bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-extracellular matrix interactions in the fluidic phase direct the topology and polarity of self-organized epithelial structures
Authors: Ouyang Mingxing , Yu Jiun-Yann , Chen Yenyu , Deng Linhong , Guo Chin-Lin 
Published: May 2020

AbstractIn vivo,cells are surrounded by extracellular matrix (ECM). To build organs from single cells, it is generally believed that ECM serves as scaffolds to coordinate cell positioning and differentiation. Nevertheless, how cells utilize cell-ECM interactions for the spatiotemporal coordination to different ECM at the tissue scale is not fully understood. Here, usingin vitroassay with engineered MDCK cells expressing H2B-mCherry (nucleus) and gp135/Podocalyxin-GFP (apical marker), we show in multi-dimensions that such coordination for epithelial morphogenesis can be determined by cell-soluble ECM interaction in the fluidic phase. The coordination depends on the native topology of ECM components such as sheet-like basement membrane (BM) and type I collagen (COL) fibers: scaffold formed by BM (COL) facilitates a close-ended (open-ended) coordination that leads to the formation of lobular (tubular) epithelium. Further, cells form apicobasal polarity throughout the entire lobule/tubule without a complete coverage of ECM at the basal side, and time-lapse two-photon scanning imaging reveals the polarization occurring early and maintained through the lobular expansion. During polarization, gp135-GFP was converged to the apical surface collectively in the lobular/tubular structures, suggesting possible intercellular communications. Under suspension culture, the polarization was impaired with multi-lumen formation in the tubules, implying the importance of ECM biomechanical microenvironment. Our results suggest a biophysical mechanism for cells to form polarity and coordinate positioning at tissue scale, and in engineering epithelium through cell-soluble ECM interaction and self-assembly.
An atlas of Arabidopsis protein S-Acylation reveals its widespread role in plant cell organisation of and function
Authors: Kumar Manoj , Carr Paul , Turner Simon 
Published: May 2020

AbstractS-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterised, largely as a result to the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. In order to address this gap in our knowledge, we have performed a comprehensive analysis of plant protein S-acylation from 6 separate tissues. In our highest confidence group, we identified 5185 cysteines modified by S-acylation, which were located in 4891 unique peptides from 2643 different proteins. This represents around 9% of the entire Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm for the first time the S-acylation of all proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity. While all three proteins have been widely predicted to possess a RING-type zinc finger at their N-terminus, for CESA4 and CESA8, we find evidence for S-acylation of cysteines in this region that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING type domain, the same region of CESA4 and CESA8 appear to have evolved a very different structure. Together, the data suggests this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrates the importance of undertaking further work in this area.
Mutations in Tomato ACC Synthase2 Uncover Its Role in Development beside Fruit Ripening
Authors: Sharma Kapil , Gupta Soni , Sarma Supriya , Rai Meenakshi , Sreelakshmi Yellamaraju , Sharma Rameshwar 
Published: May 2020

ABSTRACTThe role of ethylene in plant development is mostly inferred from its exogenous application. The usage of the mutants affecting ethylene biosynthesis proffers a better alternative to decipher its role. In tomato, 1-aminocyclopropane carboxylic acid synthase2 (ACS2) is a key enzyme regulating ripening-specific ethylene biosynthesis. We characterized two contrastingacs2mutants;acs2-1overproduces ethylene, has higher ACS activity, and increased protein levels, whileacs2-2is an ethylene under-producer, displays lower ACS activity, and protein levels than wild type. Consistent with high/low ethylene emission, the mutants show opposite phenotypes, physiological responses, and metabolomic profiles than the wild type. Theacs2-1showed early seed germination, faster leaf senescence, and accelerated fruit ripening. Conversely,acs2-2had delayed seed germination, slower leaf senescence, and prolonged fruit ripening. The phytohormone profiles of mutants were mostly opposite in the leaves and fruits. The faster/slower senescence ofacs2-1/acs2-2leaves correlated with the endogenous ethylene/zeatin ratio. The genetic analysis showed that the metabolite profiles of respective mutants co-segregated with the homozygous mutant progeny. Our results uncover that besides ripening, ACS2 participates in vegetative and reproductive development of tomato. The distinct influence of ethylene on phytohormone profiles indicates intertwining of ethylene action with other phytohormones in regulating plant development.
Range reduction of the Oblong Rocksnail,Leptoxis compacta, shapes riverscape genetic patterns
Authors: Wright Aaliyah D. , Garrison Nicole L. , Williams Ashantye’ S. , Johnson Paul D. , Whelan Nathan V. 
Published: May 2020

