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 2 Proteins specifically produced by Streptomyces scabiei in the 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)
			Day 1	Day 3	Day 5
Translational, ribosomal structure and biogenesis
C9Z241	SCAB_25261^d	30S ribosomal protein S15	0.15 ± 0.26	0.38 ± 0.27	0.03 ± 0.05
C9YW50	SCAB_36661^d	50S ribosomal protein L17	0.43 ± 0.22	0.51 ± 0.32	0.40 ± 0.32
C9YW52	SCAB_36681^d	30S ribosomal protein S11	0.31 ± 0.18	0.08 ± 0.11	nd
C9YW59	SCAB_36751^d	50S ribosomal protein L15	0.21 ± 0.18	0.42 ± 0.27	0.21 ± 0.20
C9YW62	SCAB_36781^d	50S ribosomal protein L18	0.31 ± 0.18	0.32 ± 0.11	0.24 ± 0.14
C9YW66	SCAB_36821^d	50S ribosomal protein L5	0.38 ± 0.21	0.33 ± 0.11	0.13 ± 0.05
C9YW67	SCAB_36831^d	50S ribosomal protein L24	0.06 ± 0.10	0.03 ± 0.04	nd
C9YW69	SCAB_36851^d	30S ribosomal protein S17	0.15 ± 0.10	0.38 ± 0.33	0.05 ± 0.08
C9YW71	SCAB_36871^d	50S ribosomal protein L16	0.15 ± 0.13	0.08 ± 0.10	0.01 ± 0.03
C9YW75	SCAB_36911	50S ribosomal protein L2	0.40 ± 0.28	0.97 ± 0.24	0.60 ± 0.12
C9YW76	SCAB_36921	50S ribosomal protein L23	0.24 ± 0.10	0.32 ± 0.19	0.29 ± 0.22
C9YW79	SCAB_36951^d	30S ribosomal protein S10	0.36 ± 0.05	0.32 ± 0.08	nd
C9YW95	SCAB_37121	30S ribosomal protein S12	0.24 ± 0.11	0.14 ± 0.09	0.05 ± 0.07
C9Z0W3	SCAB_39971^d	30S ribosomal protein S18 1	nd	0.07 ± 0.18	nd
C9Z0W7	SCAB_40011^d	50S ribosomal protein L28 2	nd	0.29 ± 0.10	0.17 ± 0.10
C9ZAN3	SCAB_46101^d	30S ribosomal protein S6	0.09 ± 0.16	0.23 ± 0.13	0.11 ± 0.09
C9Z2I8	SCAB_56731^d	Ribonuclease PH	0.04 ± 0.04	0.10 ± 0.03	0.11 ± 0.03
C9Z7H2	SCAB_60151^d	50S ribosomal protein L21	0.33 ± 0.08	0.36 ± 0.31	0.25 ± 0.33
C9Z7H3	SCAB_60161^d	50S ribosomal protein L27	0.22 ± 0.11	0.48 ± 0.15	0.19 ± 0.15
C9YWQ2	SCAB_69061^d	30S ribosomal protein S1	0.07 ± 0.06	nd	nd
C9Z316	SCAB_73401^d	tRNA (adenine-N(1)-)-methyltransferase	0.02 ± 0.03	0.07 ± 0.07	0.07 ± 0.04
C9Z4H9	SCAB_73971	50S ribosomal protein L35	0.57 ± 0.00	0.90 ± 0.44	0.48 ± 0.28
C9Z4I0	SCAB_73981^d	50S ribosomal protein L20	0.38 ± 0.35	0.42 ± 0.25	0.30 ± 0.13
Transcription
C9Z8G5	SCAB_28931^d	Transcription termination factor	0.03 ± 0.04	nd	nd
