Microarray analysis in the archaeon Halobacterium salinarum strain R1

PLoS ONE

Volumn 2, Issue 10, 2007, Pages

  Twellmeyer, Jens ^a   Wende, Andy ^a   Wolfertz, Jan ^a   Pfeiffer, Friedhelm ^a   Panhuysen, Markus ^b,e   Zaigler, Alexander ^c   Soppa, Jörg ^c   Welzi, Gerhard ^d   Oesterhelt, Dieter ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b MAX PLANCK INSTITUTE OF PSYCHIATRY   (Germany)

^c GOETHE UNIVERSITY   (Germany)

^d INSTITUTE OF EPIDEMIOLOGY   (Germany)

^e Affectis Pharmaceutical AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; ARCHAEAL PROTEIN; COMPLEMENTARY DNA; PRIMER DNA; RNA;

AEROBIC BACTERIUM; ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; BACTERIAL STRAIN; CELL GROWTH; CONTROLLED STUDY; DNA MICROARRAY; FILTRATION; FLUORESCENCE; GENE CONTROL; HALOBACTERIUM SALINARUM; MICROARRAY ANALYSIS; MULTIVARIATE ANALYSIS OF VARIANCE; NONHUMAN; PHOTOTROPISM; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; STRAIN IDENTIFICATION; SYSTEMS BIOLOGY; TRANSCRIPTION INITIATION; BIOCHEMISTRY; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; LIGHT; METABOLISM; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPECTROFLUOROMETRY; STATISTICAL MODEL;

ARCHAEA; HALOBACTERIUM SALINARUM;

ARCHAEAL PROTEINS; BIOCHEMISTRY; DNA PRIMERS; DNA, COMPLEMENTARY; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; HALOBACTERIUM SALINARUM; LIGHT; MODELS, STATISTICAL; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; SPECTROMETRY, FLUORESCENCE; TRANSCRIPTION, GENETIC;

EID: 38449113963     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001064     Document Type: Article

References (35)

