Metabolite profiling uncovers plasmid-induced cobalt limitation under methylotrophic growth conditions

PLoS ONE

Volumn 4, Issue 11, 2009, Pages

  Kiefer, Patrick ^a   Buchhaupt, Markus ^b   Christen, Philipp ^a   Kaup, Björn ^b   Schrader, Jens ^b   Vorholt, Julia A ^a  

^a ETH ZURICH   (Switzerland)

^b Karl Winnacker Institut   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COBALT; COBAMAMIDE; GLYOXYLIC ACID; ISOCITRATE LYASE; KANAMYCIN; METHYLMALONYL COENZYME A CARBOXYLTRANSFERASE; ACYL COENZYME A; BACTERIAL PROTEIN; ETHYLMALONYL COENZYME A; ETHYLMALONYL-COENZYME A; GLYOXYLIC ACID DERIVATIVE; MEMBRANE PROTEIN; METHANOL; METHYLMALONYL-COENZYME A; METHYLMALONYLCOENZYME A; MUTASE; TONB PROTEIN, BACTERIA;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GROWTH; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GROWTH RATE; METABOLOME; METHYLOBACTERIUM EXTORQUENS; METHYLOTROPHIC BACTERIUM; NONHUMAN; PLASMID; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; REGENERATION; WILD TYPE; BIOLOGICAL MODEL; CELL PROLIFERATION; CHEMISTRY; GENE EXPRESSION REGULATION; METABOLISM; METHYLOBACTERIUM; TRANSPORT AT THE CELLULAR LEVEL;

METHYLOBACTERIUM EXTORQUENS;

ACYL COENZYME A; BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; CELL PROLIFERATION; COBALT; COBAMIDES; GENE EXPRESSION REGULATION, BACTERIAL; GLYOXYLATES; INTRAMOLECULAR TRANSFERASES; ISOCITRATE LYASE; MEMBRANE PROTEINS; METHANOL; METHYLOBACTERIUM; MODELS, BIOLOGICAL; PLASMIDS;

EID: 70649098331     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007831     Document Type: Article

References (52)

