bluuebunny/crossref_metadata_2025_split huggingface dataset:
The bacterial virulence factors rhamnolipids and their (R)-3-hydroxyalkanoate precursors activateArabidopsisinnate immunity through two independent mechanisms
Authors: Schellenberger Romain , Crouzet Jérôme , Nickzad Arvin , Kutschera Alexander , Gerster Tim , Borie Nicolas , Dawid Corinna , Cloutier Maude , Villaume Sandra , Dhondt-Cordelier Sandrine , Hubert Jane , Cordelier Sylvain , Mazeyrat-Gourbeyre Florence , Schmid Christian , Ongena Marc , Renault Jean-Hugues , Haudrechy Arnaud , Hofmann Thomas , Baillieul Fabienne , Clément Christophe , Zipfel Cyril , Gauthier Charles , Déziel Eric , Ranf Stefanie , Dorey Stéphan 
Published: December 2020

AbstractPlant innate immunity is activated upon perception of invasion pattern molecules by plant cell-surface immune receptors. Several bacteria of the generaPseudomonasandBurkholderiaproduce rhamnolipids (RLs) from L- rhamnose and (R)-3-hydroxyalkanoate precursors (HAAs). RL and HAA secretion is required to modulate bacterial surface motility, biofilm development, and thus successful colonization of hosts. Here, we show that the lipidic secretome from the opportunistic pathogenPseudomonas aeruginosamostly comprising RLs and HAAs stimulatesArabidopsisimmunity. We demonstrate that HAAs are sensed by the bulb-type lectin receptor kinase LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION/S-DOMAIN-1-29 (LORE/SD1-29) that also mediates medium-chain 3-hydroxy fatty acid (mc-3-OH-FA) perception in the plantArabidopsis thaliana. HAA sensing induces canonical immune signaling and local resistance to plant pathogenicPseudomonasinfection. By contrast, RLs trigger an atypical immune response and resistance toPseudomonasinfection independent of LORE. Thus, the glycosyl moieties of RLs, albeit abolishing sensing by LORE, do not impair their ability to trigger plant defense. In addition, our results show that RL-triggered immune response is affected by the sphingolipid composition of the plasma membrane. In conclusion, RLs and their precursors released by bacteria can both be perceived by plants but through distinct mechanisms.SignificanceActivation of plant innate immunity relies on the perception of microorganisms through self and nonself elicitors. Rhamnolipids and their precursor HAAs are exoproducts produced by beneficial and pathogenic bacteria. They are involved in bacterial surface dissemination and biofilm development. As these compounds are released in the extracellular milieu, they have the potential to be perceived by the plant immune system. Our work shows that both compounds independently activate plant immunity. We demonstrate that HAAs are perceived by the receptor protein kinase LORE. By contrast, rhamnolipids are not senses by LORE but activate a non-canonical immune response affected by the sphingolipid composition of the plant plasma membrane. Thus, plants are able to sense bacterial molecules as well as their direct precursors to trigger a distinct immune response.
Interactive regulation between aliphatic hydroxylation and aromatic hydroxylation of thaxtomin D in TxtC: a theoretical investigation
Authors: Yuan Chang , Ouyang Qingwen , Wang Xixi , Li Xichen , Tan Hongwei , Chen Guangju 
Published: December 2020

