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Theplant cytosolic m^(6)A RNA methylome stabilizes photosynthesis in the cold

Plant Communications 2023年第6期4卷 70-84页

作者： Alexandre Magno Vicente Nikolay Manavski Paul Torben Rohn Lisa-Marie Schmid Antoni Garcia-Molina Dario Leister Charlotte Seydel Leo Bellin Torsten Möhlmann Gregor Ammann Stefanie Kaiser Jörg Meurer Plant Molecular Biology Faculty of BiologyLudwig-Maximilians-University MunichGroßhaderner Street 2-482152 Planegg-MartinsriedGermany Plant Development Faculty of BiologyLudwig-Maximilians-University MunichGroßhaderner Street 2-482152 Planegg-MartinsriedGermany Plant Physiology Faculty of BiologyUniversity of KaiserslauternErwin-Schröodinger-Street767663 KaiserslauternGermany Pharmaceutical Chemistry Goethe University FrankfurtMax-von-Laue-Str.960438 Frankfurt am MainGermany present address:loewe biochemica gmbh Möuhlweg 2a82054 SauerlachGermany present address:Center for Research in Agricultural Genomics 08193

The sessile lifestyle of plants requires an immediate response to environmental stressors that affect photosynthesis,growth,and crop ***,we showed that three abiotic perturbations—heat,cold,and high light—triggered considerable changes in the expression signatures of 42 epitranscriptomic factors(writers,erasers,and readers)with putative chloroplast-associated functions that formed clusters of commonly expressed genes in *** expression changes under all conditions were reversible upon deacclimation,identifying epitranscriptomic players as modulators in acclimation *** dysfunctions,particularly those induced by the oxidative stress-inducing norflurazon in a largely GENOME UNCOUPLED-independent manner,triggered retrograde signals to remodel chloroplastassociated epitranscriptomic expression patterns.N6-methyladenosine(m^(6)A)is known as the most prevalent RNA modification and impacts numerous developmental and physiological functions in living *** cold treatment,expression of components of the primary nuclear m^(6)A methyltransferase complex was upregulated,accompanied by a significant increase in cellular m^(6)A mRNA *** the cold,the presence of FIP37,a core component of the writer complex,played an important role in positive regulation of thylakoid structure,photosynthetic functions,and accumulation of photosystemⅠ,the Cytb6f complex,cyclic electron transport proteins,and Curvature Thylakoid1 but not that of photosystemⅡcomponents and the chloroplast ATP *** of FIP37 affected abundance,polysomal loading,and translation of cytosolic transcripts related to photosynthesis in the cold,suggesting m^(6)Adependent translational regulation of chloroplast *** summary,we identified multifaceted roles of the cellular m^(6)A RNA methylome in coping with cold;these were predominantly associated with chloroplasts and served to stabilize photosynthesis.

关键词： m^(6)A RNA methylation cold acclimation stress response Arabidopsis thaliana photosynthesis chloroplast

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Salinity Stress in Roots of Contrasting BarleyGenotypes Reveals Time-Distinct and Genotype-Specific Patterns for Defined Proteins

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Molecular Plant 2014年第2期7卷 336-355页

作者： Katja Witzel Andrea Matros Marc Strickert Stephanie Kaspar Manuela Peukert Karl H. Mühling Andreas Börner Hans-Peter Mock Leibniz Institute of Plant Genetics and Crop Plant Research Corrensstrasse 3 06466 Gatersleben Germany present address: Leibniz Institute of Vegetable and Ornamental Crops Theodor-Echtermeyer-Weg 1 14979 Großbeeren Germany present address: University of Siegen Media Systems Group Hölderlinstrasse 3 57068 Siegen Germany present address: Bruker Daltonik gmbh Fahrenheitstrasse 4 28359 Bremen Germany Institute of Plant Nutrition and Soil Science Christian Albrechts University Hermann-Rodewald-Strasse 2 24118 Kiel Germany

