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Mitotic motor CENP-E cooperates with PRC1 in temporal control of central spindle assembly

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Journal of Molecular Cell Biology 2020年第8期12卷 654-665页

作者： Xu Liu Leilei Xu Junying Li Phil Y.Yao Wanjuan Wang Hazrat Ismail Haowei Wang Bryce Liao Zhihong Yang Tarsha Ward Ke Ruan Jianchun Zhang Quan Wu Ping He Xia Ding Dongmei Wang Chuanhai Fu Zhen Dou Feng Yan Wenwen Wang Xing Liu Xuebiao Yao MOE Key Laboratory for Cellular Dynamics&Anhui Key Laboratory for Chemical Biology CAS Center for Excellence in Molecular Cell ScienceHefei National Science Center for Physical Sciences at Microscale&University of Science and Technology of ChinaHefei 230027China Department of Physiology Morehouse School of MedicineAtlantaGA 30310USA School of Basic Medical Sciences Beijing University of Chinese MedicineBeijing 100029China Department of Biology Duke University DurhamNC 27708USA institute of proteogenomics Beijing 100029China Harvard Medical School BostonMA 02115USA

Error-free cell division depends on the accurate assembly of the spindle midzone from dynamic spindle microtubules to ensure chromatid segregation during metaphase-anaphase ***,the mechanism underlying the key transition from the mitotic spindle to central spindle before anaphase onset remains *** the prevalence of chromosome instability phenotype in gastric tumorigenesis,we developed a strategy to model context-dependent cell division using a combination of light sheet microscope and 3D gastric *** sheet microscopic image analyses of 3D organoids showed that CENP-E inhibited cells undergoing aberrant metaphase-anaphase transition and exhibiting chromosome segregation errors during *** real-time imaging analyses of 2D cell culture revealed that CENP-E inhibited cells undergoing central spindle splitting and chromosome instability *** biotinylated syntelin as an affinity matrix,we found that CENP-E forms a complex with PRC1 in mitotic *** inhibition of CENP-E in metaphase by syntelin prevented accurate central spindle assembly by perturbing temporal assembly of PRC1 to the ***,CENP-E-mediated PRC1 assembly to the central spindle constitutes a temporal switch to organize dynamic kinetochore microtubules into stable midzone *** findings reveal a previously uncharacterized role of CENP-E in temporal control of central spindle *** CENP-E is absent from yeast,we reasoned that metazoans evolved an elaborate central spindle organization machinery to ensure accurate sister chromatid segregation during anaphase and cytokinesis.

关键词： organoids.cell division central spindle CENP-E syntelin PRC1

Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline

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Molecular Plant 2018年第10期11卷 1292-1307页

作者： Mingkun Yang Xiaohuang Lin Xin Liu Jia Zhang Feng Ge Key Laboratory of Algal Biology Institute of Hydrobiotegy Chinese Academy of Sciences Wuhan 430072 China University of Chinese Academy of Sciences Beijing 100039 China

Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that signifi- cantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the develop- ment of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry （MS）-based proteomics data. Our proteogenomic analysis unambigu- ously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricor- nutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https：//***/projects/gapeproteogeno mic.

关键词： Phaeodactylum tricomutum proteogenomics mass spectrometry genome annotation

A large-scale proteogenomic atlas of pear

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Molecular Plant 2023年第3期16卷 599-615页

作者： Peng Wang Xiao Wu Zebin Shi Shutian Tao Zhe Liu Kaijie Qi Zhihua Xie Xin Qiao Chao Gu Hao Yin Mengyu Cheng Xiaoyu Gu Xueying Liu Chao Tang Peng Cao Shaohang Xu Baojin Zhou Tingting Gui Yangyang Bian Juyou Wu Shaoling Zhang Sanya institute of Nanjing Agricultural University National Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing 210095China institute of Horticulture Zhejiang Academy of Agricutural SciencesHangzhou 310021China Deepxomics Co. LtdShenzhen 518000China College of Life Sciences Northwest UniversityXi'an 710127China

Pear is an important fruit tree that is widely distributed around the *** first pear genome map was reported from our laboratory approximately 10 years *** further study global protein expression patterns in pear,we generated pear proteome data based on 24 major *** tissue-resolved profiles provided evidence of the expression of 17953 *** identified 4294 new coding events and improved the pear genome annotation via the proteogenomic strategy based on 18090 peptide spectra with peptide spectrum matches>*** the eight randomly selected new short coding open reading frames that were expressed in the style,four promoted and one inhibited the growth of pear pollen *** on gene coexpression module analysis,we explored the key genes associated with important agronomic traits,such as stone cell formation in *** network regulating the synthesis of lignin,a major component of stone cells,was reconstructed,and receptor-like kinases were implicated as core factors in this regulatory ***,we constructed the online database PearEXP(http://***)to enable access to the pear proteogenomic *** study provides a paradigm for in-depth proteogenomic studies of woody plants.

