Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin

Komeil, Doaa; Padilla-Reynaud, Rebeca; Lerat, Sylvain; Simao-Beaunoir, Anne-Marie; Beaulieu, Carole

doi:10.1186/1477-5956-12-35

Proteome Science

Table 1 Proteins produced by Streptomyces scabiei with a 5-fold greater abundance in casein-suberin medium

From: Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin

Protein assignation^a	Gene assignation	Putative function	Abundance (spectrum count/MW^b) in casein-suberin medium			Abundance (spectrum count/MW^b) in casein medium
			Day 1	Day 3	Day 5	Day 1	Day 3	Day 5
Translational, ribosomal structure and biogenesis
C9Z240	SCAB_25251^d	Polyribonucleotide nucleotidyltransferase	0.04 ± 0.03	0.25 ± 0.10	0.22 ± 0.06	0.01 ± 0.01	nd^c	0.01 ± 0.01
C9Z3N7	SCAB_25991^d	Ribosome recycling factor	0.43 ± 0.13	nd	nd	0.08 ± 0.07	0.03 ± 0.05	0.10 ± 0.10
C9Z3P0	SCAB_26021^d	30S ribosomal protein S2	0.23 ± 0.12	0.05 ± 0.02	nd	0.03 ± 0.05	nd	nd
C9Z3Q3	SCAB_26151^d	50S ribosomal protein L19	0.67 ± 0.32	1.13 ± 0.56	0.68 ± 0.25	0.10 ± 0.18	nd	nd
C9YW46	SCAB_36621^d	30S ribosomal protein S9	0.42 ± 0.24	0.35 ± 0.20	0.11 ± 0.06	0.12 ± 0.13	nd	nd
C9YW47	SCAB_36631^d	50S ribosomal protein L13	0.25 ± 0.13	0.24 ± 0.10	0.10 ± 0.03	0.02 ± 0.04	nd	nd
C9YW61	SCAB_36771^d	30S ribosomal protein S5	0.33 ± 0.06	0.38 ± 0.05	0.01 ± 0.02	0.13 ± 0.23	nd	nd
C9YW63	SCAB_36791^d	50S ribosomal protein L6	0.18 ± 0.12	0.33 ± 0.16	0.02 ± 0.03	0.02 ± 0.03	nd	nd
C9YW64	SCAB_36801^d	30S ribosomal protein S8	0.17 ± 0.15	0.64 ± 0.45	0.12 ± 0.21	0.02 ± 0.04	nd	nd
C9YW68	SCAB_36841^d	50S ribosomal protein L14	0.21 ± 0.04	0.63 ± 0.47	0.54 ± 0.45	0.05 ± 0.09	nd	nd
C9YW72	SCAB_36881^d	30S ribosomal protein S3	0.17 ± 0.09	0.09 ± 0.08	0.01 ± 0.03	0.02 ± 0.04	nd	nd
C9YW73	SCAB_36891^d	50S ribosomal protein L22	0.44 ± 0.16	0.85 ± 0.60	0.67 ± 0.40	0.08 ± 0.13	nd	nd
C9YW77	SCAB_36931^d	50S ribosomal protein L4	0.62 ± 0.13	1.00 ± 0.20	0.66 ± 0.06	0.10 ± 0.14	nd	nd
C9YW78	SCAB_36941^d	50S ribosomal protein L3	0.55 ± 0.10	0.96 ± 0.26	0.56 ± 0.15	0.04 ± 0.08	nd	nd
C9YW94	SCAB_37111^d	30S ribosomal protein S7	0.51 ± 0.18	0.23 ± 0.24	nd	0.04 ± 0.07	nd	nd
C9ZAN5	SCAB_4612 ^d	30S ribosomal protein S18	0.30 ± 0.06	0.17 ± 0.18	0.06 ± 0.09	0.04 ± 0.06	nd	nd
