Ecological resource competition as a driver of metallome evolution DOI Creative Commons
Morgan S. Sobol, Holly R. Rucker, Eric Libby

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 16, 2024

Abstract Undoubtedly, Earth’s first redox revolution, which culminated ∼2.4 billion years ago in the Great Oxidation Event (GOE), fundamentally altered resources available to microbial communities, leading novel ecological competitions and evolutionary innovations. These eco-evolutionary dynamics are largely unexplored, particularly at molecular level. Here, we hypothesize that such wake of GOE explain otherwise paradoxical history metal use nitrogen fixation by nitrogenase. This ancient metalloenzyme exists three isozymes, with distinct cofactors. Recent research demonstrates most isozyme, emerging a or more before GOE, required molybdenum (Mo)-based cofactor. “Alternative” nitrogenases using iron (Fe) vanadium (V) cofactors evolved after GOE. is puzzling because Mo availability environment increased while Fe decreased , due contrasting environmental behaviors these elements. Why, then, did alternatives emerge only GOE? Using simple model constrained known quotas, demonstrate strong selection pressure for metals nitrogenase other than likely consequence competition between nitrogen-fixing prokaryotes nitrate-reducing microbes, require nitrate reduction assimilation. would have intensified increasing nitrate, explaining timing isozymes. Ecological resource therefore emerges as third driver metallome evolution deep-time, alongside relative availabilities adaptive advantages particular metals. Significance statement The biochemical widely attributed either specific their functional benefits biological systems. We propose pressure, competition, typically overlooked novelty deep time. Specifically, Mo-dependent reducers led emergence Mo-free “alternative” enzymes during early Proterozoic. hypothesis explains alternative despite ocean abundances Competition among species same drove innovations, especially response dynamically changing geochemical landscapes.

Language: Английский

The nature of the last universal common ancestor and its impact on the early Earth system DOI Creative Commons
Edmund R. R. Moody, Sandra Álvarez-Carretero, Tara Mahendrarajah

et al.

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(9), P. 1654 - 1666

Published: July 12, 2024

Abstract The nature of the last universal common ancestor (LUCA), its age and impact on Earth system have been subject vigorous debate across diverse disciplines, often based disparate data methods. Age estimates for LUCA are usually fossil record, varying with every reinterpretation. LUCA’s metabolism has proven equally contentious, some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent geochemistry. Here we infer that lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis pre-LUCA gene duplicates, calibrated using microbial fossils isotope records under new cross-bracing implementation. Phylogenetic reconciliation suggests had genome at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable modern prokaryotes. Our results suggest was prokaryote-grade anaerobic acetogen possessed an early immune system. Although is sometimes perceived as living in isolation, part established ecological would provided niche other community members hydrogen recycling by atmospheric photochemistry could supported modestly productive ecosystem.

Language: Английский

Citations

59
Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes DOI Creative Commons
Carlos Santana‐Molina, Tom A. Williams, ‎Berend Snel

et al.

Nature Ecology & Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

The origin of eukaryotes was a key event in the history life. Current leading hypotheses propose that symbiosis between an asgardarchaeal host cell and alphaproteobacterial endosymbiont represented crucial step eukaryotic metabolic cross-feeding partners provided basis for their subsequent evolutionary integration. A major unanswered question is whether metabolism modern bears any vestige this ancestral syntrophy. Here we systematically analyse origins gene repertoires mediating central carbon metabolism. Our phylogenetic sequence analyses reveal repertoire chimeric, with contributions from Asgardarchaeota Alphaproteobacteria operating predominantly glycolysis tricarboxylic acid cycle, respectively. also extent to which interplay has been remodelled via loss, transfer subcellular retargeting >2 billion years since cells, identify genetic other prokaryotic sources addition endosymbiont. work demonstrates that, contrast previous assumptions, preserves information about nature original asgardarchaeal–alphaproteobacterial interactions supports syntrophy scenarios cell. Analysis identifies Alphaproteobacteria, microbial taxa, followed by retargeting, have over time.

