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A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants

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Science China(Life Sciences) 2024年第6期67卷 1280-1291页

作者： Yong Zhang Xiaotuo Zhang Qi Tang Lei Li Ting Jiang Yixiao Fang Hong Zhang Jixian Zhai Guodong Ren Binglian Zheng state key laboratory of genetic engineering Institute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China

Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching ***,increasing evidence showed that some lariat RNA could escape *** is known about how and why these lariat RNAs could be *** comparing the atlas of lariat RNAs between the non-dividing cell(mature pollen)and three actively dividing tissues(young shoot apex,young seeds,and young roots),we identified hundreds to thousands of lariat RNA naturally retained in each tissue,and the incidence of lariat RNA retention is much less in shoot apex while much more in *** lariat RNAs derived from the same intron or different lariat RNAs from the same pre-m RNA could be retained in one tissue while degraded in the other *** deciphering lariat RNA sequences,we identified an AG-rich(RAAAAVAAAR)motif and a UC-rich(UCUCUYUCUC)motif for pollen-specific and the other three tissues-retained lariat RNAs,*** of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in ***,hundreds of lariat RNAs harbored mi RNA binding sites,and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of mi RNA target ***,our results uncover that selective retention of lariat RNA is an actively regulatory process,and provide new insights into understanding how lariat RNA metabolism may impact mi RNA activity.

关键词： intron turnover lariat RNA miRNA RNA splicing DBR1

C-terminal frameshift mutations generate viable knockout mutants with developmental defects for three essential protein kinases

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aBIOTECH 2024年第2期5卷 219-224页

作者： Yun Zhang Miao-Miao Cui Run-Nan Ke Yue-Dan Chen Kabin Xie National key laboratory of Crop genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Hubei key laboratory of plant Pathology Huazhong Agricultural UniversityWuhan 430070China

Loss-of-function mutants are fundamental resources for gene function ***,it is difficult to generate viable and heritable knockout mutants for essential ***,we show that targeted editing of the C-terminal sequence of the embryo lethal gene MITOGEN-ACTIVATED protein KINASES 1(OsMPK1)results in weak *** C-terminal-edited osmpk1 mutants displayed severe developmental defects and altered disease resistance but generated tens of viable seeds that inherited the *** the same C-terminal editing approach,we also obtained viable mutants for a wallassociated protein kinase(Os07g0493200)and a leucine-rich repeat receptor-like protein kinase(Os01g0239700),while the null mutations of these genes were *** data suggest that protein kinase activity could be reduced by introducing frameshift mutations adjacent to the C-terminus,which could generate valuable resources for gene function studies and tune protein kinase activity for signaling pathway engineering.

关键词： CRISPR/Cas9 Lethal mutant protein kinases Genome editing C-terminus

Amino acids TORC(talk)to anabolism through uncharged tRNA

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Science China(Life Sciences) 2024年第8期67卷 1775-1776页

作者： Zhen-Zhen Ma Shi-Min Zhao The Obstetrics&Gynecology Hospital of Fudan University State Key Laboratory of Genetic EngineeringShanghai Key Laboratory of Metabolic Remodelling and HealthFudan UniversityShanghai 200090China

Anabolism is essential for proliferation as well as to replenish dysfunctional macromolecules in *** to that both substantial building blocks and energy are required for anabolism,cells must double check whether these prerequisites are met before deciding to start *** acids are building blocks of protein synthesis,their sufficiency in cells is closely monitored by several mechanisms,which all are linked to protein synthesis.

关键词： synthesis. synthesis deciding

IbNIEL-mediated degradation of IbNAC087 regulates jasmonic acid-dependent salt and drought tolerance in sweet potato

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Journal of Integrative plant Biology 2024年第2期66卷 176-195页

作者： Xu Li Zhen Wang Sifan Sun Zhuoru Dai Jun Zhang Wenbin Wang Kui Peng Wenhao Geng Shuanghong Xia Qingchang Liu Hong Zhai Shaopei Gao Ning Zhao Feng Tian Huan Zhang Shaozhen He key laboratory of Sweet Potato Biology and Biotechnology Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis&Utilization and Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy&BiotechnologyChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural University Sanya 572025China state key laboratory of plant Physiology and Biochemistry National Maize Improvement CenterKey Laboratory of Biology and Genetic Improvement of MaizeBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Sweet potato(Ipomoea batatas[L.]Lam.)is a crucial staple and bioenergy *** abiotic stress tolerance holds significant importance in fully utilizing marginal *** processes regulate abiotic stress responses,yet the molecular regulatory mechanisms in sweet potato remain *** this study,a NAC(NAM,ATAF1/2,and CUC2)transcription factor,IbNAC087,was identified,which is commonly upregulated in salt-and drought-tolerant *** of IbNAC087 increased salt and drought tolerance by increasing jasmonic acid(JA)accumulation and activating reactive oxygen species(ROS)scavenging,whereas silencing this gene resulted in opposite ***-rich IbNAC087-OE(overexpression)plants exhibited more stomatal closure than wild-type(WT)and IbNAC087-Ri plants under NaCl,polyethylene glycol,and methyl jasmonate ***087 functions as a nuclear transcriptional activator and directly activates the expression of the key JA biosynthesisrelated genes lipoxygenase(IbLOX)and allene oxide synthase(IbAOS).Moreover,IbNAC087 physically interacted with a RING-type E3 ubiquitin ligase NAC087-INTERACTING E3 LIGASE(IbNIEL),negatively regulating salt and drought tolerance in sweet *** ubiquitinated IbNAC087 to promote 26S proteasome degradation,which weakened its activation on IbLOX and *** findings provide insights into the mechanism underlying the IbNIEL-IbNAC087 module regulation of JA-dependent salt and drought response in sweet potato and provide candidate genes for improving abiotic stress tolerance in crops.

