Santa Fe Institute

Chemistry of life: Following carbon fixation to the earliest branches on the tree of life

April 25, 2012 9:54 a.m.

In a study published today in PLoS Computational Biology, SFI's Rogier Braakman and D. Eric Smith map the development of life-sustaining chemistry to the history of early life and trace six methods of carbon fixation seen in modern life back to a single ancestral form.

Read the paper in PLoS Computational Biology (April 19, 2012)

Carbon fixation -- life’s mechanism for making carbon dioxide biologically useful -- forms the biggest bridge between Earth’s non-living chemistry and its living biosphere. All organisms that fix carbon do so in one of six ways. These six mechanisms have overlaps, but it was previously unclear which of the six types came first, and how their development interweaved with environmental and biological changes.

The authors used a method that creates “trees” of evolutionary relatedness based on genetic sequences and metabolic traits. From this, they were able to reconstruct the complete early evolutionary history of biological carbon–fixation, relating all ways in which life today performs this function.

The earliest form of carbon fixation identified by scientists achieved a special kind of built-in robustness -- not seen in modern cells -- by layering multiple carbon-fixing mechanisms. This redundancy allowed early life to compensate for a lack of refined control over its internal chemistry, and formed a template for the later splits that created the earliest major branches in the tree of life. For example, the first major life-form split came with the earliest appearance of oxygen on Earth, causing the ancestors of blue–green algae and most other bacteria to separate from the branch that includes Archaea, which, outside of bacteria, are the other major early group of single-celled microorganisms.

"It seems likely that the earliest cells were rickety assemblies whose parts were constantly malfunctioning and breaking down,” explains Smith, an SFI External Professor. “How can any metabolism be sustained with such shaky support? The key is concurrent and constant redundancy."

Once early cells had more refined enzymes and membranes, allowing greater control over metabolic chemistry, environmental driving forces directed life's unfolding. These forces included changes in oxygen level and alkalinity, as well as minimization of the amount of energy (in the form of ATP) used to create biomass.

In other words, the environment drove major divergences in predictable ways -- in contrast to the common widely held belief that chance dominated evolutionary innovation and that rewinding and replaying the evolutionary tape would lead to an irreconcilably different tree of life.

“Mapping cell function onto genetic history gives us a clear picture of the physiology that led to the major foundational divergences of evolution,” explains Braakman, an SFI Omidyar Fellow. “This highlights the central role of basic chemistry and physics in driving early evolution.”

With the ancestral form uncovered and evolutionary drivers pinned to branching points in the tree, the researchers now want to make the study more mathematically formal and further analyze the early evolution of metabolism.

Read the paper in PLoS Computational Biology (April 19, 2012)

Read the Yahoo! News article (April 23, 2012)

Read the Huffington Post article (April 20, 2012)

Read the MSNBC article (April 20, 2012)

Read the article in LiveScience (April 19, 2012)

Read the article in Physorg (April 19, 2012)

Learn more about Smith's and Braakman's research into the origins of life in the SFI Bulletin (2012)

Watch Rogier Braakman describe the chemistry of life (4-minute SFI video)


Image caption: Phylometabolic tree of carbon fixation. Each small black network represents a carbon-fixation pathway, and the tree describes the evolutionary process that connects them. In red are identified environmental driving forces. Through integrating phylogenetics with metabolic constraints, phylometabolic analysis allows a clear description down to the root of the tree, and shows how carbon-fixation structured the deep history of life on Earth. (Credit: Braakman and Smith)

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