Language: Английский

Citations

1
The more we learn, the more diverse it gets: structures, functions and evolution in the Phosphofructokinase Superfamily DOI Creative Commons

Jordan L. Compton,

Wayne M. Patrick

Biochemical Journal, Journal Year: 2025, Volume and Issue: 482(09), P. 467 - 483

Published: May 6, 2025

The enzyme 6-phosphofructokinase (PFK) phosphorylates d-fructose 6-phosphate, producing 1,6-bisphosphate. canonical version—discovered almost 90 years ago—is ATP-dependent, allosterically regulated and catalyses the first committed step in glycolysis. However, beyond this textbook enzyme, there is fascinating functional structural variety among PFKs across tree of life. While are found two non-homologous superfamilies, here, we review universally distributed enzymes one, Phosphofructokinase Superfamily. We focus on summarising diversity within superfamily. A key partition regards identity phosphate donor, which can be ATP or inorganic pyrophosphate (PPi). Considerable insights into evolutionary aspects ATP- PPi-dependent have come through biology, with 45 structures now available Protein Data Bank. One recent highlight was use cryoEM molecular dynamics simulations to illuminate basis allosteric regulation human liver PFK. Others were explore interactions drug-like small molecules from Trypanosoma brucei liver, revealing new routes antibiotics immune modulators, respectively. In contrast ATP-dependent enzymes, typically non-allosteric catalyse a readily reversible reaction. Some also play an additional physiological role by phosphorylating d-sedoheptulose 7-phosphate. discuss why these properties plausibly ancestral. Finally, emphasise how much remains discovered. For example, experimentally determined only 14 species. Nine decades in, it still great time studying

Language: Английский

Citations

0
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents DOI Creative Commons
András Zeke, Toby J. Gibson, László Dobson

et al.

PLoS Computational Biology, Journal Year: 2024, Volume and Issue: 20(2), P. e1011902 - e1011902

Published: Feb. 16, 2024

The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately, they are poorly understood from a molecular biology perspective, making development of mechanistically novel and selective drugs difficult. Here, we explore three functionally critical targeting short linear motif systems as well their receptors in depth, using combination structural modeling, evolutionary sequence divergence deep learning. Secretory signal peptides, endoplasmic reticulum (ER) retention motifs (KDEL motifs), autophagy signals (motifs interacting ATG8 family members) ancient essential components cellular life. Although expected be conserved amongst the kinetoplastids, observe that all show varying degree better studied equivalents animals, plants, or fungi. We not only describe behaviour, but also build models allow prediction localization potential functions for uncharacterized proteins. unusually Ala/Val-rich secretory resident proteins ending Asp-Leu-COOH atypical ATG8-like features kinetoplastid parasites. Several protein-protein interactions could serve targets antimicrobial agents against Leishmaniasis due systematic host.

Language: Английский

Citations

2
Hydrothermal seawater eutrophication triggered local macrobiological experimentation in the 2100 Ma Paleoproterozoic Francevillian sub-basin DOI
Ernest Chi Fru, Jérémie Aubineau, Olabode M. Bankole

et al.

Precambrian Research, Journal Year: 2024, Volume and Issue: 409, P. 107453 - 107453

Published: May 31, 2024

Language: Английский

Citations

2
Chimeric Origins and Dynamic Evolution of Central Carbon Metabolism in Eukaryotes DOI Creative Commons
Carlos Santana‐Molina, Tom A. Williams, ‎Berend Snel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 1, 2024

The origin of eukaryotes was a key event in the history life. Current leading hypotheses propose that symbiosis between an asgardarchaeal host cell and alphaproteobacterial endosymbiont represented crucial step eukaryotic origins invoke central role for syntrophic interactions - is, metabolic cross-feeding partners as basis their subsequent evolutionary integration. A major unanswered question is whether metabolism modern bears any vestige this ancestral interaction. To investigate detail, we systematically analyze gene repertoires mediating carbon metabolism. Our phylogenetic sequence analyses reveal repertoire chimeric, with contributions from Asgardarchaeota Alphaproteobacteria operating predominantly glycolysis TCA, respectively. Furthermore, our diverse additional other prokaryotic sources well extent to which interplay has been remodeled via loss, transfer, subcellular retargeting >2Ga since cells. Together, work demonstrates contrast previous assumptions, preserves information about nature original asgardarchaeal-alphaproteobacterial interactions, supports syntrophy scenarios on cell.

