Proteomic analysis of Staphylococcus aureus biofilm cells grown under physiologically relevant fluid shear stress conditions

Islam, Nazrul; Kim, Yonghyun; Ross, Julia M; Marten, Mark R

doi:10.1186/1477-5956-12-21

Proteome Science

Table 1 Proteins shown in the reference map were identified with a linear ion trap nano-LC-ESI-MS/MS

From: Proteomic analysis of Staphylococcus aureus biofilm cells grown under physiologically relevant fluid shear stress conditions

Spot ID	Protein name	Functional category	XC-score	pI/Mr	Cov (%)	Accession number	Location
1	Fibronectin-binding protein	Virulence mechanism	150	4.4/114	18	gi:15925493	Membrane
2	Aconitate hydratase	Carbohydrate metabolism	396	4.7/98	51	gi:15924340	transmembrane
3	Elongation factor G	Transcription and replication	548	4.6/77	49	gi:15923537	transmembrane
4	Collagen Binding Protein (Cna)	Virulence mechanism	90	5.8/133	11	gi:21284341	Membrane
5	Trigger factor	Virulence mechanism	140	4.2/49	36	gi:15924665	Cytosolic
6	DnaK protein	Stress protein	348	4.5/66	67	gi:15924570	Membrane
7	DnaK protein	Stress protein	218	4.5/66	51	gi:15924570	Membrane
8	PEP-protein phosphatase	Carbohydrate metabolism	60	4.5/63	20	gi:15926670	Membrane
9	PEP-protein phosphatase	Carbohydrate metabolism	30	4.5/63	18	gi:15926670	Membrane
10	Pyruvate kinase	Carbohydrate metabolism	150	4.1/63	25	gi:15924687	transmembrane
11	Prolyl-tRNA synthetase	Cell division	228	4.9/64	54	gi:15924253	transmembrane
12	Prolyl-tRNA synthetase	Cell division	58	4.9/64	13	gi:15924253	transmembrane
13	30S ribosomal protein	Protein synthesis	130	4.4/43	37	gi:15924466	transmembrane
14	Glutamyl- amidotransferase	Aminio acid metabolism	84	4.9/53	25	gi:21283570	transmembrane
15	Glycyl-tRNA synthetase	Cell division	90	4.9/54	20	gi:15924555	Cytosolic
16,17	Elongation factor Tu	Virulence mechanism	214	4.6/43	60	gi:15923538	Membrane
18	Pyruvate dehydrogenase	Virulence mechanism	180	4.8/41	48	gi:15924083	Membrane
19	Phosphoglycerate kinase	Carbohydrate metabolism	120	5.1/42	42	gi:15923763	transmembrane
20	Coenzyme A ligase	Protein synthesis	140	5.0/43	42	gi:21282234	transmembrane
21	DNA-directed RNA polymerase	Transcription and replication	110	4.5/35	38	gi:15925214	Cytosolic
22	Glyceraldehyde-3-PDH	Carbohydrate metabolism	108	4.8/36	44	gi:15923762	Cytosolic
23	Coenzyme A synthase	Carbohydrate metabolism	30	4.80/43	20	gi:49484747	transmembrane
24	Pyrophosphatase	Carbohydrate metabolism	30	4.5/34	15	gi:15924909	Membrane
25	Phosphotransacetylase	Others	102	4.6/35	55	gi:15923578	Cytosolic
26	Elongation factor Ts	Transcription and replication	190	5.0/32	58	gi:15924247	Cytosolic
27	General stress protein Ctc	Stress protein	50	4.2/24	29	gi:15923491	Cytosolic
28	30S ribosomal protein	Protein synthesis	106	5.3/30	30	gi:15924035	transmembrane
29	Triosephosphate isomerase	Carbohydrate metabolism	58	4.7/27	32	gi:15923764	Cytosolic
31	Superoxide dimutase	Stress protein	80	5.0/23	35	gi:15924543	Cytosolic
32	Cysteine synthase	Carbohydrate metabolism	60	5.2/33	24	gi:15923503	transmembrane
33	Malate:quinone oxidoreductase	Carbohydrate metabolism	220	6.1/56	38	gi:15925597	Membrane
35	50S ribosomal protein	Protein synthesis	174	4.5/13	96	gi:15923530	transmembrane
38	50S ribosomal protein	Protein synthesis	210	9.8/20	77	gi:15925228	Cytosolic
39	50S ribosomal protein	Protein synthesis	78	9.9/20	52	gi:15925225	Cytosolic
40	50S ribosomal protein	Protein synthesis	50	10.8/16	43	gi:15925221	Cytosolic
41	50S ribosomal protein	Protein synthesis	70	9.5/15	42	gi:15923527	Cytosolic
42	50S ribosomal protein	Protein synthesis	40	10.3/11	50	gi:15924637	Cytosolic
36,37,43	50S ribosomal protein	Protein synthesis	10	9.5/24	87	gi:15923528	Cytosolic
44	Endopeptidase	Protein degradation	438	5.4/91	57	gi:15923515	Cytosolic
45	30S ribosomal protein	Protein synthesis	100	10.1/24	44	gi:15925234	Cytosolic
46	Inositol-monophosphate DH	others	178	5.5/53	45	gi:15923380	transmembrane
47	50S ribosomal protein	Protein synthesis	80	10.2/24	36	gi:15925240	Cytosolic
48	Catalase	Stress protein	164	5.2/58	40	gi:21282950	Cytosolic
49	Pyruvate dehydrogenase E1	Virulence mechanism	90	4.8/41	24	gi:15924083	Membrane
50	Threonine dehydrogenase	Aminio acid metabolism	166	6.4/37	35	gi:15924428	Membrane
51	Poly.phosphorlase/adenylase	Others	268	4.7/77	40	gi:15924264	transmembrane
52	Glutamyl-tRNA synthetase	Cell division	116	5.0/56	31	gi:15923518	transmembrane
53	50S ribosomal protein	Protein Synthesis	60	10.3/24	17	gi:15925240	Cytosolic
54	ABC transporter	Cell division	100	5.37/48	32	gi:15923833	transmembrane
55	Adenylosuccinate synthetase	Others	150	5.0/48	41	gi:15923007	Membrane
56	Alkyl hydroperoxide reductase	Stress protein	160	4.6/55	32	gi:15923370	transmembrane
57	Akaline shock protein 23	Stress protein	156	5.0/20	48	gi:15925172	Cytosolic
58	Hypothetical protein SAV1845	Others	90	4.1/13	72	gi:15924835	Cytosolic
59	Acetate kinase	Carbohydrate metabolism	176	5.6/44	61	gi:21283383	transmembrane
60	Alcohol dehydrogenase	Carbohydrate metabolism	140	5.2/36	48	gi:21282297	transmembrane
61	Succinyl-CoA synthetase	Carbohydrate metabolism	46	5.4/32	16	gi:15924236	Not clear
62	Fructose-1,6-bioP- aldolase	Carbohydrate metabolism	190	4.7/33	50	gi:15925596	Cytosolic
63	Acid decarboxylase	Carbohydrate metabolism	240	4.7/33	78	gi:15925596	Cytosolic
64	Fructose-bi-P-aldolase	Carbohydrate metabolism	70	4.9/31	20	gi:15925115	Not clear
65	Phenylalanyl-tRNA synthetase	Aminio acid metabolism	60	4.9/22	37	gi:15924732	Cytosolic
66	Glycerate dehydrogenase	Carbohydrate metabolism	60	5.0/35	30	gi:15925295	Membrane
67	Malate-dehydrogenase	Carbohydrate metabolism	50	4.9/44	17	gi:15924692	Membrane
68	Ornithine-acid transaminase	Aminio acid metabolism	90	5.0/43	40	gi:15923947	Membrane
30,34,69	Alkyl hydroperoxide reductase	Stress protein	30	4.7/21	26	gi:15923371	Cytosolic

Gels similar to those shown in Figure 1 were subjected to image analysis to identify differentially expressed proteins. These spots were then cut from the gels, and proteins were identified via tandem mass spectrometry (MS). Protein identification was performed against NCBInr (nr.gz) databases for Staphylococcus genus. Cross correlation (XC) score is a metric associated with the quality of identification, with a score >20 indicating a positive identification; pI/Mr is isoelectric point and molecular weight (theoretical); Cov (%) is the fraction of protein sequence coverage identified via MS; Access. No. is accession number for the protein.

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ISSN: 1477-5956

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