C9Z656	SCAB_75031^d	30S ribosomal protein S4	0.51 ± 0.32	0.45 ± 0.14	0.04 ± 0.04	0.01 ± 0.02	nd	nd
Transcription
C9ZAB5	SCAB_30041^d	Cyclic nucleotide-binding protein	0.03 ± 0.01	0.18 ± 0.11	0.17 ± 0.01	0.03 ± 0.06	nd	nd
Cell wall/membrane/envelope biogenesis
C9YUC5	SCAB_4961	Glucuronoxylanase XynC	0.15 ± 0.09	0.30 ± 0.21	0.26 ± 0.10	nd	nd	0.04 ± 0.03
C9Z8V2	SCAB_45141	D-alanyl-D-alanine carboxypeptidase	0.04 ± 0.02	0.42 ± 0.07	0.40 ± 0.12	0.04 ± 0.05	nd	nd
Defense mechanisms and virulence
C9Z785	SCAB_44161^d	β-lactamase	0.43 ± 0.07	0.51 ± 0.17	0.45 ± 0.12	0.02 ± 0.04	nd	nd
C9Z160	SCAB_56441	Protease	0.39 ± 0.23	0.00 ± 0.01	nd	nd	0.21 ± 0.02	0.11 ± 0.05
Differentiation
C9Z7Z7	SCAB_89661	Factor C morphological differentiation homolog	nd	0.14 ± 0.05	0.11 ± 0.06	nd	nd	0.01 ± 0.02
Energy production and conversion
C9Z8E8	SCAB_28761^d	ATP synthase subunit β	0.28 ± 0.06	0.48 ± 0.26	0.44 ± 0.15	0.07 ± 0.11	0.06 ± 0.07	0.13 ± 0.04
C9Z8F0	SCAB_28781^d	ATP synthase subunit α	0.17 ± 0.02	0.45 ± 0.11	0.40 ± 0.20	0.05 ± 0.06	0.06 ± 0.05	0.06 ± 0.03
C9ZGW6	SCAB_34651^d	Oxidoreductase	0.05 ± 0.08	0.33 ± 0.08	0.35 ± 0.07	0.02 ± 0.04	0.04 ± 0.05	0.05 ± 0.08
C9ZE86	SCAB_79151	Cytokinin dehydrogenase	0.14 ± 0.01	0.36 ± 0.08	0.35 ± 0.07	nd	0.08 ± 0.10	0.21 ± 0.03
Lipid metabolism
C9Z707	SCAB_28481^d	Acetyl-CoA C-acetyltransferase FadA	0.04 ± 0.03	0.02 ± 0.03	nd	0.01 ± 0.01	nd	nd
C9Z5Z2	SCAB_74351	Glycerophosphoryl diester phosphodiesterase	0.09 ± 0.02	0.23 ± 0.07	0.23 ± 0.04	nd	0.05 ± 0.05	0.03 ± 0.05
C9ZCR0	SCAB_78851	Sphingolipid ceramide N-deacylase	0.24 ± 0.07	0.12 ± 0.05	0.03 ± 0.03	nd	0.15 ± 0.18	0.04 ± 0.03
Carbohydrate metabolism
C9ZBE6	SCAB_0631	α-L-fucosidase	0.03 ± 0.00	0.08 ± 0.02	0.06 ± 0.03	nd	nd	0.01 ± 0.02
C9YSR8	SCAB_3851	Fucosidase	0.18 ± 0.02	0.41 ± 0.16	0.35 ± 0.11	nd	nd	0.00 ± 0.01
C9YSS0	SCAB_3881	Arabinofuranosidase	0.13 ± 0.01	0.39 ± 0.13	0.32 ± 0.15	nd	0.18 ± 0.16	0.04 ± 0.00
C9YSS1	SCAB_3891	α-galactosidase	0.10 ± 0.06	0.22 ± 0.21	0.13 ± 0.11	nd	0.01 ± 0.01	nd
C9YVN3	SCAB_5851	Putative secreted protein	0.01 ± 0.01	0.04 ± 0.03	0.04 ± 0.04	nd	0.02 ± 0.01	nd
C9YVP9	SCAB_6021	Endo β-1.4-xylanase	0.29 ± 0.13	0.67 ± 0.20	0.65 ± 0.19	nd	0.04 ± 0.04	nd
