The 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.
"This 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," said Eric Gaucher, an associate professor in the School of Biology at the Georgia Institute of Technology.
The study, which was published April 3 in the advance online edition of the journal Nature Structural & Molecular Biology, was conducted by an international team of researchers from Georgia Tech, Columbia University and the Universidad de Granada in Spain.
Major 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.
Using 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.
To 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.
"By 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," said Gaucher.
The 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.
"Given 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," said Julio Fernández, a professor in the Department of Biological Sciences professor at Columbia University.
Fernández 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.
For 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's level of efficiency.
The 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.
"Our 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," said Fernández.
To measure the temperature range in which the enzymes operated, professor Jose Sanchez-Ruiz and graduate student Alvaro Inglés-Prieto from the Departamento de Química-Física 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.
The 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.
"Our 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," said Gaucher.
This 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.
The 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.
"The 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," added Perez-Jimenez.
This 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.
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The NAI Executive Council is comprised of the NAI Director, Carl Pilcher, Ph.D., Deputy Director, Edward Goolish, Ph.D. and the directors of the fourteen NAI teams from across the country. The purpose of the meeting is to evaluate and discuss new opportunities for NAI-wide research, space mission activities, technological development, and external partnerships.
The Georgia Tech NAI center, RiboEvo, was established in February 2009 with a five year grant of 6.4 million dollars from NASA. RiboEvo is lead by the center's director, Loren D. Williams, Ph.D., professor in the School of Chemistry and Biochemistry. RiboEvo is a multidisciplinary research center and is comprised of scientists from Georgia Tech, Emory University, John Hopkins University, the University of California at Santa Cruz and the University of Houston.
Although dispersed throughout the country, together these NAI teams work collaboratively to integrate interdisciplinary research and education in astrobiology with the goal of rewinding the tape of life. The idea being if you can understand the origin and evolution of life on earth you can then anticipate the nature of it across the universe.
RiboEvo investigators specifically focus on research surrounding the ribosome, the oldest molecular assembly in biology. Using the ribosome, RiboEvo performs molecular paleontology or mining of biophysical and inorganic chemistry from ancient biological systems.
“The ribosome tells the story of some of life’s aboriginal molecules, assemblies and chemical reactions,” Williams said. “Understanding the ribosome will uncover clues in the transition from the RNA world to the RNA-DNA-protein world.”
The work from this research center carries the potential of discovering and characterizing the oldest traceable macromolecules and machines of life, as well as the earliest discernable connection between RNA and protein.
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"Our research team seeks to understand how certain molecules in a complex mixture can work together to form highly ordered assemblies that exhibit chemical properties similar to those associated with biological molecules," said Nicholas V. Hud, a professor in the Georgia Tech School of Chemistry and Biochemistry. "Such a process was likely an essential and early stage of life, so we are also working to understand what chemicals were present on the prebiotic Earth and what processes helped these chemicals form the complex substances ultimately needed for life."
Hud will direct the effort, which is known as the Center for Chemical Evolution. The five-year grant will support research in more than 15 laboratories at institutions including Georgia Tech, Emory University, the Scripps Research Institute, the Scripps Institution of Oceanography, Jackson State University, Spelman College, Furman University and the SETI Institute.
All of the researchers will work together to accomplish the Center for Chemical Evolution's three main research goals:
To identify potential biological building blocks among the products of model prebiotic reactions,to investigate the chemical components and conditions that promote the spontaneous assembly of increasingly complex multi-component structures, and to prepare and characterize highly-ordered chemical assemblies, and to study their potential to function like biological substances.
Representatives from some of the partner institutions and the National Science Foundation (NSF) were on hand to mark the occasion with remarks and a ribbon cutting.
"The Georgia Research Alliance is proud to have at least two of our universities, Georgia Tech and Emory, collaborating with others on this project," said Susan Shows, senior vice president of the Georgia Research Alliance. "There are many groundbreaking programs under way on our campuses - more than my company can support in many cases. So when federal agencies put competitive funding into a program, it makes it easy for the GRA to know where to invest its strategic dollars."
Other speakers included: Charles Liotta, interim chair of the School of Chemistry and Biochemistry at Georgia Tech; Pat Marsteller, director of the Emory College Center for Science Education at Emory University; Loren Williams, director of Tech's NASA Ribosome Center; Katherine Covert, NSF program director for Integrative Chemistry Activities; and Matthew Platz, incoming director of the NSF Division of Chemistry.
]]>"Our research team seeks to understand how certain molecules in a complex mixture can work together to form highly ordered assemblies that exhibit chemical properties similar to those associated with biological molecules," said Nicholas V. Hud, a professor in the Georgia Tech School of Chemistry and Biochemistry. "Such a process was likely an essential and early stage of life, so we are also working to understand what chemicals were present on the prebiotic Earth and what processes helped these chemicals form the complex substances ultimately needed for life."
