Table 1.
Regulation, use, and protein or gene name | Predicted function | Annotation no.a | Fold change in protein expression | Median gene log2 ratio | qPCRf |
---|---|---|---|---|---|
Upregulated under aerobic conditions | |||||
Energy metabolism | |||||
HdrB | Heterodisulfide reductase subunit B, homolog | AFE_2586b | 9.4 | 1.0 | |
HdrB | Heterodisulfide reductase subunit B, homolog | AFE_2586b | 13.5 | ||
HdrA | Pyridine nucleotide disulfide oxidoreductase | AFE_2553b | 3.3 | ||
HdrA | Pyridine nucleotide disulfide oxidoreductase | AFE_2553b | 8.1 | ||
Conserved hypothetical protein (clusters with Hdr) | AFE_2552 | 5.4 | |||
AtpA | ATP synthase F1, α subunit (EC 3.6.3.14) | AFE_3205 | 2.1c | ||
atpC | ATP synthase F1, ε subunit | AFE_3202 | 1.0 | ||
AtpD | ATP synthase F1, β subunit (EC 3.6.3.14) | AFE_3203 | 2.3 | ||
MotA/TolQ/ExbB proton channel family protein | AFE_0768 | 0.8 | |||
tetH | Tetrathionate hydrolase | AFE_0029 | 4.3 | ||
Cyc2 | Outer membrane cytochrome c, Cyc2 | AFE_3153 | 5.6 | 0.9 | |
cyc1 | Cytochrome c4, Cyc1 | AFE_3152 | 0.7 | ||
coxA | Cytochrome c oxidase, aa3 type, subunit I | AFE_3149 | 0.9 | ||
coxC | Cytochrome c oxidase, aa3 type, subunit III | AFE_3148 | 0.9 | ||
rus | Rusticyanin | AFE_3146 | 1.7 | ||
Carbon management | |||||
Fba | Fructose bisphosphate aldolase, class II (EC 4.1.2.13) | AFE_3248b | 2.7 | O2 > Fe3+ | |
Fructose bisphosphate aldolase, putative | AFE_1802 | 4.9 | |||
Fba | Fructose-bisphosphate aldolase, class II (EC 4.1.2.13) | AFE_3248b | 3.4 | ||
Fba | Fructose bisphosphate aldolase, class II (EC 4.1.2.13) | AFE_3248b | 3.0 | ||
PdhB | Pyruvate dehydrogenase, E1 component, β subunit | AFE_3069 | 2.4 | ||
PdhB | Pyruvate dehydrogenase, E1 component, α subunit | AFE_1813 | 7.1 | 0.8 | |
Icd | NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) | AFE_0424 | 2.2 | ||
CbbL2 | RubisCO, large subunit 2 (EC 4.1.1.39) | AFE_2155 | 2.9 | O2 > Fe3+ | |
Pgi | Glucose-6-phosphate isomerase (EC 5.3.1.9) | AFE_2924 | 10.9 | ||
Rpe | Ribulose phosphate 3-epimerase (EC 5.1.3.1) | AFE_3247 | 2.5 | ||
Tal | Transaldolase (EC 2.2.1.2) | AFE_0419 | 2.2 | ||
Tkt-1 | Transketolase (EC 2.2.1.1) | AFE_1843 | 2.1 | ||
Transketolase pyridine binding domain protein | AFE_1667b | 4.0 | |||
Transketolase pyridine binding domain protein | AFE_1667b | 7.0 | |||
GlgB | 1,4-α-Glucan branching enzyme (EC 2.4.1.18) | AFE_2836 | 4.6 | 0.7 | |
6-Phosphogluconate dehydrogenase | AFE_2024 | 1.2 | |||
zwf | Glucose-6-phosphate 1-dehydrogenase | AFE_2025 | 0.9 | ||
gph-1 | Phosphoglycolate phosphatase | AFE_1823 | 0.7 | ||
Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase | AFE_2053 | 0.9 | |||
Phosphoglucomutase | AFE_2324 | 1.0 | |||
Cell wall/membrane/envelope biogenesis | |||||
OMPP1/FadL/TodX family | AFE_2542b | 1.0 | |||
OMPP1/FadL/TodX family | AFE_2542b | 2.6 | |||
