bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immediate inhibition of sucrose uptake inCorynebacterium glutamicumin response to intracellular glucose-6-phosphate accumulation requires theptsGencoded EII-permease
Authors: Petrov Dimitar P. , Goldbeck Oliver , Krämer Reinhard , Seibold Gerd M. 
Published: May 2019

ABSTRACTCorynebacterium glutamicumco-metabolizes most carbon sources, such as glucose and sucrose. Uptake of those sugars by the PTS involves a glucose- and a sucrose-specific permease EIIGlc(ptsG) and EIISuc(ptsS), respectively. Block of glycolysis by deletion ofpgi(encodes phosphoglucoisomerase) redirects glucose-driven carbon flux towards pentose phosphate pathway.C. glutamicumΔpgigrows poorly with glucose but has unaffected, good growth with sucrose. However, addition of glucose to sucrose-cultivatedC. glutamicumΔpgiimmediately arrested growth via inhibition of the EIISuc–mediated sucrose uptake and reduction ofptsS-mRNA amounts. Kinetic analyses revealed that sucrose uptake inhibition inC. glutamicumΔpgitook place within 15 s after glucose addition. We show that inhibition of PTS-mediated sucrose uptake occurs as direct response to glucose-6-P accumulation. Moreover, addition of non-PTS substrates, which are metabolized to glucose-6-P such as maltose or glucose-6-P itself (uptake was enabled by heterologously produced UhpT), led to similar growth and sucrose uptake inhibition as glucose addition. Despite EIIGlcnot being involved in uptake of these substrates, negative effects on sucrose uptake after addition of maltose and glucose-6-P were absent in the EIIGlc–deficient strainC. glutamicumΔpgiΔptsG. These results show that theptsG-encoded EIIGlcis part of a novel mechanism for perception of intracellular glucose-6-P accumulation and instantaneous inhibition of EIISuc-mediated sucrose uptake inC. glutamicum. This novel mode of control of PTS activity by an early glycolytic metabolite probably allows efficient adaptation of sugar uptake to the capacity of the central metabolism during co-metabolization, which is characteristic forC. glutamicum.IMPORTANCECoordination of substrate uptake and metabolism are a prerequisite for efficient co-utilization of substrates, a trait typical for the Gram-positiveC. glutamicum. Sucrose uptake via the PTS permease EIISucin this organism immediately was inhibited in response to intracellular accumulation of the glycolysis intermediate glucose-6-phosphate. This inhibition depends exclusively on the presence but not activity of the PTS permease EIIGluc. Thus,C. glutamicumpossesses a novel, immediate, and PTS-dependent way to control and coordinate both uptake and metabolization of multiple substrates by monitoring of their metabolic levels in the cell. This offers new insights and interesting concepts for a further rational engineering of this industrially important production organism and exemplifies a putative general strategy of bacteria for the coordination of sugar uptake and central metabolism.
Stability and dynamics interrelations in a Lipase: Mutational and MD simulations based investigations
Authors: Moharana Tushar Ranjan , Kumar Virendra , Rao N. Madhusudhana 
Published: May 2019

