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The NAC transcription factor LuNAC61 negatively regulates fiber development in flax (Linum usitatissimum L.)

Journal of Integrative Agriculture 2024年第3期23卷 795-805页

作者： Dongwei Xie Jing Li Wan Li Lijun Sun Zhigang Dai Wenzhi Zhou Jianguang Su Jian Sun School of Life Sciences Nantong UniversityNantong 226019China Institute of Crop Cultivation and Tillage Heilongjiang Academy of Agricultural SciencesHarbin 150086China Institute of Bast Fiber Crops Chinese Academy of Agricultural SciencesChangsha 410221China Jiangsu Sanshu Biotechnology Co.Ltd. Nantong 226001China

Flax is a crucial fiber crop that exhibits excellent textile properties and serves as a model plant for investigating phloem fiber development. The regulation of multiple genes significantly influences fiber development, notably involving NAC(NAM, ATAF1/2, CUC2) transcription factors in forming the fiber secondary cell wall(SCW).Overexpression of LuNAC61 in flax resulted in sparse top meristematic zone leaves and significantly reduced stem cellulose content. Scanning electron microscopy and staining observations revealed a significant reduction in fiber bundles. β-Glucuronidase(GUS) staining analysis demonstrated high activity of the LuNAC61 promoter in the bast fibers of the flax stem. Additionally, several members of the LuPLATZ and LuCesA families exhibited significant coexpression with LuNAC61. Subcellular localization indicated the presence of LuPLATZ24 protein in the nucleus and cytoplasm, LuNAC61 protein exclusively in the nucleus, and LuCesA10 in the nucleus and endoplasmic reticulum. LuPLATZ24 positively regulates LuNAC61, whereas LuNAC61 negatively affects LuCesA10, suggesting the involvement of a metabolic network in regulating flax fiber development. In conclusion, this study provides a critical opportunity for a comprehensive and in-depth analysis of the mechanisms governing flax fiber development and the potential use of biotechnology to enhance flax fiber yield.

关键词： flax fiber development Lu NAC61 gene function gene interaction

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ShCTR1 Interacts with ShRBOH1 to Positively Regulate Aerenchyma Formation in Saussurea inversa through ROS Mediation

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Phyton-International Journal of Experimental Botany 2024年第5期93卷 1023-1042页

作者： Wubin Dai Xiuting Ju Guomin Shi Jialei Guo Tao He School of Agriculture and Animal Husbandry Qinghai UniversityXining810016China Key Laboratory of Landscape Plants of Qinghai Province Qinghai UniversityXining810016China School of Ecol-Environmental Engineering Qinghai UniversityXining810016China State Key Laboratory of Plateau Ecology and Agriculture Qinghai UniversityXining810016China

Saussurea inversa is one of the Tibetan medicine with developed aerenchyma.In this study,we investigated the function of the ShCTR1 gene related to the formation of aerenchyma.The study of the occurrence and formation of aerenchyma in S.inversa has certain theoretical significance in revealing the special mechanism of alpine plants adapting to the environment.The results of yeast two-hybrid experiments showed that S.inversa ShCTR1 interacted with the ShRBOH1,which is a key producer of reactive oxygen species(ROS),and it was hypothesized that ShCTR1 regulation of aerenchyma formation in S.inversa mainly mediated by ROS.Aerenchyma induction and inhibition experiments were carried out on S.inversa seedlings,it was shown that ROS inducer(AT)and Ethene(ETH)induced the formation of aerenchyma in S.inversa well in roots,stems,and leaves,and Ethylene inhibitor(1-MCP)and ROS inhibitor DPI(diphenylene iodonium)inhibited the formation of aerenchyma of S.inversa in different degrees,which proved that ROS and ethylene(ET)were positively correlated with the formation of aerenchyma.Meanwhile,AT and ETH well induced the expression of the ShCTR1 gene,and 1-MCP and DPI inhibited the expression of the ShCTR1 gene to different degrees,which proved that ROS and ET were also positively correlated with the expression of the ShCTR1 gene.ShCTR1 was transferred into tobacco(Nicotiana tabacum L.),then repeat the above experiment.It was shown that positive rate and porosity were lowest and highest after DPI and AT treatments,respectively,it showed a positive correlation,which proved that the ShCTR1 gene was positively regulating the formation of aerenchyma.Overexpression of the ShCTR1 gene increased the content of ROS,consequently,the regulation of aerenchyma formation by the ShCTR1 gene is mainly mediated by ROS.It suggested that the formation of aerenchyma in S.inversa was related to hypoxia in the alpine environment,and ShCTR1 interacts with ShRBOH1 to positively regulate the formation of aerenchyma mainly mediated by ROS.

