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L. Felipe Benites

Publications and source records attributed to L. Felipe Benites.

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Elemental Stoichiometry as an Ecological Biosignature with Applications to Life Detection

The vast chemical space of possible small molecules, estimated at 10^60 compounds for molecules composed of just C, N, O, and S, is only sparsely occupied by biology. We propose that where life selects molecules within this space constitutes a detectable ecological signature: a fingerprint not of specific compounds, but of the statistical structure of elemental composition across molecules sam-pled from ecological systems. Here we introduce a framework combining Van Krevelen diagrams and element scaling laws to characterize the elemental composition of regions of chemical space occupied by biological systems and contrast them with other chemical systems. Applying this framework to 11,834 microbial metagenomic samples, we show that microbial metabolisms occupy a region of chemical space, which is enriched in heteroatoms such as P, S, N, and O relative to C, shifted toward higher O:C and H:C ratios. We observe sublinear element scaling with system size, yielding insights into how elemental constraints dictate how biological systems occupy chemical space. These patterns are distinct from a sample of 18,000 compounds from the comprehensive Reaxys synthetic chemical database. Critically, datasets from molecules detected in planetary science mission data occupy statistically distinct regions from both terrestrial biological and Reaxys distributions, demonstrating that with standardized methods for data collection, the approach could be developed to discriminate biotic from abiotic chemical signatures in small molecule data from planetary science missions. Our work shows how a combination of Van Krevelen fingerprinting and elemental scaling laws can provide a new class of ecological biosignatures for life detection leveraging mass spectrometric data from planetary missions, which could generalize beyond Earth's specific biochemistry.

q-bio.BM

Deep-time consistency in proteome elemental composition across cellular and viral life

Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved. One largely overlooked aspect is whether elemental composition constrains the range of viable proteomes. Here, we analyze the elemental composition of thousands of proteomes spanning cellular domains and viral realms. Despite evolutionary divergence and orders-of-magnitude variation in proteome size and gene content, proteomes exhibit strikingly consistent elemental composition. This consistency is substantially more constrained than amino acid frequencies or physicochemical properties and is not explained by evolutionary relatedness, biological function, or amino acid usage alone. Viral proteomes occupy the same elemental composition space observed in cellular organisms despite the absence of a single viral common ancestor, suggesting common biochemical constraints shape proteome organization across life. To investigate the evolutionary origins of this pattern, we compare modern proteomes with multiple independent reconstructions of the Last Universal Common Ancestor (LUCA) and with synthetic reduced-alphabet proteomes generated from primordial amino acid alphabets. LUCA proteomes occupy the same constrained elemental composition space observed in modern Bacteria and Archaea, whereas reduced primordial-like alphabets systematically generated alternative elemental regimes outside the modern range despite retaining high sequence similarity to extant proteins. Reduced alphabets disrupt fold space and reorganize relationships between elemental composition and predicted protein structural organization. Our results suggest that constrained elemental composition represents a fundamental organizational property of proteomes, which emerged early in evolution and may have contributed to the selection and stabilization of the modern amino acid alphabet.

q-bio.BM