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. 2017 Apr 19;16:64. doi: 10.1186/s12934-017-0678-9

Table 2.

Proteins showing significant changed expression levels, compared between iron excess (Fe+) and iron limitation (Fe−) conditions, as well as between the exponential growth phase (early) and the stationary phase (late)

Accession no. Protein name Cluster of orthologous groups (COG) Conserved protein domain Spot no. Fold change iron-related Fold change growth-related
Early phase higher at Late phase higher at Fe+ higher at Fe− higher at
Fe− Fe+ Fe− Fe+ Early Late Early Late
Amino acid transport and metabolism
 F502_05097 Amino peptidase 1 COG1362 Lap4 298 1.9 1.7
 F502_05412 Carbamoyl phosphate synthase large subunit COG0458 CarB 89 1.8 1.9
 F502_07028 Cysteine synthase a COG0031 CysK 449 1.8 2.1
 F502_17572 Glutamine synthetase type III COG3968 GlnA3 187 1.6 1.9
190 1.6 1.6
 F502_18676 Threonine synthase COG0498 ThrC 312 1.6 2.2
Carbohydrate transport and metabolism
 F502_03412 Propanediol dehydratase small COG4910 PduE 594 1.9 1.9
 F502_07638 Subunit flavodoxin COG0716 FldA 594
 F502_03417 Glycerol dehydratase reactivation factor large subunit No COG 220 2.1
 F502_03937 Glycogen synthase COG0297 GlgA 329 2.7 2.3
 F502_06067 Enolase COG0148 Eno 695 4.1 4.0 2.0 2.0
696 4.8 1.8 2.5
 F502_06077 Triosephosphate isomerase COG0149 TpiA 491 1.5 2.6
 F502_06087 Glyceraldehyde 3-phosphate dehydrogenase COG0057 GapA 409 1.6 2.4
 F502_07098 Glycoside hydrolase COG1543 277 2.0 1.8
 F502_12758 Dihydroxyacetone kinase COG2376 DAK1 158 1.7 2.0 1.7 2.1
179 1.7 1.7 2.2 2.3
Cell cycle control/cell division
 F502_08238 Cell division protein COG3599 DivIVA 503 2.7 2.0
Cell wall/membrane/envelope biogenesis
 F502_00655 Peptidoglycan-binding protein COG1388 LysM 233 7.9 6.1 1.6
 F502_01965 Spore coat protein Frelated protein COG5577 CotF 549 1.5 2.1 1.6
Coenzyme transport and metabolism
 F502_07578 Pyridoxal biosynthesis lyase COG0214 PdxS 460 2.5 2.2
Energy production and conversion
 F502_05017 NifU-related domain containing protein COG0822 IscU 519 0.4 2.4 0.6 1.6 1.3 0.8 0.9 1.1
520 3.7 2.9 1.9 1.5
 F502_06282 Electron transfer flavoprotein subunit alpha COG2025 FixB 440 1.5
 F502_06287 Electron transfer flavoprotein subunit alpha/beta-like protein COG2086 FixA 487 1.7
 F502_06447 Bifunctional acetaldehyde-CoA/alcohol dehydrogenase COG1012 AdhE 119 2.1 3.7 1.6
715 1.5 2.9 5.3
717 1.6 3.0 4.7
 F502_07493 Nitroreductase COG0778 NfnB 537 2.3 2.9 1.8
 F502_07643 Pyruvate: ferredoxin (flavodoxin) oxidoreductase. homodimeric COG0674 PorA 70 2.4 2.4 1.5
75 2.4 0.6 1.8
76 2.7 1.9
77 1.5 2.3
87 2.0 2.8 1.5
90 2.2 2.8 1.6 2.0
 F502_07648 Pyruvate: ferredoxin oxidoreductase COG0674 PorA 40 2.3 1.6
57 2.3 2.1
58 1.5 2.4 2.1
59 2.1 2.8
 F502_09238 Rubredoxin/flavodoxin/oxidoreductase COG0426 NorV 131 1.7 2.0
730 2.0 1.6
 F502_09488 Hydratase (aconitase A) COG1048 AcnA 156 2.4 2.5 1.9 2.0
 F502_11871 Butyrate kinase COG3426 Buk 383 1.6 1.7
 F502_11976 Pyruvate carboxylase COG1038 PycA 71 1.5 2.7 1.7
 F502_12091 F0F1 ATP synthase subunit beta COG0055 AtpD 645 2.1 1.9
646 2.2 2.4
 F502_12878 Desulfo ferrodoxin COG2033 SorL 611 2.2 2.8
 F502_13493 Flavodoxin COG0716 FldA 575 14.3 8.0 1.6
 F502_14390 [Fe] hydrogenase COG4624 Nar1 PurB 303 2.1 2.5
 F502_04707 Adenylosuccinate lyase COG0015 303
 F502_15080 Rubrerythrin COG1592 YotD 558 2.2 4.5 2.0
 F502_16610 Glycolate oxidase COG0277 GlcD 315 1.8 2.3 1.9
 F502_18287 Hydrogenase-1 COG1034 NuoG 223 4.5 1.6 2.3
224 5.1 1.9 3.6
