我々は、有用な議論のためのMPIMPに理研PSC博士とビョルンUsadelの教授斉藤和季に感謝します。 TTは、アレクサンダー·フォン·フンボルト財団から奨学金によってサポートされています。

<ol>
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L., Ishizaki, K., Nunes-Nesi, A., Larson, T. R., Tohge, T., Krahnert, I., Witt, S., Obata, T., Schauer, N., Graham, I. A., Leaver, C. J., Fernie, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+the+2-Hydroxyglutarate+and+Isovaleryl-CoA+Dehydrogenases+as+Alternative+Electron+Donors+Linking+Lysine+Catabolism+to+the+Electron+Transport+Chain+of+Arabidopsis+Mitochondria.">Identification of the 2-Hydroxyglutarate and Isovaleryl-CoA Dehydrogenases as Alternative Electron Donors Linking Lysine Catabolism to the Electron Transport Chain of Arabidopsis Mitochondria.</a> Plant Cell. 22, 1549-1563 (2010).</li><li>De Vos, R. C. H., Moco, S., Lommen, A., Keurentjes, J. J. B., Bino, R. J., Hall, R. 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I., Shibata, D., Saito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Omics-based+identification+of+Arabidopsis+Myb+transcription+factors+regulating+aliphatic+glucosinolate+biosynthesis.">Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis.</a> Proceedings of the National Academy of Sciences of the United States of America. 104, 6478-6483 (2007).</li><li>Mutwil, M., Klie, S., Tohge, T., Giorgi, F. M., Wilkins, O., Campbell, M. M., Fernie, A. 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M., Bringmann, M., Usadel, B., Persson, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptional+Wiring+of+Cell+Wall-Related+Genes+in+Arabidopsis.">Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis.</a> Molecular Plant. 2, 1015-1024 (2009).</li><li>Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., Ohta, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ATTED-II:+a+database+of+co-expressed+genes+and+cis+elements+for+identifying+co-regulated+gene+groups+in+Arabidopsis.">ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.</a> Nucleic Acids Research. 35, D863-D869 (2007).</li><li>Ogata, Y., Suzuki, H., Sakurai, N., Shibata, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CoP:+a+database+for+characterizing+co-expressed+gene+modules+with+biological+information+in+plants.">CoP: a database for characterizing co-expressed gene modules with biological information in plants.</a> Bioinformatics. 26, 1267-1268 (2010).</li><li>Persson, S., Wei, H. R., Milne, J., Page, G. P., Somerville, C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+genes+required+for+cellulose+synthesis+by+regression+analysis+of+public+microarray+data+sets.">Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets.</a> Proceedings of the National Academy of Sciences of the United States of America. 102, 8633-8638 (2005).</li><li>Tohge, T., Yonekura-Sakakibara, K., Niida, R., Watanabe-Takahashi, A., Saito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phytochemical+genomics+in+Arabidopsis+thaliana:+A+case+study+for+functional+identification+of+flavonoid+biosynthesis+genes.">Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes.</a> Pure and Applied Chemistry. 79, 811-823 (2007).</li><li>Tohge, T., Fernie, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Web-based+resources+for+mass-spectrometry-based+metabolomics:+A+user's+guide.">Web-based resources for mass-spectrometry-based metabolomics: A user's guide.</a> Phytochemistry. 70, 450-456 (2009).</li><li>Tohge, T., Fernie, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combining+genetic+diversity,+informatics+and+metabolomics+to+facilitate+annotation+of+plant+gene+function.">Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function.</a> Nature Protocols. 5, 1210-1227 (2010).</li><li>Tohge, T., Kusano, M., Fukushima, A., Saito, K., Fernie, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptional+and+metabolic+programs+following+exposure+of+plants+to+UV-B+irradiation.">Transcriptional and metabolic programs following exposure of plants to UV-B irradiation.</a> Plant Signal Behav. 6, (2011).</li><li>Tohge, T., Ramos, M. S., Nunes-Nesi, A., Mutwil, M., Giavalisco, P., Steinhauser, D., Schellenberg, M., Willmitzer, L., Persson, S., Martinoia, E., Fernie, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Towards+the+storage+metabolome:+profiling+the+barley+vacuole.">Towards the storage metabolome: profiling the barley vacuole.</a> Plant Physiol. , (2011).</li><li>Yonekura-Sakakibara, K., Tohge, T., Matsuda, F., Nakabayashi, R., Takayama, H., Niida, R., Watanabe-Takahashi, A., Inoue, E., Saito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+flavonol+profiling+and+transcriptome+coexpression+analysis+leading+to+decoding+gene-metabolite+correlations+in+Arabidopsis.">Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis.</a> Plant Cell. 20, 2160-2176 (2008).</li></ol>

