Surfaceomics and surface-enhanced Raman spectroscopy of environmental microbes: Matching cofactors with redox-active surface proteins

Proteomics

Volumn 13, Issue 18-19, 2013, Pages 2761-2765

  Carlson, Hans K ^a   Iavarone, Anthony T ^b   Coates, John D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Microbiology; SERRS; SERS; Surfaceome; Trypsin shaving

Indexed keywords

MEMBRANE PROTEIN; METALLOID; TRYPSIN;

ARTICLE; BACTERIAL CELL; CELL SURFACE; CONTRAST ENHANCEMENT; ELECTRON TRANSPORT; ENVIRONMENTAL FACTOR; MICROORGANISM; NONHUMAN; ORGANISMS BY ELECTRON DONOR; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; RAMAN SPECTROMETRY; STRUCTURAL PROTEOMICS; SURFACE PROPERTY; SURFACEOMICS;

MICROBIOLOGY; SERRS; SERS; SURFACEOME; TRYPSIN SHAVING;

BACTERIA; BACTERIAL PROTEINS; COENZYMES; ENVIRONMENTAL MICROBIOLOGY; MEMBRANE PROTEINS; OXIDATION-REDUCTION; SPECTRUM ANALYSIS, RAMAN; TRYPSIN;

EID: 84885059681     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300010     Document Type: Article

References (38)

