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

PLoS Computational Biology

Volumn 9, Issue 10, 2013, Pages

  Rex, Rene ^a   Bill, Nelli ^a   Schmidt Hohagen, Kerstin ^a   Schomburg, Dietmar ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENERGY MANAGEMENT; GENES; PHYSIOLOGY; SULFUR COMPOUNDS;

COMPUTATIONAL ANALYSIS; DIMETHYLSULFONIOPROPIONATE; DIMETHYLSULPHIDE; ENERGY DEMANDS; GAIN INSIGHT; GENOME-SCALE METABOLIC MODELING; KNOCKOUT MUTANT; LARGE-SCALES; PROTEOBACTERIA; ROSEOBACTERS;

METABOLISM;

6 PHOSPHOFRUCTOKINASE; ADENOSINE TRIPHOSPHATE; BACTERIOCHLOROPHYLL; DIMETHYL SULFIDE; LIPOPOLYSACCHARIDE;

ARTICLE; BACTERIAL GENOME; BIOMASS; CLADISTICS; DEMETHYLATION; DENITRIFICATION; DINOROSEOBACTER SHIBAE; ENERGY METABOLISM; GRAM NEGATIVE BACTERIUM; GROWTH RATE; LIGHT HARVESTING SYSTEM; METABOLISM; NONHUMAN; PHOTOSYNTHESIS; PLASMID; PROTEOBACTERIA; ROSEOBACTER; SIMULATION; SWIMMING;

ALPHAPROTEOBACTERIA; DINOROSEOBACTER SHIBAE; ROSEOBACTER;

BIOMASS; COMPUTATIONAL BIOLOGY; METABOLIC FLUX ANALYSIS; METABOLIC NETWORKS AND PATHWAYS; RHODOBACTERACEAE;

EID: 84887277438     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003224     Document Type: Article

References (67)

1. Brinkhoff T, Giebel HA, Simon M, (2008) Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Archives of microbiology 189: 531-9.
2. Buchan A, González JM, Moran MA, (2005) Overview of the marine Roseobacter lineage. Applied and environmental microbiology 71: 5665-77.
3. Biebl H, Allgaier M, Tindall BJ, Koblizek M, Lünsdorf H, et al. (2005) Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. International journal of systematic and evolutionary microbiology 55: 1089-1096.
4. Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, et al. (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. The ISME journal 4: 61-77.
5. Moran MA, Belas R, Schell MA, González JM, Sun F, et al. (2007) Ecological genomics of marine Roseobacters. Applied and environmental microbiology 73: 4559-69.
6. Geng H, Belas R, (2010) Molecular mechanisms underlying Roseobacter-phytoplankton symbioses. Current opinion in biotechnology 21: 332-8.
7. Yurkov VV, Beatty JT, (1998) Aerobic anoxygenic phototrophic bacteria. Microbiology and molecular biology reviews: MMBR 62: 695-724.
8. Petrasovits La, Purnell MP, Nielsen LK, Brumbley SM, (2007) Production of polyhydroxybutyrate in sugarcane. Plant biotechnology journal 5: 162-72.
9. Xiao N, Jiao N, (2011) Formation of polyhydroxyalkanoate in aerobic anoxygenic phototrophic bacteria and its relationship to carbon source and light availability. Applied and environmental microbiology 77: 7445-50.
10. Curson ARJ, Todd JD, Sullivan MJ, Johnston AWB, (2011) Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nature Reviews Microbiology 9 (12) ():: 849-59.
11. Tomasch J, Gohl R, Bunk B, Diez MS, Wagner-Döbler I, (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. The ISME journal 5: 1957-68.
12. Fürch T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, et al. (2009) Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade. BMC microbiology 9: 209.
13. Dickschat JS, Zell C, Brock NL, (2010) Pathways and substrate specificity of DMSP catabolism in marine bacteria of the Roseobacter clade. Chembiochem: a European journal of chemical biology 11: 417-25.
14. Holert J, Hahnke S, Cypionka H, (2011) Influence of light and anoxia on chemiosmotic energy conservation in Dinoroseobacter shibae. Environmental microbiology reports 3: 136-141.
15. Imam S, Yilmaz S, Sohmen U, Gorzalski AS, Reed JL, et al. (2011) iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC systems biology 5: 116.
16. Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY, (2011) Recent advances in reconstruction and applications of genome-scale metabolic models. Current opinion in biotechnology 23 (4) ():: 617-23.
17. Oberhardt Ma, Palsson BO, Papin Ja, (2009) Applications of genome-scale metabolic reconstructions. Molecular systems biology 5: 320.
18. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular systems biology 3: 121.
19. Thiele I, Palsson BO, (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols 5: 93-121.
20. Jarosławski S, Duquesne K, Sturgis JN, Scheuring S, (2009) High-resolution architecture of the outer membrane of the Gram-negative bacteria Roseobacter denitrificans. Molecular microbiology 74: 1211-22.
21. Yeliseev Aa, Kaplan S, (1997) Anaerobic carotenoid biosynthesis in Rhodobacter sphaeroides 2.4.1: H2O is a source of oxygen for the 1-methoxy group of spheroidene but not for the 2-oxo group of spheroidenone. FEBS Letters 403: 10-14.
22. Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, et al. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nature chemical biology 5: 593-9.
23. Harashima K, Hayasaki J, Ikari T, Shiba T, (1980) O2-stimulated synthesis of bacteriochlorophyll and carotenoids in marine bacteria. Plant and Cell Physiology 21: 1283-1294.
24. Mitchell JG, Pearson L, Bonazinga A, Dillon S, Khouri H, et al. (1995) Long lag times and high velocities in the motility of natural assemblages of marine bacteria. Applied and environmental microbiology 61: 877-82.
25. Quester S, Schomburg D, (2011) EnzymeDetector: an integrated enzyme function prediction tool and database. BMC bioinformatics 12: 376.
26. Hucka M, Finney a, Sauro HM, Bolouri H, Doyle JC, et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531.
27. Jurgenson CT, Begley TP, Ealick SE, (2009) The Structural and Biochemical Foundations of Thiamin Biosynthesis. Annual Review of Biochemistry 78: 569-603.
28. Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, et al. (2011) BRENDA, the enzyme information system in 2011. Nucleic acids research 39: D670-6.
29. Alexander K, Young IG, (1978) Alternative hydroxylases for the aerobic and anaerobic biosynthesis of ubiquinone in Escherichia coli. Biochemistry 17: 4750-5.
30. Klamt S, Grammel H, Straube R, Ghosh R, Gilles ED, (2008) Modeling the electron transport chain of purple non-sulfur bacteria. Molecular systems biology 4: 156.
31. Taglicht D, Padan E, Schuldiner S, (1993) Proton-sodium stoichiometry of NhaA, an electrogenic antiporter from Escherichia coli. The Journal of biological chemistry 268: 5382-7.
32. Arkin IT, Xu H, Jensen MO, Arbely E, Bennett ER, et al. (2007) Mechanism of Na+/H+ antiporting. Science (New York, NY) 317: 799-803.
33. Orth JD, Conrad TM, Na J, Lerman Ja, Nam H, et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Molecular systems biology 7: 535.
34. Wang XL, Quan JM, (2011) Intermediate-assisted multifunctional catalysis in the conversion of flavin to 5,6-dimethylbenzimidazole by BluB: a density functional theory study. Journal of the American Chemical Society 133: 4079-91.