利害の衝突が宣言されません。

トランスクリプトミクスとメタボロミクス技術は数年前から使用されていることを考えると、遺伝子アノテーションを支援メタボロミクスのためのデータ統合のプロセスは、一般的に未知の代謝産物を表す新たなピークの同定から始まる。この事実は、代謝物ピークの定量的な分散、またはそれらの生合成に関与すると考え、新規の候補遺伝子を評価することで次のステージへ導く。このプロトコルで説明されて戦略は、しかし、3つの主要な問題i）のピークアノテーションの難しさ、ⅱ）経路予測の複雑性、iii）の遺伝子発現データの遺伝子情報と品質の解像度を持っています。最初の問題に対処するために、ピークの注釈は、MS n分析、参照エキス、変異体の解析、代謝物データベース検索と文献調査からの情報を活用した標準化合物又はコンビナトリアルアプローチの共溶出（ 図2、12）で行われるべきである。 sのecond問題、経路の予測は、正しいピークアノテーションによって得ることができます。代謝産物の蓄積が関連遺伝子の遺伝子発現と相関する必要があるためしかし、組織特異性の代謝物プロファイリングにも、サポートのピーク注釈することができます。したがって、異なる組織や成長条件の組み合わせのプロファイルは、この第二の問題のために役立ちます。遺伝子情報の解決に関する第三の問題は、配列データの進行状況に依存します。ゲノムシーケンスの完了せずにモデル植物の場合には、他のモデル植物でオーソログ遺伝子を用いた共発現解析に便利です。アミノ酸配列の詳細なアラインメントを比較し、系統樹解析では、他の種にモデル生物を接続するためにサポートすることができます。 このプロトコルはすべての代謝に適しています。それも強力な転写Cの対象になる特徴は、中間および二次代謝の解析における最も効率的です。ontrol 1,5,11,16。いくつかの例では、共発現解析は、硫黄同化、β-酸化のための遺伝子、分岐鎖アミノ酸の分解、クロロフィルの破壊、およびリジン異化3、細胞壁代謝10,7とカスケード14に信号を送る光の中で実行することに成功しました。複合ゲノミクス、メタボロミクスと情報を介した遺伝子機能のアノテーションは転写因子の生合成遺伝子と直接レギュレータのためだけでなく、生理的なプロセスや応答を理解するためだけではありません（例えば図3 14を参照）。 モデル植物から作物種にこのアプローチを開発するために、植物種間での代謝の比較はいくつかの一般的な代謝の強力なアプローチです。たとえば、同じ化合物は、異なる植物種で検出された場合、いくつかのオーソログ遺伝子がこれらの植物種で発見され、オーソログ遺伝子を用いてクロス種の共発現解析は、STRONを提供することができますあなたの予測のgをサポートしています。 ：このアプローチは、植物種との共発現解析（6、プラネットでは、このような大麦、米、小麦、大豆などのほか重要な作物で、ポプラ、ウマゴヤシ、シロイヌナズナで行うことができ<a href="http://aranet.mpimp-golm.mpg.de/" target="_blank">http://aranet.mpimp-golm.mpg 。/ DE</a> 、、9、COP： <a href="http://webs2.kazusa.or.jp/kagiana/cop0911/" target="_blank">http://webs2.kazusa.or.jp/kagiana/cop0911/</a> 。の例を参照してください、15）。