ABSTRACTTxtC is an unusual bifunctional cytochrome P450 that is able to perform sequential aliphatic and aromatic hydroxylation of the diketopiperazine substrate thaxtomin D in two remote sites to produce thaxtomin A. Though the X-ray structure of TxtC complexed with thaxtomin D revealed a binding mode for its aromatic hydroxylation, the preferential hydroxylation site is aliphatic C14. It is thus intriguing to unravel how TxtC accomplishes such two-step catalytic hydroxylation on distinct aliphatic and aromatic carbons and why the aliphatic site is preferred in the hydroxylation step. In this work, by employing molecular docking and molecular dynamics (MD) simulation, we revealed that thaxtomin D could adopt two different conformations in the TxtC active site, which were equal in energy with either the aromatic C-H or aliphatic C14-H laying towards the active Cpd I oxyferryl moiety. Further ONIOM calculations indicated that the energy barrier for the rate-limiting hydroxylation step on the aliphatic C14site was 8.9 kcal/mol more favorable than that on the aromatic C20site. The hydroxyl group on the monohydroxylated intermediate thaxtomin B C14site formed hydrogen bonds with Ser280 and Thr385, which induced theL-Phe moiety to rotate around the Cβ−Cγbond of the 4-nitrotryptophan moiety. Thus, it adopted an energy favorable conformation with aromatic C20adjacent to the oxyferryl moiety. In addition, the hydroxyl group induced solvent water molecules to enter the active site, which propelled thaxtomin B towards the heme plane and resulted in heme distortion. Based on this geometrical layout, the rate-limiting aromatic hydroxylation energy barrier decreased to 15.4 kcal/mol, which was comparable to that of the thaxtomin D aliphatic hydroxylation process. Our calculations indicated that heme distortion lowered the energy level of the lowest Cpd I α-vacant orbital, which promoted electron transfer in the rate-limiting thaxtomin B aromatic hydroxylation step in TxtC.
Rotavirus Replication Factories Are Complex Ribonucleoprotein Condensates
Authors: Geiger Florian , Papa Guido , Arter William E. , Acker Julia , Saar Kadi L. , Erkamp Nadia , Qi Runzhang , Bravo Jack , Strauss Sebastian , Krainer Georg , Burrone Oscar R. , Jungmann Ralf , Knowles Tuomas P.J. , Engelke Hanna , Borodavka Alexander 
Published: December 2020

AbstractRNA viruses induce formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein-RNA condensates that are formed via liquid-liquid phase separation. We demonstrate that rotavirus proteins NSP5 and NSP2 undergo phase separationin vitroand form RNA-rich condensatesin vivothat can be reversibly dissolved by aliphatic diols. During infection, these RNA-protein condensates became less dynamic and impervious to aliphatic diols, indicating a transition from a liquid to solid state. Some aspects of assembly of rotavirus replication factories mirror the formation of cytoplasmic ribonucleoprotein granules, while the selective enrichment of viral transcripts appears to be a unique feature of these condensates. Such complex RNA-protein condensates that underlie replication of RNA viruses represent an attractive target for developing novel therapeutic approaches.
Arabidopsis root responses to salinity depend on pectin modification and cell wall sensing
Authors: Gigli-Bisceglia Nora , van Zelm Eva , Huo Wenying , Lamers Jasper , Testerink Christa 
Published: December 2020

AbstractSoil salinity is an increasing worldwide problem for agriculture, affecting plant growth and yield. To understand the molecular mechanisms activated in response to salt in plants, we investigated theCatharanthus roseusReceptor like Kinase 1 Like (CrRLK1L) family, which contains well described sensors previously shown to be involved in maintaining and sensing the structural integrity of the cell walls. We found thatherk1the1-4double mutants, lacking the function of theArabidopsis thalianaReceptor like Kinase HERKULES1 combined with a gain-of-function allele of THESEUS1, phenocopied the phenotypes previously reported in plants lacking FERONIA (FER) function. We report that bothfer-4andherk1the1-4mutants respond strongly to salt application, resulting in a more intense activation of early and late stress responses. We also show that salt triggers de-methyl esterification of loosely bound pectins, responsible for the activation of several salt response signaling pathways. Addition of calcium chloride or chemically inhibiting pectin methyl esterase (PME) activity reduced activation of the early signaling protein Mitogen Activated Protein Kinase 6 (MPK6) as well as amplitude of salt-induced marker gene induction. MPK6 is required for the full induction of the salt-induced gene expression markers we tested. The sodium specific root halotropism response on the other hand, appears independent of MPK6 or calcium application, and is only mildly influenced by the cell wall sensors FER/HERK1/THE1-4 or alteration of PME activity. We hypothesize a model where salt-triggered modification of pectin requires the functionality of FER alone or the HERK1/THE1 combination to attenuate salt responses. Collectively, our results show the complexity of salt stress responses and salt sensing mechanisms and their connection to cell wall modifications, responsible for several salt response pathways and ultimately plant resilience to salinity.
Artificial light at night leads to circadian disruption in a songbird: integrated evidence from behavioural, genomic and metabolomic data
Authors: Dominoni Davide M. , de Jong Maaike , van Oers Kees , O’Shaughnessy Peter , Blackburn Gavin , Atema Els , Mateman Christa A. , D’Amelio Pietro B. , Trost Lisa , Bellingham Michelle , Clark Jessica , Visser Marcel E. , Helm Barbara 
Published: December 2020

