Table 3 Genes of the Zur regulons from a range of bacteria
SpeciesExperimental approachesZn importCOG0523Ribosomal proteinsEnzymesOtherActivationRefs.
ActinobacteriaStreptomyces coelicolor*Δzur mutant; qRT-PCR. Forty-one putative Zur boxes identified by CHiP [55]znuABCyciCrpmE2, rpmF2, rpmB2, rpmG2, rpsN2, rpsR2SCO7676 (Putative fer-redoxin), 7681, 7682 (Coelibactin biosynthesis)SCO0472, 0474, 3431 (various)zitB (CDF effluxer)[16,55,69,70]
Mycobacterium tuberculosisΔzur mutant, microarrays, qRT-PCR. Thirty-two genes (probably 16 operons) up-regulatedznuABCyciCrpmB1 and B2, rpmG1, rpsN2, rpsR1Secretory proteins involved in virulence[68]
Mycobacterium avium ssp. paratuberculosisExposure to metal starvation, qRT-PCR, RNAseq. Zinc-responsive genomic islands (ZnGI)mptABC,
mptDEF
cobWrpsR2, rpsN2, rpmG2, rpmE2
rpmB1, rpmG1
sidAB and G; metallophore bio-synthesis and exportSecretory proteins involved in virulence; lamB[71]
Corynebacterium glutamicumΔzur mutant, microarrays, qRT-PCR; nine genes differentially regulated in mutantznuABCcg0794
(yciC)
cg0795 (oxidoreductase)
cg3107 (adhA)
cg0040 (secreted protein)zrf (CDF effluxer)
zra (ATPase)
[67,72]
Corynebacterium diphtheriaeΔZur mutant, qRT-PCR, reporter assaystroABCzrg (yciC)adhASeveral surface-anchored proteins[73]
FirmicutesBacillus subtilisΔzur mutant, microarrays, quantitative RT-PCRznuABC
(annotated as adcABC), ZinT
yciCrpsN2, rpmE2folE2 (yciA), yciB
ytiB (carbonic anhydrase)
[12,53]
Listeria monocytogenes*Δzur mutant, quantitative RT-PCRznuABC (2×)rpsN2[74]
Staphylococcus aureus*Transcription assaysadcBC, adcA-II
zur
yciCrpsN2, rpmG2 [75]
Enterococcus faecalis*Exposure of WT to high [Zn]; microarrays, qPCRadcBC, adcA-II, adcAyciCrpmF2 (x2), rpsN2 (x2), rpmG2 (x2) [76]
Streptococcus suisΔzur mutant, microarrays, 121 genes (72 up-, 49 down-regulated in mutant); qRT-PCRNone of the commonly Zur-regulated genes. Several enzymes and membrane proteins up-regulated in mutant, e.g. Zn-dep. NADPH-quinone reductase and 3-phosphatidyltransferase. Unclear whether genes have Zur boxes in the upstream region. Alternative sensor AdcR more common in Streptococci.[42]
Gamma-proteobacteriaE. coliΔzur mutant, qRT-PCR, EMSAznuABC, zinTrpmE2, rpmJ2pliG[17,77]
Pseudomonas aeruginosa*Δzur mutant, qRT-PCR; WT grown in high and low Zn, microarray, qRT-PCR; RNASeq of ΔznuA mutantznuABC, znuD (TonB-dR), zrmABCD (tonB-dR)yciCrpmE2, rpmJfolE2, amiA, can, pyrC2, PA5537 (glutamine synthetase)
cntOLMI (metallophore synthesis)
dksA, zbp [7881]
Pseudomonas protegens*Exposure to Zn limitation; microarrays (73 genes up-, 28 down-regulated); qRT-PCRznuABC (), 3× tonB-dRyciC, yciC2rpmJ, rpmE1folE2, amiC, can, pyrC2, hisI2dksA[82]
Yersinia pestisΔzur mutant, microarrays; 154 differentially regulated genes in response to high [Zn]znuABC ()rpmJ2
rpmE2
[83]
Vibrio choleraeBioinformatics and biochemical promoter analysisznuABC, zrgABC(DE)rpmE2, rpmJ2ribAzrgD and E: hypothetical proteins[84]
Acinetobacter baumannii*Δzur mutant, 76 genes up- and 68 genes down-regulated, qRT-PCRznuABC, 3× tonB-dR, ExbD, ExbBzigArpmE2[85]
Xanthomonas campestrisΔzur mutant, microarrays, 64 putative Zur-regulated ORFs; in vitro transcription assaysznuABC
2× tonB-dR
XC0267folE2, amiChrpX; involved in pathogenicityczcD (CDF effluxer)[86,87]
