{"id":29236,"date":"2009-11-26T19:55:00","date_gmt":"2009-11-26T18:55:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=29236"},"modified":"2024-11-14T16:27:28","modified_gmt":"2024-11-14T15:27:28","slug":"first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected\/","title":{"rendered":"First-ever blueprint of a minimal cell is more complex than expected"},"content":{"rendered":"\n<figure class=\"vf-figure wp-block-image size-large\"><a href=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2009\/11\/mycoplasma-project-yamada-2009.tif\"><img loading=\"lazy\" decoding=\"async\" width=\"1000\" height=\"701\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2009\/11\/mycoplasma-project-yamada-2009.jpg\" alt=\"This image represents the integration of genomic, metabolic, proteomic, structural and cellular information about Mycoplasma pneumoniae in this project: one layer of an Electron Tomography scan of a bottle-shaped M. pneumoniae cell (grey) is overlaid with a schematic representation of this bacterium\u2019s metabolism, where blue indicates interactions between proteins encoded in genes from the same functional unit. Apart from these expected interactions, the scientists found that, surprisingly, many proteins are multifunctional. For instance, there were various unexpected physical interactions (yellow lines) between proteins and the subunits that form the ribosome, which is depicted as an Electron microscopy image (yellow). Image credit: Takuji Yamada \/ EMBL\" class=\"wp-image-29260\" srcset=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2009\/11\/mycoplasma-project-yamada-2009.jpg 1000w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2009\/11\/mycoplasma-project-yamada-2009-300x210.jpg 300w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2009\/11\/mycoplasma-project-yamada-2009-768x538.jpg 768w\" sizes=\"auto, (max-width: 1000px) 100vw, 1000px\" \/><\/a><figcaption class=\"vf-figure__caption\">This image represents the integration of genomic, metabolic, proteomic, structural and cellular information about Mycoplasma pneumoniae in this project: one layer of an Electron Tomography scan of a bottle-shaped M. pneumoniae cell (grey) is overlaid with a schematic representation of this bacterium\u2019s metabolism, where blue indicates interactions between proteins encoded in genes from the same functional unit. Apart from these expected interactions, the scientists found that, surprisingly, many proteins are multifunctional. For instance, there were various unexpected physical interactions (yellow lines) between proteins and the subunits that form the ribosome, which is depicted as an Electron microscopy image (yellow). Image credit: Takuji Yamada  \/ EMBL<br \/>Click on image to download a high resolution image (tiff).<\/figcaption><\/figure>\n\n\n\n<p>What are the bare essentials of life, the indispensable ingredients required to produce a cell that can survive on its own? Can we describe the molecular anatomy of a cell, and understand how an entire organism functions as a system? These are just some of the questions that scientists in a partnership between the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and the Centre de Regulacio Gen\u00f2mica (CRG) in Barcelona, Spain, set out to address. In three papers published back-to-back today in <em>Science<\/em>, they provide the first comprehensive picture of a minimal cell, based on an extensive quantitative study of the biology of the bacterium that causes atypical pneumonia,<em> Mycoplasma pneumoniae<\/em>. The study uncovers fascinating novelties relevant to bacterial biology and shows that even the simplest of cells is more complex than expected.<\/p>\n\n\n\n<p><em>Mycoplasma pneumoniae<\/em> is a small, single-cell bacterium that causes atypical pneumonia in humans. It is also one of the smallest prokaryotes \u2013 organisms whose cells have no nucleus \u2013 that don\u2019t depend on a host\u2019s cellular machinery to reproduce. This is why the six research groups which set out to characterize a minimal cell in a project headed by scientists Peer Bork, Anne-Claude Gavin and Luis Serrano chose <em>M. pneumoniae<\/em> as a model: it is complex enough to survive on its own, but small and, theoretically, simple enough to represent a minimal cell \u2013 and to enable a global analysis.<\/p>\n\n\n\n<p>A network of research groups at EMBL\u2019s Structural and Computational Biology Unit and CRG\u2019s EMBL-CRG Systems Biology Partnership Unit approached the bacterium at three different levels. One team of scientists described <em>M. pneumoniae<\/em>\u2019s transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation. \u201cAt all three levels, we found <em>M. pneumoniae<\/em> was more complex than we expected\u201d, says Luis , co-initiator of the project at EMBL and now head of the Systems Biology Department at CRG.<\/p>\n\n\n\n<p>When studying both its proteome and its metabolome, the scientists found many molecules were multifunctional, with metabolic enzymes catalysing multiple reactions, and other proteins each taking part in more than one protein complex. They also found that <em>M. pneumoniae<\/em> couples biological processes in space and time, with the pieces of cellular machinery involved in two consecutive steps in a biological process often being assembled together.<\/p>\n\n\n\n<p>Remarkably, the regulation of this bacterium\u2019s transcriptome is much more similar to that of eukaryotes \u2013 organisms whose cells have a nucleus \u2013 than previously thought. As in eukaryotes, a large proportion of the transcripts produced from <em>M. pneumoniae<\/em>\u2019s DNA are not translated into proteins. And although its genes are arranged in groups as is typical of bacteria, <em>M. pneumoniae<\/em> doesn\u2019t always transcribe all the genes in a group together, but can selectively express or repress individual genes within each group.Unlike that of other, larger, bacteria, <em>M. pneumoniae<\/em>\u2019s metabolism doesn\u2019t appear to be geared towards multiplying as quickly as possible, perhaps because of its pathogenic lifestyle. Another surprise was the fact that, although it has a very small genome, this bacterium is incredibly flexible and readily adjusts its metabolism to drastic changes in environmental conditions. This adaptability and its underlying regulatory mechanisms mean <em>M. pneumoniae<\/em> has the potential to evolve quickly, and all the above are features it also shares with other, more evolved organisms.<\/p>\n\n\n\n<p>\u201cThe key lies in these shared features\u201d, explains <a href=\"http:\/\/embl.org\/groups\/gavin\/\">Anne-Claude Gavin<\/a>, an EMBL group leader who headed the study of the bacterium\u2019s proteome: \u201cThose are the things that not even the simplest organism can do without and that have remained untouched by millions of years of evolution \u2013 the bare essentials of life\u201d.<\/p>\n\n\n\n<p>This study required a wide range of expertise, to understand<em> M. pneumoniae<\/em>\u2019s molecular organisation at such different scales and integrate all the resulting information into a comprehensive picture of how the whole organism functions as a system \u2013 an approach called systems biology.<\/p>\n\n\n\n<p>\u201cWithin EMBL\u2019s Structural and Computational Biology Unit we have a unique combination of methods, and we pooled them all together for this project\u201d, says <a href=\"https:\/\/www.embl.org\/news\/science\/the-impact-of-drugs-on-gut-microbes-is-greater-than-we-thought\/\">Peer Bork<\/a>, joint head of the unit, co-initiator of the project, and responsible for the computational analysis. \u201cIn partnership with the CRG group we thus could build a complete overall picture based on detailed studies at very different levels.\u201d Bork was recently awarded the Royal Society and Acad\u00e9mie des Sciences Microsoft Award for the advancement of science using computational methods. Serrano was recently awarded a European Research Council Senior grant.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>What are the bare essentials of life, the indispensable ingredients required to produce a cell that can survive on its own? Can we describe the molecular anatomy of a cell, and understand how an entire organism functions as a system? These are just some of the questions that scientists in a&hellip;<\/p>\n","protected":false},"author":16,"featured_media":29260,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[365,883,4684,537,237,17693,991,25,1748,944],"embl_taxonomy":[19179,1806,19081],"class_list":["post-29236","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-bork","tag-cell","tag-crg","tag-dna","tag-gavin","tag-molecular-systems-biology","tag-partnership","tag-partnerships","tag-press-release","tag-structural-and-computational-biology","embl_taxonomy-bork-group","embl_taxonomy-local-alliances","embl_taxonomy-peer-bork"],"acf":{"vf_locked":false,"featured":true,"color":"#007B53","show_featured_image":true,"article_intro":"<h2>EMBL and CRG scientists reveal what a self-sufficient cell can\u2019t do without<\/h2>\n","article_sources":[{"source_description":"<p>K\u00fchner <em>et al<\/em>. Proteome Organization in a Genome-Reduced Bacterium. <em>Science<\/em>, 27 November 2009. DOI: 10.1126\/science.1176343 <\/p>\n","source_link_url":"https:\/\/science.sciencemag.org\/content\/326\/5957\/1235"},{"source_description":"<p>G\u00fcel <em>et al<\/em>. Transcriptome Complexity in a Genome-Reduced Bacterium. <em>Science<\/em>, 27 November 2009.  DOI: 10.1126\/science.1176951 <\/p>\n","source_link_url":"https:\/\/science.sciencemag.org\/content\/326\/5957\/1268"},{"source_description":"<p>Yus <em>et al<\/em>. Impact of Genome Reduction on Bacterial Metabolism and Its Regulation. <em>Science<\/em>, 27 November 2009. DOI: 10.1126\/science.1177263 <\/p>\n","source_link_url":"https:\/\/science.sciencemag.org\/content\/326\/5957\/1263"}],"related_links":false,"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","press_contact":"EMBL Generic","field_target_display":"embl","source_article":false,"field_article_language":{"value":"english","label":"English"},"article_translations":false,"languages":""},"embl_taxonomy_terms":[{"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:\"2ce7bcc2-0091-4187-b6cb-01c5b0f24f68\";}","parents":[],"name":["Bork Group"],"slug":"bork-group","description":"What &gt; Molecular Systems Biology &gt; Bork Group"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"d3050cdd-8276-4b46-ab11-1dd51da085de\";i:2;s:36:\"b318b7fd-4ca1-4bea-9713-c96d6a4cfa20\";}","parents":[],"name":["Local alliances"],"slug":"local-alliances","description":"What &gt; Institutional collaborations &gt; Local alliances"},{"uuid":"a:2:{i:0;s:36:\"4428d1fd-441a-4d6d-a1c5-5dcf5665f213\";i:1;s:36:\"87f160a6-a7bb-4d97-9709-05d4efc38819\";}","parents":[],"name":["Peer Bork"],"slug":"peer-bork","description":"Who &gt; Peer Bork"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>First-ever blueprint of a minimal cell is more complex than expected | EMBL<\/title>\n<meta name=\"description\" content=\"EMBL and CRG scientists reveal what a self-sufficient cell can\u2019t do without.\" \/>\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\/first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"First-ever blueprint of a minimal cell is more complex than expected | EMBL\" \/>\n<meta property=\"og:description\" content=\"EMBL and CRG scientists reveal what a self-sufficient cell can\u2019t do without.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected\/\" \/>\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=\"2009-11-26T18:55:00+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-11-14T15:27:28+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2009\/11\/mycoplasma-project-yamada-2009.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"701\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Guest author(s)\" \/>\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=\"Guest author(s)\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"5 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\/first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected\/\"},\"author\":{\"name\":\"Guest author(s)\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/b4d9366b2ebe691c4015c64c3619205b\"},\"headline\":\"First-ever blueprint of a minimal cell is more complex than expected\",\"datePublished\":\"2009-11-26T18:55:00+00:00\",\"dateModified\":\"2024-11-14T15:27:28+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected\/\"},\"wordCount\":902,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/first-ever-blueprint-of-a-minimal-cell-is-more-complex-than-expected\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2009\/11\/mycoplasma-project-yamada-2009.jpg\",\"keywords\":[\"bork\",\"cell\",\"crg\",\"dna\",\"gavin\",\"molecular systems biology\",\"partnership\",\"partnerships\",\"press release\",\"structural and computational biology\"],\"articleSection\":[\"Science\",\"Science &amp; 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between proteins encoded in genes from the same functional unit. Apart from these expected interactions, the scientists found that, surprisingly, many proteins are multifunctional. For instance, there were various unexpected physical interactions (yellow lines) between proteins and the subunits that form the ribosome, which is depicted as an Electron microscopy image (yellow). 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