Scaling laws in enzymes may help predict life `as we don't know it'


Date:
February 28, 2022
Source:
Santa Fe Institute
Summary:
A team of researchers is developing tools to predict the features
of life as we don't know it.



FULL STORY ==========================================================================
The only references we have for "life" are the forms we know on Earth.

Astrobiologists suspect that the search for alien life, and even for
the origins of life on Earth, may require a broader scope. A NASA-funded
team of researchers is developing tools to predict the features of life
as we don't know it. In a new study published in the Proceedings of the National Academy of Sciences, the team identifies universal patterns in
the chemistry of life that do not appear to depend on specific molecules.


==========================================================================
"We want to have new tools for identifying and even predicting features of
life as we don't know it," says Santa Fe Institute External Professor Sara Imari Walker (Arizona State University), a co-author on the paper. "To
do so, we are aiming to identify the universal laws that should apply to
any biochemical system. This includes developing quantitative theory for
the origins of life, and using theory and statistics to guide our search
for life on other planets." On Earth, life emerges from the interplay
of hundreds of chemical compounds and reactions. Some of these compounds
and reactions are found universally across Earth's organisms. Using
the Integrated Microbial Genomes and Microbiomes database, the team investigated the enzymes -- the functional drivers of biochemistry
-- found in bacteria, archaea, and eukarya to reveal a new kind of
biochemical universality.

Enzymes can be categorized into a taxonomy of broad functional classes
- - groups designated by what they do, from using water molecules to
break chemical bonds (hydrolases) to rearranging molecular structures (isomerases) to joining large molecules together (ligases). The team
compared how the abundance of enzymes in each of these functional
categories changed in relation to the overall abundance of enzymes in
an organism. They discovered various scaling laws -- almost algorithmic relationships -- between the number of enzymes in different enzyme classes
and the size of an organism's genome. They also found that these laws
don't depend on the particularenzymes in those classes.

"Here we find that you get these scaling relationships without needing
to conserve exact membership. You need a certain number of transferases,
but not particular transferases," says SFI Professor Chris Kempes, a
co-author on the paper. "There are a lot 'synonyms,' and those synonyms
scale in systematic ways." On Earth, organisms use DNA and, through RNA, create proteins. But will the macromolecules of DNA, RNA, and proteins
help us identify life across the universe, understand the origins of
life on Earth, or develop synthetic biology? "As a team, we think that's
not likely," says Kempes. The functions those macromolecules serve,
however, and the metabolic scaling relationships observed in organic, Earth-based life, just might be. "Even if life elsewhere used really
different molecules, these sort of functional categories and scaling
laws might be conserved throughout the universe," says Kempes.

Additional authors on this study are first author Dylan Gagler (New
York University Langone Health); Hyunju Kim, Bradley Karas, John Malloy,
and Veronica Mierzejewski (Arizona State University); and Aaron Goldman (Oberlin College and the Blue Marble Space Institute for Science).

Adapted from a press release published
by Arizona State University: https:// news.asu.edu/20220228-new-astrobiology-research-predicts-life-we-dont-know-it ========================================================================== Story Source: Materials provided by Santa_Fe_Institute. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Dylan C. Gagler, Bradley Karas, Christopher P. Kempes, John Malloy,
Veronica Mierzejewski, Aaron D. Goldman, Hyunju Kim, Sara I. Walker.

Scaling laws in enzyme function reveal a new kind of biochemical
universality. Proceedings of the National Academy of Sciences,
2022; 119 (9): e2106655119 DOI: 10.1073/pnas.2106655119 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/02/220228161618.htm

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