AbstractGlobally increasing levels of artificial light at night (ALAN) are associated with shifts in circadian rhythms of behaviour in many wild species. However, it is still unclear whether changes in behavioural timing are underlined by parallel shifts in the molecular clock, and whether such internal shifts may differ between different tissues and physiological pathways, which could highlight circadian disruption. We tackled these questions in a comprehensive study that integrated behavioural, gene expression and metabolomic analyses. We exposed captive male great tits (Parus major) to three ALAN intensities or to dark nights, recorded their activity rhythms and obtained mid-day and midnight samples of brain, liver, spleen and blood. ALAN advanced wake-up time, and this shift was paralleled by an advance in the expression of the clock geneBMAL1in all tissues, suggesting close links of brain and peripheral clock gene expression with activity rhythms. However, several metabolic and immune genes were desynchronised the shiftedBMAL1expression, suggesting circadian disruption of behaviour and physiology. This result was reinforced by untargeted metabolomic profiling, which showed that only 9.7% of the 755 analysed metabolites followed the behavioural shift. We suggest circadian as a key mediator of the health impacts of ALAN on wild animals.
Where are they now? Tracking the Mediterranean Lionfish Invasion via Local Dive Centers
Authors: Phillips Elizabeth W , Kotrschal Alexander 
Published: December 2020

AbstractInvasive species are globally on the rise due to human-induced environmental change and are often a source of harm to their new ecosystems. Tracking the spread of invaders is crucial to better management of invasive species, and citizen science is often used to collect sighting data. However, this can be unreliable due to the general public’s limited expertise for accurate identification and a lack of clear absence data. Here, we introduce a refined method of citizen science by tracking the spread of the invasive lionfish (Pterois miles) in the Mediterranean Sea using dive centers’ expertise on local marine wildlife. We contacted 1131 dive centers on the Mediterranean coast via email and received 216 responses reporting whether or not lionfish were present in their area and, if present, the year they were first sighted. Currently, lionfish sightings are observed in the eastern half of the Mediterranean, though the front is continuing to move west with the furthest sighting as far as Corfu, Greece (19.939423°E, 39.428017°N). In 2020, lionfish also expanded their invasive range north on the Turkish Aegean coast to Karaburun (26.520657°E, 38.637033°N), showing that the invasion is ongoing. We found that the invasive range is now exceeding previous invasion models, highlighting the need for additional research on lionfish biology to inform management efforts. Continuous monitoring of invasive fronts based on dive center reports and a better understanding of what makes lionfish so invasive is crucial to mitigating their negative impact on native ecosystems.
The Behavior of Molecular Measures of Natural Selection after a Change in Population Size
Authors: Müller Rebekka , Kaj Ingemar , Mugal Carina F. 
Published: December 2020

ABSTRACTA common model to describe natural selection at the molecular level is the nearly neutral theory, which emphasizes the importance of mutations with slightly deleterious fitness effects as they have a chance to get fixed due to genetic drift. Since genetic drift is stronger in smaller than in larger populations, a negative relationship between molecular measures of selection and population size is expected within the nearly neutral theory. Originally, this hypothesis was formulated under equilibrium conditions. A change in population size, however, pushes the selection-drift balance off equilibrium leading to alterations in the efficacy of selection. To investigate the nonequilibrium behavior, we relate measures of natural selection and genetic drift to each other, considering both, measures of micro- and macroevolution. Specifically, we use a Poisson random field framework to modelπN/πSandωas time-dependent measures of selection and assess genetic drift by an effective population size. This analysis reveals a clear deviation from the expected equilibrium selection-drift balance during nonequilibrium periods. Moreover, we find that microevolutionary measures quickly react to a change in population size and reflect a recent change well, at the same time as they quickly lose the knowledge about it. Macroevolutionary measures, on the other hand, react more slowly to a change in population size but instead capture the influence of ancient changes longer. We therefore conclude that it is important to be aware of the different behaviors of micro- and macroevo- lutionary measures when making inference in empirical studies, in particular when comparing results between studies.
Disentangling environmental drivers of circadian metabolism in desert-adapted mice
Authors: Colella Jocelyn P. , Blumstein Danielle M. , MacManes Matthew D. 
Published: December 2020

