TY - JOUR A1 - Pfeiffer, F. A1 - Bagyan, I. A1 - Alfaro Espinoza, Gabriela A1 - Zamora-Lagos, M.-A. A1 - Habermann, B. A1 - Marin-Sanguino, A. A1 - Oesterhelt, D. A1 - Kunte, Hans-Jörg T1 - Revision and reannotation of the Halomonas elongata DSM 2581(T) genome N2 - The genome of the Halomonas elongata type strain DSM 2581, an industrial producer, was reevaluated using the Illumina HiSeq2500 technology. To resolve duplication-associated ambiguities, PCR products were generated and sequenced. Outside of duplications, 72 sequence corrections were required, of which 24 were point mutations and 48 were indels of one or few bases. Most of these were associated with polynucleotide stretches (poly-T stretch overestimated in 19 cases, poly-C underestimated in 15 cases). These problems may be attributed to using 454 technology for original Genome sequencing. On average, the original genome sequence had only one error in 56 kb. There were 23 frameshift error corrections in the 29 protein-coding genes affected by sequence revision. The genome has been subjected to major reannotation in order to substantially increase the annotation quality. KW - Frameshift KW - Genome annotation KW - Genome sequencing KW - Halomonas elongata KW - Halophilic bacteria KW - Sequence revision PY - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-403292 SN - 2045-8827 VL - 6 IS - 4 SP - Article e465, 1 EP - 6 PB - Wiley AN - OPUS4-40329 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kindzierski, V. A1 - Raschke, Silvia A1 - Knabe, Nicole A1 - Siedler, F. A1 - Scheffer, B. A1 - Pflüger-Grau, K. A1 - Pfeiffer, F. A1 - Oesterhelt, D. A1 - Marin-Sanguino, A. A1 - Kunte, Hans-Jörg T1 - Osmoregulation in the halophilic bacterium halomonas elongata: A case study for integrative systems biology N2 - 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. KW - Halomonas elongata KW - Systems biology KW - Flux balance analysis KW - Proteomic analysis PY - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-391172 SN - 1932-6203 VL - 12 IS - 1 SP - Article e0168818, 1 EP - 22 AN - OPUS4-39117 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -