TABLE 1.

RyhB-regulated genes

GeneaBlattner no.Fold change when RyhB is expressedDescriptionbReference or source
Wild typefur mutant+ FeSO4
acnB b0118−4.4−2.0−1.4Aconitate hydrase B [4Fe-4S], major, exponential phase
cueO c b0123−2.1−1.3−1.2Multicopper oxidase, phenoloxidase and ferroxidase activities 36
sdhC b0721−6.1−2.5−4.5Succinate dehydrogenase, cytochrome b556
sdhD b0722−6.1−2.3−5.0Succinate dehydrogenase, hydrophobic subunit
sdhA b0723−4.0−2.6−3.0Succinate dehydrogenase, flavoprotein subunit
sdhB b0724−5.1−2.8−1.9Succinate dehydrogenase, 2Fe-2S, 3Fe-4S, 4Fe-4S
cydA b0733−1.9−2.2−2.4Cytochrome d terminal oxidase, polypeptide subunit I
cydB b0734−1.7−1.8−2.2Cytochrome d terminal oxidase, polypeptide subunit II
pflA b0902−3.8−2.9−2.8Pyruvate formate lyase activating enzyme 1, 4Fe-4S
acnA d b1276−1.7−1.3−3.8Aconitate hydrase A
ydbK b1378−2.9−2.8−1.3Putative oxidoreductase, 4Fe-4S
fumA b1612−7.6−3.8−3.2Fumarase A = fumarate hydratase Class I, 4Fe-4S
ydhD b1654−3.0−3.1−1.7Similar to some glutaredoxins
sodB b1656−19.3−10.6−20.9Iron superoxide dismutase
yeaC b1777−2.0−2.3−1.6Hypothetical protein
msrB b1778−2.8−1.9−2.2Methionine sulfoxide reductase 17
mrp/apbC b2113−4.7−3.0−3.3Fe-S cluster formation/repair in Salmonella enterica 43
nuoN b2276−3.0−2.5−4.1NADH dehydrogenase I chain N
nuoM b2277−4.1−3.5−4.2NADH dehydrogenase I chain M
nuoL b2278−4.3−3.2−4.8NADH dehydrogenase I chain L
nuoK b2279−5.0−3.3−5.0NADH dehydrogenase I chain K
nuoJ b2280−5.5−3.9−6.6NADH dehydrogenase I chain J
nuoI b2281−8.2−3.5−7.7NADH dehydrogenase I chain I, 4Fe-4S
nuoH b2282−6.8−3.5−5.8NADH dehydrogenase I chain H
nuoG b2283−4.9−3.7−4.3NADH dehydrogenase I chain G, 2Fe-2S, 4Fe-4S
nuoF b2284−3.2−2.4−2.5NADH dehydrogenase I chain F, potential 4Fe-4S
nuoE b2285−3.6−2.5−3.0NADH dehydrogenase I chain E, potential 2Fe-2S
nuoC b2286−4.5−3.0−4.7NADH dehydrogenase I chain C, D
nuoB b2287−4.4−2.3−3.9NADH dehydrogenase I chain B, potential 4Fe-4S
nuoA b2288−3.6−2.5−3.3NADH dehydrogenase I chain A
sseB b2522−2.5−2.0−1.3Enhanced serine sensitivity
pepB b2523−2.7−2.1−2.5Peptidase B
iscX b2524−5.6−3.5−4.7Open reading frame, hypothetical protein
fdx b2525−4.3−3.6−3.1Ferredoxin [2FE-2S], electron carrer protein
hscA b2526−2.9−2.6−2.4Heat shock protein, chaperone, member of Hsp70 protein family
hscB b2527−3.7−2.6−4.4Scaffold protein involved in iron-sulfur cluster assembly
iscA b2528−3.5−2.3−2.5Putative regulator
iscU b2529−4.9−2.8−3.2Scaffold protein involved in iron-sulfur cluster assembly
iscS b2530−6.1−3.8−5.1Subunit of cysteine desulfurase
iscR b2531−1.6−1.2−1.3IscR transcriptional regulator
yggG b2936−3.0−2.1−2.7Putative metalloproteaseExPASy
hybG b2990+0.9−1.1−1.1Maturation of large subunit of hydrogenase-2
hybF b2991+0.9−2.8−2.3May modulate levels of hydrogenase-2
hybE b2992−1.2−1.4−1.5Member of hyb operon
hybD b2993−1.2+0.9−1.4Probable processing element for hydrogenase-2
hybC b2994−1.3−6.1−9.2Large subunit, hydrogenase-2
hybB b2995−2.1−1.9−3.0Probable cytochrome Ni/Fe component of hydrogenase-2
hybA b2996−2.3−1.6−2.1Hydrogenase-2 small subunit, 4Fe-4S, 3Fe-4S
hybO b2997−2.4−1.6−8.8Small hydrogenase subunit, 4Fe-4S, 3Fe-4S
fdoI b3892−3.8−2.6−3.4Formate dehydrogenase, cytochrome b556 subunit
fdoH b3893−5.6−3.1−5.2Formate dehydrogenase-O, iron-sulfur subunit
fdoG b3894−5.0−3.3−4.2Formate dehydrogenase-O, major subunit
frdD b4151−6.0−2.6−2.3Fumarate reductase, anaerobic, membrane anchor polypeptide
frdC b4152−10.7−3.3−2.5Fumarate reductase, anaerobic, membrane anchor polypeptide
frdB b4153−5.3−1.8−1.9Fumarate reductase, anaerobic, iron-sulfur protein subunit
frdA b4154−4.4−2.6−2.6Fumarate reductase, anaerobic, flavoprotein subunit
  • a Individual genes or operons are grouped by lightface or boldface gene names. The gene orientation from top to bottom is clockwise on the chromosome.

  • b Descriptions are mostly from Affymetrix or, when mentioned, from ExPASy (http://au.expasy.org ) or cited reference.

  • c While cueO is weakly regulated by RyhB in the fur mutant, it is not repressed by Fur.

  • d acnA is repressed by RyhB as previously shown by Northern blotting (30).