<table border="1"><tbody><tr><td> 試薬の名前 </td><td> 会社 </td><td> カタログ番号 </td></tr><tr><td>蒸留水ULC / MS卒業生</td><td> BIOSOLVE </td><td> 23214102 </td></tr><tr><td>アセトニトリル（ACN）ULC / MSグレード</td><td> BIOSOLVE </td><td> 01204102 </td></tr><tr><td>メタノール（MeOH）ULC / MSグレード</td><td> BIOSOLVE </td><td> 13684102 </td></tr><tr><td>液体クロマトグラフィー用ギ酸（HCOOH）ULC / MSグレード</td><td> BIOSOLVE </td><td> 06914131 </td></tr><tr><td>標準化合物</td><td> EXTRASYNTHESE </td><td></td></tr><tr><td>リニアイオントラップ（IT）ESI-MSシステムフィニガン-LTQ </td><td>サーモフィニガン</td><td></td></tr><tr><td> HPLCシステムのサーベイ</td><td>サーモフィニガン</td><td></td></tr><tr><td> C18分析カラムのルナ（2）、2.0ミリメートルの直径150ミリメートルの長さは、100Åの細孔サイズと3mmの球状粒子</td><td> Phenomenex </td><td> 00F-4251-B0 </td></tr><tr><td> Xcaliburソフトウェア</td><td>サーモフィニガン</td><td></td></tr></tbody></table>

annotation of plant gene function via combined genomics, metabolomics and informatics

完全なゲノム配列が利用可能であり、このようなノックアウト変異体、野生のアクセッションおよび高度な繁殖個体群として生物資源の豊富されるモデル植物種の拡大を続ける数を考えると、遺伝子機能アノテーションのための上昇の負担があります。このプロトコルでは、結合された共発現遺伝子解析、メタボロミクスと情報を用いた植物遺伝子の機能注釈が（ 図1）提供されています。このアプローチは、メタボロミクスを介してターゲット化合物の同定と、特定の代謝過程に関与する非注釈付き遺伝子の同定可能性が高い可能にするために既知の関数のターゲット遺伝子を用いての理論に基づいています。戦略が楽であるこれらのどれにもかかわらず、順方向と逆遺伝学のアプローチによって生成された集団では、この情報を適用するための前方に置かれます。当然の結果では、このアプローチは、新しいまたは特定のSEを表す未知のピークを特徴付けるためのアプローチとして使用することができます現在植物の代謝を理解する上で重要な試験である限られた組織、植物種やストレス治療のcondary代謝物。

Watch this Scientific Journal Video about Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics at JoVE.com

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

代謝を介したゲノム、共発現遺伝子の解析と標的化合物の同定の組み合わせは、遺伝子の機能アノテーションを付与します。

複合ゲノミクス、メタボロミクスと情報を介した植物遺伝子の機能注釈

Given the ever expanding number of model plant species for which complete genome sequences are available and the abundance of bio-resources such as ...

annotation-plant-gene-function-via-combined-genomics-metabolomics

Universidad de Cartagena UDEC

Research

JoVE Journal

Biology

19.6K ビュー.  Max-Planck-Institut. 代謝を介したゲノム、共発現遺伝子の解析と標的化合物の同定の組み合わせは、遺伝子の機能アノテーションを付与します。

ビデオ: Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to particular habitats and management practices. This article shows how certain terroir signatures can be detected in the berry metabolome and transcriptome of the grapevine cultivar Corvina using multivariate statistical analysis. The method first requires an appropriate sampling plan. In this case study, a specific clone of the Corvina cultivar was selected to minimize genetic differences, and samples were collected from seven vineyards representing three different macro-zones during three different growing seasons. An untargeted LC-MS metabolomics approach is recommended due to its high sensitivity, accompanied by efficient data processing using MZmine software and a metabolite identification strategy based on fragmentation tree analysis. Comprehensive transcriptome analysis can be achieved using microarrays containing probes covering ~99% of all predicted grapevine genes, allowing the simultaneous analysis of all differentially expressed genes in the context of different terroirs. Finally, multivariate data analysis based on projection methods can be used to overcome the strong vintage-specific effect, allowing the metabolomics and transcriptomics data to be integrated and analyzed in detail to identify informative correlations.

