Global Chromosomal Structural Instability in a Subpopulation of Starving Escherichia coli Cells

Abstract

Copy-number variations (CNVs) constitute very common differences between individual humans and possibly all genomes and may therefore be important fuel for evolution, yet how they form remains elusive. In starving Escherichia coli, gene amplification is induced by stress, controlled by the general stress response. Amplification has been detected only encompassing genes that confer a growth advantage when amplified. We studied the structure of stress-induced gene amplification in starving cells in the Lac assay in Escherichia coli by array comparative genomic hybridization (aCGH), with polymerase chain reaction (pcr) and DNA sequencing to establish the structures generated. About 10% of 300 amplified isolates carried other chromosomal structural change in addition to amplification. Most of these were inversions and duplications associated with the amplification event. This complexity supports a mechanism similar to that seen in human non-recurrent copy number variants. We interpret these complex events in terms of repeated template switching during DNA replication. Importantly, we found a significant occurrence (6 out of 300) of chromosomal structural changes that were apparently not involved in the amplification event. These secondary changes were absent from 240 samples derived from starved cells not carrying amplification, suggesting that amplification happens in a differentiated subpopulation of stressed cells licensed for global chromosomal structural change and genomic instability. These data imply that chromosomal structural changes occur in bursts or showers of instability that may have the potential to drive rapid evolution.

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

“…The mutation rate increase is indeed also restricted to subpopulations of cells, because it appears the hypermutation is mostly restricted to about 1% of stressed cells that have double-strand breaks in DNA (258). Also, the stress-induced GDA changes may be in subpopulations of bacteria that show repeated template switching during DNA replication (181). All this mutational heterogeneity in subpopulations adds to the rich variation from which adaptive strategies can emerge in bacteria.…”

Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements

“…The MMBIR model has since been used to explain telomere healing (Lowden, et al, 2011; Yatsenko, et al, 2012) and CGRs in a number of diseases including cancer (Lawson et al, 2011; Vissers et al, 2009; Wang et al, 2015). In addition, MMBIR-like events have been described in various model systems including bacteria (Slack et al, 2006; Lin et al, 2011), yeast (Payen et al, 2008), Arabidopsis (Kwon et al, 2010; Marechal et al, 2009), Caenorhabditis elegans (Meier et al, 2014), and mouse embryonic stem cells (Arlt et al, 2012). However, despite the broad occurrence of MMBIR and its important role in CGR formation, what triggers initiation of MMBIR remains unknown.…”

Multiple Pathways of Duplication Formation with and Without Recombination (RecA) in Salmonella enterica

“…This structure is later modified by deletions that leave the observed REP and SJ duplications. The proposed pathway is supported by the amplified TID structures found following selection for increased gene copy number in E. coli, Salmonella, and yeast (Rattray et al 2005;Narayanan et al 2006;Kugelberg et al 2010;Brewer et al 2011;Lin et al 2011).…”

“…Tandem inversion duplication: This duplication type was identified in Lac + revertants isolated after prolonged selection of a leaky lac mutant for improved growth on lactose (Kugelberg et al 2006;Kugelberg et al 2010;Lin et al 2011). Roughly 20% of the Lac + revertants with an amplification of the region ABCD had multiple tandem copies of a basic structure that could be described as: ABCD-C9B9A9-BCD.…”

“…Some selected amplifications (20%) have repeated tandem inversion duplications (TID), in which a parental sequence element (e.g., ABCD) is repeated three times in alternating orientation ABCD-D9C9B9A9-ABCD and amplified by exchanges between flanking direct repeats. The parent sequence ABCD can be .10 kb and the initial TID junctions are flanked by extensive perfectly complementary sequences that can be rendered asymmetric (ABCD-C9B9A9-BCD) by junction deletions (Kugelberg et al 2010;Lin et al 2011). …”