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Table 3 B. cenocepacia J2315 genes identified using the second generation cep box motif

From: Identification of potential CepR regulated genes using a cep box motif-based search of the Burkholderia cenocepacia genome

Motif namea Positionb bpc gened Gene/domain and predicted functione (Adjacent downstream genes possibly in operon)
Cell Surface or Membrane
MST2008 (-) 1:806161 45 BCAL0738(-) COG0793: Periplasmic protease; cell envelope biogenesis
MST2009 (+) 1:901874 295 BCAL0831 (+) phaP: phasin-like protein
MST2031 (-) 1:2662911 104 BCAL2406(-) COG0859, rfaF, LPS heptosyltransferase (rfa L,rfaG; LPS biosynthesis genes)
MST2048 (-) 2:211218 106 BCAM0183 (+) COG3468, autotransporter type V secretion, shdA homolog: adhesin
MST2050 (+) 2:1129604 172 BCAM1015(-) COG3203: Outer membrane protein
MST2068 (-) 3:174253 153 BCAS0156(+) COG1680: ampC, β-lactamase class C
Hypothetical Protein
MST2014 (-) 1:1228119 131 BCAL1124 (+) Conserved hypothetical protein
MST2020 (+) MST028 f 1:1484174 140 BCAL1354(-) COG4104: conserved hypothetical protein (vgrG: vgr related protein)
MST2030 (-) 1:2567308 41 BCAL2313 (+) hypothetical protein
MST2052 (+) 2:1249946 118 BCAM1149 (+) hypothetical protein
MST2056 (-) 2:1667312 57 BCAM1502 (+) hypothetical protein (Chemoreceptor mcpA)
MST2063 (-) 2:2720454 -19 BCAM2417 (+) hypothetical protein
MST2067 (+) 2:3070180 254 BCAM2713(-) hypothetical protein
MST2071 (+) 3:836110 63 BCAS0753(+) hypothetical protein
Metabolism
MST2002 (-) 1:273243 21 BCAL0232 (+) Elongation factor Tu
MST2005 (+) 1:390962 47 BCAL0358 (-) COG0308: Aminopeptidase N
MST2007 (+) MST011 1:778996 101 BCAL0716 (+) COG1250: fadB, 3-hydroxyacyl-CoA dehydrogenase; lipid metabolism
MST2010 (-) 1:963495 59 BCAL0886 (+) COG0183: paaJ, Probable beta-ketoadipyl CoA thiolase (caiD; lipid metabolism)
MST2022 (-) 1:1602043 50 BCAL1448(-) COG0525: valS, Valyl-tRNA synthetase
MST2023 (-) 1:1626201 104 BCAL1468(-) COG0644: fixC, electron transfer flavoprotein-ubiquinone oxidoreductase
MST2027 (+) 1:2465614 32 BCAL2229(-) Hypothetical signal peptide protein (COG3000: Sterol desaturase, lipid metabolism)
MST2029 (-) 1:2554533 153 BCAL2302(-) COG0556,uvrB: Helicase subunit of the DNA excision repair complex
MST2029 (-) 1:2554533 106 BCAL2303 (+) COG1448, tyrB: aspartate/tyrosine/aromatic aminotransferase
MST2034 (+) 1:2903040 55 BCAL2638 (+) COG0165,argH: Argininosuccinate lyase, arginine biosynthesis
MST2035 (+) MST052 1:3009329 9 BCAL2739 (+) COG0480, fusA: Translation elongation factor
MST2038 (+) 1:3351536 -15 BCAL3058 (+) COG0043, ubiD: 3-polyprenyl-4-hydroxybenzoate decarboxylase (rhtB, Putative threonine efflux or homoserine/homoserine lactone efflux)
MST2039(+) MST059 f 1:3488874 117 BCAL3191(+) COG1960: caiA, acyl CoA dehydrogenase
MST2043 (+) 1:3745369 60 BCAL3419 (+) COG0757: aroQ: 3-dehydroquinate dehydratase II
MST2045 (+) 2:11142 137 BCAM0010(+) kbl homolog, AKB ligase
MST2046 (+) MST072 f 2:84847 55 BCAM0077(-) COG0654: ubiH or mhpA, hydroxylase
MST2055 (+) 2:1564008 139 BCAM1405(-) sacB: Levansucrase (sacC: Levanase precursor)
MST2059 (+) f 2:2088113 71 BCAM1870 (+) cepI: homoserine lactone synthase
MST2061(+) 2:2134837 112 BCAM1922(+) repA: replication protein
MST2064 (-) 2:2839793 44 BCAM2502(-) COG0757: aroQ: 3-dehydroquinate dehydratase II (aroE: Shikimate 5-dehydrogenase)
MST2064 (-) 2:2839793 125 BCAM2503(+) COG3185: hppD, 4-hydroxyphenylpyruvate dioxygenase
MST2065 (-) 2:2938113 48 BCAM2588(-) menG: putative S-adenosylmethionine:2 demethylmenaquinone methyltransferase
Phage genes
MST2024 (+) 1:1735446 71 BCAL1564 (-) Hypothetical proteins Mup46, Mup47 and Mup48 [phage tail protein]
MST2060 (+) 2:2096677 28 BCAM1879 (+) Phage antirepressor
Regulatory gene