This article describes the application of untargeted metabolomics, transcriptomics and multivariate statistical analysis to grape berry transcripts and metabolites in order to gain insight into the terroir concept, i.e., the impact of the environment on berry quality traits.

グレープベリーメタボロミクスとトランスクリプトを通して解釈テロワールコンセプト

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to ...

遺伝学

mRNA Interactome Capture from Plant Protoplasts

RNA-binding proteins (RBPs) determine the fates of RNAs. They participate in all RNA biogenesis pathways and especially contribute to post-transcriptional gene regulation (PTGR) of messenger RNAs (mRNAs). In the past few years, a number of mRNA-bound proteomes from yeast and mammalian cell lines have been successfully isolated through the use of a novel method called &#34;mRNA interactome capture,&#34; which allows for the identification of mRNA-binding proteins (mRBPs) directly from a physiological environment. The method is composed of in vivo ultraviolet (UV) crosslinking, pull-down and purification of messenger ribonucleoprotein complexes (mRNPs) by oligo(dT) beads, and the subsequent identification of the crosslinked proteins by mass spectrometry (MS). Very recently, by applying the same method, several plant mRNA-bound proteomes have been reported simultaneously from different Arabidopsis tissue sources: etiolated seedlings, leaf tissue, leaf mesophyll protoplasts, and cultured root cells. Here, we present the optimized mRNA interactome capture method for Arabidopsis thaliana leaf mesophyll protoplasts, a cell type that serves as a versatile tool for experiments that include various cellular assays. The conditions for optimal protein yield include the amount of starting tissue and the duration of UV irradiation. In the mRNA-bound proteome obtained from a medium-scale experiment (107 cells), RBPs noted to have RNA-binding capacity were found to be overrepresented, and many novel RBPs were identified. The experiment can be scaled up (109 cells), and the optimized method can be applied to other plant cell types and species to broadly isolate, catalog, and compare mRNA-bound proteomes in plants.

Here, we present an interactome capture protocol applied to Arabidopsis thaliana leaf mesophyll protoplasts. This method critically relies on in vivo UV crosslinking and allows for the isolation and identification of plant mRNA-binding proteins from a physiological environment.

植物のプロトプラストからのmRNAインターアクチベント捕獲

RNA-binding proteins (RBPs) determine the fates of RNAs. They participate in all RNA biogenesis pathways and especially contribute to post-transcriptional ...

生化学

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Recently, a new implementation of a previously described method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and released. The Pathway Association Study Tool (PAST) was developed to address concerns with user-friendliness and slow-running analyses. This new user-friendly tool has been released on Bioconductor and Github. In testing, PAST ran analyses in less than one hour that previously required twenty-four or more hours. In this article, we present the protocol for using either the Shiny application or the R console to run PAST.

By running the Pathway Association Study Tool (PAST), either through the Shiny application or through the R console, researchers can gain a deeper understanding of the biological meaning of their genome-wide association study (GWAS) results by investigating the metabolic pathways involved.

代謝経路情報のGWAS解析のための経路関連研究ツール

Recently, a new implementation of a previously described method for interpreting genome-wide association study (GWAS) data using metabolic pathway ...

A Multi-Omics Extraction Method for the In-Depth Analysis of Synchronized Cultures of the Green Alga Chlamydomonas reinhardtii

Microalgae have been the focus of research for their applications in the production of high value compounds, food and fuel. Moreover, they are valuable photosynthetic models facilitating the understanding of the basic cellular processes. System wide studies enable comprehensive and in-depth understanding of molecular functions of the organisms. However, multiple independent samples and protocols are required for proteomics, lipidomics and metabolomics studies introducing higher error and variability. A robust high throughput extraction method for the simultaneous extraction of chlorophyll, lipids, metabolites, proteins and starch from a single sample of the green alga Chlamydomonas reinhardtii is presented here. The illustrated experimental setup is for Chlamydomonas cultures synchronized using 12 h/12 h light/dark conditions. Samples were collected over a 24 h cell cycle to demonstrate that the metabolites, lipids and starch data obtained using various analytical platforms are well conformed. Furthermore, protein samples collected using the same extraction protocol were used to conduct detailed proteomics analysis to evaluate their quality and reproducibility. Based on the data, it can be inferred that the illustrated method provides a robust and reproducible approach to advance understanding of various biochemical pathways and their functions with greater confidence for both basic and applied research.

