Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA

Abstract

The isolation of aerobic citrate-utilizing Escherichia coli (Cit ؉ ) in long-term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit ؉ mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested with wild-type E. coli strain B and with K-12 and three K-12 derivatives: an E. coli ⌬rpoS::kan mutant (impaired for stationaryphase survival), an E. coli ⌬citT::kan mutant (deleted for the anaerobic citrate/succinate antiporter), and an E. coli ⌬dctA::kan mutant (deleted for the aerobic succinate transporter). E. coli underwent adaptation to aerobic citrate metabolism that was readily and repeatedly achieved using minimal medium supplemented with citrate (M9C), M9C with 0.005% glycerol, or M9C with 0.0025% glucose. Forty-six independent E. coli Cit ؉ mutants were isolated from all E. coli derivatives except the E. coli ⌬citT:: kan mutant. Potentiation/actualization mutations occurred within as few as 12 generations, and refinement mutations occurred within 100 generations. Citrate utilization was confirmed using Simmons, Christensen, and LeMaster Richards citrate media and quantified by mass spectrometry. E. coli Cit ؉ mutants grew in clumps and in long incompletely divided chains, a phenotype that was reversible in rich media. Genomic DNA sequencing of four E. coli Cit ؉ mutants revealed the required sequence of mutational events leading to a refined Cit ؉ mutant. These events showed amplified citT and dctA loci followed by DNA rearrangements consistent with promoter capture events for citT. These mutations were equivalent to the amplification and promoter capture CitT-activating mutations identified in the LTEE. H ow genetic information evolves to generate new phenotypes/ species is a central issue in biology. Long-term evolution experiments (LTEE) using microorganisms have been initiated by several groups, in part to empirically observe this phenomenon (1). LTEE using bacteria, bacteriophage, or yeast have distinct advantages that include high population numbers, rapid generation times, and the opportunity to freeze intermittent populations (frozen fossils) to track mutations over time. Coupled with wholegenome sequencing, evolutionary changes can be genetically characterized to identify a mutation(s) required for a specific phenotypic change and frozen intermediates can be revived to replay and confirm the events. The most famous and meticulously documented LTEE are those, initiated in 1988, in Richard Lenski's laboratory (2). Twelve parallel cultures of Escherichia coli REL606 (an E. coli B strain) have been growing aerobically in minimal salts medium with low glucose concentrations (0.0025%) for 27 years. Cultures are transferred daily into fresh medium. Frozen samples are preserved for each culture every 500 generations, providing a tremendous resource to study long-term bacterial adaptation under controlled conditio...

Reinterpreting Long-Term Evolution Experiments: Is Delayed Adaptation an Example of Historical Contingency or a Consequence of Intermittent Selection?

“…n this issue, Van Hofwegen, Hovde, and Minnich suggest that the long-term evolution experiments (LTEE) of Lenski and coworkers may need to be reinterpreted (1). In those experiments, 12 parallel cultures of Escherichia coli have been serially subcultured daily for over 25 years (2).…”

No genome is an island: toward a 21st century agenda for evolution

“…The appearance of this strain, which activated expression of a citrate transporter (CitT) by a nonhomologous transcriptional fusion, was originally interpreted as resulting from such an unusual genomic change as to be considered the equivalent of a paleontological speciation event . However, when E. coli cultures were subjected to selection for citrate utilization under conditions where they first experienced the triggering effect of aerobic starvation on the surface of Petri dishes, the same class of CitT‐activating fusions was obtained repeatedly in each of a series of replicate cultures within a matter of days …”

“…We can anticipate at least three different ways the different coding regions can become available for transcription: (1) modification of nearby sequences to create active transcription signals; (2) insertion of active transcription modules, such as mobile DNA elements, upstream of the coding sequence; or (3) creation of a genome rearrangement that fuses the unexpressed coding sequence to active transcription signals. Both changes (1) and (2) are classic examples of NGE and have been observed in the E. coli citrate utilization system described above . This qualitative analysis is critical because it may turn out that the spectrum of mutational changes is different for single‐locus selection and multilocus selection at one or more of the genome regions being tested.…”

“…Both changes (1) and (2) are classic examples of NGE and have been observed in the E. coli citrate utilization system described above. 156,159 This qualitative analysis is critical because it may turn out that the spectrum of mutational changes is different for single-locus selection and multilocus selection at one or more of the genome regions being tested. The finding that multilocus selection produces qualitatively distinct genome changes would be a further indication of a special multilocus NGE functionality.…”

Cellular adaptation through fitness-directed transcriptional tuning

“…This is true because under any conceivable environment, the activities of some genes are beneficial, whereas those of others are futile or even actively detrimental [1,3,4]. In fact, if the initial fitness defect is not lethal, a population of cells may slowly adapt to an unfamiliar environment through the accumulation of genetic mutations that rewire regulatory networks thereby achieving more optimal gene expression states [3,[5][6][7][8][9][10][11][12].…”