Application of High-Throughput Proteomics
EMSL Project ID
18427
Abstract
The understanding of how cells function at the systems level will greatly benefit from the development of new approaches capable of making global measurements of protein expression (proteome). The aim of this project is to apply new capabilities that are being developed for quantitative and high throughput proteomic measurements, based primarily upon high resolution separations combined with the unique high field Fourier transform ion cyclotron resonance mass spectrometry technology developed at PNNL. The project focuses on biological applications involving studies of the proteomes of several microorganisms including Shewanella oneidensis MR1, Deinococcus radiodurans R1, Rhodobacter sphaeroides and Geobacter sulfurreducens that play significant roles in bioremediation, carbon sequestration or radiation resistance. These efforts are proceeding in collaboration with biologists with expertise in each of these biological systems. The Shewanella research is focusing on the characterization of the organism cultured with different electron acceptors and is closely aligned with the Shewanella Federation. Comparative expression studies with D. radiodurans are being conducted in conjunction with Dr. Michael Daly (USUHS) and PNNL microbiologists to determine the affect of metals on radiation resistance. The Rhodobacter project performed in collaboration with Dr. Timothy Donohue and Dr. Samuel Kaplan focuses on life style dependent protein expression patterns. Finally the Geobacter project, in collaboration with Dr. Derek Lovely is characterization of the cytochrome proteins with extension to global proteomics.
Project Details
Start Date
2006-03-16
End Date
2009-03-22
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Brown RN, MF Romine, AA Schepmoes, RD Smith, and MS Lipton. 2010. "Mapping the Subcellular Proteome of Shewanella oneidensis MR-1 using Sarkosyl-based fractionation and LC-MS/MS protein identification." Journal of Proteome Research 9(9):4454-4463. doi:10.1021/pr100215h
Chin MH, W Qian, H Wang, VA Petyuk, JS Bloom, DM Sforza, G Lacan, D Liu, AH Khan, RM Cantor, DJ Bigelow, WP Melega, DG Camp, II, RD Smith, and DJ Smith. 2008. "Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson’s disease." Journal of Proteome Research 7(2):666-677. doi:10.1021/pr070546l
Du X, SJ Callister, NP Manes, JN Adkins, RA Alexandridis, X Zeng, JH Roh, WE Smith, TJ Donohue, S Kaplan, RD Smith, and MS Lipton. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7(7):2595-2604. doi:10.1021/pr0704837
Elias DA, SL Tollaksen, DW Kennedy, HM Mottaz, CS Giometti, JS Mclean, EA Hill, GE Pinchuk, MS Lipton, JK Fredrickson, and YA Gorby. 2008. "The Influence of Cultivation Methods on Shewanella oneidensis Physiology and Proteome Expression ." Archives of Microbiology 189(4):313-324. doi:10.1007/s00203-007-0321-y
Eraso JM, JH Roh, X Zeng, SJ Callister, MS Lipton, and S Kaplan. 2008. "Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis." Journal of Bacteriology 190(14):4831-4848. doi:10.1128/JB.00301-08
Merkley ED, KC Wrighton, C Castelle, BJ Anderson, MJ Wilkins, V Shah, T Arbour, JN Brown, SW Singer, RD Smith, and MS Lipton. 2014. "Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis." Journal of Proteome Research epub ahead of print:, doi:10.1021/pr500983v
Raymond J. DiDonato Jr., Nelson D. Young, Jessica E. Butler, Kuk-Jeong Chin, Kim K. Hixson, Paula
Mouser, Mary S. Lipton, Robert DeBoy, Barbara A. Methe´. 2010 "Genome Sequence of the Deltaproteobacterial Strain NaphS2 and Analysis of Differential Gene Expression during Anaerobic Growth on Naphthalene." PLoS ONE 5(11): e14072. doi:10.1371/journal.pone.0014072
Smith DP, JB Kitner, AD Norbeck, TRW Clauss, MS Lipton, MS Schwalbach, L Steindler, CD Nicora, RD Smith, and SJ Giovannoni. 2010. "Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique." PLoS One 5(5):Article Number: e10487.
Sowell SM, L Wilhelm, AD Norbeck, MS Lipton, CD Nicora, DF Barofsky, C carlson, RD Smith, and SJ Giovannoni. 2009. " Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3(1):93-105
Zhang H, RN Brown, W Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9(5):2160-2169.