A Multi-Omics Extraction Method for the In-Depth Analysis of Synchronized Cultures of the Green Alga Chlamydomonas reinhardtii

System-wide analysis of multiple biomolecules is crucial to gain functional and mechanistic insights into biological processes. Hereby, an extensive protocol is described for high throughput extraction of lipids, metabolites, proteins and starch from a single sample harvested from synchronized Chlamydomonas culture.

緑藻クラミドモナス・ラインハルトティの同期培養物の詳細分析のためのマルチオミクス抽出法

Microalgae have been the focus of research for their applications in the production of high value compounds, food and fuel. Moreover, they are valuable ...

発生生物学

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

The chemical space covered by natural products is immense and widely unrecognized. Therefore, convenient methodologies to perform wide-ranging evaluation of their functions in nature and potential human benefits (e.g., for drug discovery applications) are desired. This protocol describes the combination of genome mining (GM) and molecular networking (MN), two contemporary approaches that match gene cluster-encoded annotations in whole genome sequencing with chemical structure signatures from crude metabolic extracts. This is the first step towards the discovery of new natural entities. These concepts, when applied together, are defined here as MS-guided genome mining. In this method, the main components are previously designated (using MN), and structurally related new candidates are associated with genome sequence annotations (using GM). Combining GM and MN is a profitable strategy to target new molecule backbones or harvest metabolic profiles in order to identify analogues from already known compounds.

A mass spectrometry-guided genome mining protocol is established and described here. It is based on genome sequence information and LC-MS/MS analysis and aims to facilitate identification of molecules from complex microbial and plant extracts.

新しい天然物を発見するためのツールとしての質量分析誘導ゲノムマイニング

The chemical space covered by natural products is immense and widely unrecognized. Therefore, convenient methodologies to perform wide-ranging evaluation ...

化学

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization

Both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) are widely used metabolomics approaches to detect and quantify hundreds of thousands of metabolite features. However, the application of these techniques to a large number of samples is subject to more complex interactions, particularly for genome-wide association studies (GWAS). This protocol describes an optimized metabolic workflow, which combines an efficient and fast sample preparation with the analysis of a large number of samples for legume crop species. This slightly modified extraction method was initially developed for the analysis of plant and animal tissues and is based on extraction in methyl tert-butyl ether: methanol solvent to allow the capture of polar and lipid metabolites. In addition, we provide a step-by-step guide for reducing analytical variations, which are essential for the high-throughput evaluation of metabolic variance in GWAS.

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

In this protocol, we present an optimized workflow, which combines an efficient and fast sample preparation of many samples. In addition, we provide a step-by-step guide to reduce analytical variations for high-throughput evaluation of metabolic GWAS studies.

大規模マルチオミクスゲノムワイド関連研究(Mo-GWAS):サンプル調製と正規化のためのガイドライン

Both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) are widely used metabolomics approaches to detect ...

13C6-グルコース標識を用いた薬用植物における一次臓器の同定

13C6&#45;Glucose Labeling Associated with LC&#45;MS&#58; Identification of Plant Primary Organs in Secondary Metabolite Synthesis

