Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation

Pieper, Rembert; Huang, Shih-Ting; Parmar, Prashanth P; Clark, David J; Alami, Hamid; Fleischmann, Robert D; Perry, Robert D; Peterson, Scott N

doi:10.1186/1471-2180-10-30

Table 1 Abundance differences of Y. pestis proteins profiled in periplasmic fractions of iron-rich vs. iron-starved cells

From: Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation

Spot No a)	Gene locus b)	gene name c)	Protein description c)	Subc. Loc. d)	Fur/RyhB e)	Mascot Score f)	exp Mr (Da)	exp pI	26°C, Vs (-Fe) g)	26°C, Vs (+Fe) h)	26-ratio -Fe/+Fe i)	26°C P-value j)	37-ratio -Fe/+Fe k)
53	y0028	malE	periplasmic maltose-binding protein	PP		2150	43937	5.53	0.72	5.98	0.121	0.000	0.760
54	y0137	degQ	serine endoprotease	PP		1077	55588	6.43	0.39	0.11	2.41	0.0177	0.900
55	y0291	-	putative tospovirus resistance protein D	U		486	18721	5.44	2.05	0.47	4.320	0.000	N.D.
56	y0541	hmuT	hemin-binding periplasmic protein	PP	Fur	228	27164	5.85	0.46	0.11	4.328	0.000	> 20
57	y0542	hmuS	hemin uptake system component	U	Fur	989	38188	5.56	0.53	0.19	2.780	0.000	2.091
58	y0869	cybC	cytochrome b(562)	PP	Fur	626	5035	5.64	0.13	0.03	4.746	N.D.	3.160
59	y0964	frsA	fermentation/respiration switch protein	U		586	51326	5.98	0.15	0.07	2.208	0.000	1.875
60	y1128	bglX	putative beta-glucosidase	PP		2324	81506	5.43	3.01	0.52	5.822	0.000	1.740
61	y1189	gltI	solute-binding periplasmic protein of glutamate/aspartate ABC transporter	PP		2512	35927	7.20	0.41	2.91	0.141	0.005	N.D.
62	y1223	nrdE	ribonucleoside-diphosphate reductase 2, alpha subunit	U	Fur	198	79914	6.32	0.03	-	> 20	N.D.	N.D.
63	y1222	nrdF	ribonucleoside-diphosphate reductase 2, beta chain	U	Fur	561	39335	5.11	0.77	-	> 20	N.D.	> 20
64	y1430	-	putative putative periplasmic iron-binding signal peptide protein	U		3359	41211	6.09	-	0.57	< 0.05	N.D.	< 0.05
65	y1526	yfuA	putative solute-binding protein for iron ABC transporter	PP	Fur	1979	39620	6.65	2.36	1.46	1.618	0.061	N.D.
66	y1607	hisJ	histidine-binding periplasmic protein of high-affinity histidine transport system	PP		1494	31529	5.01	0.29	0.93	0.309	0.000	0.350
67	y1744	-	hypothetical protein y1744	CY		324	5183	5.92	0.38	-	> 20	N.D.	4.510
68	y1897	yfeA	periplasmic-binding protein for iron and manganese ABC transporter	CM	Fur	1201	31395	5.80	2.87	0.63	4.576	0.000	4.780
69	y1936	sufC	iron-sulfur cluster assembly protein SufC, ATPase component	ML	Fur	726	28460	5.10	0.16	0.02	7.514	0.000	> 20
70	y1937	sufD	cysteine desulfurase activator complex subunit SufD	U	Fur	369	60476	6.76	0.06	-	> 20	N.D.	N.D.
71	y2358	hmsF	hemin storage system, HmsF protein	U		542	61790	5.47	0.40	0.12	3.467	0.000	1.480
72	y2368	-	putative ferrous iron transport protein	U		532	13556	5.29	1.71	1.64	1.030	0.390	2.330
73	y2394	ybtS	anthranilate synthase	CY	Fur	1323	50265	5.82	1.65	0.36	4.538	0.000	> 20
74	y2401	ybtU	thiazolinyl-S-HMWP1 reductase of Ybt system	U	Fur	351	48765	6.63	0.33	0.11	3.057	0.006	N.D.
76	y2403	ybtE	salicyl-AMP ligase	CY	Fur	1205	58276	5.43	2.04	0.31	6.660	0.000	7.060
77	y2451	efeO	putative ferrous iron transport protein	U		998	38614	4.96	1.71	0.90	1.896	0.000	1.274
78	y2638	ysuG	siderophore biosynthetic protein of the Ysu system	U	Fur	182	77918	5.36	0.06	-	> 20	N.D.	N.D.
79	y2662	mglB	periplasmic D-galactose-binding ABC transport protein	PP		1440	33113	5.40	0.51	1.53	0.330	0.000	0.251
80	y2828	pheA	putative chorismate mutase	PP		630	14433	5.88	0.86	0.05	19.293	0.000	2.817
81	y2842	-	putative periplasmic binding protein of iron/siderophore ABC transporter	U		1096	51189	5.97	0.62	1.87	0.332	0.000	0.501
82	y2875	yiuA	solute-binding periplasmic protein of iron/siderophore ABC transporter	U	Fur	1690	46030	6.69	0.73	0.37	1.957	0.002	N.D.
83	y3037	modA	molybdate-binding periplasmic protein of molybdate ABC transporter	PP		2136	27031	5.55	0.17	0.72	0.234	0.000	2.089
84	y0815	sodC	periplasmic superoxide dismutase (Cu-Zn)	PP		695	16562	7.54	0.55	0.63	0.89	0.4490	N.D.
85	y3165	ptr	protease III	PP		1794	96878	5.60	2.71	1.86	1.454	0.001	1.032
86	y3676	-	putative type VI secretion system protein	CY		375	50035	4.81	0.29	-	> 20	N.D.	N.D.
87	y3772	lsrB	putative periplasmic autoinducer II-binding protein	U		917	36377	6.30	0.31	1.96	0.159	0.000	N.D.
88	y3812	dsbA	protein disulfide isomerase I	PP		1587	22454	5.91	2.57	1.18	2.176	0.000	0.910
89	y3825	dppA	periplasmic dipeptide transport protein of ABC transporter	PP		1253	54903	5.52	0.68	2.46	0.277	0.000	0.696
90	y3837	yhjJ	predicted zinc-dependent peptidase	U		1215	62177	5.10	0.44	0.17	2.613	0.000	0.720
91	y3956	crp	cAMP-regulatory protein	CY		220	26494	7.82	0.06	-	> 20	N.D.	N.D.
92	y3977	fkpA	FKBP-type peptidyl-prolyl cis-trans isomerase	PP		2031	33670	6.94	5.50	3.45	1.594	0.007	N.D.
93	y4125	-	putative solute-binding periplasmic protein precursor for ABC transporter	PP		2766	30250	6.27	6.09	3.67	1.661	0.001	2.264

