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. 2013 Sep;195(18):4231–4245. doi: 10.1128/JB.00154-13

Table 1.

Differentially expressed genes in A. vinosum after growth on different reduced sulfur compounds in comparison with growth on malatea

Locus tag Gene Annotation Strand Avg fold change after growth onb:
Sulfide Thiosulfate Sulfur Sulfite
Alvin_0040 atpB ATP synthase F0, A-subunit + 0.93 0.74 0.17 0.35
Alvin_0041 atpE ATP synthase F0, C-subunit + 1.17 0.79 0.17 0.50
Alvin_0042 atpF ATP synthase F0, B-subunit + 1.13 0.87 0.20 0.44
Alvin_0043 atpH ATP synthase F1, δ-subunit + 1.15 1.18 0.12 0.44
Alvin_0044 atpA ATP synthase F1, α-subunit + 1.30 1.14 0.20 0.61
Alvin_0629 α/β-Hydrolase fold protein − 4.02 0.61 0.15 1.01
Alvin_0741 sufD FeS assembly protein SufD + 0.20 0.47 4.12 1.30
Alvin_0742 FeS assembly SUF system protein + 0.20 0.51 4.12 1.46
Alvin_0852 TonB-dependent vitamin B12 receptor − 3.18 0.61 0.19 0.65
Alvin_0913 gcvP Glycine dehydrogenase (decarboxylating) − 0.43 0.35 0.40 0.44
Alvin_0982 rpmI Ribosomal protein L35 + 1.06 0.51 0.19 0.49
Alvin_1093 fccA Cytochrome c class I − 0.13 1.99 0.56 1.39
Alvin_1095 NapC/NirT cytochrome c domain protein − 0.08 1.27 0.80 0.90
Alvin_1196 Hypothetical protein Alvin_1196 + 0.03 1.42 98.00 3.95
Alvin_1197 Hypothetical protein Alvin_1197 + 0.03 1.37 116.63 3.88
Alvin_1420 Transcriptional regulator, BadM/Rrf2 family + 0.07 0.99 8.70 1.86
Alvin_1436 Cold shock DNA-binding domain protein + 2.29 0.71 0.10 0.29
Alvin_1525 feoB Ferrous iron transport protein B − 0.20 4.31 4.07 0.73
Alvin_1527 feoA FeoA family protein − 0.20 2.37 3.92 0.52
Alvin_1848 aceA Isocitrate lyase − 0.02 1.01 15.40 2.92
Alvin_2012 Hypothetical protein Alvin_2012 + 4.48 0.78 0.20 1.36
Alvin_2245 hemP Hemin uptake protein HemP + 0.17 1.78 2.71 1.06
Alvin_2262 metE 5-Methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase + 0.39 0.59 0.08 0.44
Alvin_2337 rplQ Ribosomal protein L17 − 1.10 0.90 0.18 0.61
Alvin_2338 rpoA DNA-directed RNA polymerase, α-subunit − 0.94 0.55 0.17 0.63
Alvin_2339 rpsD Ribosomal protein S4 − 1.04 0.58 0.16 0.60
Alvin_2340 rpsK 30S ribosomal protein S11 − 1.26 0.70 0.18 0.54
Alvin_2341 rpsM 30S ribosomal protein S13 − 1.12 0.57 0.20 0.68
Alvin_2342 rpmJ Ribosomal protein L36 − 1.27 1.03 0.18 0.70
Alvin_2343 secY Preprotein translocase, SecY subunit − 0.64 0.64 0.14 0.57
Alvin_2357 rpsC Ribosomal protein S3 − 1.02 0.76 0.15 0.55
Alvin_2358 rplV Ribosomal protein L22 − 0.92 0.73 0.14 0.46
Alvin_2359 rpsS Ribosomal protein S19 − 0.91 0.79 0.12 0.48
Alvin_2360 rplB Ribosomal protein L2 − 0.95 0.71 0.13 0.37
Alvin_2361 Ribosomal protein L25/L23 − 0.85 0.63 0.15 0.55
Alvin_2362 Ribosomal protein L4/L1e − 0.92 0.69 0.14 0.41
Alvin_2363 rplC 50S ribosomal protein L3 − 0.73 0.48 0.16 0.53
Alvin_2364 rpsJ Ribosomal protein S10 − 0.80 0.67 0.17 0.70
Alvin_2371 Ribosomal protein L7/L12 − 1.47 0.91 0.12 0.59
Alvin_2372 rplJ Ribosomal protein L10 − 1.07 0.61 0.10 0.43
Alvin_2373 rplA Ribosomal protein L1 − 0.85 0.61 0.17 0.62
Alvin_2374 rplK Ribosomal protein L11 − 0.64 0.91 0.17 0.80
Alvin_2440 cysB Transcriptional regulator, LysR family − 0.06 0.07 0.61 0.27
Alvin_2441 cysA Sulfate ABC transporter, ATPase subunit, CysA − 0.17 0.22 0.70 0.40
Alvin_2442 cysW Sulfate ABC transporter, inner membrane subunit, CysW − 0.09 0.11 0.65 0.35
Alvin_2443 cysT Sulfate ABC transporter, inner membrane subunit, CysT − 0.06 0.07 0.66 0.25
Alvin_2444 cysP Sulfate ABC transporter, periplasmic sulfate-binding protein, CysP + 0.04 0.28 1.35 0.35
Alvin_2446 cysI Nitrite and sulfite reductase 4Fe-4S region, CysI + 0.01 0.02 0.48 0.16
Alvin_2447 cysH Adenylylsulfate reductase, thioredoxin dependent, CysH + 0.01 0.01 0.46 0.14
Alvin_2448 cysD Sulfate adenylyltransferase, small subunit, CysD + 0.01 0.02 0.53 0.19
Alvin_2449 cysN Sulfate adenylyltransferase, large subunit, CysN + 0.02 0.04 0.76 0.19
Alvin_2451 Molybdopterin oxidoreductase 4Fe-4S region + 0.15 0.66 1.17 3.36
Alvin_2767 DEAD/DEAH box helicase domain protein + 0.95 0.76 0.16 0.33
a

Data are compiled for genes for which transcription levels decreased at least 5-fold on one sulfur source or at least 2-fold on all tested sulfur sources; the average fold change for the corresponding microarray ratio(s) is highlighted in bold. Genes involved in light harvesting are excluded here; they are summarized in Table S2 in the supplemental material.

b

The complete microarray data sets can be found in Table S3 in the supplemental material and in the GEO database (see Materials and Methods).