bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tm-22 resistance targets a conserved cysteine essential for tobacco mosaic virus (TMV) movement
Authors: Hak Hagit , Raanan Hagai , Schwarz Shahar , Sherman Yifat , Dinesh-Kumar Savithramma P , Spiegelman Ziv 
Published: October 2022

ABSTRACTThe tomato Tm-22 gene was considered one of the most durable resistance genes in agriculture, protecting against viruses of the Tobamovirus genus, such as Tomato mosaic virus (ToMV) and Tobacco mosaic virus (TMV). However, an emerging tobamovirus, Tomato brown rugose fruit virus (ToBRFV), has overcome Tm-22, damaging tomato production worldwide. Tm-22 encodes a nucleotide-binding leucine-rich repeat (NLR) class immune receptor that recognizes its effector, the tobamovirus movement protein (MP). Previously, we found that ToBRFV MP (MPToBRFV) enabled the virus to overcome Tm-22- mediated resistance. Yet, it was unknown how Tm-22 remained durable against other tobamoviruses, such as TMV and ToMV, for over 60 years. Here, we show that the presence of a conserved cysteine (C68) in the MP of TMV (MPTMV) is both sufficient to trigger Tm-22 resistance and essential for viral movement. Substitution of MPToBRFV amino acid H67 with the corresponding amino acid in MPTMV (C68) activated Tm-22-medited resistance. However, replacement of C68 in TMV and ToMV disabled the infectivity of both viruses. Phylogenetic and structural prediction analysis revealed that C68 is conserved among all Solanaceae-infecting tobamoviruses except ToBRFV, and localizes to a predicted jelly-roll fold common to various MPs. Cell-to-cell, and subcellular movement analysis showed that C68 is required for the movement of TMV, by regulating the MP interaction with the endoplasmic reticulum and targeting it to plasmodesmata. The dual role of C68 in viral movement and Tm-22 immune activation could explain how TMV was unable to overcome this resistance for such a long period.
Toxoplasma gondii importin α shows weak auto-inhibition
Authors: Bhambid Manasi , Dey Vishakha , Walunj Sujata , Patankar Swati 
Published: October 2022

ABSTRACTImportin α is a nuclear transporter that binds to nuclear localization signals (NLSs), consisting of 7-20 positively charged amino acids found within cargo proteins. In addition to cargo binding, intramolecular interactions also occur within the importin α protein due to binding between the importin β-binding (IBB) domain and the NLS-binding sites, a phenomenon called auto-inhibition. The interactions causing auto-inhibition are driven by a stretch of basic residues, similar to an NLS, in the IBB domain. Consistent with this, importin α proteins that do not have some of these basic residues lack auto-inhibition; a naturally occurring example of such a protein is found in the apicomplexan parasite Plasmodium falciparum. In this report, we show that importin α from another apicomplexan parasite, Toxoplasma gondii, harbors basic residues (KKR) in the IBB domain and exhibits auto-inhibition. This protein has a long, unstructured hinge motif (between the IBB domain and the NLS-binding sites) that does not contribute to auto-inhibition. However, the IBB domain may have a higher propensity to form an α-helical structure, positioning the wild-type KKR motif in an orientation that results in weaker interactions with the NLS-binding site than a KRR mutant. We conclude that the importin α protein from T. gondii shows auto-inhibition, exhibiting a different phenotype from that of P. falciparum importin α. However, our data indicate that T. gondii importin α may have a low strength of auto-inhibition. We hypothesize that low levels of auto-inhibition may confer an advantage to these important human pathogens.
The roles and evolution of the four LEAFY homologues in floral patterning and leaf development in woodland strawberry
Authors: Zhang Yunming , Kan Lijun , Hu Shaoqiang , Cheng Laichao , Liu Zhongchi , Kang Chunying 
Published: October 2022

AbstractThe plant-specific transcription factor LEAFY (LFY), generally maintained as a single copy gene in most angiosperm species, plays critical roles in flower and leaf development. However, wild strawberry Fragaria vesca possesses four LFY homologues in the genome, their respective functions and evolution remain unknown. Through chemical mutagenesis screen, we identified two allelic mutations in one of the four LFY homologues, FveLFYa, in F. vesca, causing homeotic conversion of floral organs and reiterative outgrowth of ectopic florets. Both CRISPR-knockout and transgenic rescue confirmed the identity of FveLFYa. Ectopic expression in Arabidopsis lfy-5 mutant revealed that only FveLFYa and FveLFYb can rescue the flower defects and induce solitary flowers in leaf axils. Disruption of FveLFYc, the second abundantly expressed LFY homologue, caused no obvious morphology phenotypes in F. vesca. FveLFYb and FveLFYd are barely expressed. Expression of FveAP1, homologue of the well-known LFY target AtAP1, is not changed in the fvelfya flowers, possibly caused by an absence of any FveLFYa binding site in its promoter. Loss of Axillary Meristems encodes a GRAS transcription factor essential for stamen initiation. The ectopic florets are eliminated in fvelfya lam, suggesting that LAM is required for floret production. Moreover, approximately 30% of mature leaves have smaller or fewer leaflets in fvelfya. Among these homologues, only FveLFYa is syntenic to the homologues in other species. Overall, the detailed analyses of the four LFY homologues in woodland strawberry demonstrate that only FveLFYa plays crucial roles in floral patterning with rewired gene network.
Pump-Rest-Leak-Repeat: regulation of the mammalian-brain V-ATPase via ultra-slow mode-switching
Authors: Kosmidis Eleftherios , Shuttle Christopher G. , Preobraschenski Julia , Ganzella Marcelo , Johnson Peter J. , Veshaguri Salome , Møller Mads P. , Marantos Orestis , Pedersen Jesper L. , Jahn Reinhard , Stamou Dimitrios 
Published: October 2022

Summary paragraphVacuolar-type adenosine triphosphatases (V-ATPases)1–3 are electrogenic rotary mechanoenzymes structurally related to F-type ATP synthases4,5. They hydrolyze ATP to establish electrochemical proton gradients for a plethora of cellular processes1,3. In neurons, the loading of all neurotransmitters into synaptic vesicles is energized by ~1 V-ATPase molecule per synaptic vesicle6,7. To shed light into this bona fide single-molecule biological process, we investigated electrogenic proton pumping by single mammalian-brain V-ATPases, using individual synaptic vesicles fused with immobilized liposomes. We show V-ATPases do not pump continuously in time, as hypothesized by observing the rotation of bacterial homologs8 and assuming strict ATP/proton coupling. Instead, they stochastically switch between three novel ultra-long-lived proton-pumping, inactive, and proton-leaky modes. Upending conventional wisdom, direct observation of pumping revealed that physiologically relevant concentrations of ATP do not regulate the intrinsic pumping rate. Instead, ATP regulates V-ATPase activity via the switching probability of the proton-pumping mode. In contrast, electrochemical proton gradients regulate the pumping rate and the switching of the pumping and inactive modes. This work reveals and emphasises the mechanistic and biological importance of mode-switching in protein regulation.
Drug repurposing screens identifies compounds that inhibit α-synuclein oligomers’ membrane disruption and block antibody interactions
Authors: Somavarapu Arun Kumar , Kleijwegt Giulia , Nagaraj Madhu , Alam Parvez , Nielsen Janni , Otzen Daniel 
Published: October 2022

ABSTRACTSmall soluble oligomers of the protein α-synuclein (αSO) have been linked to disruptions in neuronal homeostasis, contributing to the development of Parkinson’s Disease (PD). While this makes αSO an obvious drug target, the development of effective therapeutics against αSO are challenged by its low abundance and structural and morphological complexity. Here we employ two different approaches to neutralize toxic interactions made by αSOs with different cellular components. Firstly, we use available data to identify four neuronal proteins as likely candidates for αSO interactions, namely Cfl1, Uchl1, Sirt2 and SerRS. However, despite promising results when immobilized, all 4 proteins only bind weakly to αSO in solution in microfluidic assays, making them inappropriate for screening. In contrast, the formation of stable contacts formed between αSO and vesicles consisting of anionic lipids not only mimics a likely biological role of αSO but also provided a platform to screen two small molecule libraries for disruptors of these contacts. Of the 11 leads obtained in this way, 2 significantly impaired αSO contacts with other proteins in a sandwich ELISA assay using αSO-binding monoclonal antibodies and nanobodies. In addition, 5 of these leads suppressed α-synuclein amyloid formation. Thus a repurposing screening that directly targets a key culprit in PD pathogenesis shows therapeutic potential.HighlightsThe toxic oligomer formed by α-synuclein (αSO) is an important drug target.Neuronal proteins found by pull-down assays do not bind αSOs in solution.Liposome assay identifies 7 approved drugs reducing αSO membrane disruption.We identify different inhibitory mechanisms used by different compounds.Two top drug hits disrupt αSO binding to oligomer-specific antibodies.Graphical Abstract
Convergent evolution of plant pattern recognition receptors sensing cysteine-rich patterns from three microbial kingdoms
Authors: Yang Yuankun , Steidele Christina E. , Löffelhardt Birgit , Kolb Dagmar , Leisen Thomas , Zhang Weiguo , Ludwig Christina , Felix Georg , Seidl Michael F. , Nürnberger Thorsten , Hahn Matthias , Gust Bertolt , Gross Harald , Hückelhoven Ralph , Gust Andrea A. 
Published: October 2022

AbstractThe Arabidopsis thaliana receptor-like protein RLP30 contributes to immunity against the fungal pathogen Sclerotinia sclerotiorum. Here we identified the RLP30-ligand as a small cysteine-rich protein (SCP) that occurs in many fungi and oomycetes and is also recognized by the Nicotiana benthamiana RLP RE02. However, RLP30 and RE02 share little sequence similarity and respond to different parts of the native/folded protein. Interestingly, some Brassicaceae other than Arabidopsis also respond to a linear SCP peptide, suggesting that SCP is an eminent immune target that led to the convergent evolution of distinct immune receptors in plants. Surprisingly, RLP30 shows a second ligand specificity for a SCP-nonhomologous protein secreted by bacterial Pseudomonads. RLP30 expression in N. tabacum resulted in lower susceptibility to bacterial, fungal and oomycete pathogens, thus demonstrating that detection of immunogenic patterns by Arabidopsis RLP30 is involved in defense against pathogens from three microbial kingdoms.
Synchronization in collectively moving inanimate and living active matter
Authors: Riedl Michael , Merrin Jack , Sixt Michael , Hof Björn 
Published: October 2022

ABSTRACTRegardless of whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinement, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the essential requirements to reach the corresponding collective state, i.e. the synchronization of the individuals’ internal oscillators. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for emergent, self-organized motion of cell collectives.
Capsid-mediated chromatin state of the AAV vector genome controls host species range
Authors: Gonzalez-Sandoval Adriana , Tsuji Shinnosuke , Zhang Feijie , Hung King L. , Chang Howard Y. , Pekrun Katja , Kay Mark A. 
Published: October 2022

SummaryRecombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. We used a primate specific capsid, AAV-LK03, and demonstrated that the limitation of this capsid towards transduction of mouse cells was unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enabled efficient transduction and the accumulation of active histone marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in determining the chromatin status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species.
Aquaponics versus conventional farming: effects on the growth, nutritional and chemical compositions of Celosia argentea L., Corchorus olitorius L., and Ocimum gratissimum L.
Authors: Olanrewaju Gbolaga O. , Sarpong David D. , Aremu Abiola O. , Ade-Ademilua Elizabeth O. 
Published: October 2022

ABSTRACTThis study examined the practicality and sustainability of growing leafy vegetables in aquaponics instead of traditional soil-based farming systems by comparing the physiological growth patterns, nutritional compositions, and phytochemical constituents of Celosia argentea L., Corchorus olitorius L. and Ocimum gratissimum L. grown in aquaponics with those of other conventional systems. The results of this study indicate that the growth and accumulation of biomass by plants grown in aquaponics were similar to those obtained in unamended loamy soil but better than those of plants grown in inorganic hydroponics. However, plants grown in NPK-supplemented soil showed significantly (p<0.05) higher biomass accumulation than those grown in aquaponics. Likewise, C. argentea, C. olitorius, and O. gratissimum grown in aquaponics had significantly higher nutrient compositions than those grown in inorganic medium, and at the same time, similar to that of plants grown in unamended loamy soil. C. argentea and C. olitorius grown in inorganic medium had significantly higher concentrations of the observed phytochemicals than those grown in aquaponics, whereas the opposite was true for O. gratissimum. The three plant species were able to serve as filters for the effective maintenance of nitrogen dynamics in the constructed African catfish aquaponics, while utilizing nitrogenous waste for biomass production.
A plasma membrane-associated glycolytic metabolon is functionally coupled to KATPchannels in pancreatic α and β cells from humans and mice
Authors: Ho Thuong , Potapenko Evgeniy , Davis Dawn B. , Merrins Matthew J. 
Published: October 2022