1. Weber, K. A., Achenbach, L. A., Coates, J. D., Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. Nat. Rev. Microbiol. 2006, 4, 752-764.
2. Carlson, H. K., Clark, I. C., Melnyk, R. A., Coates, J. D., Toward a mechanistic understanding of anaerobic nitrate-dependent iron oxidation: balancing electron uptake and detoxification. Front Microbiol. 2012, 3, 57.
3. Shi, L., Squier, T. C., Zachara, J. M., Fredrickson, J. K., Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes. Mol. Microbiol. 2007, 65, 12-20.
4. Carlson, H. K., Iavarone, A. T., Gorur, A., Yeo, B. S. et al., Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 1702-1707.
5. Walian, P. J., Allen, S., Shatsky, M., Zeng, L. et al., High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J. Proteome Res. 2012, 11, 5720-5735.
6. Wohlbrand, L., Kube, M., Mussmann, M., Jarling, R. et al., Complete genome, catabolic sub-proteomes and key-metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound-degrading, sulfate-reducing bacterium. Environ. Microbiol. 2013, 15, 1334-1355.
7. D41. Proteomics 2012, 12, 3180-3192.
8. Bird, L. J., Bonnefoy, V., Newman, D. K., Bioenergetic challenges of microbial iron metabolisms. Trends Microbiol. 2011, 19, 330-340.
9. Culha, M., Adiguzel, A., Yazici, M. M., Kahraman, M. et al., Characterization of thermophilic bacteria using surface-enhanced raman scattering. Appl. Spectrosc. 2008, 62, 1226-1232.
10. Biju, V., Pan, D., Gorby, Y. A., Fredrickson, J. et al., Combined spectroscopic and topographic characterization of nanoscale domains and their distributions of a redox protein on bacterial cell surfaces. Langmuir 2007, 23, 1333-1338.
11. Jarvis, R. M., Law, N., Shadi, I. T., O'Brien, P. et al., Surface-enhanced Raman scattering from intracellular and extracellular bacterial locations. Anal. Chem. 2008, 80, 6741-6746.
12. Clark, I. C., Carlson, H. K., Iavarone, A. T., Coates, J. D., Bioelectrical redox cycling of anthraquinone-2, 6-disulfonate coupled to perchlorate reduction. Energy Environ. Sci. 2012, 5, 7970-7978.
13. Tjalsma, H., Lambooy, L., Hermans, P. W., Swinkels, D. W., Shedding & shaving: disclosure of proteomic expressions on a bacterial face. Proteomics 2008, 8, 1415-1428.
14. Calvo, E., Pucciarelli, M. G., Bierne, H., Cossart, P. et al., Analysis of the Listeria cell wall proteome by two-dimensional nanoliquid chromatography coupled to mass spectrometry. Proteomics 2005, 5, 433-443.
15. Thein, M., Sauer, G., Paramasivam, N., Grin, I. et al., Efficient subfractionation of gram-negative bacteria for proteomics studies. J. Proteome Res. 2010, 9, 6135-6147.
16. Cordwell, S. J., Technologies for bacterial surface proteomics. Curr. Opin. Microbiol. 2006, 9, 320-329.
17. Wolff, S., Antelmann, H., Albrecht, D., Becher, D. et al., Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches. J. Chromatogr. B Analyt. Technol. Biomed. Life. Sci. 2007, 849, 129-140.
18. Brown, R. N., Romine, M. F., Schepmoes, A. A., Smith, R. D. et al., Mapping the subcellular proteome of Shewanella oneidensis MR-1 using sarkosyl-based fractionation and LC-MS/MS protein identification. J. Proteome Res. 2010, 9, 4454-4463.
19. Walther, T. C., Mann, M., Mass spectrometry-based proteomics in cell biology. J. Cell Biol. 2010, 190, 491-500.
20. Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-553.
21. Zhang, H., Brown, R. N., Qian, W. J., Monroe, M. E. et al., Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling. J. Proteome Res. 2010, 9, 2160-2169.
22. Solis, N., Larsen, M. R., Cordwell, S. J., Improved accuracy of cell surface shaving proteomics in Staphylococcus aureus using a false-positive control. Proteomics 2010, 10, 2037-2049.
23. Stiles, P. L., Dieringer, J. A., Shah, N. C., Van Duyne, R. P., Surface-enhanced Raman spectroscopy. Annu. Rev. Anal. Chem. (Palo Alto Calif) 2008, 1, 601-626.
24. Jarvis, R. M., Goodacre, R., Characterisation and identification of bacteria using SERS. Chem. Soc. Rev. 2008, 37, 931-936.
25. Premasiri, W. R., Moir, D. T., Klempner, M. S., Krieger, N. et al., Characterization of the surface enhanced raman scattering (SERS) of bacteria. J. Phys. Chem. B 2005, 109, 312-320.
26. Premasiri, W. R., Moir, D. T., Klempner, M. S., Krieger, N. et al., Characterization of the surface enhanced raman scattering (SERS) of bacteria. J. Phys. Chem. B 2005, 109, 312-320.
27. Porter, M. D., Lipert, R. J., Siperko, L. M., Wang, G. et al., SERS as a bioassay platform: fundamentals, design, and applications. Chem. Soc. Rev. 2008, 37, 1001-1011.
28. Lee, P. C., Meisel, D., Adsorption and surface-enhanced Raman of dyes on silver and gold sols. J. Phys. Chem. 1982, 86, 3391-3395.
29. Moerl, L., Pettinger, B., The role of Cu atoms on silver electrodes in surface enhanced Raman-scattering from pyridine-giant enhancement by a minority of adsorbed molecules. Solid State Commun. 1982, 43, 315-320.
30. Stockle, R. M., Deckert, V., Fokas, C., Zenobi, R., Controlled formation of isolated silver islands for surface-enhanced Raman scattering. Appl. Spectrosc. 2000, 54, 1577-1583.
31. McNay, G., Eustace, D., Smith, W. E., Faulds, K. et al., Surface-enhanced Raman scattering (SERS) and surface-enhanced resonance Raman scattering (SERRS): a review of applications. Appl. Spectrosc. 2011, 65, 825-837.
32. Kleinman, S. L., Frontiera, R. R., Henry, A. I., Dieringer, J. A. et al., Creating, characterizing, and controlling chemistry with SERS hot spots. Phys. Chem. Chem. Phys. 2013, 15, 21-36.
33. Hudson, S. D., Chumanov, G., Bioanalytical applications of SERS (surface-enhanced Raman spectroscopy). Anal. Bioanal. Chem. 2009, 394, 679-686.
34. Picorel, R., Lu, T., Holt, R. E., Cotton, T. M. et al., Surface-enhanced resonance raman scattering spectroscopy of bacterial photosynthetic membranes: orientation of the carotenoids of Rhodobacter sphaeroides 2.4.1. Biochemistry 1990, 29, 707-712.
35. Picorel, R., Holt, R. E., Cotton, T. M., Seibert, M., Surface-enhanced resonance Raman scattering spectroscopy of bacterial photosynthetic membranes. The carotenoid of Rhodospirillum rubrum. J. Biol. Chem. 1988, 263, 4374-4380.
36. Seibert, M., Picorel, R., Kim, J. H., Cotton, T. M., Surface-enhanced Raman scattering spectroscopy of photosynthetic membranes and complexes. Meth. Enzymol. 1992, 213, 31-42.
37. Busalmen, J. P., Esteve-Nunez, A., Berna, A., Feliu, J. M., ATR-SEIRAs characterization of surface redox processes in G. sulfurreducens. Bioelectrochemistry 2010, 78, 25-29.
38. Busalmen, J. P., Esteve-Nunez, A., Berna, A., Feliu, J. M., C-type cytochromes wire electricity-producing bacteria to electrodes. Angew. Chem. Int. Ed. Engl. 2008, 47, 4874-4877.