{"id":34446,"date":"2020-12-09T17:20:00","date_gmt":"2020-12-09T16:20:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=34446"},"modified":"2024-03-22T11:22:23","modified_gmt":"2024-03-22T10:22:23","slug":"heating-proteins-to-understand-how-genes-work","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/","title":{"rendered":"Heating proteins to understand how genes work"},"content":{"rendered":"\n<p>Understanding how genes work and how they interact with one another is a major goal of biology. This poses huge challenges in terms of both methods and the sheer numbers of experiments required. Recent advances have transformed scientists\u2019 ability to map gene function and interactions, and EMBL researchers are developing innovative techniques to measure the activity of thousands of genes at once. A new paper from EMBL\u2019s Savitski team and Typas group is <a href=\"https:\/\/www.nature.com\/articles\/s41586-020-3002-5\" target=\"_blank\" rel=\"noreferrer noopener\">published in <em>Nature<\/em><\/a> this week, describing their work on <em>E. coli<\/em> and how it brings a greater understanding of the way genes function and interact.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"a1\"><strong>Thermal proteome profiling unravels the function of bacterial proteins&nbsp; &nbsp;<\/strong><\/h2>\n\n\n\n<p>Central to this work is thermal proteome profiling (TPP), which was developed by EMBL team leader <a href=\"https:\/\/science.sciencemag.org\/content\/346\/6205\/1255784\">Mikhail Savitski in 2014.<\/a> TPP is based on the principle that exposure to heat causes the structure of proteins to break down \u2013 they\u2019re said to \u2018denature\u2019 and they become insoluble. It\u2019s the same process that causes an egg white to become solid when cooked.<\/p>\n\n\n\n<p>The team used the TPP approach on live <em>E. coli<\/em> bacteria, heating cells to different temperatures to investigate how much of each individual protein in the cell remained soluble at each temperature. The temperature at which a protein denatures can tell researchers about the state of a protein, whether it is active and\/or interacting with, for example, a drug or another protein. This is because the structure of a protein changes when it takes part in any interaction, and different structures of the same protein require different levels of heat before they denature.<\/p>\n\n\n\n<p>The team conducted this experiment on 121 <em>E. coli<\/em> mutants, with each having one gene removed. They profiled these mutants one by one using TPP, and looked at how all the proteins in the cell were expressed and the temperature at which they denatured. This information provided unique insights into the interactions and functions of each protein, including hundreds of less well-understood proteins.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"a2\"><strong>The difficulty of working with essential proteins<\/strong><\/h2>\n\n\n\n<p>One frequently used way to study individual proteins is to delete the genes encoding them and monitor the impact on how a cell behaves. Yet such an approach is impossible to use with essential proteins \u2013 those that a cell relies on for survival \u2013 because their absence would cause the cell to die. The technique used by the Typas and Savitski researchers in this study represents a big step forward in the study of essential proteins. \u201cWe found that although the levels of these proteins did not change across the mutants we studied \u2013 a feature which makes these proteins difficult to study by measuring their expression \u2013 their thermal stability changed quite often,\u201d says Andr\u00e9 Mateus, a postdoc in the Savitski team and Typas group, and first author of the paper. The change in thermal stability of essential proteins is because of changes in their activity.<\/p>\n\n\n\n<p>While this research was conducted on <em>E. coli<\/em> \u2013 arguably the most studied bacterial species \u2013 the researchers hope to apply a similar approach to other organisms that are much less well understood. One such target is the human gut microbiome: the ecosystem made up of all the microorganisms in the gut. This ecosystem is a major focus of EMBL\u2019s future research plans, and is increasingly being linked to multiple aspects of human health and disease \u2013 everything from brain function to how our immune system operates.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"a3\"><strong>EMBL\u2019s unique interdisciplinary approach<\/strong><\/h2>\n\n\n\n<p>The research highlighted in this paper is a great example of the impact that <a href=\"https:\/\/www.embl.de\/training\/postdocs\/08-eipod\/\">EMBL\u2019s Interdisciplinary Postdocs (EIPOD) initiative<\/a> is making. EIPOD arises from EMBL\u2019s commitment to interdisciplinary research, building on the EMBL tradition of highly collaborative study between groups in different research units. Postdoc Andr\u00e9 Mateus sits in both the Typas group and Savitski team, and believes that the EIPOD approach brings great possibilities for research. \u201cBy building on EMBL\u2019s interdisciplinary approach, and enabling work that overlaps separate scientific fields, we can explore a greater range of questions and ultimately gain a much deeper understanding of gene function and interaction. It\u2019s something EMBL really does well.