AbstractDynamics plays crucial role in the function and stability of proteins. Earlier studies have provided ambivalent nature of these interrelations. Epistatic effects of amino acid substitutions on dynamics are an interesting strategy to investigate such relations. In this study we investigated the interrelation between dynamics with that of stability and activity ofBacillus subtilislipase (BSL) using experimental and molecular dynamics simulation (MDS) approaches. Earlier we have identified many stabilising mutations in BSL using directed evolution. In this study these stabilizing mutations were clustered based on their proximity in the sequence into four groups (CM1 to 4). Activity, thermal stability, protease stability and aggregations studies were performed on these four mutants, along with the wild type BSL, to conclude that the mutations in each region contributed additively to the overall stability of the enzyme without suppressing the activity. Root mean square fluctuation and amide bond squared order parameter analysis from MDS revealed that dynamics has increased for CM1, CM2 and CM3 compared to the wild type in the amino acid region 105 to 112 and for CM4 in the amino acid region 22 to 30. In all the mutants core regions dynamics remained unaltered, while the dynamics in the rigid outer region (RMSF <0.05 nm) has increased. Alteration in dynamics, took place both in the vicinity (CM2, 0.41 nm) as well as far away from the mutations (CM1, 2.6 nm; CM3 1.5 nm; CM4 1.7 nm). Our data suggests that enhanced dynamics in certain regions in a protein may actually improve stability.Statement of SignificanceHow does a protein readjust its dynamics upon incorporation of an amino acid that improved its stability? Are the stabilizing effects of a substitution being local or non-local in nature? While there is an excellent documentation (from x-ray studies) of both local and non-local adjustments in interactions upon incorporation of a stabilizing mutations, the effect of these on the protein dynamics is less investigated. The stability and MD data presented here on four mutants, stabilized around four loop regions of a lipase, suggests that stabilizing effects of these mutations influence two specific regions leaving rest of the protein unperturbed. In addition, our data supports, observations by others, wherein enhancement in stability in a protein need not result in dampening of dynamics of a protein.
Evidence of transcription at polyT short tandem repeats
Authors: Bessière Chloé , Saraswat Manu , Grapotte Mathys , Menichelli Christophe , Ramilowski Jordan A. , Severin Jessica , Hayashizaki Yoshihide , Itoh Masayoshi , Hasegawa Akira , Suzuki Harukazu ,   FANTOM consortium, Carninci Piero , Hoon Michiel J.L. de , Wasserman Wyeth W. , Bréhélin Laurent , Lecellier Charles-Henri 
Published: May 2019

AbstractBackgroundUsing the Cap Analysis of Gene Expression technology, the FANTOM5 consortium provided one of the most comprehensive maps of Transcription Start Sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers.ResultsHere, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at short tandem repeats (STRs) corresponding to homopolymers of thymidines (T). Additional analyse confirm that these CAGEs are truly associated with transcriptionally active chromatin marks. Furthermore, we train a sequence-based deep learning model able to predict CAGE signal at T STRs with high accuracy (~81%) Extracting features learned by this model reveals that transcription at T STRs is mostly directed by STR length but also instructions lying in the downstream sequence. Excitingly, our model also predicts that genetic variants linked to human diseases affect this STR-associated transcription.ConclusionsTogether, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism. We also provide a new metric that can be considered in future studies of STR-related complex traits.
Emergence of consistent intra-individual locomotor patterns during zebrafish development
Authors: Fitzgerald Jennifer A. , Kirla Krishna T. , Zinner Carl P. , vom Berg Colette M. 
Published: May 2019

AbstractThe analysis of larval zebrafish locomotor behavior has emerged as a powerful indicator of perturbations in the nervous system and is used in many fields of research, such as neuroscience, toxicology or drug discovery. The behavior of larval zebrafish, however, is highly variable, resulting in the use of high numbers of animals and the inability to detect small effects. In this study, we analyzed whether individual locomotor behavior is stable over development and whether behavioral parameters correlate with physiological and morphological features of the larvae, with the aim to better understand variability and predictability of larval locomotor behavior. We found that locomotor activity of individuals is consistent within the same day and becomes predictable during development especially during dark phases, when larvae are performing exploratory light-searching behavior and display increased activity. Stimulus induced startle responses were less predictable for an individual, and response strength did not correlate with inherent locomotor activity. Moreover, locomotor activity was not associated with physiological and morphological features of the larva (resting heart rate, body length, size of the swim bladder). These findings highlight the areas of intra-individual consistency, which could be used to improve the sensitivity of assays using zebrafish locomotor activity as an endpoint.
A cytochrome P450 from juvenile mustard leaf beetles hydroxylates geraniol, a key step in iridoid biosynthesis
Authors: Fu Nanxia , Yang Zhi-ling , Pauchet Yannick , Paetz Christian , Brandt Wolfgang , Boland Wilhelm , Burse Antje 
Published: May 2019