a) spot number as denoted in Figures 1 and 2; b) protein accession number and locus tag as listed in Y. pestis KIM genome database (NCBI); c) gene name and protein description from the KIM database or a conserved E. coli K12 ortholog http://www.ecocyc.org, if >65 pct. sequence identity; d) subcellular localization based on PSORTb data: CY, cytoplasm; ML: multiple localizations; CM: inner membrane; PP, periplasm; U: unknown; e) proven or putative regulation by Fur or a Fur-dependent small RNA (e.g. RyhB); f) highest Mascot score for a protein from LC-MS/MS or MALDI data; g) Vs (-Fe): average spot volume (n ≥ 3) in 2D gels for iron-depleted growth conditions at 26°C as shown in Figures 1-2; h) Vs (+Fe): average spot volume (n ≥ 3) in 2D gels for iron-supplemented growth conditions at 26°C; i) spot volume ratio (-Fe/+Fe) at 26°C, N.D.: not determined; -: no spot detected; j) two-tailed t-test p-value for spot abundance change at 26°C; 0.000 stands for < 0.001; k) average spot volume ratio (-Fe/+Fe) at 37°C; additional data for the statistical spot analysis at 37°C are part of Additional Table 1. exp.pI/Mr = experimental pI and Mr values.

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ISSN: 1471-2180

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