Table 3. Potential members of PlcR regulon in Bce ATCC 14579.

Bce CDSs with a putative PlcR-binding site in the upstream region / Other Bce CDSs in a putative PlcR-regulated operon / Ortholog in Ban / Function / Comment
1. Toxins
BC1110* (BC1111) / (-) / Cytotoxin K
BC1809 / BA_2389† / Non-hemolytic enterotoxin lytic component L2
BC1810 / BA_2390 / Non-hemolytic enterotoxin lytic component L1
BC1811 / BA_2391 / Hypothetical protein in nhe operon
BC3104 / (-) / Hemolysin BL lytic component L2
BC3103 / (-) / Hemolysin BL lytic component L1
BC3102 / (-) / Hemolysin BL binding component precursor
BC5101 / BA_3854 / Thiol-activated cytolysin (cereolysin O)
2. Phospholipases
BC0670 / Phospholipase C
BC0671 / BA_1265, BA_1266 / Sphingomyelin phosphodiesterase
BC0672 / BA_1267 / Hypothetical protein
BC0671 / BA_1268 / Flavin-dependent dehydrogenase
BC3761 / BA_4362 / 1-phosphatidylinositol phosphodiesterase precursor (EC 3.1.4.10) / Upstream sequence in Ban is not known
3. Proteases
BC3161 / BA_3802‡ / Microbial collagenase (EC 3.4.24.3)
BC2735 / BA_3252† / Bacillolysin (EC 3.4.24.28)
BC3384 / BA_3939‡ / Enhancin (EC 3.4.24.-)
BC3383 / BA_3938 / Bacillolysin (EC 3.4.24.28)
BC3762* (BC3763) / BA_4363† / Microbial collagenase (EC 3.4.24.3)
BC5351* (BC5350) / (-) / Bacillolysin (EC 3.4.24.28)
BC5359 / BA_0463† / Aminopeptidase Y (EC 3.4.11.-)
BC2466 / (-) / Microbial collagenase (EC 3.4.24.3) / Truncated CDS
4. Cell wall machinery and surface proteins
BC4511*
(BC4510) / BA_5177† / Acid phosphatase
BC0991 / BA_1550‡ / S-layer homology domain / Putative murein endopeptidase
BC0992 / (-) / Hypothetical protein
BC3763* (BC3762) / BA_4364† / Cell wall hydrolase
BC2464 / BA_2322 / SLH-domain protein / Peptidoglycan endo-beta-N-acetylglucosaminidase (EC 3.2.1.-) / PlcR-binding site in the coding region of BC2463, not conserved in Ban
5. Transporters
BC4510* (BC4511) / BA_5176† / Sodium export ATP-binding protein
BC4509 / BA_5175 / Sodium export permease protein
BC0442 / BA_0974† / Tellurium resistance protein terD
BC0443 / BA_0975 / Tellurium resistance protein terD
BC0444 / BA_0976 / Tellurium resistance protein terD
BC0445 / BA_0977 / TerC-like protein
BC0446 / BA_0978 / ABC transporter solute-binding protein
BC0447 / BA_0979 / Tellurite resistance protein
BC2410 / BA_2973 / Transcription regulator, TetR family / PlcR-binding motif not conserved in Ban
BC2411 / BA_2974 / Macrolide-efflux protein
BC1430 / BA_1969, BA_1970† / Sodium-dependent tryptophan transporter / Functional assignment is based on the finding of a T-box upstream of the gene
BC1734 / BA_2299† / Export ABC transporter ATP-binding protein / Transporter is similar to the streptolysin S exporter SagGHI
BC1735 / BA_2300 / Export ABC transporter permease protein
BC1736 / BA_2301 / Export ABC transporter permease protein
BC5093 / (-) / Xanthine permease / Fragment; PlcR-binding site in the coding region of BC5092
BC4140 / (-) / Mg(2+) transport ATPase, P-type (EC 3.6.3.2) / PlcR-binding site is ~900 bp upstream of the start site
BC4141 / (-) / Mg(2+) transport ATPase protein C
6. Chemotaxis proteins
BC1641 / BA_2190‡ / Flagellar basal-body rod protein flgB
BC1642 / BA_2191 / Flagellar basal-body rod protein flgC
BC1643 / BA_2192 / Flagellar hook-basal body complex protein fliE
BC1644 / BA_2193 / Flagellar M-ring protein fliF
BC1645 / BA_2195 / Flagellar motor switch protein fliG
BC1646 / BA_2196 / Hypothetical protein
BC1647 / BA_2197 / Flagellum-specific ATP synthase (EC 3.6.3.14)
BC1648 / BA_2198 / Hypothetical protein
BC1649 / BA_2199, BA_2200 / Hypothetical protein
BC1650 / BA_2201 / Basal-body rod modification protein flgD
BC1651 / BA_2202 / Flagellar hook protein flgE
BC1652 / BA_2203 / Hypothetical protein
BC3385 / BA_0943 / Methyl-accepting chemotaxis protein / PlcR-binding motif is not conserved in Ban
BC0576 / BA_1155† / Methyl-accepting chemotaxis protein
BC0577 / BA_1156 / Two-component sensor kinase yufL (EC 2.7.3.-) / Putative malate-specific sensor kinase
BC0578 / BA_1157 / Two-component response regulator yufM / Putative malate-specific regulator
BC0579 / BA_1158 / Malate-sodium symport
BC0580 / BA_1159 / NAD-dependent malic enzyme (EC 1.1.1.38)
7. DNA metabolism
BC3739 / BA_4343‡ / Exodeoxyribonuclease III (EC 3.1.11.2)
BC3740 / BA_4344 / Ada regulatory protein
BC3741 / BA_4345 / O6-methylguanine-DNA methyltransferase (EC 2.1.1.63)
BC3742 / BA_4346 / DNA-3-methyladenine glycosylase II (EC 3.2.2.21)
BC4142 / BA_4823, BA_4822† / DNA polymerase IV (EC 2.7.7.7) / PlcR-binding site in the coding region of BC4143
8. Regulators
BC5350* (BC5351) / BA_0453† / Transcriptional activator PlcR
BC5349 / BA_0452† / PapR (PlcR pheromone)
BC2770 / BA_3290† / Transcriptional regulator, DeoR family / PlcR-binding site in the coding region of BC2771; homolog of B. subtilis GlcR (glycerol-3-phosphate operon repressor)
BC2769 / BA_3289 / Acetyltransferase (EC 2.3.1.-)
BC2768 / BA_3288 / Hypothetical cytosolic protein
BC2767 / BA_3287 / Hypothetical membrane associated protein
BC2766 / BA_3286 / Sigma-54-dependent transcriptional activator
BC3194 / BA_3731 / Transcriptional regulator, MarR family / PlcR-binding site upstream of BC3195, not conserved in Ban
BC1715* (BC1713) / BA_2279‡ / Transcriptional regulator
BC1716 / BA_2280, BA_2281 / Na+ driven multidrug efflux pump
9. Sporulation-related proteins
BC4794* (BC4795) / BA_5469† / Spore germination protein PF / There are 2 putative PlcR-binding sites between the two divergent genes
BA_5470 / SLH domain protein / CDS inserted upstream of BA_5469, PlcR-binding site is upstream of this CDS
BC3528 / (-) / Sporulation kinase B (EC 2.7.3.-)
BC5287 / BA_0382† / Sporulation protein SpoIID
BC5286 / BA_0381, BA_0379 / Transcriptional regulator with ABC transporter ATP-binding domain and LytTR DNA-binding domain
BC5285 / BA_0378 / Bacitracin transport ATP-binding protein bcrA
BC5284 / BA_0377 / ABC transporter permease protein
BC5283 / BA_0376 / Stage II sporulation protein Q
10. Metabolic genes
BC2137 / BA_2643† / Nitric oxide-dependent regulator DnrN
BC2136 / BA_2642 / Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
BC2135 / BA_2641 / Nitrite reductase [NAD(P)H] small subunit (EC 1.7.1.4)
BC2134 / BA_2640 / Uroporphyrin-III methyltransferase (EC 2.7.1.107) / Uroporphyrinogen-III synthase (EC 4.2.1.75)
BC2133 / BA_2639 / CbiX protein
BC2132 / BA_2638 / Precorrin-2 oxidase (EC 1.-.-.-) / Ferrochelatase (EC 4.99.1.-)
BC1350* (BC1349) / BA_1891‡ / Hypothetical protein
BC1351 / BA_1892 / Hypothetical protein
BC1352 / (-) / Hypothetical protein / Orthologous CDS in Ban wasn't identified in GenBank
BC1353 / BA_1893 / NrdI protein
BC1354 / BA_1894, BA_1896 / Ribonucleoside-diphosphate reductase alpha chain (EC 1.17.4.1)
BA_1895 / Intron-encoded endonuclease
BC1355 / BA_1897 / Ribonucleoside-diphosphate reductase beta chain (EC 1.17.4.1)
BC5335 / BA_0436‡ / Fructose-bisphosphate aldolase (EC 4.1.2.13)
BC4957 / (-) / Hypothetical protein / PlcR-binding site in the coding region of BC4956
BC4958 / BA_0063 / NAD(P)H dehydrogenase [quinone] (EC 1.6.99.2)
BC2974 / BA_3499† / Gamma-glutamyl phosphate reductase (EC 1.2.1.41) / PlcR-binding site in the coding region of BC2975
BC3184 / (-) / Broad specificity phosphatase / Truncated CDS; PlcR-binding site in the coding region of BC3185
11. Hypothetical proteins
BC4999 / BA_0109† / Membrane protein (CAAX amino terminal protease family)
BC1655 / BA_2208† / Hypothetical protein / Hypothetical protein in chemotaxis cluster
BC2552 / (-) / Hypothetical protein
BC0362 / (-) / Hypothetical protein
BC0361 / BA_0900 / Polysaccharide deacetylase
BC0360 / BA_0899 / Aminopeptidase (EC 3.4.11.-)
BC0916 / (-) / Hypothetical protein / Putative prophage protein
BC0917 / (-) / Hypothetical cytosolic protein
BC1713* (BC1715) / (-)‡ / Hypothetical membrane spanning protein / Orthologous CDS in Ban wasn't identified in GenBank
BC1273 / BATRNA026 / tRNA-Val-GAC / Putative PlcR-binding site is more than 1000 bp upstream of the start site
BC1082* (BC1083) / BA_1636† / Acetyltransferase (EC 2.3.1.-)
BC1083* (BC1082) / BA_1635† / Hypothetical protein
BC1349* (BC1350) / BA_1890‡ / Acetyltransferase (EC 2.3.1.-)
BC1975 / BA_2479† / Hypothetical exported protein / PlcR-binding site in the coding region of BC1974
BC1976 / (-) / Membrane protein, MgtC/SapB family / The homolog of BC1976is elsewhere on the scaffold of Ban chromosome (BA_0001)
BC1977 / BA_2481 / Acetyltransferase (EC 2.3.1.-)
BC2707, BC2706 / BA_3220† / Acetyltransferase (EC 2.3.1.-) / PlcR-binding site in the coding region of BC2708
BC4346 / BA_5019 / Hypothetical membrane spanning protein / PlcR-binding site in the coding sequence of BC4347, sequence in Ban is not known
BC1111* (BC1110) / BA_1656, BA_1657, BA_1658 / phosphoesterase (EC 3.1.-.-) / Upstream sequence is not conserved in Ban, protein is truncated
BC1112 / BA_1659 / Metal-dependent phosphohydrolase / Homolog of B. megaterium oxetanocin A resistance protein
BC4795* (BC4794) / (-), BA_5471† / Hypothetical membrane spanning protein / EpiH/GdmH-related protein
BC4796 / BA_5472 / Membrane protein

* - Putative PlcR-binding site was found between two divergent genes; †- PlcR-binding site conserved in Ban; ‡ - PlcR-binding site has 1 mismatch in Ban