Epistasis has substantial impacts on evolution, in particular, the rate of adaptation. We generated
combinations of beneficial mutations that arose in a lineage during rapid adaptation of …

… Here, we used a DhprA strain (Marx, 2008) that lacks a key enzyme (hydroxypyruvate
reductase) for assimilating carbon from methylamine. In media with lactose and methylamine, the …

Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader,
has one of the two largest known bacterial genomes and is the first nonpathogenic …

… pCM110 was constructed by inserting the 0·4 kb HindIII–NsiI fragment of pCM27 containing
PmxaF into pCM60 (CJ Marx & ME Lidstrom, unpublished results) which had been cut with …

Complete genome sequences are now available for many bacterial species that lack sophisticated
genetic tools. We describe the development of a broad-host-range crelox system that …

Background Methylotrophy describes the ability of organisms to grow on reduced organic
compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative …

… extorquens AM1, pCM62 (CJ Marx and ME Lidstrom, unpublished data), to create … Bult
CJ, White O., Olsen GJ, Zhou L., Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, … Marx …

… Citation: Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, Ferguson-Noel N, et al.
(2012) … Smith, and members of the Marx lab for helpful dicussion; and R. Kofler for sharing …

Genome reduction has been observed in many bacterial lineages that have adapted to
specialized environments. The extreme genome degradation seen for obligate pathogens and …

Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely
encoded by a specific subset of possible codons. Within individual genes, codon bias is …