The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation

The Archean atmosphere

(2020) David C. Catling et al.   Science Advances

A New Analysis of Archaea–Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution

(2020) Sarah J Berkemer et al.   MOLECULAR BIOLOGY AND EVOLUTION

The number and type of O2-utilizing enzymes indicates aerobic vs. anaerobic phenotype

(2019) Jagoda Jabłońska et al.   FREE RADICAL BIOLOGY AND MEDICINE

Oxidative opening of the aromatic ring: tracing the natural history of a large superfamily of dioxygenase domains and their relatives

(2019) A. Maxwell Burroughs et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Living with Oxygen

(2018) Harry B. Gray et al.   ACCOUNTS OF CHEMICAL RESEARCH

Dating phototrophic microbial lineages with reticulate gene histories

(2018) C. Magnabosco et al.   Geobiology

Modern rather than Mesoarchaean oxidative weathering responsible for the heavy stable Cr isotopic signatures of the 2.95 Ga old Ijzermijn iron formation (South Africa)

(2018) Gülüm Albut et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Isotopic evidence for oxygenated Mesoarchaean shallow oceans

(2018) Benjamin Eickmann et al.   Nature Geoscience

The last universal common ancestor between ancient Earth chemistry and the onset of genetics

(2018) Madeline C. Weiss et al.   PLoS Genetics

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

(2018) Holly C. Betts et al.   Nature Ecology & Evolution

Early Archean origin of Photosystem II

(2018) Tanai Cardona et al.   Geobiology

A Mesoarchean shift in uranium isotope systematics

(2018) Xiangli Wang et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modern diversification of the amino acid repertoire driven by oxygen

(2017) Matthias Granold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Timing and tempo of the Great Oxidation Event

(2017) Ashley P. Gumsley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths

(2017) Gudrun Gygli et al.   PLoS Computational Biology

Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans

(2017) Donato Giovannelli et al.   eLife

Effect of the environment on horizontal gene transfer between bacteria and archaea

(2017) Clara A. Fuchsman et al.   PeerJ

Phylogenetic rooting using minimal ancestor deviation

(2017) Fernando Domingues Kümmel Tria et al.   Nature Ecology & Evolution

Evolution of Oxygenic Photosynthesis

(2016) Woodward W. Fischer et al.   Annual Review of Earth and Planetary Sciences

Enzymatic Antioxidant Systems in Early Anaerobes: Theoretical Considerations

(2016) Ireneusz Ślesak et al.   ASTROBIOLOGY

One step beyond a ribosome: The ancient anaerobic core

(2016) Filipa L. Sousa et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Crown group Oxyphotobacteria postdate the rise of oxygen

(2016) P. M. Shih et al.   Geobiology

The physiology and habitat of the last universal common ancestor

(2016) Madeline C. Weiss et al.   Nature Microbiology

Rapid oxygenation of Earths atmosphere 2.33 billion years ago

(2016) G. Luo et al.   Science Advances

Improved gene tree error correction in the presence of horizontal gene transfer

(2015) Mukul S. Bansal et al.   BIOINFORMATICS

Horizontal gene transfer and genome evolution in Methanosarcina

(2015) Sofya K. Garushyants et al.   BMC EVOLUTIONARY BIOLOGY

Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code

(2015) G. P. Fournier et al.   JOURNAL OF MOLECULAR EVOLUTION

Benthic perspective on Earth’s oldest evidence for oxygenic photosynthesis

(2015) Stefan V. Lalonde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chlorite dismutases - a heme enzyme family for use in bioremediation and generation of molecular oxygen

(2014) Stefan Hofbauer et al.   Biotechnology Journal

Origins of major archaeal clades correspond to gene acquisitions from bacteria

(2014) Shijulal Nelson-Sathi et al.   NATURE

Evidence for oxygenic photosynthesis half a billion years before the Great Oxidation Event

(2014) Noah J. Planavsky et al.   Nature Geoscience

Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities

(2013) Z. J. Jay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantifying the areal extent and dissolved oxygen concentrations of Archean oxygen oases

(2013) Stephanie L. Olson et al.   CHEMICAL GEOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Atmospheric oxygenation three billion years ago

(2013) Sean A. Crowe et al.   NATURE

Oxygen and Hydrogen Peroxide in the Early Evolution of Life on Earth: In silico Comparative Analysis of Biochemical Pathways

(2012) Ireneusz Ślesak et al.   ASTROBIOLOGY

Microaerobic steroid biosynthesis and the molecular fossil record of Archean life

(2011) J. R. Waldbauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Dating the cyanobacterial ancestor of the chloroplast

(2010) Luisa I Falcón et al.   ISME Journal

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Phylogeny of prokaryotes: does it exist and why should we care?

(2009) Simonetta Gribaldo et al.   RESEARCH IN MICROBIOLOGY

Evolution of the haem copper oxidases superfamily: a rooting tale

(2009) Simonetta Gribaldo et al.   TRENDS IN BIOCHEMICAL SCIENCES

A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land

(2008) F. U. Battistuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION