Bioinformatics Analysis of NprR-NprX Quorum-Sensing System of Bacillus thuringiensis Isolates from the Papaloapan Region, Oaxaca-Mexico
Author(s)
Humberto Rafael Bravo-D1,
Alain Cruz-Nolasco1,
Luis Raúl Gutiérrez-Lucas2,
Ana Karin Navarro-Mtz2*
Affiliation(s)
1 División de Estudios de Posgrado, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, Tuxtepec, Oaxaca, México. 2 Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, Tuxtepec, Oaxaca, México.
1 División de Estudios de Posgrado, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, Tuxtepec, Oaxaca, México. 2 Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, Tuxtepec, Oaxaca, México.
ABSTRACT
Quorum sensing is a chemical communication process that bacteria use to regulate collective behaviors. In Gram-positive bacteria, oligopeptides (called autoinducers) are the signaling molecules to elicit quorum sensing. In Bacillus thuringiensis, NprR is a transcriptional regulator whose activity depends on the NprX signalling peptide. Bacillus thuringiensis is closely related to Bacillus cereus and Bacillus anthracis. The principal difference between them is that Bacillus thuringiensis is the only one that produced Cry protein. The aim of this study is to explore the relation of nprR and 16S rRNA genes in Bacillus thurin-giensis. Phylogenetic trees of nucleotide sequences of nprR and 16S rRNA genes were built. Sequences of fourteen new isolates from Papaloapan region were included in those phylo-genetic trees. In order to identify the isolates, a simple and fast methodology considering the Cry protein formation was used. The 16S rRNA phylogenetic tree allows identify eight isolates as Bacillus thuringiensis and the others as Bacillus spp. The nprR phylogenetic tree does not match with the 16S rRNA phylogenetic tree. This confirms that nprR is not a molecular marker for evolution. Most of the new isolates have the same NprR sequence (WTSDIVG). However, the SKPDIVG is the most common NprR sequence in thuringiensis species.
Quorum sensing is a chemical communication process that bacteria use to regulate collective behaviors. In Gram-positive bacteria, oligopeptides (called autoinducers) are the signaling molecules to elicit quorum sensing. In Bacillus thuringiensis, NprR is a transcriptional regulator whose activity depends on the NprX signalling peptide. Bacillus thuringiensis is closely related to Bacillus cereus and Bacillus anthracis. The principal difference between them is that Bacillus thuringiensis is the only one that produced Cry protein. The aim of this study is to explore the relation of nprR and 16S rRNA genes in Bacillus thurin-giensis. Phylogenetic trees of nucleotide sequences of nprR and 16S rRNA genes were built. Sequences of fourteen new isolates from Papaloapan region were included in those phylo-genetic trees. In order to identify the isolates, a simple and fast methodology considering the Cry protein formation was used. The 16S rRNA phylogenetic tree allows identify eight isolates as Bacillus thuringiensis and the others as Bacillus spp. The nprR phylogenetic tree does not match with the 16S rRNA phylogenetic tree. This confirms that nprR is not a molecular marker for evolution. Most of the new isolates have the same NprR sequence (WTSDIVG). However, the SKPDIVG is the most common NprR sequence in thuringiensis species.
Cite this paper
Bravo-D, H. , Cruz-Nolasco, A. , Gutiérrez-Lucas, L. and Navarro-Mtz, A. (2015) Bioinformatics Analysis of NprR-NprX Quorum-Sensing System of Bacillus thuringiensis Isolates from the Papaloapan Region, Oaxaca-Mexico. Advances in Biological Chemistry, 5, 293-304. doi: 10.4236/abc.2015.57027.
Bravo-D, H. , Cruz-Nolasco, A. , Gutiérrez-Lucas, L. and Navarro-Mtz, A. (2015) Bioinformatics Analysis of NprR-NprX Quorum-Sensing System of Bacillus thuringiensis Isolates from the Papaloapan Region, Oaxaca-Mexico. Advances in Biological Chemistry, 5, 293-304. doi: 10.4236/abc.2015.57027.
