Metabolism Archives

Overall information on the first and second nitrogen replacements in a benzene ring.

Biochemistry & Organic Chemistry, Genomics, Proteomics, Bioinformatics, Imaging & Spectroscopy, Origin & Evolution of Life, Status Report, Water/Hycean Worlds & Oceanography

Novel Chemical Pathways For The Formation Of Nucleobase Precursors Via Benzene π-Bond Addition To HCN

by Keith CowingMay 13, 2026May 13, 2026

We propose a simple and efficient pathway for the formation of precursors to core nucleobases in DNA and RNA using a suite of computational chemistry methods.

Energetics associated with the occupancy of the K1 site and the position of the M2 ion. (A) Free energy surface of the concerted motions of Prp11 Lys10 and M2, with the initial PDB conformation marked by a yellow star. (B–D) Representative structures of three metastable states from metadynamics simulations. State 1 (B) represents a PDB-like arrangement where Lys10 (slate blue sticks) remains at the K1 site, and M2 (yellow sphere) is properly positioned at the U6 snRNA triple-helix (yellow cartoon). State 2 (C): Lys10 leaves the K1 site, allowing a K+ ion to occupy it and stabilize M2 in place. State 3 (D): M2 directly coordinates G52, losing its catalytic position and partially occupying the K1 site. -- PNAS

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Status Report

Computational Chemistry And Supercomputers To Help Understand The Mechanisms Of Life

by Keith CowingApril 13, 2026April 13, 2026

A new study from the Italian Institute of Technology (IIT), in collaboration with Uppsala University (Sweden) and AstraZeneca, shows how computational chemistry and supercomputers can help scientists better understand the […]

Graphical Abstract -- Journal of the American Chemical Society

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Status Report

Entropy-Driven Amino Acid-Based Coacervates with Enzyme-Free Metabolism and Prebiotic Robustness

by Keith CowingJanuary 3, 2026January 2, 2026

Protocells capable of nonenzymatic metabolism and environmental adaptation are essential models for understanding the emergence of cellular life.

The phylogenetic tree showed the amino acid of xoxF and mxaF genes in MAGs from lava tubes, Haikou City, Hainan Province. The blue words indicated the acquired MAGs in this study. -- JGR Planets via x-mol.net

Analog Studies, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Caves, Craters, Mountains, Subsurface, Lava Tubes, Extremeophiles and Extreme Environments, Habitable Zones, Mars, Microbiology & Virology, Status Report, Terraforming & Geoengineering

Microbial Diversity and Metabolic Adaptations in Mars‐Analog Lava Tubes

by Keith CowingJanuary 3, 2026January 2, 2026

Lunar and Martian lava tubes will offer stable temperatures and radiation protection, making them potential habitats for extraterrestrial life. The Martian atmosphere, containing gases like H2, CO, and CH4, could […]

Processes occurring in the protocell at each time step. Continuous arrows show polymers being produced, segmented arrows show peptide catalysis of CO2 fixation and templated polymerisation, and dotted arrows indicate RNA acting as templates for copying and translation. Note that sequences shown here are illustrative, and the model only keeps track of hydrophobicity and length of sequences, and not sequence order. -- biorxiv.org

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

First Growth, Then Information: The Path To Genetic Heredity In Protocells

by Keith CowingDecember 15, 2025December 15, 2025

Most theoretical work on the origin of heredity has focused on how genetic information can be maintained without mutational degradation in the absence of error-proofing systems. A simple and parsimonious […]

Ribosome biogenesis processes and sets of RBFs in bacteria. a)Schematic view of multi-step ribosome biogenesis including the list of RBFs and tertiary structure of RPs, 70S, 50S and 30S subunits (PDB code: 4YBB, 5UYN, 6ENF, and 1RQU). The structure was visualized using CueMol. b) Boxplot representation of the number of BFs across different phyla in bacteria. Firmicutes are divided into seven groups in the AnnoTree database. * indicates fau-1, recently designated as a gene of RNase W (Vayssières et al. 2024). ** indicates a P-value of ≤ 0.01. -- Molecular Biology and Evolution

Genomics, Proteomics, Bioinformatics, Status Report

Evolutionary Flexibility of Ribosome Biogenesis in Bacteria

by Keith CowingDecember 11, 2025December 10, 2025

Ribosomes are essential for protein synthesis and require ribosome biogenesis factors for assembly.

