1887

Abstract

Five genes encoding enzymes required for -gluconate catabolism, together with genes encoding components of putative ABC transporters, are located in a cluster in the genome of sp. 43P. A gene encoding a transcriptional regulator in the IclR family, , is located in front of the cluster in the opposite direction. Reverse transcription PCR analysis indicated that the cluster was transcribed as an operon, termed the operon. Two promoters, P and P, are divergently located in the intergenic region, and transcription from these promoters was induced by addition of -gluconate or -idonate, a catabolite of -gluconate. Deletion of resulted in constitutive expression of , and , indicating that encodes a repressor protein for the expression of the operon and itself. Electrophoretic mobility shift assay and DNase I footprinting analyses revealed that recombinant LgnR binds to both P and P, indicating that LgnR represses transcription from these promoters by competing with RNA polymerase for binding to these sequences. -Idonate was identified as a candidate effector molecule for dissociation of LgnR from these promoters. Phylogenetic analysis revealed that LgnR formed a cluster with putative proteins from other genome sequences, which is distinct from those proteins of known regulatory functions, in the IclR family of transcriptional regulators. Additionally, the phylogeny suggests an evolutionary linkage between the -gluconate catabolic pathway and -galactonate catabolic pathways distributed in , , and .

Funding
This study was supported by the:
  • , JSPS KAKENHI , (Award 21380054)
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2014-03-01
2021-01-18
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References

