The transcriptomic and proteomic ramifications of segmental amplification

Abstract

AbstractGene duplication and subsequent amplification can drive adaptation by rapidly increasing the cellular dosage of critical gene products. Gene duplication events often encompass large genomic segments surrounding the gene(s) under selection for higher dosage. Overexpression of co-amplified genes imposes a significant 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 can modulate the 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 anEscherichia colimutant 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 were detected in all populations. These amplifications ranged in size, from 9 to 125 kb, and copy number, from 2 to 12 copies. We performed RNA-seq and label-free quantitative proteomics to quantify the expression of amplified genes present at 2, 6, and 12 copies. mRNA expression generally scales with gene copy number, but protein expression scales poorly with both gene copy number and mRNA expression. We propose mechanisms to explain these discrepancies for several cases in which expression is either higher or lower than expected based on gene copy number. We also show that segmental amplifications can have system-wide consequences by indirectly altering expression of non-amplified genes. Overall, our findings indicate that the fitness benefit derived from segmental amplification depends on the combined effects of amplicon size, copy number, and gene content.