Team:Szeged SA RMG/references

The Scientific Articles used by our Team

1. Alit, H. & Murrell, J. C. Development and validation of promoter-probe vectors for the study of methane monooxygenase gene expression in Methylococcus capsulatus Bath. Microbiology 155, 761–771 (2009).

2. Anthony, C. & Williams, P. The structure and mechanism of methanol dehydrogenase. in Biochimica et Biophysica Acta - Proteins and Proteomics 1647, 18–23 (2003).

3. Baani, M. & Liesack, W. Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc. Natl. Acad. Sci. 105, 10203–10208 (2008).

4. Boettcher, M. & McManus, M. T. Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. Molecular Cell (2015). doi:10.1016/j.molcel.2015.04.028

5. Bowman, J. P., Sly, L. I., Nichols, P. D. & Hayward, a. C. Revised Taxonomy of the Methanotrophs: Description of Methylobacter gen. nov., Emendation of Methylococcus, Validation of Methylosinus and Methylocystis Species, and a Proposal that the Family Methylococcaceae Includes Only the Group I Methanotrophs. Int. J. Syst. Bacteriol. 44, 375–375 (1994).

6. Brantl, S. Antisense-RNA regulation and RNA interference. Biochim Biophys Acta 1575, 15–25. (2002).

7. Cardy, D. L. N., Laidler, V., Salmond, G. P. C. & Murrell, J. C. The methane monooxygenase gene cluster of Methylosinus trichosporium: cloning and sequencing of the mmoC gene. Arch. Microbiol. 156, 477–483 (1991).

8. Cardy, D. L. N., Laidler, V., Salmond, G. P. C. & Murrell, J. C. Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b. Mol. Microbiol. 5, 335–342 (1991).

9. Carter, P. Site-directed mutagenesis. Biochem. J. 237, 1–7 (1986).

10. Coufal, D. E. et al. Sequencing and analysis of the Methylococcus capsulatus (Bath) soluble methane monooxygenase genes. Eur. J. Biochem. 267, 2174–2185 (2000).

11. Culpepper, M. A. & Rosenzweig, A. C. Structure and Protein–Protein Interactions of Methanol Dehydrogenase from\n Methylococcus capsulatus\n (Bath). Biochemistry 53, 6211–6219 (2014).

12. Csáki, R., Bodrossy, L., Klem, J., Murrell, J. C. & Kovács, K. L. Genes involved in the copper-dependent regulation of soluble methane monooxygenase of Methylococcus capsulatus (Bath): Cloning, sequencing and mutational analysis. Microbiology (2003). doi:10.1099/mic.0.26061-0

13. de Souza, N. Prokaryotic RNAi. Nat. Publ. Gr. 9, 220–221 (2012).

14. Dietrich, P., Sanders, D. & Hedrich, R. The role of ion channels in light-dependent stomatal opening. J. Exp. Bot. 52, 1959–1967 (2001).

15. Farhan Ul Haque, M., Gu, W., DiSpirito, A. A. & Semrau, J. D. Marker exchange mutagenesis of mxaF, encoding the large subunit of the Mxa methanol dehydrogenase, in Methylosinus trichosporium OB3b. Appl. Environ. Microbiol. 82, 1549–1555 (2016).

16. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).

17. Fodor, B. D. et al. Modular Broad-Host-Range Expression Vectors for Single-Protein and Protein Complex Purification. 70, 712–721 (2004).

18. Foster, J. W. & Davis, R. H. A methane-dependent coccus, with notes on classification and nomenclature of obligate, methane-utilizing bacteria. J. Bacteriol. 91, 1924–1931 (1966).

19. Fox, B. G., Borneman, J. G., Wackett, L. P. & Lipscomb, J. D. Haloalkene oxidation by the soluble methane monooxygenase from Methylosinus trichosporium OB3b: mechanistic and environmental implications. Biochemistry 29, 6419–6427 (1990).

20. Giver, L. Methane and Methanotrophic Bacteria as a Biotechnological Platform Calysta overview. (2015).

21. Good, L. & Stach, J. E. M. Synthetic RNA silencing in bacteria - antimicrobial discovery and resistance breaking. Front. Microbiol. 2, 1–11 (2011).

