biorxiv.org Archives

Conceptual model illustrating a possible evolutionary trajectory of ATP-generating enzymes. Under prebiotic conditions with a limited amino acid repertoire, kinase-like proteins resembling Arc1-12KR or Arc1-11K may have generated ATP through ADP disproportionation (2ADP → ATP + AMP). As the amino acid alphabet expanded toward the LUCA era, this chemistry was likely superseded by the emergence of modern NDKs, which catalyze phosphoryl transfer between NTPs and NDPs, and by adenylate kinases, which catalyze the reversible reaction 2ADP ⇌ ATP + AMP. Ultimately, the evolution of rotary ATP synthases enabled efficient ATP production from ADP and inorganic phosphate. -- biorxiv.org

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Emergence Of A Potentially Ancestral ATP-synthesizing Activity Under Prebiotic Amino Acid Constraints

by Keith CowingFebruary 25, 2026February 25, 2026

The earliest enzymes are thought to have been composed of the limited amino acid repertoire available on prebiotic Earth. However, how such compositional simplicity shaped catalytic capability remains unclear.

AtubAB dynamic instability revealed by TIRF microscopy. (A) Inset: assay design; biotinylated, GMPCPP-stabilised AtubAB dimers (labelled with 20% Alexa Fluor 647, shown as red) were anchored via NeutrAvidin to PEG Silane. Free AtubAB dimers (4 µM 20% Atto 488-labelled, cyan) were added, and filament polymerisation was observed by TIRF (total internal reflection fluorescence) microscopy. Field view revealing red GMPCPP seeds with plus- and minus-end growth (cyan). Only this used 20% tagged (unlabelled) AtubAhBs to observe dynamics at high concentrations needed for field views. Scale bar = 10 µm. B) Timelapse of plus-end growth of untagged AtubAB filament. The 10th image down shows the moment just after catastrophe, the ultra-rapid depolymerisation of the mini microtubule. Scale bar 5 µm. C) Kymograph (time vertical, filament axis horizontal) showing an untagged AtubAB filament growing and undergoing catastrophe at the plus-end. One growth episode (line) and one catastrophe event (arrowhead) are highlighted - it is the same as in panel B. Scale bars, 2 min / 2 µm. See also Supplementary Figures S4A & B and Movie M5. D) Asgard archaeal 4- pf mini microtubules show all the hallmarks of eukaryotic 13-protofilament microtubules - but are much thinner. We therefore suggest it is possible that Asgard mini microtubules are the evolutionary precursors of eukaryotic microtubules. Arrows do not indicate evolutionary distances or complexity. -- biorxiv.org

Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Asgard Archaeal Origin Of Microtubules

by Keith CowingFebruary 25, 2026February 25, 2026

Eukaryotic cells change their shapes, actively segregate their DNA and contain membrane networks, facilitated by a complex cytoskeleton containing actin filaments, microtubules made from tubulin, and other components.

The experimental pipeline, from design to characterization, of peptides comprising the Xeno 1 and Xeno 2 amino acid alphabets. Design begins with a library of commercially available amino acids. The physicochemical properties (Van der Waals volume and hydrophobicity at pH 7) are then estimated for a xeno alphabet heuristic search. The potential energy surfaces for each amino acid which returns in the search is calculated and two xeno amino acid alphabets, Xeno 1 and Xeno 2, are selected based on post-search metrics (e.g. PCA and EMD). The similarity of these alphabets to the E10 is further assessed via calculation of HOMO-LUMO gaps and LogS: their ability to form secondary structures is measured in vitro with ECD, IR, and NMR spectroscopy for random combinatorial 25-mer libraries and for designed sequences. -- biorxiv.org

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Press Release

Xeno Amino Acid Alphabets Form Peptides With Familiar Secondary Structure

by Keith CowingFebruary 10, 2026

The central dogma of molecular biology describes how genetic information stored in nucleic acids guides the formation of structured proteins from a single molecular alphabet of twenty amino acids (C20)1,2.

GC content, total number and their frequencies of PQS in H. volcanii genome. (A) Schematic presentation of a G-quartet (left) and a G-quadruplex (right). (B) Total PQS counts, percentage of GC and PQS frequency characteristics for the main chromosome and mini-chromosomes. (C,D) G4 prediction in H. volcanii’s promoters: number and localisation relative to the TSS. -- biorxiv.org

Biochemistry & Organic Chemistry, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Archaeal G-Quadruplexes: A Novel Model for Understanding Unusual DNA/RNA Structures Across the Tree of Life

by Keith CowingFebruary 10, 2026February 10, 2026

Archaea, a domain of microorganisms found in diverse environments including the human microbiome, represent the closest known prokaryotic relatives of eukaryotes.

