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Genetic insights into adaptation of alfalfa

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Molecular Plant 2024年第8期17卷 1170-1171页

作者： Yafei Guo Lipeng Kang Fei Lu State Key laboratory of Plant cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina Key laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChineseAcademyof SciencesBeijingChina University of Chinese Academy of Sciences BeijingChina CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

Climate change is increasingly affecting agricultural outputs,as evidenced by the changing global temperature and extreme weather events that significantly impact crop yields(Lesk et al.,2016).To address this challenge,there is a growing interest in developing crops that can endure these adverse conditions to ensure food *** examples in nature show how crops have adapted to diverse environments(Gutaker and Purugganan,2023),leaving behind a rich genomic *** genomics has started to provide insights into these adaptive processes from evolutionary and genetic perspectives(Savolainen et al.,2013;Aguirre-Liguori et al.,2021;Sang et al.,2022).Recently,Zhang et al.(Zhang et al.,2024)investigated alfalfa(Medicago sativa ***),known as the"queen of forages,"for its broad *** analyzing whole-genome sequencing data of 702 accessions from 24 Medicago species,this study enriches our understanding of how to develop crops and meet the challenges of climate change.

关键词： sativa crops environments

Stress Knowledge Map:A knowledge graph resource for systems biology analysis of plant stress responses

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Plant Communications 2024年第6期5卷 17-31页

作者： Carissa Bleker Ziva Ramsak Andras Bittner Vid Podpecan Maja Zagorscak Bernhard Wurzinger Spela Baebler Marko Petek Maja Kriznik Annelotte van Dieren Juliane Gruber Leila Afjehi-Sadat Wolfram Weckwerth Anze Zupanic Markus Teige Ute CVothknecht Kristina Gruden Department of Biotechnology and Systems biology National Institute of BiologyVecna pot 1211000 LjubljanaSlovenia Plant cell biology Institute of Cellular and Molecular BotanyUniversity of BonnKirschallee 153115 BonnGermany Department of Knowledge Technologies Jozef Stefan InstituteJamova cesta 391000 LjubljanaSlovenia Department of Functional&evolutionary Ecology University of ViennaDjerassiplatz 11030 ViennaAustria Mass Spectrometry Unit Core Facility Shared ServicesUniversity of ViennaDjerassiplatz 11030 ViennaAustria

Stress Knowledge Map(SKM;https://***)is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical,signaling,and regulatory molecular interactions in plants:a highly curated model of plant stress signaling(PSS;543 reactions)and a large comprehensive knowledge network(488390 interactions).Both were constructed by domain experts through systematic curation of diverse literature and database *** provides a single entry point for investigations of plant stress response and related growth trade-offs,as well as interactive explorations of current *** is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital ***,we describe the features of SKM and show,through two case studies,how it can be used for complex analyses,including systematic hypothesis generation and design of validation experiments,or to gain new insights into experimental observations in plant biology.

关键词： knowledge graph plant stress responses plant signaling systems biology plant digital twin

The DUF579 proteins GhIRX15s regulate cotton fiber development by interacting with proteins involved in xylan synthesis

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The Crop Journal 2024年第4期12卷 1112-1125页

作者： Mengyun Li Feng Chen Jingwen Luo Yanan Gao Jinglong Cai Wei Zeng Monika S.Doblin Gengqing Huang Wenliang Xu Hubei Key laboratory of Genetic Regulation and Integrative biology School of Life SciencesCentral China Normal UniversityWuhan 430079HubeiChina Zhejiang Provincial Key laboratory of Plant evolutionary Ecology and Conservation School of Life SciencesTaizhou UniversityTaizhou 318000ZhejiangChina La Trobe Institute for Sustainable Agriculture&Food School of AgricultureBiomedicine and EnvironmentLa Trobe UniversityBundooraVIC 3086Australia

Cotton provides the most abundant natural fiber for the textile *** mature cotton fiber largely consists of secondary cell walls with the highest proportion of cellulose and a small amount of hemicellulose and *** dissect the roles of hemicellulosic polysaccharides during fiber development,four IRREGULAR XYLEM 15(IRX15)genes,GhIRX15-1/-2/-3/-4,were functionally characterized in *** genes encode DUF579 domain-containing proteins,which are homologs of AtIRX15 involved in xylan *** four GhIRX15 genes were predominantly expressed during fiber secondary wall thickening,and the encoded proteins were localized to the Golgi *** GhIRX15 gene could restore the xylan deficient phenotype in the Arabidopsis irx15irx15l double *** of GhIRX15s in cotton resulted in shorter mature fibers with a thinner cell wall and reduced cellulose content as compared to the wild ***,GhIRX15-2 and GhIRX15-4 formed homodimers and *** addition,the GhIRX15s showed physical interaction with glycosyltransferases GhGT43C,GhGT47A and GhGT47B,which are responsible for synthesis of the xylan backbone and reducing end ***,the GhIRX15s can form heterocomplexes with enzymes involved in xylan modification and side chain synthesis,such as GhGUX1/2,GhGXM1/2 and *** findings suggest that GhIRX15s participate in fiber xylan biosynthesis and modulate fiber development via forming large multiprotein complexes.

