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Erschienen in:

2016 | OriginalPaper | Buchkapitel

3. A Genome-Scale Metabolic Model of M. maripaludis S2 for CO₂ Capture and Conversion to Methane

verfasst von : Nishu Goyal

Erschienen in: In silico Modeling and Experimental Validation for Improving Methanogenesis from CO2 via M. maripaludis

Verlag: Springer Singapore

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Abstract

Methane is a major energy source for heating and electricity. Its production by methanogenic bacteria is widely known in nature. M. maripaludis S2 is a fully sequenced hydrogenotrophic methanogen and an excellent laboratory strain with robust genetic tools. However, a quantitative systems biology model to complement these tools is absent in the literature.

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Vorheriges Kapitel Literature Review

Nächstes Kapitel Flux Measurements and Maintenance Energy for CO2 Utilization by M. maripaludis

Terzer M, ND Maynard, Covert MW, Jörg Stelling (2009) Genome-scale metabolic networks. Wiley Interdisc Rev: Syst Biol Med 3:285–297

Senger RS, Papoutsakis ET (2008) Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnol Bioeng 101:1036–1052CrossRef

Zou W, Liu L, Zhang J, Yang H, Zhou M, Hua Q, Chen J (2012) Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001. J Biotechnol 161:42–48CrossRef

Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, Conway de Macario E, Dodsworth JA, Gillett W, Graham DE, et al (2004) Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol 186:6956–6969

Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:D109–D114CrossRef

Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C et al (2008) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome Databases. Nucleic Acids Res 36:D623–D631CrossRef

Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Sohngen C, Stelzer M, Thiele J, Schomburg D (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res 39:D670–D676CrossRef

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRef

Lee D-Y, Yun H, Park S, Lee SY (2003) MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 19:2144–2146CrossRef

10.

Li C, Courtot M, Le Novère N, Laibe C (2010) BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Briefings in bioinformatics 11:270–277CrossRef

11.

Lee J, Yun H, Feist AM, Palsson BO, Lee SY (2008) Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol 80:849–862CrossRef

12.

Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA (2007) Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 3:92CrossRef

13.

Lombard J, Lopez-Garcia P, Moreira D (2012) Phylogenomic investigation of phospholipid synthesis in archaea. Archaea 2012:630910CrossRef

14.

Tenchov B, Vescio EM, Sprott GD, Zeidel ML, Mathai JC (2006) Salt tolerance of archaeal extremely halophilic lipid membranes. J Biol Chem 281:10016–10023CrossRef

15.

Yu J-P, Ladapo J, Whitman WB (1993) Pathway of glycogen metabolism in Methanococcus maripaludis. J Bacteriol 176:325–332

16.

Verduyn C, Stouthamer AH, Scheffers WA, Dijken JP (1991) A theoretical evaluation of growth yields of yeasts. Antonie Van Leeuwenhoek 59:49–63CrossRef

17.

Jones WJ, Paynter MJB, Gupta R (1983) Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment. Arch Microbiol 135:91–97CrossRef

18.

Xia Q, Wang T, Hendrickson EL, Lie TJ, Hackett M, Leigh JA (2009) Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis. BMC Microbiol 9:149CrossRef

19.

Reed JL, Famili I, Thiele I, Palsson BO (2006) Towards multidimensional genome annotation. Nat Rev Genet 7:130–141CrossRef

20.

Sivashankari S, Shanmughavel P (2006) Functional annotation of hypothetical proteins–A review. Bioinformation 1:335CrossRef

21.

Kral TA, Brink KM, Miller SL, McKay CP (1998) Hydrogen consumption by methanogens on the early earth. Orig Life Evol Biosph 28:311–319CrossRef

22.

Lupa B, Hendrickson EL, Leigh JA, Whitman WB (2008) Formate-dependent H₂ production by the mesophilic methanogen Methanococcus maripaludis. Appl Environ Microbiol 74:6584–6590CrossRef

23.

Whitman WB, Shieh J, Sohn S, Caras DS, Premachandran U (1986) Isolation and characterization of 22 mesophilic methanococci. Syst Appl Microbiol 7:235–240CrossRef

24.

Haydock AK, Porat I, Whitman WB, Leigh JA (2004) Continuous culture of Methanococcus maripaludis under defined nutrient conditions. FEMS Microbiol Lett 238:85–91

25.

Lin W, Whitman WB (2004) The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis. Arch Microbiol 181:68–73CrossRef

26.

Lie TJ, Leigh JA (2003) A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis. Mol Microbiol 47:235–246CrossRef

27.

Lie TJ, Leigh JA (2002) Regulatory response of Methanococcus maripaludis to Alanine, an intermediate Nitrogen Source. J Bacteriol 184:5301–5306CrossRef

28.

Costa KC, Yoon SH, Pan M, Burn JA, Baliga NS, Leigh JA (2013) Effects of H₂ and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. J Bacteriol 195:1456–1462CrossRef

29.

Shieh J, Whitman WB (1987) Pathway of acetate assimilation in autotrophic and heterotrophic methanococci. J Bacteriol 169:5327–5329

30.

Feist AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2

31.

Graupner M, White RH (2001) Methanococcus jannaschii Generates L-Proline by Cyclization of L-Ornithine. J Bacteriol 183:5203–5205CrossRef

32.

