Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity.

ABSTRACT: The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in the fossil record. The great majority of the increase is accounted for by 2 discrete steps of approximately equal magnitude: the first in the middle of the Paleoproterozoic Era (approximately 1.9 Gya) and the second during the late Neoproterozoic and early Paleozoic eras (0.6-0.45 Gya). Each size step required a major innovation in organismal complexity--first the eukaryotic cell and later eukaryotic multicellularity. These size steps coincide with, or slightly postdate, increases in the concentration of atmospheric oxygen, suggesting latent evolutionary potential was realized soon after environmental limitations were removed.

SUBMITTER: Payne JL

PROVIDER: S-EPMC2607246 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Tracking of Ubiquitin Signaling through 3.5 Billion Years of Combinatorial Conjugation.

Project description:Ubiquitination is an evolutionary, ancient system of post-translational modification of proteins that occurs through a cascade involving ubiquitin activation, transfer, and conjugation. The maturation of this system has followed two main pathways. The first is the conservation of a universal structural fold of ubiquitin and ubiquitin-like proteins, which are present in both Archaea and Bacteria, as well as in multicellular Eukaryotes. The second is the rise of the complexity of the superfamily of ligases, which conjugate ubiquitin-like proteins to substrates, in terms of an increase in the number of enzyme variants, greater variation in structural organization, and the diversification of their catalytic domains. Here, we examine the diversity of the ubiquitination system among different organisms, assessing the variety and conservation of the key domains of the ubiquitination enzymes and ubiquitin itself. Our data show that E2 ubiquitin-conjugating enzymes of metazoan phyla are highly conservative, whereas the homology of E3 ubiquitin ligases with human orthologues gradually decreases depending on "molecular clock" timing and evolutionary distance. Surprisingly, Chordata and Echinodermata, which diverged over 0.5 billion years ago during the Cambrian explosion, share almost the same homology with humans in the amino acid sequences of E3 ligases but not in their adaptor proteins. These observations may suggest that, firstly, the E2 superfamily already existed in its current form in the last common metazoan ancestor and was generally not affected by purifying selection in metazoans. Secondly, it may indicate convergent evolution of the ubiquitination system and highlight E3 adaptor proteins as the "upper deck" of the ubiquitination system, which plays a crucial role in chordate evolution.

| S-EPMC11354881 | biostudies-literature

Conservation of protein structure over four billion years.

Project description:Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis.

| S-EPMC3774310 | biostudies-literature

Helium in diamonds unravels over a billion years of craton metasomatism.

Project description:Chemical events involving deep carbon- and water-rich fluids impact the continental lithosphere over its history. Diamonds are a by-product of such episodic fluid infiltrations, and entrapment of these fluids as microinclusions in lithospheric diamonds provide unique opportunities to investigate their nature. However, until now, direct constraints on the timing of such events have not been available. Here we report three alteration events in the southwest Kaapvaal lithosphere using U-Th-He geochronology of fluid-bearing diamonds, and constrain the upper limit of He diffusivity (to D ≈ 1.8 × 10-19 cm2 s-1), thus providing a means to directly place both upper and lower age limits on these alteration episodes. The youngest, during the Cretaceous, involved highly saline fluids, indicating a relationship with late-Mesozoic kimberlite eruptions. Remnants of two preceding events, by a Paleozoic silicic fluid and a Proterozoic carbonatitic fluid, are also encapsulated in Kaapvaal diamonds and are likely coeval with major surface tectonic events (e.g. the Damara and Namaqua-Natal orogenies).

| S-EPMC8113505 | biostudies-literature

Networks of bZIP protein-protein interactions diversified over a billion years of evolution.