1. Sumper M, Reitmeier H, Oesterhelt D (1976) Biosynthesis of the purple membrane of halobacteria. Angew Chem Int Ed Engl 15: 187-94.
2. Sumper M, Herrmann G (1976) Biogenesis of purple membrane: regulation of bacterio-opsin synthesis. FEBS Lett 69: 149-52.
3. Oesterhelt D, Krippahl G (1983) Phototrophic growth of halobacteria and its use for isolation of photosynthetically-deficient mutants. Ann Microbiol B134: 137-150.
4. Shand RF, Betlach MC (1991) Expression of the bop Gene Cluster of Halobacterium halobium Is Induced by Low Oxygen Tension and by Light. J Bacteriol 173: 4692-4699.
5. Peck RF, Echavarri-Erasun C, Johnson EA, Ng WV, Kennedy SP, et al. (2001) brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum. J Biol Chem 276: 5739-5744.
6. Baliga NS, Kennedy SP, Ng WV, Hood L, DasSarma S (2001) Genomic and genetic dissection of an archaeal regulon. Proc Natl Acad Sci USA 98:2521-2525.
7. Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, et al. (2002) Coordinate regulation of energy transduction modules in Halobacterim sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A 99: 14913-14918.
8. Bisle B, Schmidt A, Scheibe B, Klein C, Tebbe A, et al. (2006) Quantitative profiling of the membrane protcome in a halophilic archaeon. Mol Cell Proteomics 5: 1543-1558.
9. Klein C, Garcia-Rizo C, Bisle B, Scheffer B, Zischka H, et al. (2005) The membrane protcome of Halobacterium salinarum. Proteomics 5: 180-197.
10. Tebbe A, Klein C, Bisle B, Siedler F, Scheffer B, et al. (2005) Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation. Proteomics 5: 168-179.
11. Lee ML, Kuo FC, Whitmore GA, Sklar J (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A 97: 9834-9839.
12. Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3: 579-588.
13. Wu H, Kerr MK, Cui X, Churchill CA (2003) MAANOVA: a software package for the analysis of spotted cDNA microarray experiments. In: Parmigiani G, Garrett E, Irizarry R, Zeger S, eds. The Analysis of Gene Expression Data: Methods and Software. New York: Springer-Verlag. pp 313-341.
14. Rousseeuw PJ, Leroy AM (1987) Robust Regression & Outlier Detection. New York: Wiley.
15. Mary-Huard T, Daudin JJ, Robin S, Bitton F, Cabannes E, et al. (2004) Spotting effect in microarray experiments. BMC Bioinformatics 5: 63.
16. Trovanskaya O, Cantor M, Sherlock G, Brown P, Hastic T, et al. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics 17: 520-525.
17. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate - A practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Method 57: 289-300.
18. Gropp F, Betlach MC (1994) The bat gene of Halobacterium halobium encodes a transacting oxygen inducibility factor. Proc Natl Acad Sci U S A 91: 5475-5479.
19. Muller JA, DasSarma S (2005) Genomic Analysis of Anaerobic Respiration in the Archaeon Halobacterium sp. Strain NRC-1: Dimethyl Sulfoxide and Trimethylamine N-Oxide as Terminal Electron Acceptors. J Bacteriol 187: 1659-1667.
20. Rudolph J, Oesterhelt D (1995) Chemotaxis and phototaxis require a CheA histidine kinase in the archaeon Halobacterium salinarium. EMBO J 14: 667-673.
21. Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, et al. (2000) Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 97: 12176-12181.
22. Yao VJ, Spudich JL (1992) Primary structure of an archaebactctial transducer, a methylaccepting protein associated with sensory rhodopsin I. Proc Natl Acad Sci U S A 89: 11915-11919.
23. Brooun A, Bell J, Freitas T, Larsen RW, Alam M (1998) An archaeal aerotaxis transducer combines subunit I core structures of eukaryotic cytochrome c oxidase and eubacterial methylaccepting chemotaxis proteins. J Bacteriol 180: 1642-1646.
24. Kokoeva MV, Oesterhelt D (2000) BasT, a membrane-bound transducer protein for amino acid detection in Halobacterium salinarum. Mol Microbiol 35: 647-656.
25. Stoeckenius W, Kunau WH (1968) Further characterization of particulate fractions from lysed cell envelopes of Halobacterium halobium and isolation of gas vacuole membranes. J Cell Biol 38: 337-357.
26. DasSarma S, Halladay JT, Jones JG, Donovan JW, Giannasca PJ, et al. (1988) High-frequency mutations in a plasmid-enccoded gas vesicle gene in Halobacterium halobium. Proc Natl Acad Sci U S A 85: 6861-6865.
27. Dharmadi Y, Gonzalez R (2004) DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol Prog 20: 1309-1324.
28. Ruepp A, Soppa J (1996) Fermentative arginine degradation in Halobacterium salinarum (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcR4CB gene cluster. J Bacteriol 178: 4942-7.
29. Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, et al. (2006) An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol 2: 47.
30. Oesterhelt D (1982) Anaerobic Growth of Halobacteria. Methods Enzymol 88: 417-420.
31. Raddatz G, Dehio M, Meyer TF, Dehio C (2001) PrimeArray: genome-scale primer design for DNA-microarray construction. Bioinformatics 17; 98-99.
32. Diehl F, Grahlmann S, Beier M, Hoheisel JD (2001) Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucl Acids Res methods online 29: 38, doi:10.1093/nar/29.7.e38.
33. Zaigler A, Schuster SC, Soppa J (2003) Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii. Mol Microbiol 48: 1089-1105.
34. Freeman WM, Walker SJ, Vrana KE (1999) Quantitative RI-PCR: pitfalls and potential. Biotechniques 26: 112-125.
35. Aregger M (2003) Ph.D thesis. Munich: Ludwig-Maximilians-University.