Erratum: Part I: Characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2 (Analytical and Bioanalytical Chemistry DOI: 10.1007/s00216-010-3955-6);Part I: Characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2

Analytical and Bioanalytical Chemistry

Volumn 398, Issue 1, 2010, Pages 377-389

  Muddiman, David ^a   Andrews, Genna ^a   Lewis, Derrick ^b   Notey, Jaspreet ^b   Kelly, Robert ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b North Carolina State University   (United States)

Author keywords

Caldicellulosiruptor saccharolyticus; Sample preparation; Secretome; Thermophile

Indexed keywords

ACETONE; ACTIVATION ANALYSIS; BACTERIA; BIOLOGICAL MEMBRANES; ECOLOGY; HIDDEN MARKOV MODELS; PHYSIOLOGY; PURIFICATION;

CALDICELLULOSIRUPTOR SACCHAROLYTICUS; CONSOLIDATED BIO-PROCESSING; HIGH-TEMPERATURE ENVIRONMENT; SAMPLE PREPARATION; SAMPLE PREPARATION TECHNIQUES; SECRETOME; THERMOPHILE; THERMOPHILIC MICROORGANISMS;

PROTEINS;

BACTERIA (MICROORGANISMS); CALDICELLULOSIRUPTOR SACCHAROLYTICUS;

EID: 77955956751     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-010-4102-0     Document Type: Erratum

References (55)