关键词： abiotic tolerance IbNAC087 IbNIEL JA sweet potato

A growth-regulating factor 7(GRF7)-mediated gene regulatory network promotes leaf growth and expansion in sugarcane

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The Crop Journal 2024年第2期12卷 422-431页

作者： Qiaoyu Wang Yihan Li Dadong Lin Xiaoxi Feng Yongjun Wang Tianyou Wang Hongyan Ding Jisen Zhang state key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi key Lab for Saccharum Biology Guangxi UniversityNanning 530005GuangxiChina Center for Genomics and Biotechnology/Fujian Provincial key laboratory of Haixia Applied plant Systems Biology/key laboratory of Saccharum Biology and genetic Breeding/National engineering Research Center for Saccharum Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina

Knowledge of the function of growth-regulating factors(GRFs)in sugarcane(Saccharum officinarum and ***)growth and development could assist breeders in selecting desirable plant ***,limited information about GRFs is available in Saccharum due to their *** this study,22 GRFs were identified in the two species and their conserved domains,gene structures,chromosome location,and synteny were ***7 expression varied among tissues and responded to diurnal ***7-YFP was localized preferentially in the nucleus and appears to act as a transcriptional ***7 positively regulated the size and length of rice leaves,possibly by regulating cell size and plant *** seven potential transcription factors binding to the SsGRF7 promoter in ***,four showed positive expression patterns,and two showed negative expression patterns relative to SsGRF7.

关键词： Expression analysis Growth-regulating factor Leaf development Sugarcane Transcription factors

OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng state key laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus

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mLife 2024年第1期3卷 129-142页

作者： Pingping Wu Wenjuan Mo Tian Tian Kunfeng Song Yilin Lyu Haiyan Ren Jungang Zhou Yao Yu Hong Lu state key laboratory of genetic engineering School of Life SciencesFudan UniversityShanghaiChina Shanghai engineering Research Center of Industrial Microorganisms ShanghaiChina

Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous *** the yield in *** remains a challenge and incorporating large-scale functional modules poses a technical obstacle in *** address these issues,linear and circular yeast artificial chromosomes of ***(KmYACs)were constructed and loaded with disulfide bond formation modules from Pichia pastoris or *** modules contained up to seven genes with a maximum size of 15 *** carried telomeres either from *** or *** were transferred successfully into *** and stably propagated without affecting the normal growth of the host,regardless of the type of telomeres and configurations of *** increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous *** high-density fermentation,the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l,the highest reported level to date in *** and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis,enhanced flux entering the tricarboxylic acid cycle,and a preferred demand for lysine and arginine as features of cells overexpressing heterologous ***,supplementing lysine or arginine further improved the ***,KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental *** the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins,and this strategy may be applied to optimize other microbial cell factories.

关键词： disulfide bond formation expression of heterologous proteins Kluyveromyces marxianus telomere yeast artificial chromosome

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

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plant Diversity 2024年第3期46卷 372-385页

作者： Shanni Cao Xue Zhao Zhuojin Li Ranran Yu Yuqi Li Xinkai Zhou Wenhao Yan Dijun Chen Chao He state key laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China National key laboratory of Crop genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific *** we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis *** atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological *** integration spans a broad spectrum of tissues,including both below-and above-ground *** a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell *** systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene *** together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.

关键词： Arabidopsis Single cell transcriptome Gene regulatory network Data integration plant cell atlas

Revealing the role of CCoAOMT1: fine-tuning bHLH transcription factors for optimal anther development

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Science China(Life Sciences) 2024年第3期67卷 565-578页

作者： Zesen Lai Jianzheng Wang Ying Fu Menghan Wang Hong Ma Shiqing Peng Fang Chang state key laboratory of genetic engineering Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity SciencesInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China School of Tropical Agriculture and Forestry Agriculture-Rural Affairs and Rural RevitalizationHainan UniversityHaikou 570228China key laboratory of Biology and genetic Resources of Tropical Crops Ministry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou 571101China Department of Biology Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPA 16802USA

The tapetum,a crucial innermost layer encompassing male reproductive cells within the anther wall,plays a pivotal role in normal pollen *** transcription factors (TFs) bHLH010/089/091 redundantly facilitate the rapid nuclear accumulation of DYSFUNCTIONAL TAPETUM 1,a gatekeeper TF in the ***,the regulatory mechanisms governing the activity of bHLH010/089/091 remain *** this study,we reveal that caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1) is a negative regulator affecting the nuclear localization and function of bHLH010 and bHLH089,probably through their K259 *** findings underscore that CCoAOMT1 promotes the nuclear export and degradation of bHLH010 and ***,elevated CCoAOMT1 expression resulted in defective pollen development,mirroring the phenotype observed in bhlh010 bhlh089 ***,our investigation revealed that the K259A mutation in the bHLH089 protein disrupted its translocation from the nucleus to the cytosol and impeded its degradation induced by ***,transgenic plants with the probHLH089::bHLH089^(K259A)construct failed to rescue proper pollen development or gene expression in bhlh010 bhlh089 ***,these findings emphasize the need to maintain balanced TF homeostasis for male *** firmly establish CCoAOMT1 as a pivotal regulator that is instrumental in achieving equilibrium between the induction of the tapetum transcriptional network and ensuring appropriate anther development.

关键词： anther development nuclear localization bHLH O-methyltransferase transcription factor homeostasis