E-GEOD-42116 - Restoration and reinforcement of acclimatizing responses during the adaptation of an unfit, metabolically engineered strain

Status
Released on 8 November 2012, last updated on 20 November 2012
Organism
Methylobacterium extorquens AM1
Samples (30)
Array (1)
Protocols (8)
Description
Organisms cope with physiological stressors through acclimatizing mechanisms in the short-term, and through adaptive mechanisms over evolutionary timescales. Whereas the former offer a consistent and largely predictable buffer against stressors, myriad paths of adaptation are often possible. Our work examined whether knowledge of acclimatizing responses could be informative of  aspects of future adaptation, using as a model system a strain of Methylobacterium extorquens AM1 that was experimentally engineered and then evolved with a novel central metabolism. The engineered strain is markedly slower and less fit than wild-type, which is reflected in microarray analyses by hundreds of genes with differential expression, and also altered levels NAD(P)(H) metabolites. Yet after 600 generations of evolution in the lab, eight replicate populations founded from an engineered ancestor showed substantial but variable improvements in growth using the engineered metabolic pathway. Using information from wild-type, engineered, and adapted physiological states, we determined the extent to which physiological processes were restored, unrestored, reinforced, or novel after experimental evolution. Overall, we found that the vast majority of gene expression perturbations from the engineered strain are restored to wild-type like conditions after experimental evolution but were accompanied by a modest number of unrestored processes, varying instances of novel expression, and a few rare instances where expression changes from acclimation were reinforced through adaptive evolution. One such example was in the reinforced up-regulation of pntAB transhydrogenase, whose increased expression and activity correlated with the restoration of NAD(P)(H) metabolism towards wild-type levels and with increased growth rate in the evolved lineages. Thus, while trajectories of physiological adaptation may still be difficult to predict a priori, our results demonstrate that information from acclimatizing responses can provide a “direction” to hypothesize which changes in physiology arose as a consequence of adaptation versus those that may have caused it . Single-color microarray hydridization of total RNA isolated from mid-exponentially grown cultures of wildtype, engineered, and eight experimentally evolved populations of Methylobacterium extorquens AM1, each represented by three biological replicates
Experiment type
transcription profiling by array 
Contacts
Sean Michael Carroll <scarroll@oeb.harvard.edu>, Christopher J Marx, Sean M Carroll
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-42116.idf.txt
Sample and data relationshipE-GEOD-42116.sdrf.txt
Raw data (1)E-GEOD-42116.raw.1.zip
Processed data (1)E-GEOD-42116.processed.1.zip
Array designA-GEOD-16255.adf.txt
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