关键词： Cotton fiber Xylan biosynthesis GhIRX15s Protein-protein interaction Protein complexes

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Genome editing in plants using the TnpB transposase system

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aBIOTECH 2024年第2期5卷 225-230页

作者： Qi Li Yongqiang Wang Zhuoting Hou Hang Zong Xuping Wang Yong EZhang Haoyi Wang Haitao Chen Wen Wang Kang Duan School of Ecology and Environment Northwestern Polytechnical UniversityXi’an 710129China Sanjie Institute of Forage Yangling 712100China Key laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101China State Key laboratory of Stem cell and Reproductive biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China

The widely used clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)system is thought to have evolved from IS200/IS605 *** proteins,encoded by one type of IS200/IS605 transposon,are considered to be the evolutionary ancestors of Cas12 nucleases,which have been engineered to function as RNA-guided DNA endonucleases for genome editing in bacteria and human *** nucleases,which are smaller than Cas nucleases,have been engineered for use in genome editing in animal systems,but the feasibility of this approach in plants remained ***,we obtained stably transformed genome-edited mutants in rice(Oryza sativa)by adapting three recently identified TnpB genome editing vectors,encoding distinct TnpB nucleases(ISAam1,ISDra2,and ISYmu1),for use in plants,demonstrating that the hypercompact TnpB proteins can effectively edit plant ***2 and ISYmu1 precisely edited their target sequences,with no off-target mutations detected,showing that TnpB transposon nucleases are suitable for development into a new genome editing tool for *** modifications improving the genome-editing efficiency of the TnpB system will facilitate plant functional studies and breeding programs.

关键词： ISAam1 ISDra2 ISYmu1 Plant genome editing Rice TnpB transposon endonuclease

The challenge of defining rare genetic programs by single-cell RNA sequencing:Insights from phloem studies

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Molecular Plant 2024年第1期17卷 22-25页

作者： Xiaomin Liu Pawel Roszak YkäHelariutta State Key laboratory of Tree Genetics and Breeding College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China The Sainsbury laboratory University of CambridgeCB21TN CambridgeUK Wood Development Group University of Helsinki00100 HelsinkiFinland Organismal and evolutionary biology Research Programme Faculty of Biological and Environmental Sciences and Viikki Plant Science CentreUniversity of Helsinki00100 HelsinkiFinland

Single-cell RNA sequencing technology provides unprecedented opportunities to capture the spatiotemporal aspects of genetic programs that drive cell *** is a subtype of vascular tissue that is crucial for transporting sugars,proteins,and other organic *** critical role in the redistribution of carbon between photosynthetically active“source”organs(leaves,shoots)and“sink”tissues/organs incapable of fixing carbon(wood,storage organs,root system,etc.)has made phloem development and its transcriptional regulation a prime research focus.

关键词： organs sugar rare

Procyanidin Aand its digestive products inhibit acrylamide-induced IPEC-J2 cell damage: apoptosis and cell cycle arrest

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Food Science and Human Wellness 2024年

作者： Fangfang Yan Si Qin Chengming Wang Wolfram Weckwerth Qun Lu Rui Liu Lab of Food Function and Nutrigenomics， College of Food Science and Technology， Hunan Agricultural University College of Food Science and Technology， Huazhong Agricultural University Key laboratory of Environment Correlative Dietology (Huazhong Agricultural University)， Ministry of Education Molecular Systems biology， Department of Functional and evolutionary Ecology， University of Vienna

Our previous study has demonstrated that procyanidin A1(A1) and its simulated digestive product (D-A1) can prevent acrylamide （ACR）-induced cytotoxicity in small intestine cells. However， the potential mechanism remains poorly understood. In this study， ACR treatment was found to increase the levels of 8-hydroxy-deoxyguanine （8-OHdG） and phosphorated histone H2AX (γH2AX)， two DNA damage markers， thereby resulting in cell cycle arrest in the G2/M phase; whereas both A1and D-A1could prevent the phosphorylation of ataxia telangiectasia mutated （ATM） and checkpoint kinase 2 （Chk2）， and then regulate the expression of G2/M phase-related proteins， finally maintaining normal cell cycle progression. Moreover， A1and D-A1could increase the B cell lymphoma 2 （Bcl-2）/Bcl2-associated X （Bax） ratio and decrease the expression of cleaved caspase-3 and cleaved caspase-9 proteins to alleviate ACR-induced cell apoptosis， which might be related to the inhibition of the mitogen-activated protein kinase （MAPK） pathway. More importantly， A1showed no remarkable variation in inhibitory effect before and after digestion， indicating that it can endure gastrointestinal digestion and may be a promising phytochemical to alleviate ACR-induced intestinal cell damage.

