Development of an Optimized Medium, Strain and High-Throughput Culturing Methods for Methylobacterium extorquens

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Delaney, Nigel F ^a   Kaczmarek, Maria E ^a,c   Ward, Lewis M ^a,d   Swanson, Paige K ^a   Lee, Ming Chun ^a,e   Marx, Christopher J ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^d CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^e UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

CITRIC ACID; BACTERIAL PROTEIN; CARBON; CHELATING AGENT; CULTURE MEDIUM;

ACCURACY; ARTICLE; AUTOMATION; BACTERIAL GENE; BACTERIAL GROWTH; BIOFILM; CELLULOSE SYNTHASE GENE; CHELATION; CONTROLLED STUDY; CULTURE MEDIUM; GENE SEQUENCE; GROWTH RATE; HIGH THROUGHPUT SCREENING; METHYLOBACTERIUM EXTORQUENS; MICROTITER PLATE ASSAY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; REPRODUCIBILITY; CHEMISTRY; DRUG EFFECTS; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MUTATION;

METHYLOBACTERIUM; METHYLOBACTERIUM EXTORQUENS;

BACTERIAL PROTEINS; CARBON; CHELATING AGENTS; CULTURE MEDIA; METHYLOBACTERIUM EXTORQUENS; MUTATION;

EID: 84876965085     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062957     Document Type: Article

References (47)

