Review of Jewish Tradition and the Challenge of Darwinism, Geoffery Cantor and Marc Swetlitz, eds.

This is a book review

Review of Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis

This is a book review

Differential expression analysis for multiple conditions

As high-throughput sequencing has become common practice, the cost of sequencing large amounts of genetic data has been drastically reduced, leading to much larger data sets for analysis. One important task is to identify biological conditions that lead to unusually high or low expression of a particular gene. Packages such as DESeq implement a simple method for testing differential signal when exactly two biological conditions are possible. For more than two conditions, pairwise testing is typically used. Here the DESeq method is extended so that three or more biological conditions can be assessed simultaneously. Because the computation time grows exponentially in the number of conditions, a Monte Carlo approach provides a fast way to approximate the $p$-values for the new test. The approach is studied on both simulated data and a data set of {\em C. jejuni}, the bacteria responsible for most food poisoning in the United States

Escherichia coli Lacking RpoS Are Rare in Natural Populations of Non-Pathogens

The alternative sigma factor RpoS controls a large regulon that allows E. coli to respond to a variety of stresses. Mutations in rpoS can increase rates of nutrient acquisition at the cost of a decrease in stress resistance. These kinds of mutations evolve rapidly under certain laboratory conditions where nutrient acquisition is especially challenging. The frequency of strains lacking RpoS in natural populations of E. coli is less clear. Such strains have been found at frequencies over 20% in some collections of wild isolates. However, laboratory handling can select for RpoS-null strains and may have affected some of these strain collections. Other studies have included an unknown diversity of strains or only used a phenotypic proxy as a measure of RpoS levels. We directly measured RpoS levels in a collection of E. coli that includes the full diversity of the species and that was handled in a manner to minimize the potential for laboratory evolution. We found that only 2% of strains produce no functional RpoS. Comparison of these strains in multiple labs shows that these rpoS mutations occurred in the laboratory. Earlier studies reporting much higher levels of RpoS polymorphism may reflect the storage history of the strains in laboratories rather than true frequency of such strains in natural populations

The transcriptional response of genes to RpoS concentration in Escherichia coli is not determined by core promoter sequences

The alternative sigma factor RpoS is an important regulatory protein in Escherichia coli, responsible for mediating the general stress response. RpoS levels vary continuously in response to different stresses. Previous work has shown that genes vary in their responsiveness to increasing RpoS concentrations, with some genes being "sensitive," requiring only a low level of RpoS to be relatively highly expressed, while other genes are "insensitive," only being highly expressed in the presence of high levels of RpoS. In other systems, this type of variation is caused by interactions between the regulatory protein and the DNA it binds. To see if this is the case for RpoS, we measured twelve RpoS binding site mutants for their effects on maximal expression and responsiveness to increasing RpoS concentration. While maximal expression varied over an order of magnitude across these twelve constructs, the responsiveness to increasing RpoS concentration was largely unaffected, suggesting that the RpoS binding site alone is not responsible for a genes' sensitivity or insensitivity to RpoS. In addition, we swapped the RpoS binding region between sensitive and insensitive promoters and found no change in the behavior of the promoter. Taken together, these results argue that differences in sensitivity of the RpoS-dependent promoters are not due to interactions between RpoS and the various DNA sites it binds

Size Doesn\u27t Matter: Microbial Selection Experiments Address Ecological Phenomena

Experimental evolution is relevant to ecology because it can connect physiology, and in particular metabolism, to questions in ecology. The investigation of the linkage between the environment and the evolution of metabolism is tractable because these experiments manipulate a very simple environment to produce predictable evolutionary outcomes. In doing so, microbial selection experiments can examine the causal elements of natural selection: how specific traits in varying environments will yield different fitnesses. Here, we review the methodology of microbial evolution experiments and address three issues that are relevant to ecologists: genotype-by-environment interactions, ecological diversification due to specialization, and negative frequency-dependent selection. First, we expect that genotype-by-environment interactions will be ubiquitous in biological systems. Second, while antagonistic pleiotropy is implicated in some cases of ecological specialization, other mechanisms also seem to be at work. Third, while negative frequency-dependent selection can maintain ecological diversity in laboratory systems, a mechanistic (biochemical) analysis of these systems suggests that negative frequency dependence may only apply within a narrow range of environments if resources are substitutable. Finally, we conclude that microbial experimental evolution needs to avail itself of molecular techniques that could enable a mechanistic understanding of ecological diversification in these simple systems