Project description:Differences in biomolecular sequence and function underlie dramatic ranges of appearance and behavior among species. We studied the basic region-leucine zipper (bZIP) transcription factors and quantified bZIP dimerization networks for five metazoan and two single-cell species, measuring interactions in vitro for 2891 protein pairs. Metazoans have a higher proportion of heteromeric bZIP interactions and more network complexity than the single-cell species. The metazoan bZIP interactomes have broadly similar structures, but there has been extensive rewiring of connections compared to the last common ancestor, and each species network is highly distinct. Many metazoan bZIP orthologs and paralogs have strikingly different interaction specificities, and some differences arise from minor sequence changes. Our data show that a shifting landscape of biochemical functions related to signaling and gene expression contributes to species diversity.

| S-EPMC4115154 | biostudies-literature

Organic carbon concentrations in 3.5-billion-year-old lacustrine mudstones of Mars.

Project description:The Sample Analysis at Mars instrument stepped combustion experiment on a Yellowknife Bay mudstone at Gale crater, Mars revealed the presence of organic carbon of Martian and meteoritic origins. The combustion experiment was designed to access refractory organic carbon in Mars surface sediments by heating samples in the presence of oxygen to combust carbon to CO2. Four steps were performed, two at low temperatures (less than ∼550 °C) and two at high temperatures (up to ∼870 °C). More than 950 μg C/g was released at low temperatures (with an isotopic composition of δ13C = +1.5 ± 3.8‰) representing a minimum of 431 μg C/g indigenous organic and inorganic Martian carbon components. Above 550 °C, 273 ± 30 μg C/g was evolved as CO2 and CO (with estimated δ13C = -32.9‰ to -10.1‰ for organic carbon). The source of high temperature organic carbon cannot be definitively confirmed by isotopic composition, which is consistent with macromolecular organic carbon of igneous origin, meteoritic infall, or diagenetically altered biomass, or a combination of these. If from allochthonous deposition, organic carbon could have supported both prebiotic organic chemistry and heterotrophic metabolism at Gale crater, Mars, at ∼3.5 Ga.

| S-EPMC9271195 | biostudies-literature

Ingredients for microbial life preserved in 3.5 billion-year-old fluid inclusions.

Project description:It is widely hypothesised that primeval life utilised small organic molecules as sources of carbon and energy. However, the presence of such primordial ingredients in early Earth habitats has not yet been demonstrated. Here we report the existence of indigenous organic molecules and gases in primary fluid inclusions in c. 3.5-billion-year-old barites (Dresser Formation, Pilbara Craton, Western Australia). The compounds identified (e.g., H2S, COS, CS2, CH4, acetic acid, organic (poly-)sulfanes, thiols) may have formed important substrates for purported ancestral sulfur and methanogenic metabolisms. They also include stable building blocks of methyl thioacetate (methanethiol, acetic acid) - a putative key agent in primordial energy metabolism and thus the emergence of life. Delivered by hydrothermal fluids, some of these compounds may have fuelled microbial communities associated with the barite deposits. Our findings demonstrate that early Archaean hydrothermal fluids contained essential primordial ingredients that provided fertile substrates for earliest life on our planet.

| S-EPMC7889642 | biostudies-literature

Southern Africa crustal anisotropy reveals coupled crust-mantle evolution for over 2 billion years.

Project description:The long-term stability of Precambrian continental lithosphere depends on the rheology of the lithospheric mantle as well as the coupling between crust and mantle lithosphere, which may be inferred by seismic anisotropy. Anisotropy has never been detected in cratonic crust. Anisotropy in southern Africa, detected by the seismological SKS-splitting method, usually is attributed to the mantle due to asthenospheric flow or frozen-in features of the lithosphere. However, SKS-splitting cannot distinguish between anisotropy in the crust and the mantle. We observe strong seismic anisotropy in the crust of southern African cratons by Receiver Function analysis. Fast axes are uniform within tectonic units and parallel to SKS axes, orogenic strike in the Limpopo and Cape fold belts, and the strike of major dyke swarms. Parallel fast axes in the crust and mantle indicate coupled crust-mantle evolution for more than 2 billion years with implications for strong rheology of the lithosphere.

| S-EPMC6884544 | biostudies-literature

Reproducibility and Temporal Structure in Weekly Resting-State fMRI over a Period of 3.5 Years.

