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Protein ubiquitination in plant peroxisomes

Journal of Integrative Plant Biology 2023年第2期65卷 371-380页

作者： delara akhter Yuchan Zhang Jianping Hu Ronghui Pan State Key Laboratory of Rice Biology Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesCollege of Agriculture and Biotechnology&ZJU-Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou 310058/311200China Zhejiang Laboratory Hangzhou 311121China Department of Genetics and Plant Breeding Sylhet Agricultural UniversitySylhet 3100Bangladesh Department of Energy Plant Research Laboratory and Plant Biology Department Michigan State UniversityEast LansingMichiganUSA Department of Plant Biology Michigan State UniversityEast LansingMichiganUSA

Protein ubiquitination regulates diverse cellular processes in eukaryotic organisms,from growth and development to stress *** subjected to ubiquitination can be found in virtually all subcellular locations and organelles,including peroxisomes,singlemembrane and highly dynamic organelles ubiquitous in *** contain metabolic functions essential to plants and animals such as lipid catabolism,detoxification of reactive oxygen species(ROS),biosynthesis of vital hormones and cofactors,and *** peroxisomes possess a complex proteome with functions varying among different tissue types and developmental stages,and during plant response to distinct environmental ***,how these diverse functions are regulated at the post-translational level is poorly understood,especially in *** this review,we summarized current knowledge of the involvement of protein ubiquitination in peroxisome protein import,remodeling,pexophagy,and metabolism,focusing on plants,and referencing discoveries from other eukaryotic systems when *** on previous ubiquitinomics studies,we compiled a list of 56 ubiquitinated Arabidopsis peroxisomal proteins whose functions are associated with all the major plant peroxisomal metabolic *** discovery suggests a broad impact of protein ubiquitination on plant peroxisome functions,therefore substantiating the need to investigate this significant regulatory mechanism in peroxisomes at more depths.

关键词： peroxins peroxisome peroxisome biogenesis peroxisome metabolism pexophagy ubiquitination

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SRG1,Encoding a Kinesin-4 Protein,Is an Important Factor for Determining Grain Shape in Rice

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Rice science 2018年第6期25卷 297-307页

作者： QIN Ran delara akhter YANG Chengcong Ujjal Kumar NATH Jamal ESHAG JIN Xiaoli SHI Chunhai Department of Agronomy Zhejiang University Department of Genetics and Plant Breeding Sylhet Agricultural University Department of Genetics and Plant Breeding Bangladesh Agricultural University

Grain shape is one of the important agronomic traits, which is closely related to the yield of rice.A new rice mutant, named small and round grain(srg1), was isolated from an indica cultivar Zhenong 34 by ethyl methane sulfonate(EMS) mutagenesis. The microscopic analysis showed that the cell length of spikelet in srg1 was decreased compared with that in wild type(WT), which caused the grain length ***, the grains of srg1 were wider than those of WT because of the increased cell layers in spikelet in the lateral direction. Therefore, the inhibition of cell expansion and increased cell proliferation collectively led to the small and round grain. By map-based cloning, the gene SRG1 was located on the short arm of chromosome 9, which encodes a kinesin-4 protein, represented by the gene LOC_Os09 g02650. A single nucleotide polymorphism, occurred in the 16 th exon of SRG1, led to premature translation stop in mutant. The cell cycle-related genes were up-regulated in srg1, which conferred that SRG1 controlled grain width through the cell proliferation. Since the role of SRG1 in regulating grain shape was not clarified well before, it is valuable to explore the mechanism of grain development. This study could, hence, provide a morphogenesis and molecular basis for elucidating the function of SRG1, as well as a new germplasm resource for the further study of grain development.