Language: Английский

Citations

1
Challenges in Assembling the Dated Tree of Life DOI Creative Commons
Carlos G. Schrago, Beatriz Mello

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(10)

Published: Oct. 1, 2024

Abstract The assembly of a comprehensive and dated Tree Life (ToL) remains one the most formidable challenges in evolutionary biology. complexity life's history, involving both vertical horizontal transmission genetic information, defies its representation by simple bifurcating phylogeny. With advent genome metagenome sequencing, vast amounts data have become available. However, employing this information for phylogeny divergence time inference has introduced significant theoretical computational hurdles. This perspective addresses some key methodological assembling ToL, namely, identification classification homologous genes, accounting gene tree-species tree mismatch due to population-level processes along with duplication, loss, transfer, accurate dating events. Ultimately, success endeavor requires new approaches that integrate knowledge databases optimized phylogenetic algorithms capable managing complex models.

Language: Английский

Citations

0
Completing a molecular timetree of primates DOI Creative Commons
Jack M. Craig, S. Blair Hedges, Sudhir Kumar

et al.

Frontiers in Bioinformatics, Journal Year: 2024, Volume and Issue: 4

Published: Dec. 16, 2024

Primates, consisting of apes, monkeys, tarsiers, and lemurs, are among the most charismatic well-studied animals on Earth, yet there is no taxonomically complete molecular timetree for group. Combining latest large-scale genomic primate phylogeny 205 recognized species with 400-species literature consensus tree available from TimeTree.org yields a just 405 primates, 50 still missing despite having sequence data in NCBI GenBank. In this study, we assemble 455 incorporating every which available. We use synthetic approach review published timetrees,

Language: Английский

Citations

0
Ecological resource competition as a driver of metallome evolution DOI Creative Commons
Morgan S. Sobol, Holly R. Rucker, Eric Libby

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 16, 2024

Abstract Undoubtedly, Earth’s first redox revolution, which culminated ∼2.4 billion years ago in the Great Oxidation Event (GOE), fundamentally altered resources available to microbial communities, leading novel ecological competitions and evolutionary innovations. These eco-evolutionary dynamics are largely unexplored, particularly at molecular level. Here, we hypothesize that such wake of GOE explain otherwise paradoxical history metal use nitrogen fixation by nitrogenase. This ancient metalloenzyme exists three isozymes, with distinct cofactors. Recent research demonstrates most isozyme, emerging a or more before GOE, required molybdenum (Mo)-based cofactor. “Alternative” nitrogenases using iron (Fe) vanadium (V) cofactors evolved after GOE. is puzzling because Mo availability environment increased while Fe decreased , due contrasting environmental behaviors these elements. Why, then, did alternatives emerge only GOE? Using simple model constrained known quotas, demonstrate strong selection pressure for metals nitrogenase other than likely consequence competition between nitrogen-fixing prokaryotes nitrate-reducing microbes, require nitrate reduction assimilation. would have intensified increasing nitrate, explaining timing isozymes. Ecological resource therefore emerges as third driver metallome evolution deep-time, alongside relative availabilities adaptive advantages particular metals. Significance statement The biochemical widely attributed either specific their functional benefits biological systems. We propose pressure, competition, typically overlooked novelty deep time. Specifically, Mo-dependent reducers led emergence Mo-free “alternative” enzymes during early Proterozoic. hypothesis explains alternative despite ocean abundances Competition among species same drove innovations, especially response dynamically changing geochemical landscapes.

Language: Английский

Citations

0