Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis

Journal of Microbiological Methods

Volumn 67, Issue 1, 2006, Pages 36-43

  Culley, David E ^a   Kovacik Jr , William P ^a   Brockman, Fred J ^a   Zhang, Weiwen ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Methanosarcina barkeri; Microarray; RNA isolation

Indexed keywords

LIQUID NITROGEN; OLIGONUCLEOTIDE;

ARCHAEBACTERIUM; ARTICLE; CONTROLLED STUDY; CYTOLYSIS; DNA MICROARRAY; DNA MODIFICATION; GENE EXPRESSION; METHANOGENESIS; METHANOSARCINA BARKERI; NONHUMAN; PRIORITY JOURNAL; REPRODUCIBILITY; RNA ISOLATION; VALIDATION PROCESS;

GENE EXPRESSION; METHANE; METHANOSARCINA BARKERI; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA; RNA, BACTERIAL;

ARCHAEA; METHANOSARCINA BARKERI;

EID: 33747764232     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2006.02.014     Document Type: Article

References (23)

1. Balch W.E., Fox G.E., Magrum L.J., Woese C.R., and Wolfe R.S. Methanogens: reevaluation of a unique biological group. Microbiol. Rev. 43 (1979) 260-296
2. Chien Y.T., and Zinder S.H. Cloning, DNA sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum. J. Bacteriol. 176 (1994) 6590-6598
3. Chien Y.T., Auerbuch V., Brabban A.D., and Zinder S.H. Analysis of genes encoding an alternative nitrogenase in the archaeon Methanosarcina barkeri 227. J. Bacteriol. 182 (2000) 3247-3253
4. Chomczynski P., and Sacchi N. Single step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162 (1987) 156-159
5. Deppenmeier U. The unique biochemistry of methanogenesis. Prog. Nucleic Acid Res. Mol. Biol. 71 (2002) 223-283
6. Galagan J.E., Nusbaum C., Roy A., Endrizzi M.G., Macdonald P., FitzHugh W., Calvo S., Engels R., Smirnov S., Atnoor D., Brown A., Allen N., Naylor J., Stange-Thomann N., DeArellano K., Johnson R., Linton L., McEwan P., McKernan K., Talamas J., Tirrell A., Ye W., Zimmer A., Barber R.D., Cann I., Graham D.E., Grahame D.A., Guss A.M., Hedderich R., Ingram-Smith C., Kuettner H.C., Krzycki J.A., Leigh J.A., Li W., Liu J., Mukhopadhyay B., Reeve J.N., Smith K., Springer T.A., Umayam L.A., White O., White R.H., Conway de Macario E., Ferry J.G., Jarrell K.F., Jing H., Macario A.J., Paulsen I., Pritchett M., Sowers K.R., Swanson R.V., Zinder S.H., Lander E., Metcalf W.W., and Birren B. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12 (2002) 532-542
7. Hovey R., Lentes S., Ehrenreich A., Salmon K., Saba K., Gottschalk G., Gunsalus R.P., and Deppenmeier U. DNA microarray analysis of Methanosarcina mazei Go1 reveals adaptation to different methanogenic substrates. Mol. Genet. Genomics 273 (2005) 225-239
8. Ibrahim A., and Ahring B.K. Extraction of intact ribosomal RNA from anaerobic bioreactor samples for molecular ecological studies. Biotechniques 27 (1999) 1132-1138
9. Jarvis G.N., Strompl C., Burgess D.M., Skillman L.C., Moore E.R., and Joblin K.N. Isolation and identification of ruminal methanogens from grazing cattle. Curr. Microbiol. 40 (2000) 327-332
10. Jones W.J., Nagle Jr. D.P., and Whitman W.B. Methanogens and the diversity of archaebacteria. Microbiol. Rev. 51 (1987) 135-177
11. Karlin S., and Mrazek J. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182 (2000) 5238-5250
12. Liljedahl U., Fredriksson M., Dahlgren A., and Syvanen A.C. Detecting imbalanced expression of SNP alleles by minisequencing on microarrays. BMC Biotechnol. 4 (2004) 24
13. Lovley D.R., and Klug M.J. Intermediary metabolism of organic matter in the sediments of a eutrophic lake. Appl. Environ. Microbiol. 43 (1982) 552-560
14. Macario A.J., Lange M., Ahring B.K., and De Macario E.C. Stress genes and proteins in the archaea. Microbiol. Mol. Biol. Rev. 63 (1999) 923-967
15. Mazumder T.K., Nishio N., Fukuzaki S., and Nagai S. Effect of sulfur-containing compounds on growth of Methanosarcina barkeri in defined medium. Appl. Environ. Microbiol. 52 (1986) 617-622
16. Nuwaysir E.F., Huang W., Albert T.J., Singh J., Nuwaysir K., Pitas A., Richmond T., Gorski T., Berg J.P., Ballin J., McCormick M., Norton J., Pollock T., Sumwalt T., Butcher L., Porter D., Molla M., Hall C., Blattner F., Sussman M.R., Wallace R.L., Cerrina F., and Green R.D. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12 (2002) 1749-1755
17. Sambrook J.M., and Russell D.W. Molecular Cloning: A Laboratory Manual. 3rd ed. (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
18. Singh-Gasson S., Green R.D., Yue Y., Nelson C., Blattner F., Sussman M.R., and Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 17 (1999) 974-978
19. Smith P.H., and Mah R.A. Kinetics of acetate metabolism during sludge digestion. Appl. Microbiol. 14 (1966) 368-371
20. Sowers K.R., and Gunsalus R.P. Adaptation for growth at various saline concentrations by the archaebacterium Methanosarcina thermophila. J. Bacteriol. 170 (1988) 998-1002
21. Ushida K., Newbold C.J., and Jouany J.P. Interspecies hydrogen transfer between the rumen ciliate Polyplastron multivesiculatum and Methanosarcina barkeri. J. Gen. Appl. Microbiol. 43 (1997) 129-131
22. Van Dessel W., Van Mellaert L., Geukens N., Lammertyn E., and Anne J. Isolation of high quality RNA from Streptomyces. J. Microbiol. Methods 58 (2004) 135-137
23. Zinder S.H. Physiological ecology of methanogens. In: Ferry J.G. (Ed). Methanogenesis (1993), Chapman Hall Routledge, New York 128-206