Response from Matthews.

Dr Valdivia raises an issue of concern to microbiologists of every stripe: how small a change in gene expression is likely to be physiologically significant? Valdivia suggests that a twofold increase in gene expression is unlikely to play a critical role in microbial adaptation to a new environment. When considering the significance of twofold changes in gene expression, the main concerns are the amplitude and speed of the response. With no further amplification of the signal, as our simulation indicates, it would take ten generations for the protein product to double in concentration. However, this is not a linear increase; rather, the concentration increases hyperbolically towards an asymptote of doubled value. As Valdivia notes, and the simulations suggest, the amplitude of the response could be increased by synergistic increases in translation initiation, mRNA half-life or activity modulation.We would also add that, for a multisubunit protein, subunit association will increase as an exponential power of the protein concentration. Therefore, if the preshift subunit concentration is close to but below the Kd, then a doubling of protein concentration will much more than double the concentration of active protein. The effect of small changes in subunit concentration on a multimeric DNA-binding protein cooperatively occupying adjacent DNA-binding sites is dramatically illustrated in the case of the lambda repressor1xA Genetic Switch. Ptashne, M. See all References1. Because of limits on the sensitivity of our analytical methods, twofold changes must be regarded with some caution – but this caution should not be confused with an assumption that such changes (where real) are irrelevant. When a difference of only tens of seconds in the generation time can lead to the takeover of a population, such twofold changes could, indeed, be highly relevant. It seems to us that the burden of proof lies in demonstrating that the ∼1300 genes showing ∼twofold changes in transcription during a shift in yeast carbon source2xDiRisi, J.L., Lyer, V.R., and Brown, P.O. Science. 1997; 278: 680–686Crossref | PubMed | Scopus (3268)See all References2 represent a physiologically irrelevant artefact. We agree that the debate can only be resolved experimentally, but would argue that the type of experiment required is one in which the expression of the gene is artificially manipulated, for example by IPTG, and the phenotype of the cell is then examined as a function of the gene product’s concentration in the cell. Such an experiment has been performed using a construct in which the level of Lrp in Escherichia coli was regulated by IPTG (Ref. 3xBorst, D.W., Blumenthal, R.M., and Matthews, R.G. J. Bacteriol. 1996; 178: 6904–6912PubMedSee all ReferencesRef. 3). A change in the concentration of Lrp from 0.2 ng ml−1 to 0.4 ng ml−1 of cell extract resulted in a change in the doubling time of the culture from 82 to 70 minutes. Many small changes in gene expression could result from passive reallocation of the cell’s limited transcription and translation capacities. We agree that only a subset of these are likely to have significant phenotypic effects. At present, we are focused on trying to understand which changes in expression permit active adaptation to changes in the environment. It may be some time before we begin to understand the compensatory changes that allow reallocation of transcription and translation.