bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional analysis of deoxyhexose sugar utilization inEscherichia colireveals fermentative metabolism under aerobic conditions
Authors: Millard Pierre , Pérochon Julien , Letisse Fabien 
Published: April 2021

ABSTRACTL-rhamnose and L-fucose are the two main 6-deoxyhexosesEscherichia colican use as carbon and energy sources. Deoxyhexose metabolism leads to the formation of lactaldehyde whose fate depends on oxygen availability. Under anaerobic conditions, lactaldehyde is reduced to 1,2-propanediol whereas under aerobic condition, it should be oxidised into lactate and then channelled into the central metabolism. However, although this all-or-nothing view is accepted in the literature, it seems overly simplistic since propanediol is also reported to be present in the culture medium during aerobic growth on L-fucose. To clarify the functioning of 6-deoxyhexose sugar metabolism, a quantitative metabolic analysis was performed to determine extra- and intracellular fluxes inE. coliK-12 MG1655 (a laboratory strain) and inE. coliNissle 1917 (a human commensal strain) during anaerobic and aerobic growth on L-rhamnose and L-fucose. As expected, lactaldehyde is fully reduced to 1,2-propanediol in anoxic conditions allowing complete reoxidation of the NADH produced by glyceraldehyde-3-phosphate-dehydrogenase. We also found that net ATP synthesis is ensured by acetate production. More surprisingly, lactaldehyde is also primarily reduced into 1,2-propanediol under aerobic conditions. For growth on L-fucose,13C-metabolic flux analysis revealed a large excess of available energy, highlighting the need to better characterize ATP utilization processes. The probioticE. coliNissle 1917 strain exhibits similar metabolic traits, indicating that they are not the result of the K-12 strain’s prolonged laboratory use.IMPORTANCEE. coli’s ability to survive, grow and colonize the gastrointestinal tract stems from its use of partially digested food and hydrolysed glycosylated proteins (mucins) from the intestinal mucus layer as substrates. These include L-fucose and L-rhamnose, two 6-deoxyhexose sugars, whose catabolic pathways have been established by genetic and biochemical studies. However, the functioning of these pathways has only partially been elucidated. Our quantitative metabolic analysis provides a comprehensive picture of 6-deoxyhexose sugar metabolism inE. coliunder anaerobic and aerobic conditions. We found that 1,2-propanediol is a major by-product under both conditions, revealing the key role of fermentative pathways in 6-deoxyhexose sugar metabolism. This metabolic trait is shared by bothE. colistrains studied here, a laboratory strain and a probiotic strain. Our findings add to our understanding ofE. coli’s metabolism and of its functioning in the bacterium’s natural environment.
Formins play important role inLeishmaniaphysiology by acting as cytosolic actin bundlers
Authors: Kushwaha Renu , Seth Arunava , Jijumon A.S. , Reshmi P.B. , Dileep Drisya , Datta Rupak , Maiti Sankar 
Published: April 2021

AbstractFormins are a highly conserved eukaryotic family of proteins that regulate actin dynamics. They play important physiological roles in cell adhesion, motility, vesicular trafficking and cytokinesis. Although sequence analysis of Trypanosomatida genomes predicted multiple formin-encoding genes, none of them are functionally characterized yet. We report here experimental identification and functional characterization of two constitutively expressed formins from the trypanosomatid protozoaLeishmania majorviz. LmForminA and LmForminB. These formins exhibited irregular cytosolic distribution that co-localized with actin patches. Co-sedimentation assay and surface plasmon resonance confirmed that purified LmForminA and B FH2 domains can bind actin, albeit with differential affinity. Interestingly, both LmForminA and B FH2 domains were found to be actin bundlers as revealed by low-speed co-sedimentation assay and TIRF microscopy. LmForminA and B also had actin-nucleating activities, which was abolished by mutating their conserved Ile residue crucial for actin assembly. The Ile-mutant formins, however, retained their actin binding and bundling properties. Treatment ofLeishmaniacells with formin inhibitor SMIFH2 severely perturbed parasite growth and morphology indicating that Lmformins are physiologically important and may be considered as novel drug targets.
A species-specific signature residue in the PB2 subunit of the bat influenza virus polymerase restricts viral RNA synthesis
Authors: Banerjee Saptarshi , De Aratrika , Kedia Nandita , Linfa Wang , Mondal Arindam 
Published: April 2021

