Precarious balance of genome stability

Living organisms adapt to altered environments by the stepwise selection of genomic changes that lead to the optimization of fitness under the altered conditions. Conversely, what would happen if one tinkers with the genome while outside conditions remain more or less unaltered? In the case of critical genes (whose functionality is maintained by strong purifying selection), loss of function rapidly results in the accumulation of compensatory secondary mutation/s, a phenomenon known as suppression. What about deletion of non-essential genes?

Under laboratory settings, we often create targeted deletions of “non essential” genes, in order to understand their function. What are the consequences of such genomic perturbations under normal lab conditions (normal in this context means the absence of deliberate selection)? Deleting an apparently, “non-essential” gene might not threaten survival under laboratory conditions but is likely to lead to a reduction in fitness under specific natural environments, a consequence of disrupting millions of years of natural selection at work.

Xinchen Teng et al from Johns Hopkins University School of Medicine, Baltimore, ( have systematically explored the consequence of genome-wide single gene knockouts available in yeast. They have come up with the startling conclusion that “mutation of any single gene may cause a genomic imbalance with consequences sufficient to drive adaptive genetic changes”. They consider this to be a “logical consequence of losing a functional unit originally acquired under pressure during evolution”.

They have screened for hidden heterogeneities in the survivability of the knockout strains by observing heat stress response as well as nutrient sensing under low amino acid conditions using replicates of the deletion strains obtained from different colonies. The presence of secondary mutations was confirmed by following their segregation in tetrads, confirming by whole genomes sequencing in specific cases. Strains carrying deletions in the same gene, obtained from different sources, were evolved under non-stress conditions to determine whether they accumulate the same secondary mutation.

Crux of the study:

Genomic analysis reveals that these heterogeneities are due to secondary genomic changes and not due to stochastic changes in gene-expression or other epigenetic changes, as both are often used to explain the heterogeneity in presumably isogenic populations. Moreover, the driver for these secondary changes is the original gene that is knocked out as evident from the observation that independently constructed deletions of the same gene most often accumulated the same secondary mutations or mutations in the same complementary group. In many cases, the secondary mutations arose while growing the replicates of the deletion strains from individual colonies without selection whereas in some cases they preexisted in the original deletion strain.

 These results reinforce the fact that one must be cautious while interpreting the gene interaction studies involving deletions. Though the rest of the background is supposedly isogenic, the deletions may have unexpected consequence on the fitness of the strain resulting in the accumulation of second site suppressor mutations that are not documented. Next time you are struggling to reproduce your previous result with a knockout, testing multiple biological replicates might help, well…to some extent. I know it is more work but it is better than discarding everything. In fact, you might get a hint about the pathway in which you original gene (that is knocked out) works without the bias of strong selection. For details, check out the original article!