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Osmoregulation in the halophilic bacterium halomonas elongata: A case study for integrative systems biology

  • 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 thisHalophilic 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.zeige mehrzeige weniger

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Autor*innen:V. Kindzierski, Silvia Raschke, Nicole Knabe, F. Siedler, B. Scheffer, K. Pflüger-Grau, F. Pfeiffer, D. Oesterhelt, A. Marin-Sanguino, Hans-Jörg KunteORCiD
Dokumenttyp:Zeitschriftenartikel
Veröffentlichungsform:Verlagsliteratur
Sprache:Englisch
Titel des übergeordneten Werkes (Englisch):PLoS ONE
Jahr der Erstveröffentlichung:2017
Veröffentlichende Institution:Bundesanstalt für Materialforschung und -prüfung (BAM)
Herausgeber (Institution):PLoS
Jahrgang/Band:12
Ausgabe/Heft:1
Erste Seite:Article e0168818, 1
Letzte Seite:22
DDC-Klassifikation:Technik, Medizin, angewandte Wissenschaften / Ingenieurwissenschaften / Sanitär- und Kommunaltechnik; Umwelttechnik
Freie Schlagwörter:Flux balance analysis; Halomonas elongata; Proteomic analysis; Systems biology
DOI:10.1371/journal.pone.0168818
URN:urn:nbn:de:kobv:b43-391172
ISSN:1932-6203
Verfügbarkeit des Dokuments:Datei für die Öffentlichkeit verfügbar ("Open Access")
Lizenz (Deutsch):License LogoCreative Commons - Namensnennung
Datum der Freischaltung:08.02.2017
Referierte Publikation:Ja
Datum der Eintragung als referierte Publikation:16.02.2017
Schriftenreihen ohne Nummerierung:Wissenschaftliche Artikel der BAM
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