检索结果-南通市图书馆

Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond

Plant Communications 2023年第1期4卷 304-323页

作者： Andreas S.Richter Thomas Nägele Bernhard Grimm kerstin kaufmann Michael Schroda Dario Leister Tatjana Kleine Physiology of Plant Metabolism Institute for BiosciencesUniversity of RostockAlbert-Einstein-Str.318059 RostockGermany Plant Evolutionary Cell Biology Faculty of BiologyLudwig-Maximilians-Universität München82152 Planegg-MartinsriedGermany Institute of Biology/Plant Physiology Humboldt-Universität zu BerlinPhilippstr.1310115 BerlinGermany Plant Cell and Molecular Biology Institute of BiologyHumboldt-Universität zu BerlinPhilippstr.1310115 BerlinGermany Molecular Biotechnology and Systems Biology TU KaiserslauternKaiserslauternGermany Plant Molecular Biology(Botany) Faculty of BiologyLudwig-Maximilians-Universität München82152 Planegg-MartinsriedGermany

Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling,allowing nuclear gene expression to be adjusted appropriately.Signaling during plastid biogenesis and responses of mature chloroplasts to environmental changes are designated“biogenic”and“operational”controls,respectively.A prominent example of the investigation of biogenic signaling is the screen for gun(genomes uncoupled)mutants.Although the first five gun mutants were identified 30 years ago,the functions of GUN proteins in retrograde signaling remain controversial,and that of GUN1 is hotly disputed.Here,we provide background information and critically discuss recently proposed concepts that address GUN-related signaling and some novel gun mutants.Moreover,considering heme as a candidate in retrograde signaling,we revisit the spatial organization of heme biosynthesis and export from plastids.Although this review focuses on GUN pathways,we also highlight recent progress in the identification and elucidation of chloroplast-derived signals that regulate the acclimation response in green algae and plants.Here,stress-induced accumulation of unfolded/misassembled chloroplast proteins evokes a chloroplast-specific unfolded protein response,which leads to changes in the expression levels of nucleus-encoded chaperones and proteases to restore plastid protein homeostasis.We also address the importance of chloroplast-derived signals for activation of flavonoid biosynthesis leading to production of anthocyanins during stress acclimation through sucrose non-fermenting 1-related protein kinase 1.Finally,a framework for identification and quantification of intercompartmental signaling cascades at the proteomic and metabolomic levels is provided,and we discuss future directions of dissection of organelle-nucleus communication.

关键词： chloroplast chloroplast unfolded protein response genomes uncoupled gun retrograde signaling subcellular proteomes subcellular metabolomes

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants

引用

Molecular Plant 2019年第6期12卷 743-763页

作者： Xuelei Lai Arnaud Stigliani Gilles Vachon Cristel Carles Cezary Smaczniak Chloe Zubieta kerstin kaufmann Francois Parcy CNRS Univ. Grenoble Alpes CEA INRA BIG-LPCV 38000 Grenoble France Department for Plant Cell and Molecular Biology Institute for Biology Humboldt-Universitat zu Berlin Berlin Germany

Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.

关键词： Transcription factor binding site Gene regulation flower development

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

ChIP-Hub: an integrative platform for exploring plant regulome

ChIP-Hub: an integrative platform for exploring plant regulo...

引用

第十九届中国作物学会学术年会

作者： Liang-Yu Fu Zhigui Wu kerstin kaufmann 陈迪俊 State Key Laboratory of Pharmaceutical Biotechnology School of Life Sciences Nanjing University Department for Plant Cell and Molecular Biology Institute for Biology Humboldt-Universit?t zu Berlin

ChIP-seq and complementary assays are powerful methods to measure protein-DNA binding events and chemical modifications of histone proteins at genome-wide level. In recent years, an explosion of regulome data are being generated in plants. However, reuse and comparison of data generated by different laboratories is not straightforward, hampering data integration to generate novel hypotheses for further investigation. Here, we adapt the standard provided by the ENCODE consortium to set up computational pipelines and systematically reanalyze public ChIP-seq(as well as DAP-seq) data in plants. We further present an integrative web-based platform(ChIP-Hub) for exploring the comprehensive reanalysis of more than 8000 ChIP-seq datasets in 42 plant species. The resources are bundled in a well-accessible database that also allows visualization and meta-analyses. This resource will allow experimental biologists from various fields to comprehensively use all available epigenomic information to get novel insights into their specific questions. ChIP-Hub is available at http://***/.

关键词： plants regulome ChIP-seq ChIP-Hub

来源： cnki会议评论

在线全文

cnki会议

学校读者我要写书评

暂无评论

欢迎您,

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

在线全文

在线全文

请选择保存的检索档案：

请选择收藏分类：

通借通还

欢迎您,

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

在线全文

在线全文

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：