1. Bailey JE (1993) Host-vector interactions in Escherichia coli. Adv Biochem Eng Biotechnol 48: 29-52.
2. Bailey JE, Da Silva NA, Peretti SW, Seo JH, Srienc F (1986) Studies of hostplasmid interactions in recombinant microorganisms. Ann N Y Acad Sci 469: 194-211.
3. Glick BR (1995) Metabolic load and heterologous gene expression. Biotechnol Adv 13: 247-261.
4. Cheah UE, Weigand WA, Stark BC (1987) Effects of recombinant plasmid size on cellular processes in Escherichia coli. Plasmid 18: 127-134.
5. Khosravi M, Ryan W, Webster DA, Stark BC (1990) Variation of oxygen requirement with plasmid size in recombinant Escherichia coli. Plasmid 23: 138-143.
6. Ryan W, Parulekar SJ, Stark BC (1989) Expression of beta-lactamase by recombinant Escherichia coli strains containing plasmids of different sizes-effects of pH, phosphate, and dissolved oxygen. Biotechnol Bioeng 34: 309-319.
7. Birnbaum S, Bailey JE (1991) Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant Escherichia coli. Biotechnol Bioeng 37: 736-745.
8. Seo JH, Bailey JE (1985) Effects of recombinant plasmid content on growth properties and cloned gene product formation in Escherichia coli. Biotechnol Bioeng 27: 1668-1674.
9. da Silva NA, Bailey JE (1986) Theoretical growth yield estimates for recombinant cells. Biotechnol Bioeng 28: 741-746.
10. Diaz Ricci JC, Hernandez ME (2000) Plasmid effects on Escherichia coli metabolism. Crit Rev Biotechnol 20: 79-108.
11. Ow DS, Lee DY, Yap MG, Oh SK (2008) Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol Prog 25: 61-67.
12. Ow DS-W, Nissom PM, Philp R, Oh SK-W, Yap MG-S (2006) Global transcriptional analysis of metabolic burden due to plasmid maintenance in Escherichia coli DH5 [alpha] during batch fermentation. Enzyme and Microbial Technology 39: 391-398.
13. Marciano DC, Karkouti OY, Palzkill T (2007) A fitness cost associated with the antibiotic resistance enzyme SME-1 beta-lactamase. Genetics 176: 2381-2392.
14. Moyed HS, Bertrand KP (1983) Mutations in multicopy Tn10 tet plasmids that confer resistance to inhibitory effects of inducers of tet gene expression. J Bacteriol 155: 557-564.
15. Lee SW, Edlin G (1985) Expression of tetracycline resistance in pBR322 derivatives reduces the reproductive fitness of plasmid-containing Escherichia coli. Gene 39: 173-180.
16. Nielsen J, Oliver S (2005) The next wave in metabolome analysis. Trends Biotechnol 23: 544-546.
17. Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63: 477-499.
18. 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.
19. Bosch G, Skovran E, Xia Q, Wang T, Taub F, et al. (2008) Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions. Proteomics 8: 3494-3505.
20. Guo X, Lidstrom ME (2008) Metabolite profiling analysis of Methylobacterium extorquens AM1 by comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. Biotechnol Bioeng 99: 929-940.
21. Kiefer P, Portais JC, Vorholt JA (2008) Quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry. Anal Biochem 382: 94-100.
22. Laukel M, Rossignol M, Borderies G, Volker U, Vorholt JA (2004) Comparison of the proteome of Methylobacterium extorquens AM1 grown under methylotrophic and nonmethylotrophic conditions. Proteomics 4: 1247-1264.
23. Okubo Y, Skovran E, Guo X, Sivam D, Lidstrom ME (2007) Implementation of microarrays for Methylobacterium extorquens AM1. OMICS 11: 325-340.
24. Schrader J, Schilling M, Holtmann D, Sell D, Filho MV, et al. (2009) Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends Biotechnol 27: 107-115.
25. Marx CJ, Lidstrom ME (2001) Development of improved versatile broad-hostrange vectors for use in methylotrophs and other Gram-negative bacteria. Microbiol 147: 2065-2075.
26. Chistoserdova L, Chen S-W, Lapidus A, Lidstrom ME (2003) Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol 185: 2980-2987.
27. Vorholt JA (2002) Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch Microbiol 178: 239-249.
28. Anthony C (1982) The biochemistry of methylotrophs. Academic Press, London, UK.
29. Large PJ, Quayle JR (1963) Microbial growth on C(1) compounds. 5. Enzyme activities in extracts of Pseudomonas AM1. Biochem J 87: 386-396.
30. 2-units involving crotonyl-CoA carboxylase/ reductase: the ethylmalonyl-CoA pathway. Proc Natl Acad Sci USA 104: 10631-10636.
31. 13C metabolomics. Proc Natl Acad Sci USA 106: 4846-4851.
32. 13C-labeled cell extracts as internal standards. Anal Biochem 336: 164-171.
33. Erb TJ, Retey J, Fuchs G, Alber BE (2008) Ethylmalonyl-CoA mutase from Rhodobacter sphaeroides defines a new subclade of coenzyme B12-dependent acyl-CoA mutases. J Biol Chem 283: 32283-32293.
34. Korotkova N, Lidstrom ME (2004) MeaB is a component of the methylmalonyl-CoA mutase complex required for protection of the enzyme from inactivation. J Biol Chem 279: 13652-13658.
35. Leadlay PF (1981) Purification and characterization of methylmalonyl-CoA epimerase from Propionibacterium shermanii. Biochem J 197: 413-419.
36. Stabler SP, Marcell PD, Allen RH (1985) Isolation and characterization of DL-methylmalonyl-coenzyme A racemase from rat liver. Arch Biochem Biophys 241: 252-264.
37. Levy SB, McMurry L (1978) Plasmid-determined tetracycline resistance involves new transport systems for tetracycline. Nature 276: 90-92.
38. Yamaguchi A, Udagawa T, Sawai T (1990) Transport of divalent cations with tetracycline as mediated by the transposon Tn10-encoded tetracycline resistance protein. J Biol Chem 265: 4809-4813.
39. Korotkova N, Lidstrom ME (2001) Connection between poly-beta-hydroxybutyrate biosynthesis and growth on C(1) and C(2) compounds in the methylotroph Methylobacterium extorquens AM1. J Bacteriol 183: 1038-1046.
40. Legoffic F, Martel A, Capmau ML, Baca B, Goebel P, et al. (1976) New plasmid-mediated nucleotidylation of aminoglycoside antibiotics in Staphylococcus aureus. Antimicrobial Agents and Chemotherapy 10: 258-264.
41. Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, et al. (2007) Antibiotic stress, genetic response and altered permeability of E. coli. PLoS One 2: e365.
42. Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T (2006) Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J Bacteriol 188: 317-327.
43. Schauer K, Gouget B, Carriere M, Labigne A, de Reuse H (2007) Novel nickel transport mechanism across the bacterial outer membrane energized by the TonB/ExbB/ExbD machinery. Mol Microbiol 63: 1054-1068.
44. Schauer K, Rodionov DA, de Reuse H (2008) New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'? Trends Biochem Sci 33: 330-338.
45. Chou HH, Berthet J, Marx CJ (2009) Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. PLoS Genet 5: e1000652.
46. Schönheit P, Moll J, Thauer RK (1979) Nickel, cobalt, and molybdenum requirement for growth of Methanobacterium thermoautotrophicum. Arch Microbiol 123: 105-107.
47. Thauer RK (1998) Biochemistry of methanogenesis: a tribute to Marjory Stephenson. 1998 Marjory Stephenson Prize Lecture. Microbiol 144: 2377-2406.
48. Gonzalez-Gil G, Kleerebezem R, Lettinga G (1999) Effects of nickel and cobalt on kinetics of methanol conversion by methanogenic sludge as assessed by online CH4 monitoring. Appl Environ Microbiol 65: 1789-1793.
49. Rohwerder T, Breuer U, Benndorf D, Lechner U, Müller RH (2006) The alkyl tert-butyl ether intermediate 2-hydroxyisobutyrate is degraded via a novel cobalamin-dependent mutase pathway. Appl Environ Microbiol 72: 4128-4135.
50. Sambrook J, Russell DW, eds (2001) Molecular cloning - a laboratory manual. New York: Cold Spring Harbor Press.
51. Bolten CJ, Kiefer P, Letisse F, Portais JC, Wittmann C (2007) Sampling for metabolome analysis of microorganisms. Anal Chem 79: 3843-3849.
52. Mashego MR, Wu L, Van Dam JC, Ras C, Vinke JL, et al. (2004) MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotechnol Bioeng 85: 620-628.