AbstractJuveniles of the leaf beetle Phaedon cochleariae synthesize iridoid via the mevalonate pathway to repel predators. The normal terpenoid biosynthesis is integrated into the dedicated defensive pathway by the ω-hydroxylation of geraniol to 8-hydroxygeraniol. Here we identify and characterize the geraniol 8-hydroxylase as a P450 monooxygenase using integrated transcriptomic and proteomic analyses. In the fat body, 73 individual cytochrome P450s were identified. The double stranded RNA (dsRNA)-mediated knock down of CYP6BH5 led to a significant reduction of 8-hydroxygeraniol-glucoside in the hemolymph and, later, of the chrysomelidial in the defensive secretion. Heterologously expressed CYP6BH5 converted geraniol to 8-hydroxygeraniol. In addition to geraniol, CYP6BH5 also catalyzes other monoterpenols, such as nerol and citronellol, into the corresponding α, ω-dihydroxy compounds.HighlightsThe geraniol 8-hydroxylase in Phaedon cochleariae was identified as a cytochrome P450 CYP6BH5.RNA interference emphasized the importance of CYP6BH5 in iridoid biosynthesis.In vitro enzyme assays showed that recombinant CYP6BH5 is a substrate promiscuous enzyme, converting the ω-hydroxylation of geraniol, nerol, citronellol but not linalool.Homology modeling suggested the -OH group of the substrate plays an important role in coordinating the substrates with the enzyme’s catalytic cavity.
MCC950/CRID3 potently targets the NACHT domain of wildtype NLRP3 but not disease-associated mutants for inflammasome inhibition
Authors: Vande Walle Lieselotte , Stowe Irma B. , Šácha Pavel , Lee Bettina L. , Demon Dieter , Fossoul Amelie , Van Hauwermeiren Filip , Saavedra Pedro H. V. , Šimon Petr , Šubrt Vladimír , Kostka Libor , Stivala Craig E. , Pham Victoria C. , Staben Steven T. , Yamazoe Sayumi , Konvalinka Jan , Kayagaki Nobuhiko , Lamkanfi Mohamed 
Published: May 2019

SummaryThe NLRP3 inflammasome drives pathological inflammation in a suite of autoimmune, metabolic, malignant and neurodegenerative diseases. Additionally,NLRP3gain-of-function point mutations cause systemic periodic fever syndromes that are collectively known as cryopyrin-associated periodic syndromes (CAPS). There is significant interest in the discovery and development of diarylsulfonylurea Cytokine Release Inhibitory Drugs (CRIDs) such as MCC950/CRID3, a potent and selective inhibitor of the NLRP3 inflammasome, for the treatment of CAPS and other diseases. However, drug discovery efforts have been constrained by the lack of insight in the molecular target and mechanism by which these CRIDs inhibit the NLRP3 inflammasome. Here, we show that the NACHT domain of NLRP3 is the molecular target of diarylsulfonylurea inhibitors. Interestingly, we find photoaffinity labelling of the NACHT domain requires an intact (d)ATP-binding pocket and is substantially reduced for most CAPS-associated NLRP3 mutants. In concordance, MCC950/CRID3 failed to inhibit NLRP3- driven inflammatory pathology in two mouse models of CAPS. Moreover, it abolished circulating levels of interleukin (IL)-1β and IL-18 in LPS-challenged wildtype mice but not inNlrp3L351Pknock-in mice and ex vivo-stimulated mutant macrophages. These results identify wildtype NLRP3 as the molecular target of MCC950/CRID3, and show that CAPS-related NLRP3 mutants escape efficient MCC950/CRID3 inhibition. Collectively, this work suggests that MCC950/CRID3-based therapies may effectively treat inflammation driven by wildtype NLRP3, but not CAPS-associated mutants.
Infection-driven activation of transglutaminase 2 boosts glucose uptake and hexosamine biosynthesis
Authors: Maffei Benoit , Laverrière Marc , Wu Yongzheng , Triboulet Sébastien , Perrinet Stéphanie , Duchateau Magalie , Matondo Mariette , Hollis Robert L. , Gourley Charlie , Rupp Jan , Keillor Jeffrey W. , Subtil Agathe 
Published: May 2019

