Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis

OMICS A Journal of Integrative Biology

Volumn 8, Issue 3, 2004, Pages 239-254

  Romine, Margaret F ^a   Elias, Dwayne A ^a   Monroe, Matthew E ^a   Auberry, Kenneth ^a   Fang, Ruihua ^a   Fredrickson, Jim K ^a   Anderson, Gordon A ^a   Smith, Richard D ^a   Lipton, Mary S ^a,b  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACRB PROTEIN; ACRD PROTEIN; ACRF PROTEIN; ALKALINE PHOSPHATASE; AMINO ACID; BACTERIAL PROTEIN; CHORISMATE SYNTHASE; FLAGELLAR HOOK ASSOCIATED PROTEIN FLGK; FORMATE DEHYDROGENASE; GENE PRODUCT; GLUTAMATE TRANSFER RNA LIGASE; INITIATION FACTOR; METHYL ACCEPTING CHEMOTAXIS PROTEIN; NUCLEOTIDE PYROPHOSPHATASE; PEPTIDE CHAIN RELEASE FACTOR 3; PEPTIDE DERIVATIVE; PHOSPHATIDYLSERINE DECARBOXYLASE; PROTEIN MR 1; PROTEIN SLYX; PROTEOME; RIBOSOME PROTEIN; SELENOCYSTEINE; SENSORY BOX PROTEIN; SIDEROPHORE RECEPTOR; TRANSLATION INITIATION FACTOR IF 1; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; CELL FUNCTION; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENETIC CONSERVATION; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN ANALYSIS; SHEWANELLA ONEIDENSIS; STOP CODON; VALIDATION PROCESS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROTEOME; SEQUENCE HOMOLOGY, AMINO ACID; SHEWANELLA;

BACTERIA (MICROORGANISMS); SHEWANELLA; SHEWANELLA ONEIDENSIS MR-1;

EID: 7044241336     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2004.8.239     Document Type: Article

References (20)

1. BARANOV, P.V., GURVICH, O.L., HAMMER, A.W., et al. (2003). RECODE. Nucleic Acids Res 31, 87-89.
2. DARASELIA, N., DERNOVOY, D., TIAN, Y., et al. (2003). Reannotation of Shewanella oneidensis genome. OMICS 7, 171-175.
3. ENG, J.K., MCCORMACK, A.L., and YATES, J.R. (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.
4. HARKEWICZ, R., ANDERSON, O.A., PASA-TOLIC, L., et al. (2001). Data-dependent external ion selection in the quadrupole ion guide of an external source ESI-FTICR mass spectrometer. J Am Soc Mass Spectrom 13, 144-154.
5. HEIDELBERG, J.F., PAULSEN, I.T., NELSON, K.E., et al. (2002). Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol 20, 1118-1123.
6. III in smectite by a pure culture of Shewanella putrefaciens strain MR-1. Clays Clay Miner 44, 522-529.
7. LAWRENCE, J. (2003). When ELFs are ORFs, but don't act like them. Trends Genet 19, 131-132.
8. LERCHER, M.J., and HURST, L.D. (2002). Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet 18, 337-340.
9. LIPTON, M.S., PASA-TOLIC, L., ANDERSON, G.A., et al. (2002). Global analysis of the Deinococcus radiodurans R1 proteome by using accurate mass tags. Proc Nat Acad Sci USA 99, 11049-11054.
10. LOVLEY, D.R., PHILLIPS, E.J.P., GORBY, Y.A., et al. (1991). Microbial reduction of uranium. Nature 350, 413-417.
11. LUKASHIN, A.V., and BORODOVSKY, M. (1998). GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26, 1107-1115.
12. III in Shewanella putrefaciens MR-1. J Bacteriol 172, 6232-6238.
13. MYERS, C.R., and MYERS, J.M. (1994). Ferric iron reduction-linked growth yields of Shewanella putrefaciens MR-1. J Appl Bacteriol 76, 253-258.
14. OCHMAN, H. (2002). Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet 18, 335-337.
15. SHEN, Y., ZHAO, R., RODRIGUEZ, N., et al. (2002). High-efficiency packed narrow capillary liquid chromatography (NanoLC) coupled on-line with mass spectrometry through nanoESI for high-sensitivity proteomics. Anal Chem 74, 4235-4249.
16. SKOVGAARD, M., JENSEN, L.J., BRUNAK, S., et al. (2001). On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 18, 425-428.
17. SMITH, R.D., ANDERSON, G.A., LIPTON, M.S., et al. (2002). An accurate mass tag strategy for quantitative and high throughput proteome measurements. Proteomics 2, 513-523.
18. VENTER, J.C., REMINGTON, K., HEIDELBERG, J.F., et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74.
19. WASHBURN, M.P., WOLTERS, D., and YATES, J.R. (2001). Large-scale analysis of the yeast proteome by multi-dimensional protein identification technology. Nat Biotechnol 19, 242-247.
20. 3+ oxides in single phase suspensions and subsurface materials. Am Miner 83, 1426-1443.