Upregulated under anaerobiosis | |||||
Energy metabolism | |||||
Pyridine nucleotide disulfide oxidoreductase (DsrE-like) | AFE_2556 | 1.3 | |||
tusA | Hypothetical protein (similar to SirA) | AFE_2557 | 0.9 | ||
sreA | Sulfur reductase molybdopterin subunit | AFE_2177 | Fe3+ > O2 | ||
SreB | Sulfur reductase, iron-sulfur binding subunit | AFE_2178 | Unique | Fe3+ > O2 | |
sreC | Sulfur reductase, membrane subunit, putative | AFE_2179 | Fe3+ > O2 | ||
sreD | Sulfur reductase | AFE_2181 | Fe3+ > O2 | ||
AtpF | ATP synthase F0, subunit b (EC 3.6.3.14) | AFE_3207 | Unique | 1.5 | |
atpE | ATP synthase C chain | AFE_3208 | 1.4 | ||
atpB | ATP synthase F0, A subunit | AFE_3209 | 1.0 | ||
cycA2 | Cytochrome c4, CycA2 | AFE_2727 | 0.9 | ||
petA2 | Ubiquinol-cytochrome c reductase, iron-sulfur subunit | AFE_2729 | 0.9 | ||
petB2 | Ubiquinol-cytochrome c reductase, cytochrome b subunit | AFE_2730 | 1.1 | ||
ubiE | Ubiquinone/menaquinone biosynthesis methyltransferase | AFE_0289 | 0.7 | ||
Carbon management | |||||
CbbS1 | RubisCO, small subunit (EC 4.1.1.39) | AFE_1690 | 3.8 | Fe3+ > O2 | |
CscE | Carboxysome shell peptide | AFE_1683 | 3.1 | ||
AcnA | Aconitate hydratase, putative | AFE_0423 | 2.0 | ||
cbbp | Phosphoribulokinase | AFE_0536 | 0.7 | Fe3+ > O2 | |
cscC | Carboxysome shell peptide | AFE_1685 | 1.6 | ||
tkt-2 | Transketolase | AFE_3252 | 0.9 | ||
Cell wall/membrane/envelope biogenesis | |||||
OMPP1/FadL/TodX family | AFE_2542b | Unique | |||
OMPP1/FadL/TodX family | AFE_2542b | Unique | |||
OMPP1/FadL/TodX family | AFE_2542b | 9.6d | |||
OMPP1/FadL/TodX family | AFE_2542b | 6.8d | |||
OMPP1/FadL/TodX family | AFE_2542b | 1.7d | |||
Posttranslational modification/protein turnover/chaperone functions and inorganic ion transport and metabolism | |||||
surA | Survival protein SurA | AFE_3035 | 1.4 | ||
Amino acid metabolism and transport | |||||
Sulfite reductase hemoprotein, β component | AFE_3122 | 0.9 | |||
cysH | Adenylylsulfate reductase | AFE_3123 | 1.5 |
The annotation number is that of GenBank accession number NC011761.
Identification of multiple spots for a single gene in the proteomics is likely due to posttranslational modifications.
The protein spot contains a mixture or proteins. No conclusions regarding upregulation of the individual proteins can be drawn.
Fold change values are not comparable to the remaining data in the table, as these protein spots were not considered for final analyses. Values are given here to show the gradual increase of the different isoforms of the same protein in gels of outer membrane-enriched fractions for anaerobic conditions.
Details are given in Tables S2 and S3 in the supplemental material.
O2 > Fe3+ denotes that a higher mRNA content was detected by qPCR analysis during aerobic growth than with anaerobic growth; vice versa for Fe3+ > O2.