Nucleic Acids Research, 2000, Vol. 28, No. 5 1206-1210
© 2000 Oxford University Press
Evaluation and characterization of catabolite-responsive elements (cre) of Bacillus subtilis
Faculty of Engineering, Fukuyama University, Fukuyama 729-0292, Japan and 1Computer Laboratory, National Institute for Basic Biology, Okazaki 444-8585, Japan
A global mechanism of catabolite repression of the genus Bacillus comprises negative regulation exerted through the binding of the CcpA protein to the catabolite-responsive elements (cres) of the target genes. We searched for cre sequences in the Bacillus subtilis genome using a query sequence, WTGNAANCGNWNNCW (N and W stand for any base and A or T, respectively), picking out 126 putative and known cre sequences. To examine their cre function, we integrated spac promoter (Pspac)-cre-lacZ fusions into the amyE locus. Examination of catabolite repression of ß-galactosidase synthesis in the integrants led us to the following conclusions: (i) lower mismatching of cre sequences to the query sequence is required for their function; (ii) although cre sequences are partially palindromic, low mismatching in the same direction as that of transcription of the target genes is more critical for their function than that in the inverse direction; and (iii) yet, a more palindromic nature of cre sequences is desirable for a better function. Furthermore, the alignment of 22 cres that function in vivo implicated a consensus sequence, WWTGNAARCGNWWWCAWW (R stands for G or A). Interestingly, in the case where cre sequences are located in the protein-coding regions of the target genes, their conserved bases are preferentially the third bases of codons where base degeneracy is allowed.
* To whom correspondence should be addressed at: Department of Biotechnology, Faculty of Engineering, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan. Tel: +81 849 36 2111; Fax: +81 849 36 2459; Email: yfujita@bt.fubt.fukuyama-u.ac.jp Present address: Atsushi Ogiwara, Tsukuba Research Laboratories, Glaxo Wellcome K.K., Tsukuba 300-4247, Japan
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Avila, M. Jaquet, D. Moine, T. Requena, C. Pelaez, F. Arigoni, and I. Jankovic Physiological and biochemical characterization of the two {alpha}-L-rhamnosidases of Lactobacillus plantarum NCC245 Microbiology, August 1, 2009; 155(8): 2739 - 2749. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Ujiie, T. Matsutani, H. Tomatsu, A. Fujihara, C. Ushida, Y. Miwa, Y. Fujita, H. Himeno, and A. Muto Trans-Translation is Involved in the CcpA-Dependent Tagging and Degradation of TreP in Bacillus subtilis J. Biochem., January 1, 2009; 145(1): 59 - 66. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Seidl, M. Bischoff, and B. Berger-Bachi CcpA Mediates the Catabolite Repression of tst in Staphylococcus aureus Infect. Immun., November 1, 2008; 76(11): 5093 - 5099. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. J. G. van de Werken, M. R. A. Verhaart, A. L. VanFossen, K. Willquist, D. L. Lewis, J. D. Nichols, H. P. Goorissen, E. F. Mongodin, K. E. Nelson, E. W. J. van Niel, et al. Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Appl. Envir. Microbiol., November 1, 2008; 74(21): 6720 - 6729. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. D. Sriramulu, M. Liang, D. Hernandez-Romero, E. Raux-Deery, H. Lunsdorf, J. B. Parsons, M. J. Warren, and M. B. Prentice Lactobacillus reuteri DSM 20016 Produces Cobalamin-Dependent Diol Dehydratase in Metabolosomes and Metabolizes 1,2-Propanediol by Disproportionation J. Bacteriol., July 1, 2008; 190(13): 4559 - 4567. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Seidl, C. Goerke, C. Wolz, D. Mack, B. Berger-Bachi, and M. Bischoff Staphylococcus aureus CcpA Affects Biofilm Formation Infect. Immun., May 1, 2008; 76(5): 2044 - 2050. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Abdou, C. Boileau, P. de Philip, S. Pages, H.-P. Fierobe, and C. Tardif Transcriptional Regulation of the Clostridium cellulolyticum cip-cel Operon: a Complex Mechanism Involving a Catabolite-Responsive Element J. Bacteriol., March 1, 2008; 190(5): 1499 - 1506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. C. Almengor, T. L. Kinkel, S. J. Day, and K. S. McIver The Catabolite Control Protein CcpA Binds to Pmga and Influences Expression of the Virulence Regulator Mga in the Group A Streptococcus J. Bacteriol., December 1, 2007; 189(23): 8405 - 8416. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Inacio and I. de Sa-Nogueira trans-Acting Factors and cis Elements Involved in Glucose Repression of Arabinan Degradation in Bacillus subtilis J. Bacteriol., November 15, 2007; 189(22): 8371 - 8376. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. E. Kaufman and J. Yother CcpA-Dependent and -Independent Control of Beta-Galactosidase Expression in Streptococcus pneumoniae Occurs via Regulation of an Upstream Phosphotransferase System-Encoding Operon J. Bacteriol., July 15, 2007; 189(14): 5183 - 5192. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Macek, I. Mijakovic, J. V. Olsen, F. Gnad, C. Kumar, P. R. Jensen, and M. Mann The Serine/Threonine/Tyrosine Phosphoproteome of the Model Bacterium Bacillus subtilis Mol. Cell. Proteomics, April 1, 2007; 6(4): 697 - 707. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Yu, M. Tangney, H. C. Aass, and W. J. Mitchell Analysis of the Mechanism and Regulation of Lactose Transport and Metabolism in Clostridium acetobutylicum ATCC 824 Appl. Envir. Microbiol., March 15, 2007; 73(6): 1842 - 1850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Zomer, G. Buist, R. Larsen, J. Kok, and O. P. Kuipers Time-Resolved Determination of the CcpA Regulon of Lactococcus lactis subsp. cremoris MG1363 J. Bacteriol., February 15, 2007; 189(4): 1366 - 1381. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Shulami, G. Zaide, G. Zolotnitsky, Y. Langut, G. Feld, A. L. Sonenshein, and Y. Shoham A Two-Component System Regulates the Expression of an ABC Transporter for Xylo-Oligosaccharides in Geobacillus stearothermophilus Appl. Envir. Microbiol., February 1, 2007; 73(3): 874 - 884. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Asai, T. Ootsuji, K. Obata, T. Matsumoto, Y. Fujita, and Y. Sadaie Regulatory role of RsgI in sigI expression in Bacillus subtilis Microbiology, January 1, 2007; 153(1): 92 - 101. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Deutscher, C. Francke, and P. W. Postma How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria Microbiol. Mol. Biol. Rev., December 1, 2006; 70(4): 939 - 1031. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. J. Goh, C. Zhang, A. K. Benson, V. Schlegel, J.-H. Lee, and R. W. Hutkins Identification of a Putative Operon Involved in Fructooligosaccharide Utilization by Lactobacillus paracasei Appl. Envir. Microbiol., December 1, 2006; 72(12): 7518 - 7530. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Spence, W. G. Wells, and C. J. Smith Characterization of the Primary Starch Utilization Operon in the Obligate Anaerobe Bacteroides fragilis: Regulation by Carbon Source and Oxygen J. Bacteriol., July 1, 2006; 188(13): 4663 - 4672. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Marr, B. Joseph, S. Mertins, R. Ecke, S. Muller-Altrock, and W. Goebel Overexpression of PrfA Leads to Growth Inhibition of Listeria monocytogenes in Glucose-Containing Culture Media by Interfering with Glucose Uptake J. Bacteriol., June 1, 2006; 188(11): 3887 - 3901. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Seidl, M. Stucki, M. Ruegg, C. Goerke, C. Wolz, L. Harris, B. Berger-Bachi, and M. Bischoff Staphylococcus aureus CcpA Affects Virulence Determinant Production and Antibiotic Resistance. Antimicrob. Agents Chemother., April 1, 2006; 50(4): 1183 - 1194. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Schumacher, G. Seidel, W. Hillen, and R. G. Brennan Phosphoprotein Crh-Ser46-P Displays Altered Binding to CcpA to Effect Carbon Catabolite Regulation J. Biol. Chem., March 10, 2006; 281(10): 6793 - 6800. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Barrangou, M. A. Azcarate-Peril, T. Duong, S. B. Conners, R. M. Kelly, and T. R. Klaenhammer Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays PNAS, March 7, 2006; 103(10): 3816 - 3821. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Joseph, K. Przybilla, C. Stuhler, K. Schauer, J. Slaghuis, T. M. Fuchs, and W. Goebel Identification of Listeria monocytogenes Genes Contributing to Intracellular Replication by Expression Profiling and Mutant Screening J. Bacteriol., January 15, 2006; 188(2): 556 - 568. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. L. Lorca, Y. J. Chung, R. D. Barabote, W. Weyler, C. H. Schilling, and M. H. Saier Jr Catabolite Repression and Activation in Bacillus subtilis: Dependency on CcpA, HPr, and HprK J. Bacteriol., November 15, 2005; 187(22): 7826 - 7839. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Aleksandrzak-Piekarczyk, J. Kok, P. Renault, and J. Bardowski Alternative Lactose Catabolic Pathway in Lactococcus lactis IL1403 Appl. Envir. Microbiol., October 1, 2005; 71(10): 6060 - 6069. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-K. Choi and M. H. Saier Jr. Regulation of sigL Expression by the Catabolite Control Protein CcpA Involves a Roadblock Mechanism in Bacillus subtilis: Potential Connection between Carbon and Nitrogen Metabolism J. Bacteriol., October 1, 2005; 187(19): 6856 - 6861. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Labrie, C. Bart, C. Vadeboncoeur, and S. Moineau Use of an {alpha}-Galactosidase Gene as a Food-Grade Selection Marker for Streptococcus thermophilus J Dairy Sci, July 1, 2005; 88(7): 2341 - 2347. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Lopez-Contreras, K. Gabor, A. A. Martens, B. A. M. Renckens, P. A. M. Claassen, J. van der Oost, and W. M. de Vos Substrate-Induced Production and Secretion of Cellulases by Clostridium acetobutylicum Appl. Envir. Microbiol., September 1, 2004; 70(9): 5238 - 5243. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Cochu, C. Vadeboncoeur, S. Moineau, and M. Frenette Genetic and Biochemical Characterization of the Phosphoenolpyruvate:Glucose/Mannose Phosphotransferase System of Streptococcus thermophilus Appl. Envir. Microbiol., September 1, 2003; 69(9): 5423 - 5432. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Inacio, C. Costa, and I. de Sa-Nogueira Distinct molecular mechanisms involved in carbon catabolite repression of the arabinose regulon in Bacillus subtilis Microbiology, September 1, 2003; 149(9): 2345 - 2355. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Watanabe, M. Hamano, H. Kakeshita, K. Bunai, S. Tojo, H. Yamaguchi, Y. Fujita, S.-L. Wong, and K. Yamane Mannitol-1-Phosphate Dehydrogenase (MtlD) Is Required for Mannitol and Glucitol Assimilation in Bacillus subtilis: Possible Cooperation of mtl and gut Operons J. Bacteriol., August 15, 2003; 185(16): 4816 - 4824. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Barrangou, E. Altermann, R. Hutkins, R. Cano, and T. R. Klaenhammer Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus PNAS, July 22, 2003; 100(15): 8957 - 8962. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Nessler, S. Fieulaine, S. Poncet, A. Galinier, J. Deutscher, and J. Janin HPr Kinase/Phosphorylase, the Sensor Enzyme of Catabolite Repression in Gram-Positive Bacteria: Structural Aspects of the Enzyme and the Complex with Its Protein Substrate J. Bacteriol., July 15, 2003; 185(14): 4003 - 4010. [Full Text] [PDF]
|
|
|
|
|
|
J. B. Warner, C. Magni, and J. S. Lolkema CcpA-Independent Regulation of Expression of the Mg2+-Citrate Transporter Gene citM by Arginine Metabolism in Bacillus subtilis J. Bacteriol., February 1, 2003; 185(3): 854 - 859. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Fieulaine, S. Morera, S. Poncet, I. Mijakovic, A. Galinier, J. Janin, J. Deutscher, and S. Nessler X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr PNAS, October 15, 2002; 99(21): 13437 - 13441. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lapierre, B. Mollet, and J.-E. Germond Regulation and Adaptive Evolution of Lactose Operon Expression in Lactobacillus delbrueckii J. Bacteriol., February 15, 2002; 184(4): 928 - 935. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K.-I. Yoshida, Y. Yamamoto, K. Omae, M. Yamamoto, and Y. Fujita Identification of Two myo-Inositol Transporter Genes of Bacillus subtilis J. Bacteriol., February 15, 2002; 184(4): 983 - 991. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Miwa and Y. Fujita Involvement of Two Distinct Catabolite-Responsive Elements in Catabolite Repression of the Bacillus subtilis myo-Inositol (iol) Operon J. Bacteriol., October 15, 2001; 183(20): 5877 - 5884. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Yamamoto, M. Serizawa, J. Thompson, and J. Sekiguchi Regulation of the glv Operon in Bacillus subtilis: YfiA (GlvR) Is a Positive Regulator of the Operon That Is Repressed through CcpA and cre J. Bacteriol., September 1, 2001; 183(17): 5110 - 5121. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K.-i. Yoshida, K. Kobayashi, Y. Miwa, C.-M. Kang, M. Matsunaga, H. Yamaguchi, S. Tojo, M. Yamamoto, R. Nishi, N. Ogasawara, et al. Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis Nucleic Acids Res., February 1, 2001; 29(3): 683 - 692. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Jankovic, O. Egeter, and R. Brückner Analysis of Catabolite Control Protein A-Dependent Repression in Staphylococcus xylosus by a Genomic Reporter Gene System J. Bacteriol., January 15, 2001; 183(2): 580 - 586. [Abstract] [Full Text]
|
|
|
|
|
|
J. B. Warner, B. P. Krom, C. Magni, W. N. Konings, and J. S. Lolkema Catabolite Repression and Induction of the Mg2+-Citrate Transporter CitM of Bacillus subtilis J. Bacteriol., November 1, 2000; 182(21): 6099 - 6105. [Abstract] [Full Text]
|
|
|
|
|
|
L. A. Rivas, V. Parro, M. Moreno-Paz, and R. P. Mellado The Bacillus subtilis 168 csn gene encodes a chitosanase with similar properties to a Streptomyces enzyme Microbiology, November 1, 2000; 146(11): 2929 - 2936. [Abstract] [Full Text]
|
|