ABSTRACTTransglutaminase 2 (TG2) is a ubiquitous enzyme with transamidating activity. We report here that the expression and activity of TG2 are enhanced in cells infected with the obligate intracellular bacteriaChlamydia trachomatis. Genetic or pharmacological inhibition of TG2 activity impair bacterial development. We show that TG2 increases glucose import by up-regulating the transcription of the glucose transporter genesGLUT-1andGLUT-3. Furthermore, TG2 activation drives one specific glucose-dependent pathway in the host, i.e. hexosamine biosynthesis. Mechanistically, we identify the glucosamine:fructose-6-phosphate amidotransferase (GFPT) among the substrates of TG2. GFPT modification by TG2 increases its enzymatic activity, resulting in higher levels of UDP-N-acetylglucosamine biosynthesis. As a consequence, TG2 activation results in increased proteinO-GlcNAcylation. The correlation between TG2 transamidating activity andO-GlcNAcylation is disrupted in infected cells because host hexosamine biosynthesis is being exploited by the bacteria, in particular to assist their division. In conclusion, our work establishes TG2 as a key player in controlling glucose-derived metabolic pathways in mammalian cells, themselves hijacked byC. trachomatisto sustain their own metabolic needs.
BIOTIN ATTACHMENT DOMAIN-CONTAINING proteins, inhibitors of ACCase, are regulated by WRINKLED1
Authors: Liu Hui , Zhai Zhiyang , Kuczynski Kate , Keereetaweep Jantana , Schwender Jorg , Shanklin John 
Published: May 2019

AbstractWRINKLED1 (WRI1) is a transcriptional activator that binds to AW boxes in the promoters of many genes from central metabolism and FA synthesis, resulting in their transcription. BIOTIN ATTACHMENT DOMAIN-CONTAINING (BADC) proteins are homologs of BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) that lack a biotin-attachment domain and are therefore inactive. In the presence of excess FA, BADC1 and BADC3 are primarily responsible for the observed long-term irreversible inhibition of ACETYL-COA CARBOXYLASE (ACCase), and consequently FA synthesis. Purified WRI1 bound with high affinity (Kds in the low nanomolar range) to canonical AW-boxes from the promoters of all three BADC genes. Consistent with this observation, the expression of BADC1, BADC2 and BADC3 genes and BADC1 protein levels were reduced in wri1-1 relative to wild type (WT), and BADCs gene expression and BADC1 protein levels also were elevated upon WRI1 overexpression. The double mutant badc1badc2 phenocopied wri1-1 with respect to both reduction in root length, and elevation of indole-3-acetic acid-Asp (IAA-Asp) levels relative to WT. Overexpression of BADC1 in wri1-1 decreased its IAA-Asp and partially rescued its short-root phenotype demonstrating a role for BADCs in seedling establishment. That WRI1 positively regulates genes encoding both FA synthesis and BADCs i.e., conditional inhibitors of FA synthesis, represents a coordinated mechanism to achieve lipid homeostasis in which plants couple the transcription their FA synthetic capacity with their capacity to biochemically downregulate it.One sentence summaryWRI1 regulates genes encoding both fatty acid synthesis and inhibitors of FA synthesis (BADCs), creating a lipid homeostatic mechanism in which the transcription of FA synthetic capacity is coordinated with the capacity to biochemically downregulate FA synthesis.
Probing RNA conformational equilibria within the functional cellular context
Authors: Ganser Laura R. , Chu Chia-Chieh , Bogerd Hal P. , Kelly Megan L. , Cullen Bryan R. , Al-Hashimi Hashim M. 
Published: May 2019

SummaryMany regulatory RNAs undergo changes in their structure from the dominant ground-state (GS) toward short-lived low-abundance ‘excited-states’ (ES) that reorganize local elements of secondary structure. ESs are increasingly observedin vitroand implicated in the folding and biological activities of regulatory RNAs and as targets for developing therapeutics. However, whether these ESs also form with comparable abundance within the complex cellular environment remains unknown. Here, we developed an approach for assessing the relative stability and abundance of RNA ESs within the functional cellular context. The approach uses point substitution mutations to increase the population of an inactive ES relative to the active GS. The cellular activity of such ES-stabilizing mutants then provides an indirect measure of any residual population of the active GS within the functional cellular context. Compensatory rescue mutations that restore the GS are used to control for changes in cellular activity arising due to changes in sequence. The approach is applied to probe ESs in two highly conserved and functionally important regulatory RNAs from HIV-1: the transactivation response element (TAR) and the Rev response element (RRE). For both RNAs, ES-stabilizing mutations inhibited cellular activity to a degree that correlates with the extent to which they stabilize the ES relative to the GSin vitro. These results indicate that the non-native ESs of TAR and RRE likely form in cells with abundances comparable to those measuredin vitroand their targeted stabilization provides a new avenue for developing anti-HIV therapeutics.
VE-PTP participates in vasculogenic mimicry by preventing autophagic degradation of VE-cadherin
Authors: Delgado-Bellido Daniel , Bueno-Galera Concepción , Garcia-Diaz Angel , Oliver F. Javier 
Published: May 2019