Francisella tularensis and F. novicidaΔzur mutant, RNASeq, qRT-PCRzupT (FN)FTN_0880FTN_0395; ArsR family transcrip-tional regulator[88]
Alpha-proteobacteriaCaulobacter crescentusMicroarrays, transcription assays. Twenty-eight genes (7 up-, 21 down-) regulated in Δzur mutantznuGHI
tonB-dR (znuK, L and M)
zrpXrpUI, rpmAzrpW (putative transporter)RND systems, ATPase,
tonB-dRs
[89]
Agrobacterium tumefaciens*Δzur mutant, qRT-PCRznuABC/troABC, zinTyciC (2×)[90,91]
Paracoccus denitrificans*RNASeq (Zn-chelated/depleted/replete), 147 genes (133 up-, 14 down-regulated in low [Zn]), qRT-PCRznuABC, aztABCyciC[46]
Beta-proteobacteriaNeisseria meningitidisΔzur mutant, microarrays, qRT-PCR; 17 genes differentially regulated in mutantznuABC,
TonB-dR
rpmE2, rpmJqueC, queFadhP[65]
Cupriavidus metalliduransΔzur mutant, microarrays, Zur binding to promoter regions was testedzupT
tonB-dR
Op0317f
cobW1 W2, W3
NodehH2dksA1σ-factor fliA; cadA but not zntA[92,93]
CyanobacteriaAnabaena PCC 7120Promoter mapping, screening for putative Zur boxes, qRT-PCR, 23 genes identified [60]
Δzur mutant, semiquant. qRT-PCR, EMSA [62]
znuABC, 3 tonB-dR, (alr3243, alr4031)alr1197, all1751,
all4722
hemB2, thrS2, folE2, glycosyl-transferase [60]; sodA, catalase, peroxiredoxin [62], several more predictedaztR
all1474, alr3495
[60,62]
Synechococcus PCC 7002*Δzur mutant, RNASeqznuABChemB2, folE2 (+2 more)[94]

In most cases, Zur regulation has been confirmed experimentally. Some entries have been complemented by data extracted from the RegPrecise database [52]; experimentally confirmed Zur-regulated genes are printed in bold. Actinobacteria and Firmicutes have a single membrane; all other bacterial groups are Gram-negative and have an outer and inner membrane and a periplasm. Asterisks (*) indicate species in which zur expression is subject to autoregulation. Also see Figure 1 regarding uptake/efflux proteins. Abbreviations: znuABC, znuGHI, troABC, adcABC, aztABC, zrgABC are all ABC-type zinc uptake systems; zinT and adcA: periplasmic zinc-binding proteins; the latter has both a ZnuA and ZinT-like domain; zupT: zinc importer of the ZIP family; zitB: zinc exporter of the cation diffusion facilitator (CDF) family; tonB-dR: TonB-dependent receptor; exbB/D: parts of energy transduction system for TonB-dependent receptors; oprD: outer-membrane porin; aztR, smtB: zinc excess sensors; cobW/yciC: frequently used labels for COG0523 proteins; ribosomal proteins: rpmE = L31, rpmJ = L36, rpUI = L21, rpmA = L27, rpmB = L28, rpmG = L33, rpsN2 = S14p, rpsR1 = S18, rpmF2 = L32p; zrpW: zinc-regulated protein; zbp: putative zinc-binding protein; pliG: periplasmic lysozyme inhibitor; dksA: zinc-independent transcription factor; can: gamma-carbonic anhydrase; pyrC2: dihydroorotase; amiA/amiC: N-acetyl-muramoyl-l-alanine amidase; adhA: zinc-dependent alcohol dehydrogenase; adhP: alcohol dehydrogenase; folE2 and ribA: GTP cyclohydrolases; (tetrahydrofolate biosynthesis); dehH2: haloacetate dehydrogenase; hemB: delta-aminolevulinic acid dehydratase (tetrapyrrole biosynthesis); thrS2: threonyl-tRNA synthetase; hrpX: hypersensitivity-pathogenicity regulatory gene; queC: 7-cyano-7-deazaguanine synthase; queF: NADPH-dependent 7-cyano-7-deazaguanine reductase; Other abbreviations such as alr1197 and XC0267 are locus tags.