AbstractBat influenza A viruses (H17N10 and H18N11) are genetically distant from conventional influenza A viruses and replicates poorly in non-bat hosts species. However, the reason behind the lower replication fitness of these viruses are yet to be elucidated. In this work, we have identified species-specific signature residues, present in viral PB2 protein, which is a major determinant of polymerase fitness in human, avian and bat cell lines. Through extensive sequence and structural comparison between the bat and non-bat influenza virus RNA polymerases, we have identified a previously uncharacterized PB2-282 residue, which is serine in bat virus PB2 protein but harbours highly conserved glutamic acid in conventional influenza A viruses. Introduction of these bat specific signatures in the polymerase of a human adapted strain of influenza A/H1N1 virus drastically reduces its polymerase activity and replication efficiency in cell lines of human, bat and canine origin. In contrast, introduction of the human specific signatures in bat virus PB2 (H17N10), significantly enhances its function in the context of a chimeric RNA polymerase. Interestingly, the PB2-282 resides within an evolutionary conserved “S-E-S” motif present across different genera of influenza viruses but is replaced with a “S-S-T” motif in bat influenza viruses, indicating that this E to S transition may serve as a species-specific adaptation signature that modulates the activity of bat virus polymerase in other host species.ImportanceRecent isolation of influenza A like viruses (H17N10 and H18N11) in bats raised concerns about their potential of zoonotic transmission in human. Here we present species-specific signature residues present in the bat influenza virus polymerase, which may act as critical modulators of bat virus propagation in non-bat host species. We utilize bioinformatics based comparative analysis followed by functional screening in order to identify the PB2-282ndposition, which harbors a highly conserved glutamic acid in conventional influenza A viruses, but contains an unusual serine in case of bat influenza viruses. Human adapted polymerase, harboring bat specific signature (PB2-S282) performs poorly, while bat PB2 protein harboring human specific signature (PB2-E282) shows increased fitness in human cells. Together, our data identifies novel species-specific signatures present within the influenza virus polymerase that may serve as a key factor in the adaptation of influenza viruses from bat to non-bat host species and vice versa.
The C-terminus of the prototypical M2 muscarinic receptor localizes to the mitochondria and regulates cell respiration under stress conditions
Authors: Fasciani Irene , Petragnano Francesco , Wang Ziming , Edwards Ruairidh , Telegu Narasimha , Pietrantoni Ilaria , Zabel Ulrike , Zauber Henrik , Grieben Marlies , Terzenidou Maria E. , Di Gregorio Jacopo , Pellegrini Cristina , Santini Silvano , Taddei Anna R. , Pöhl Barbel , Aringhieri Stefano , Carli Marco , Aloisi Gabriella , Marampon Francesco , Charlesworth Eve , Roman Alexandra , Diecke Sebastian , Flati Vincenzo , Giorgi Franco , Amicarelli Fernanda , Tobin Andrew B. , Scarselli Marco , Tokatlidis Kostas , Rossi Mario , Lohse Martin J. , Annibale Paolo , Maggio Roberto 
Published: April 2021

AbstractMuscarinic acetylcholine receptors are prototypical G protein-coupled receptors (GPCRs), members of a large family of seven transmembrane receptors mediating a wide variety of extracellular signals. We show here, in cultured cells and in a murine model, that the carboxyl terminal fragment of the muscarinic M2receptor, comprising the transmembrane regions 6 and 7 (M2tail), is expressed by virtue of an internal ribosome entry site localized in the third intracellular loop. Single cell imaging and import in isolated yeast mitochondria reveals that M2tail, whose expression is upregulated in cells undergoing integrated stress response, does not follow the normal route to the plasma membrane, but is almost exclusively sorted to the mitochondria inner membrane: here it controls oxygen consumption, cell proliferation and the formation of reactive oxygen species by reducing oxidative phosphorylation. Crispr/Cas9 editing of the key methionine where cap-independent translation begins in human induced pluripotent stem cells, reveals the physiological role of this process in influencing cell proliferation and oxygen consumption at the endogenous level. The expression of the C-terminal domain of a GPCR, capable of regulating mitochondrial function, constitutes a hitherto unknown mechanism notably unrelated to its canonical signalling function as a GPCR at the plasma membrane. This work thus highlights a potential novel mechanism thar cells may use for controlling their metabolism under variable environmental conditions, notably as a negative regulator of cell respiration.
SUFFICIENT ACTIVITY OF THE UBIQUITIN PROTEASOME SYSTEM IN AGED MICE AND DURING RETINAL DEGENERATION SUPPORTS DHFR-BASED CONDITIONAL CONTROL OF PROTEIN ABUNDANCE IN THE RETINA
Authors: Peng Hui , Ramadurgum Prerana , Woodard DaNae R. , Daniel Steffi , Renwick Marian , Aredo Bogale , Datta Shyamtanu , Chen Bo , Ufret-Vincenty Rafael , Hulleman John D. 
Published: April 2021