C9YWA1	SCAB_37181^d	DNA-directed RNA polymerase subunit β	nd	0.01 ± 0.02	nd
C9YWA2	SCAB_37191^d	DNA-directed RNA polymerase subunit β	nd	0.02 ± 0.02	0.01 ± 0.01
Posttranslational modification, protein turnover, chaperones
C9YYX4	SCAB_23161^d	Membrane protease	nd	0.04 ± 0.06	0.10 ± 0.07
C9YYJ3	SCAB_84021^d	Carbamoyltransferase	nd	0.14 ± 0.11	0.17 ± 0.07
Cell wall/membrane/envelope biogenesis
C9Z1V1	SCAB_9441^d	Sugar isomerase	nd	0.00 ± 0.01	0.02 ± 0.02
C9Z234	SCAB_25191^d	Dihydrodipicolinate synthase	0.02 ± 0.04	0.01 ± 0.03	0.04 ± 0.05
C9ZAN0	SCAB_46061^d	Alanine racemase	0.01 ± 0.02	0.01 ± 0.02	0.01 ± 0.02
C9Z2W0	SCAB_72801	Glycosyl hydrolase	0.28 ± 0.15	0.90 ± 0.20	0.83 ± 0.12
Signal transduction mechanism
C9YYC2	SCAB_70311^d	TerD-like stress protein	nd	0.01 ± 0.02	0.04 ± 0.03
Defense mechanism
C9ZAA4	SCAB_29931^d	Nickel superoxide dismutase	0.16 ± 0.08	nd	0.01 ± 0.03
C9YZ91	SCAB_38731^d	β-lactamase	0.63 ± 0.05	0.54 ± 0.07	0.34 ± 0.11
C9Z5I1	SCAB_42661^d	β-lactamase	0.10 ± 0.02	nd	nd
C9ZGZ0	SCAB_49661^d	Peroxiredoxin	nd	0.03 ± 0.06	0.09 ± 0.11
C9Z043	SCAB_84821	β-lactamase	0.02 ± 0.03	0.18 ± 0.04	0.11 ± 0.05
Secondary metabolites biosynthesis, transport and catabolism
C9YYT5	SCAB_8041	Aminohydrolase	0.01 ± 0.02	0.26 ± 0.11	0.22 ± 0.11
C9YWT5	SCAB_69391^d	Pseudouridine-5'-phosphate glycosidase	nd	0.03 ± 0.05	0.02 ± 0.03
C9YU69	SCAB_82441	Poly(3-hydroxyalkanoate) depolymerase C	nd	0.01 ± 0.01	0.03 ± 0.03
C9Z6A5	SCAB_88391^d	2-hydroxyhepta-2.4-diene-1.7-dioate isomerase	nd	nd	0.04 ± 0.05
Energy production and conversion
C9ZBX1	SCAB_31271^d	Ferredoxin	0.10 ± 0.04	nd	nd
C9YU38	SCAB_82111^d	Oxidoreductase	0.03 ± 0.04	0.02 ± 0.03	0.01 ± 0.02
Lipid metabolism
C9ZD66	SCAB_16601^d	CoA transferase	nd	nd	0.01 ± 0.02
C9Z6Y2	SCAB_28231^d	Acetate/propionate kinase	nd	0.01 ± 0.02	0.04 ± 0.04
C9ZGV4	SCAB_34521^d	Enoyl-CoA hydratase	0.03 ± 0.03	nd	nd
C9Z776	SCAB_44071^d	Esterase-lipase	0.18 ± 0.05	0.10 ± 0.07	0.07 ± 0.02
C9YTK3	SCAB_51091	Esterase-lipase	nd	0.14 ± 0.05	0.13 ± 0.05
C9YY49	SCAB_54571^d	Acetyl CoA acyl transferase	0.01 ± 0.01	0.10 ± 0.09	0.14 ± 0.07
