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

MC Weiss, M Preiner, JC Xavier, V Zimorski… - PLoS …, 2018 - journals.plos.org
All known life forms trace back to a last universal common ancestor (LUCA) that witnessed
the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the …

[HTML][HTML] The evolution of metabolism: How to test evolutionary hypotheses at the genomic level

F Scossa, AR Fernie - Computational and Structural Biotechnology Journal, 2020 - Elsevier
The origin of primordial metabolism and its expansion to form the metabolic networks extant
today represent excellent systems to study the impact of natural selection and the potential …

[PDF][PDF] Confronting the catalytic dark matter encoded by sequenced genomes

KW Ellens, N Christian, C Singh… - Nucleic acids …, 2017 - academic.oup.com
The post-genomic era has provided researchers with a deluge of protein sequences.
However, a significant fraction of the proteins encoded by sequenced genomes remains …

Living organisms author their read-write genomes in evolution

JA Shapiro - Biology, 2017 - mdpi.com
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from
complex cellular activities altering genome content and expression:(i) Symbiogenetic cell …

Functional annotations of paralogs: a blessing and a curse

R Zallot, KJ Harrison, B Kolaczkowski… - Life, 2016 - mdpi.com
Gene duplication followed by mutation is a classic mechanism of neofunctionalization,
producing gene families with functional diversity. In some cases, a single point mutation is …

Enzyme promiscuity, metabolite damage, and metabolite damage control systems of the tricarboxylic acid cycle

TD Niehaus, KB Hillmann - The FEBS Journal, 2020 - Wiley Online Library
Promiscuous enzymes and spontaneous chemical reactions can convert normal cellular
metabolites into noncanonical or damaged metabolites. These damaged metabolites can be …

The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force

DR Sannino, FA Arroyo… - Proceedings of the …, 2023 - National Acad Sciences
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped
individual is a million times the volume of Escherichia coli. To better understand the …

Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts

C Gonçalves, P Gonçalves - Proceedings of the National …, 2019 - National Acad Sciences
Horizontal acquisition of bacterial genes is presently recognized as an important
contribution to the adaptation and evolution of eukaryotic genomes. However, the …

Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions

JG Jeffryes, C Lerma-Ortiz, F Liu, A Golubev… - Metabolic …, 2022 - Elsevier
Spontaneous reactions between metabolites are often neglected in favor of emphasizing
enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be …

Alternate routes to mnm5s2U synthesis in Gram-positive bacteria

M Jaroch, G Sun, HCT Tsui, C Reed, J Sun… - Journal of …, 2024 - Am Soc Microbiol
The wobble bases of tRNAs that decode split codons are often heavily modified. In bacteria,
tRNAGlu, Gln, Asp contains a variety of xnm5s2U derivatives. The synthesis pathway for …