关键词： Saussurea inversa aerenchyma ROS gene function

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Applications of virus-induced gene silencing for identification of gene function in fruit

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Food Quality and Safety 2021年第3期5卷 222-230页

作者：刘港帅李泓利傅达奇 Laboratory of Fruit Biology College of Food Science&Nutritional EngineeringChina Agricultural UniversityBeijingChina

With the development of bioinformatics,it is easy to obtain information and data about thousands of genes,but the determi nation of the functions of these genes depends on methods for rapid and effective functi on al identification.Virus-induced gene sile ncing(VIGS)is a mature method of gene functional identification developed over the last 20 years,which has been widely used in many research fields involving many species.Fruit quality formation is a complex biological process,which is closely related to ripening.Here,we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.

关键词： gene function virus-induced gene silencing fruit viral vector.

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A Method of gene-function Annotation Based on Variable Precision Rough Sets

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Journal of Bionic Engineering 2007年第3期4卷 177-184页

作者： Zhi-li Pei Xiao-hu Shi Meng Niu Xu-ning Tang Li-sha Liu Ying Kong Yan-chun Liang College of Computer Science and Technology Jilin University Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Changchun 130012 P. R. China College of Mathematics and Computer Science Inner Mongolia University for NationalitiesTongliao 028043 P. R. China College of Software Jilin University Changchun 130012 P. R. China Department of Biochemistry and Molecular Biology Institution of Glycobiology Dalian Medical University Dalian 116027 P. R. China

It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.

关键词： gene function annotation variable precision rough set GO BLAST

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genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2023年第12期24卷 1069-1092页

作者： Sakura KARUNARATHNE Esther WALKER Darshan SHARMA Chengdao LI Yong HAN Western Crop genetics Alliance College of ScienceHealthEngineering and EducationMurdoch UniversityMurdochWA6150Australia Department of Primary Industries and Regional Development South PerthWA6151Australia

Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern geneediting platforms. In particular, clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.

关键词： Clustered regularly interspaced short palindromic repeats(CRISPR) gene function Drought genetic improvement Transcription regulation Breeding

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Exploiting plant transcriptomic databases:Resources,tools,and approaches

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Plant Communications 2022年第4期3卷 1-13页

作者： Peng Ken Lim Xinghai Zheng Jong Ching Goh Marek Mutwi School of Biological Sciences Nanyang Technological University60 Nanyang DriveSingapore 637551Singapore

There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plant species.The expression data have great value,as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data.Because gene expression provides essential clues to where and when a gene is active,the data provide powerful tools for predicting gene function,and comparative analyses allow us to study plant evolution from a new perspective.This review describes how we can gain new knowledge from gene expression profiles,expres-sion specificities,co-expression networks,differential gene expression,and experiment correlation.We also introduce and demonstrate databases that provide user-friendly access to these tools.

关键词： gene expression comparative transcriptomics gene function co-express ion differential expr ession databases

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A Nimble Cloning-compatible vector system for high-throughput gene functional analysis in plants

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Plant Communications 2023年第2期4卷 65-76页

作者： Pu Yan Decai Tuo Wentao Shen Haida Deng Peng Zhou Xinzheng Gao Key Laboratory of Biology and genetic Resources of Tropical Crops Sanya Research InstituteInstitute of Tropical Biosciences and BiotechnologyChinese Academy of Tropical Agricultural Science&Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan ProvinceHainan Institute of Tropical Agricultural ResourcesHaikou 571101China Department of Biology Hainan Medical UniversityHaikouChina

Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding.The gene of interest is transferred to the vector by molecular cloning technology.Nimble Cloning is a newly developed molecular cloning method with the advantages of simplicity,efficiency,and standardization.In this study,we developed a"pNC"vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in plants.These vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble Cloning.We demonstrate that the pNC vectors are convenient and effective for the functional analysis of plant genes,including the study of gene ectopic expression,protein subcellular localization,protein-protein interaction,gene silencing(RNAi),virus-induced gene silencing,promoter activity,and CRISPR-Cas9-mediated genome editing.The"pNC"vector system represents a high-throughput toolkit that can facilitate the large-scale analysis of plant functional genomics.