SummaryTheEscherichia colidihydrofolate reductase (DHFR) destabilizing domain (DD) serves as a promising approach to conditionally regulate protein abundance in a variety of tissues. In the absence of TMP, a DHFR stabilizer, the DD is degraded by the ubiquitin proteasome system (UPS). To test whether this approach could be effectively applied to a wide variety of aged and disease-related ocular mouse models, which may have a compromised UPS, we evaluated the DHFR DD system in aged mice (up to 24 mo), a light-induced retinal degeneration (LIRD) model, and two genetic models of retinal degeneration (rd2andAbca4−/−mice). Aged, LIRD, andAbca4−/−mice all had similar proteasomal activities and high-molecular weight ubiquitin levels compared to control mice. However,rd2mice displayed compromised chymotrypsin activity compared to control mice. Nonetheless, the DHFR DD was effectively degraded in all model systems, includingrd2mice. Moreover, TMP increased DHFR DD-dependent retinal bioluminescence in all mouse models, however the fold induction was slightly, albeit significantly, lower inAbca4−/−mice. Thus, the destabilized DHFR DD-based approach allows for efficient control of protein abundance in aged mice and retinal degeneration mouse models, laying the foundation to use this strategy in a wide variety of mice for the conditional control of gene therapies to potentially treat multiple eye diseases.
β-RA targets mitochondrial metabolism and adipogenesis, leading to therapeutic benefits against CoQ deficiency and age-related overweight
Authors: Hidalgo-Gutiérrez Agustín , Barriocanal-Casado Eliana , Díaz-Casado María Elena , González-García Pilar , Chiozzi Riccardo Zenezini , Acuña-Castroviejo Darío , López Luis Carlos 
Published: April 2021

AbstractPrimary mitochondrial diseases are caused by mutations in mitochondrial or nuclear genes, leading to abnormal function of specific mitochondrial pathways. Mitochondrial dysfunction is also a secondary event in more common pathophysiological conditions, such as obesity and metabolic syndrome. In both cases, the improvement and management of mitochondrial homeostasis remains challenging. Here, we show that beta-resorcylic acid (β-RA), a natural phenolic compound, competesin vivowith 4-hydroxybenzoic acid, the natural precursor of Coenzyme Q biosynthesis. This leads to a decrease of demethoxyubiquinone, an intermediate metabolite of CoQ biosynthesis that is abnormally accumulated inCoq9R239Xmice. As a consequence, β-RA rescues the phenotype ofCoq9R239Xmice, a model of primary mitochondrial encephalopathy. Moreover, we observe that long-term treatment with β-RA also reduces the size and content of the white adipose tissue (WAT) that is normally accumulated during aging in wild-type mice, leading to a prevention of hepatic steatosis and an increase in survival at the old stage of life. The reduction in WAT content is due to a decrease in adipogenesis, an adaptation of the mitochondrial proteome in the kidneys, and a stimulation of glycolysis and acetyl-CoA metabolism. Therefore, our results demonstrate that β-RA acts through different cellular mechanisms, with effects on mitochondrial metabolism, and it may be used for the treatment of primary Coenzyme Q deficiency, overweight, and hepatic steatosis.
Novel amiloride derivatives that inhibit bacterial motility across multiple strains and stator types
Authors: Islam MI , Bae JH , Ishida T , Ridone P , Lin J , Kelso MJ , Sowa Y , Buckley BJ , Baker MAB 
Published: April 2021

