Skip to main content
. 2013 Apr;79(7):2172–2181. doi: 10.1128/AEM.03057-12

Table 1.

Gene product concentration levels (microarrays and qPCR) and protein spot intensities (proteomics) from Acidithiobacillus ferrooxidans grown under aerobic and anaerobic conditionse

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
a

The annotation number is that of GenBank accession number NC011761.

b

Identification of multiple spots for a single gene in the proteomics is likely due to posttranslational modifications.

c

The protein spot contains a mixture or proteins. No conclusions regarding upregulation of the individual proteins can be drawn.

d

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.

e

Details are given in Tables S2 and S3 in the supplemental material.

f

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.