关键词： nimble cloning plant expression vector gene function ectopic expression genome editing

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Decoupling gene functions from knockout effects by evolutionary analyses

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National Science Review 2020年第7期7卷 1169-1180页

作者： Li Liu Mengdi Liu Di Zhang Shanjun Deng Piaopiao Chen Jing Yang Yunhan Xie Xionglei He State Key Laboratory of Biocontrol School of Life Sciences Sun Yat-sen University

Genic functions have long been confounded by pleiotropic mutational effects. To understand such genetic effects, we examine HAP4, a well-studied transcription factor in Saccharomyces cerevisiae that functions by forming a tetramer with HAP2, HAP3 and HAP5. Deletion of HAP4 results in highly pleiotropic gene expression responses, some of which are clustered in related cellular processes(clustered effects) while most are distributed randomly across diverse cellular processes(distributed effects). Strikingly, the distributed effects that account for much of HAP4 pleiotropy tend to be non-heritable in a population,suggesting they have few evolutionary consequences. Indeed, these effects are poorly conserved in closely related yeasts. We further show substantial overlaps of clustered effects, but not distributed effects, among the four genes encoding the HAP2/3/4/5 tetramer. This pattern holds for other biochemically characterized yeast protein complexes or metabolic pathways. Examination of a set of cell morphological traits of the deletion lines yields consistent results. Hence, only some deletion effects of a gene support related biochemical understandings with the rest being often pleiotropic and evolutionarily decoupled from the gene's normal functions. This study suggests a new framework for reverse genetic analysis.

关键词： pleiotropy mutational effects heritability reverse genetics gene function

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Advances in the use of the RNA interference technique in Hemiptera

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Insect Science 2013年第1期20卷 31-39页

作者： Jie Li Xiao-Ping Wang Man-Qun Wang Wei-Hua Ma Hong-Xia Hua Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory Colleage of Plant Science and Technology Huazhong Agricultural University Wuhan China

RNA interference （RNAi） suppresses the expression of target genes by post- transcriptional regulation. Because double-stranded RNA （dsRNA） mediated gene silenc- ing is a conserved mechanism in many eukaryotes, RNAi has become a valuable tool for unveiling gene function in many model insects. Recent research has also shown that RNAi can also be effective in the downregulation of target genes in Hemiptera. In this review, we discuss the use of the RNAi technique in gene functional analysis in hemipterans, highlighting the methods of dsRNA uptake by these insects and discuss the knock-down efficiency of these techniques. Although the RNAi technique has disadvantages, our pri- mary goal here is to determine whether it can be exploited further in the discovery of new ~ene functions, and as a oest control strategy, in some important HemiDteran oests.

关键词： dsRNA gene function Hemiptera pest control RNA interference

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Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins

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Genomics, Proteomics & Bioinformatics 2020年第5期18卷 549-564页

作者： Arup Panda Tamir Tuller Department of Biomedical Engineering Tel Aviv UniversityTel Aviv 69978Israel

Intrinsically disordered proteins(IDPs)are an important class of proteins in all domains of life for their functional importance.However,how nature has shaped the disorder potential of prokaryotic and eukaryotic proteins is still not clearly known.Randomly generated sequences are free of any selective constraints,thus these sequences are commonly used as null models.Considering different types of random protein models,here we seek to understand how the disorder potential of natural eukaryotic and prokaryotic proteins differs from random sequences.Comparing proteomewide disorder content between real and random sequences of 12 model organisms,we noticed that eukaryotic proteins are enriched in disordered regions compared to random sequences,but in prokaryotes such regions are depleted.By analyzing the position-wise disorder profile,we show that there is a generally higher disorder near the N-and C-terminal regions of eukaryotic proteins as compared to the random models;however,either no or a weak such trend was found in prokaryotic proteins.Moreover,here we show that this preference is not caused by the amino acid or nucleotide composition at the respective sites.Instead,these regions were found to be endowed with a higher fraction of protein-protein binding sites,suggesting their functional importance.We discuss several possible explanations for this pattern,such as improving the efficiency of protein-protein interaction,ribosome movement during translation,and post-translational modification.However,further studies are needed to clearly understand the biophysical mechanisms causing the trend.

关键词： Intrinsically disordered protein Comparative genomics gene function Proteome evolution Z-score

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