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Macroalgal deep genomics illuminate multiple paths to aquatic,photosynthetic multicellularity

Molecular Plant 2024年第5期17卷 747-771页

作者： David R.Nelson Alexandra Mystikou Ashish Jaiswal Cecilia Rad-Menendez Michael J.Preston Frederik De Boever Diana C.El Assal Sarah Daakour Michael W.Lomas Jean-Claude Twizere David H.Green William C.Ratcliff Kourosh Salehi-Ashtiani Division of Science and Math New York University Abu DhabiAbu DhabiUAE Center for genomics and Systems Biology(CGSB) New York University Abu DhabiAbu DhabiUAE Biotechnology Research Center Technology Innovation InstitutePO Box 9639Masdar CityAbu DhabiUAE culture Collection of Algae and Protozoa Scottish Association for Marine ScienceObanScotlandUK National Center for marine Algae and Microbiota Bigelow Laboratory for Ocean SciencesEast BoothbayMEUSA laboratory of Viral Interactomes GIGA InstituteUniversity of LiegeLiegeBelgium School of Biological Sciences Georgia Institute of TechnologyAtlantaGAUSA

Macroalgae are multicellular,aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering,which are directly linked to their multicellularity ***,their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain *** this study,we sequenced 110 macroalgal genomes from diverse climates and phyla,and identified key genomic features that distinguish them from their microalgal *** for cell adhesion,extracellular matrix formation,cell polarity,transport,and cell differentiation distinguish macroalgae from microalgae across all three major phyla,constituting conserved and unique gene sets supporting multicellular *** genes show phylum-and climate-specific expansions that may facilitate niche ***,our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.

关键词： macroalgae multicellularity comparative genomics evolution adhesome endogenous viral elements

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Characteristics of cell motility during cell collision

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Chinese Physics B 2024年第2期33卷 72-77页

作者：马一凯李娜陈唯 State Key laboratory of Surface Physics and Department of Physics Fudan UniversityShanghai 200438China China National Center for Bioinformation Beijing 100101China National genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China

Quantitative examination of cellular motion and intercellullar interactions possesses substantial relevance for both biology and ***,the effects of intercellular interactions during cellular locomotion remain under-explored in experimental *** such,this study seeks to bridge this research gap,adopting Dictyostelium discoideum(Dicty)cells as a paradigm to investigate variations in cellular motion during reciprocal *** aim to attain a comprehensive understanding of how cell interactions influence cell *** observing and processing the motion trajectories of colliding cells under diverse chemical environments,we calculated the diffusion coefficient(D)and the persistence time(τ),using mean square *** analysis of the relationship dynamics between D andτprior to the collisions reveals intricate and non-monotonic alterations in cell movements during *** quantitatively scrutinizing theτtrend,we were able to categorize the cellular responses to interactions under different ***,we ascertained that the effect of cell interactions during collisions in Dicty cells emulates a classical sigmoid *** discovery suggests that cellular responses might comply with a pattern akin to the Weber–Fechner law.

关键词： cell migration random walk cell-cell interaction

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Spatial search weighting information contained in cell velocity distribution

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Chinese Physics B 2024年第2期33卷 522-528页

cell migration plays a significant role in physiological and pathological *** the characteristics of cell movement is crucial for comprehending biological processes such as cell functionality,cell migration,and cell–cell *** of the fundamental characteristics of cell movement is the specific distribution of cell speed,containing valuable information that still requires comprehensive *** article investigates the distribution of mean velocities along cell trajectories,with a focus on optimizing the efficiency of cell food search in the context of the entire *** confirm that the specific velocity distribution in the experiments corresponds to an optimal search efficiency when spatial weighting is *** simulation results indicate that the distribution of average velocity does not align with the optimal search efficiency when employing average spatial ***,when considering the distribution of central spatial weighting,the specific velocity distribution in the experiment is shown to correspond to the optimal search *** simulations reveal that for any given distribution of average velocity,a specific central spatial weighting can be identified among the possible central spatial weighting that aligns with the optimal search ***,our work presents a method for determining the spatial weights embedded in the velocity distribution of cell *** results have provided new avenues for further investigation of significant topics,such as relationship between cell behavior and environmental conditions throughout their evolutionary history,and how cells achieve collective cooperation through cell-cell communication.