This paper presents a novel and efficient method for certifying primary organs involved in secondary metabolite synthesis. As the most important secondary metabolite in Parispolyphylla var. yunnanensis (Franch.) Hand. -Mzt. (PPY), Paris saponin (PS) has a variety of pharmacological activities and PPY is in increasing demand. This study established leaf, rhizome, and stem-vascular-bundle 13C6-Glucose feeding and non-feeding four treatments to precisely certify the primary organs involved in Paris saponins VII (PS VII) synthesis. By combining liquid chromatography-mass spectrometry (LC-MS), the 13C/12C ratios of leaf, rhizome, stem, and root in different treatments were quickly and accurately calculated, and four types of PS isotopic ion peak(M&#8722;) ratios were found: (M+1) &#8722;/M&#8722;, (M+2) &#8722;/M&#8722;, (M+3) &#8722;/M&#8722; and (M+4) &#8722;/M&#8722;. The results showed that the ratio of 13C/12C in the rhizomes of the stem-vascular-bundle and rhizome feeding treatments was significantly higher than that in the non-feeding treatment. Compared to the non-feeding treatment, the ratio of PS VII molecules (M+2) &#8722;/M&#8722; in the leaves increased significantly under leaf and stem-vascular-bundle feeding treatments. Simultaneously, compared to the non-feeding treatment, the ratio of PS VII molecules (M+2) &#8722;/M&#8722; in the leaves under rhizome treatment showed no significant difference. Furthermore, the ratio of PS VII molecules (M+2) &#8722;/M&#8722; in the stem, root, and rhizome showed no differences among the four treatments. Compared to the non-feeding treatment, the ratio of the Paris saponin II (PS II) molecule (M+2) &#8722;/M&#8722; in leaves under leaf feeding treatment showed no significant difference, and the (M+3) &#8722;/M&#8722; ratio of PS II molecules in leaves under leaf feeding treatment were lower. The data confirmed that the primary organ for the synthesizing of PS VII is the leaves. It lays the foundation for future identification of the primary organs and pathways involved in the synthesis of secondary metabolites in medicinal plants.

著者スポットライト: 13C6-グルコース標識と LC-MS を使用した植物一次臓器プロファイリング(英語)

The developed method of 13C6-Glucose labeling combined with liquid chromatography high-resolution mass spectrometry is versatile and lays the foundation for future studies on the primary organs and pathways involved in the synthesis of secondary metabolites in medicinal plants, as well as the comprehensive utilization of these secondary metabolites.

13名LC-MSに関連するC6-グルコース標識:二次代謝物合成における植物一次器官の同定

This paper presents a novel and efficient method for certifying primary organs involved in secondary metabolite synthesis. As the most important secondary ...

Fluorescence-microscopy Screening and Next-generation Sequencing: Useful Tools for the Identification of Genes Involved in Organelle Integrity

This protocol describes a fluorescence microscope-based screening of Arabidopsis seedlings and describes how to map recessive mutations that alter the subcellular distribution of a specific tagged fluorescent marker in the secretory pathway. Arabidopsis is a powerful biological model for genetic studies because of its genome size, generation time, and conservation of molecular mechanisms among kingdoms. The array genotyping as an approach to map the mutation in alternative to the traditional method based on molecular markers is advantageous because it is relatively faster and may allow the mapping of several mutants in a really short time frame. This method allows the identification of proteins that can influence the integrity of any organelle in plants. Here, as an example, we propose a screen to map genes important for the integrity of the endoplasmic reticulum (ER). Our approach, however, can be easily extended to other plant cell organelles (for example see1,2), and thus represents an important step toward understanding the molecular basis governing other subcellular structures.

A fundamental quest in cell biology is to define the mechanisms that underlie the identity of the organelles that make eukaryotic cells. Here we propose a method to identify the genes responsible for the morphological and functional integrity of plant organelles using fluorescence microscopy and next-generation sequencing tools.

蛍光顕微鏡スクリーニングと次世代シーケンシング：オルガネラの整合性に関与する遺伝子の同定のための有用なツール

This protocol describes a fluorescence microscope-based screening of Arabidopsis seedlings and describes how to map recessive mutations that alter the ...

複合ゲノミクス、メタボロミクスと情報を介した植物遺伝子の機能注釈

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¹³名LC-MSに関連するC₆-グルコース標識:二次代謝物合成における植物一次器官の同定

¹³名LC-MSに関連するC₆-グルコース標識:二次代謝物合成における植物一次器官の同定

¹³名LC-MSに関連するC₆-グルコース標識:二次代謝物合成における植物一次器官の同定

蛍光顕微鏡スクリーニングと次世代シーケンシング：オルガネラの整合性に関与する遺伝子の同定のための有用なツール