Soil salinity is one of the most severe abiotic stress factors threatening agriculture worldwide. Hence,particular interest exists in unraveling mechanisms leading to salt tolerance and improved crop plant performance onsaline soils. Barley is considered to be one of the most salinity-tolerant crops, but varying levels of tolerance are wellcharacterized. A proteomic analysis of the roots of two contrasting cultivars （cv. Steptoe and cv. Morex） is *** plants were exposed to a period of 1, 4, 7, or 10 d at 0, 100, or 150mM NaCI. The root proteome was analyzedbased on two-dimensional gel electrophoresis. A number of cultivar-specific and salinity stress-responsive proteins wereidentified. Mass spectrometry-based identification was successful for 74 proteins, and a hierarchical clustering analysisgrouped these into five clusters based on similarity of expression profile. The rank product method was applied to sta-tistically access the early and late responses, and this delivered a number of new candidate proteins underlying salinitytolerance in barley. Among these were some germin-like proteins, some pathogenesis-related proteins, and numerousas-yet uncharacterized proteins. Notably, proteins involved in detoxification pathways and terpenoid biosynthesis weredetected as early responsive to salinity and may function as a means of modulating growth-regulating mechanisms andmembrane stability via fine tuning of phytohormone and secondary metabolism in the root.

关键词： barley genotypes mass spectrometry proteome analysis salinity stress two-dimensional gel electrophoresis

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Identification of Early Nuclear Target Genes of Plastidial Redox Signals that Trigger the Long- Term Response of Arabidopsis to Light Quality Sh∽ts

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Molecular Plant 2015年第8期8卷 1237-1252页

作者： Lars Dietzel Christine Glaeer Monique Liebers Stefan Hiekel Florence Courtois Olaf Czarneckit Hagen Schlicke Yan Zubo Thomas Borner Klaus Mayer Bernhard Grimm Thomas Pfannschmidt Department of Plant Physiology Institute of General Botany and Plant Physiology Friedrich-Schiller-University of Jena Domburger Strasse 159 07743 JenaGermany MIPS/IBI Helmholtz Zentrum MGnchen German Research Center for Environmental Health (GmbH) Ingolst~dter Landstrasse 1 85764 Neuherberg Germany Institute of Biology/Plant Physiology Humboldt-University Berlin Philippstrasse 13 Building 12 10115 Berlin Germany Institute of Biology Genetics Humboldt-University Berlin Chausseestrasse 117 10115 Berlin Germany present address: Institut fer Molekulare Biowissenschaften Pflanzliche Zellphysiologie Max-von-Laue-Strasse 9 Biozentrum Goethe-Universit~t Frankfurt 60438Frankfurt am Main Germany present address: Zentrum fur Molekulare Biologie an der Universitat zu Heidelberg (ZMBH) Im Neuenheimer Feld 282 69120 Heidelberg Germany present address: Universite Grenoble-Alpes F-38000 Grenoble France present address: CNRS UMR5168 F-38054 Grenoble France present address: CEA iRTSV Laboratoire de Physiologie Cellulaire & Vgetale F-38054 Grenoble France present address: INRA USC1359 F-38054 Grenoble France present address: Plant Reproductive Biology Group Department of Physiology and Ceil-Biology Leibniz Institute of Rant Genetics and Crop Plant Research (IPK)OT Gatersleben Corrensstrasse 3 D-06466 Stadt Seeland Germany present address: KWS Saat AG Grimsehlstrasse 31 37555 Einbeck Germany present address: Dartmouth College Department of Biological Sciences Ufe Sciences Center 78 College Street Hanover NH 03755 USA