C9Z0D5	SCAB_8871	Endoglucanase	0.03 ± 0.00	0.05 ± 0.02	0.08 ± 0.05	nd	0.02 ± 0.01	0.02 ± 0.01
C9Z1T6	SCAB_9291	Lactonase	nd	0.14 ± 0.05	0.20 ± 0.07	nd	0.02 ± 0.03	nd
C9Z507	SCAB_11431	Glycosyl hydrolase	0.39 ± 0.10	0.88 ± 0.30	0.64 ± 0.17	nd	0.42 ± 0.13	0.33 ± 0.14
C9Z878	SCAB_13491	Glycosyl hydrolase	nd	0.03 ± 0.02	0.04 ± 0.02	nd	nd	0.01 ± 0.01
C9ZD50	SCAB_16431	Cellulase	0.43 ± 0.29	1.52 ± 0.86	1.04 ± 0.61	nd	0.93 ± 0.72	0.39 ± 0.04
C9ZD59	SCAB_16521	Arabinofuranosidase	0.38 ± 0.12	1.07 ± 0.39	0.96 ± 0.36	nd	0.33 ± 0.24	0.33 ± 0.17
C9ZEP9	SCAB_17001	Cellulase	0.05 ± 0.04	1.05 ± 0.47	1.05 ± 0.38	nd	0.29 ± 0.14	0.19 ± 0.14
C9ZEQ0	SCAB_17011	Cellulase	0.15 ± 0.04	0.85 ± 0.26	0.73 ± 0.21	nd	0.02 ± 0.02	0.02 ± 0.02
C9YT14	SCAB_19051	Solute-binding lipoprotein	nd	0.12 ± 0.05	0.21 ± 0.11	nd	0.09 ± 0.08	0.02 ± 0.02
C9YT63	SCAB_19561	β-xylosidase	0.09 ± 0.10	0.23 ± 0.17	0.24 ± 0.17	nd	0.36 ± 0.18	0.20 ± 0.05
C9YUL1	SCAB_19941	Glycosyl hydrolase	0.47 ± 0.08	0.46 ± 0.29	0.33 ± 0.18	0.04 ± 0.03	0.38 ± 0.12	0.26 ± 0.12
C9YYV2	SCAB_22931	Arabinofuranosidase	0.24 ± 0.07	0.40 ± 0.20	0.35 ± 0.14	nd	0.22 ± 0.16	0.12 ± 0.03
C9Z271	SCAB_25571	Glycosyl hydrolase	nd	0.22 ± 0.17	0.17 ± 0.07	nd	0.10 ± 0.09	nd
C9YUZ2	SCAB_36371	Xylanase/cellulase	0.24 ± 0.10	0.51 ± 0.16	0.47 ± 0.13	0.02 ± 0.02	0.23 ± 0.18	0.14 ± 0.09
C9Z5L1	SCAB_42951	Glucose / Sorbosone dehydrogenase	0.87 ± 0.12	4.30 ± 2.73	4.18 ± 1.77	0.14 ± 0.14	0.91 ± 0.35	0.60 ± 0.22
C9Z737	SCAB_43661	Galactan endo-1.6-β-galactosidase	0.20 ± 0.08	0.32 ± 0.11	0.18 ± 0.08	0.01 ± 0.02	nd	nd
C9Z7A0	SCAB_44311	α-galactosidase	0.13 ± 0.07	0.15 ± 0.03	0.12 ± 0.07	nd	0.07 ± 0.05	0.06 ± 0.05
C9Z7A1	SCAB_44321	Glycosyl hydrolase	0.17 ± 0.05	0.05 ± 0.05	0.07 ± 0.04	nd	nd	0.01 ± 0.01
C9YTK2	SCAB_51081	Cellulase	0.01 ± 0.01	0.57 ± 0.25	0.46 ± 0.13	nd	0.05 ± 0.07	nd
C9Z2N2	SCAB_57161	Endo-β-1.6-galactanase	0.07 ± 0.03	0.36 ± 0.11	0.35 ± 0.04	nd	nd	0.02 ± 0.02
C9Z451	SCAB_57751	Cellobiose-binding transport system	nd	0.11 ± 0.07	0.18 ± 0.06	nd	0.02 ± 0.02	nd
C9ZDW4	SCAB_63891	ABC-type xylose transport system	0.13 ± 0.10	0.63 ± 0.14	0.34 ± 0.18	0.03 ± 0.04	1.00 ± 0.30	0.75 ± 0.15
C9ZFW2	SCAB_66021	β-xylosidase	0.09 ± 0.02	0.23 ± 0.19	0.23 ± 0.18	nd	0.01 ± 0.02	0.01 ± 0.02