The Effect of Mobile Element IS10 on Experimental Regulatory Evolution in Escherichia coli

Mobile genetic elements are widespread in bacteria, where they cause several kinds of mutations. Although their effects are on the whole negative, rare beneficial mutations caused by insertion sequence elements are frequently selected in some experimental evolution systems. For example, in earlier work, we found that strains of Escherichia coli that lack the sigma factor RpoS adapt to a high-osmolarity environment by the insertion of element IS10 into the promoter of the otsBA operon, rewiring expression from RpoS dependent to RpoS independent. We wished to determine how the presence of IS10 in the genome of this strain shaped the evolutionary outcome. IS10 could influence the outcome by causing mutations that confer adaptive phenotypes that cannot be achieved by strains without the element. Alternatively, IS10 could influence evolution by increasing the rate of appearance of certain classes of beneficial mutations even if they are no better than those that could be achieved by a strain without the element. We found that populations evolved from an IS10-free strain did not upregulate otsBA. An otsBA-lacZY fusion facilitated the recovery of a number of mutations that upregulate otsB without involving IS10 and found that two caused greater fitness increases than IS10 insertion, implying that evolution could have upregulated otsBA in the IS10-free strain. Finally, we demonstrate that there is epistasis between the IS10 insertion into the otsBA promoter and the other adaptive mutations, implying that introduction of IS10 into the otsBA promoter may alter the trajectory of adaptive evolution. We conclude that IS10 exerts its effect not by creating adaptive phenotypes that could not otherwise occur but by increasing the rate of appearance of certain adaptive mutations

The transcriptional response of genes to RpoS concentration in Escherichia coli is not determined by core promoter sequences

The alternative sigma factor RpoS is an important regulatory protein in Escherichia coli, responsible for mediating the general stress response. RpoS levels vary continuously in response to different stresses. Previous work has shown that genes vary in their responsiveness to increasing RpoS concentrations, with some genes being "sensitive," requiring only a low level of RpoS to be relatively highly expressed, while other genes are "insensitive," only being highly expressed in the presence of high levels of RpoS. In other systems, this type of variation is caused by interactions between the regulatory protein and the DNA it binds. To see if this is the case for RpoS, we measured twelve RpoS binding site mutants for their effects on maximal expression and responsiveness to increasing RpoS concentration. While maximal expression varied over an order of magnitude across these twelve constructs, the responsiveness to increasing RpoS concentration was largely unaffected, suggesting that the RpoS binding site alone is not responsible for a genes' sensitivity or insensitivity to RpoS. In addition, we swapped the RpoS binding region between sensitive and insensitive promoters and found no change in the behavior of the promoter. Taken together, these results argue that differences in sensitivity of the RpoS-dependent promoters are not due to interactions between RpoS and the various DNA sites it binds

Bacterial Nucleoid-Associated Protein Uncouples Transcription Levels from Transcription Timing

The histone-like nucleoid-structuring (H-NS) protein binds to horizontally acquired genes in the bacterium Salmonella enterica serovar Typhimurium, silencing their expression. We now report that overcoming the silencing effects of H-NS imposes a delay in the expression of genes activated by the transcriptional regulator PhoP. We determine that PhoP-activated genes ancestral to Salmonella are expressed before those acquired horizontally. This expression timing reflects the in vivo occupancy of the corresponding promoters by the PhoP protein. These results are surprising because some of these horizontally acquired genes reached higher mRNA levels than ancestral genes expressed earlier and were transcribed from promoters harboring PhoP-binding sites with higher in vitro affinity for the PhoP protein. Our findings challenge the often-made assumption that for genes coregulated by a given transcription factor, early genes are transcribed to higher mRNA levels than those transcribed at later times. Moreover, they provide a singular example of how gene ancestry can impact expression timing.This work was supported, in part, by grant AI49561 from the National Institutes of Health to E.A.G., who is an Investigator of the Howard Hughes Medical Institute