关键词： small and round grain kinesin-4 protein gene mapping rice

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Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution

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The Crop Journal 2023年第6期11卷 1782-1792页

作者： Yanlei Feng Yukang Wang Hejun Lu Jun Li delara akhter Fang Liu Ting Zhao Xingxing Shen Xiaobo Li James Whelan Tianzhen Zhang Jianping Hu Ronghui Pan College of Agriculture and Biotechnology&ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 310058/311215ZhejiangChina Zhejiang Laboratory Hangzhou 311121ZhejiangChina Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024ZhejiangChina Department of Genetics and Plant Breeding Sylhet Agricultural UniversitySylhet 3100Bangladesh State Key Laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 450000HenanChina Institute of Biology Westlake Institute for Advanced StudyHangzhou 310024ZhejiangChina College of Life Science Zhejiang UniversityHangzhou 310058ZhejiangChina Michigan State University Department of Energy Plant Research Laboratory and Plant Biology DepartmentEast LansingMI 48824USA

Cotton is a major crop that provides the most important renewable textile fibers in the *** of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin,evolution,and cultivation of polyploid *** studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber ***,with only a few mitogenomes assembled in the cotton genus Gossypium,our knowledge about their roles in cotton evolution and speciation is still *** close this gap,here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades(A–G,K,and AD genomes)and 5 cotton relatives using short and long sequencing *** analyses uncovered a high level of mitochondrial gene sequence conservation,abundant sequence repeats and many insertions of foreign sequences,as well as extensive structural variations in cotton *** sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general,while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content,RNA editing,and gene expression ***,we further revealed the specific presence and expression of two novel mitochondrial open reading frames(ORFs)in lint-fiber cotton ***,these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.

关键词： Cotton evolution Cotton phylogeny Lint fiber cotton Mitochondrial genome Mitochondrial genes

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Transport properties of dilute ammonia-noble gas mixtures from new intermolecular potential energy functions

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Chinese Journal of Chemical Engineering 2017年第12期25卷 1727-1734页

作者： Farshid Zargari delara Mohammad-Aghaie Maryam Lotfi Masoume Ghorbanipour Mohammad Mehdi Alavianmehr Omolbanin Shahraki Department of Chemistry Shiraz University of Technology Shiraz Iran Medicinal and Natural Products Chemistry Research Center Shiraz University of Medical Sciences Shiraz Iron Department of Physical Chemistry University of Tabriz Tabriz Iran Zahedan University of Medical Sciences Zahedan Iran

Previously we have determined the dilute mixture transport properties of slightly polar fluorocarbons using the inverted intermolecular potential energies(Ind. Eng. Chem. Res. 45(2006) 9211–9223). In the present paper, the corresponding states correlations for reduced viscosity collision integrals were employed to obtain effective unlike interaction potential models for dilute binary mixtures of highly polar molecule ammonia with noble *** inverted potentials were fitted to the Morse–Spline–van der Waals(MSV), model potential. The method of least-squares fitting was then applied to identify best consistence force parameters for each ammonia-noble gas mixture, taking advantage of experimental viscosities, diffusion coefficients and thermal *** proposed potential models were compared with those obtained from other sources, in order to assess the extent of their *** potentials were later employed to calculate transport properties of the studied mixtures. Then, results were compared with those reported in the literature, which led to the acceptable agreement.

关键词： lntermolecular potential energy Transport properties Inversion pmcedure Mixture Ammonia Noble gas

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Determination of Transport Properties of Dilute Binary Mixtures Containing Carbon Dioxide through Isotropic Pair Potential Energies

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Chinese Journal of Chemical Engineering 2014年第3期22卷 274-286页

作者： delara Mohammad-Aghaie Mohammad Mehdi Papari Amjad Reza Ebrahimi Department of Chemistry Shiraz University of Technology

