Table 2.
Proteomics data | Microarray data | ||||||
---|---|---|---|---|---|---|---|
Biological process / protein | Gene name, functional description | Spectr. count ratio MeOH/Succin (log2)b) | Sum (log2)c) | q-value d) | Avg. ratio MeOH/Succin (log10) | Avg. p-value | SAM δ=1.25 score e) |
Methylotrophy | |||||||
RMQ12669 | fdh2A, NAD-linked formate dehydrogenase, α-subunit | 8.46 | 9.460 | 0.000086 | 0.9510 | 0.000000 | 15.8053 |
RMQ12670 | fdh2B, NAD-linked formate dehydrogenase, β-subunit | 8.11 | 9.11 | 0.000000 | 0.3144 | 0.000005 | 4.2410 |
RMQ04236 | fdh2C, NAD-linked formate dehydrogenase, γ-subunit | 4.66 | 5.71 | 0.000000 | 0.8310 | 0.000000 | 12.1072 |
MELfdh2D | Molybdenum-dependent formate dehydrogenase | 5.67 | 6.70 | 0.000000 | 0.6008 | 0.000000 | 8.8664 |
RMQ06989 | mtkA, malate thiokinase, α-subunit | 4.21 | 10.56 | 0.000000 | 0.4131 | 0.000000 | 5.6789 |
RMQ06988 | mtkB, malate thiokinase, β-subunit | 3.47 | 9.65 | 0.000000 | 0.9416 | 0.000000 | 15.6636 |
RMQ12088 | sga, serine glyoxylate aminotransferase | 3.42 | 12.33 | 0.000000 | 1.0458 | 0.000000 | 12.5071 |
RMQ06990 | fch, methenyltetrahydrofolate cyclohydrolase | 2.67 | 10.32 | 0.000000 | 0.3522 | 0.000051 | 4.0102 |
RMQ09318 | mauA, methylamine dehydrogenase, small subunit | 3.15 | 5.720 | 0.000000 | 0.0784 | 0.256444 | - |
Electron transfer | |||||||
RMQ08074 | Cytochrome C | 5.04 | 6.30 | 0.000000 | 0.5614 | 0.000289 | 7.8708 |
RMQ09050 | Ferredoxin | 3.20 | 4.85 | 0.000000 | -0.2022 | 0.111892 | -1.8364 |
RMQ 07487 | Alkanesulfonate monooxygenase | 2.63 | 4.51 | 0.000182 | 0.0682 | 0.210289 | - |
RMQ04804 | Flavohemoprotein | 2.96 | 4.13 | 0.000749 | 0.0316 | 0.281579 | - |
RMQ02158 | Cytochrome d ubiquinol oxidase subunit I | 2.83 | 4.02 | 0.002249 | -0.0103 | 0.494911 | - |
Transport and binding | |||||||
RMQ06614 | Oligopeptide transporter | 3.20 | 4.09 | 0.000604 | 0.0169 | 0.719162 | - |
RMQ05821 | Transporter | 3.03 | 4.20 | 0.000264 | 0.1787 | 0.221674 | 3.1046 |
RMQ06652 | Alkanesulfonates binding protein | 2.85 | 4.26 | 0.000489 | -0.0313 | 0.646506 | - |
Bacteriochlorophyll biosynthesis | |||||||
RMQ06356 | Light-independent protochlorophyllide reductase subunit N | 3.51 | 4.64 | 0.000000 | 0.8791 | 0.016483 | 5.9173 |
RMQ01543 | Light-independent protochlorophyllide reductase subunit B | 2.60 | 4.24 | 0.001349 | 0.1087 | 0.104357 | - |
RMQ08201 | Mg-protoporphyrin IX monomethyl ester oxidative cyclase (aerobic) | 2.54 | 4.19 | 0.001234 | 0.5887 | 0.000000 | 6.3932 |
Others | |||||||
RMQ05833 | 2-keto-4-pentenoate hydratase | 4.51 | 6.16 | 0.000000 | 0.0694 | 0.319367 | - |
RMQ07275 | 2-dehydropantoate 2-reductase | 2.68 | 7.25 | 0.000000 | 0.1800 | 0.017278 | 3.6012 |
RMQ01118 | CoA synthetase | 2.67 | 7.53 | 0.000000 | 0.1550 | 0.123622 | 1.9451 |
RMQ06057 | Acetyl-CoA:acetoacetyl-CoA transferase α-subunit | 3.91 | 9.75 | 0.000000 | 0.5693 | 0.000000 | 7.4182 |
RMQ04459 | SSU ribosomal protein S12P | 4.23 | 5.30 | 0.000000 | -0.1007 | 0.264939 | - |
RMQ02615 | Universal stress protein family | 3.04 | 6.35 | 0.000000 | -0.0957 | 0.459547 | - |
RMQ12593 | Glucose-fructose oxidoreductase | 2.72 | 4.14 | 0.001534 | 0.0125 | 0.765129 | - |
RMQ07739 | fliM, Flagellar motor switch protein | 3.20 | 4.09 | 0.000036 | 0.0300 | 0.712640 | - |
RMQ12403 | Metal-dependent hydrolase | 2.92 | 4.10 | 0.001086 | 0.2390 | 0.088655 | 2.5209 |
Unknown function / hypothetical | |||||||
RMQ11509 | Unknown function | 4.28 | 5.10 | 0.000000 | -0.0184 | 0.666193 | - |
RMQ05835 | Hypothetical protein | 3.07 | 4.23 | 0.000000 | 0.2744 | 0.001003 | 1.9523 |
RMQ11790 | Unknown function | 2.72 | 4.14 | 0.001061 | 0.1396 | 0.182216 | 1.7696 |
RMQ08996 | Unknown function | 2.59 | 5.23 | 0.000000 | 0.0027 | 0.545101 | - |
Included in Table 2 are those proteins showing the 33 highest observed methanol vs. succinate ratios, with q-values < 0.01, i.e. those proteins that showed the strongest induction under methanol. For reasons of clarity, proteome level abundance changes are represented by spectral count values only. For a complete listing of all observed spectral counting and intensity ratios, see supplemental Tables S1 and S2. A subset of proteins relevant to methylotrophy is shown in Table S3. See Section 2.3 for instructions for accessing Tables S1 and S2.
Global log2 ratio of the average of the normalized total spectral count values for MeOH vs. Succininate: log2[(MeOH_1 + MeOH_2) ÷ (Succin_1 + Succin_2).
The sum of the normalized spectral counts for both MeOH and Succinate, providing an estimate of the degree to which a particular ORF is represented in the dataset