High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture...

Area of Science:

• Evolutionary Biology
• Genomics
• Molecular Biology

Background:

• Understanding cellular evolution is crucial for medical interventions and bioengineering.
• The adaptome, comprising genetic changes driving adaptation, can be mapped by tracking beneficial variants during clonal evolution.

Purpose of the Study:

• To characterize mutations in Escherichia coli genes under selection using a novel sequencing method.
• To demonstrate the utility of multiplex adaptome capture sequencing (mAdCap-seq) for deep profiling of a cell's adaptome.

Main Methods:

• Multiplex adaptome capture sequencing (mAdCap-seq), combining unique molecular identifiers and hybridization-based enrichment.
• Characterization of mutations in eight Escherichia coli genes in a laboratory environment.
• Tracking 301 mutations at frequencies as low as 0.01%.

Main Results:

• Inferred fitness effects for 240 mutations.
• Identified distinct molecular signatures of selection on protein structure and function for genes with the most beneficial mutations.
• Successfully profiled a targeted portion of the cell's adaptome.

Conclusions:

• mAdCap-seq is an effective method for deeply profiling a cell's adaptome.
• The study provides insights into the genetic basis of adaptation in Escherichia coli.
• Findings can inform strategies for medical interventions and bioengineering involving cellular evolution.