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ESCRT-Ⅲ component OsSNF7.2 modulates leaf rolling by trafficking and endosomal degradation of auxin biosynthetic enzyme OsYUC8 in rice

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Journal of Integrative plant Biology 2023年第6期65卷 1408-1422页

作者： Liang Zhou Saihua Chen Maohong Cai Song Cui Yulong Ren Xinyue Zhang Tianzhen Liu Chunlei Zhou Xin Jin Limin Zhang Minxi Wu Shuyi Zhang Zhijun Cheng Xin Zhang Cailin Lei Qibing Lin Xiuping Guo Jie Wang Zhichao Zhao Ling Jiang Shanshan Zhu Jianmin Wan State key laboratory for Crop genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095China National key Facility for Crop Gene Resources and genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China 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 Agricultural College of Yangzhou UniversityYangzhou 225009China

The endosomal sorting complex required for transport(ESCRT)is highly conserved in eukaryotic cells and plays an essential role in the biogenesis of multivesicular bodies and cargo degradation to the plant vacuole or *** ESCRT components affect a variety of plant growth and development processes,their impact on leaf development is rarely ***,we found that OsSNF7.2,an ESCRT-Ⅲ component,controls leaf rolling in rice(Oryza sativa).The Ossnf7.2 mutant rolled leaf 17(rl17)has adaxially rolled leaves due to the decreased number and size of the bulliform ***7.2is expressed ubiquitously in all tissues,and its protein is localized in the endosomal ***7.2 homologs,including OsSNF7,OsSNF7.3,and OsSNF7.4,can physically interact with OsSNF7.2,but their single mutation did not result in leaf *** ESCRT complex subunits,namely OsVPS20,OsVPS24,and OsBRO1,also interact with *** assays revealed that OsSNF7.2 interacts with OsYUC8 and aids its vacuolar *** Osyuc8and rl17 Osyuc8 showed rolled leaves,indicating that OsYUC8 and OsSNF7.2 function in the same pathway,conferring leaf *** study reveals a new biological function for the ESCRT-Ⅲcomponents,and provides new insights into the molecular mechanisms underlying leaf rolling.

关键词： bulliform cell leaf rolling OsSNF7.2 OsYUC8 rice(Oryza sativa) vacuolar degradation

A comparative genomic analysis of plant hormone related genes in different species

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Journal of genetics and Genomics 2010年第4期37卷 219-230页

作者： Zhiqiang Jiang Hongwei Guo laboratory of Protein engineering and plant genetic engineering College of Life Sciences Peking University Beijing 100871 China

plant hormones are small molecules that play important roles throughout the life span of a plant, known as auxin, gibberellin, cyto- kinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. genetic and molecular studies in the model organism Arabidopsis thaliana have revealed the individual pathways of various plant hormone responses. In this study, we selected 479 genes that were convincingly associated with various hormone actions based on genetic evidence. By using these 479 genes as queries, a genome-wide search for their orthologues in several species （microorganisms, plants and animals） was performed. Meanwhile, a com- parative analysis was conducted to evaluate their evolutionary relationship. Our analysis revealed that the metabolisms and functions of plant hormones are generally more sophisticated and diversified in higher plant species. In particular, we found that several phytohor- mone receptors and key signaling components were not present in lower plants or animals. Meanwhile, as the genome complexity in- creases, the orthologue genes tend to have more copies and probably gain more diverse functions. Our study attempts to introduce the classification and phylogenic analysis of phytohormone related genes, from metabolism enzymes to receptors and signaling components, in different species.

关键词： comparative genomics Arabidopsis hormone related gene plant hormone orthologue

Resequencing-based QTL mapping for yield and resistance traits reveals great potential of Oryza longistaminata in rice breeding

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作物学报:英文版 2023年第5期11卷 1541-1549页

作者： Weixiong Long Nengwu Li Jie Jin Jie Wang Dong Dan Fengfeng Fan Zhiyong Gao Shaoqing Li State key laboratory of Hybrid Rice Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of AgricultureEngineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life SciencesWuhan UniversityWuhan 430072HubeiChina Hongshan laboratory of Hubei Province Wuhan 430072HubeiChina

As a natural genetic reservoir, wild rice contains many favorable alleles and mutations conferring high yield and resistance to biotic and abiotic stresses. However, there are few reports describing favorable genes or QTL from the AA genome wild rice O. longistaminata, which is characterized by tall and robust habit and long tassels and anthers and shows high potential for use in cultivated rice improvement. We constructed a stable BC_(2)F_(20) backcross inbred line(BIL) population of 152 lines from the cross of 9311 × ***. Some BILs showed large panicles, large seeds, and strong resistance to rice false smut, bacterial leaf blight, rice blast spot, and brown planthopper. Genomic resequencing showed that the 152 BILs covered about 99.6% of the O. longistaminata genome. QTL mapping with 2432 bin markers revealed 13QTL associated with seven yield traits and eight with resistance to brown planthopper and to four diseases. Of these QTL, 12 for grain yield and 11 for pest and disease resistance are novel in Oryza species.A large-panicle NIL1880 line containing QTL qPB8.1 showed a nearly 50% increase in spikelet number and27.5% in grain yield compared to the recurrent parent 9311. These findings support the potential value of O. longistaminata for cultivated rice improvement.