C9YYE5	SCAB_70541	Lipolytic enzyme	0.07 ± 0.09	nd	nd
C9Z7Q3	SCAB_75771^d	Acyl-CoA dehydrogenase	0.02 ± 0.01	0.02 ± 0.03	nd
Degradation of aromatic compounds
C9Z2P6	SCAB_57301	3-oxo-5.6-dehydrosuberyl-CoA semialdehyde dehydrogenase	0.13 ± 0.17	nd	nd
Carbohydrate metabolism
C9YSY4	SCAB_4561	Glycosyl hydrolase	0.00 ± 0.00	0.02 ± 0.02	0.00 ± 0.00
C9YVM5	SCAB_5761	Glycosyl hydrolase	nd	0.04 ± 0.05	0.01 ± 0.01
C9YVN4	SCAB_5861	Carbohydrate esterase	nd	0.01 ± 0.01	0.06 ± 0.06
C9YVP5	SCAB_5981	Cellulase B	0.09 ± 0.06	0.31 ± 0.19	0.20 ± 0.13
C9YVP8	SCAB_6011	Glycosyl hydrolase/xylanase	0.01 ± 0.01	nd	0.03 ± 0.04
C9YX59	SCAB_6471	α-L-fucosidase	nd	0.09 ± 0.11	0.06 ± 0.09
C9Z1U5	SCAB_9381	Exo-α-sialidase	0.16 ± 0.08	0.34 ± 0.17	0.37 ± 0.14
C9Z885	SCAB_13561	Glycosyl hydrolase	0.02 ± 0.03	0.01 ± 0.01	0.00 ± 0.01
C9ZBJ5	SCAB_15481^d	α-mannosidase	nd	0.04 ± 0.03	0.07 ± 0.07
C9ZD61	SCAB_16551	Mannosidase	0.02 ± 0.04	0.18 ± 0.14	0.15 ± 0.12
C9ZD71	SCAB_16651	SugarP isomerase	0.01 ± 0.02	0.05 ± 0.03	0.02 ± 0.02
C9ZEQ1	SCAB_17021	Cellulase	0.04 ± 0.02	0.47 ± 0.13	0.36 ± 0.10
C9ZEQ3	SCAB_17041	Glycosyl transferase	0.02 ± 0.03	nd	nd
C9Z574	SCAB_26801	Polysaccharide lyase	nd	0.04 ± 0.03	0.05 ± 0.04
C9YUZ7	SCAB_36421^d	β-xylosidase	nd	0.05 ± 0.02	0.05 ± 0.02
C9YW88	SCAB_37051	Cellulase/xylanase	0.09 ± 0.03	0.24 ± 0.09	0.35 ± 0.14
C9Z725	SCAB_43531	Polysaccharide lyase	0.00 ±	0.02 ± 0.03	0.04 ± 0.05
C9Z789	SCAB_44201	β-galactosidase	0.01 ± 0.02	0.02 ± 0.02	0.00 ± 0.00
C9Z4A0	SCAB_58271	Glycosyl hydrolase	nd	0.01 ± 0.01	0.02 ± 0.03
C9ZDV4	SCAB_63781^d	α-L-arabinofuranosidase	nd	0.01 ± 0.01	0.04 ± 0.04
C9YYE3	SCAB_70521	Bifunctional pectate lyase/pectinesterase	0.02 ± 0.02	nd	nd
C9YYE6	SCAB_70551	Pectate lyase	0.91 ± 0.12	0.01 ± 0.01	nd
C9YYE7	SCAB_70561	Pectinesterase	0.30 ± 0.04	0.05 ± 0.02	0.03 ± 0.03
C9YYE8	SCAB_70571	Pectinesterase	0.24 ± 0.08	0.07 ± 0.02	0.04 ± 0.03
C9YYF0	SCAB_70591	Pectate lyase	0.36 ± 0.09	0.41 ± 0.18	0.29 ± 0.30
C9Z2Z4	SCAB_73161	Secreted protein	0.36 ± 0.06	0.17 ± 0.17	0.04 ± 0.06
C9Z623	SCAB_74681	Licheninase	0.07 ± 0.07	0.34 ± 0.07	0.27 ± 0.11