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Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in neuroblastoma

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Frontiers of Medicine 2024年第4期18卷 690-707页

作者： Zhe Nian Dan Wang Hao Wang Wenxu Liu Zhenyi Ma Jie Yan Yanna Cao Jie Li Qiang Zhao Zhe Liu Department of Immunology School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China Zhejiang Key laboratory of Medical Epigenetics Department of Cell BiologySchool of Basic Medical SciencesHangzhou Normal UniversityHangzhou311121China Department of Pediatric Oncology Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin’s Clinical Research Center for CancerTianjin300060China Collaborative Innovation Center for Cancer Personalized Medicine Nanjing Medical UniversityNanjing211166China

Neuroblastoma(NB)is one of the most common childhood *** percent of patients present with widely disseminated clinical signs at diagnosis and exhibit poor ***,the molecular mechanisms triggering NB metastasis remain largely *** this study,we generated a transcriptomic atlas of 15447 NB cells from eight NB samples,including paired samples of primary tumors and bone marrow *** used time-resolved analysis to chart the evolutionary trajectory of NB cells from the primary tumor to the metastases in the same patient and identified a common‘starter’subpopulation that initiates tumor development and ***‘starter’population exhibited high expression levels of multiple cell cycle-related genes,indicating the important role of cell cycle upregulation in NB tumor *** addition,our evolutionary trajectory analysis demonstrated the involvement of partial epithelial-to-mesenchymal transition(p-EMT)along the metastatic route from the primary site to the bone *** study provides insights into the program driving NB metastasis and presents a signature of metastasis-initiating cells as an independent prognostic indicator and potential therapeutic target to inhibit the initiation of NB metastasis.

关键词： single-cell RNA sequencing metastasis neuroblastoma epithelial-to-mesenchymal transition

Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2024年

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity Ocean University of China Marine College Shandong University Zoology Department College of Science King Saud University Department of biology Bradley University laboratory for Marine biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase II and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Bactericidal ability of target acidic phospholipids and phagocytosis of CDC42 GTPase-mediated cytoskeletal rearrangement underlie functional conservation of CXCL12 in vertebrates

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Science China Life Sciences 2024年

作者： Yanqi Zhang Ning Xia Yazhen Hu Wentao Zhu Chunrong Yang Jianguo Su Hubei Hongshan laboratory College of Fisheries Huazhong Agricultural University laboratory for Marine biology and Biotechnology Qingdao Marine Science and Technology Center School of Marine Sciences Ningbo University College of Veterinary Medicine Huazhong Agricultural University

Chemokine CXCL12 plays a crucial role in both direct bactericidal activity and phagocytosis in humans. However, the mechanisms and evolutionary functions of these processes in vertebrates remain largely unknown. In this study, we found that the direct bactericidal activity of CXCL12 is highly conserved across various vertebrate lineages, including Arctic lamprey (Lampetra japonica), Basking shark (Cetorhinus maximus), grass carp (Ctenopharyngodon idella), Western clawed frog (Xenopus tropicalis), Green anole (Anolis carolinensis), chicken(Gallus gallus), and human (Homo sapiens). CXCL12 also has been shown to promote phagocytosis in lower and higher vertebrates. We then employed C. idella CXCL12a (CiCXCL12a) as a model to further investigate its immune functions and underlying mechanisms. CiCXCL12a exerts direct broad-spectrum antibacterial activity by targeting bacterial acidic phospholipids, resulting in bacterial cell membrane perforation, and eventual lysis. Monocytes/macrophages are attracted to the infection sites for phagocytosis through the rapid production of CiCXCL12a during bacterial infection. CiCXCL12a induces CDC42 and CDC42 GTPase activation, which in turn mediates F-actin polymerization and cytoskeletal rearrangement. The interaction between F-actin and Aeromonas hydrophila facilitates bacterial internalization into monocytes/macrophages. Additionally, A. hydrophila is colocalized within early endosomes, late endosomes and lysosomes, ultimately degrading within phagolysosomes. CiCXCL12a also activates PI3K-AKT, JAK-STAT5 and MAPK-ERK signaling pathways. Notably, only the PI3K-AKT signaling pathway inhibits LPS-induced monocyte/macrophage apoptosis. Thus, CiCXCL12a plays key roles in reducing tissue bacterial loads, attenuating organ injury, and decreasing mortality rates. Altogether, our findings elucidate the conserved mechanisms underlying CXCL12-mediated bactericidal activity and phagocytosis, providing novel perspectives into the immune functions

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