SummaryThe ATP-sensitive K+channel (KATP) is a key regulator of hormone secretion from pancreatic islet endocrine cells. Using direct measurements of KATPchannel activity in pancreatic β cells and the lesser-studied α cells, from both humans and mice, we demonstrate that a glycolytic metabolon locally controls KATPchannels on the plasma membrane. The two ATP-consuming enzymes of upper glycolysis, glucokinase and phosphofructokinase, generate ADP that activates KATP. Substrate channeling of fructose 1,6-bisphosphate through the enzymes of lower glycolysis fuels pyruvate kinase, which directly consumes the ADP made by phosphofructokinase to raise ATP/ADP and close the channel. We further demonstrate the presence of a plasma membrane NAD+/NADH cycle, whereby lactate dehydrogenase is functionally coupled to glyceraldehyde-3-phosphate dehydrogenase. These studies provide direct electrophysiological evidence of a KATP-controlling glycolytic signaling complex and demonstrate its relevance to islet glucose sensing and excitability.Graphical abstractHoet al. demonstrate that the enzymes of glycolysis, as well as lactate dehydrogenase, form a plasma membrane-associated metabolon with intrinsic ATP/ADP and NAD+/NADH cycles. The subcellular location of this signaling complex allows both ATP-consuming and ATP-producing enzymes to locally control the activity of ATP-sensitive K+channels in pancreatic α and β cells from humans and mice.HighlightsKATPchannels are regulated by a glycolytic metabolon on the plasma membrane.Substrate channeling occurs between the consecutive enzymes of glycolysis.Upper glycolysis produces ADP that is used directly by lower glycolysis to make ATP.LDH and GADPH facilitate a plasma membrane-associated NAD+/NADH redox cycle.
Time-lapse mechanical imaging of neural tube closure in live embryo using Brillouin microscopy
Authors: Handler Chenchen , Scarcelli Giuliano , Zhang Jitao 
Published: October 2022

ABSTRACTNeural tube closure (NTC) is a complex process of embryonic development involving molecular, cellular, and biomechanical mechanisms. While the genetic factors and biochemical signaling have been extensively investigated, the role of tissue biomechanics remains mostly unexplored due to the lack of tools. Here, we developed a new optical modality that can conduct time-lapse mechanical imaging of neural plate tissue as the embryo is experiencing neurulation. This technique is based on the combination of a confocal Brillouin microscope and an on-stage incubator for the modified ex ovo culturing of chick embryo. With this technique, for the first time, we captured the mechanical evolution of the neural plate tissue with live embryos. Specifically, we observed the continuous stiffening of the neural plate during NTC for ex ovo cultured embryos, which is consistent with the data of in ovo culture as well as previous studies. Beyond that, we found the tissue stiffening was highly correlated with the tissue thickening and bending. We foresee this non-contact and label-free technique can open new opportunities to understand the biomechanical mechanisms in development.Summary statementAn all-optical technique is developed to capture the evolution of tissue mechanics during neural tube closure of live chick embryo.
Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus
Authors: Hickey Glenn , Monlong Jean , Ebler Jana , Novak Adam , Eizenga Jordan M. , Gao Yan ,   Human Pangenome Reference Consortium, Marschall Tobias , Li Heng , Paten Benedict 
Published: October 2022

AbstractReference genomes provide mapping targets and coordinate systems but introduce biases when samples under study diverge sufficiently from them. Pangenome references seek to address this by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but thanks to advances in long-read sequencing, high-quality phased assemblies are becoming widely available. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph’s ability to consistently represent variation at different scales and reduces biases introduced by reference-based variant calls. Pangenome construction in this way is equivalent to multiple genome alignment. Here we present the Minigraph-Cactus pangenome pipeline, a method to create pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium (HPRC). This tool was designed to build graphs containing all forms of genetic variation while still being practical for use with current mapping and genotyping tools. We show that this graph is useful both for studying variation within the input haplotypes, but also as a basis for achieving state of the art performance in short and long read mapping, small variant calling and structural variant genotyping. We further measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes, and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods, even after projecting back to GRCh38. We also demonstrate that our method can apply to nonhuman data by showing improved mapping and variant detection sensitivity with aDrosophila melanogasterpangenome.
Kinetics of blood cell differentiation during hematopoiesis revealed by quantitative long-term live imaging
Authors: Ho Kevin Y.L. , Carr Rosalyn L. , Dvoskin Alexandra D. , Tanentzapf Guy 
Published: October 2022

AbstractStem cells typically reside in a specialized physical and biochemical environment that facilitates regulation of their behavior. For this reason, stem cells are ideally studied in contexts that maintain this precisely constructed microenvironment while still allowing for live imaging. Here, we describe a long-term organ culture and imaging strategy for hematopoiesis in flies that takes advantage of powerful genetic and transgenic tools available in this system. We find that fly blood progenitors undergo symmetric cell divisions and that their division is both linked to cell size and is spatially oriented. Using quantitative imaging to simultaneously track markers for stemness and differentiation in progenitors, we identify two types of differentiation that exhibit distinct kinetics. Moreover, we find that infection-induced activation of hematopoiesis occurs through modulation of the kinetics of cell differentiation. Overall, our results show that even subtle shifts in proliferation and differentiation kinetics can have large and aggregate effects to transform blood progenitors from a quiescent to an activated state.