Hypothetical sequence of events that led to the origin of the purple-green photosymbiosis of P. tenue. See main text for details. Note that all ancestors and extant species remain phagotrophic (or mixotrophic in the case of photosymbiosis). This study has revealed the order of endosymbiont acquisition in P. tenue and potential pre adaptations that facilitated the symbiosis. These insights have, in turn, shed light on the question of how two contrasting photosynthetic symbionts came to exist within the same host. Moreover, we have expanded the known diversity of the genus Pseudoblepharisma by discovering new non photosymbiotic species and confidently establishing the sister relationship between the genera Pseudoblepharisma and Spirostomum in the family Spirostomidae. Our genome-based predictions on the physiology of photosymbiotic Pseudoblepharisma species represent the basis for future experimental work on the identity of the metabolites that are exchanged among symbiotic partners. -- biorxiv.org

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

The Phylogenetic Context For The Origin Of A Unique Purple-green Photosymbiosis

by Keith CowingFebruary 9, 2026February 9, 2026

Symbioses are widespread in nature and have been the source of much evolutionary innovation. While some types of symbioses evolved multiple times across space and time (e.g., oxygenic photosymbioses or […]

Iron disruption through endosymbiosis: An overview of disruptive effects of iron throughout endosymbiosis, from ecological associations and biochemistries of archaea and bacteria (69) to LECA (90, 94). These effects may underlie a mechanistic connection between the cessation of marine iron deposition and the radiation of the earliest eukaryotes. -- biorxiv.org

Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Origin & Evolution of Life, Status Report

Did Iron Suppress Eukaryote Emergence and Early Radiation?

by Keith CowingFebruary 5, 2026June 11, 2026

The last eukaryotic common ancestor (LECA) is widely thought to have been an oxygen-respiring organism, arising through endosymbiosis when a free-living bacterium became the mitochondrion.

iss070e014729 (Oct. 29, 2023) -- Orbital nighttime peeks through the International Space Station's cupola, or "window to the world," nearly 270 miles above the Indian Ocean. In the right window, the cymbal-shaped solar array that powers Northrop Grumman's Cygnus spacecraft can be seen. Media Credit: NASA

Life Support Systems, Microbiology & Virology, Microgravity, Space Life Science, Space Physiology & Medicine, Space Stations, Status Report

A Next Generation Space Antimicrobial: Assessing Microbial Activity And Reduction Across The ISS

by Keith CowingJanuary 28, 2026January 28, 2026

Microbial contamination in spacecraft poses a threat to crew health and operational integrity. Currently, microbial reduction aboard the International Space Station (ISS) relies on rigorous cleaning, which is time-consuming for […]

Selection protocol used to isolate ligase ribozymes.

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Emergence Of Diverse Ligase Reactivities From A Single RNA Evolution Experiment

by Keith CowingJanuary 23, 2026January 23, 2026

RNA-catalyzed assembly of RNA strands was one of the most essential enzymatic functions in a primordial RNA-based biology.

Schematic drawing of a Fiersviridae (formely Leviviridae) virion (cross section and side view) ViralZone, SIB Swiss Institute of Bioinformatics: Levivirus CC BY 4.0 via Wikipedia

Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Habitable Zones, Mars, Microbiology & Virology, Status Report

Regolith as a Refuge: Differential Survival of Bacteriophage Qβ in Mars-Analog Environments

by Keith CowingJanuary 19, 2026January 19, 2026

Viruses are among the simplest biological entities capable of replication. Their robustness and adaptability make them relevant not only to terrestrial ecosystems but also to astrobiological exploration.

Phylogenetic trees constructed using the GTDB-Tk. The trees of (a) 197 bacterial and (b) 27 archaeal high-quality MAGs obtained in this study. The concentric rings surrounding each tree represent, from innermost to outermost, the sediment depth from which the MAG was recovered (5 m to 295 m), the phylum-level classification, and the average MAG coverage. In the bacterial tree (a), clusters marked in red text indicate groups of six or more MAGs with an ANI>97%, which were selected to analyse recombination-to-mutation ratios. The scale bar indicates the expected number of substitutions per site. ANI average nucleotide identity, GTDB-Tk Genome Taxonomy Database Toolkit, MAG metagenome-assembled genome. -- biorxiv.org

Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Status Report

Evolutionary Stasis And Homogeneous Selection Structure Microbial Communities In The Deep Subseafloor Sedimentary Biosphere

by Keith CowingJanuary 14, 2026January 14, 2026

The subseafloor biosphere, one of the Earth’s largest and most stable microbial habitats, mainly consists of energy-limited sediments where microbial life persists over geological timescales.

biorxiv.org

Emergence Of A Potentially Ancestral ATP-synthesizing Activity Under Prebiotic Amino Acid Constraints

Asgard Archaeal Origin Of Microtubules

Xeno Amino Acid Alphabets Form Peptides With Familiar Secondary Structure

Archaeal G-Quadruplexes: A Novel Model for Understanding Unusual DNA/RNA Structures Across the Tree of Life

The Phylogenetic Context For The Origin Of A Unique Purple-green Photosymbiosis

Did Iron Suppress Eukaryote Emergence and Early Radiation?

A Next Generation Space Antimicrobial: Assessing Microbial Activity And Reduction Across The ISS

Emergence Of Diverse Ligase Reactivities From A Single RNA Evolution Experiment

Regolith as a Refuge: Differential Survival of Bacteriophage Qβ in Mars-Analog Environments

Evolutionary Stasis And Homogeneous Selection Structure Microbial Communities In The Deep Subseafloor Sedimentary Biosphere

Astrobiologist Dale Andersen’s Antarctic Field Report: 9 November 2026: Lake Untersee Basecamp Update

Astrochemistry: Hubble and JWST Observe Star Formation in The Carina Nebula

Mapping the Historical Roots of Astrobiology: A Reference Publication Year Spectroscopy (RPYS) Analysis

The Agentic Observer Hackathon: Autonomous Decision-making in Simulated Astronomical Surveys

Tracking The Evolution of sub-Neptunes. I. Gyrochronology of Planet Hosting Stars