AbstractMany freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail,Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range ofL. compactaare unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show thatL. compactahas likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey.Leptoxis compactadoes not display an isolation by distance pattern, contrasting patterns seen in many riverine taxa. Our findings also indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution ofL. compactaallows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.
Comment on Pescott & Jitlal 2020: Failure to account for measurement error undermines their conclusion of a weak impact of nitrogen deposition on plant species richness
Authors: Smart SM , Stevens CJ , Tomlinson SJ , Maskell LC , Henrys PA 
Published: May 2020

AbstractEstimation of the impacts of atmospheric nitrogen (N) deposition on ecosystems and biodiversity is a research imperative. Analyses of large-scale spatial gradients, where an observed response is correlated with measured or modelled deposition, have been an important source of evidence. A number of problems beset this approach. For example, if responses are spatially aggregated then treating each location as statistically independent can lead to biased confidence intervals and a greater probably of false positive results.Using sophisticated methods that account for residual spatial autocorrelation Pescott & Jitlal (2020) re-analysed two large-scale spatial gradient datasets from Britain where modelled N deposition at 5×5km resolution had been previously correlated with species richness in small quadrats. They found that N deposition effects were weaker than previously demonstrated leading them to conclude that“..previous estimates of Ndep impacts on richness from space-for-time substitution studies are likely to have been over-estimated”. We use a simple simulation study to show that their conclusion is flawed. They failed to recognise that an influential fraction of the residual spatially structured variation could itself be attributable to N deposition. This arises because the covariate used was modelled N deposition at 5×5km resolution leaving open the possibility that measured or modelled N deposition at finer resolutions could explain more variance in the response. Explicitly treating this as spatially auto-correlated error ignores this possibility and leads directly to their unreliable conclusion. We further demonstrate the plausibility of this scenario by showing that significant variation in N deposition at the 1km square resolution is indeed averaged at 5×5km resolution.Further analyses are required to explore whether estimation of the size of the N deposition effect on plant species richness and other measures of biodiversity is indeed dependent on the accuracy and hence measurement error of the N deposition covariate. Until then the conclusions of Pescott & Jitlal (2020) should be considered premature and not proven.
Promiscuous enzymes cooperate at the substrate level en route to lactazole A
Authors: Vinogradov Alexander A. , Shimomura Morito , Kano Naokazu , Goto Yuki , Onaka Hiroyasu , Suga Hiroaki 
Published: May 2020

AbstractEnzymes involved in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis often have relaxed specificity profiles and are able to modify diverse substrates. When several such enzymes act together during precursor peptide maturation, a multitude of products can form, and yet usually, the biosynthesis converges on a single natural product. For the most part, the mechanisms controlling the integrity of RiPP assembly remain elusive. Here, we investigate biosynthesis of lactazole A, a model thiopeptide produced by five promiscuous enzymes from a ribosomal precursor peptide. Using ourin vitrothiopeptide production (FIT-Laz) system, we determine the order of biosynthetic events at the individual modification level, and supplement this study with substrate scope analysis for participating enzymes. Combined, our results reveal a dynamic thiopeptide assembly process with multiple points of kinetic control, intertwined enzymatic action, and the overall substrate-level cooperation between the enzymes. This work advances our understanding of RiPP biosynthesis processes and facilitates thiopeptide bioengineering.
Tracing two causative SNPs reveals SARS-CoV-2 transmission in North America population
Authors: Ou Xumin , Yang Zhishuang , Zhu Dekang , Mao Sai , Wang Mingshu , Jia Renyong , Chen Shun , Liu Mafeng , Yang Qiao , Wu Ying , Zhao Xinxin , Zhang Shaqiu , huang Juan , Gao Qun , Liu Yunya , Zhang Ling , Peopplenbosch Maikel , Pan Qiuwei , Cheng Anchun 
Published: May 2020

AbstractDuring the COVID-19 pandemic, precisely tracing the route of the SARS-CoV-2 transmission in human population remains challenging. Because this RNA virus can mutate massively without a specifically tracing maker. Herein, using a geographic stratified genome-wide association study (GWAS) of 2599 full-genome sequences, we identified that two SNPs (i.e., 1059.C>T and 25563.G>T) of linkage disequilibrium were presented in approximately half of North America SARS-CoV-2 population (p = 2.44 x 10−212and p = 2.98 x 10−261), resulting two missense mutations (i.e., Thr 265 Ile and Gln 57 His) in ORF1ab and ORF3a, respectively. Interestingly, these two SNPs exclusively occurred in the North America dominated clade 1, accumulated during mid to late March, 2020. We did not find any of these two SNPs by retrospectively tracing the two SNPs in bat and pangolin related SARS-CoV-2 and human SARS-CoV-2 from the first epicenter Wuhan or other regions of China mainland. This suggested that the SARS-CoV-2 population of Chinese mainland were different from the prevalent strains of North America. Time-dependently, we found that these two SNPs first occurred in Europe SARS-CoV-2 (26-Feb-2020) which was 3 days early than the occurring date of North America isolates and 17 days early for Asia isolates (Taiwan China dominated). Collectively, this population genetic analysis highlights a well-confidential transmission route of the North America isolates and the two SNPs we newly identified are possibly novel diagnosable or druggable targets for surveillance and treatment.
Structure of SARS-CoV-2 main protease in the apo state reveals the inactive conformation
Authors: Zhou Xuelan , Zhong Fangling , Lin Cheng , Hu Xiaohui , Zhang Yan , Xiong Bing , Yin Xiushan , Fu Jinheng , He Wei , Duan Jingjing , Fu Yang , Zhou Huan , Wang Qisheng , Li Jian , Zhang Jin 
Published: May 2020

AbstractMprois of considerable interest as a drug target in the treatment of COVID-19 since the proteolytic activity of this viral protease is essential for viral replication. Here we report the first insight of the structure Mprofor SARS-CoV-2 in the inactive conformation under conditions close to the physiological state (pH 7.5) to an overall resolution of 1.9 Å. The comparisons of Mproin different states reveal that substrate binding site and the active site are more flexible in the inactive conformation than that in the active conformations. Notably, compared with the active conformation of the apo state structure in pH7.6 of SARS, the SARS-CoV-2 apo state is in the inactive conformation under condition close to physiological state (pH7.5). Two water molecules are present in the oxyanion hole in our apo state structure, whereas in the ligand-bound structure, water molecular is absence in the same region. This structure provides novel and important insights that have broad implications for understanding the structural basis underlying enzyme activity, and can facilitate rational, structure-based, approaches for the design of specific SARS-CoV-2 ligands as new therapeutic agents.
Splicing factor SRSF1 expands the regulatory logic of microRNA expression
Authors: Dargyte Marija , Philipp Julia , Palka Christina D. , Stone Michael D. , Sanford Jeremy R. 
Published: May 2020

AbstractThe serine and arginine-rich splicing factor SRSF1 is an evolutionarily conserved, essential pre-mRNA splicing factor. Through a global protein-RNA interaction survey we discovered SRSF1 binding sites 25-50nt upstream from hundreds of pre-miRNAs. Using primary miRNA-10b as a model we demonstrate that SRSF1 directly regulates microRNA biogenesis bothin vitroandin vivo. Selective 2’ hydroxyl acylation analyzed by primer extension (SHAPE) defined a structured RNA element located upstream of the precursor miRNA-10b stem loop. Our data support a model where SRSF1 promotes initial steps of microRNA biogenesis by relieving the repressive effects ofcis-regulatory elements within the leader sequence.
Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation
Authors: Sosa Robert P. , Florez-Ariza Alfredo J. , Díaz-Celis César , Onoa Bibiana , Cassago Alexandre , de Oliveira Paulo S. L. , Portugal Rodrigo V. , Guerra Daniel G. , Bustamante Carlos J. 
Published: May 2020

AbstractDuring transcription initiation, the RNA polymerase holoenzyme (RNAP) and the promoter form an open complex. For many promoters, this interaction involves upstream DNA wrapping, downstream promoter bending, and associated large-scale protein rearrangements. Although these processes have been reported across the life kingdom, their structure, energetics, and role in transcription remain an area of active research. Using optical tweezers, we find that these processes become energetically and reversibly coupled after the formation of the open promoter complex, providing the main contribution to their stability. Using electron microscopy and single particle analysis, we find that the interaction encompasses from positions −76 to +18 along the template, that it involves an overall DNA bent angle of ~245°, and that the upstream wrapping is enabled by interactions between the C-terminal domains of RNAP’s alpha subunits and proximal and middle upstream promoter regions. The energy associated with upstream wrapping, downstream bending and its coupling to downstream rearrangements does not require specific upstream promoter sequence, and correlate positively with the rate of transcription DNA bubble formation as reported by a real-time fluorescence assay. Our results suggest that the coupling between upstream and downstream events are part of acis-regulatory network established after the opening of the DNA bubble, that could furnish a control mechanism of gene expression by protein factors and regulatory metabolites.SummaryThe first step of gene expression involves transcription of DNA into RNA by RNA polymerase (RNAP). RNAP recognizes a promoter sequence forming the transcriptionally active open complex. For several promoters, DNA wraps around the RNAP. We find that upstream wrapping contacts are energetically coupled and occur cooperatively with downstream rearrangements in the open complexes, providing the largest contribution to their stability. We also determined that upstream wrapping is enabled by interactions between non-specific upstream promoter regions and RNAP α subunit C-terminal domains. Significantly, the strength of these contacts correlates with the rate of DNA bubble opening, and is regulated by factors such as the transcriptional regulator ppGpp. We suggest that any modulator altering upstream wrapping and downstream rearrangements could finely tune gene expression in response to the needs of the cell
High temperature inhibits cnidarian-dinoflagellate symbiosis establishment through nitric oxide signaling
Authors: Hill Lilian J. , Salgado Leonardo T. , Salomon Paulo S. , Guse Annika 
Published: May 2020

Disclaimer StatementThe authors have withdrawn their manuscript after further experiments based on reviewer comments did not support the conclusions of the paper. Therefore, the authors do not wish this work to be cited as reference for the project. The authors thank the anonymous reviewer for a critical assessment. If you have any questions, please contact the corresponding authors.
A novel Ca2+signalling pathway co-ordinates environmental phosphorus sensing and nitrogen metabolism in marine diatoms
Authors: Helliwell K. E. , Harrison E. , Christie-Oleza J. , Rees A. P. , Downe J. , Aguilo-Ferretjans M. M. , Al-Moosawi L. , Brownlee C. , Wheeler G. L. 
Published: May 2020

AbstractDiatoms are a diverse and globally important phytoplankton group, responsible for an estimated 20% of carbon fixation on Earth. They frequently form spatially extensive phytoplankton blooms, responding rapidly to increased availability of nutrients including phosphorus and nitrogen. Although it is well established that diatoms are common first-responders to nutrient influxes in aquatic ecosystems, little is known of the sensory mechanisms that they employ for nutrient perception. Here we show that diatoms use a novel and highly-sensitive Ca2+-dependent signalling pathway, not previously described in eukaryotes, to sense and respond to the critical macronutrient phosphorus. We demonstrate that phosphorus-Ca2+signalling is essential for regulating diatom recovery from phosphorus limitation, by controlling rapid and substantial increases in nitrogen assimilation. Phosphorus-Ca2+signalling thus mediates fundamental cross-talk between the vital nutrients P and N to maximise resource competition, and likely governs the success of diatoms as major bloom formers in regions of pulsed nutrient supply. Importantly, our study demonstrates that distinct mechanisms for nutrient sensing have evolved in photosynthetic eukaryotes.
iDePP: a genetically encoded system for the inducible depletion of PI(4,5)P2inArabidopsis thaliana
Authors: Doumane Mehdi , Colin Léia , Lebecq Alexis , Fangain Aurélie , Bareille Joseph , Hamant Olivier , Belkhadir Youssef , Jaillais Yvon , Caillaud Marie-Cécile 
Published: May 2020

ABSTRACTPhosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is a low abundant lipid present at the plasma membrane of eukaryotic cells. Extensive studies in animal cells revealed the pleiotropic functions of PI(4,5)P2. In plant cells, PI(4,5)P2is involved in various cellular processes including the regulation of cell polarity and tip growth, clathrin-mediated endocytosis, polar auxin transport, actin dynamics or membrane-contact sites. To date, most studies investigating the role of PI(4,5)P2in plants have relied on mutants lacking enzymes responsible for PI(4,5)P2synthesis and degradation. However, such genetic perturbations only allow steady-state analysis of plants undergoing their life cycle in PI(4,5)P2deficient conditions and the corresponding mutants are likely to induce a range of non-causal (untargeted) effects driven by compensatory mechanisms. In addition, there are no small molecule inhibitors that are available in plants to specifically block the production of this lipid. Thus, there is currently no system to fine tune PI(4,5)P2content in plant cells. Here we report a genetically encoded and inducible synthetic system, iDePP (InducibleDepletion ofPI(4,5)P2inPlants), that efficiently removes PI(4,5)P2from the plasma membrane in different organs ofArabidopsis thaliana, including root meristem, root hair and shoot apical meristem. We show that iDePP allows the inducible depletion of PI(4,5)P2in less than three hours. Using this strategy, we reveal that PI(4,5)P2is critical for cortical microtubule organization. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P2in given cellular or developmental responses but also to evaluate the importance of this lipid in protein localization.Research OrganismA. thaliana