Biology subjects

Brandon Gaut

Publications and source records attributed to Brandon Gaut.

3 recordsLinked to original sources

bioRxiv2016

Lazarus effects: the frequency and genetic causes of Escherichia coli population recovery under lethal heat stress

Sometimes populations crash and yet recover before being lost completely. Such recoveries have been observed incidentally in evolution experiments using Escherichia coli, and this phenomenon has been termed the \"Lazarus effect.\" To investigate how often recovery occurs and the genetic changes that drive it, we evolved ~300 populations of E. coli at lethally high temperatures (43.0{degrees}) for five days and sequenced the genomes of recovered populations. Our results revealed that the Lazarus effect is uncommon, but frequent enough, at ~9% of populations, to be a potent source of evolutionary innovation. Population sequencing uncovered a set of mutations adaptive to lethal 43.0{degrees}C that were mostly distinct from those that were beneficial at a high but nonlethal temperature (42.2{degrees}). Mutations within two operons--the heat shock hslUV operon and the RNA polymerase rpoBC operon--drove adaptation to lethal temperature. Mutations in hslUV exhibited little antagonistic pleiotropy at 37.0{degrees}C and may have arisen neutrally prior to subjection to lethal temperature. In contrast, rpoBC mutations provided greater fitness benefits than hslUV mutants, but were less prevalent and caused stronger fitness tradeoffs at lower temperatures. Recovered populations fixed mutations in only one operon or the other, but not both, indicating that epistatic interactions between beneficial mutations were important even at the earliest stages of adaptation.

Evolutionary Biology↗

bioRxiv2015

CG methylation covaries with differential gene expression between leaf and floral bud tissues of Brachypodium distachyon

DNA methylation has the potential to influence plant growth and development through its influence on gene expression. To date, however, the evidence from plant systems is mixed as to whether patterns of DNA methylation vary significantly among tissues and, if so, whether these differences affect tissue-specific gene expression. To address these questions, we analyzed both bisulfite sequence (BSseq) and transcriptomic sequence data from three biological replicates of two tissues (leaf and floral bud) from the model grass species Brachypodium distachyon. Our first goal was to determine whether tissues were more differentiated in DNA methylation than explained by variation among biological replicates. Tissues were more differentiated than biological replicates, but the analysis of replicated data revealed high (>50%) false positive rates for the inference of differentially methylated sites (DMSs) and differentially methylated regions (DMRs). Comparing methylation to gene expression, we found that differential CG methylation consistently covaried negatively with gene expression, regardless as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expression and either CHG or CHH methylation was less consistent. In total, CG methylation in promoters explained 9% of the variation in tissue-specific expression across genes, suggesting that CG methylation is a minor but appreciable factor in tissue differentiation.

Genomics↗

bioRxiv2015

First-step Mutations during Adaptation to Thermal Stress Shift the Expression of Thousands of Genes Back toward the Pre-stressed State

The temporal change of phenotypes during the adaptive process remain largely unexplored, as do the genetic changes that affect these phenotypic changes. Here we focused on three mutations that rose to high frequency in the early stages of adaptation within 12 Escherichia coli populations subjected to thermal stress (42{degrees}C). All of the mutations were in the rpoB gene, which encodes the RNA polymerase beta subunit. For each mutation, we measured the growth curves and gene expression (mRNAseq) of clones at 42{degrees}C. We also compared growth and gene expression to their ancestor under unstressed (37{degrees}C) and stressed conditions (42{degrees}C). Each of the three mutations changed the expression of hundreds of genes and conferred large fitness advantages, apparently through the restoration of global gene expression from the stressed towards the pre-stressed state. Finally, we compared the phenotypic characteristics of one mutant, I572L, to two high-temperature adapted clones that have this mutation plus additional background mutations. The background mutations increased fitness, but they did not substantially change gene expression. We conclude that early mutations in a global transcriptional regulator cause extensive changes in gene expression, many of which are likely under positive selection for their effect in restoring the pre-stress physiology.

Evolutionary Biology↗