Identification of a Chloroform-soluble Membrane Miniprotein in Escherichia Coli and Its Homolog in Salmonella Typhimurium

Overview

Journal Anal Biochem

Publisher Elsevier

Specialty Biochemistry

Date 2010 Nov 6

PMID 21050835

Citations 5

Authors

Ziqiang Guan

Xiaoyuan Wang

Christian R H Raetz

Affiliations

Soon will be listed here.

Abstract

Two homologous 29 amino acid-long highly hydrophobic membrane miniproteins were identified in the Bligh-Dyer lipid extracts of Escherichia coli and Salmonella typhimurium using liquid chromatography/tandem mass spectrometry (LC/MS/MS). The amino acid sequences of the proteins were determined by collision-induced dissociation tandem mass spectrometry, in conjunction with a translating BLAST (tBLASTn) search, i.e., comparing the MS/MS-determined protein query sequence against the six-frame translations of the nucleotide sequences of the E. coli and S. typhimurium genomes. Further MS characterization revealed that both proteins retain the N-terminal initiating formyl-methionines. The methodologies described here may be amendable for detecting and characterizing small hydrophobic proteins in other organisms that are difficult to annotate or analyze by conventional methods.

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References

Girvin M, Rastogi V, Abildgaard F, Markley J, Fillingame R . Solution structure of the transmembrane H+-transporting subunit c of the F1F0 ATP synthase. Biochemistry. 1998; 37(25):8817-24. DOI: 10.1021/bi980511m. View

Murphy R, Fiedler J, Hevko J . Analysis of nonvolatile lipids by mass spectrometry. Chem Rev. 2001; 101(2):479-526. DOI: 10.1021/cr9900883. View

Hemm M, Paul B, Schneider T, Storz G, Rudd K . Small membrane proteins found by comparative genomics and ribosome binding site models. Mol Microbiol. 2009; 70(6):1487-501. PMC: 2614699. DOI: 10.1111/j.1365-2958.2008.06495.x. View

Greer J, Lees M . Myelin proteolipid protein--the first 50 years. Int J Biochem Cell Biol. 2002; 34(3):211-5. DOI: 10.1016/s1357-2725(01)00136-4. View

Roepstorff P, Fohlman J . Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom. 1984; 11(11):601. DOI: 10.1002/bms.1200111109. View

Adams J, Capecchi M . N-formylmethionyl-sRNA as the initiator of protein synthesis. Proc Natl Acad Sci U S A. 1966; 55(1):147-55. PMC: 285768. DOI: 10.1073/pnas.55.1.147. View

Guan Z, Breazeale S, Raetz C . Extraction and identification by mass spectrometry of undecaprenyl diphosphate-MurNAc-pentapeptide-GlcNAc from Escherichia coli. Anal Biochem. 2005; 345(2):336-9. DOI: 10.1016/j.ab.2005.07.002. View

Bokoch G, Reed P . Stimulation of arachidonic acid metabolism in the polymorphonuclear leukocyte by an N-formylated peptide. Comparison with ionophore A23187. J Biol Chem. 1980; 255(21):10223-6. View

Whitelegge J . HPLC and mass spectrometry of intrinsic membrane proteins. Methods Mol Biol. 2004; 251:323-40. DOI: 10.1385/1-59259-742-4:323. View

10.

LEES M, Chao B, Laursen R, LItalien J . A hydrophobic tryptic peptide from bovine white matter proteolipid. Biochim Biophys Acta. 1982; 702(1):117-24. DOI: 10.1016/0167-4838(82)90034-6. View

11.

Webster R, Engelhardt D, Zinder N . In vitro protein synthesis: chain initiation. Proc Natl Acad Sci U S A. 1966; 55(1):155-61. PMC: 285769. DOI: 10.1073/pnas.55.1.155. View

12.

Takeda M, Webster R . Protein chain initiation and deformylation in B. subtilis homogenates. Proc Natl Acad Sci U S A. 1968; 60(4):1487-94. PMC: 224945. DOI: 10.1073/pnas.60.4.1487. View

13.

Hemm M, Paul B, Miranda-Rios J, Zhang A, Soltanzad N, Storz G . Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies. J Bacteriol. 2009; 192(1):46-58. PMC: 2798279. DOI: 10.1128/JB.00872-09. View

14.

Gassel M, Mollenkamp T, Puppe W, Altendorf K . The KdpF subunit is part of the K(+)-translocating Kdp complex of Escherichia coli and is responsible for stabilization of the complex in vitro. J Biol Chem. 1999; 274(53):37901-7. DOI: 10.1074/jbc.274.53.37901. View

15.

MARCKER K, SANGER F . N-FORMYL-METHIONYL-S-RNA. J Mol Biol. 1964; 8:835-40. DOI: 10.1016/s0022-2836(64)80164-9. View

16.

BLIGH E, Dyer W . A rapid method of total lipid extraction and purification. Can J Biochem Physiol. 1959; 37(8):911-7. DOI: 10.1139/o59-099. View

17.

Ferguson J, Wenger C, Metcalf W, Kelleher N . Top-down proteomics reveals novel protein forms expressed in Methanosarcina acetivorans. J Am Soc Mass Spectrom. 2009; 20(9):1743-50. PMC: 2832193. DOI: 10.1016/j.jasms.2009.05.014. View

18.

Milligan D, Koshland Jr D . The amino terminus of the aspartate chemoreceptor is formylmethionine. J Biol Chem. 1990; 265(8):4455-60. View

19.

Adams J . On the release of the formyl group from nascent protein. J Mol Biol. 1968; 33(3):571-89. DOI: 10.1016/0022-2836(68)90307-0. View

20.

Carroll J, Altman M, Fearnley I, Walker J . Identification of membrane proteins by tandem mass spectrometry of protein ions. Proc Natl Acad Sci U S A. 2007; 104(36):14330-5. PMC: 1952138. DOI: 10.1073/pnas.0706817104. View