  1. Babbitt P. C., Mrachko G. T., Hasson M. S., Huisman G. W., Kolter R., Ringe D., Petsko G. A., Kenyon G. L., Gerlt J. A. ( 1995). A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids. Science 267:1159–1161 [CrossRef][PubMed]
    [Google Scholar]
  2. Baker S. C., Ferguson S. J., Ludwig B., Page M. D., Richter O. M., van Spanning R. J. ( 1998). Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility. Microbiol Mol Biol Rev 62:1046–1078[PubMed]
    [Google Scholar]
  3. Browning D. F., Busby S. J. ( 2004). The regulation of bacterial transcription initiation. Nat Rev Microbiol 2:57–65 [CrossRef][PubMed]
    [Google Scholar]
  4. Campos E., de la Riva L., Garces F., Giménez R., Aguilar J., Baldoma L., Badia J. ( 2008). The yiaKLX1X2PQRS and ulaABCDEFG gene systems are required for the aerobic utilization of l-ascorbate in Klebsiella pneumoniae strain 13882 with l-ascorbate-6-phosphate as the inducer. J Bacteriol 190:6615–6624 [CrossRef][PubMed]
    [Google Scholar]
  5. Chao H., Zhou N. Y. ( 2013). GenR, an IclR-type regulator, activates and represses the transcription of gen genes involved in 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum. . J Bacteriol 195:1598–1609 [CrossRef][PubMed]
    [Google Scholar]
  6. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T. J., Higgins D. G., Thompson J. D. ( 2003). Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res 31:3497–3500 [CrossRef][PubMed]
    [Google Scholar]
  7. Deacon J., Cooper R. A. ( 1977). D-Galactonate utilisation by enteric bacteria. The catabolic pathway in Escherichia coli. . FEBS Lett 77:201–205 [CrossRef][PubMed]
    [Google Scholar]
  8. Gerischer U., Segura A., Ornston L. N. ( 1998). PcaU, a transcriptional activator of genes for protocatechuate utilization in Acinetobacter. . J Bacteriol 180:1512–1524[PubMed]
    [Google Scholar]
  9. Gui L., Sunnarborg A., Pan B., LaPorte D. C. ( 1996). Autoregulation of iclR, the gene encoding the repressor of the glyoxylate bypass operon. J Bacteriol 178:321–324[PubMed]
    [Google Scholar]
  10. Harley C. B., Reynolds R. P. ( 1987). Analysis of E. coli promoter sequences. Nucleic Acids Res 15:2343–2361 [CrossRef][PubMed]
    [Google Scholar]
  11. Hutner S. H., Provasoli L., Schatz A., Haskins C. P. ( 1950). Some approaches to the study of the role of metals in the metabolism of microorganisms. Proc Am Philos Soc 94:152–170
    [Google Scholar]
  12. Ibañez E., Campos E., Baldoma L., Aguilar J., Badia J. ( 2000). Regulation of expression of the yiaKLMNOPQRS operon for carbohydrate utilization in Escherichia coli: involvement of the main transcriptional factors. J Bacteriol 182:4617–4624 [CrossRef][PubMed]
    [Google Scholar]
  13. Jahn C. E., Charkowski A. O., Willis D. K. ( 2008). Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. J Microbiol Methods 75:318–324 [CrossRef][PubMed]
    [Google Scholar]
  14. Kim J., Kang Y., Choi O., Jeong Y., Jeong J. E., Lim J. Y., Kim M., Moon J. S., Suga H., Hwang I. ( 2007). Regulation of polar flagellum genes is mediated by quorum sensing and FlhDC in Burkholderia glumae. . Mol Microbiol 64:165–179 [CrossRef][PubMed]
    [Google Scholar]
  15. Kovach M. E., Elzer P. H., Hill D. S., Robertson G. T., Farris M. A., Roop R. M. II, Peterson K. M. ( 1995). Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175–176 [CrossRef][PubMed]
    [Google Scholar]
  16. Krell T., Molina-Henares A. J., Ramos J. L. ( 2006). The IclR family of transcriptional activators and repressors can be defined by a single profile. Protein Sci 15:1207–1213 [CrossRef][PubMed]
    [Google Scholar]
  17. Laemmli U. K. ( 1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685 [CrossRef][PubMed]
    [Google Scholar]
  18. Livak K. J., Schmittgen T. D. ( 2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔ C T method. Methods 25:402–408 [CrossRef][PubMed]
    [Google Scholar]
  19. Lu Y., Rashidul I. M., Hirata H., Tsuyumu S. ( 2011). KdgR, an IClR family transcriptional regulator, inhibits virulence mainly by repression of hrp genes in Xanthomonas oryzae pv. oryzae. J Bacteriol 193:6674–6682 [CrossRef][PubMed]
    [Google Scholar]
  20. Maddocks S. E., Oyston P. C. ( 2008). Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154:3609–3623 [CrossRef][PubMed]
    [Google Scholar]
  21. Maloy S. R., Nunn W. D. ( 1982). Genetic regulation of the glyoxylate shunt in Escherichia coli K-12. J Bacteriol 149:173–180[PubMed]
    [Google Scholar]
  22. Manso I., Torres B., Andreu J. M., Menéndez M., Rivas G., Alfonso C., Díaz E., García J. L., Galán B. ( 2009). 3-Hydroxyphenylpropionate and phenylpropionate are synergistic activators of the MhpR transcriptional regulator from Escherichia coli. . J Biol Chem 284:21218–21228 [CrossRef][PubMed]
    [Google Scholar]
  23. Molina-Henares A. J., Krell T., Eugenia Guazzaroni M., Segura A., Ramos J. L. ( 2006). Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol Rev 30:157–186 [CrossRef][PubMed]
    [Google Scholar]
  24. Moore S., Link K. P. ( 1940). Carbohydrate characterization. J Biol Chem 133:293–311
    [Google Scholar]
  25. Nasser W., Reverchon S., Robert-Baudouy J. ( 1992). Purification and functional characterization of the KdgR protein, a major repressor of pectinolysis genes of Erwinia chrysanthemi. . Mol Microbiol 6:257–265 [CrossRef][PubMed]
    [Google Scholar]
  26. Pan Y., Fiscus V., Meng W., Zheng Z., Zhang L. H., Fuqua C., Chen L. ( 2011). The Agrobacterium tumefaciens transcription factor BlcR is regulated via oligomerization. J Biol Chem 286:20431–20440 [CrossRef][PubMed]
    [Google Scholar]
  27. Pouyssegur J., Stoeber F. ( 1974). Genetic control of the 2-keto-3-deoxy-d-gluconate metabolism in Escherichia coli K-12: kdg regulon. J Bacteriol 117:641–651[PubMed]
    [Google Scholar]
  28. Rakus J. F., Fedorov A. A., Fedorov E. V., Glasner M. E., Hubbard B. K., Delli J. D., Babbitt P. C., Almo S. C., Gerlt J. A. ( 2008). Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry 47:9944–9954 [CrossRef][PubMed]
    [Google Scholar]
  29. Reverchon S., Nasser W., Robert-Baudouy J. ( 1991). Characterization of kdgR, a gene of Erwinia chrysanthemi that regulates pectin degradation. Mol Microbiol 5:2203–2216 [CrossRef]
    [Google Scholar]
  30. Rojas A., Segura A., Guazzaroni M. E., Terán W., Hurtado A., Gallegos M. T., Ramos J. L. ( 2003). In vivo and in vitro evidence that TtgV is the specific regulator of the TtgGHI multidrug and solvent efflux pump of Pseudomonas putida. . J Bacteriol 185:4755–4763 [CrossRef][PubMed]
    [Google Scholar]
  31. Shimizu T., Takaya N., Nakamura A. ( 2012). An L-glucose catabolic pathway in Paracoccus species 43P. J Biol Chem 287:40448–40456 [CrossRef][PubMed]
    [Google Scholar]
  32. Simon R., Priefer U., Pühler A. ( 1983). A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Nat Biotechnol 1:784–791 [CrossRef]
    [Google Scholar]
  33. Sunnarborg A., Klumpp D., Chung T., LaPorte D. C. ( 1990). Regulation of the glyoxylate bypass operon: cloning and characterization of iclR. . J Bacteriol 172:2642–2649[PubMed]
    [Google Scholar]
  34. Szumiło T. ( 1981). Pathway for D-galactonate catabolism in nonpathogenic mycobacteria. J Bacteriol 148:368–370[PubMed]
    [Google Scholar]
  35. Tamura K., Dudley J., Nei M., Kumar S. ( 2007). MEGA4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [CrossRef][PubMed]
    [Google Scholar]
  36. Yamamoto K., Ishihama A. ( 2003). Two different modes of transcription repression of the Escherichia coli acetate operon by IclR. Mol Microbiol 47:183–194 [CrossRef][PubMed]
    [Google Scholar]
  37. Yamazaki H., Ohnishi Y., Horinouchi S. ( 2003). Transcriptional switch on of ssgA by A-factor, which is essential for spore septum formation in Streptomyces griseus. . J Bacteriol 185:1273–1283 [CrossRef][PubMed]
    [Google Scholar]
  38. Zhou Y., Huang H., Zhou P., Xie J. ( 2012). Molecular mechanisms underlying the function diversity of transcriptional factor IclR family. Cell Signal 24:1270–1275 [CrossRef][PubMed]
    [Google Scholar]
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