title: Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology.
abstract: Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem. However, as more of these reconstructions become available, it becomes clear that processes predicted by genome annotation may not reflect the processes that are active in vivo. As a case in point, E. coli is unable to grow aerobically on citrate in spite of having all the necessary genes to do it. It has also been shown that the realization of this genetic potential into an actual capability to metabolize citrate is an extremely unlikely event under normal evolutionary conditions. Moreover, many marine bacteria seem to have the same pathways to metabolize glucose but each species uses a different one. In this work, a metabolic network inferred from genomic annotation of the halophilic bacterium Halomonas elongata and proteomic profiling experiments are used as a starting point to motivate targeted experiments in order to find out some of the defining features of the osmoregulatory strategies of this bacterium. This new information is then used to refine the network in order to describe the actual capabilities of H. elongata, rather than its genetic potential.
authors.affiliation: Faculty of Mechanical Engineering, Specialty Division for Systems Biotechnology, Technische Universität München, München, Germany.
authors.forename: Viktoria
authors.initials: V
authors.lastname: Kindzierski
authors.affiliation: Federal Institute for Materials Research and Testing (BAM), Division 4.1 Biodeterioration and Reference Organisms, Berlin, Germany.
authors.forename: Silvia
authors.initials: S
authors.lastname: Raschke
authors.affiliation: Federal Institute for Materials Research and Testing (BAM), Division 4.1 Biodeterioration and Reference Organisms, Berlin, Germany.
authors.forename: Nicole
authors.initials: N
authors.lastname: Knabe
authors.affiliation: Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Siedler
authors.affiliation: Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
authors.forename: Beatrix
authors.initials: B
authors.lastname: Scheffer
authors.affiliation: Faculty of Mechanical Engineering, Specialty Division for Systems Biotechnology, Technische Universität München, München, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Pflüger-Grau
authors.affiliation: Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
authors.forename: Friedhelm
authors.initials: F
authors.lastname: Pfeiffer
authors.affiliation: Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
authors.forename: Dieter
authors.initials: D
authors.lastname: Oesterhelt
authors.affiliation: Faculty of Mechanical Engineering, Specialty Division for Systems Biotechnology, Technische Universität München, München, Germany.
authors.forename: Alberto
authors.initials: A
authors.lastname: Marin-Sanguino
authors.affiliation: Federal Institute for Materials Research and Testing (BAM), Division 4.1 Biodeterioration and Reference Organisms, Berlin, Germany.
authors.forename: Hans-Jörg
authors.identifier: http://orcid.org/0000-0003-1455-7822
authors.initials: HJ
authors.lastname: Kunte
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D020632:Halomonas / Q000235:genetics / Q000378:metabolism*; D064587:Osmoregulation / Q000502:physiology*; D020543:Proteome / Q000096:biosynthesis* / Q000235:genetics; D049490:Systems Biology
chemical_list: D001426:Bacterial Proteins; D020543:Proteome