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A new paper from EMBL\u2019s Savitski team and Typas group describes their work on E. coli and how it brings a greater understanding of the way genes function and interact.<\/p>\n","protected":false},"author":98,"featured_media":34448,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[774,749,496,43,704,45,434,669,582],"embl_taxonomy":[9796,19371,19391],"class_list":["post-34446","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-e-coli","tag-eipod","tag-genome-biology","tag-heidelberg","tag-proteins","tag-proteomics","tag-savitski","tag-thermal-proteome-profiling","tag-typas","embl_taxonomy-embl-heidelberg","embl_taxonomy-savitski-team","embl_taxonomy-typas-group"],"acf":{"featured":true,"show_featured_image":false,"color":"#007B53","link_color":"#fff","article_intro":"<p>A technique known as thermal proteome profiling, developed by EMBL team leader Mikhail Savitski, has been used at an unprecedented scale to systematically map gene function<\/p>\n","related_links":[{"link_description":"Savitski Team","link_url":"https:\/\/www.embl.de\/research\/units\/genome_biology\/savitski\/index.html"},{"link_description":"Typas Group","link_url":"https:\/\/www.embl.de\/research\/units\/genome_biology\/typas\/"},{"link_description":"EMBL Interdisciplinary Postdocs (EIPOD) initiative","link_url":"https:\/\/www.embl.de\/training\/postdocs\/08-eipod\/"}],"article_sources":[{"source_description":"<p>Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM. <i>Nature,<\/i> DOI: http:\/\/dx.doi.org\/10.1038\/s41586-020-3002-5<\/p>\n","source_link_url":"https:\/\/doi.org\/10.1038\/s41586-020-3002-5"}],"in_this_article":[{"heading_description":"Thermal proteome profiling unravels the function of bacterial proteins","anchor":"#a1"},{"heading_description":"The difficulty of working with essential proteins","anchor":"#a2"},{"heading_description":"EMBL\u2019s unique interdisciplinary approach","anchor":"#a3"}],"youtube_url":"","mp4_url":"","video_caption":"","press_contact":"None","translations":false,"embl_taxonomy_term_who":false,"embl_taxonomy_term_what":false,"embl_taxonomy_term_where":false,"vf_locked":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"ab46b6d4-71d8-49f8-b2f4-b326d4c8ea4e\";}","parents":[],"name":["EMBL Heidelberg"],"slug":"embl-heidelberg","description":"Where &gt; All EMBL sites &gt; EMBL Heidelberg"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"bd910dd7-0cda-4618-8bfa-d37fbda8438e\";i:2;s:36:\"b75f6f46-874c-40e5-a44f-a2bc5b173198\";}","parents":[],"name":["Savitski Team"],"slug":"savitski-team","description":"What &gt; Molecular Systems Biology &gt; Savitski Team"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"bd910dd7-0cda-4618-8bfa-d37fbda8438e\";i:2;s:36:\"94ddaf2b-18a5-4239-9017-bb23f22f3e9f\";}","parents":[],"name":["Typas Group"],"slug":"typas-group","description":"What &gt; Molecular Systems Biology &gt; Typas Group"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Heating proteins to understand how genes work | EMBL<\/title>\n<meta name=\"description\" content=\"A paper from the Savitski team and Typas group describes their work on E. coli to understand the way genes function and interact.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Heating proteins to understand how genes work | EMBL\" \/>\n<meta property=\"og:description\" content=\"A paper from the Savitski team and Typas group describes their work on E. coli to understand the way genes function and interact.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2020-12-09T16:20:00+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T10:22:23+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2020\/12\/E-Coli_Proteome_Savitski_1000x600px.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"600\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Edward Prior\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@embl\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Edward Prior\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/\"},\"author\":{\"name\":\"Edward Prior\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/24af9e0be5466790b9d7b6e4526d94f6\"},\"headline\":\"Heating proteins to understand how genes work\",\"datePublished\":\"2020-12-09T16:20:00+00:00\",\"dateModified\":\"2024-03-22T10:22:23+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/\"},\"wordCount\":686,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2020\/12\/E-Coli_Proteome_Savitski_1000x600px.jpg\",\"keywords\":[\"e. coli\",\"eipod\",\"genome biology\",\"heidelberg\",\"proteins\",\"proteomics\",\"savitski\",\"thermal proteome profiling\",\"typas\"],\"articleSection\":[\"Science\",\"Science &amp; 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