AbstractThe bacterial flagellar motor (BFM) is a protein complex that confers motility to cells and contributes to survival and virulence. The BFM consists of stators that are ion-selective membrane protein complexes and a rotor that directly connects to a large filament, acting as a propeller. The stator complexes couple ion transit across the membrane to torque that drives rotation of the motor. The most common ion gradients that drive BFM rotation are protons (H+) and sodium ions (Na+). The sodium-powered stators, like those in the PomAPomB stator complex of Vibrio spp, can be inhibited by sodium channel inhibitors, in particular, by phenamil, a potent and widely used inhibitor. However, relatively few new sodium-motility inhibitors have been described since the discovery of phenamil. In this study, we characterised two possible motility inhibitors HM2-16F and BB2-50F from a small library of previously reported amiloride derivatives. We used three approaches: effect on rotation of tethered cells, effect on free swimming bacteria and effect on rotation of marker beads. We showed that both HM2-16F and BB2-50F stopped rotation of tethered cells driven by Na+motors comparable to phenamil at matching concentrations, and could also stop rotation of tethered cells driven by H+motors. Bead measurements in presence and absence of stators confirmed that the compounds did not inhibit rotation via direct association with the stator, in contrast to the established mode of action of phenamil. Overall, HM2-16F and BB2-50F stopped swimming in both Na+and H+stator types, and in pathogenic and non-pathogenic strains.ImportanceHere we characterised two novel amiloride derivatives in the search for antimicrobial compounds that target bacterial motility. Our two compounds were shown to inhibit flagellar motility at 10 μM across multiple strains, from non-pathogenicE. coliwith flagellar rotation driven by proton or chimeric sodium-powered stators, to proton-powered pathogenicE. coli(EHEC/UPEC) and lastly in sodium-poweredVibrio alginolyticus. Broad anti-motility compounds such as these are important tools in our efforts control virulence of pathogens in health and agricultural settings.
Towards a comprehensive delineation of white matter tract-related deformation
Authors: Zhou Zhou , Li Xiaogai , Liu Yuzhe , Fahlstedt Madelen , Georgiadis Marios , Zhan Xianghao , Raymond Samuel J. , Grant Gerald , Kleiven Svein , Camarillo David , Zeineh Michael 
Published: April 2021

AbstractFinite element (FE) models of the human head are valuable instruments to explore the mechanobiological pathway from external loading, localized brain response, and resultant injury risks. The injury predictability of these models depends on the use of effective criteria as injury predictors. The FE-derived normal deformation along white matter (WM) fiber tracts (i.e., tract-oriented strain) has recently been suggested as an appropriate predictor for axonal injury. However, the tract-oriented strain only represents a partial depiction of the WM fiber tract deformation. A comprehensive delineation of tract-related deformation may improve the injury predictability of the FE head model by delivering new tract-related criteria as injury predictors. Thus, the present study performed a theoretical strain analysis to comprehensively characterize the WM fiber tract deformation by relating the strain tensor of the WM element to its embedded fiber tract. Three new tract-related strains with exact analytical solutions were proposed, measuring the normal deformation perpendicular to the fiber tracts (i.e., tract-perpendicular strain), and shear deformation along and perpendicular to the fiber tracts (i.e., axial-shear strain and lateral-shear strain, respectively). The injury predictability of these three newly-proposed strain peaks along with the previously-used tract-oriented strain peak and maximum principal strain (MPS) were evaluated by simulating 151 impacts with known outcome (concussion or non-concussion). The results preliminarily showed that four tract-related strain peaks exhibited superior performance than MPS in discriminating concussion and non-concussion cases. This study presents a comprehensive quantification of WM tract-related deformation and advocates the use of orientation-dependent strains as criteria for injury prediction, which may ultimately contribute to an advanced mechanobiological understanding and enhanced computational predictability of brain injury.
Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes
Authors: Schneider-Lunitz Valentin , Ruiz-Orera Jorge , Hubner Norbert , van Heesch Sebastiaan 
Published: April 2021

ABSTRACTRNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism. We searched for such previously undiscovered multifunctionality within a set of 143 RBPs, by defining the predictive value of RBP abundance for the transcription and translation levels of known RBP target genes across 80 human hearts. This led us to newly associate 27 RBPs with cardiac translational regulationin vivo. Of these, 21 impacted both RNA expression and translation, albeit for virtually independent sets of target genes. We highlight a subset of these, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved through differential affinity for target length, by which separate biological processes are controlled. Similar to the RNA helicase DDX3X, the known splicing factors EFTUD2 and PRPF8 - all identified as multifunctional RBPs by our analysis - selectively influence target translation rates depending on 5’ UTR structure. Our analyses identify dozens of RBPs as being multifunctional and pinpoint potential novel regulators of translation, postulating unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression.
Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa
Authors: Hartop Emily , Srivathsan Amrita , Ronquist Fredrik , Meier Rudolf 
Published: April 2021

AbstractNew, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa”, that we here define as clades for which <10% of all species are described and the estimated diversity exceeds 1000 species. Species delimitation for these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop explicit methods to avoid this by applying Large-scale Integrative Taxonomy (LIT). Preliminary species hypotheses are generated based on inexpensive data that are obtained quickly and cost-effectively in a technical exercise. The validation step is then based on a more expensive type of data that are only obtained for specimens selected based on objective criteria. We here use this approach to sort 18 000 scuttle flies (Diptera: Phoridae) from Sweden into 315 preliminary species hypotheses based on NGS barcode (313bp) clusters. These clusters were subsequently tested with morphology and used to develop quantitative indicators for predicting which barcode clusters are in conflict with morphospecies. For this purpose, we first randomly selected 100 clusters for in-depth validation with morphology. Afterwards, we used a linear model to demonstrate that the best predictors for conflict between barcode clusters and morphology are maximum p-distance within the cluster and cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that conflict with morphology. The morphological validation step in our study involved only 1 039 specimens (5.8% of all specimens), but a newly proposed simplified protocol would only require the study of 915 (5.1%: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of conflict are similar across Objective Clustering (OC), Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP) and Refined Single Linkage (RESL) (used by Barcode of Life Data System (BOLD) to assign Barcode Index Numbers (BINs)). OC and ABGD achieved a maximum congruence score with morphology of 89% while PTP was slightly less effective (84%). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1 714 haplotypes were 86% congruent with morphology while the values were 89% for OC, 74% for PTP, and 72% for ABGD.
The transcriptomic landscape of the photoperiodic stress response in Arabidopsis thaliana resembles the response to pathogen infection
Authors: Cortleven Anne , Roeber Venja M. , Frank Manuel , Bertels Jonas , Lortzing Vivien , Beemster Gerrit , Schmülling Thomas 
Published: April 2021

ABSTRACTPlants are exposed to regular diurnal rhythms of light and dark. Changes in the photoperiod by the prolongation of the light period cause photoperiod stress in short day-adapted Arabidopsis thaliana. Here we report on the transcriptional response to photoperiod stress of wild-type A. thaliana and photoperiod stress-sensitive cytokinin signalling and clock mutants. Transcriptomic changes induced by photoperiod stress included numerous changes in reactive oxygen (ROS)-related transcripts and showed a strong overlap with changes occurring in response to ozone stress and pathogen attack, which have in common the induction of an apoplastic oxidative burst. A core set of photoperiod stress-responsive genes has been identified, including salicylic acid (SA) biosynthesis and signalling genes. Genetic analysis revealed a central role for NPR1 in the photoperiod stress response as npr1-1 mutants were stress-insensitive. Photoperiod stress treatment led to a strong increase in camalexin levels which is consistent with shared photoperiod stress and pathogen response pathways. Photoperiod stress induced resistance of Arabidopsis plants to a subsequent infection by Pseudomonas syringae cv. tomato DC3000 indicating priming of the defence response. Together, photoperiod stress causes transcriptional reprogramming resembling plant pathogen defence responses and induces systemic acquired resistance in the absence of a pathogen.One sentence summaryPhotoperiod stress results in significant dynamic transcriptomic changes related to oxidative stress similar to those caused by pathogen attack and primes the defence response against a subsequent pathogen infection.