The transcriptomic and proteomic ramifications of segmental amplification

Gene amplification can drive adaptation by rapidly increasing the cellular dosage of critical gene products. Segmental amplifications often encompass large genomic regions surrounding the gene(s) under selection for higher dosage. Overexpression of co-amplified neighboring genes imposes a substantial metabolic burden. While compensatory mutations can decrease inappropriate overexpression of co-amplified genes, it takes time for such mutations to arise. The extent to which intrinsic regulatory mechanisms modulate expression of co-amplified genes in the immediate aftermath of segmental amplification is largely unknown. To address the collateral effects of segmental amplification, we evolved replicate cultures of an Escherichia coli mutant under conditions that select for higher dosage of an inefficient enzyme whose weak activity limits growth rate. Segmental amplifications encompassing the gene encoding the weak-link enzyme arose in all populations. Amplicons ranged in size (9 to 125 kb) and copy number (2 to 12 copies). We performed RNA-seq and label-free proteomics to quantify expression of amplified genes present at 2, 6, and 12 copies. mRNA expression generally scales with gene copy number, but protein expression scales less well with both gene copy number and mRNA expression. We characterize the molecular mechanisms underlying discrepancies between gene copy number and expression for several cases. We also show that segmental amplifications can have system-wide consequences by indirectly altering expression of non-amplified genes. Our findings indicate that the fitness benefit derived from segmental amplification depends on the combined effects of amplification size, gene content, and copy number as well as collateral effects on non-amplified genes. Significance StatementGene amplification frequently drives rapid adaptation when organisms are challenged by harsh conditions. However, gene amplification rarely amplifies only the gene(s) under selection for higher dosage. Segmental amplifications often include many co-amplified neighbor genes. Because segmental amplifications can reach very high copy number, overexpression of co-amplified genes can impose an energetic burden and perturb physiology, yet this aspect of gene amplification has received little attention. Here, we performed transcriptomic and proteomic analysis of laboratory-evolved Escherichia coli strains containing large, high-copy-number amplifications. We found that mRNA levels, but often not protein levels, scale well with gene copy number. We identified amplified genes that exhibit discrepancies between gene copy number and mRNA/protein expression and examine the molecular mechanisms underlying these discrepancies.