Liu Y (2010) Adaptations of Methanococcus maripaludis to its unique lifestyle. The University of Georgia

33.

Hausinger RP, Orme-Johnson WH, Walsh C (1985) Factor 390 chromophores: phosphodiester between AMP or GMP and methanogenic factor 420. Biochemistry 24:1629–1633CrossRef

34.

Namboori SC, Graham DE (2008) Acetamido sugar biosynthesis in the Euryarchaea. J Bacteriol 190:2987–2996CrossRef

35.

White RH (2004) L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. Biochemistry 43:7618–7627CrossRef

36.

Worrell V, Nagle D Jr (1988) Folic acid and pteroylpolyglutamate contents of archaebacteria. J Bacteriol 170:4420–4423

37.

Ragsdale SW (2002) Biocatalytic One-Carbon Conversion. Encyclopedia Catal (Wiley Inc.)

38.

Strassman M, Ceci LN (1964) Enzymatic formation of homocitric acid, an intermediate in lysine biosynthesis. Biochem Biophys Res Commun 14:262CrossRef

39.

Ladapo J, Whitman WB (1990) Method for isolation of auxotrophs in the methanogenic archaebacteria: role of the acetyl-CoA pathway of autotrophic CO2 fixation in Methanococcus maripaludis. Proc Natl Acad Sci 87:5598–5602CrossRef

40.

Belay N, Sparling R, Daniels L (1986) Relationship of formate to growth and methanogenesis by Methanococcus thermolithotrophicus. Appl Environ Microbiol 52:1080–1085

41.

Cheng S, Xing D, Call DF, Logan BE (2009) Direct biological conversion of electrical current into methane by electromethanogenesis. Environ Sci Technol 43:3953–3958CrossRef

42.

Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2

43.

Mahadevan R, Bond D, Butler J, Esteve-Nunez A, Coppi M, Palsson B, Schilling C, Lovley D (2006) Characterization of metabolism in the Fe (III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol 72:1558–1568CrossRef

44.

Porat I, Sieprawska-Lupa M, Teng Q, Bohanon FJ, White RH, Whitman WB (2006) Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Mol Microbiol 62:1117–1131CrossRef

45.

Lie TJ, Costa KC, Lupa B, Korpole S, Whitman WB, Leigh JA (2012) Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis. Proc Natl Acad Sci U S A 109:15473–15478CrossRef

46.

Major TA, Liu Y, Whitman WB (2010) Characterization of energy-conserving hydrogenase B in Methanococcus maripaludis. J Bacteriol 192:4022–4030CrossRef

47.

Wood GE, Haydock AK, Leigh JA (2003) Function and regulation of the formate dehydrogenase genes of the methanogenic archaeon methanococcus maripaludis. J Bacteriol 185:2548–2554CrossRef

48.

Costa KC, Lie TJ, Jacobs MA, Leigh JA (2013) H₂-independent growth of the hydrogenotrophic methanogen Methanococcus maripaludis. MBio 4

49.

Kessler PS, Daniel C, Leigh JA (2001) Ammonia switch-off of nitrogen fixation in the methanogenic archaeon Methanococcus maripaludis: mechanistic features and requirement for the novel GlnB homologues, Nif I(1) and NifI(2). J Bacteriol 183:882–889CrossRef

50.

Lie TJ, Leigh JA (2002) A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis. Mol Microbiol 47:235–246CrossRef

51.

Belay N, Sparling R, Choi B-S, Roberts M, Roberts J, Daniels L (1988) Physiological and ¹⁵N-NMR analysis of molecular nitrogen fixation by Methanococcus thermolithotrophicus, Methanobacterium bryantii and Methanospirillum hungatei. Biochimica et Biophysica Acta (BBA)-Bioenergetics 971:233–245

52.

Fardeau M-L, Peillex J-P, Belaich J-P (1987) Energetics of the growth of Methanobacterium thermoautotrophicum and Methanococcus thermolithotrophicus on ammonium chloride and dinitrogen. Arch Microbiol 148:128–131CrossRef

53.

Satish Kumar V, Ferry JG, Maranas CD (2011) Metabolic reconstruction of the archaeon methanogen Methanosarcina acetivorans. BMC Syst Biol 5:28

54.

Ulas T, Riemer SA, Zaparty M, Siebers B, Schomburg D (2012) Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS ONE 7:e43401CrossRef

55.

Shima S, Pilak O, Vogt S, Schick M, Stagni MS, Meyer-Klaucke W, Warkentin E, Thauer RK, Ermler U (2008) The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Science 321:572–575CrossRef

56.

Berg IA, Kockelkorn D, Buckel W, Fuchs G (2007) A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318:1782–1786CrossRef

57.

Benedict MN, Gonnerman MC, Metcalf WW, Price ND (2012) Genome-scale metabolic reconstruction and hypothesis testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A. J Bacteriol 194:855–865CrossRef

Titel: A Genome-Scale Metabolic Model of M. maripaludis S2 for CO2 Capture and Conversion to Methane
verfasst von: Nishu Goyal
Verlag: Springer Singapore
Buch: In silico Modeling and Experimental Validation for Improving Methanogenesis from CO2 via M. maripaludis
Print ISBN: 978-981-10-2509-9

Electronic ISBN: 978-981-10-2510-5

Copyright-Jahr: 2016
DOI: https://doi.org/10.1007/978-981-10-2510-5_3