An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis

Journal of Bacteriology

Volumn 193, Issue 18, 2011, Pages 4758-4765

  Beck, David A C ^a,b   Hendrickson, Erik L ^a   Vorobev, Alexey ^a   Wang, Tiansong ^b   Lim, Sujung ^b   Kalyuzhnaya, Marina G ^b   Lidstrom, Mary E ^a,b   Hackett, Murray ^a   Chistoserdova, Ludmila ^a  

^a University of Washington   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; AMMONIA; METHANOL; NITRATE; NITROGEN; OXIDOREDUCTASE; OXYGEN; PROTEIN XOXF; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; DENITRIFICATION; DOWN REGULATION; ELECTRON; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ASSOCIATION; LIQUID CHROMATOGRAPHY; METABOLISM; METHYLOBACTERIUM; METHYLOTENERA MOBILIS; NITROGEN METABOLISM; NONHUMAN; OXIDATION; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEOMICS; RNA SEQUENCE; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY; TRANSCRIPTOMICS;

ELECTRONS; GENE EXPRESSION PROFILING; METABOLIC NETWORKS AND PATHWAYS; METHANOL; METHYLOPHILACEAE; NITRATES; OXIDATION-REDUCTION; OXYGEN; PROTEOME;

METHYLOBACILLUS; METHYLOPHILUS; METHYLOTENERA; METHYLOVORUS;

EID: 80052519363     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05375-11     Document Type: Article

References (30)

1. Anthony, C. 2004. The quinoprotein dehydrogenases for methanol and glucose. Arch. Biochem. Biophys. 428:2-9.
2. Bolstad, B. M., R. A. Irizarry, M. Astrand, and T. P. Speed. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
3. Bosch, G., et al. 2008. Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions. Proteomics 8:3494-3505.
4. Bosch, G., et al. 2009. Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis. Microbiology 155:1103-1110.
5. Callister, S. J., et al. 2008. Comparative bacterial proteomics: analysis of the core genome concept. PLoS One 3:e1542.
6. Cianciotto, N. P. 2005. Type II secretion: a protein secretion system for all seasons. Trends Microbiol. 13:581-588.
7. Chistoserdova, L. 2011. Modularity of methylotrophy, revisited. Environ. Microbiol. [Epub ahead of print.] doi:10.1111/j.1462-2920.2011.02464.x.
8. Chistoserdova, L., et al. 2007. Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J. Bacteriol. 189:4020-4027.
9. Croucher, N. J., and N. R. Thomson. 2010. Studying bacterial transcriptomes using RNA-seq. Curr. Opin. Microbiol. 13:619-624.
10. Elias, J. E., F. D. Gibbons, O. D. King, F. P. Roth, and S. P. Gygi. 2004. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22:214-219.
11. Eng., J. K., A. L. McCormack, and J. R. Yates III. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976-989.
12. Gao, J., G. J. Opiteck, M. S. Friedrichs, A. R. Dongre, and S. A. Hefta. 2003. Changes in the protein expression of yeast as a function of carbon source. J. Proteome Res. 2:643-649.
13. Hendrickson, E. L., et al. 2010. Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy. J. Bacteriol. 192:4859-4867.
14. Kalyuzhnaya, M. G., D. A. C. Beck, and L. Chistoserdova. 2011. Functional metagenomics of methylotrophs. Methods Enzymol. 495:81-98.
15. Kalyuzhnaya, M. G., et al. 2010. Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed through transcriptomics. ISME J. 4:388-398.
16. Kalyuzhnaya, M. G., et al. 18 February 2011. Novel methylotrophic isolates from Lake Washington sediment and description of a new species in the genus Methylotenera, Methylotenera versatilis sp. nov. Int. J. Syst. Evol. Microbiol.[Epub ahead of print.] doi:10.1099/ijs.0.029165-0.
17. Kalyuzhnaya, M. G., S. Bowerman, M. E. Lidstrom, and L. Chistoserdova. 2006. Methylotenera mobilis, gen. nov., sp. nov., an obligately methylamineutilizing bacterium within the family Methylophilaceae. Int. J. Syst. Evol. Microbiol. 56:2819-2823.
18. Kalyuzhnaya, M. G., et al. 2009. Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis. Environ. Microbiol. Rep. 1:385-392.
19. Lapidus, A., et al. 2011. Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of Methylophilaceae. J. Bacteriol. 15:3757-3764.
20. Li, H., and R. Durbin. 2009. Fast and accurate short read alignment with Burrows Wheeler transform. Bioinformatics 25:1754-1760.
21. Lidstrom, M. E. 2006. Aerobic methylotrophic prokaryotes, p. 618-634. In A. Balows, H. G. Truper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes, vol. 2. Springer-Verlag, New York, NY.
22. Liu, H., R. G. Sadygov, and J. R. Yates III. 2004. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76:4193-4201.
23. Mortazavi, A., B. A. Williams, K. McCue, L. Schaeffer, and B. Wold. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5:621-628.
24. Okubo, Y., E. Skovran, X. Guo, D. Sivam, and M. E. Lidstrom. 2007. Implementation of microarrays for Methylobacterium extorquens AM1. OMICS 11:325-340.
25. Ozsolak, F., and P. M. Milos. 2011. RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12:87-98.
26. Peng, J., J. E. Elias, C. C. Thoreen, L. J. Licklider, and S. P. Gygi. 2003. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2:43-50.
27. Porteus, B., C. Kocharunchitt, R. E. Nilsson, T. Ross, and J. P. Bowman. 2011. Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms. Appl. Microbiol. Biotechnol. 90:407-416.
28. Skovran, E., G. J. Crowther, X. Guo, S. Yang, and M. E. Lidstrom. 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.
29. Storey, J. D., and R. R. Tibshirani. 2003. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 100:9440-9445.
30. Tinberg, C. E., et al. 2010. Characterization of iron dinitrosyl species formed in the reaction of nitric oxide with a biological Rieske center. J. Am. Chem. Soc. 132:18168-18176.