Scaling laws in enzyme function reveal a new kind of biochemical universality

Abstract

All life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to known biochemistry and does not allow quantitative predictions about examples not yet observed. Here, we introduce a more generalizable concept of biochemical universality that is more akin to the kind of universality found in physics. Using annotated genomic datasets including an ensemble of 11,955 metagenomes, 1,282 archaea, 11,759 bacteria, and 200 eukaryotic taxa, we show how enzyme functions form universality classes with common scaling behavior in their relative abundances across the datasets. We verify that these scaling laws are not explained by the presence of compounds, reactions, and enzyme functions shared across known examples of life. We demonstrate how these scaling laws can be used as a tool for inferring properties of ancient life by comparing their predictions with a consensus model for the last universal common ancestor (LUCA). We also illustrate how network analyses shed light on the functional principles underlying the observed scaling behaviors. Together, our results establish the existence of a new kind of biochemical universality, independent of the details of life on Earth’s component chemistry, with implications for guiding our search for missing biochemical diversity on Earth or for biochemistries that might deviate from the exact chemical makeup of life as we know it, such as at the origins of life, in alien environments, or in the design of synthetic life.

Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs

“…Gly is favored in all the triad microenvironments, especially around the Naa, in agreement with the dominant Gly-Xaa-Ser-Xaa-Gly enzyme motif in α/β hydrolase folds. , The X 1 position, adjacent to the active residues, stands out in all microenvironments as it often contains charged aa (Glu, Asp, His) when adjacent to the Naa, the acidic Asp when adjacent to the Aaa, and an oscillating polar/nonpolar character in proximity of Baa. This suggests that the triad hydrolytic mechanism might have additional layers of complexity in the evolutionary or microenvironment sense, prompting new questions for further research . Furthermore, positions directly adjacent to the Naa residue are likely used for substrate stabilization and selection based on their properties and codependencies on oxyanion hole and substrate types.…”

Neuro-evolutionary evidence for a universal fractal primate brain shape

“…Indeed, our previously proposed model (Mota and Herculano-Houzel, 2015) for cortical gyrification is very simple, which is both a strength and a weakness. There are many complex phenomena in nature that display simple and universal scaling that can be derived from first principles (Barenblatt, 1996;Gagler et al, 2022;West et al, 1997). In addition, recent results suggest simplicity and symmetry are generically favoured on statistical-ensemble grounds by evolution (Johnston et al, 2022).…”

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“…It is thought that life might appear on a body in the Universe once favorable physical-chemical conditions are established. However, the possible alien lives might have been created under exotic environments and thus could be based on chemistries utterly different from life on Earth ( Bains, 2004 ; Benner et al, 2004 ; Schulze-Makuch and Irwin, 2008 ; Gagler et al, 2022 ). Hence, a formal definition of “life” is not possible for astrobiologists since we do not know what life will be like elsewhere in the cosmos and because we only have the sole example of Earth life ( Cleland, 2019a , b ; Gagler et al, 2022 ).…”

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