References
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http://dx.doi.org/10.1016/S0196-9781(01)00488-0 [6] Pottathil, M. and Lazazzera, B.A. (2003) The Extracellular Phr Peptide-Rap Phosphatase Signaling Circuit of Bacillus subtilis. Frontiers in Bioscience, 8, 32-45.
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http://dx.doi.org/10.1074/jbc.M401881200 [10] Muniady, S., Rathinam, X. and Subramaniam, S. (2011) Quick Isolation and Characterization for the Confirmation of a Novel Bacillus thuringiensis Strains from Chicken Manure Samples. African Journal of Microbiology Research, 5, 3131-3137. [11] Wabiko, H. and Yasuda, E. (1995) Bacillus thuringiensis Protoxin: Location of Toxic Border and Requirement of Non-Toxic Domain for High-Level in Vivo Production of Active Toxin. Microbiology, 141, 629-639.
http://dx.doi.org/10.1099/13500872-141-3-629 [12] Navarro, A.K., Farrera, R.R., Lopez, R. and Perez-Guevara, F. (2006) Relationship between Poly-β-Hydroxybutirate Production and δ-Endotoxin for Bacillus thuringiensis var. kurstaki. Biotechnology Letters, 28, 641-644.
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http://dx.doi.org/10.1038/nprot.2007.131 [16] Thompson, J., Higgins, D. and Gibson, T. (1994) Clustal W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Research, 22, 4673-4680.
http://dx.doi.org/10.1093/nar/22.22.4673 [17] Bavykin, S., Lysov, Y., Zakhariev, V., Kelly, J., Jackman, J., Stahl, D. and Cherni, A. (2004) Use of 16S rRNA, 23S rRNA, and gyrB Gene Sequence Analysis to Determine Phylogenetic Relationships of Bacillus cereus Group Microorganisms. Journal of Clinical Microbiology, 42, 3711-3730.
http://dx.doi.org/10.1128/JCM.42.8.3711-3730.2004 [18] Helgason, E., Okstad, O.E., Caugant, D.A., Johansen, H.A., Fouet, A., Mock, M., Hegna, I. and Kolsto, A.B. (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis One Species on the Basis of Genetic Evidence. Applied and Environmental Microbiology, 66, 2627-2630.
http://dx.doi.org/10.1128/AEM.66.6.2627-2630.2000 [19] Zasada, A. and Gierczyński, R. (2006) Some Bacillus thuringiensis Strains Share rpoB Nucleotide Polymorphisms Also Present in Bacillus anthracis. Journal of Clinical Microbiology, 44, 1606-1607.
http://dx.doi.org/10.1128/JCM.44.4.1606-1607.2006
[1] Waters, C.M. and Bassler, B.L. (2005) Quorum Sensing: Cell-to-Cell Communication in Bacteria. Annual Review of Cell and Developmental Biology, 21, 319-346.
http://dx.doi.org/10.1146/annurev.cellbio.21.012704.131001 [2] Monnet, V. and Gardan, R. (2015) Quorum-Sensing Regulators in Gram-Positive Bacteria: Cherchez le Peptide. Molecular Microbiology, 97, 181-184.
http://dx.doi.org/10.1111/mmi.13060 [3] Perchat, S., Dubois, T., Zouhir, S., Gominet, M., Poncet, S., Lemy, C., Aumont-Nicaise, M., Deutscher, J., Gohar, M., Nessler, S. and Lereclus, D. (2011) A Cell-Cell Communication System Regulates Protease Production during Sporulation in Bacteria of the Bacillus cereus Group. Molecular Microbiology, 82, 619-633.
http://dx.doi.org/10.1111/j.1365-2958.2011.07839.x [4] Rocha, J., Flores, V., Cabrera, R., Soto-Guzman, A., Granados, G., Juaristi, E., Guarneros, G. and de la Torre, M. (2012) Evolution and Some Functions of the NprR-NprRB Quorum-Sensing System in the Bacillus cereus Group. Applied Microbiology and Biotechnology, 94, 1069-1078.
http://dx.doi.org/10.1007/s00253-011-3775-4 [5] Lazazzera, B.A. (2001) The Intracellular Function of Extracellular Signaling Peptides. Peptides, 22, 1519-1527.
