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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

Development of a rapid and efficient system for CR genes identification based on hairy root transformation in Brassicaceae

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Horticultural Plant Journal 2024年第4期10卷 1049-1060页

作者： Wenlin Yu Lu Yang Yuanyuan Xiang Rongde Li Xueqing Zhou Longcai Gan Xianyu Xiang Yunyun Zhang Lei Yuan Yanqing Luo Genze Li Youning Wang Yinhua Chen Peng Chen Chunyu Zhang National Key Laboratory of Crop genetic Improvement and College of Plant Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China National Key Laboratory for Tropical Crop Breeding Sanya Nanfan Research InstituteHainan UniversitySanyaHainan 572025China National Agro-Tech Extension and Service Center Beijing 100125China Industrial Crops Research Institute Yunnan Academy of Agricultural SciencesKunmingYunnan 650221China College ofAgronomy NorthwestA&F UniversityYanglingShaanxi712100China

Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by Plasmodiophora brassicae *** of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this *** traditional way of R gene functional validation requires stable transformation that is both time-and *** this study,a rapid and efficient hairy-root transgenic protocol mediated by Agrobacterium rhizogenes was *** transformation positive rate was over 80%in Brassica napus showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable *** system was applicable to different *** varieties and other cruciferous crops including Brassica rapa and Brassica *** particular,two known CR genes,CRA3.7.1 and CRA8.2.4 were used respectively,as example to show that the system works well for CR gene study combined with subsequent *** infection in *** importantly,it works both in over-expression that led to disease resistance,as well as in RNAi which led to disease susceptible ***,this system can be used in batch-wise identification of CR genes,and also offered the possibility of manipulating key genes within the *** genome that could improve our knowledge on host-pathogen interaction.

关键词： Brassicaceae Agrobacterium rhizogenes Hairy root transformation Clubroot gene function

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

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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

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 *** this study,we investigated the function of the ShCTR1 gene related to the formation of *** study of the occurrence and formation of aerenchyma in *** has certain theoretical significance in revealing the special mechanism of alpine plants adapting to the *** results of yeast two-hybrid experiments showed that *** 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 *** mainly mediated by *** induction and inhibition experiments were carried out on *** seedlings,it was shown that ROS inducer(AT)and Ethene(ETH)induced the formation of aerenchyma in *** well in roots,stems,and leaves,and Ethylene inhibitor(1-MCP)and ROS inhibitor DPI(diphenylene iodonium)inhibited the formation of aerenchyma of *** in different degrees,which proved that ROS and ethylene(ET)were positively correlated with the formation of ***,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 ***1 was transferred into tobacco(Nicotiana tabacum L.),then repeat the above *** 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 *** of the ShCTR1 gene increased the content of ROS,consequently,the regulation of aerenchyma formation by the ShCTR1 gene is mainly mediated by *** suggested that the formation of aerenchyma in *** was related to hypoxia in the alpine environment,and ShCTR1 interacts with ShRBOH1 to positively regulate the formation of a

关键词： Saussurea inversa aerenchyma ROS gene function

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

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 *** gene of interest is transferred to the vector by molecular cloning *** Cloning is a newly developed molecular cloning method with the advantages of simplicity,efficiency,and *** this study,we developed a"pNC"vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in *** vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble *** 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 ***"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

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

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 ***,how nature has shaped the disorder potential of prokaryotic and eukaryotic proteins is still not clearly *** generated sequences are free of any selective constraints,thus these sequences are commonly used as null *** different types of random protein models,here we seek to understand how the disorder potential of natural eukaryotic and prokaryotic proteins differs from random *** 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 *** 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 ***,here we show that this preference is not caused by the amino acid or nucleotide composition at the respective ***,these regions were found to be endowed with a higher fraction of protein-protein binding sites,suggesting their functional *** discuss several possible explanations for this pattern,such as improving the efficiency of protein-protein interaction,ribosome movement during translation,and post-translational ***,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

Changing Gly311 to an acidic amino acid in the MATE family protein DTX6 enhances Arabidopsis resistance to the dihydropyridine herbicides

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Molecular Plant 2021年第12期14卷 2115-2125页

作者： Zeyu Lv Mingming Zhao Wenjing Wang Qi Wang Mengqi Huang Chaoqun Li Qichao Lian Jinqiu Xia Ji Qi Chengbin Xiang Huiru Tang Xiaochun Ge State Key Laboratory of genetic Engineering Department of Biochemistry and BiophysicsSchool of Life SciencesFudan UniversityShanghai 200438China School of Life Sciences and Division of Molecular&Cell Biophysics Hefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaHefeiAnhui Province 230027China

In modern agriculture,frequent application of herbicides may induce the evolution of resistance in plants,but the mechanisms underlying herbicide resistance remain largely ***,we report the char-acterization of rtp 1(resistant to paraquat 1),an Arabidopsis mutant showing strong resistance to the widely used herbicides paraquat and *** rtp1 mutant is semi-dominant and carries a point mutation in the gene encoding the multidrug and toxic compound extrusion family protein DTX6,leading to the change of glycine to glutamic acid at residue 311(G311E).The wild-type DTX6 with glycine 311 conferred weak para-quat and diquat resistance when overexpressed,while mutation of glycine 311 to a negatively charged amino acid(G311E or G311D)markedly increased the paraquat and diquat resistance of plants,whereas mutation to a positively charged amino acid(G311R or G311K)compromised the resistance,suggesting that the charge property of residue 311 of DTX6 is critical for the paraquat and diquat resistance of Arabi-dopsis ***6 is localized in the endomembrane trafficking system and may undergo the endosomal sorting to localize to the vacuole and plasma *** with the V-ATPase inhibitor ConA reduced the paraquat resistance of the rtp1 *** release and uptake assays demonstrated that DTX6 is involved in both exocytosis and vacuolar sequestration of ***6 and DTX5 show functional redundancy as the dtx5 dtx6 double mutant but not the dtx6 single mutant plants were more sen-sitive to paraquat and diquat than the wild-type ***,our work reveals a potential mecha-nism for the evolution of herbicide resistance in weeds and provides a promising gene for the manipulation of plant herbicide resistance.

关键词： paraquat diquat point mutation DTX6 gene function multidrug and toxic compound extrusion