ABSTRACTMetabolism is a complex phenotype shaped by natural environmental rhythms, as well as behavioral, morphological, and physiological adaptations. Although historically studied under constant environmental conditions, continuous metabolic phenotyping through environmental transitions now offers a window into the physiological responses of organisms to changing environments. Here, we use flow-through respirometry to compare metabolic responses of the desert-adapted cactus mouse (Peromyscus eremicus) between diurnally variable and constant environmental conditions. We contrast metabolic responses to circadian cycles in photoperiod, temperature, and humidity, against those recorded under constant hot-and-dry and constant cold-and-wet conditions. We found significant sexual dimorphism in metabolic responses, despite no measurable difference in body weight. Males seem to be more heat tolerant and females more cold tolerant. Under circadian environmental cycling, the ratio of CO2produced to O2consumed (the respiratory quotient or respiratory exchange ratio) reached greater than one, a pattern that strongly suggests that lipogenesis is contributing to the production of energy and endogenous water in this species. This hypothesis is consistent with the results of previous dehydration experiments in this species, which documented significant weight loss in response to dehydration, without other physiological impairment. Our results are also consistent with historical descriptions of circadian torpor in this species (torpid by day, active by night), but reject the hypothesis that this pattern is driven by food restriction or negative water balance, as both resources were available to animals throughout the experiments.SUMMARY STATEMENTContinuous metabolic phenotyping of desert-adapted cactus mice (Peromyscus eremicus) identifies significant metabolic differences between the sexes and circadian patterning consistent with lipogenesis and environmental entrainment.
Enhanced reproductive thermotolerance is associated with increased accumulation of flavonols in pollen of the tomatohigh-pigment2 mutant
Authors: Rutley Nicholas , Miller Golan , Wang Fengde , Harper Jeffrey F , Miller Gad , Lieberman-Lazarovich Michal 
Published: December 2020

SummaryClimate change has created an environment where heat stress conditions are becoming more frequent as temperatures continue to rise in crop production areas around the world. This situation leads to decreased crop production due to plant sensitivity to heat stress. Reproductive success is critically dependent on plants’ ability to produce functional pollen grains, which are the most thermo-sensitive tissue. Flavonols are plant secondary metabolites known for their potent antioxidative activity, essential for male fertility in several species including tomato, and implicated in heat stress tolerance. Since flavonols are highly abundant in fruits of the tomatohigh pigment-2(hp2) mutant, we tested the level of flavonols in pollen of this mutant, under the hypothesis that increased accumulation of flavonols would render pollen more tolerant to heat stress. Indeed, pollen from three alleles of thehp2mutant were found to have flavonols levels increased by 40% on average compared with wild-type under moderate chronic heat stress conditions. This mutant produced on average 7.8-fold higher levels of viable pollen and displayed better germination competence under heat stress conditions. The percentage of fully seeded fruits and the number of seeds per fruit were maintained in the mutant under heat stress conditions while decreased in wild-type plants. Our results strongly suggest that increased pollen flavonols content enhances pollen thermotolerance and reproductive success under heat stress conditions. Thus, the high flavonols trait may help frame the model for improving crop resilience to heat stress.
Activation of MrgprA3 and MrgprC11 on bladder-innervating afferents induces peripheral and central hypersensitivity to bladder distension
Authors: Grundy Luke , Caldwell Ashlee , Garcia-Caraballo Sonia , Grundy David , Spencer Nick J. , Dong Xinzhong , Castro Joel , Harrington Andrea M. , Brierley Stuart M. 
Published: December 2020