The present work is concerned with extracting information about intermolecular potential energies of binary mixtures of CO2 with C2H6, C3H8, n-C4Hlo and iso-C4Hlo, by the usage of the inversion method, and then predicting the dilute gas transport properties of the mixtures. Using the inverted pair potential energies, the Chap- man-Enskog version of the kinetic theory was applied to calculate transport properties, except thermal conductivity of mixtures. The calculation of thermal conductivity through the methods of Schreiber et al. and Uribe et al. was discussed. Calculations were performed over a wide temperature range and equimolar composition. Rather accurate correlations for the viscosity coefficients of the mixtures in the temperature range were reproduced from the pre- sent unlike intermolecular potential energies. Our estimated accuracies for the viscosity are within ±2%. Acceptable agreement between the predicted values of the viscosity and thermal conductivity with the literature values demon- strates the predictive power of the inversion scheme. In the case of thermal conductivity our results are in favor of the preference of Uribe et al.＇s method over Schreiber et al.＇s scheme.

关键词： intermolecular potential transport properties carbon dioxide inversion scheme

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基于线粒体基因组数据的裂腹鱼类系统发育研究

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中国水产科学 2022年第6期29卷 781-791页

作者：迪丽娜·茹斯坦木袁晓倩张琪韩洁新疆大学生命科学与技术学院北京师范大学生命科学学院生物多样性与生态工程教育部重点实验室

关于裂腹鱼类(Schizothoracids)的分类系统一直存在学术争议。本研究利用最大似然法和贝叶斯分析法,对Gen Bank数据库中的64种裂腹鱼类的线粒体基因组数据进行分析。建立了13个蛋白质编码基因(PCGs)和13个蛋白质编码基因加2个r RNA基因(... 详细信息

关于裂腹鱼类(Schizothoracids)的分类系统一直存在学术争议。本研究利用最大似然法和贝叶斯分析法,对Gen Bank数据库中的64种裂腹鱼类的线粒体基因组数据进行分析。建立了13个蛋白质编码基因(PCGs)和13个蛋白质编码基因加2个r RNA基因(13 PCGs&2 rDNAs)两个联合基因数据集,分别采用基于核苷酸替代模型的数据多分区和单分区分析策略重建系统发育关系。结果显示,裂腹鱼类“原始”、“特化”和“高度特化”3个等级各自的聚类明确;“原始”等级的裂腹鱼和鲃亚科(Barbinae)鲈鲤属(Percocypris)形成一个单系群,“特化”与“高度特化”等级的裂腹鱼类群形成另一演化支,“高度特化”类群与部分“特化”类群具有最近共同祖先。研究结果不支持裂腹鱼类为一独立亚科,笔者支持将“特化”和“高度特化”类群合并为Schizopygopsini族,将“原始”等级的裂腹鱼和鲈鲤属鱼归为Schizothoracini族。分析中,采用不同的数据集和不同的数据分区分析策略对解决裂腹鱼类的系统发育关系没有显著影响。以地质学证据和线粒体基因演化速率为先验,利用13 PCGs联合基因数据集,采用基于核苷酸替代模型的数据单分区分析策略和贝叶斯方法估算主要类群的最近共祖时间(t MRCA),结果显示裂腹鱼类与鲈鲤属的t MRCA在中新世中期大约13.16 Ma前,现生的“原始”等级裂腹鱼的t MRCA在上新世距今约4.94 Ma,“特化”和“高度特化”等级裂腹鱼的最近共同祖先则是在9.64 Ma前开始分化,“高度特化”等级裂腹鱼起源于约5.40 Ma。由分布区的地理历史推断,裂腹鱼类的起源可能与印度与欧亚板块后碰撞期晚期有关,其各个等级的分化和成种事件与青藏高原的阶段式演化和气候波动密不可分。

关键词：线粒体基因组系统发育裂腹鱼类最近共祖时间

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GenBank中裂腹鱼类CO I基因序列的分子标记有效性

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中国水产科学 2022年第7期29卷 1073-1090页