C9ZFW3	SCAB_66031	Arabinofuranosidase	0.46 ± 0.06	0.73 ± 0.26	0.67 ± 0.14	0.03 ± 0.03	0.32 ± 0.15	0.26 ± 0.12
C9YY63	SCAB_69711^d	Phosphoglycerate kinase	0.07 ± 0.05	0.02 ± 0.02	0.00 ± 0.01	0.02 ± 0.02	nd	nd
C9Z2V1	SCAB_72711	Endo β-1.4-xylanase	0.29 ± 0.12	0.20 ± 0.11	0.25 ± 0.05	nd	nd	0.05 ± 0.05
C9Z4J7	SCAB_74141	α-N-furanosidase	0.34 ± 0.14	0.19 ± 0.11	0.20 ± 0.11	nd	0.01 ± 0.01	0.03 ± 0.02
C9ZB22	SCAB_77441	α-arabinanase	0.06 ± 0.01	0.05 ± 0.01	0.06 ± 0.02	0.01 ± 0.02	0.08 ± 0.02	0.11 ± 0.02
C9ZCR4	SCAB_78891	Glycosyl hydrolase	0.08 ± 0.06	0.28 ± 0.16	0.16 ± 0.06	nd	0.00 ± 0.01	0.11 ± 0.06
C9ZE94	SCAB_79241	Arabinofuranosidase	0.60 ± 0.16	1.90 ± 0.61	1.51 ± 0.68	nd	0.25 ± 0.11	0.07 ± 0.06
C9ZE95	SCAB_79251	Xylanase A	0.79 ± 0.30	3.26 ± 1.60	3.17 ± 1.14	0.04 ± 0.01	0.13 ± 0.06	0.12 ± 0.06
C9Z041	SCAB_84801	Arabinase	0.17 ± 0.06	0.46 ± 0.20	0.45 ± 0.15	0.03 ± 0.06	0.61 ± 0.11	0.47 ± 0.11
C9Z1I5	SCAB_85231	Chitinase	0.17 ± 0.02	0.80 ± 0.13	0.46 ± 0.16	nd	0.42 ± 0.19	0.26 ± 0.16
C9Z351	SCAB_86311	Endoglucanase	nd	0.29 ± 0.16	0.27 ± 0.21	nd	0.01 ± 0.02	0.02 ± 0.03
C9Z674	SCAB_88071	Arabinofuranosidase	0.05 ± 0.04	0.14 ± 0.04	0.14 ± 0.06	nd	0.05 ± 0.05	0.02 ± 0.03
C9Z804	SCAB_89741	Cellulose-binding protein	0.33 ± 0.09	0.96 ± 0.23	0.55 ± 0.12	nd	0.33 ± 0.14	0.24 ± 0.03
C9Z9L5	SCAB_90081	Cellulase B	0.21 0.08	0.21 0.08	0.11 ± 0.03	nd	0.03 0.04	0.03 0.03
C9Z9L6	SCAB_90091	Cellulase	0.30 ± 0.09	0.85 ± 0.30	0.67 ± 0.22	nd	0.07 ± 0.06	0.06 ± 0.04
C9Z9L7	SCAB_90101	Cellulase	0.59 ± 0.21	1.03 ± 0.39	0.75 ± 0.40	nd	0.56 ± 0.47	0.19 ± 0.07
Amino acid metabolism
C9Z1W0	SCAB_9531^d	Catalase-peroxidase	0.10 ± 0.01	0.06 ± 0.06	0.04 ± 0.05	0.06 ± 0.05	nd	nd
C9Z862	SCAB_13321	X-prolyl-dipeptidyl aminopeptidase	0.21 ± 0.16	0.28 ± 0.02	0.18 ± 0.09	0.02 ± 0.03	nd	nd
C9ZGG7	SCAB_18081	γ-glutamyltranspeptidase	0.39 ± 0.06	0.32 ± 0.08	0.32 ± 0.08	0.01 ± 0.01	nd	0.02 ± 0.02
C9ZGM2	SCAB_18661	Serine protease	0.19 ± 0.17	nd	nd	0.01 ± 0.02	0.17 ± 0.16	nd
C9Z6V3	SCAB_27921	Neutral zinc metalloprotease	0.23 ± 0.12	0.04 ± 0.02	0.04 ± 0.01	0.01 ± 0.02	0.03 ± 0.03	nd
C9ZAN4	SCAB_46111	Single-stranded DNA-binding protein	0.16 ± 0.05	0.26 ± 0.12	0.29 ± 0.09	0.04 ± 0.06	0.05 ± 0.05	0.11 ± 0.05
