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Expression profiles of evolved clones isolated at various stages during adaptive experimental evolution of E. coli

ABSTRACT: An Eschericia coli strain was constructed in which the PaeR7 restriction-modification gene complex was present under an unstable condition on a partially duplicated chromosomal region so that it may continuously attack the host genome to accelerate its evolution. This strain was grown for more than a hundred of generations through repeated cycles of saturation and dilution. The winners of this competition showed faster growth than the ancestor. Analysis of their genome and transcriptome revealed that they have acquired rearrangements in genes affecting their growth. The global expression pattern changes may have realized growth advantage during the adaptation experiment. Keywords: time course during adaptive evloution Overall design: We used microarrays to know the genetic mechanism underlying adaptive evolution process, and to know the global expression changes that realize advantage in growth during adaptation. Four populations of the parent strain (YA027) and two populations of isogenic r-m+ strain (YA074), for control, were grown and serially propagated in amino acid rich medium (Davis’s MM supplied with 20 amino acids) with Cm (chloramphenicol) and Km (kanamycin), daily with 100-fold dilution. One passage corresponds to 6 - 7 generations, though it might be changed with evolution. Their growth was monitored daily. The growth curve shifted upwards every day in every population, reflecting improvement both in the initial growth rate and the saturation cell density through the evolution. To follow genome changes and global expression changes during adaptive evolution, we selected clones that might represent several stages of evolution with respect to growth from an r+m+ population (population #3) at the 11th, 84th, and 172th passage (corresponding 70, 500, and 1000 generations, respectively): 3-11-2, 3-11-4, 3-11-9, and 3-11-10 from the 11th passage; 3-84-2, 3-84-4, 3-84-6, and 3-84-10 from the 84th passage, and 3-172-1, 3-172-9, and 3-172-10 from the 172nd passage. We subjected them to transcriptome analysis. All gene expression measurements were duplicated or triplicated.

INSTRUMENT(S): [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array

SUBMITTER: Yoko Asakura  

PROVIDER: GSE21869 | GEO | 2011-07-26



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Evolutionary genome engineering using a restriction-modification system.

Asakura Yoko Y   Kojima Hiroyuki H   Kobayashi Ichizo I  

Nucleic acids research 20110723 20

Modification of complex microbial cellular processes is often necessary to obtain organisms with particularly favorable characteristics, but such experiments can take many generations to achieve. In the present article, we accelerated the experimental evolution of Escherichia coli populations under selection for improved growth using one of the restriction-modification systems, which have shaped bacterial genomes. This resulted in faster evolutionary changes in both the genome and bacterial grow  ...[more]

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