Table 4. Genes in B.subtilis predicted to be members of the Spo0A-phosphate regulon, including both known and new members.
| TU | Evidence | Functions of genes in TU | Position | Score |
|---|---|---|---|---|
| abrB*† | a, b, c | Transcriptional pleiotropic regulator of transition state genes | –59 | 9.93 |
| divIVA* | a, b, c | Cell-division initiation protein | –359 | 8.82 |
| spo0A*† | a, b, c | Two-component response regulator central for the initiation of sporulation | –182c, –166, –61 | 9.93, 7.87, 9.93 |
| ypjD-dapB-ypjFG*H-papS-birA | a, b, c | Unknown; dihydrodipicolinate reductase, transcriptional repressor of the biotin operon | –56 | 7.87 |
| yqeGH-aroD-yqeIJK*LM | a, b, c | Unknown | –94, –36c | 9.93, 9.93 |
| yqhL* | a, b, c | Unknown | –75 | 9.93 |
| yvyE*†-yvhJ* | a, b, c | Unknown | –154 | 8.82 |
| spoIIE† | a, b | Serine phosphatase | –63c | 7.87 |
| valS-folC | a, b | Valyl-tRNA synthetase | –348 | 7.43 |
| yerQ | a, b | Unknown | –367 | 7.43 |
| yloI-priA-def-fmt-yloMNOPQRS-spoVM | a, b | Unknown | –391 | 8.82 |
| ypjC | a, b | Unknown | –307c | 7.87 |
| yvyD | a, b | Unknown | –99c | 9.93 |
| flgBC*-fliE*F*G* | a, c | Flagellar basal-body rod proteins | –42c | 7.35 |
| fruR*B*A | a, c | Transcriptional repressor of the fructose operon, fructose 1-phosphate kinase, PTS fructose-specific enzyme IIABC component | –170 | 9.93 |
| spoIIGA*†sigE* | a, c | Protease (processing of pro-sigma-E to active sigma-E), RNA polymerase sporulation mother cell-specific (early) sigma factor | –130c | 7.35 |
| yfkQRST* | a, c | Similar to spore germination response | –366, –222c | 7.35, 9.93 |
| yhbAB*-cspR-yhbDEF | a, c | Unknown | –120 | 7.43 |
| yttP* | a, c | Unknown | –132c | 8.82 |
| ywqC*D*E* | a, c | Unknown; similar to capsular polysaccharide biosynthesis | –95 | 8.82 |
| fbaA* | b, c | Fructose-1,6-bisphosphate aldolase | –340, –137 | 7.43, 9.93 |
| spo0F*† | b, c | Two-component response regulator involved in the initiation of sporulation | –29 | 7.43 |
| yfnA* | b, c | Unknown; similar to metabolite transporter | –64c | 9.93 |
| ylbQ-yllA* | b, c | Unknown; similar to 2-dehydropantoate 2-reductase | –383, –166 | 7.87, 7.87 |
| ylxY-ymxGH* | b, c | Unknown | –215 | 7.87 |
| yttI-accA* | b, c | Acetyl-CoA carboxylase (beta and alpha subunit) | –207, –176c | 9.93, 7.87 |
| ctrA | a | CTP synthetase | –347 | 7.43 |
| degS | a | Two-component sensor histidine kinase involved in degradative enzyme and competence regulation | –61c | 8.82 |
| spoVB | a | Involved in spore cortex synthesis (stage V sporulation) | –311c | 7.43 |
| topA-gid-codV-clpQY-codY | a | DNA topoisomerase I, glucose-inhibited division protein, site-specific integrase, two-component ATP-dependent protease, transcriptional pleiotropic repressor | –172c | 7.87 |
| yfkO | a | Similar to NAD(P)H-flavin oxidoreductase | –176c | 7.35 |
| ygaH-ygxA | a | Unknown | –194c | 8.82 |
| yhcWX | a | Unknown | –186 | 8.82 |
| yhdYZ | a | Unknown | –306c | 8.82 |
