Proteomic Signature Library for
Staphylococcus aureus COL

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please cite

If Aureolib enriched your work we would like to ask to cite us:

Aureolib - a proteome signature library: towards an understanding of Staphylococcus aureus pathophysiology.
Fuchs S, Zühlke D, Pané-Farré J, Kusch H, Wolf C, Reiß S, Binh le TN, Albrecht D, Riedel K, Hecker M, Engelmann S.
PLoS One. 2013 Aug 13;8(8):e70669. doi: 10.1371/journal.pone.0070669. eCollection 2013.

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experiments

Data of following signatures are available in the library (see references for experimental details):
 
:: experiment description imported reference
1 hydrogen peroxide stress of exponentially grown cells (CDM; OD 0.5; 37°C) by H2O2 [10 mM] 2012-05-18 Wolf et al., 2008
2 diamide stress of exponentially grown cells (CDM; OD 0.5; 37°C) by diamide [1 mM] 2012-05-18 Wolf et al., 2008
3 paraquat stress of exponentially grown cells (CDM; OD 0.5; 37°C) by paraquat [0.01 µM] 2012-05-18 Wolf et al., 2008
4 nitric oxide stress of exponentially grown cells (CDM; OD 0.5; 37°C) by NO [500 µM] 2012-05-18 Hochgräfe et al., 2008
5 fermentation shift of exponentially grown cells (CDM; OD 0.5; 37°C) to oxygen limitation 2012-05-18 Fuchs et al., 2007
6 nitrate respiration shift of exponentially grown cells (CDM + NO3 [8mM]; OD 0.5; 37°C) to oxygen limitation 2012-05-18 Fuchs et al., 2007
7 heat shift of exponentially grown cells (CDM; OD 0.5; 37°C) to 48°C 2015-07-15 Fuchs et al., 2013
8 puromycin stress of exponentially grown cells (CDM; OD 0.5; 37°C) by puromycin [3 µM] 2015-07-15 Fuchs et al., 2013
9 mupirocin stress of exponentially grown cells (CDM; OD 0.5; 37°C) by mupirocin [0.03 µg/ml] 2012-05-18 Reiß et al., 2012
 

sampling

Timepoints and number of independent biological replicates used for the 35S-methionine labeling:
 
:: experiment controls samples
0'60' 1'5'10'20'30'40'60'120'
1 hydrogen peroxide 2--22-222-
2 diamide 2--22-222-
3 paraquat 2--22-2-22
4 nitric oxide 2-222-2-2-
5 fermentation 22--222-2-
6 nitrate respiration 22--222-2-
7 heat 3--33-2-3-
8 puromycin 33-33-3-3-
9 mupirocin 22--2-2-2-
 

transfer of identification labels

A reference map (mastergel) containing the identification data as so-called labels were created. These labels were manually transferred to each experiment. Only labels transferred without any doubt and within experiment-specifically detected spot borders are considered.
 
:: experiment considered labels considered protein spots
1 hydrogen peroxide 542 490
2 diamide 579 539
3 paraquat 566 511
4 nitric oxide 547 503
5 fermentation 598 542
6 nitrate respiration 548 503
7 heat 516 496
8 puromycin 576 543
9 mupirocin 593 565
 

statistical analyses

For statistical analysis ANOVA (1st level, end controls excluded) and t-test (2nd level, single timepoints vs control at t0) were perfomed applying the following parameters (see references for details of analysis):
 
:: experiment ANOVA t-TEST reference
1 hydrogen peroxide α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
2 diamide α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
3 paraquat α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
4 nitric oxide α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
5 fermentation α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
6 nitrate respiration α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
7 heat α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
8 puromycin α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
9 mupirocin α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
 

regulons & regulatory elements

Considered regulons and regulatoric elements:
 
:: regulator/
regulatory element
assigned proteins for which expression data is available assigned proteins for which expression data is NOT available
1 AgrA 0 5
2 ArcR 0 5
3 ArgR 2 14
4 ArsR 0 3
5 BglR 0 3
6 BirA 0 12
7 BlaI 0 0
8 CcpA 18 102
9 CodY 49 97
10 CtsR 8 4
11 CymR 4 15
12 CzrA 0 2
13 FapR 6 2
14 FMN 2 3
15 FruR 0 2
16 Fur 3 46
17 GapR 6 0
18 GlmS 1 0
19 GlnR 1 2
20 GltC 1 2
21 GlvR 0 1
22 Glycine 1 2
23 GntR 0 3
24 HisR 0 13
25 HrcA 5 1
26 HssR 0 2
27 HutR 0 4
28 IcaR 0 4
29 L10_leader 2 0
30 L13_leader 0 2
31 L19_leader 0 1
32 L20_leader 0 3
33 LacR 0 7
34 LexA 6 10
35 Lysine 7 2
36 MalR 0 9
37 ManR 0 2
38 MecI 0 2
39 MepR 0 2
40 MntR 0 4
41 MtlR 2 2
42 MurR 0 4
43 NrdR 2 3
44 NreC 0 12
45 PdxR 1 1
46 PerR 15 2
47 PreQ1 0 4
48 Purine 3 1
49 PurR 12 2
50 PyrR 6 2
51 RbsR 0 3
52 SaeR 1 25
53 SAM 2 4
54 ScrR 2 1
55 T-box(Ala) 1 0
56 T-box(Asn) 1 1
57 T-box(Cys) 1 1
58 T-box(Gly) 1 0
59 T-box(Ile) 1 0
60 T-box(Leu) 1 0
61 T-box(Met) 5 0
62 T-box(Phe) 2 0
63 T-box(Ser) 1 0
64 T-box(Thr) 1 0
65 T-box(Trp) 0 7
66 T-box(Tyr) 1 0
67 T-box(Val) 1 0
68 TPP 0 7
69 TreR 0 3
70 YtrA 0 5
71 yybP-ykoY 0 1
72 Zur 1 11
73 SigB- 4 62
74 SigB+ 40 186
75 Rex 8 18
 

the online system

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Data content includes:
9 signatures
94 autoradiograms
698 expression profiles
 
The changelog can be found here.
 

funds

Universität Greifswald TRR 34
 

imprint & contact

idea, concept, design, programming:
Stephan Fuchs

domain holder:
Stephan Fuchs

contact:
Stephan Fuchs

Institut der Mikrobiologie
Friedrich-Ludwig-Jahn-Str. 15a
17487 Greifswald

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