35. Choi-Rhee E, Cronan JE, (2005) A nucleosidase required for in vivo function of the S-adenosyl-L-methionine radical enzyme, biotin synthase. Chemistry & biology 12: 589-93.
36. Kriek M, Martins F, Challand MR, Croft A, Roach PL, (2007) Thiamine biosynthesis in Escherichia coli: identification of the intermediate and by-product derived from tyrosine. Angewandte Chemie (International ed in English) 46: 9223-6.
37. Sowa Y, Berry RM, (2008) Bacterial flagellar motor. Quarterly reviews of biophysics 41: 103-32.
38. Johansen J, Pinhassi J, Blackburn N, Zweifel U, Hagström A, (2002) Variability in motility characteristics among marine bacteria. Aquatic Microbial Ecology 28: 229-237.
39. Mitchell J, (1991) The influence of cell size on marine bacterial motility and energetics. Microbial ecology 22: 227-238.
40. Riemer SA, Rex R, Schomburg D, (2013) A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC systems biology 7: 33.
41. Moran MA, Reisch CR, Kiene RP, Whitman WB, (2012) Genomic Insights into Bacterial DMSP Transformations. Annual Review of Marine Science 4: 523-542.
42. Thomas Ma, Suntharalingam P, Pozzoli L, Devasthale A, Kloster S, et al. (2011) Rate of non-linearity in DMS aerosol-cloud-climate interactions. Atmospheric Chemistry and Physics 11: 11175-11183.
43. Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, et al. (2000) Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290: 481-486.
44. Biebl H, Wagner-Döbler I, (2006) Growth and bacteriochlorophyll a formation in taxonomically diverse aerobic anoxygenic phototrophic bacteria in chemostat culture: Influence of light regimen and starvation. Process Biochemistry 41: 2153-2159.
45. Koblízek M, Mlcousková J, Kolber Z, Kopecký J, (2010) On the photosynthetic properties of marine bacterium COL2P belonging to Roseobacter clade. Archives of microbiology 192: 41-9.
46. González JM, Kiene RP, Moran MA, (1999) Transformation of sulfur compounds by an abundant lineage of marine bacteria in the alpha-subclass of the class Proteobacteria. Applied and environmental microbiology 65: 3810-9.
47. Shapleigh JP, (2011) Oxygen control of nitrogen oxide respiration, focusing on α-Proteobacteria. Biochemical Society transactions 39: 179-83.
48. Doi M, Shioi Y, (1991) Enhancement of denitrifying activity in cells of Roseobacter denitrificans grown aerobically in the light. Plant and cell physiology 32: 365-370.
49. Wagner-Döbler I, Biebl H, (2006) Environmental biology of the marine Roseobacter lineage. Annual review of microbiology 60: 255-80.
50. Puchałka J, Oberhardt Ma, Godinho M, Bielecka A, Regenhardt D, et al. (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS computational biology 4: e1000210.
51. Berghoff BA, Glaeser J, Nuss AM, Zobawa M, Lottspeich F, et al. (2011) Anoxygenic photosynthesis and photooxidative stress: a particular challenge for Roseobacter. Environmental microbiology 13: 775-91.
52. Matyash V, Liebisch G, Kurzchalia T, Shevchenko A, Schwudke D, (2008) Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. Journal of lipid research 49: 1137-1146.
53. Lowry O, Rosebrough N, Farr A, Randall R, et al. (1951) Protein measurement with the Folin phenol reagent. J biol chem 193: 265-275.
54. Sambrook J, Russell D (2001) Molecular cloning: a laboratory manual, volume 2. CSHL press.
55. Karr D, Waters J, Emerich D, (1983) Analysis of poly-β-hydroxybutyrate in Rhizobium japonicum bacteroids by ion-exclusion high-pressure liquid chromatography and uv detection. Applied and environmental microbiology 46: 1339-1344.
56. Poblete-Castro I, Escapa I, Jäger C, Puchalka J, Lam C, et al. (2012) The metabolic response of P. putida kt2442 producing high levels of polyhydroxyalkanoate under single-and multiple-nutrient-limited growth: Highlights from a multi-level omics approach. Microbial Cell Factories 11: 34.
57. Hiller K, Hangebrauk J, Jäger C, Spura J, Schreiber K, et al. (2009) MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Analytical chemistry 81: 3429-39.
58. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, et al. (2012) Icy: an open bioimage informatics platform for extended reproducible research. Nature Methods 9: 690-696.
59. Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, et al. (2013) Dynamics of amino acid utilization in phaeobacter inhibens dsm 17395. Proteomics [epub ahead of print] doi: 10.1002/pmic.201200560.
60. Caspi R, Altman T, Dreher K, Fulcher Ca, Subhraveti P, et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic acids research 40: D742-53.
61. Meister M, Lowe G, Berg HC, (1987) The proton flux through the bacterial flagellar motor. Cell 49: 643-650.
62. Berg HC, (2003) The rotary motor of bacterial flagella. Annual review of biochemistry 72: 19-54.
63. Vázquez J, González M, Murado M, (2004) A new marine medium. Enzyme and Microbial Technology 35: 385-392.
64. Fell DA, Small JR, (1986) Fat synthesis in adipose tissue. An examination of stoichiometric constraints. The Biochemical journal 238: 781-6.
65. Orth JD, Thiele I, Palsson BO, (2010) What is flux balance analysis? Nature Biotechnology 28: 245-248.
66. Mahadevan R, Schilling C, (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Engineering 5: 264-276.
67. Gudmundsson S, Thiele I, (2010) Computationally efficient flux variability analysis. BMC bioinformatics 11: 489.