AbstractAberrant extra-vascular expression of VE-cadherin has been observed in metastasis associated with Vasculogenic Mimicry (VM); we have recently shown that in VM prone (VM+) tumor cells VE-cadherin is mainly in the form of pVE-cadherin in Y658 allowing an increased plasticity that potentiates VM development. As excessive VE-cadherin phosphorylation is regulated by the phosphatase VEPTP in endothelial cells in the current study we analysed its role in this aberrant phenotype in malignant tumor cells. We show that human malignant melanoma cells VM+, also express VE-PTP although at lower levels than endothelial cells. The complex VE-PTP/VE-Cadherin/p120-catenin act as a safeguard to prevent VE-cadherin degradation by autophagy. Indeed, silencing of VE-PTP results in complete degradation of VE-cadherin with the features of autophagy and increases the global p120 tyrosine phosphorylation status. In summary, we show that VE-PTP is involved in VM formation and disruption of VE-PTP/VE-Cadherin/p120 complex results in enhanced autophagy in aggressive VM+ cells.
Frontal theta and beta oscillations during lower-limb movement in Parkinson’s disease
Authors: Singh Arun , Cole Rachel C. , Espinoza Arturo I. , Brown Darin , Cavanagh James F. , Narayanan Nandakumar 
Published: May 2019

ABSTRACTBackgroundMotor and cognitive dysfunction has been linked in patients with Parkinson’s disease (PD). EEG theta and beta rhythms are reliably associated with cognitive and motor functions, respectively. We tested the hypothesis that PD patients with lower-limb abnormalities would exhibit abnormal beta and theta rhythms in the mid-frontal region during action initiation.MethodsWe recruited thirty-nine subjects, including PD patients with FOG (PDFOG+; n=13) and without FOG (PDFOG−; n=13), and demographically-matched healthy subjects (n=13). Scalp electroencephalogram (EEG) signals were collected during a lower-limb pedaling motor task, which required intentional initiation and stopping of a motor movement.ResultsFOG scores were correlated with disease severity and cognition. PDFOG+ patients pedaled with reduced speed and decreased acceleration compared to PDFOG− patients and to controls. PDFOG+ patients exhibited attenuated theta-band (4-8 Hz) power and increased beta-band (13-30 Hz) power at mid-frontal electrode Cz during pedaling. Frontal theta- and beta-band oscillations also correlated with lower-limb movement in PD patients.ConclusionsFrontal theta and beta oscillations are predictors of lower-limb motor symptoms in PD. These data provide insight into the mechanism of lower-limb dysfunction in PD, and could be used to design neuromodulation for PD-related lower-limb abnormalities.
Mixed support for the idea that lower elevation animals are better competitors than their upper elevation relatives
Authors: Freeman Benjamin G. 
Published: May 2019

AbstractWhat factors set species’ range edges? One general hypothesis, often attributed to Darwin and MacArthur, is that interspecific competition prevents species from inhabiting the warmest portions along geographic gradients (i.e., low latitudes or low elevations). A prediction arising from the Darwin-MacArthur hypothesis is that lower elevation species are better competitors than are related upper elevation species. I tested this prediction by conducting a meta-analysis of studies that have measured behavioral competition between related species along elevational gradients. I found that (1) interspecific aggression appears to be a reliable indicator of interspecific competition; (2) as predicted, lower elevation species showed stronger interspecific aggression, but only for tropical species-pairs tested with playback experiments (nearly all songbirds); (3) for a broader range of taxa where authors directly observed behavioral interactions, upper elevation species showed stronger interspecific aggression; and (4) in general, larger species showed greater interspecific aggression. One potential explanation for why upper elevation species often show more interspecific aggression is that they tend to be larger (Bergmann’s rule; larger body sizes in colder environments). Supporting this possibility, tropical species tested with playback experiments, which do not follow Bergmann’s rule, were the only group that matched predictions arising from the Darwin-MacArthur hypothesis. Hence, available evidence does not consistently support the longstanding hypothesis that relative range position predicts the outcome of interspecific competition. Instead, body size is a better predictor of behavioral competition. Last, I consider these results in the context of the hypothesis that behavioral interactions may impact rates of upslope range shifts associated with recent warming.