关键词： cell migration foraging efficiency random walk spatial search weight

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Combining QTL Mapping and Multi-Omics Identify Candidate Genes for Nutritional Quality Traits during Grain Filling Stage in Maize

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1441-1453页

作者： Pengcheng Li Tianze Zhu Yunyun Wang Shuangyi Yin Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Zefeng Yang Chenwu Xu Jiangsu Key laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhou225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou225009China

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and ***,the genetic basis underlying these nutritional quality traits during grainﬁlling remains poorly *** this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages *** the traits exhibited considerable phenotypic *** the grain-ﬁlling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with signiﬁcant changes observed between 30 and 40 days after *** trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,*** QTLs were consistently detectable across different time *** integrating QTL analysis,glo-bal gene expression proﬁling,and comparative genomics,we identiﬁed 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,*** gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein *** study offers signiﬁcant insights into the genetic architecture of maize kernel nutritional quality and identiﬁes promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.

关键词： Maize protein oil starch QTL mapping candidate genes

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Applications of genetic code expansion technology in eukaryotes

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Protein & cell 2024年第5期15卷 331-363页

作者： Qiao-ru Guo Yu J.Cao State Key laboratory of Chemical Oncogenomic Guangdong Provincial Key Laboratory of Chemical GenomicsPeking University Shenzhen Graduate SchoolShenzhen 518055China Institute of Chemical Biology Shenzhen Bay LaboratoryShenzhen 518132China

Unnatural amino acids(UAAs)have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to *** eukaryotes,genetic code expansion(GCE)enables the incorporation of UAAs and facilitates posttranscriptional modification(PTM),which is not feasible in prokaryotic *** is also a powerful tool for cell or animal imaging,the monitoring of protein interactions in target cells,drug development,and switch ***,there is keen interest in utilizing GCE in eukaryotic *** review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.

关键词： genetic code expansion unnatural amino acid eukaryotes basic research therapeutic applications

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Phase separation of S-RNase promotes self-incompatibility in Petunia hybrida

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Journal of Integrative Plant Biology 2024年第5期66卷 986-1006页

作者： Huayang Tian Hongkui Zhang Huaqiu Huang Yu'e Zhang Yongbiao Xue The State Key laboratory of Plant cell and Chromosome Engineering Institute of Genetics and Developmental Biologythe Chinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 100049China Beiing Institute of genomics Chinese Academy of SciencesNational Center for BioinformationBeijing 100101China

Self-incompatibility(SI)is an intraspecific reproductive barrier widely present in *** SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F-box(SLF)genes found in the Solanaceae,Plantaginaceae,Rosaceae,and *** studies reveal that non-self S-RNase is degraded by the Skip Cullin F-box(SCF)SLF-mediated ubiquitin–proteasome system in a collaborative manner in Petunia,but how self-RNase functions largely remains ***,we show that S-RNases form S-RNase condensates(SRCs)in the self-pollen tube cytoplasm through phase separation and the disruption of SRC formation breaks SI in self-incompatible Petunia *** further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h together with a reduced state of the pollen tube all promote the expansion of SRCs,which then sequester several actin-binding proteins,including the actin polymerization factor PhABRACL,the actin polymerization activity of which is reduced by S-RNase in ***,we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for pollen tube growth *** together,our results demonstrate that phase separation of S-RNase promotes SI response in ***,revealing a new mode of S-RNase action.

关键词： self-incompatibility S-RNase phase separation

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Insufficient TRPM5 Mediates Lipotoxicity-induced Pancreaticβ-cell Dysfunction

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Current Medical Science 2024年第2期44卷 346-354页

作者： Kai-yuan WANG Shi-mei WU Zheng-jian YAO Yun-xia ZHU Xiao HAN Key laboratory of Human Functional genomics of Jiangsu Province Department of Biochemistry and Molecular BiologyNanjing Medical UniversityNanjing 211166China

Objective:While the reduction of transient receptor potential channel subfamily M member 5(TRPM5)has been reported in islet cells from type 2 diabetic(T2D)mouse models,its role in lipotoxicity-induced pancreaticβ-cell dysfunction remains *** study aims to study its ***:Pancreas slices were prepared from mice subjected to a high-fat-diet(HFD)at different time points,and TRPM5 expression in the pancreaticβcells was examined using immunofluorescence ***-stimulated insulin secretion(GSIS)defects caused by lipotoxicity were mimicked by saturated fatty acid palmitate(Palm).Primary mouse islets and mouse insulinoma MIN6 cells were treated with Palm,and the TRPM5 expression was detected using qRT-PCR and Western ***-induced GSIS defects were measured following siRNA-based Trpm5 *** detrimental effects of Palm on primary mouse islets were also assessed after overexpressing Trpm5 via an adenovirus-derived Trpm5(Ad-Trpm5).Results:HFD feeding decreased the mRNA levels and protein expression of TRPM5 in mouse pancreatic *** reduced TRPM5 protein expression in a time-and dose-dependent manner in MIN6 *** also inhibited TRPM5 expression in primary mouse *** of Trpm5 inhibited insulin secretion upon high glucose stimulation but had little effect on insulin *** of Trpm5 reversed Palm-induced GSIS defects and the production of functional maturation molecules unique toβ***:Our findings suggest that lipotoxicity inhibits TRPM5 expression in pancreaticβcells both in vivo and in vitro and,in turn,drivesβ-cell dysfunction.

