(This series of three posts is taken from a review article I am planning to submit for publication. I have removed references from the posts, but will be happy to supply them on request.)
Stress Directed Mutations
In 1988, a paper by John Cairns and his colleagues data showed that bacteria could produce beneficial mutations targeted specifically to relieve severe stress. Cairns’ paper took a major step away from the “purely random” concept for mutation. These beneficial mutations (now called stress-directed mutations or SDM) are produced at rates up to 5 times higher than other mutations with neutral effects. Numerous researchers have confirmed this phenomenon, and have found a number of molecular mechanisms to account for it. Hypermutability of specific stress-related genes can result from a variety of environmental stressors, like starvation, or changes in osmolarity, temperature or anaerobiosis.
Stress leads to derepression of specific genes, whose function are related to the stress. The resulting higher level of transcription of these genes allows for unpaired and exposed bases in loop structures that are more susceptible to mutation. Several investigators have found evidence that mutants arising from SDM in starving bacteria arise from different molecular mechanisms than the ordinary mutational events. Most mutations due to SDM occur in newly derepressed genes. Derepression of genes can lead to supercoiling and much higher mutation rates in the genes affected. Supercoliing of DNA during selective gene transcription is one of the leading molecular precursors of SDM in bacteria. Such changes in supercoiling that can lead to hypermutability can result from a variety of environmental stressors, like changes in osmolarity, temperature or anaerobiosis.
Natural Genetic Engineering
Over the past decades, microbiologist James Shapiro has applied many findings on how cells can accomplish major genomic alterations to develop a model he calls Natural Genetic Engineering (NGE). His view is that the cell can control the genome as much as the genome controls the cell. When applied to evolution, these sources of genetic variation do not fit the neo-Darwinian model of slow progressive changes, but are rapid, dramatic, and involve grand molecular events such as whole genome duplication, transposition of DNA sections leading to massive re-engineering of proteins, horizontal transfer of coding regions from plastids, viruses and other organisms.
One such revolutionary event was the huge evolutionary step taken when a cell engulfed a bacterium that remained alive and functional within its host, giving rise to eukaryotic cells with mitochondria. Nobody thinks that event was a slow stepwise process. Dawkins has described it as a one-time incredibly lucky accident, more or less equivalent to the origin of life. (In fact it happened at least twice, since chloroplasts also started out as bacteria swallowed by an ancient plant cell.)