Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching.

Multiheme c-type cytochromes (proteins with covalently attached heme c moieties) play important roles in extracellular metal respiration in dissimilatory metal-reducing bacteria. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of c-type cytochromes is hindered by the presence of multiple heme groups, since the heme c modified peptides are typically not observed or, if observed, not identified. Using a recently reported histidine affinity chromatography (HAC) procedure, we enriched heme c tryptic peptides from purified bovine heart cytochrome c, two bacterial decaheme cytochromes, and subjected these samples to LC-MS/MS analysis. Enriched bovine cytochrome c samples yielded 3- to 6-fold more confident peptide-spectrum matches to heme c containing peptides than unenriched digests. In unenriched digests of the decaheme cytochrome MtoA from Sideroxydans lithotrophicus ES-1, heme c peptides for 4 of the 10 expected sites were observed by LC-MS/MS; following HAC fractionation, peptides covering 9 out of 10 sites were obtained. Heme c peptide spiked into E. coli lysates at mass ratios as low as 1×10(-4) was detected with good signal-to-noise after HAC and LC-MS/MS analysis. In addition to HAC, we have developed a proteomics database search strategy that takes into account the unique physicochemical properties of heme c peptides. The results suggest that accounting for the double thioether link between heme c and peptide, and the use of the labile heme fragment as a reporter ion, can improve database searching results. The combination of affinity chromatography and heme-specific informatics yielded increases in the number of peptide-spectrum matches of 20-100-fold for bovine cytochrome c.

[1]  Ming L. Wu,et al.  Bacterial oxygen production in the dark , 2012, Front. Microbio..

[2]  M. Lipton,et al.  Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1 , 2012, Front. Microbio..

[3]  Leland Wilkinson,et al.  Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams , 2012, IEEE Transactions on Visualization and Computer Graphics.

[4]  Ronald J. Moore,et al.  Identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation. , 2011, Analytical chemistry.

[5]  John M. Zachara,et al.  Structure of a bacterial cell surface decaheme electron conduit , 2011, Proceedings of the National Academy of Sciences.

[6]  B. Polacco,et al.  Discovering Mercury Protein Modifications in Whole Proteomes Using Natural Isotope Distributions Observed in Liquid Chromatography-Tandem Mass Spectrometry* , 2011, Molecular & Cellular Proteomics.

[7]  Bin Cao,et al.  Extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms: characterization by infrared spectroscopy and proteomics. , 2011, Environmental microbiology.

[8]  Jeffrey A. Gralnick,et al.  Towards Electrosynthesis in Shewanella: Energetics of Reversing the Mtr Pathway for Reductive Metabolism , 2011, PloS one.

[9]  Kara L Bren,et al.  A heme fusion tag for protein affinity purification and quantification , 2010, Protein science : a publication of the Protein Society.

[10]  S. Kerisit,et al.  The Roles of Outer Membrane Cytochromes of Shewanella and Geobacter in Extracellular Electron Transfer , 2010 .

[11]  P. Pevzner,et al.  The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search* , 2010, Molecular & Cellular Proteomics.

[12]  Derek R Lovley,et al.  The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments. , 2010, BMC Genomics.

[13]  Richard D. Smith,et al.  Mapping the subcellular proteome of Shewanella oneidensis MR-1 using sarkosyl-based fractionation and LC-MS/MS protein identification. , 2010, Journal of proteome research.

[14]  W. D. Gould,et al.  Biochemical and genomic facets on the dissimilatory reduction of radionuclides by microorganisms – A review , 2010 .

[15]  Dong-Woo Lee,et al.  Cytochrome c biogenesis: the Ccm system. , 2010, Trends in microbiology.

[16]  Ronald J. Moore,et al.  Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling. , 2010, Journal of proteome research.

[17]  Elaine Stephens,et al.  Aberrant attachment of heme to cytochrome by the Ccm system results in a cysteine persulfide linkage. , 2010, Journal of the American Chemical Society.

[18]  Paul C Mills,et al.  Characterization of an electron conduit between bacteria and the extracellular environment , 2009, Proceedings of the National Academy of Sciences.

[19]  Yiguo Hong,et al.  Bacterial anaerobic respiration and electron transfer relevant to the biotransformation of pollutants , 2009 .

[20]  Kenneth H. Williams,et al.  Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation , 2009, Applied and Environmental Microbiology.

[21]  Navdeep Jaitly,et al.  Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data , 2009, BMC Bioinformatics.

[22]  Richard D. Smith,et al.  Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor. , 2008, Biochimica et biophysica acta.

[23]  D. Lovley.  The microbe electric: conversion of organic matter to electricity. , 2008, Current opinion in biotechnology.

[24]  P. Pevzner,et al.  Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. , 2008, Journal of proteome research.

[25]  Joshua N. Adkins,et al.  MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features , 2008, Comput. Biol. Chem..

[26]  Navdeep Jaitly,et al.  DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra , 2008, Bioinform..

[27]  V. Stojanoff,et al.  High resolution X‐ray crystallographic structure of bovine heart cytochrome c and its application to the design of an electron transfer biosensor , 2007, Proteins.

[28]  Ronald J Moore,et al.  Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. , 2008, Analytical chemistry.

[29]  Brett S Phinney,et al.  Shotgun cross-linking analysis for studying quaternary and tertiary protein structures. , 2007, Journal of proteome research.

[30]  M. Tien,et al.  Characterization of Protein-Protein Interactions Involved in Iron Reduction by Shewanella oneidensis MR-1 , 2007, Applied and Environmental Microbiology.

[31]  D. Newman,et al.  Extracellular respiration , 2007, Molecular microbiology.

[32]  J. Fredrickson,et al.  Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes , 2007, Molecular microbiology.

[33]  D. Lovley.  Bug juice: harvesting electricity with microorganisms , 2006, Nature Reviews Microbiology.

[34]  Richard D. Smith,et al.  The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions. , 2006, Biochimica et biophysica acta.

[35]  Richard D. Smith,et al.  Advances in proteomics data analysis and display using an accurate mass and time tag approach. , 2006, Mass spectrometry reviews.

[36]  Matthew E Monroe,et al.  Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR‐1 using LC‐MS based proteomics , 2005, Proteomics.

[37]  Richard D. Smith,et al.  Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry. , 2005, Journal of proteome research.

[38]  L. M. Markillie,et al.  Overexpression of multi-heme C-type cytochromes. , 2005, BioTechniques.

[39]  Matthew E Monroe,et al.  Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis. , 2004, Omics : a journal of integrative biology.

[40]  D. Frishman,et al.  Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. , 2004, Omics : a journal of integrative biology.

[41]  P. De Bièvre,et al.  Atomic weights of the elements. Review 2000 (IUPAC Technical Report) , 2009 .

[42]  J A Eisen,et al.  Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments , 2003, Science.

[43]  B. Ruotolo,et al.  Surface-induced dissociation on a MALDI-ion mobility-orthogonal time-of-flight mass spectrometer: sequencing peptides from an "in-solution" protein digest. , 2001, Analytical chemistry.

[44]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[45]  F. McLafferty,et al.  Automated reduction and interpretation of , 2000, Journal of the American Society for Mass Spectrometry.

[46]  S J Ferguson,et al.  Still a puzzle: why is haem covalently attached in c-type cytochromes? , 1999, Structure.

[47]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[48]  R. S. Burkhalter,et al.  Characterization of heme c peptides by mass spectrometry. , 1993, Journal of inorganic biochemistry.

[49]  A. S. Wexler.  Determination of Phenolic Substances by Ultraviolet Difference Spectroscopy. , 1963 .