Microbial strains and growth conditions
Construction of P. chlororaphis O6 gacA mutant
Phenotypic assays related to biocontrol traits
2-D PAGE analysis
Table 1
Spot number | Observed migrationa | Identified protein by ProFound Search | Fold change | ||||||
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Mr (kDa) | pI | Est’s Zb | Identified gene and protein in P. chlororapis O6 (locus_tag)c | Mr (kDa) | pI | Meand | SEd | p-valuee | |
113 | 28 | 4.45 | 1.50 | pppA, serine/threonine phosphatase (PchlO6_3739) | 26 | 4.95 | -2.6 | 0.5 | 0.020 |
1123 | 27 | 4.74 | 2.26 | phage portal protein, HK97 family (PchlO6_1242) | 45 | 5.84 | >-100 | 0.008 | |
1827 | 87 | 4.79 | 2.35 | ptsP, phosphoenolpyruvate-protein phosphotransferase (PchlO6_5904) | 84 | 5.44 | >-100 | 0.018 | |
2503 | 52 | 4.96 | 1.71 | emhC, efflux transporter, outer membrane factor (PchlO6_1402) | 52 | 5.69 | >-100 | 0.025 | |
2628 | 59 | 5.09 | 2.40 | tssC2, type VI secretion protein TssC2 (PchlO6_6187) | 56 | 5.24 | >-100 | 0.007 | |
3519 | 54 | 5.16 | 2.32 | arcA, arginine deiminase (PchlO6_4747) | 47 | 5.49 | >-100 | 0.010 | |
5013 | 20 | 5.76 | 1.71 | type VI secretion system effector, Hcp1 family (PchlO6_0238) | 19 | 5.63 | >-100 | 0.016 | |
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6713 | 81 | 6.02 | 2.35 | parE, DNA topoisomerase IV, B subunit (PchlO6_0539) | 70 | 5.73 | >100 | 0.005 | |
8902 | 139 | 7.37 | 2.37 | narG, nitrate reductase, alpha subunit (PchlO6_3628) | 140 | 6.31 | >100 | 0.001 |
a The Mr and pI values were estimated from 2-dimensional gels obtained in three independent experiments.
b Estimated Z score by ProFound program. Z scores of 1.281, 1.645, 2.326, and 3.090 mean that the search are in the 90th, 95th, 99th and 99.9th percentiles.
Table 2
Spot number | Observed migrationa | Identified protein | Fold change | ||||||
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Mr (kDa) | pI | Identified protein in P. chlororaphis O6 (locus_tag)b | Ion Score or Matching sequenced | Mr (kDa) | pI | Meanc | SEc | p-valuec | |
1318 | 39 | 4.71 | oxidoreductase, zinc-binding dehydrogenase (PchlO6_0868) | DYGDYVRNFWGGGERKP | 15 | 6.14 | >-100 | 0.001 | |
1719 | 72 | 4.82 | protein-export membrane protein SecD (PchlO6_5012) | AIYHFFR NGGAFVNPIVALAR | 68 | 5.22 | >-100 | 0.001 | |
2315 | 41 | 5.13 | lipase, class 3 (PchlO6_3236) | KISITHAYVVNNSAR RTSVPASISPGTAIRKK | 36 | 5.31 | >-100 | 0.002 | |
2621 | 67 | 5.11 | type VI secretion protein TssC1 (PchlO6_3748) | LPYHGHFNR IFTTPEHPAVSR | 55 | 5.37 | >-100 | 0.016 | |
2721 | 72 | 4.96 | putative ATP-dependent helicase (PchlO6_5564) | CAALLNCYFPGAR | 158 | 6.05 | >-100 | 0.016 | |
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316 | 39 | 4.57 | extracellular solute-binding protein (PchlO6_3412) | R.AVDAEFWVDHGEELEQR.F(80)R.FNAWAAR.(21) | 38 | 5.10 | >100 | 0.025 | |
1014 | 15 | 4.91 | MaoC-like protein (PchlO6_5497) | R.INLFAEATGDFQFIHVDPVK.A(87)K.KPGQWLLK.A(43)K.MVVNYGLDSVR.F(39) | 17 | 5.20 | >100 | 0.018 | |
2209 | 38 | 5.05 | TonB-dependent outer membrane receptor(PchlO6_3670) | CAAVSLDLENHFP EGAHDPPFALDER | 86 | 5.57 | 2.8 | 0.6 | 0.021 |
3001 | 24 | 5.14 | antioxidant, AhpC/TSA family (PchlO6_4904) | KAYDVESEGGVAFRG (66)R.SQIVNDLPLGR.N (32)R.NVEVIAVSIDSHFTHNAWR.N (14) | 22 | 5.18 | >100 | 0.013 | |
6703 | 80 | 5.89 | monovalent cation/proton antiporter, MnhAB/PhaAB subunit (PchlO6_2634) | SSLAKHYWLP | 105 | 9.55 | >100 | 0.014 | |
6706 | 73 | 5.92 | hypothetical protein (PchlO6_2333) | ESLLMEADPSSH KLDGVADSADVENGLSPPG | 57 | 6.25 | >100 | 0.021 |
a The Mr and pI values were estimated from 2-dimensional gels obtained in three independent experiments. Ions score is -10*Log (P), where P is the probability that the observed match is a random event. Individual ions scores > 49 indicate identity or extensive homology (p<0.05). Protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits. Amino acid sequences without ion scores were determined by Q-TOF analysis.