Genomes of diverse microbes point to early evolution of a rudimentary immune system

The last ancestor shared by all living organisms was a microbe that lived 4.2 billion years ago, had a fairly large genome encoding some 2600 proteins, enjoyed a diet of hydrogen gas and carbon dioxide, and harbored a rudimentary immune system for fighting off viral invaders. That’s the conclusion of a new study that compared the genomes of a diverse range of 700 modern microbes and looked for commonalities to identify which features arose first. Although the analysis doesn’t reveal how life got its start, it suggests a complex cellular organism somewhat similar to modern microbes evolved only a few hundred million years after Earth’s formation.

“I was quite excited,” says Betül Kaçar, an evolutionary biologist at the University of Wisconsin–Madison who saw the research presented this week at the Society for Molecular Biology & Evolution meeting in Puerto Vallarta, Mexico. (The study is also published today in Nature Ecology & Evolution.) “It’s a comprehensive analysis and a good example of how to do this work.”

It’s not the first attempt to sketch the identity of the hypothetical last universal common ancestor, or LUCA. In 2016, for example, researchers led by William Martin, an evolutionary biologist at Heinrich Heine University Düsseldorf, used a related approach of comparing known microbial genomes to provide the most compelling genetic evidence yet that LUCA likely was an anaerobe that grew in an environment devoid of oxygen required by most cells today. Martin’s genetic analysis also found evidence suggesting it was a “thermophile,” a heat-loving microbe, that fed on hydrogen gas (H2). That combination suggested it may have lived near deep-sea ocean vents near underwater volcanoes...

The common ancestry of all extant cellular life is evidenced by the universal genetic code, machinery for protein synthesis, shared chirality of the almost-universal set of 20 amino acids and use of ATP as a common energy currency1. The last universal common ancestor (LUCA) is the node on the tree of life from which the fundamental prokaryotic domains (Archaea and Bacteria) diverge. As such, our understanding of LUCA impacts our understanding of the early evolution of life on Earth. Was LUCA a simple or complex organism? What kind of environment did it inhabit and when? Previous estimates of LUCA are in conflict either due to conceptual disagreement about what LUCA is2 or as a result of different methodological approaches and data3,4,5,6,7,8,9. Published analyses differ in their inferences of LUCA’s genome, from conservative estimates of 80 orthologous proteins10 up to 1,529 different potential gene families4. Interpretations range from little beyond an information-processing and metabolic core6 through to a prokaryote-grade organism with much of the gene repertoire of modern Archaea and Bacteria8, recently reviewed in ref. 7. Here we use molecular clock methodology, horizontal gene-transfer-aware phylogenetic reconciliation and existing biogeochemical models to address questions about LUCA’s age, gene content, metabolism and impact on the early Earth system.

Estimating the age of LUCA

Life’s evolutionary timescale is typically calibrated to the oldest fossil occurrences. However, the veracity of fossil discoveries from the early Archaean period has been contested11,12. Relaxed Bayesian node-calibrated molecular clock approaches provide a means of integrating the sparse fossil and geochemical record of early life with the information provided by molecular data; however, constraining LUCA’s age is challenging due to limited prokaryote fossil calibrations and the uncertainty in their placement on the phylogeny. Molecular clock estimates of LUCA13,14,15 have relied on conserved universal single-copy marker genes within phylogenies for which LUCA represented the root. Dating the root of a tree is difficult because errors propagate from the tips to the root of the dated phylogeny and information is not available to estimate the rate of evolution for the branch incident on the root node. Therefore, we analysed genes that duplicated before LUCA with two (or more) copies in LUCA’s genome16...