关键词： type 2 diabetes β-cell dysfunction lipotoxicity TRPM5

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Endomembrane-biased dimerization of ABCG16 and ABCG25 transporters determines their substrate selectivity in ABA-regulated plant growth and stress responses

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Molecular Plant 2024年第3期17卷 478-495页

作者： Yeling Zhou Yuzhu Wang Dong Zhang Jiansheng Liang institute of Plant and Food Science Department of BiologySchool of Life SciencesSouthern University of Science and Technology(SUSTech)Shenzhen 518055China Key laboratory of Molecular Design for Plant cell Factory of Guangdong Higher Education Institutes Southern University of Science and Technology(SUSTech)Shenzhen 518055China jiangsu Key laboratory of Crop Genetics and Physiology/Co-lnnovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009China

ATP-binding cassette(ABC)transporters are integral membrane proteins that have evolved diverse func-tions fulfilled via the transport of various *** Arabidopsis,the G subfamily of ABC proteins is particularly abundant and participates in multiple signaling pathways during plant development and stress *** this study,we revealed that two Arabidopsis ABCG transporters,ABCG16 and ABCG25,engage in ABA-mediated stress responses and early plant growth through endomembrane-specific dimerization-coupled transport of ABA and ABA-glucosyl ester(ABA-GE),*** first revealed that ABCG16 contributes to osmotic stress tolerance via ABA *** specifically,ABCG16 induces cellular ABA efflux in both yeast and plant *** FRET analysis,we showed that ABCG16 forms oblig-atory homodimers for ABA export activity and that the plasma membrane-resident ABCG16 homodimers specifically respond to ABA,undergoing notable conformational ***,we demonstrated that ABCG16 heterodimerizes with ABCG25 at the endoplasmic reticulum(ER)membrane and facilitates the ER entry of ABA-GE in both Arabidopsis and tobacco *** specific responsiveness of the ABCG16-ABCG25 heterodimer to ABA-GE and the superior growth of their double mutant support an inhib-itory role of these twoABCGs in early seedling establishment via regulation of ABA-GE translocation across the ER *** endomembrane-specific analysis of the FRET signals derived from the homo-or heterodimerized ABcG complexes allowed us to link endomembrane-biased dimerization to the transloca-tion of distinct substrates by ABcG transporters,providing a prototypic framework for understanding the omnipotence of ABcG transporters in plant development and stress responses.

关键词： abscisic acid ABCG transporter dimerization endomembrane substrate selectivity

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Auxin-brassinosteroid crosstalk:Regulating rice plant architecture and grain shape

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The Crop Journal 2024年第4期12卷 953-963页

作者： Meidi Wu Jing Zhou Qian Li Dunfan Quan Qingwen Wang Yong Gao Jiangsu Key laboratory of Crop genomics and Molecular Breeding/Key laboratory of Plant Functional genomics of the Ministry of Education/Jiangsu Key laboratory of Crop Genetics and Physiology Yangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of EducationYangzhou UniversityYangzhou 225009JiangsuChina

Rice(Oryza sativa)plant architecture and grain shape,which determine grain quality and yield,are modulatedby auxin and brassinosteroid via regulation of cell elongation and *** review the signaltransduction of these h... 详细信息

关键词： Auxin Brassinosteroid Auxin-brassinosteroid crosstalk Plant architecture Grain shape

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Epigenetic regulators as the foundation for molecular classification of colorectal cancer

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Cancer Biology & Medicine 2024年第7期21卷 547-552页

作者： Zhenyu Liu Xin Zhou Fuchou Tang School of Life Sciences Biomedical Pioneering Innovation Center Department of General Surgery Third Hospital Peking University Beijing Advanced Innovation Center for genomics (ICG) Ministry of Education Key Laboratory of Cell Proliferation and Differentiation Peking University Third Hospital Cancer Center Academy for Advanced Interdisciplinary Studies Peking University

Colorectal cancer （CRC） accounts for approximately 10% of newly diagnosed cancer cases and cancer-related deaths worldwide1. The identification of molecular subtypes of CRCs has significantly advanced treatment stra... 详细信息

关键词： ISLAND METHYLATOR PHENOTYPE MICROSATELLITE INSTABILITY BRAF MUTATION SUBTYPES COLON

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