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

All Life Copies DNA Unambiguously Into Proteins. Archaea May Be The Exception.

by Keith CowingDecember 2, 2025December 2, 2025

The beauty of the DNA code is that organisms interpret it unambiguously. Each three-letter nucleotide sequence, or codon, in a gene codes for a unique amino acid that’s added to […]

Summary of different extracellular electron transfer (EET) pathways. While it is common to classify EET based on the nature and function of the mediators, here the emphasis is on the means of electron transport. (A) Electrons are transported between cells via direct interspecies electron transfer (DIET) through (1) direct contact via conductive pili and/or nanowires, (2) conductive particles smaller than the cells (e.g., magnetite), and (3) conductive particles larger than the cells (e.g., activated carbon). (B) Electrons are exported from cells to the solid surface via outward EET through (1), (4) direct contact via redox-active proteins, (5) diffusive soluble electron shuttles, and (6) redox mediators or enzymes. (C) Electrons are taken up by cells from the solid surface via inward EET or extracellular electron uptake (EEU) through (1), (4)–(6). Asterisks denote that not the exact same mechanism is employed by outward EET and inward EET when redox-active proteins are involved. -- mLife

Biophysics, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Habitable Zones, Magnetic Fields, Electromagnetism, bioelectricity,, Microbiology & Virology, Origin & Evolution of Life, Status Report

Current Understanding Of Electroautotrophy And Its Relevance In Astrobiology-related Research

by Keith CowingOctober 28, 2025October 28, 2025

Electroautotrophy—the use of extracellular electrons as the primary energy source for autotrophic metabolism—remains understudied compared to photoautotrophy and chemoautotrophy.

Researcher Issaku Kohl recorded this image at a historic mining district in Spain, which scientists now an analog for the surface of Mars. It shows the mixing zone on the Rio Tinto, where green water, rich in the Fe2+ ion of iron, containing very high O₂ content sulfate, is discharging from a mine tailings pile. This water is mixing into the river’s main branch red waters, where most of the iron occurs as Fe3+ and sulfate oxygen is mostly sourced from water. -- University of Utah

Analog Studies, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Mars, Press Release

How A Pyrite-oxidizing Microbe Helps Preserve Atmospheric Oxygen In Sulfate

by Keith CowingOctober 27, 2025October 27, 2025

Because oxygen-bearing sulfate minerals trap and preserve signals from Earth’s atmosphere, scientists closely study how they form. Sulfates are stable over billions of years, so their oxygen isotopes are seen […]

Conceptual model for the evolution of exoenzymes and the recycling of organic matter across the Great Oxidation Event (GOE). (A) In the Archean Ocean, prior to the GOE, the recycling of organic matter depended entirely on the activity of fermenters. This resulted in low recycling efficiency, elevated carbon burial, and limited regeneration of essential nutrients back into seawater. This scarcity of particulate organic matter (POM) also reduced the availability of niches for microbial colonization, thus limiting the selective pressure for the evolution of exoenzyme systems. (b) Following the GOE, rising oxygen levels increased the availability of high-energy electron acceptors (e.g. O2, nitrate and ferric iron), supporting the expansion of metabolic groups with high exoenzyme capacity, such as aerobic heterotrophs, dissimilatory nitrate reducers and dissimilatory ferric iron reducers. Concurrently, increases in POM abundance and microbial cell densities would have amplified the selective pressure to produce exoenzymes. Collectively, these changes in the Paleoproterozoic promoted more efficient recycling of organic matter and regeneration of nutrients back into the water column, ultimately fueling greater primary productivity and oxygen release. This feedback between exoenzyme evolution, nutrient cycling, and oxygen production would have amplified Earth’s progressive oxygenation. -- biorxiv.org

Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Gaia - Planetary Perspectives, Origin & Evolution of Life, Status Report, Water/Hycean Worlds & Oceanography

Microbial Exoenzymes Catalyzed The Transition To An Oxygenated Earth

by Keith CowingOctober 11, 2025October 11, 2025

Microbial exoenzymes—extracellular enzymes secreted to degrade complex organic polymers— are essential for recycling carbon and nutrients, thus sustaining primary productivity in today’s oceans.

Metabolism

Novel Chemical Pathways For The Formation Of Nucleobase Precursors Via Benzene π-Bond Addition To HCN

Computational Chemistry And Supercomputers To Help Understand The Mechanisms Of Life

Entropy-Driven Amino Acid-Based Coacervates with Enzyme-Free Metabolism and Prebiotic Robustness

Microbial Diversity and Metabolic Adaptations in Mars‐Analog Lava Tubes

First Growth, Then Information: The Path To Genetic Heredity In Protocells

Evolutionary Flexibility of Ribosome Biogenesis in Bacteria

All Life Copies DNA Unambiguously Into Proteins. Archaea May Be The Exception.

Current Understanding Of Electroautotrophy And Its Relevance In Astrobiology-related Research

How A Pyrite-oxidizing Microbe Helps Preserve Atmospheric Oxygen In Sulfate

Microbial Exoenzymes Catalyzed The Transition To An Oxygenated Earth

Ancient Layers On Mars Exposed By A Crater Within A Crater In Terra Sirenum

Send Your Name to Titan Aboard NASA’s Dragonfly Astrobiology Mission

Reconciling Giant Impacts with the Radius Valley: The Role of Silicate-Hydrogen Miscibility for Sub-Neptunes

Comprehensive Visible and Near-infrared Keck and Gemini Monitoring and Characterization of Interstellar Comet 3I/ATLAS during its Encounter with the Solar System

ExoVetter and a TESS Exoplanet Transit Search of Kepler Stars as Ground Truth