C9YTK4	SCAB_51101^d	Phosphoserine aminotransferase	0.14 ± 0.09	0.41 ± 0.23	0.50 ± 0.16	0.06 ± 0.05	0.09 ± 0.05	0.07 ± 0.06
C9Z498	SCAB_58251	Tripeptidyl aminopeptidase	0.26 ± 0.03	0.10 ± 0.06	0.08 ± 0.05	0.10 ± 0.11	0.06 ± 0.05	0.01 ± 0.01
C9ZHG5	SCAB_66881^d	Glutamine synthetase	0.05 ± 0.04	0.30 ± 0.09	0.09 ± 0.05	0.01 ± 0.02	nd	0.03 ± 0.01
C9YY61	SCAB_69691	Zinc-binding carboxypeptidase	0.16 ± 0.04	0.05 ± 0.01	0.04 ± 0.02	0.02 ± 0.01	0.07 ± 0.02	0.05 ± 0.02
C9YZP9	SCAB_70761	Solute-binding protein	0.11 ± 0.05	0.46 ± 0.22	0.35 ± 0.17	nd	0.43 ± 0.19	0.29 ± 0.08
C9Z1E7	SCAB_72231	Serine protease	0.28 ± 0.15	0.58 ± 0.20	0.50 ± 0.13	0.01 ± 0.02	0.25 ± 0.07	0.24 ± 0.12
C9Z1N0	SCAB_85681^d	Tyrosinase	0.31 ± 0.05	0.02 ± 0.03	0.01 ± 0.01	0.01 ± 0.02	0.01 ± 0.02	nd
Nucleotide metabolism
C9ZGX4	SCAB_49491	5'-nucleotidase	0.17 ± 0.07	0.12 ± 0.05	0.06 ± 0.04	0.01 ± 0.01	nd	nd
Inorganic ion metabolism
C9ZH91	SCAB_66141	Alkaline phosphatase	0.21 ± 0.07	0.25 ± 0.03	0.18 ± 0.08	nd	nd	0.03 ± 0.03
General function prediction only
C9Z871	SCAB_13411	Oxidoreductase	1.04 ± 0.30	0.87 ± 0.20	0.70 ± 0.28	0.22 ± 0.16	0.16 ± 0.21	0.02 ± 0.03
C9ZAW6	SCAB_62471	Aminopeptidase	0.30 ± 0.07	0.54 ± 0.28	0.43 ± 0.17	0.01 ± 0.01	0.19 ± 0.14	0.02 ± 0.02
C9ZE96	SCAB_79261	Feruloyl esterase	0.30 ± 0.16	0.48 ± 0.29	0.41 ± 0.20	nd	0.03 ± 0.04	0.03 ± 0.02
Unknown function
C9YVL7	SCAB_5681		0.44 ± 0.20	0.61 ± 0.19	0.54 ± 0.31	nd	0.11 ± 0.14	nd
C9YUN3	SCAB_20171		0.11 ± 0.11	0.08 ± 0.06	0.09 ± 0.03	nd	0.09 ± 0.05	0.03 ± 0.05
C9ZGQ1	SCAB_33981		1.19 ± 0.44	3.88 ± 1.18	2.99 ± 0.95	0.18 ± 0.09	1.95 ± 0.48	1.33 ± 0.32
C9YUT0	SCAB_35731		0.14 ± 0.05	nd	nd	nd	nd	0.06 ± 0.05
C9Z411	SCAB_41931		0.07 ± 0.12	nd	nd	nd	0.07 ± 0.12	nd
C9ZHG0	SCAB_66831		0.09 ± 0.04	0.12 ± 0.07	0.09 ± 0.11	0.09 ± 0.00	0.01 ± 0.03	nd
C9Z4J0	SCAB_74081		0.30 ± 0.06	0.44 ± 0.32	0.32 ± 0.17	nd	0.02 ± 0.04	0.01 ± 0.01
C9Z7P8	SCAB_75721		0.29 ± 0.04	0.34 ± 0.08	0.24 ± 0.09	nd	0.01 ± 0.02	0.10 ± 0.07

^aUniprot accession number; ^bData are the mean of three replicates; ^cnd: not detected; ^dProtein with intracellular localisation prediction.

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