 F502_18651 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase COG1012 AdhE 736 2.7 1.5 2.1
 F502_19556 Formate acetyltransferase COG1882 PflD 174 4.5 5.7
175 8.0 6.5
178 2.5 3.4
181 3.7 1.7 7.4
Function unknown/general function prediction only
 F502_02435 Aldo/keto reductase COG1453 362 2.6 2.9
 F502_05012 Hypothetical protein (GGGtGRT protein) No COG 400 7.1 2.2 3.0
 F502_05962 Hypothetical protein No COG 635 2.0 1.5
 F502_06682 Hypothetical protein COG2607 318 3.4 3.8 1.7 2.0
 F502_15420 Hypothetical protein No COG 597 1.7 2.8 1.5
 F502_16320 Hypothetical protein COG0393 YbjQ 637 2.3 2.0
Lipid transport and metabolism
 F502_06297 3-Hydroxybutyryl-CoA dehydratase COG1024 CaiD 472 2.1 2.2
 F502_10483 Biotin carboxylase COG0439 AccC 302 2.5 1.6 2.1 1.9
Nucleotide transport and metabolism
 F502_17300 Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase COG0138 PurH 281 1.7 1.6
Posttranslational modification/Protein turnover/Chaperones
 F502_03242 Heat shock protein (molecular chaperone GrpE) COG0576 GrpE 481 2.1 2.2
 F502_03247 Molecular chaperone DnaK COG0443 Dank 217 1.6 1.8
 F502_03987 peptidase COG1026 Cym1 106 2.3 2.1
107 3.6 1.6 2.4
 F502_05557 ATP-dependent Clp protease ATP-binding subunit COG0542 ClpA 165 1.8 2.1
168 1.9 1.7
 F502_06242 Chaperonin COG0459 GroEL 258 1.6 2.0
 F502_06247 Co-chaperonin COG0234 GroES 613 1.5 2.6
 F502_07608 Thij/PfpI family protein COG0693 ThiJ 553 1.8 1.6
 F502_10228 Heat shock protein (molecular chaperone IbpA) COG0071 IbpA 600 2.5 3.0 6.9
 F502_15425 Heat shock protein 90 COG0326 HtpG 196 2.2 2.4
206 1.6 1.5
 F502_18446 Clpb protein COG0542 ClpA 138 1.8 1.5 2.8
716 2.5 2.4 4.4
 F502_18743 ATPase with chaperone activity clpC. two ATP-binding domain protein COG0542 ClpA 147 2.1 2.1 2.0 2.0
ClpA 149 2.5 1.7 2.4 1.6
Signal transduction/stress response/defense mechanism
 F502_04082 GTP-binding protein COG1217 TypA 47 1.7 1.8
148 1.7 2.4 2.1
 F502_07703 Chemotaxis histidine kinase. CheA (contains CheW-like adaptor domain) COG0643 CheA 155 3.6 2.2 1.6
 F502_10768 Lipid hydroperoxide peroxidase COG2077 Tpx 572 3.9 2.2 2.5
 F502_13258 CBS domain-containing protein COG0517 CBS 606 4.5 4.8 1.7 1.9
 F502_14770 Serine protein kinase COG2766 PrkA 193 4.7 1.5 3.4
197 3.7 2.6 2.1
200 6.2 1.9 3.6
201 3.8 2.6
 F502_16565 Nitrogen regulatory protein
P-II		 COG0347 GlnK 638 3.1 1.8
 F502_17612 Alkyl hydroperoxide reductase COG0450 AhpC 567 5.3 2.9 2.4
 F502_17637 Spore coat protein COG3546 CotJC 548 2.3 3.9 2.1
 F502_18092 Stage V sporulation protein T COG2002 AbrB 544 6.1 4.5 1.7
Transcription/Defense mechanisms
 F502_12326 Transcription accessory protein COG2183 Tex 160 1.7 1.8 4.7 1.5
Translation/Ribosomal structure and biogenesis
 F502_04537 30S ribosomal protein S2 COG0052 RpsB 497 2.1 2.1 2.7 2.7
500 2.4 1.9
 F502_06817 Ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5 COG1825 RplY 504 3.5 3.9
 F502_12196 Ribosome-associated protein Y (PSrp-1) COG1544 RaiA 565 2.4 2.4
 F502_18808 Elongation factor Tu COG0050 TufB 327 1.7 1.5 1.5 1.4
 F502_18833 50S ribosomal protein L1 COG0081 RplA 681 2.4 1.5 2.0
 F502_18948 50S ribosomal protein L5 COG0094 RplE 752 2.1 1.8
 F502_18963 50S ribosomal protein L6 COG0097 RplF 753 2.4 2.3

*1 COG: according to the annotation for C. pasteurianum DSMZ 525 by BioCyc database collection (http://www.biocyc.org/organism-summary?object=CPAS1262449)

*2 Conserved Protein Domain Family: according to the definition by NCBI Conserved Domains and Protein Classification (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml)