{"65366":{"#nid":"65366","#data":{"type":"news","title":"Adaptation in Proteins Provides Evidence that Organisms on Early Earth Lived in a Hot, Acidic Environment","body":[{"value":"\u003Cp\u003EA new study reveals that a group of ancient enzymes adapted to substantial changes in ocean temperature and acidity during the last four billion years, providing evidence that life on Early Earth evolved from a much hotter, more acidic environment to the cooler, less acidic global environment that exists today.\u003C\/p\u003E\n\u003Cp\u003EThe study found that a group of ancient enzymes known as thioredoxin were chemically stable at temperatures up to 32 degrees Celsius (58 degrees Fahrenheit) higher than their modern counterparts. The enzymes, which were several billion years old, also showed increased activity at lower pH levels -- which correspond to greater acidity.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022This study shows that a group of ubiquitous proteins operated in a hot, acidic environment during early life, which supports the view that the environment progressively cooled and became more alkaline between four billion and 500 million years ago,\u0022 said Eric Gaucher, an associate professor in the School of Biology at the Georgia Institute of Technology.\n\u003C\/p\u003E\n\u003Cp\u003EThe study, which was published April 3 in the advance online edition of the journal \u003Cem\u003ENature Structural \u0026amp; Molecular Biology\u003C\/em\u003E, was conducted by an international team of researchers from Georgia Tech, Columbia University and the Universidad de Granada in Spain.\n\u003C\/p\u003E\n\u003Cp\u003EMajor funding for this study was provided by two grants from the National Aeronautics and Space Administration to Georgia Tech, a grant from the National Institutes of Health to Columbia University, and a grant from the Spanish Ministry of Science and Innovation to the Universidad de Granada.\n\u003C\/p\u003E\n\u003Cp\u003EUsing a technique called ancestral sequence reconstruction, Gaucher and Georgia Tech biology graduate student Zi-Ming Zhao reconstructed seven ancient thioredoxin enzymes from the three domains of life -- archaea, bacteria and eukaryote -- that date back between one and four billion years. \n\u003C\/p\u003E\n\u003Cp\u003ETo resurrect these enzymes, which are found in nearly all known modern organisms and are essential for life in mammals, the researchers first constructed a family tree of the more than 200 thioredoxin sequences available from the three domains of life. Then they reconstructed the sequences of the ancestral thioredoxin enzymes using statistical methods based on maximum likelihood. Finally, they synthesized the genes that encoded these sequences, expressed the ancient proteins in the cells of modern Escherichia coli bacteria and then purified the proteins.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022By resurrecting proteins, we are able to gather valuable information about the adaptation of extinct forms of life to climatic, ecological and physiological alterations that cannot be uncovered through fossil record examinations,\u0022 said Gaucher.\n\u003C\/p\u003E\n\u003Cp\u003EThe reconstructed enzymes from the Precambrian period -- which ended about 542 million years ago -- were used to examine how environmental conditions, including pH and temperature, affected the evolution of the enzymes and their chemical mechanisms.\u003C\/p\u003E\n\u003Cp\u003E\u0022Given the ancient origin of the reconstructed thioredoxin enzymes, with some of them predating the buildup of atmospheric oxygen, we thought their catalytic chemistry would be simple, but we found that thioredoxin enzymes use a complex mixture of chemical mechanisms that increases their efficiency over the simpler compounds that were available in early geochemistry,\u0022 said Julio Fern\u00e1ndez, a professor in the Department of Biological Sciences professor at Columbia University.\n\u003C\/p\u003E\n\u003Cp\u003EFern\u00e1ndez led a team that included Columbia University postdoctoral researchers Raul Perez-Jimenez, Jorge Alegre-Cebollada and Sergi Garcia-Manyes, and graduate student Pallav Kosuri in using an assay based on single molecule force spectroscopy to measure the activity level of the thioredoxin enzymes under different pH levels. \n\u003C\/p\u003E\n\u003Cp\u003EFor their experiments, the researchers used an atomic force microscope to pick up and stretch an engineered protein in a solution containing thioredoxin. They first applied a constant force to the protein, causing it to rapidly unfold and expose its disulfide bonds to the thioredoxin enzymes. The rate at which a thioredoxin enzyme snipped the disulfide bonds determined the enzyme\u0027s level of efficiency. \n\u003C\/p\u003E\n\u003Cp\u003EThe study results showed that the three oldest thioredoxin enzymes -- those thought to have inhabited Earth 4.2 to 3.5 billion years ago -- were able to operate in lower pH environments than the modern thioredoxin enzymes.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022Our analysis indicates that ancient thioredoxin enzymes were well adapted to function under acidic conditions and that they maintained their high level of activity as they evolved in more alkaline environments,\u0022 said Fern\u00e1ndez.\n\u003C\/p\u003E\n\u003Cp\u003ETo measure the temperature range in which the enzymes operated, professor Jose Sanchez-Ruiz and graduate student Alvaro Ingl\u00e9s-Prieto from the Departamento de Qu\u00edmica-F\u00edsica at the Universidad de Granada in Spain used a technique called differential scanning calorimetry. This method measures the stability of enzymes by heating the enzymes at a constant rate and measuring the heat change associated with their unfolding.