关键词： Oryza longistaminata High yield High disease and pest resistance QTL

The chromatin remodeling complex imitation of switch controls stamen filament elongation by promoting jasmonic acid biosynthesis in Arabidopsis

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Journal of genetics and Genomics 2021年第2期48卷 123-133页

作者： Youshang Zhao Ting Jiang Lei Li Xiaotuo Zhang Tianyu Yang Cuimei Liu Jinfang Chu Binglian Zheng State key laboratory of genetic engineering Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China National Centre for plant Gene Research(Beijing) Innovation Academy for Seed DesignInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100039China

plant reproduction requires the coordinated development of both male and female reproductive *** acid(JA)plays an essential role in stamen filament ***,the mechanism by which the JA biosynthesis genes are regulated to promote stamen elongation remains ***,we show that the chromatin remodeling complex Imitation of Switch(ISWI)promotes stamen filament elongation by regulating JA *** show that AT-Rich Interacting Domain 5(ARID5)interacts with CHR11,CHR17,and RLT1,several known subunits of *** in ARID5 and RLTs caused a reduced seed set due to greatly shortened stamen ***-seq analyses reveal that the expression of key genes responsible for JA biosynthesis is significantly down-regulated in the arid5 and rlt ***,the JA levels are drastically decreased in both arid5 and rlt *** immunoprecipitationquantitative PCR analyses further show that ARID5 is recruited to the chromatin of JA biosynthesis ***,exogenous JA treatments can fully rescue the defects of stamen filament elongation in both arid5 and rlt mutants,leading to the partial recovery of *** results provide a clue how JA biosynthesisis positively regulated by the chromatin remodeling complex ISWI,thereby promoting stamen filament elongation in Arabidopsis.

关键词： ARID Chromatin remodeling ISWI Stamen filaments Jasmonate biosynthesis

An integrated rice panicle phenotyping method based on X-ray and RGB scanning and deep learning

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The Crop Journal 2021年第1期9卷 42-56页

作者： Lejun Yu Jiawei Shi Chenglong Huang Lingfeng Duan Di Wu Debao Fu Changyin Wu Lizhong Xiong Wanneng Yang Qian Liu Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for OptoelectronicsKey Laboratory of Ministry of Education for Biomedical PhotonicsDepartment of Biomedical EngineeringHuazhong University of Science and TechnologyWuhan 430074HubeiChina National key laboratory of Crop genetic Improvement National Center of Plant Gene ResearchAgricultural Bioinformatics Key Laboratory of Hubei ProvinceCollege of EngineeringHuazhong Agricultural UniversityWuhan 430070HubeiChina School of Biomedical engineering Hainan UniversityHaikou 570228HainanChina

Rice panicle phenotyping is required in rice breeding for high yield and grain *** fully evaluate spikelet and kernel traits without threshing and hulling,using X-ray and RGB scanning,we developed an integrated rice panicle phenotyping system and a corresponding image analysis *** compared five methods of counting spikelets and found that Faster R-CNN achieved high accuracy(R~2 of 0.99)and *** R-CNN was also applied to indica and japonica classification and achieved 91%*** proposed integrated panicle phenotyping method offers benefit for rice functional genetics and breeding.

关键词： Rice(O.satiua) Panicle traits RGB imaging X-ray scanning Faster R-CNN

Lysohexaenetides A and B,linear lipopeptides from Lysobacter *** 3655 identified by heterologous expression in Streptomyces

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Chinese Journal of Natural Medicines 2023年第6期21卷 454-458页

作者： XU Qiushuang ZOU Haochen PAN Chen WANG Haoxin SHEN Yuemao LI Yaoyao key laboratory of Chemical Biology of ministry of education School of Pharmaceutical SciencesCheeloo College of MedicineShandong UniversityJinan 250012China State key laboratory of microbial Technology Shandong UniversityQingdao 266237China

Lysobacter harbors a plethora of cryptic biosynthetic gene clusters(BGCs),albeit only a limited number have been analyzed to *** this study,we described the activation of a cryptic polyketide synthase(PKS)/nonribosomal peptide synthetase(NRPS)gene cluster(lsh)in Lysobacter *** 3655 through promoter engineering and heterologous expression in Streptomyces *** a result of this methodology,we were able to isolate two novel linear lipopeptides,lysohexaenetides A(1)and B(2),from the recombinant strain ***,we proposed the biosynthetic pathway for lysohexaenetides and identified LshA as another example of entirely iterative bacterial *** study highlights the potential of heterologous expression systems in uncovering cryptic biosynthetic pathways in Lysobacter genomes,particularly in the absence of genetic manipulation tools.