| yheM | a | Similar to D-alanine aminotransferase | –151 | 9.93 |
| yjlA | a | Unknown | –84c | 7.43 |
| ykuL | a | Unknown | –71c | 9.93 |
| yugGH | a | Similar to transcriptional regulator (Lrp/AsnC family) | –52c | 7.43 |
| ywbI-thiKC | a | Unknown | –356c | 8.82 |
| alsSD | b | Alpha-acetolactate synthase, alpha-acetolactate decarboxylase | –313c | 7.35 |
| dnaA | b | Initiation of chromosome replication | –141 | 9.93 |
| dnaBI-2635002-ytxC | b | Initiation of chromosome replication/membrane attachment protein, primosome component | –217 | 7.43 |
| ykuJ | b | Unknown | –241c | 7.87 |
| ymfC | b | Unknown; similar to transcriptional regulator (GntR family) | –63c | 9.93 |
| yodC | b | Unknown | –313c | 9.93 |
| ypoP | b | Unknown; similar to transcriptional regulator (MarR family) | –195c | 7.43 |
| yqhM | b | Unknown | –114c | 9.93 |
| yrkHIJ | b | Unknown | –398 | 7.87 |
| ysfE | b | Unknown | –28 | 8.82 |
| yusM | b | Unknown | –142 | 9.93 |
| yutLM | b | Unknown | –269c | 7.43 |
| ywiC | b | Unknown | –210c | 9.93 |
| addBA*-sbcD | c | ATP-dependent deoxyribonuclease (subunit B, A), exonuclease SbcD homolog | –45c | 7.43 |
| appD*F* | c | Oligopeptide ABC transporter | –25c | 7.87 |
| comFA*FBFC-yvyF | c | Late competence gene | –369c | 7.87 |
| ecsAB*C | c | ABC transporter | –265c, –162c | 7.87, 7.87 |
| fliK*-ylxG*-flgE* | c | Flagellar hook proteins | –253 | 7.43 |
| ftsE*X | c | Cell-division ATP binding protein, cell-division protein | –66 | 9.93 |
| gbsAB* | c | Glycine betaine aldehyde dehydrogenase, alcohol dehydrogenase | –342c | 7.43 |
| gerCACB*CC | c | Heptaprenyl diphosphate synthase | –270c | 7.35 |
| gspA* | c | General stress protein | –243 | 7.43 |
| hom*-thrCB | c | Homoserine dehydrogenase, threonine synthase, homoserine kinase | –105 | 7.87 |
| iolDEFG*H* | c | Myo-inositol catabolism | –79 | 9.93 |
| kinA*† | c | Two-component sensor histidine kinase involved in the initiation of sporulation | –37 | 8.82 |
| med*-yjzA | c | Positive regulator of comK, | –115c, –42 | 9.93, 7.87 |
| NarQ*†A* | c | Required for formate dehydrogenase activity | –55c | 9.93 |
| nasB*C | c | Assimilatory nitrate reductase | –13c | 7.43 |
| rbsR*K*D*A*C*B* | c | Transcriptional repressor of the ribose operon, ribokinase, ribose ABC transporters | –146 | 7.87 |
| sacV* | c | Transcriptional regulator of the levansucrase gene | –309 | 7.35 |
| sinI*†R | c | Antagonist of SinR, and SinR is transcriptional regulator of post-exponential-phase responses genes | –163c | 8.82 |
| spoIIAA*†-spoIIAB*-sigF* | c | Anti-anti-sigma factor, anti-sigma factor/serine kinase, RNA polymerase sporulation forespore-specific (early) sigma factor | –319 | 7.43 |
| spoIIB* | c | Spatial and temporal regulation of the dissolution of septal peptidoglycan during engulfment | –120 | 7.43 |
| spoVAA-VAB-VAC-VAD-VAE*-VAF | c | Mutants lead to the production of immature spores | –310c | 7.87 |
| spoVFA*-VFB | c | Dipicolinate synthase subunit B and A | –191c | 7.35 |
| xylA* | c | Xylose isomerase | –263c | 7.87 |