1. Large P, Peel D, Quayle J, (1961) Microbial growth on C1 compounds. 2. Synthesis of cell constituents by methanol-and formate-grown Pseudomonas AM1, and methanol-grown Hyphomicrobium vulgare. Biochemical Journal 81: 470.
2. Chistoserdova L, Chen SW, Lapidus A, Lidstrom ME, (2003) Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol 185: 2980-2987.
3. Marx CJ, (2008) Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Res Notes 1: 1.
4. Chou HH, Marx CJ, (2012) Optimization of gene expression through divergent mutational paths. Cell Reports 1: 133-140.
5. Marx CJ, Lidstrom ME, (2004) Development of an insertional expression vector system for Methylobacterium extorquens AM1 and generation of null mutants lacking mtdA and/or fch. Microbiology 150: 9-19.
6. Marx CJ, Lidstrom ME, (2002) Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. BioTechniques 33: 1062-1067.
7. Marx CJ, Lidstrom ME, (2001) Development of improved versatile broad-host-range vectors for use in methylotrophs and other Gram-negative bacteria. Microbiology 147: 2065-2075.
8. Marx CJ, Bringel F, Chistoserdova L, Moulin L, Farhan UHM, et al. (2012) Complete genome sequences of six strains of the genus Methylobacterium. J Bacteriol 194: 4746.
9. Vuilleumier S, Chistoserdova L, Lee MC, Bringel F, Lajus A, et al. (2009) Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS One 4: e5584.
10. Peyraud R, Schneider K, Kiefer P, Massou S, Vorholt JA, et al. (2011) Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Syst Biol 5: 189.
11. Skovran E, Crowther GJ, Guo X, Yang S, Lidstrom ME, (2010) A systems biology approach uncovers cellular strategies used by Methylobacterium extorquens AM1 during the switch from multi- to single-carbon growth. PLoS One 5: e14091.
12. Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, et al. (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6: 1378-1390.
13. Lee MC, Chou HH, Marx CJ, (2009) Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates. Evolution 63: 2816-2830.
14. Chou HH, Chiu HC, Delaney NF, Segrè D, Marx CJ, (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332: 1190.
15. Marx CJ, (2012) Recovering from a bad start: rapid adaptation and tradeoffs to growth below a threshold density. BMC Evol Biol 12: 109.
16. Warringer J, Blomberg A, (2003) Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. Yeast 20: 53-67.
17. Bollenbach T, Quan S, Chait R, Kishony R, (2009) Nonoptimal microbial response to antibiotics underlies suppressive drug interactions. Cell 139: 707-718.
18. Hermann R, Lehmann M, Büchs J, (2003) Characterization of gas-liquid mass transfer phenomena in microtiter plates. Biotechnol Bioeng 81: 178-186.
19. Blomberg A, (2011) Measuring growth rate in high-throughput growth phenotyping. Curr Opin Biotechnol 22: 94-102.
20. Sparkes A, Aubrey W, Byrne E, Clare A, Khan MN, et al. (2010) Review Towards Robot Scientists for autonomous scientific discovery. Autom Exp 2.
21. Chou HH, Berthet J, Marx CJ, (2009) Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. PLoS Genetics 5: e1000652.
22. Kiefer P, Buchhaupt M, Christen P, Kaup B, Schrader J, et al. (2009) Metabolite profiling uncovers plasmid-induced cobalt limitation under methylotrophic growth conditions. PLoS One 4: e7831.
23. Anthony C, Zatman L, (1964) The microbial oxidation of methanol. Biochem J 92: 614-621.
24. Chan H, Anthony C, (1992) The mechanism of inhibition by EDTA and EGTA of methanol oxidation by methylotrophic bacteria. FEMS Microbiol Lett 96: 231-234.
25. Dales SL, Anthony C, (1995) The interaction of methanol dehydrogenase and its cytochrome electron acceptor. Biochemical Journal 312: 261.
26. Neidhardt FC, Bloch PL, Smith DF, (1974) Culture medium for enterobacteria. Journal of bacteriology 119: 736.
27. Box GEP, Hunter JS, Hunter WG (2005) Statistics for experimenters: design, innovation, and discovery: Wiley Online Library.
28. Wu CJ, Hamada MS (2011) Experiments: planning, analysis, and optimization: Wiley.
29. Atlas RM (2004) Handbook of microbiological media: CRC.
30. Overmann J, (2006) Principles of enrichment, isolation, cultivation, and preservation of Prokaryotes. The Prokaryotes 1: 80-136.
31. Kim P, Kim JH, Oh DK, (2003) Improvement in cell yield of Methylobacterium sp. by reducing the inhibition of medium components for poly-β-hydroxybutyrate production. World J Microbiol Biotechnol 19: 357-361.
32. Dworkin M, Falkow S (2006) The prokaryotes: a handbook on the biology of bacteria. Springer Verlag. 257-265.
33. Knief C, Frances L, Vorholt JA, (2010) Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microbial ecology 60: 440-452.
34. Peel D, Quayle J, (1961) Microbial growth on C1 compounds. 1. Isolation and characterization of Pseudomonas AM1. Biochem J 81: 465.
35. Delaney NF, Echenique JR, Marx CJ (2012) Clarity: An Open Source Manager for Laboratory Automation. J Lab Autom.
36. Lee MC, Marx CJ, (2012) Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genetics 8: e1002651.
37. Marx C, (2008) Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Research Notes 1: 1.
38. Tsuchiya Y, Nishio N, Nagai S, (1980) Medium optimization for a methanol utilizing bacterium based on chemostat theory. Applied microbiology and biotechnology 9: 121-127.
39. Schmidt S (2010) Functional investigation of methanol dehydrogenase-like protein XoxF in Methylobacterium extorquens AM1 [Dissertation]: ETH Zurich.
40. Choi J, Kim J, Daniel M, Lebeault J, (1989) Optimization of growth medium and poly-β-hydroxybutyric acid production from methanol in Methylobacterium organophilum. Kor J Appl Microbiol Bioeng 17: 392-396.
41. Kensy F, Zimmermann HF, Knabben I, Anderlei T, Trauthwein H, et al. (2005) Oxygen transfer phenomena in 48-well microtiter plates: Determination by optical monitoring of sulfite oxidation and verification by real-time measurement during microbial growth. Biotechnol Bioeng 89: 698-708.
42. Marx CJ, Miller JA, Chistoserdova L, Lidstrom ME, (2004) Multiple formaldehyde oxidation/detoxification pathways in Burkholderia fungorum LB400. J Bacteriol 186: 2173-2178.
43. Morel F, Hering JG (1993) Principles and applications of aquatic chemistry: Wiley-Interscience.
44. Mokhtari-Hosseini ZB, Vasheghani-Farahani E, Heidarzadeh-Vazifekhoran A, Shojaosadati SA, Karimzadeh R, et al. (2009) Statistical media optimization for growth and PHB production from methanol by a methylotrophic bacterium. Bioresource technology 100: 2436-2443.
45. Mokhtari-Hosseini ZB, Vasheghani-Farahani E, Shojaosadati SA, Karimzadeh R, Khosravi-Darani K (2009) Media selection for poly (hydroxybutyrate) production from methanol by Methylobacterium extorquens DSMZ 1340. Iran J Chem Chem Eng Vol 28.
46. McIntire WS, Wemmer DE, Chistoserdov A, Lidstrom ME, (1991) A new cofactor in a prokaryotic enzyme: tryptophan tryptophylquinone as the redox prosthetic group in methylamine dehydrogenase. Science 252: 817-824.
47. Laukel M, Chistoserdova L, Lidstrom ME, Vorholt JA, (2003) The tungsten containing formate dehydrogenase from Methylobacterium extorquens AM1: Purification and properties. Eur J Biochem 270: 325-333.