关键词： Natural products Lysobacter Lipopeptides Heterologous expression

Panicle-3D: A low-cost 3D-modeling method for rice panicles based on deep learning, shape from silhouette, and supervoxel clustering

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The Crop Journal 2022年第5期10卷 1386-1398页

作者： Dan Wu Lejun Yu Junli Ye Ruifang Zhai Lingfeng Duan Lingbo Liu Nai Wu Zedong Geng Jingbo Fu Chenglong Huang Shangbin Chen Qian Liu Wanneng Yang Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronicsand Key Laboratory of Ministry of Education for Biomedical PhotonicsDepartment of Biomedical EngineeringHuazhong University of Science and TechnologyWuhan 430074HubeiChina School of Biomedical engineering Hainan UniversityHaikou 570228HainanChina National key laboratory of Crop genetic Improvement National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan 430070HubeiChina

Self-occlusions are common in rice canopy images and strongly influence the calculation accuracies of panicle traits. Such interference can be largely eliminated if panicles are phenotyped at the 3 D *** on 3 D panicle phenotyping has been limited. Given that existing 3 D modeling techniques do not focus on specified parts of a target object, an efficient method for panicle modeling of large numbers of rice plants is lacking. This paper presents an automatic and nondestructive method for 3 D panicle modeling. The proposed method integrates shoot rice reconstruction with shape from silhouette, 2 D panicle segmentation with a deep convolutional neural network, and 3 D panicle segmentation with ray tracing and supervoxel clustering. A multiview imaging system was built to acquire image sequences of rice canopies with an efficiency of approximately 4 min per rice plant. The execution time of panicle modeling per rice plant using 90 images was approximately 26 min. The outputs of the algorithm for a single rice plant are a shoot rice model, surface shoot rice model, panicle model, and surface panicle model, all represented by a list of spatial coordinates. The efficiency and performance were evaluated and compared with the classical structure-from-motion algorithm. The results demonstrated that the proposed method is well qualified to recover the 3 D shapes of rice panicles from multiview images and is readily adaptable to rice plants of diverse accessions and growth stages. The proposed algorithm is superior to the structure-from-motion method in terms of texture preservation and computational efficiency. The sample images and implementation of the algorithm are available online. This automatic, cost-efficient, and nondestructive method of 3 D panicle modeling may be applied to high-throughput 3 D phenotyping of large rice populations.

关键词： Panicle phenotyping Deep convolutional neural network 3D reconstruction Shape from silhouette Point-cloud segmentation Ray tracing Supervoxel clustering

The F-box protein HAWAIIAN SKIRT is required for mimicry target-induced microRNA degradation in Arabidopsis

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Journal of Integrative plant Biology 2019年第11期61卷 1121-1127页

作者： Jun Mei Ning Jiang Guodong Ren State key laboratory of genetic engineering and ministry of education key laboratory for Biodiversity Science and Ecological engineering School of Life SciencesFudan UniversityShanghai 200438China laboratory of Population&Quantitative genetics Institute of Genetics and BiostatisticsSchool of Life SciencesFudan UniversityShanghai 200438China

Mimicry target-directed micro RNA degradation is widespread and highly conserved among eukaryotes. However, little is known about its mechanism of action. In this letter, by using STTM160(target mimic of mi R160) as a reporter, we show that dysfunction of HAWAIIAN SKIRT(HWS) suppresses the pleiotropic phenotype of STTM160. Small RNA sequencing and Northern blot analyses suggested that HWS only affects a subset of micro RNAs. Intriguingly,we identified a stable coexistence of mi R160/mi R399 and their mimicry targets within the AGO1 complex when HWS is compromised, pointing to a possible role of HWS in the clearance of RNA-induced silencing complexes associated with mimicry target.

关键词： mimicry letter HAWAII

Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology

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Synthetic and Systems Biotechnology 2018年第2期3卷 90-96页

作者： Lihong Jiang Jiarun Zhao Jiazhang Lian Zhinan Xu key laboratory of Biomass Chemical engineering of ministry of education College of Chemical and Biological EngineeringZhejiang UniversityHangzhou 310027China

Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past ***,due to complexity of cellular metabolism,the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic ***,cell-free protein synthesis system(CFPS)has been emerging as an enabling alternative to address challenges in *** review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits(biosensors)to speed up design-build-test(DBT)cycles of metabolic engineering and synthetic biology.

关键词： Cell-free protein synthesis Metabolic pathway optimization genetic circuits Metabolic engineering Synthetic biology