Natural illumination conditions are highly variable and because of their sessile life style, plants are forced to acclimate to them at the cellular and molecular level. Changes in light intensity or quality induce changes in the reduction/oxidation （redox） state of the photosynthetic electron chain that acts as a trigger for compen- satory acclimation responses comprising functional and structural adjustments of photosynthesis and metabolism. Such responses include redox-controlled changes in plant gene expression in the nucleus and organelles. Here we describe a strategy for the identification of early redox-regulated genes （ERGs） in the nucleus of the model organism Arabidopsis thaliana that respond significantly 30 or 60 min after the generation of a reduction signal in the photosynthetic electron transport chain. By comparing the response of wild-type plants with that of the acclimation mutant stn7, we could specifically identify ERGs. The results reveal a significant impact of chloroplast redox signals on distinct nuclear gene groups including genes for the mitochondrial electron transport chain, tetrapyrrole biosynthesis, carbohydrate metabolism, and signaling lipid synthesis. These expression profiles are clearly different from those observed in response to the reduction of photosynthetic electron transport by high light treatments. Thus, the ERGs identified are unique to redox imbalances in photosynthetic electron transport and were then used for analyzing potential redox-responsive cis-elements, trans-factors, and chromosomal regulatory hot spots. The data identify a novel redox-responsive element and indicate extensive redox control at transcriptional and chromosomal levels that point to an unprecedented impact of redox signals on epigenetic processes.

关键词： plastidial redox signaling,early redox-regulated gene Arabidopsis thaliana Molecular Plant

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Impact of human sequences in variable domains of therapeutic antibodies on the location of CD4 T-cell epitopes

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Cellular & Molecular Immunology 2020年第6期17卷 656-658页

作者： Sylvain Meunier Moustafa Hamze Anette Karle Marie de Bourayne Abdelaziz Gdoura Sebastian Spindeldreher Bernard Maillère CEA-Saclay Institut Frederic JoliotSIMOPROUniversitéParis-Saclay91191 Gif sur YvetteFrance Novartis Pharma AG BaselSwitzerland present address:Integrated Biologix gmbh BaselSwitzerland

The clinical efficacy of therapeutic antibodies is recognized in many indications,explaining their rapid rise in the worldwide drug ***,therapeutic antibodies can be immunogenic by inducing a specific immune response characterized by the production of anti-drug antibodies(ADAs).ADAs can potentially increase the clearance of therapeutic antibodies,decrease their therapeutic effects1 and induce hypersensitivity *** humans are thought to be tolerant to their own proteins,sequences of the therapeutic antibodies have been humanized or human antibodies have been directly generated by technologies using human ***,human(ized)antibodies exhibit highly variable levels of immunogenicity,1,2 illustrating the poor understanding of the role of sequence humanization in mitigating the immunogenicity of therapeutic *** lines of evidence highlight the role of CD4 T lymphocytes during the initiation of an ADA response,3 but few T-cell epitopes of marketed therapeutic antibodies have been described to date.

关键词： therapeutic antibodies clinical

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The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants

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Molecular Plant 2020年第2期13卷 215-230页

作者： Bernard Gutmann Santana Royan Mareike Schallenberg-Rudinger Henning Lenz Ian R.Castleden Rose McDowell Michael AVacher Julian Tonti-Filippini Charles SBond Volker Knoop Ian D.Small Australian Research Council Centre of Excellence in Plant Energy Biology The University of Western AustraliaCrawleyPerth 6009WAAustralia School of Molecular Sciences The University of Western AustraliaCrawleyPerth 6009WAAustralia IZMB-Institut fur Zellulare und Molekulare Botanik Abteilung Molekulare EvolutionUniversitat BonnKirschallee 153115 BonnGermany present address:EditForce Inc. West zone#429Kyushu University744 MotookaNishi-KuFukuokaJapan present address:IBG-2:Plant Sciences Forschungszentrum Jiilich GmbH52425 JulichGermany present address:Australian eHealth Research Centre Commonwealth Scientific and Industrial Research OrganisationFloreatPerth 6014WAAustralia

The RNA-binding pentatricopeptide repeat(PPR)family comprises hundreds to thousands of genes in most plants,but only a few dozen in algae,indicating massive gene expansions during land plant *** nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant *** this study,we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family,focusing on the proteins typically associated with RNA editing,which show the most spectacular variation in numbers and domain composition across the plant *** characterize over 2250000 PPR motifs in over 400000 *** lycophytes,polypod ferns,and hornworts,nearly 10%of expressed protein-coding genes encode putative PPR editing factors,whereas they are absent from algae and complex-thalloid *** show that rather than a single expansion,most land plant lineages with high numbers of editing factors have continued to generate novel sequence *** identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing ***,using the sequence variations across the datasets,we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors,given their phylogenetic distribution and sequence characteristics.