作者：袁晓倩迪丽娜·茹斯坦木张琪韩洁新疆大学生命科学与技术学院北京师范大学生命科学学院生物多样性与生态工程教育部重点实验室

裂腹鱼类(Schizothoracids)分布有复杂的水系格局,在形态学鉴定时有些鱼种容易混淆。线粒体细胞色素C氧化酶亚基I(COI)基因是动物学研究中常用的物种分子条形码,分析GenBank数据库中裂腹鱼类COI作为分子标记的有效性,可以加深理解和认... 详细信息

裂腹鱼类(Schizothoracids)分布有复杂的水系格局,在形态学鉴定时有些鱼种容易混淆。线粒体细胞色素C氧化酶亚基I(COI)基因是动物学研究中常用的物种分子条形码,分析GenBank数据库中裂腹鱼类COI作为分子标记的有效性,可以加深理解和认识前人用这些数据所做的研究工作,也为今后更合理地使用这些数据提供参考依据。本研究对GenBank数据库中裂腹鱼类CO I基因的分子标记有效性进行分析评估,通过同源性比对、参考序列间遗传分歧的估算和系统发育关系重建等方法,判断GenBank数据库中裂腹鱼类CO I基因序列的同源性、序列所属鱼种鉴定的准确性,以及序列信息对系统发育关系的解析力。通过对下载的1431条序列进行多重比对发现,有3条序列与其他序列存在显著差异,同源性存疑,数据信息经BLAST相似性搜索和核查确认为,以CO I基因的互补链形式提交的序列,比对前应先进行互补链转换。全部序列的比对结果显示,GenBank数据库中裂腹鱼类的CO I基因片段序列均为该基因近5’端至中部的序列。权衡序列的数量和长度后,舍弃较短的35条序列,保留长度为527 bp的1396条序列进行分析,结果共定义了228个单倍型,在有多条序列的鱼种中,普遍存在种内共享单倍型,还有41个单倍型为种间共享。裂腹鱼类COI单倍型的平均p-距离为9.5%,与鱼类的属级水平相当,原始、特化和高度特化类群各自的平均p-距离值更低,体现近期辐射演化的特征,可能与它们随着青藏高原演化成种的历史较短有关。GenBank中一些裂腹鱼类CO I基因序列的鱼种鉴定存在错误,在使用时应先与参考序列对比,或从系统发育分析的角度做出判断。总体来看,COI基因序列能够有力解析裂腹鱼类各演化等级裂腹鱼类之间的亲缘关系,可用于分类和演化的初步分析。结合形态学、生态学、线粒体和核基因的多样性及系统发育关系等进行综合分析,将有助于更准确地界定裂腹鱼种类,同时也为深入探讨杂交和成种过程等问题奠定基础。

关键词：裂腹鱼类 CO I 分子标记有效性 GenBank

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吸烟者支气管形态学的3DCT测量:与健康者比较

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国际医学放射学杂志 2009年第4期32卷 409-409页

作者： M. Montaudon P. Berger M. Lederlin R. Marthan J. M. Tunon-delara F. Laurent 杨秀娟（译）刘筠（校） Unite d＇Imagerie Thoracique Hopital Cariologique 5 avenue de Magellan 33600 Pessac France. 不详

由于支气管倾斜、支气管分支难于识别以及可以测量的支气管分支数有限．CT用于气道病变病人的气道面积的评价受到制约。本研究的目的：①分析CT影像上所有可显示的经自动正交重建的支气管横断面面积；②将吸烟者与非吸烟者支气管形态测... 详细信息

由于支气管倾斜、支气管分支难于识别以及可以测量的支气管分支数有限．CT用于气道病变病人的气道面积的评价受到制约。本研究的目的：①分析CT影像上所有可显示的经自动正交重建的支气管横断面面积；②将吸烟者与非吸烟者支气管形态测量进行比较。将18例男性分为2组，其中9例吸烟者、9例非吸烟者，均行CT扫描与肺功能检测。应用可精确测量CT影像上所有可显示支气管的专业3D软件测量管壁面积（WA）和管腔面积（LA）。

关键词：气道 CT 吸烟者影像分析

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