C9ZAZ8	SCAB_77201	Glycosyl hydrolase	0.12 ± 0.08	0.95 ± 0.25	0.71 ± 0.14
C9ZB17	SCAB_77391	Glycosyl hydrolase	0.01 ± 0.02	0.10 ± 0.11	0.06 ± 0.06
C9ZE74	SCAB_79011	Acetyl-xylan esterase	nd	0.59 ± 0.13	0.52 ± 0.09
C9ZEB7	SCAB_79481	Xylanase A	0.01 ± 0.02	0.02 ± 0.03	0.02 ± 0.03
C9ZFY5	SCAB_79861^d	Xylose isomerase	0.04 ± 0.01	0.10 ± 0.06	0.11 ± 0.05
C9YU11	SCAB_81841	Glycosyl hydrolase	0.13 ± 0.11	0.06 ± 0.06	0.01 ± 0.01
C9YU29	SCAB_82021	β-mannosidase	nd	0.22 ± 0.06	0.24 ± 0.07
C9YU66	SCAB_82411	Pectate lyase	nd	0.07 ± 0.08	0.06 ± 0.07
C9Z820	SCAB_89901^d	β-D-xylosidase	nd	0.02 ± 0.02	0.02 ± 0.02
Amino acid metabolism
C9YVT3	SCAB_6381	Extracellular small neutral protease	0.25 ± 0.21	0.08 ± 0.11	0.05 ± 0.08
C9YYP7	SCAB_7651	Zinc metalloprotease	0.13 ± 0.05	0.04 ± 0.04	0.03 ± 0.02
C9YYX3	SCAB_23151^d	Arginine deaminase	nd	0.00 ± 0.01	0.03 ± 0.02
C9Z238	SCAB_25231^d	Dihydrodipicolinate reductase	nd	0.03 ± 0.05	0.01 ± 0.03
C9Z281	SCAB_25691^d	4-aminobutyrate aminotransferase	0.01 ± 0.03	0.04 ± 0.04	0.02 ± 0.01
C9Z5A0	SCAB_27061^d	Ketol-acid reductoisomerase	0.02 ± 0.02	0.02 ± 0.02	0.00 ± 0.01
C9YTF8	SCAB_35641^d	Serine hydroxymethyltransferase 4	0.02 ± 0.02	nd	0.01 ± 0.01
C9Z8U5	SCAB_45071^d	Zinc aminopeptidase	0.04 ± 0.01	0.05 ± 0.01	0.07 ± 0.03
C9ZC37	SCAB_46731^d	Xaa-Pro aminopeptidase	0.01 ± 0.01	0.06 ± 0.04	0.16 ± 0.12
C9Z7B6	SCAB_59611^d	Aminopeptidase N	0.05 ± 0.04	nd	nd
C9Z4N7	SCAB_87271	Peptidase	0.03 ± 0.05	0.10 ± 0.13	0.04 ± 0.04
Coenzyme metabolism
C9Z1Y4	SCAB_9771^d	Cobalamin biosynthesis protein	0.02 ± 0.02	0.18 ± 0.04	0.12 ± 0.07
C9Z3M4	SCAB_25861^d	Aminotransferase	nd	0.00 ± 0.01	0.03 ± 0.03
C9Z402	SCAB_41841^d	Aminotransferase	nd	0.00 ± 0.01	0.01 ± 0.03
C9Z638	SCAB_74841^d	Pyridoxal biosynthesis lyase pdxS	0.03 ± 0.05	nd	nd
C9Z7L0	SCAB_75311^d	S-adenosylmethionine synthase	nd	0.01 ± 0.02	0.02 ± 0.02
Nucleotide metabolism
C9Z407	SCAB_41891^d	Adenylosuccinate synthetase	0.01 ± 0.03	nd	nd
C9ZDR6	SCAB_47861^d	Phosphoribosylformylglycinamidine cyclo-ligase	0.01 ± 0.02	0.00 ± 0.01	0.03 ± 0.02
C9Z7F8	SCAB_60011^d	Nucleoside diphosphate kinase	0.02 ± 0.04	0.08 ± 0.09	0.09 ± 0.13