AbstractUnderstanding the sensory mechanisms innervating the bladder is paramount to developing efficacious treatments for chronic bladder hypersensitivity conditions. The contribution of Mas-gene-related G protein-coupled receptors (Mrgpr) to bladder signalling is currently unknown. Here we show in mice with single-cell RT-PCR that sub-populations of dorsal root ganglion (DRG) neurons innervating the mouse bladder expressMrgprA3(14%) andMrgprC11 (38%), either individually or in combination, with high levels of co-expression withTrpv1(81-89%). Calcium imaging studies demonstrated MrgprA3 and MrgprC11 agonists (chloroquine, BAM8-22 and neuropeptide FF) activated sub-populations of bladder-innervating DRG neurons, showing functional evidence of co-expression between MrgprA3, MrgprC11 and TRPV1. Inex vivobladder-nerve preparations chloroquine, BAM8-22 and neuropeptide FF all evoked mechanical hypersensitivity in sub-populations (20-41%) of bladder afferents. These effects were absent in recordings fromMrgpr-clusterΔ−/−mice.In vitrowhole-cell patch clamp recordings showed that application of an MrgprA3/C11 agonist cocktail induced neuronal hyper-excitability in 44% of bladder-innervating DRG neurons. Finally,in vivoinstillation of an MrgprA3/C11 agonist cocktail into the bladder of wild-type mice induced a significant activation of dorsal horn neurons within the lumbosacral spinal cord, as quantified by pERK-immunoreactivity. This MrgprA3/C11 agonist-induced activation was particularly apparent within the superficial dorsal horn and the sacral parasympathetic nuclei of wild-type, but notMrgpr-clusterΔ−/−mice. This study demonstrates, for the first time, functional expression of MrgprA3 and MrgprC11 in bladder afferents. Activation of these receptors is not required for normal bladder function but does trigger hypersensitivity to distension, a critically valuable factor for therapeutic target development.Significance statementDetermining how bladder afferents become sensitized is the first step in finding effective treatments for common urological disorders such as overactive bladder and interstitial cystitis/bladder pain syndrome. Here we show that two of the key receptors, MrgprA3 and MrgprC11, that mediate itch from the skin are also expressed on afferents innervating the bladder. Activation of these receptors results in sensitization of bladder afferents, resulting in sensory signals being sent into the spinal cord that prematurely indicate bladder fullness. Targeting bladder afferents expressing MrgprA3 or MrgprC11 and preventing their sensitisation may provide a novel approach for treating overactive bladder and interstitial cystitis/bladder pain syndrome.
Sterilizing immunity against SARS-CoV-2 in hamsters conferred by a novel recombinant subunit vaccine
Authors: Wu Yangtao , Huang Xiaofen , Yuan Lunzhi , Wang Shaojuan , Zhang Yali , Xiong Hualong , Chen Rirong , Ma Jian , Qi Ruoyao , Nie Meifeng , Xu Jingjing , Zhang Zhigang , Chen Liqiang , Wei Min , Zhou Ming , Cai Minping , Shi Yang , Zhang Liang , Yu Huan , Hong Junping , Wang Zikang , Hong Yunda , Yue Mingxi , Li Zonglin , Chen Dabing , Zheng Qingbing , Li Shaowei , Chen Yixin , Cheng Tong , Zhang Jun , Zhang Tianying , Zhu Huachen , Zhao Qinjian , Yuan Quan , Guan Yi , Xia Ningshao 
Published: December 2020

AbstractA safe and effective SARS-CoV-2 vaccine is essential to avert the on-going COVID-19 pandemic. Here, we developed a subunit vaccine, which is comprised of CHO-expressed spike ectodomain protein (StriFK) and nitrogen bisphosphonates-modified zinc-aluminum hybrid adjuvant (FH002C). This vaccine candidate rapidly elicited the robust humoral response, Th1/Th2 balanced helper CD4 T cell and CD8 T cell immune response in animal models. In mice, hamsters, and non-human primates, 2-shot and 3-shot immunization of StriFK-FH002C generated 28- to 38-fold and 47- to 269-fold higher neutralizing antibody titers than the human COVID-19 convalescent plasmas, respectively. More importantly, the StriFK-FH002C immunization conferred sterilizing immunity to prevent SARS-CoV-2 infection and transmission, which also protected animals from virus-induced weight loss, COVID-19-like symptoms, and pneumonia in hamsters. Vaccine-induced neutralizing and cell-based receptor-blocking antibody titers correlated well with protective efficacy in hamsters, suggesting vaccine-elicited protection is immune-associated. The StriFK-FH002C provided a promising SARS-CoV-2 vaccine candidate for further clinical evaluation.