Table 1.
Proteins produced by Streptomyces scabiei with a 5-fold greater abundance in casein-suberin medium
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_25251d |
Polyribonucleotide nucleotidyltransferase |
0.04 ± 0.03 |
0.25 ± 0.10 |
0.22 ± 0.06 |
0.01 ± 0.01 |
ndc |
0.01 ± 0.01 |
C9Z3N7 |
SCAB_25991d |
Ribosome recycling factor |
0.43 ± 0.13 |
nd |
nd |
0.08 ± 0.07 |
0.03 ± 0.05 |
0.10 ± 0.10 |
C9Z3P0 |
SCAB_26021d |
30S ribosomal protein S2 |
0.23 ± 0.12 |
0.05 ± 0.02 |
nd |
0.03 ± 0.05 |
nd |
nd |
C9Z3Q3 |
SCAB_26151d |
50S ribosomal protein L19 |
0.67 ± 0.32 |
1.13 ± 0.56 |
0.68 ± 0.25 |
0.10 ± 0.18 |
nd |
nd |
C9YW46 |
SCAB_36621d |
30S ribosomal protein S9 |
0.42 ± 0.24 |
0.35 ± 0.20 |
0.11 ± 0.06 |
0.12 ± 0.13 |
nd |
nd |
C9YW47 |
SCAB_36631d |
50S ribosomal protein L13 |
0.25 ± 0.13 |
0.24 ± 0.10 |
0.10 ± 0.03 |
0.02 ± 0.04 |
nd |
nd |
C9YW61 |
SCAB_36771d |
30S ribosomal protein S5 |
0.33 ± 0.06 |
0.38 ± 0.05 |
0.01 ± 0.02 |
0.13 ± 0.23 |
nd |
nd |
C9YW63 |
SCAB_36791d |
50S ribosomal protein L6 |
0.18 ± 0.12 |
0.33 ± 0.16 |
0.02 ± 0.03 |
0.02 ± 0.03 |
nd |
nd |
C9YW64 |
SCAB_36801d |
30S ribosomal protein S8 |
0.17 ± 0.15 |
0.64 ± 0.45 |
0.12 ± 0.21 |
0.02 ± 0.04 |
nd |
nd |
C9YW68 |
SCAB_36841d |
50S ribosomal protein L14 |
0.21 ± 0.04 |
0.63 ± 0.47 |
0.54 ± 0.45 |
0.05 ± 0.09 |
nd |
nd |
C9YW72 |
SCAB_36881d |
30S ribosomal protein S3 |
0.17 ± 0.09 |
0.09 ± 0.08 |
0.01 ± 0.03 |
0.02 ± 0.04 |
nd |
nd |
C9YW73 |
SCAB_36891d |
50S ribosomal protein L22 |
0.44 ± 0.16 |
0.85 ± 0.60 |
0.67 ± 0.40 |
0.08 ± 0.13 |
nd |
nd |
C9YW77 |
SCAB_36931d |
50S ribosomal protein L4 |
0.62 ± 0.13 |
1.00 ± 0.20 |
0.66 ± 0.06 |
0.10 ± 0.14 |
nd |
nd |
C9YW78 |
SCAB_36941d |
50S ribosomal protein L3 |
0.55 ± 0.10 |
0.96 ± 0.26 |
0.56 ± 0.15 |
0.04 ± 0.08 |
nd |
nd |
C9YW94 |
SCAB_37111d |
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_75031d |
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_30041d |
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_44161d |
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_28761d |
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_28781d |
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_34651d |
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_28481d |
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_69711d |
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_9531d |
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_51101d |
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_66881d |
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_85681d |
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.