C9YVK8	SCAB_68841	5' nucleotidase	0.03 ± 0.02	0.15 ± 0.09	0.08 ± 0.07
Inorganic ion metabolism
C9YVE4	SCAB_68191^d	Alkaline phosphatase	0.13 ± 0.04	0.06 ± 0.04	0.06 ± 0.05
C9ZB70	SCAB_77971	Alkaline phosphatase	0.16 ± 0.01	0.19 ± 0.07	0.17 ± 0.11
General function prediction only
C9YSY7	SCAB_4591	Acyltransferases	0.07 ± 0.07	0.02 ± 0.03	nd
C9YVP7	SCAB_6001^d	Feruloyl esterase	nd	0.05 ± 0.04	0.06 ± 0.06
C9Z3D2	SCAB_10131	Glycosyl hydrolase	nd	0.06 ± 0.03	0.06 ± 0.03
C9YT61	SCAB_19541	Carbohydrate esterase	0.02 ± 0.03	0.05 ± 0.03	0.01 ± 0.02
C9Z233	SCAB_25181^d	B lactamase	0.01 ± 0.01	0.03 ± 0.04	0.05 ± 0.03
C9Z6S2	SCAB_27611^d	Phage tail sheath protein FI	nd	0.03 ± 0.01	0.09 ± 0.05
C9Z8S0	SCAB_44821^d	Phosphatase	0.03 ± 0.05	0.00 ± 0.01	nd
C9Z994	SCAB_61611^d	Protease	0.05 ± 0.04	0.14 ± 0.03	0.03 ± 0.03
C9ZAQ7	SCAB_61831^d	Metalloendopeptidase	nd	nd	0.03 ± 0.03
C9ZAU3	SCAB_62211	Phosphatase	nd	0.11 ± 0.05	0.17 ± 0.07
C9ZDW7	SCAB_63921^d	Dehydratase	nd	0.04 ± 0.05	0.07 ± 0.03
C9ZHB0	SCAB_66321^d	F420-dependent NADP reductase	nd	0.02 ± 0.03	0.05 ± 0.05
C9ZB18	SCAB_77401	Glycosyl hydrolase	nd	0.06 ± 0.03	0.05 ± 0.04
C9ZCL9	SCAB_78431	Tripeptidylaminopeptidase	0.13 ± 0.01	0.14 ± 0.04	0.14 ± 0.11
C9ZEA8	SCAB_79391	Glycosyl hydrolase	nd	0.13 ± 0.07	0.11 ± 0.09
C9ZEC6	SCAB_79571	Glycosyl hydrolase	nd	0.03 ± 0.03	0.01 ± 0.02
C9YYG1	SCAB_83671^d	Acetyl esterase	nd	0.00 ± 0.01	0.02 ± 0.05
C9Z047	SCAB_84861	Amidase	0.21 ± 0.05	0.11 ± 0.03	0.06 ± 0.06
Unknown function
C9Z6Q2	SCAB_12841		0.44 ± 0.12	0.70 ± 0.25	0.59 ± 0.17
C9ZBK5	SCAB_15581^d		0.04 ± 0.04	0.03 ± 0.02	0.03 ± 0.03
C9YVU0	SCAB_20641		0.07 ± 0.04	0.34 ± 0.09	0.38 ± 0.11
C9Z0X8	SCAB_40131		0.28 ± 0.13	0.14 ± 0.05	0.07 ± 0.03
C9Z5E6	SCAB_42301^d		nd	0.03 ± 0.06	0.03 ± 0.06
C9ZGX5	SCAB_49501		0.06 ± 0.06	nd	nd
C9YV55	SCAB_52141^d		0.02 ± 0.03	0.03 ± 0.03	0.08 ± 0.09
C9Z1G8	SCAB_72441		0.17 ± 0.06	0.27 ± 0.09	0.32 ± 0.10
C9Z609	SCAB_74541		0.12 ± 0.14	nd	0.02 ± 0.04
C9ZG06	SCAB_80071		0.02 ± 0.03	nd	nd

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

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