Selection of ade novogene that can promote survival ofE. coliby modulating protein homeostasis pathways

Abstract

Cells sometime adapt to challenging environments by turning non-functional loci into functional genes in a process termedde novogene birth. But how proteins with random amino acid sequences integrate into existing cellular pathways to provide a benefit remains poorly understood. Here, we screened ~108random genes for their ability to rescue growth arrest ofE. colicells producing the ribonuclease toxin MazF. Approximately 2,000 random genes could promote growth by reducing transcription from the promoter drivingmazFexpression. Additionally, one gene, namedrandomantitoxin ofMazF(ramF), whose protein product was well-tolerated in cells and neutralized MazF by interacting with chaperones, leading to MazF proteolysis. We show that the specificity of RamF for MazF relative to other toxins relies on the degron-like function of MazF's first 10 amino acids. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for howde novogene birth can produce new, functional proteins that are integrated into complex cellular systems and provide a benefit to cells.

Random, de novo, and conserved proteins: How structure and disorder predictors perform differently

“…However, to which extent is yet unknown, [8][9][10] Several studies have previously utilized randomly generated proteins to draw conclusions about the origin, structure, and activities of de novo proteins. [11][12][13][14][15][16][17] De novo proteins, particularly those of a more recent origin, have been found to differ from evolutionary conserved proteins and instead exhibit a similarity to random proteins, as they have not yet been subjected to natural selection. 8,9,13 Libraries of random sequences constrained only by a close to natural distribution of amino acids have been shown to form secondary structural elements.…”

“…Devoid of sequence homology outside their evolutionary trajectory, de novo proteins are considered to be distant in sequence space from evolutionarily conserved proteins and might instead resemble unevolved random proteins. However, to which extent is yet unknown, 8–10 Several studies have previously utilized randomly generated proteins to draw conclusions about the origin, structure, and activities of de novo proteins 11–17 . De novo proteins, particularly those of a more recent origin, have been found to differ from evolutionary conserved proteins and instead exhibit a similarity to random proteins, as they have not yet been subjected to natural selection 8,9,13 .…”

Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the noncanonical translatome

“…Carvunis et al 16 found de novo cORFs are enriched for the GO term 'response to stress'. Other studies showed examples of how de novo ORFs could be involved in stress response 29,64 or homeostasis 64,65 . For instance the de novo antifreeze glycoprotein AFGP allows Arctic codfish to live in colder environments 29 or MDF1 in yeast, provides resistance to certain toxins and mediates ion homeostasis 66 .…”

Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins

“…Future studies that leverage the ever-increasing global metagenomic sequences will be useful to tackle that question. Additionally, experimental evidence shows that the emergence of functional proteins via de novo gene evolution from noncoding sequences can provide adaptation in Escherichia coli (Babina et al 2023; Frumkin & Laub 2023). Thus, de novo evolution may be more plausible, and prevalent, than usually assumed.…”