\n\u003C\/p\u003E\n\u003Cp\u003EThe researchers found that the ancient proteins were stable at temperatures up to 32 degrees Celsius higher than the modern thioredoxins. The experiments showed that the enzymes exhibited higher temperature stability the older they were. The results provide evidence that ancestral thioredoxins adapted to the cooling trend of ancient oceans, as inferred from geological records.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022Our results confirm that life has the remarkable ability to adapt to a wide range of historical environmental conditions; and by extension, life will undoubtedly adapt to future environmental changes, albeit at some cost to many species,\u0022 said Gaucher.\n\u003C\/p\u003E\n\u003Cp\u003EThis study also showed that the experimental resurrection of ancient proteins together with the sensitivity of single-molecule techniques can be a powerful tool for understanding the origin and evolution of life on Earth. \n\u003C\/p\u003E\n\u003Cp\u003EThe researchers are currently using this strategy to assess other enzymes to get a clearer picture of what life was like on Early Earth. They are also applying these tools to the field of biotechnology, where enzymes play important roles in many industrial processes. \n\u003C\/p\u003E\n\u003Cp\u003E\u0022The functions and characteristics we observed in the ancestral enzymes show that our techniques can be implemented to generate improved enzymes for a wide range of applications,\u0022 added Perez-Jimenez.\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cem\u003EThis project was supported by the National Aeronautics and Space Administration (NASA) (Award Nos. NNX08AO12G and NNA09DA78A). The content is solely the responsibility of the principal investigator and does not necessarily represent the official view of NASA.\u003C\/em\u003E\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EResearch News \u0026amp; Publications Office\u003Cbr \/\u003E\nGeorgia Institute of Technology\u003Cbr \/\u003E\n75 Fifth Street, N.W., Suite 314\u003Cbr \/\u003E\nAtlanta, Georgia  30308  USA\u003C\/strong\u003E\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EMedia Relations Contacts:\u003C\/strong\u003E Abby Robinson (abby@innovate.gatech.edu; 404-385-3364) or John Toon (jtoon@gatech.edu; 404-894-6986)\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EWriter:\u003C\/strong\u003E Abby Robinson\u003C\/p\u003E\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EA new study reveals that a group of ancient enzymes adapted to substantial changes in ocean temperature and acidity during the last four billion years, providing evidence that life on Early Earth evolved from a much hotter, more acidic environment.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"Protein adaptation provides evidence for hot, acidic Early Earth."}],"uid":"27206","created_gmt":"2011-04-04 00:00:00","changed_gmt":"2016-10-08 03:08:18","author":"Abby Vogel Robinson","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2011-04-04T00:00:00-04:00","iso_date":"2011-04-04T00:00:00-04:00","tz":"America\/New_York"},"extras":[],"hg_media":{"65367":{"id":"65367","type":"image","title":"Eric Gaucher and Zi-Ming Zhao","body":null,"created":"1449176831","gmt_created":"2015-12-03 21:07:11","changed":"1475894577","gmt_changed":"2016-10-08 02:42:57","alt":"Eric Gaucher and Zi-Ming Zhao","file":{"fid":"192226","name":"twj48150.jpg","image_path":"\/sites\/default\/files\/images\/twj48150_0.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/twj48150_0.jpg","mime":"image\/jpeg","size":1357353,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/twj48150_0.jpg?itok=UWn3ridx"}},"65368":{"id":"65368","type":"image","title":"Eric Gaucher","body":null,"created":"1449176831","gmt_created":"2015-12-03 21:07:11","changed":"1475894577","gmt_changed":"2016-10-08 02:42:57","alt":"Eric Gaucher","file":{"fid":"192227","name":"tdy48150.jpg","image_path":"\/sites\/default\/files\/images\/tdy48150_0.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/tdy48150_0.jpg","mime":"image\/jpeg","size":1043179,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/tdy48150_0.jpg?itok=IAAwLQAG"}}},"media_ids":["65367","65368"],"related_links":[{"url":"http:\/\/dx.doi.org\/10.1038\/nsmb.2020","title":"Nature Structural \u0026 Molecular Biology paper"},{"url":"http:\/\/www.biology.gatech.edu\/people\/eric-gaucher","title":"Eric Gaucher"},{"url":"http:\/\/www.biology.gatech.edu\/","title":"School of Biology"}],"groups":[{"id":"1188","name":"Research Horizons"}],"categories":[{"id":"154","name":"Environment"},{"id":"146","name":"Life Sciences and Biology"},{"id":"135","name":"Research"}],"keywords":[{"id":"12665","name":"Acidity"},{"id":"12662","name":"Ancestral"},{"id":"12663","name":"ancestral proteins"},{"id":"12657","name":"ancient protein"},{"id":"4896","name":"College of Sciences"},{"id":"12661","name":"Early Earth"},{"id":"807","name":"environment"},{"id":"7735","name":"enzyme"},{"id":"5079","name":"Eric Gaucher"},{"id":"9854","name":"Origin Of Life"},{"id":"12660","name":"Origin Of Species"},{"id":"12664","name":"PH"},{"id":"12659","name":"Precambrian"},{"id":"12666","name":"Protein Stability"},{"id":"12667","name":"resurrected protein"},{"id":"7510","name":"temperature"},{"id":"12658","name":"thioredoxin"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003E\u003Cstrong\u003EAbby Robinson\u003C\/strong\u003E\u003Cbr \/\u003EResearch News and Publications\u003Cbr \/\u003E\u003Ca href=\u0022http:\/\/www.gatech.edu\/contact\/index.html?id=avogel6\u0022\u003EContact Abby Robinson\u003C\/a\u003E\u003Cbr \/\u003E\u003Cstrong\u003E404-385-3364\u003C\/strong\u003E\u003C\/p\u003E","format":"limited_html"}],"email":["abby@innovate.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}