关键词： RNA editing RNA-binding protein organelles

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Targeting α-synuclein by PD03 AFFITOPE■ and Anle 138b rescues neurodegenerative pathology in a model of multiple system atrophy:clinical relevance

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Translational Neurodegeneration 2020年第3期9卷 484-497页

作者： Miguel Lemos Serena Venezia Violetta Refolo Antonio Heras-Gavin Sabine Schmidhuber Armin Giese Andrei Leonov Sergey Ryazanov Christian Griesinger Gergana Galabova Guenther Safer Gregor Karl Wenning Nadia Stefanova Division of Neurobiology Department of NeurologyInnsbruck Medical University6020 InnsbruckAustria AFFIRIS AG ViennaAustria Center for Neuropathology and Prion Research Ludwig-Maximilians-UniversityMunichGermany Max Planck Institute for Biophysical Chemistry GottingenGermany present address:Origenis gmbh MunichGermany

Background:Misfolded oligomeric α-synuclein plays a pivotal role in the pathogenesis of a-synucleinopathies including Parkinson's disease and multiple system atrophy,and its detection parallels activation of microglia and a loss of neurons in the substantia nigra pars *** we aimed to analyze the therapeutic efficacy of PD03,a new AFFITOPE■ immunotherapy approach,either alone or in combination with Anle138b,in a PLP-α-syn mouse ***:The PLP-α-syn mice were treated with PD03 immunotherapy,Anle138b,or a combination of *** months after study initiation,the mice underwent behavioral testing and were sacrificed for neuropathological *** treatment groups were compared to the vehicle group with regard to motor performance,nigral neuronal loss,microglial activation and α-synuclein ***:The PLP-α-syn mice receiving the PD03 or Anle138b single therapy showed improvement of gait deficits and preservation of nigral dopaminergic neurons associated with the reduced α-synuclein oligomer levels and decreased microglial *** combined therapy with Anle138b and PD03 resulted in lower lgG binding in the brain as compared to the single immunotherapy with ***:PD03 and Anle138b can selectively target oligomeric α-synuclein,resulting in attenuation of neurodegeneration in the PLP-α-syn *** approaches are potential therapies that should be developed further for disease modification in α-synucleinopathies.

关键词： α-Synuclein Immunotherapy Oligomer modulation Target engagement Substantia nigra Microglia

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Performance of two complementary machine-learned potentials in modelling chemically complex systems

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npj Computational Materials 2023年第1期9卷 1008-1022页

作者： Konstantin Gubaev Viktor Zaverkin Prashanth Srinivasan Andrew Ian Duff Johannes Kästner Blazej Grabowski Institute for Materials Science University of StuttgartPfaffenwaldring 5570569 StuttgartGermany Institute for Theoretical Chemistry University of StuttgartPfaffenwaldring 5570569 StuttgartGermany Scientific Computing Department STFC Daresbury LaboratoryWarrington WA44ADUK present address:NEC Laboratories Europe gmbh Kurfürsten-Anlage 3669115 HeidelbergGermany

Chemically complex multicomponent alloys possess exceptional properties derived from an inexhaustible compositional *** complexity however makes interatomic potential development *** explore two complementary machine-learned potentials—the moment tensor potential(MTP)and the Gaussian moment neural network(GM-NN)—in simultaneously describing configurational and vibrational degrees of freedom in the Ta-V-Cr-W alloy *** models are equally accurate with excellent performance evaluated against *** achieve root-mean-square-errors(RMSEs)in energies of less than a few meV/atom across 0 K ordered and high-temperature disordered configurations included in the *** for compositions not in training,relative energy RMSEs at high temperatures are within a few meV/***-temperature molecular dynamics forces have similarly small RMSEs of about 0.15 eV/Åfor the disordered quaternary included in,and ternaries not part of *** achieve faster convergence with training size;GM-NNs are faster in *** learning is partially beneficial and should be complemented with conventional human-based training set generation.