22. Guyton, A. C. & Hall, J. E. Textbook of Medical Physiology. 2011 XXXIII, (2011).

23. Hammond, S. M. Dicing and slicing: The core machinery of the RNA interference pathway. FEBS Letters 579, 5822–5829 (2005).

24. Hanson, R. S. & Hanson, T. E. Methanotrophic bacteria. Microbiol. Rev. 60, 439–471 (1996).

25. Harwood, J. H., Williams, E. & Bainbridge, B. W. Mutation of the Methane Oxidizing Bacterium, Methylococcus capsulatus. J. Appl. Bacteriol. 35, 99–108 (1972).

26. Henard, C. A. et al. Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Sci. Rep. 6, 21585 (2016).

27. Henckel, T. et al. Molecular Analyses of the Methane-Oxidizing Microbial Community in Rice Field Soil by Targeting the Genes of the 16S rRNA , Particulate Methane Monooxygenase , and Methanol Dehydrogenase Molecular Analyses of the Methane-Oxidizing Microbial Community in R. Appl. Environ. Microbiol. 65, 1980–1990 (1999).

28. Herrero, M., De Lorenzo, V. & Timmis, K. N. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J. Bacteriol. (1990). doi:10.1128/jb.172.11.6557-6567.1990

29. Kalyuzhnaya, M. G., Puri, A. W. & Lidstrom, M. E. Metabolic engineering in methanotrophic bacteria. Metab. Eng. 29, 142–152 (2015).

30. Keates, A. C., Fruehauf, J., Xiang, S. & Li, C. J. TransKingdom RNA interference: a bacterial approach to challenges in RNAi therapy and delivery. Biotechnol. Genet. Eng. Rev. 25, 113–27 (2008).

31. Kelly, W. J. et al. in Genome Announcements 4, e00232-16 (2016).

32. Khalifa, A. Y. Z. Mutagenesis of a Copper P-Type ATPase Encoding Genein Methylococcus capsulatus (Bath) Results inCopper-Resistance. Int. J. Biosci. Biochem. Bioinforma. (2013). doi:10.7763/IJBBB.2013.V3.159

33. Kitmitto, A., Myronova, N., Basu, P. & Dalton, H. Characterization and structural analysis of an active particulate methane monooxygenase trimer from Methylococcus capsulatus (Bath). Biochemistry 44, 10954–10965 (2005).

34. Larsen, ??ivind & Karlsen, O. A. Transcriptomic profiling of Methylococcus capsulatus (Bath)during growth with two different methane monooxygenases. Microbiologyopen 5, 254–267 (2016).

35. Lawton, T. J. & Rosenzweig, A. C. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. J. Am. Chem. Soc. 138, 9327–9340 (2016).

36. Lemos, S. S., Perille Collins, M. L., Eaton, S. S., Eaton, G. R. & Antholine, W. E. Comparison of EPR-visible Cu(2+) sites in pMMO from Methylococcus capsulatus (Bath) and Methylomicrobium album BG8. Biophys. J. 79, 1085–1094 (2000).


38. Lloyd, J. S., Bhambra, A., Murrell, J. C. & Dalton, H. Inactivation of the regulatory protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath) by proteolysis can be overcome by a Gly to Gln modification. Eur. J. Biochem 248, 72–79 (1997).

39. Lo, H. C., Haskel, A., Kapon, M. & Keinan, E. TpPt(IV)Me(H)2 forms a σ-CH4 complex that is kinetically resistant to methane liberation. J. Am. Chem. Soc. 124, 3226–3228 (2002).

40. M??ller, J. E. N. et al. Engineering Escherichia coli for methanol conversion. Metab. Eng. 28, 190–201 (2015).

41. Macalady, J. L., McMillan, A. M. S., Dickens, A. F., Tyler, S. C. & Scow, K. M. Population dynamics of type I and II methanotrophic bacteria in rice soils. Environ. Microbiol. (2002). doi:10.1046/j.1462-2920.2002.00278.x

42. Makarova, K. S., Grishin, N. V, Shabalina, S. A., Wolf, Y. I. & Koonin, E. V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7 (2006).

43. Manuscript, A., Thomason, M. K. & Storz, G. Bacterial antisense RNAs: How many are there and what are they doing? Analysis 324, 167–188 (2011).