http://dx.doi.org/10.1016/S0196-9781(01)00488-0 [6] Pottathil, M. and Lazazzera, B.A. (2003) The Extracellular Phr Peptide-Rap Phosphatase Signaling Circuit of Bacillus subtilis. Frontiers in Bioscience, 8, 32-45.
http://dx.doi.org/10.2741/913 [7] Raymond, B., Johnston, P.R., Nielsen-LeRoux, C., Lereclus, D. and Crickmore, N. (2010) Bacillus thuringiensis: An Impotent Pathogen? Trends in Microbiology, 18, 189-194.
http://dx.doi.org/10.1016/j.tim.2010.02.006 [8] Rowe, G.E. and Margaritis, A. (1987) Bioprocess Development in the Production of Bioinsecticides by Bacillus thuringiensis. Critical Reviews in Biotechnology, 6, 87-127.
http://dx.doi.org/10.3109/07388558709086986 [9] Ito, A., Sasaguri, Y., Kitada, S., Kusaka, Y., Kuwano, K., Masutomi, K., Mizuki, E., Akao, T. and Ohba, M. (2004) A Bacillus thuringiensis Crystal Protein with Selective Cytocidal Action to Human Cells. Journal of Biological Chemistry, 279, 21282-21286.
http://dx.doi.org/10.1074/jbc.M401881200 [10] Muniady, S., Rathinam, X. and Subramaniam, S. (2011) Quick Isolation and Characterization for the Confirmation of a Novel Bacillus thuringiensis Strains from Chicken Manure Samples. African Journal of Microbiology Research, 5, 3131-3137. [11] Wabiko, H. and Yasuda, E. (1995) Bacillus thuringiensis Protoxin: Location of Toxic Border and Requirement of Non-Toxic Domain for High-Level in Vivo Production of Active Toxin. Microbiology, 141, 629-639.
http://dx.doi.org/10.1099/13500872-141-3-629 [12] Navarro, A.K., Farrera, R.R., Lopez, R. and Perez-Guevara, F. (2006) Relationship between Poly-β-Hydroxybutirate Production and δ-Endotoxin for Bacillus thuringiensis var. kurstaki. Biotechnology Letters, 28, 641-644.
http://dx.doi.org/10.1007/s10529-006-0029-0 [13] Weisburg, W., Barns, S., Pelletier, D. and Lane, D. (1991) 16S Ribosomal DNA Amplification for Phylogenetic Study. Journal of Bacteriology, 173, 697-703. [14] Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28, 2731-2739.
http://dx.doi.org/10.1093/molbev/msr121 [15] Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. (2007) Locating Proteins in the Cell Using Target P, Signal P, and Related Tools. Nature Protocols, 2, 953-971.
http://dx.doi.org/10.1038/nprot.2007.131 [16] Thompson, J., Higgins, D. and Gibson, T. (1994) Clustal W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Research, 22, 4673-4680.
http://dx.doi.org/10.1093/nar/22.22.4673 [17] Bavykin, S., Lysov, Y., Zakhariev, V., Kelly, J., Jackman, J., Stahl, D. and Cherni, A. (2004) Use of 16S rRNA, 23S rRNA, and gyrB Gene Sequence Analysis to Determine Phylogenetic Relationships of Bacillus cereus Group Microorganisms. Journal of Clinical Microbiology, 42, 3711-3730.
http://dx.doi.org/10.1128/JCM.42.8.3711-3730.2004 [18] Helgason, E., Okstad, O.E., Caugant, D.A., Johansen, H.A., Fouet, A., Mock, M., Hegna, I. and Kolsto, A.B. (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis One Species on the Basis of Genetic Evidence. Applied and Environmental Microbiology, 66, 2627-2630.
http://dx.doi.org/10.1128/AEM.66.6.2627-2630.2000 [19] Zasada, A. and Gierczyński, R. (2006) Some Bacillus thuringiensis Strains Share rpoB Nucleotide Polymorphisms Also Present in Bacillus anthracis. Journal of Clinical Microbiology, 44, 1606-1607.
http://dx.doi.org/10.1128/JCM.44.4.1606-1607.2006