Hud will direct the effort, which is known as the Center for Chemical Evolution. The five-year grant will support research in more than 15 laboratories at institutions including Georgia Tech, Emory University, the Scripps Research Institute, the Scripps Institution of Oceanography, Jackson State University, Spelman College, Furman University and the SETI Institute.
All of the researchers will work together to accomplish the Center for Chemical Evolution’s three main research goals:
* To identify potential biological building blocks among the products of model prebiotic reactions,
* To investigate the chemical components and conditions that promote the spontaneous assembly of increasingly complex multi-component structures, and
* To prepare and characterize highly-ordered chemical assemblies, and to study their potential to function like biological substances.
"We will work backward from the complex substances found in living organisms today, such as proteins and DNA, and make materials that are a little bit different and simpler in chemical structure," explained Hud. "We will then strive to determine if there were possibly chemicals and conditions on the early Earth that would have given rise to these and similar substances."
In addition, the researchers will translate technological developments into commercially viable products. Facundo Fernandez, an associate professor in the Georgia Tech School of Chemistry and Biochemistry, is leading the Center's commercialization efforts.
For the first research theme, which is being led by Georgia Tech chemistry professor Thomas Orlando, creating a model inventory of the chemicals present on the early Earth will require the development of new tools and approaches for analyzing and sorting complex mixtures.
"Complex mixtures are found in many chemical industries - including petroleum, food and pharmaceuticals," said Fernandez. "The instruments and protocols we develop to sort through the complex mixtures that result from model prebiotic chemical reactions are going to be valuable to these industries too."
Charles Liotta, a Regents professor in the Georgia Tech School of Chemistry and Biochemistry, is leading the second research theme, which involves exploring alternative media that could have facilitated the assembly of complex substances in the prebiotic world. This research could produce environmentally-friendly procedures leading to new chemical processes, according to the team.
In the third research theme, led by David Lynn, chair of the Department of Chemistry at Emory University, and Ram Krishnamurthy, an associate professor of chemistry at the Scripps Research Institute, methods will be developed to create polymers and assemblies that mimic natural macromolecules, such as DNA and proteins. The resulting methods could be used as a platform to create a range of substances with broad commercial applications across the spectrum of therapeutics, diagnostics and drug delivery materials. Lynn will also lead the Center's education and public outreach programs.
The research efforts of the Center will build on the knowledge and results gained during the past three years, during which time a smaller group of laboratories were funded by the National Science Foundation to conduct collaborative research projects and to develop a larger center.
Research progress made during the initial phase of funding includes a paper published June 14 in the journal ChemBioChem. Center laboratories showed for the first time that guanine, a component of DNA, could be produced from formamide (H2NCOH), a simple chemical known to exist in outer space.
Previous research had shown that the other three building blocks of nucleic acids - cytosine, adenine and uracil - could be synthesized by heating formamide in the presence of mineral catalysts, but not guanine.
Center researchers produced guanine from formamide by subjecting the sample to ultraviolet light during the heating process. The results also demonstrated that guanine, adenine and another building block called hypoxanthine could be produced at lower temperatures than previously reported.
"Our ultimate goal is to create a complete chemical pathway showing how relatively simple substances can interact with the environment and each other to spontaneously produce complex assemblies that exhibit properties normally associated with biological substances, and perhaps shed some light on the earliest stages of life on Earth," noted Hud.
]]>Nick Hud, Professor of Chemistry & Biochemistry and Associate Director of Georgia Tech's Institute for Bioengineering & Bioscience, has research on "Molecular Midwives" featured in Daily Times India.
Scientists at the Georgia Institute of Technology have discovered that small molecules could have acted as "molecular midwives" in helping the building blocks of life's genetic material form long chains and may have assisted in selecting the base pairs of the DNA double helix. "Our hypothesis is that before there were protein enzymes to make DNA and RNA, there were small molecules present on the pre-biotic Earth that helped make these polymers by promoting molecular self-assembly," said Nicholas V. Hud, professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology.
]]>Chimps are more promiscuous than humans and thus may have higher mutation rates in their males' DNA.ALAMY. A genetic analysis has called into question the controversial claim that early humans and chimpanzees interbred before splitting into separate species. "Many evolutionary biologists were pretty skeptical" about the interbreeding scenario, says evolutionary geneticist Soojin Yi of the Georgia Institute of Technology in Atlanta. She argues that her explanation — which stems from promiscuity differences among primate species — is "simpler and hence more likely".... Now Yi, together with Daven Presgraves of the University of Rochester, have reanalysed the data and suggest that species differences in the levels of female promiscuity can account for the chromosomal inconsistency. The original hypothesis is "way more of a headache for evolutionary biologists", says Yi. The data "can also be explained very well by well-established ideas in molecular evolution"
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