Project description:Resting-state functional MRI (rs-fMRI) permits study of the brain's functional networks without requiring participants to perform tasks. Robust changes in such resting state networks (RSNs) have been observed in neurologic disorders, and rs-fMRI outcome measures are candidate biomarkers for monitoring clinical trials, including trials of extended therapeutic interventions for rehabilitation of patients with chronic conditions. In this study, we aim to present a unique longitudinal dataset reporting on a healthy adult subject scanned weekly over 3.5 years and identify rs-fMRI outcome measures appropriate for clinical trials. Accordingly, we assessed the reproducibility, and characterized the temporal structure of, rs-fMRI outcome measures derived using independent component analysis (ICA). Data was compared to a 21-person dataset acquired on the same scanner in order to confirm that the values of the single-subject RSN measures were within the expected range as assessed from the multi-participant dataset. Fourteen RSNs were identified, and the inter-session reproducibility of outcome measures-network spatial map, temporal signal fluctuation magnitude, and between-network connectivity (BNC)-was high, with executive RSNs showing the highest reproducibility. Analysis of the weekly outcome measures also showed that many rs-fMRI outcome measures had a significant linear trend, annual periodicity, and persistence. Such temporal structure was most prominent in spatial map similarity, and least prominent in BNC. High reproducibility supports the candidacy of rs-fMRI outcome measures as biomarkers, but the presence of significant temporal structure needs to be taken into account when such outcome measures are considered as biomarkers for rehabilitation-style therapeutic interventions in chronic conditions.

| S-EPMC4627782 | biostudies-literature

Genetics, energetics and allostery during a billion years of hydrophobic protein core evolution

Project description:Protein folding is driven by the burial of hydrophobic amino acids in a tightly-packed core that excludes water. The genetics, biophysics and evolution of hydrophobic cores are not well understood, in part because of a lack of systematic experimental data on sequence combinations that do - and do not - constitute stable and functional cores. Here we randomize protein hydrophobic cores and evaluate their stability and function at scale. The data show that vast numbers of amino acid combinations can constitute stable protein cores but that these alternative cores frequently disrupt protein function because of allosteric effects. These strong allosteric effects are not due to complicated, highly epistatic fitness landscapes but rather, to the pervasive nature of allostery, with many individually small energy changes combining to disrupt function. Indeed both protein stability and ligand binding can be accurately predicted over very large evolutionary distances using additive energy models with a small contribution from pairwise energetic couplings. As a result, energy models trained on one protein can accurately predict core stability across hundreds of millions of years of protein evolution, with only rare energetic couplings that we experimentally identify limiting the transplantation of cores between highly diverged proteins. Our results reveal the simple energetic architecture of protein hydrophobic cores and suggest that allostery is a major constraint on sequence evolution.

2024-05-13 | GSE266299 | GEO

Orbital forcing of climate 1.4 billion years ago.

Project description:Fluctuating climate is a hallmark of Earth. As one transcends deep into Earth time, however, both the evidence for and the causes of climate change become difficult to establish. We report geochemical and sedimentological evidence for repeated, short-term climate fluctuations from the exceptionally well-preserved ?1.4-billion-year-old Xiamaling Formation of the North China Craton. We observe two patterns of climate fluctuations: On long time scales, over what amounts to tens of millions of years, sediments of the Xiamaling Formation record changes in geochemistry consistent with long-term changes in the location of the Xiamaling relative to the position of the Intertropical Convergence Zone. On shorter time scales, and within a precisely calibrated stratigraphic framework, cyclicity in sediment geochemical dynamics is consistent with orbital control. In particular, sediment geochemical fluctuations reflect what appear to be orbitally forced changes in wind patterns and ocean circulation as they influenced rates of organic carbon flux, trace metal accumulation, and the source of detrital particles to the sediment.

| S-EPMC4378410 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data