1. Antranikian G, Egorova K (2007) Extremophiles, a unique resource of biocatalysts for industrial biotechnology. In: Gerday C, Glansdorff N (eds) Physiology and biochemistry of extremophiles. ASM Press, Washington, pp 361-406
2. AL VanFossen DL Lewis JD Nichols RM Kelly 2008 Polysaccharide degradation and synthesis by extremely nermophilic anaerobes Ann NY Acad Sci 1125 322 337 10.1196/annals.1419.017 (Pubitemid 351451163)
3. C Vafiadi E Topakas P Biely P Christakopoulos 2009 Purification, characterization and mass spectrometric sequencing of a thermophilic glucuronoyl esterase from Sporotrichum thermophile FEMS Microbiol Lett 296 178 184 10.1111/j.1574-6968.2009.01631.x
4. RD Barabote G Xie DH Leu P Normand A Necsulea V Daubin C Medigue WS Adney XC Xu A Lapidus RE Parales C Detter P Pujic D Bruce C Lavire JF Challacombe TS Brettin AM Berry 2009 Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations Genome Res 19 1033 1043 10.1101/gr.084848.108
5. Y Asada S Endo Y Inoue H Mamiya A Hara N Kunishima T Matsunaga 2009 Biochemical and structural characterization of a short-chain dehydrogenase/reductase of Thermus thermophilus HB8 A hyperthermostable aldose-1-dehydrogenase with broad substrate specificity Chem Biol Interact 178 117 126 10.1016/j.cbi.2008.09.018
6. SA Muhammad S Ahmad A Hameed 2009 Antibiotic production by Thermophilic bacillus specie Sat-4 Pak J Pharm Sci 22 339 345
7. TZ Esikova YV Temirov SL Sokolov YB Alakhov 2002 Secondary antimicrobial metabolites produced by thermophilic Bacillus spp. strains VK2 and VK21 Appl Biochem Microbiol 38 226 231 10.1023/A:1015463122840
8. S Sato CA Hutchison JI Harris 1977 Thermostable sequence-specific endonuclease from Thermus aquaticus PNAS 74 542 546 10.1073/pnas.74.2.542 (Pubitemid 8038838)
9. H Tjalsma A Bolhuis JDH Jongbloed S Bron JM van Dijl 2000 Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome Microbiol Mol Biol Rev 64 515 547 10.1128/MMBR.64.3.515-547. 2000
10. M Zhou J Boekhorst C Francke RJ Siezen 2008 LocateP: genome-scale subcellular-location predictor for bacterial proteins BMC Bioinform 9 173 10.1186/1471-2105-9-173 (Pubitemid 351587133)
11. Y Hathout 2007 Approaches to the study of the cell secretome Expert Rev Proteomics 4 239 248 10.1586/14789450.4.2.239 (Pubitemid 46588459)
12. FA Rainey AM Donnison PH Janssen D Saul A Rodrigo PL Bergquist RM Daniel E Stackebrandt HW Morgan 1994 Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium FEMS Microbiol Lett 120 263 266 10.1111/j.1574-6968.1994.tb07043.x
13. SE Blumer-Schuette I Kataeva J Westpheling MWW Adams RM Kelly 2008 Extremely thermophilic microorganisms for biomass conversion: status and prospects Curr Opin Biotechnol 19 210 217 10.1016/j.copbio.2008.04.007
14. K Rezaul LF Wu V Mayya SI Hwang D Han 2005 A systematic characterization of mitochondrial proteome from human T leukemia cells Mol Cell Proteomics 4 169 181
15. JD Bendtsen H Nielsen G von Heijne S Brunak 2004 Improved prediction of signal peptides: SignalP 3.0 J Mol Biol 340 783 795 10.1016/j.jmb.2004.05.028 (Pubitemid 38829638)
16. H Nielsen J Engelbrecht S Brunak G von Heijne 1997 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Protein Eng 10 1 6 10.1093/protein/10.1.1
17. van der Does C, Nouwen N, Driessen AJM (2003) The Sec translocase. In: Oudega B (ed) Protein secretion pathways in bacteria. Kluwer Academic Publishers, Boston, p 296
18. JD Bendtsen H Nielsen D Widdick T Palmer S Brunak 2005 Prediction of twin-arginine signal peptides BMC Bioinform 6 167 10.1186/1471-2105-6-167 (Pubitemid 41372498)
19. A Muesch E Hartmann K Rohde A Rubartelli R Sitia TA Rapoport 1990 A novel pathway for secretory proteins Trends Biochem Sci 15 86 88 10.1016/0968- 0004(90)90186-F
20. A Rubartelli F Cozzolino M Talio R Sitia 1990 A novel secretory pathway for interleukin-1-beta, a protein lacking a signal sequence EMBO J 9 1503 1510
21. G Harth DL Clemens MA Horwitz 1994 Glutamine synthetase of Mycobacterium tuberculosis: extracellular release and characterization of its enzymatic activity PNAS 91 9342 9346 10.1073/pnas.91.20.9342
22. G Harth MA Horwitz 1997 Expression and efficient export of enzymatically active Mycobacterium tuberculosis glutamine synthetase in Mycobacterium smegmatis and evidence that the information for export is contained within the protein J Biol Chem 272 22728 22735 10.1074/jbc.272.36.22728 (Pubitemid 27386090)
23. JD Bendtsen L Kiemer A Fausboll S Brunak 2005 Non-classical protein secretion in bacteria BMC Microbiol 5 58 10.1186/1471-2180-5-58 (Pubitemid 41561577)
24. A Krogh B Larsson G von Heijne ELL Sonnhammer 2001 Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J Mol Biol 305 567 580 10.1006/jmbi.2000.4315 (Pubitemid 33032862)
25. L Kall A Krogh ELL Sonnhammer 2004 A combined transmembrane topology and signal peptide prediction method J Mol Biol 338 1027 1036 10.1016/j.jmb.2004.03. 016 (Pubitemid 38542831)
26. L Kall A Krogh ELL Sonnhammer 2007 Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server Nucleic Acids Res 35 W429 W432 10.1093/nar/gkm256
27. HJG van de Werken MRA Verhaart AL VanFossen K Willquist DL Lewis JD Nichols HP Goorissen EF Mongodin KE Nelson EWJ van Niel AJM Stams DE Ward WM de Vos J van der Oost RM Kelly SWM Kengen 2008 Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus Appl Environ Microbiol 74 6720 6729 10.1128/AEM.00968-08
28. Pierce Technical Resource (2004) TR00490. Pierce Technical Resource, Rockford, IL., USA
29. L Jiang L He M Fountoulakis 2004 Comparison of protein precipitation methods for sample preparation prior to proteomic analysis J Chromatogr A 1023 317 320 10.1016/j.chroma.2003.10.029 (Pubitemid 37494806)
30. DM Sauve DT Ho M Roberge 1995 Concentration of dilute protein for gel-electrophoresis Anal Biochem 226 382 383 10.1006/abio.1995.1242
31. RL Winston MC Fitzgerald 1998 Concentration and desalting of protein samples for mass spectrometry analysis Anal Biochem 262 83 85 10.1006/abio.1998.2754 (Pubitemid 28440691)
32. A Shevchenko H Tomas J Havlis JV Olsen M Mann 2006 In-gel digestion for mass spectrometric characterization of proteins and proteomes Nat Protoc 1 2856 2860 10.1038/nprot.2006.468
33. GL Andrews CM Shuford JC Burnett AM Hawkridge DC Muddiman 2009 Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides J Chromatogr B 877 948 954 10.1016/j.jchromb.2009.02.040
34. DN Perkins DJC Pappin DM Creasy JS Cottrell 1999 Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 3551 3567 10.1002/(SICI)1522-2683(19991201)20: 18<3551::AID-ELPS3551>3.0.CO;2-2
35. Y Benjamini Y Hochberg 1995 Controlling the false discovery rate-a practical and powerful approach to multiple testing J R Stat Soc Ser B Stat Methodol 57 289 300
36. DB Weatherly JA Atwood TA Minning C Cavola RL Tarleton R Orlando 2005 A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results Mol Cell Proteomics 4 762 772 10.1074/mcp.M400215-MCP200 (Pubitemid 40873005)
37. J Zakowski 1931 On the purification of soya-urease through precipitation with acetone and carbonic acids. Hoppe-Seyler's Z Physiol Chem 202 67 82
38. V Thongboonkerd KR McLeish JM Arthur JB Klein 2002 Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation J Am Soc Nephrol 13 119A 119A
39. TS Collier AM Hawkridge DR Georgianna GA Payne DC Muddiman 2008 Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer Anal Chem 80 4994 5001 10.1021/ac800254z (Pubitemid 351956307)
40. M Sahyun CL Alsberg 1930 On rabbit liver glycogen and its preparation J Biol Chem 89 33 39
41. M Chevallet H Diemer A Van Dorssealer C Villiers T Rabilloud 2007 Toward a better analysis of secreted proteins: the example of the myeloid cells secretome Proteomics 7 1757 1770 10.1002/pmic.200601024 (Pubitemid 46910996)
42. JW Palmer TD Gerlough 1940 A simple method for preparing antigenic substances from the typhoid bacillus Science 92 155 156 10.1126/science.92.2381. 155
43. R Marusyk A Sergeant 1980 A simple method for dialysis of small-volume samples Anal Biochem 105 403 404 10.1016/0003-2697(80)90477-7
44. HR Bergen G Vasmatzis WA Cliby KL Johnson AL Oberg DC Muddiman 2003 Discovery of ovarian cancer biomarkers in serum using NanoLC electrospray ionization TOF and FT-ICR mass spectrometry Dis Markers 19 239 249
45. KL Johnson CJ Mason DC Muddiman JE Eckel 2004 Analysis of the low molecular weight fraction of serum by LC-dual ESI-FT-ICR mass spectrometry: precision of retention time, mass, and ion abundance Anal Chem 76 5097 5103 10.1021/ac0497003 (Pubitemid 39180339)
46. MA Basrai P Hieter JD Boeke 1997 Small open reading frames: beautiful needles in the haystack Genome Res 7 768 771
47. J Gough K Karplus R Hughey C Chothia 2001 Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure J Mol Biol 313 903 919 10.1006/jmbi.2001.5080 (Pubitemid 33063435)
48. M Bantscheff M Schirle G Sweetman J Rick B Kuster 2007 Quantitative mass spectrometry in proteomics: a critical review Anal Bioanal Chem 389 1017 1031 10.1007/s00216-007-1486-6 (Pubitemid 47482251)
49. J Gao MS Friedrichs AR Dongre GJ Opiteck 2005 Guidelines for the routine application of the peptide hits technique J Am Soc Mass Spectrom 16 1231 1238 10.1016/j.jasms.2004.12.002 (Pubitemid 41059559)
50. HB Liu RG Sadygov JR Yates 2004 A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal Chem 76 4193 4201 10.1021/ac0498563 (Pubitemid 38943698)
51. WM Old K Meyer-Arendt L Aveline-Wolf KG Pierce A Mendoza JR Sevinsky KA Resing NG Ahn 2005 Comparison of label-free methods for quantifying human proteins by shotgun proteomics Mol Cell Proteomics 4 1487 1502 10.1074/mcp.M500084-MCP200 (Pubitemid 41555475)
52. B Zybailov MK Coleman L Florens MP Washburn 2005 Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling Anal Chem 77 6218 6224 10.1021/ac050846r (Pubitemid 41436955)
53. B Zybailov AL Mosley ME Sardiu MK Coleman L Florens MP Washburn 2006 Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae J Proteome Res 5 2339 2347 10.1021/pr060161n (Pubitemid 44330827)
54. LR Lynd PJ Weimer WH van Zyl IS Pretorius 2002 Microbial cellulose utilization: fundamentals and biotechnology Microbiol Mol Biol Rev 66 506 577 10.1128/MMBR.66.3.506-577.2002 (Pubitemid 35005827)
55. LR Lynd RT Elander CE Wyman 1996 Likely features and costs of mature biomass ethanol technology Appl Biochem Biotechnol 57-8 741 761 10.1007/BF02941755