关键词： pear Pyrus proteome transcriptome proteogenomics genome annotation database

Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics

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Journal of Pharmaceutical Analysis 2023年第9期13卷 1070-1079页

作者： Xiaoxiao Luo Qirui Bi Dongdong Huang Yun Li Changliang Yao Jianqing Zhang Wenlong Wei Jiayuan Li Zhenwei Li Jingxian Zhang Shen Ji Yurong Wang De-an Guo School of Basic Medicine and Clinical Pharmacy China Pharmaceutical UniversityNanjing211198China Shanghai Research Center for Modernization of Traditional Chinese Medicine National Engineering Research Center of TCM Standardization TechnologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China University of Chinese Academy of Sciences Beijing100049China NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China

Pheretima,also called“earthworms”,is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines(CPMs)in Chinese Pharmacopoeia(2020 edition).However,its zoological origin is unclear,both in the herbal market and *** this study,a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms(restricted search,open search,and de novo)was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima,including Pheretima aspergillum(PA),Pheretima vulgaris(PV),and Metaphire magna(MM).We identified 10,477 natural peptides in the PA,7,451 in PV,and 5,896 in MM *** specific signature peptides were screened and then validated using synthetic peptides;these demonstrated robust specificity for the authentication of PA,PV,and ***,all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills,revealing the inconsistent Pheretima species used in these *** conclusion,our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines,especially non-model species with poorly annotated protein databases.

关键词： Pheretima Natural peptides Label-free peptidomics proteogenomics Animal derived medicine

Quantitative Proteomics Using Isobaric Labeling:A Practical Guide

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Genomics, Proteomics & Bioinformatics 2021年第5期19卷 689-706页

作者： Xiulan Chen Yaping Sun Tingting Zhang Lian Shu Peter Roepstorff Fuquan Yang Key Laboratory of Protein and Peptide Pharmaceuticals&Laboratory of Proteomics Institute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100149China Department of Biochemistry and Molecular Biology University of Southern DenmarkCampusvej 55DK-5230 Odense MDenmark

In the past decade,relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological *** its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions,its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification ***,we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling *** also discuss which precautions should be taken at each step of the isobaric labeling workflow,to obtain reliable quantification results in large-scale quantitative proteomics *** the last section,we discuss the broad applications of the isobaric labeling technology in biological and clinical studies,with an emphasis on thermal proteome profiling and proteogenomics.

关键词： Quantitative proteomics Isobaric labeling iTRAQ TMT Mass spectrometry

Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy

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Marine Life Science & Technology 2023年第1期5卷 102-115页

作者： Xiao-Huang Chen Ming-Kun Yang Yuan-Yuan Li Zhang-Xian Xie Shu-Feng Zhang Mats Töpel Shady A.Amin Lin Lin Feng Ge Da-Zhi Wang State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology Xiamen UniversityXiamen361005China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Sun Yat-Sen UniversityZhuhai519082China Key Laboratory of Algal Biology Institute of HydrobiologyChinese Academy of SciencesWuhan430072China College of Chemistry Chemical Engineering and EnvironmentMinnan Normal UniversityZhangzhou363000China Department of Marine Sciences University of GothenburgBox 46140530GothenburgSweden IVL-Swedish Environmental Research institute Box 5302140014GothenburgSweden New York University Abu Dhabi Saadiyat Island129188Abu DhabiUnited Arab Emirates

Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20%of global carbon fixation and 40%of marine primary productivity;thus,they are essential for global carbon biogeochemical cycling and *** availability of ten diatom genome sequences has facilitated evolutionary,biological and ecological research over the past decade;however,a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still ***,we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic ***-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins,accounting for~81%of the predicted protein-coding *** analysis identified 1235 novel genes,975 revised genes,104 splice variants and 234 single amino acid ***,our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient *** findings substantially improve the genome annotation of *** and provide insights into new biological functions of *** relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.

关键词： Marine diatoms Thalassiosira pseudonana Proteome proteogenomics

Genome annotation of a model diatom Phaeodactylum tricornutum using an integrated proteogenomic pipeline

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Genome annotation of a model diatom Phaeodactylum tricornutu...

iNID： An Analytical Framework for Identifying Network Models for Interplays among Developmental Signaling in Arabidopsis

中国生物化学与分子生物学会2019年全国学术会议暨学会成立四十周年

作者： Mingkun Yang Xiaohuang Lin Xin Liu Jia Zhang Feng Ge Key Laboratory of Algal Biology Institute of Hydrobiology Chinese Academy of Sciences University of Chinese Academy of Sciences

Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high quality genome annotation has still not been obtained for this diatom. Here we develop a systematic approach for conducting an integrated proteogenomic analysis of P. tricornutum using mass spectrometry(MS) based proteomics data. Our proteogenomic analysis unambiguously identifies close to 8300 genes and reveals 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of posttranslational modifications in P. tricornutum. We experimentally confirm a subset of novel events and provide MS-evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscapes of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryotes and so represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https://***/projects/gapeproteogenomic.

关键词： Phaeodactylum tricornutum proteogenomics mass spectrometry(MS) genome annotation

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Molecular Plant 2014年第5期7卷 792-813页

作者： Daeseok Choi Jaemyung Choi Byeongsoo Kang Seungchul Lee Young-hyun Cho Ildoo Hwang Daehee Hwang School of Interdisciplinary Bioscience and Bioengineering POSTECH 790-784 Pohang Republic of Korea Department of Life Sciences POSTECH 790-784 Pohang Republic of Korea Department of New Biology DGIST Daegu 711-873 Republic of Korea Division of Integrative Biosciences and Biotechnologies POSTECH 790-784 Pohang Republic of Korea Center for Systems Biology of Plant Senescence and-Life History Institute for BasicScience DGIST Daegu 711-873 Republic of Korea

Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors （IEFs）. However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling （iNID） in Arabidopsis. iNID provides a comprehensive resource of （1） transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and （2） protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of （1） phytohormones and light and （2） phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid （BR）-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs.

关键词： transcriptome analysis network analysis signal interplays development Arabidopsis.