Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae

被引:12
作者
Rex, Rene [1 ]
Bill, Nelli [1 ]
Schmidt-Hohagen, Kerstin [1 ]
Schomburg, Dietmar [1 ]
机构
[1] Tech Univ Carolo Wilhelmina Braunschweig, Dept Bioinformat & Biochem, D-38106 Braunschweig, Germany
关键词
ANOXYGENIC PHOTOTROPHIC BACTERIA; ESCHERICHIA-COLI; MARINE-BACTERIA; FLUX; RECONSTRUCTION; BIOSYNTHESIS; MOTILITY; ENZYME; GROWTH; POLYHYDROXYALKANOATE;
D O I
10.1371/journal.pcbi.1003224
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The Roseobacter clade is a ubiquitous group of marine alpha-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae.
引用
收藏
页数:16
相关论文
共 50 条
  • [11] Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae
    Maier, Tobias
    Marcos, Josep
    Wodke, Judith A. H.
    Paetzold, Bernhard
    Liebeke, Manuel
    Gutierrez-Gallego, Ricardo
    Serrano, Luis
    MOLECULAR BIOSYSTEMS, 2013, 9 (07) : 1743 - 1755
  • [12] An integrative computational model for large-scale identification of metalloproteins in microbial genomes: a focus on iron-sulfur cluster proteins
    Estellon, Johan
    de Choudens, Sandrine Ollagnier
    Smadja, Myriam
    Fontecave, Marc
    Vandenbrouck, Yves
    METALLOMICS, 2014, 6 (10) : 1913 - 1930
  • [13] A large-scale nanoscopy and biochemistry analysis of postsynaptic dendritic spines
    Helm, Martin S.
    Dankovich, Tal M.
    Mandad, Sunit
    Rammner, Burkhard
    Jahne, Sebastian
    Salimi, Vanessa
    Koerbs, Christina
    Leibrandt, Richard
    Urlaub, Henning
    Schikorski, Thomas
    Rizzoli, Silvio O.
    NATURE NEUROSCIENCE, 2021, 24 (08) : 1151 - 1162
  • [14] Scale-Up Analysis for a CHO Cell Culture Process in Large-Scale Bioreactors
    Xing, Zizhuo
    Kenty, Brian N.
    Li, Zheng Jian
    Lee, Steven S.
    BIOTECHNOLOGY AND BIOENGINEERING, 2009, 103 (04) : 733 - 746
  • [15] Computational minimization of the specific energy demand of large-scale aerobic fermentation processes based on small-scale data
    Kreyenschulte, Dirk
    Emde, Frank
    Regestein, Lars
    Buechs, Jochen
    CHEMICAL ENGINEERING SCIENCE, 2016, 153 : 270 - 283
  • [16] iGTP: A software package for large-scale gene tree parsimony analysis
    Chaudhary, Ruchi
    Bansal, Mukul S.
    Wehe, Andre
    Fernandez-Baca, David
    Eulenstein, Oliver
    BMC BIOINFORMATICS, 2010, 11
  • [17] Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways
    Schulz, Juliane Caroline
    Zampieri, Mattia
    Wanka, Stefanie
    von Mering, Christian
    Sauer, Uwe
    SCIENCE SIGNALING, 2014, 7 (353)
  • [18] Improved Quadrant Analysis for Large-Scale Events Detection in Turbulent Transport
    Wang, Ye
    Wang, Baomin
    Lan, Changxing
    Fang, Renzhi
    Zheng, Baofeng
    Lu, Jieying
    Zheng, Dan
    ATMOSPHERE, 2022, 13 (03)
  • [19] Automated segmentation and tracking for large-scale analysis of focal adhesion dynamics
    Wuerflinger, T.
    Gamper, I.
    Aach, T.
    Sechi, A. S.
    JOURNAL OF MICROSCOPY, 2011, 241 (01) : 37 - 53
  • [20] Large-Scale Structural Analysis of the Classical Human Protein Tyrosine Phosphatome
    Barr, Alastair J.
    Ugochukwu, Emilie
    Lee, Wen Hwa
    King, Oliver N. F.
    Filippakopoulos, Panagis
    Alfano, Ivan
    Savitsky, Pavel
    Burgess-Brown, Nicola A.
    Mueller, Susanne
    Knapp, Stefan
    CELL, 2009, 136 (02) : 352 - 363