| xylR* | c | Transcriptional repressor of the xylose operon | –79 | 7.87 |
| ybcO*P*QST*-ybdA*BD* | c | Unknown | –76c | 9.93 |
| yceC*DE*F | c | Unknown | –130c | 7.43 |
| yczJ* | c | Unknown | –343 | 7.43 |
| ydcPQ*R* | c | Unknown | –325 | 7.43 |
| ydfL* | c | Unknown; similar to multidrug-efflux transporter regulator | –216c | 7.87 |
| ydhB* | c | Unknown | –68c | 7.43 |
| yerI* | c | Unknown | –256 | 8.82 |
| yfhK* | c | Unknown; similar to cell-division inhibitor | –27 | 7.87 |
| yfmH*G* | c | Unknown | –309 | 9.93 |
| yfmT*S* | c | Unknown; similar to benzaldehyde dehydrogenase, similar to methyl-accepting chemotaxis protein | –184 | 9.93 |
| ygaN* | c | Unknown | –126 | 7.87 |
| ygaO* | c | Unknown | –325c, –310 | 7.43, 9.93 |
| yhdX* | c | Unknown | –50c | 8.82 |
| yjcP*Q | c | Unknown | –64c | 9.93 |
| yjfC* | c | Unknown | –13c | 7.87 |
| ykaA*†B* | c | Unknown | –56c | 9.93 |
| yknW*X*Y*Z* | c | Unknown | –357 | 7.43 |
| ykuA* | c | Unknown | –302c | 7.87 |
| ykzF* | c | Unknown | –110 | 8.82 |
| ylqB* | c | Unknown | –93 | 7.87 |
| ylxM*-ffh | c | Unknown | –82c | 7.87 |
| yncM* | c | Unknown | –89 | 7.43 |
| yolA*B* | c | Unknown | –399 | 7.87 |
| yopT*, yopU | c | Unknown | –365c | 8.82 |
| yosB*CD*EFGHI*JK | c | Unknown | –70c | 8.82 |
| ypjA*B | c | Unknown | –134 | 7.87 |
| yppDE* | c | Unknown | –132 | 9.93 |
| yppF* | c | Unknown | –100 | 7.87 |
| ypvA* | c | Unknown; similar to methyl-accepting chemotaxis protein | –27 | 8.82 |
| yqaRST-yqbABCDEFG*HIJ | c | Unknown; similar to phage related protein | –62c | 9.93 |
| yqgTU*V | c | Unknown | –119c | 7.43 |
| yqzD*†C | c | Unknown | –247, –89c | 8.82, 7.35 |
| yraIJ* | c | Unknown | –80 | 9.93 |
| ythP*Q | c | Unknown | –380c | 7.43 |
| ytpAB* | c | Unknown | –369c | 7.43 |
| yusN* | c | Unknown | –209c | 9.93 |
| yuxH*† | c | Unknown | –54c | 7.43 |
| yvcE* | c | Unknown; similar to cell wall binding protein | –216 | 9.93 |
| yvfB*CDE | c | Unknown | –396 | 7.87 |
| yvfI* | c | Unknown; similar to transcriptional regulator (GntR family) | –7, –278c | 9.93, 7.87 |
| yvqI*H | c | Unknown | –264 | 9.93 |
| ywjG* | c | Unknown | –379c, –135c | 7.43, 7.43 |
| ywmB-murA* | c | Unknown | –68 | 7.43 |
| ywsC*-ywtABC | c | Unknown; similar to capsular polyglutamate biosynthesis | –12 | 8.82 |
| yydA* | c | Unknown | –364 | 9.93 |
Genes whose expression is 3-fold dependent on spo0A are labeled with a star, and genes from the combined training set are labeled with a dagger. Types of evidence for the predicted TUs are: a, conserved between B.subtilis and B.halodurans; b, conserved between B.subtilis and B.anthracis; c, transcript level at least 3-fold dependent on spo0A from microarray analysis. Locations of sites are relative to the translation start of the first downstream gene. In the ‘Position’ column, c indicates complementary strand. Score unit: nat. Functions of specific genes are obtained from the SubtiList Web Server (http://genolist.pasteur.fr/SubtiList/).