next, we showed that ADAM22 and ADAM23 acted as chaperones to promote axonal vesicular transport of LGI1 reducing its density at the AIS. Moreover, live-cell imaging of fluorescently labelled CAMs indicated that LGI1 was co-transported in axonal vesicles with ADAM22 or ADAM23. Finally, we showed that ADAM22 and ADAM23 also associate with Caspr2 and TAG-1 to be selectively targeted within different axonal sub-regions. The combinatorial expression of Kv1-associated CAMs may be critical to tune intrinsic excitability in a physiological or an epileptogenic context.
The lost world of Cuatro Cienegas Basin, a relictual bacterial niche in a desert oasis
Authors: Souza V. , Moreno-Letelier A. , Travisano M. , Alcaraz L. D. , Olmedo-Alvarez G. , Eguiarte L. E. 
Published: April 2018

AbstractBarriers to immigration can lead to localized adaptive radiations and increased endemism. We propose that extreme oligotrophy can be a strong barrier to immigration over geological timescales, and facilitate the evolution of diverse and coevolved microbial communities. We show here that the endangered oasis of Cuatro Ciénegas Basin can be a model for a lost world, where the ancient niche of extreme oligotrophy favoured survival of ancestral microorganisms that persisted due to environmental stability and low extinction rates, generating a diverse and unique bacteria diversity. Diversification/extinction rates in Bacillus showed several CCB endemic clades that diverged from the rest of Bacillus spp. in different times of the Paleozoic and Mesozoic, in contrast to more recent Bacillus, Clostridium and Bacteroidetes lineages. CCB conservation is vital to the understanding of early evolutionary and ecological processes.
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
Authors: Alshahrani Mona , Hoehndorf Robert 
Published: April 2018

AbstractMotivationIn the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease’s (or patient’s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse.ResultsWe developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.Availabilityhttps://github.com/bio-ontology-research-group/SmuDGEContactrobert.hoehndorf@kaust.edu.sa