Editor’s note: As we expand outward from Earth to other worlds we are almost certainly going to encounter things we did not expect to find – things that are unlikely or impossible on Earth. Life on other worlds may arise from a totally different set of chemical pathways than was the case on Earth. Or it may follow a very similar path. Or both. How do we estimate what could exist such that we are better prepared to search for the unexpected? Using systems such these researchers have done to identify the plethora of compounds that are possible and functional in Earth life is one way to start to figure that out. This barcoding technology could find future application in understanding two things: how Earth life responds and/or adapts to novel extraterrestrial environments and understanding how alien genomic systems work – and also adapt to new environments.
[biorxiv.org] Saturation mutagenesis is a powerful tool for understanding and engineering the function of biological systems, and has been applied successfully to characterize the mutational landscape of individual proteins and genetic loci.
However, it has not been applied at the whole genome scale due to the challenges of both creating and quantifying a saturating set of mutations. Here we introduce BioBloom, a retron based method for barcoded saturation mutagenesis at the scale of a whole bacterial genome.
We constructed a barcoded BioBloom library with >99% projected sampling of saturating single nucleotide polymorphism (SNP) mutations of the E. coli genome, and applied it to identify beneficial mutations under salt and antibiotic selection. Relative to other techniques like CRISPR enabled mutagenesis or Adaptive Laboratory Evolution, BioBloom excels at identifying diverse causal SNPs quickly and at smaller working volumes.
A barcoded, saturating mutation library is also a shared resource, and we are releasing the updated BioBloom Ec. 2.0 library to the scientific community for broader adoption and application. Together, BioBloom makes barcoded saturation mutagenesis accessible at whole genome scale, creating new opportunities for large scale data collection and bacterial engineering.
BioBloom, a method for barcoded saturation mutagenesis of an entire bacterial genome, biorxiv.org
Astrobiology, Genomics