关键词： alloy faster complex

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Inhibition of Cdk5 increases osteoblast differentiation and bone mass and improves fracture healing

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Bone Research 2022年第3期10卷 469-481页

作者： Mubashir Ahmad Benjamin Thilo Krüger Torsten Kroll Sabine Vettorazzi Ann-Kristin Dorn Florian Mengele Sooyeon Lee Sayantan Nandi Dilay Yilmaz Miriam Stolz Naveen Kumar Tangudu David Carro Vázquez Johanna Pachmayr Ion Cristian Cirstea Maja Vujic Spasic Aspasia Ploubidou Anita Ignatius Jan Tuckermann Institute of Comparative Molecular Endocrinology(CME) Ulm UniversityHelmholtzstrasse 8/189081 UlmGermany Institute of Orthopedic Research and Biomechanics Ulm UniversityHelmholtzstrasse 1489081 UlmGermany Leibniz Institute on Aging–Fritz Lipmann Institute(FLI) Beutenbergstrasse 11D-07745 JenaGermany Praxisklinik für Orthopädie Unfall-und Neurochirurgie Prof.Bischoff/Dr.Spies/Dr.Mengele89231 Neu-UlmGermany Paracelsus Medizinische Privatuniverstät Institute of PharmacyStrubergasse 215020 SalzburgAustria Department of Endocrinology Ludwig Maximilians University MunichMunich 80336Germany present address:Institute of Orthopedic Research and Biomechanics Ulm UniversityHelmholtzstrasse 1489081 UlmGermany present address:UPMC Hillman Cancer Center Department of Pharmacology and Chemical BiologyUniversity of Pittsburgh5115 Center Avenue15232 PittsburghPAUSA present address:TAmiRNA gmbh Leberstrasse 201110 ViennaAustria

Identification of regulators of osteoblastogenesis that can be pharmacologically targeted is a major goal in combating osteoporosis,a common disease of the elderly population. Here, unbiased kinome RNAi screening in primary murine osteoblasts identified cyclin-dependent kinase 5(Cdk5) as a suppressor of osteoblast differentiation in both murine and human preosteoblastic cells. Cdk5 knockdown by si RNA, genetic deletion using the Cre-lox P system, or inhibition with the small molecule roscovitine enhanced osteoblastogenesis in vitro. Roscovitine treatment significantly enhanced bone mass by increasing osteoblastogenesis and improved fracture healing in mice. Mechanistically, downregulation of Cdk5 expression increased Erk phosphorylation, resulting in enhanced osteoblast-specific gene expression. Notably, simultaneous Cdk5 and Erk depletion abrogated the osteoblastogenesis conferred by Cdk5 depletion alone, suggesting that Cdk5 regulates osteoblast differentiation through MAPK pathway modulation. We conclude that Cdk5 is a potential therapeutic target to treat osteoporosis and improve fracture healing.

关键词： Cdk5 healing expression

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Winery by‑products as a feed source with functional properties:dose–response effect of grape pomace,grape seed meal,and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2439-2453页

作者： Ratchaneewan Khiaosa‑ard Mubarik Mahmood Elsayed Mickdam Catia Pacifico Julia Meixner Laura‑Sophie Traintinger Institute of Animal Nutrition and Functional Plant Compounds Department for Farm Animals and Veterinary Public HealthUniversity of Veterinary Medicine ViennaVeterinaerplatz 11210 ViennaAustria. Animal Nutrition Section Department of Animal SciencesSub Campus JhangUniversity of Veterinary and Animal Sciences12 Km Chiniot RoadJhang 35200LahorePakistan. Nutrition and Clinical Nutrition Department Faculty of Veterinary MedicineSouth Valley UniversityQena 83523Egypt. present address:Biome Diagnostics gmbh ViennaAustria.