MST2006 (-) 1:616909 88 BCAL0562(-) COG2747, flgM: Negative regulator of flagellin synthesis (flgN; Flagellar biosynthesis/type III secretory pathway)
MST2007 (+) MST011 f 1:778996 59 BCAL0715(-) COG0583: LysR-type transcriptional regulator
MST2013 (+) 1:1085981 40 BCAL0999 (+) COG3073: RseA; Negative regulator of sigma E activity (RseB or MucB, negative regulator for alginate biosynthesis)
MST2019 (-) 1:1437591 385 BCAL1318 (+) COG3707, nasR: nitrate-and nitrite-responsive positive regulator
MST2026 (+) 1:2016418 259 BCAL1826 (+) gltF: regulator of gltBDF operon, glutamate synthaseenzymes
MST2036 (-) 1:3153030 18 BCAL2871(-) COG3073, rseA: Negative regulator of sigma E activity (mucB/rseB, mucD)
MST2039 (+) MST059 1:3488874 102 BCAL3190(-) COG1414: Transcriptional regulator, IclR family
MST2040 (-) 1:3502381 36 BCAL3205(-) COG1396: hipB homolog, Putative transcription regulator
MST2045 (+) MST068 f 2:11142 22 BCAM0009(-) COG1396: hipB homolog, Predicted transcriptional regulator
MST2046 (+) MST072 2:84847 58 BCAM0076(-) COG1309: ArcR domain: Bacterial regulatory proteins, tetR family
MST2055(+) 2:1564008 64 BCAM1406(+) COG: aglR, HTH-type transcriptional regulator
MST2057 (+) 2:1959876 36 BCAM1750 (+) COG1846: Transcriptional regulator, MarR family
MST2058f (+) 2:2087487 31 BCAM1868(-) cepR: Transcriptional regulator, LuxR family
MST2071 (+) 3:836110 40 BCAS0752(-) COG0583: LysR type Transcriptional regulator
Secretion or secreted product
MST2003 (+) 1:351306 25 BCAL0321 (+) COG3671: Predicted membrane protein (tatA, tatB, tatC secretion pathway)
MST2004 (+) MST005 f 1:366026 206 BCAL0340 (+) COG0457: TPR repeat, (evpA and evpB, evpC, evpE, evpF, and evpG virulence and possible secretion)
MST2070(-) f 3:478440 108 BCAS0409 (+) zmpA: extracellular zinc metalloprotease
Transport
MST2001 (-) 1:61816 272 BCAL0051 (+) COG0834: ABC-type amino acid transport/signal transduction systems
MST2066 (+) f 2:2974227 115 BCAM2626 (+) phuR: Haem/Haemoglobin uptake outer membrane receptor precursor (phuS, phuT, phuU phuV
MST2072 (+) P:55610 113 PBCA053 (-) COG1638,dctP homolog: TRAP-type C4-dicarboxylate transport system,
Unknown
MST2004 (+) MST005 1:366026 181 BCAL0339(-) COG3521: Uncharacterized protein conserved in bacteria
MST2025 (+) 1:1979817 274 BCAL1791 (-) COG2606: Uncharacterized conserved protein
MST2047 (-) 2:169540 86 BCAM0148 (+) Putative vgr-related protein (pldA: Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases)
MST2051 (-) 2:1150388 -37 BCAM1044(-) no homology (COG1536: Flagellar motor switch protein)
MST2053 (-) 2:1467792 28 BCAM1328-329 (+) Unknown proteins
MST2061 (+) 2:2134837 59 BCAM1921-919 (-) no homologs
MST2069 (+)f 3:329197 160 BCAS0293(-) aidA, intracellular protein of unknown function involved in nematode virulence; (second aid A)
  1. a MSTs were identified by searching the B. cenocepacia J2315 genome with the position specific scoring matrix (PSSM) from the second generation motif. Only genes with a motif match within a potential promoter and within 300 bp of the predicted start codon are reported.
  2. b The location center of the predicted motif is reported as chromosome:nucleotide. (+) or (-) refers to the DNA strand encoding the motif sequence. The motif names in bold were used to generate the PSSM file.
  3. c Number of base pairs between the centre of the motif and the predicted translational start site.
  4. d Open reading frame number from the unpublished annotation of the B. cenocepacia J2315 genome. (+) and (-) refer to the DNA strand.
  5. e Gene and domain homologies were obtained using the standard protein-protein BlastP program as described in the methods. Genes in parantheses are downstream of the first orf following the motif and may be in the same operon.
  6. f Confirmed to be CepR regulated by either lux or lacZ transcriptional fusions.