IN SILICO PHYLOGENETIC ANALYSIS, CHEMORECEPTOR AND SIGNAL TRANSDUCTION OF BACTERIAL CONTAMINATION DENTAL UNIT
In Silico Analysis of Bacterial Contamination
Abstract
The importance of patient safety when carrying out dental and oral care processes is essential. However, the high levels of contamination that have been reported in dental units are of particular concern, so it is necessary to identify and study the patterns of bacterial contaminants and the transduction mechanisms of bacterial responses to their environment. This study investigates the diversity of bacterial contamination in dental units, chemotaxtic signals, and pathways from chemoreceptors through in silico approched. In silico research was carried out using several online and offline software tools utilizing a genomic sequence database from bacteria-contaminated with dental units. Phylogenetic analysis of the tree based on the 16s rRNA gene using MEGA 6 software, protein signaling interactions were analyzed using MiST 3.0 (https://mistdb.com/), signal transduction and protein structure (https://pfam.xfam.org/), the role of chemotaxis using interPro Ebi (https://www.ebi.ac.uk/interpro/structure/), dan biological process using Ebi QuickGo (https://www.ebi.ac.uk/QuickGO/). The analysis showed that 58 species of bacterial contamination showed a similarity test > 95%. Chemosensory pathway analysis of P. aeruginosa with a genome length of 6.538 Mbp through 8 signaling mechanism pathways for a total of 48 MCP. Signaling pathways.MCP signaling analysis classes are 24H, 36H, 40H, and 44H, while the identification of MCP classes is grouped based on chemosensory classes, namely CheW, CheA, CheR, CheB, Chev, CheD, and CheZ. The conclusion of this study, the complexity of the chemoreceptor interaction pathway in adapting quickly to the environment.
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Tuttlebee, C. M., O’Donnell, M. J., Keane, C. T., Russell, R. J., Sullivan, D. J., Falkiner, F., & Coleman, D. C. (2002). Effective control of dental chair unit waterline biofilm and marked reduction of bacterial contamination of output water using two peroxide-based disinfectants. Journal of Hospital Infection, 52(3), 192–205. https://doi.org/10.1053/jhin.2002.1282
Ulrich, L. E., Koonin, E. V., & Zhulin, I. B. (2005). One-component systems dominate signal transduction in prokaryotes. In Trends in Microbiology (Vol. 13, Issue 2, pp. 52–56). https://doi.org/10.1016/j.tim.2004.12.006
Wuichet, K., & Zhulin, I. B. (2010). Origins and diversification of a complex signal transduction system in prokaryotes. Science Signaling, 3(128). https://doi.org/10.1126/scisignal.2000724
Alexander, R. P., & Zhulin, I. B. (2007). Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. Proceedings of the National Academy of Sciences of the United States of America, 104(8), 2885–2890. https://doi.org/10.1073/pnas.0609359104
Alkhulaifi, M. M., Alotaibi, D. H., Alajlan, H., & Binshoail, T. (2020). Assessment of nosocomial bacterial contamination in dental unit waterlines: Impact of flushing. Saudi Dental Journal, 32(2), 68–73. https://doi.org/10.1016/j.sdentj.2019.07.003
Binns, D., Dimmer, E., Huntley, R., Barrell, D., O’Donovan, C., & Apweiler, R. (2009). QuickGO: A web-based tool for Gene Ontology searching. Bioinformatics, 25(22), 3045–3046. https://doi.org/10.1093/bioinformatics/btp536
Coleman, D. C., O’Donnell, M. J., Shore, A. C., & Russell, R. J. (2009). Biofilm problems in dental unit water systems and its practical control. Journal of Applied Microbiology, 106(5), 1424–1437. https://doi.org/10.1111/j.1365-2672.2008.04100.x
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., Sonnhammer, E. L. L., Hirsh, L., Paladin, L., Piovesan, D., Tosatto, S. C. E., & Finn, R. D. (2019). The Pfam protein families database in 2019. Nucleic Acids Research, 47(D1), D427–D432. https://doi.org/10.1093/nar/gky995
Elzen, A. S., Altayyar, I. A., Abdalla, A. M., Alsanousi, A., Elzen, G., & Elbreki, M. F. (2016). Prevalence and Antibiotic Susceptibility Pattern of Pseudomonas aeruginosa Isolated from Hospital Environment in South Libya Antibiotic resistance View project Plant extract antimicrobial effect View project Prevalence and Antibiotic Susceptibility Patter. Journal of Advanced Laboratory Research in Biology, 7(2). https://www.researchgate.net/publication/300690714
EMBL-EBI. (2018). Train online - What is genomics? Genomics: An Introduction to EMBL-EBI Resources. https://www.ebi.ac.uk/training/online/course/genomics-introduction-ebi-resources/what-genomics
García-Fontana, C., Lugo, A. C., & Krell, T. (2014). Structural biology: Specificity of the CheR2 methyltransferase in pseudomonas aeruginosa is directed by a C-terminal pentapeptide in the McpB chemoreceptor. Science Signaling, 7(320). https://doi.org/10.1126/scisignal.2004849
García-Fontana, C., Reyes-Darias, J. A., Muñoz-Martínez, F., Alfonso, C., Morel, B., Ramos, J. L., & Krell, T. (2013). High specificity in CheR methyltransferase function: CheR2 of pseudomonas putida is essential for chemotaxis, whereas CheR1 is involved in biofilm formation. Journal of Biological Chemistry, 288(26), 18987–18999. https://doi.org/10.1074/jbc.M113.472605
Ghane, M., & Azimi, Z. (2014). Isolation, Identification and Antimicrobial Susceptibility of Pseudomonas spp. Isolated from Hospital Environment in Tonekabon, North of Iran. Journal of Applied & Environmental Microbiology, 2(4), 97–101. http://pubs.sciepub.com/jaem/2/4/2
Gumerov, V. M., Ortega, D. R., Adebali, O., Ulrich, L. E., & Zhulin, I. B. (2020). MiST 3.0: An updated microbial signal transduction database with an emphasis on chemosensory systems. Nucleic Acids Research, 48(D1), D459–D464. https://doi.org/10.1093/nar/gkz988
Güvener, Z. T., & Harwood, C. S. (2007). Subcellular location characteristics of the Pseudomonas aeruginosa GGDEF protein, WspR, indicate that it produces cyclic-di-GMP in response to growth on surfaces. Molecular Microbiology, 66(6), 1459–1473. https://doi.org/10.1111/j.1365-2958.2007.06008.x
Hajardhini, P., Susilowati, H., & Yulianto, H. D. K. (2020). RONGGA MULUT SEBAGAI RESERVOIR POTENSIAL UNTUK INFEKSI Pseudomonas aeruginosa. ODONTO : Dental Journal, 7(2), 125. https://doi.org/10.30659/odj.7.2.125-133
Huangyutitham, V., Güvener, Z. T., & Harwood, C. S. (2013). Subcellular clustering of the phosphorylated WspR response regulator protein stimulates its diguanylate cyclase activity. MBio, 4(3). https://doi.org/10.1128/mBio.00242-13
Kasi, P. D., Ariandi, & Tenriawaru, E. P. (2019). Identifikasi Bakteri Asam Laktat dari Limbah Cair Sagu dengan Gen 16S rRNA. Majalah Ilmiah Biologi Biosfera, 36(1), 35–40. https://doi.org/10.20884/1.mib.2019.36.1.924
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
Masyeni, S., Sukmawati, H., Siskayani, A. S., Dharmayanti, S., & Sari, K. (2018). Antimicrobial susceptibility pattern of pathogens isolated from various specimens in denpasar-bali: A two years retrospective study. Biomedical and Pharmacology Journal, 11(1), 493–502. https://doi.org/10.13005/bpj/1399
Mokodompit, M. F. M., Wowor, V. N. S., & Mintjelungan, C. N. (2019). Pencegahan dan Pengendalian Infeksi Silang pada Tindakan Ekstraksi Gigi di Poliklinik Gigi Rumah Sakit Pancaran Kasih Manado. Jurnal E-Biomedik, 7(2). https://doi.org/10.35790/ebm.7.2.2019.23878
O’Connor, J. R., Kuwada, N. J., Huangyutitham, V., Wiggins, P. A., & Harwood, C. S. (2012). Surface sensing and lateral subcellular localization of WspA, the receptor in a chemosensory-like system leading to c-di-GMP production. Molecular Microbiology, 86(3), 720–729. https://doi.org/10.1111/mmi.12013
Ortega, D. R., Fleetwood, A. D., Krell, T., Harwood, C. S., Jensen, G. J., & Zhulin, I. B. (2017). Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 114(48), 12809–12814. https://doi.org/10.1073/pnas.1708842114
Tuttlebee, C. M., O’Donnell, M. J., Keane, C. T., Russell, R. J., Sullivan, D. J., Falkiner, F., & Coleman, D. C. (2002). Effective control of dental chair unit waterline biofilm and marked reduction of bacterial contamination of output water using two peroxide-based disinfectants. Journal of Hospital Infection, 52(3), 192–205. https://doi.org/10.1053/jhin.2002.1282
Ulrich, L. E., Koonin, E. V., & Zhulin, I. B. (2005). One-component systems dominate signal transduction in prokaryotes. In Trends in Microbiology (Vol. 13, Issue 2, pp. 52–56). https://doi.org/10.1016/j.tim.2004.12.006
Wuichet, K., & Zhulin, I. B. (2010). Origins and diversification of a complex signal transduction system in prokaryotes. Science Signaling, 3(128). https://doi.org/10.1126/scisignal.2000724
Published
2021-12-27
How to Cite
WARDANA, tirta.
IN SILICO PHYLOGENETIC ANALYSIS, CHEMORECEPTOR AND SIGNAL TRANSDUCTION OF BACTERIAL CONTAMINATION DENTAL UNIT.
Mandala Of Health, [S.l.], v. 14, n. 2, p. 111-123, dec. 2021.
ISSN 2615-6954.
Available at: <http://jos.unsoed.ac.id/index.php/mandala/article/view/5161>. Date accessed: 24 apr. 2024.
doi: https://doi.org/10.20884/1.mandala.2021.14.2.5161.
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