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. Author manuscript; available in PMC: 2009 Sep 1.
Published in final edited form as: Proteomics. 2008 Sep;8(17):3494–3505. doi: 10.1002/pmic.200800152

Table 2.

Highest abundance changes a) estimated by spectral counting values for select proteins under methanol vs. succinate growth conditions, compared with the corresponding transcription array ratios by Okubo, Skovran et al. [16].

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 -
a)

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.

b)

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).

c)

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

d)

See Section 2.6 and the supplementary notes for Tables S1-S3. Any value less than 1 × 10-6 is shown as zero.

e)

SAM δ=1.25: Significance Analysis of Microarrays score, as previously published [16]. See the supplementary notes for Tables S1-S3 for more detail regardins the SAM score.