44. Martin, H. & Murrell, J. C. Methane monooxygenase mutants of Methylosinus trichosporium constructed by marker-exchange mutagenesis. FEMS Microbiol. Lett. 127, 243–248 (1995).

45. Marx, C. J. & Lidstrom, M. E. Development of improved versatile broad-host-range vectors for use in methylotrophs and other gram-negative bacteria. Microbiology 147, 2065–2075 (2001).

46. Mocellin, S. & Provenzano, M. RNA interference: learning gene knock-down from cell physiology. J. Transl. Med. 2, 39 (2004).

47. Morita, T., Mochizuki, Y. & Aiba, H. Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc. Natl. Acad. Sci. U. S. A. 103, 4858–63 (2006).

48. Murrell, J. C. Genetics and molecular biology of methanotrophs. FEMS Microbiol. Rev. 88, 233–248 (1992).

49. Nakamura, T. et al. Soluble and particulate methane monooxygenase gene clusters in the marine methanotroph Methylomicrobium sp. strain NI. FEMS Microbiol. Lett. 277, 157–164 (2007).

50. Neuwirth, G. & Szemerszki, M. Tehetséggondozás a középiskolában, tehetségek a felsőoktatásban. Educatio 18, 204–218 (2009).

51. Omay, D. & Guvenilir, Y. Synthesis and characterization of poly(d,l-lactic acid) via enzymatic ring opening polymerization by using free and immobilized lipase. Biocatal. Biotransformation 31, 132–140 (2013).

52. Park, D. & Lee, J. Biological conversion of methane to methanol. Korean J. Chem. Eng. 30, 977–987 (2013).

53. Patel, R. N. & Hoare, D. S. Oxidation of C-1 Compounds capsulatus Physiological Studies of Methane and Methanol- Oxidizing Bacteria : Oxidation of C-1 Compounds by Methylococcus caps ulatus. J. Bacteriol. 107, 187–192 (1971).

54. Pratt, A. J. & MacRae, I. J. The RNA-induced silencing complex: A versatile gene-silencing machine. J. Biol. Chem. 284, 17897–17901 (2009).

55. Puri, A. W. et al. Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense. Appl. Environ. Microbiol. 81, 1775–1781 (2015).

56. Rasmussen, L. C. V., Sperling-Petersen, H. U. & Mortensen, K. K. Hitting bacteria at the heart of the central dogma: sequence-specific inhibition. Microb. Cell Fact. 6, 24 (2007).

57. Rhee, M. S. et al. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1. Stand. Genomic Sci. (2011). doi:10.4056/sigs.2365342

58. Róbert, C. et al. Szolubilis metán monooxigenáz rézfüggő szabályozásának vizsgálata Methylococcus capsulatus (Bath) törzsben. (2005).

59. Sander, J. D. & Joung, J. K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347–55 (2014).

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61. Sauer, N. J. et al. Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol. 170, pp.01696.2015 (2016).

62. Sharpe, P. L. et al. Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C 40 carotenoid synthesis. Appl. Environ. Microbiol. 73, 1721–1728 (2007).

63. Sirajuddin, S. & Rosenzweig, A. C. Enzymatic oxidation of methane. Biochemistry 54, 2283–2294 (2015).

64. Stainthorpe, A. C., Lees, V., Salmond, G. P. C., Dalton, H. & Murrell, J. C. The methane monooxygenase gene cluster of Methylococcus capsulatus (Bath). Gene 91, 27–34 (1990).

65. Stolyar, S., Franke, M. & Lidstrom, M. E. Expression of individual copies of Methylococcus capsulatus Bath particulate methane monooxygenase genes. J. Bacteriol. 183, 1810–1812 (2001).

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67. Strong, P. J., Xie, S. & Clarke, W. P. Methane as a resource: Can the methanotrophs add value? Environmental Science and Technology 49, 4001–4018 (2015).

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76. West, C. A., Salmond, G. P. C., Dalton, H. & Murrell, J. C. Functional expression in Escherichia coli of proteins B and C from soluble methane monooxygenase of Methylococcus capsulatus (Bath). J. Gen. Microbiol. 138, 1301–1 (1992).

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