Gerth M.L.,New Zealand Institute for Advanced Study |
Ferla M.P.,Massey University |
Rainey P.B.,New Zealand Institute for Advanced Study |
Rainey P.B.,Max Planck Institute for Evolutionary Biology
Environmental Microbiology | Year: 2012
Pseudomonas proliferate in a wide spectrum of harsh and variable environments. In many of these environments, amino acids, such as histidine, are a valuable source of carbon, nitrogen and energy. Here, we demonstrate that the histidine uptake and utilization (hut) pathway of Pseudomonas aeruginosa PAO1 contains two branches from the intermediate formiminoglutamate to the product glutamate. Genetic analysis revealed that the four-step route is dispensable as long as the five-step route is present (and vice versa). Mutants with deletions of either the four-step (HutE) or five-step (HutFG) branches were competed against each other and the wild-type strain to test the hypothesis of ecological redundancy; that is, that the presence of two pathways confers no benefit beyond that delivered by the individual pathways. Fitness assays performed under several environmental conditions led us to reject this hypothesis; the four-step pathway can provide an advantage when histidine is the sole carbon source. An IclR-type regulator (HutR) was identified that regulates the four-step pathway. Comparison of sequenced genomes revealed that P. aeruginosa strains and P. fluorescens Pf-5 have branched hut pathways. Phylogenetic analyses suggests that the gene encoding formiminoglutamase (hutE) was acquired by horizontal gene transfer from a Ralstonia-like ancestor. Potential barriers to inter-species transfer of the hutRE module were explored by transferring it from P. aeruginosa PAO1 to P. fluorescens SBW25. Transfer of the operon conferred the ability to utilize histidine via the four-step pathway in a single step, but the fitness cost of acquiring this new operon was found to be environment dependent. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.
Schwerdtfeger P.,New Zealand Institute for Advanced Study |
Assadollahzadeh B.,New Zealand Institute for Advanced Study |
Hermann A.,University of Auckland |
Hermann A.,MacDiarmid Institute for Advanced Materials and Nanotechnology
Physical Review B - Condensed Matter and Materials Physics | Year: 2010
Complete basis set limit calculations are carried out for the fcc lattices of solid neon and argon, using second- to fourth-order Møller-Plesset theory, MP2-MP4, and coupled-cluster calculations, CCSD(T), to describe electron correlation within a many-body expansion of the interaction potential up to third order. A correct description of the three-body Axilrod-Teller-Muto term for the solid state is only obtained from third order on in the many-body expansion of the correlation energy, correcting the severe underestimation of long-range three-body effects at the MP2 level of theory. MP4 shows good agreement with the CCSD(T) results, and the latter are in good agreement with experimental lattice constants, cohesive energies, and bulk moduli. However, with increasing pressures the convergence of the Møller-Plesset series deteriorates as the electronic band gap decreases, resulting in rather large deviations for the equation of state (pressure-volume dependence). For neon, however, the errors in the MP2 two- and three-body terms almost cancel, i.e., at a volume of V=3 cm3 /mol the MP2 pressure is underestimated by only 1 GPa compared to the pressure of P=251 GPa calculated at the CCSD(T) level of theory. In contrast, for argon this is not the case, and at V=5.5 cm3 /mol the calculated MP2 pressure of 228 GPa deviates substantially from the CCSD(T) result of 252 GPa. © 2010 The American Physical Society.