Background Grape and winery by-products have nutritional values for cattle and also contain functional compounds like phenols,which not only bind to protein but can also directly affect microbiota and their function in the *** characterized the nutritional and functional effects of grape seed meal and grape pomace as well as an effective dosage of grape phenols on ruminal microbiota and fermentation characteristics using a rumen simulation *** Six diets(each n=8)were compared including a control diet(CON,no by-product),a positive control diet(EXT,CON+3.7%grape seed extract on a dry matter(DM)basis),two diets with grape seed meal at 5%(GS-low)and 10%(GS-high),and two diets with grape pomace:at 10%(GP-low)and 20%(GP-high),on a DM *** inclusion of the by-product supplied total phenols at 3.4%,0.7%,1.4%,1.3%,and 2.7%of diet DM for EXT,GS-low,GS-high,GP-low,and GP-high,*** were tested in four experimental *** treatments decreased ammonia concentrations and the disappearances of DM and OM(P<0.05)compared to *** and GP-high lowered butyrate and odd-and branch-chain short-chain fatty acids while increased acetate compared to CON(P<0.05).Treatments did not affect methane *** decreased the abundance of many bacterial genera including those belonging to the core ***-high and EXT consistently decreased Olsenella and Anaerotipes while increased Ruminobacter *** The data suggest that the inclusion of winery by-products or grape seed extract could be an option for reducing excessive ammonia *** to grape phenols at a high dosage in an extract form can alter the rumen microbial ***,however,does not necessarily alter the effect of grape phenols on the microbial community function compared to feeding high levels of winery *** suggests the dominant role of dosage over the form or source of the grape phenols in affecting ruminal microbial *** conclusion,

关键词： Functional feed Grape pomace Grape seed Protein degradation Rumen microbiota

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Survey of Rice Cropping Systems in Kampong Chhnang Province,Cambodia

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Rice science 2013年第2期20卷 154-164页

作者： Volker KLEINHENZ Sophon CHEA Ngin HUN Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) gmbh #17Street 306P.O.Box 81Phnom PenhCambodia Provincial Department of Agriculture (PDA) Kampong Chhnang Sangkat KsamKampong ChhnangCambodia present address:The Herbals Joint Stock Company 8 th FloorBAC A BuildingNo.9Dao Duy Anh StreetDong Da DistrictHanoiVietnam

Although Cambodia might have achieved self-sufficiency and an exported surplus in rice production,its rice-based farming systems are widely associated with low productivity,low farmer income and rural *** study is based on a questionnaire village survey in 14 communes containing 97 villages of Kampong Chhnang Province from March to June,*** analyzes the prevailing rice-based cropping systems and evaluates options for their *** in cropping systems depend on the distance from the Tonle Sap water *** distances greater than 10 km,transplanted wet-season rice cropping system with low productivity of about 1.6 t/hm 2 *** deficiency can be primarily attributed to soils with high coarse sand fractions and low pH （〈 4.0）,use of ＇late＇ cultivars,and exclusive use of self-propagated *** improve this cropping system,commercial ＇medium＇ cultivars help prevent crop failure by shortening the cultivation period by one month and complementation of wet-season rice with non-rice crops should be *** adjacent （≤ 1 km） to the water bodies become inundated for up to seven months between July until January of each *** this area,soils contain more fine sand,silt and clay,and their pH is higher （〉 4.0）.Farmers predominantly cultivate dry-season recession rice between January and ***-nine percent of the area is sown directly and harvested by *** ratio of commercial rice seeds is 59% and yields average 3.2 t/hm *** of the second dry-season rice between April and July may double annual yields in this rice cropping *** upgrading other cultivation technologies,using seeds from commercial sources will improve yield and rice *** with rice,farmers grow non-rice crops at different intensities ranging from single annual crops to intensive sequences at low yields.

关键词： rice cropping system socioeconomic indicator on-farm activity rice production

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