Genome analysis of Lysinibacillus sphaericus isolate 6.2 pathogenic to Culex quinquefasciatus Say, 1823 (Diptera: Culicidae)
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Abstract. Viersanova A, Purwanto H. 2021. Genome analysis of Lysinibacillus sphaericus isolate 6.2 pathogenic to Culex quinquefasciatus Say, 1823 (Diptera: Culicidae). Biodiversitas 22: 5211-5222. Lysinibacillus sphaericus is an entomopathogenic bacteria that is specific to vector mosquitoes, especially Culex spp., and Anopheles spp., so it has been widely used as a bioinsecticide. L. sphaericus has a wide variation of toxicity efficiencies, which have led to continuous exploration of new isolates with higher toxicity and a new toxin to deal with resistance problems. This study aimed to identify the genomic characteristics and toxin characteristics of isolate 6.2 based on whole genome analysis and analyze the identification of isolate 6.2. Isolate 6.2 was previously obtained from rhizosphere in Yogyakarta. To analyze the genome and toxins, the NGS technique was used and then the analysis was carried out using a couple of freely available bioinformatics tools. Molecular identification was carried out with the 16SrRNA gene and the relationship was analyzed by reconstructing the phylogenetic tree using Neighbours-Joining. The genomic analysis of isolate 6.2 showed good results with G+C content and genome size that matched the reference genome of L. sphaericus. The result of the 16SrRNA gene blasting showed that the closest related gene of isolate 6.2 is L. fusiformis (NR_042072.1). However, the reconstructed phylogenetic tree did not show the formation of clusters according to the species. Toxin analysis indicates that isolate 6.2 has Mtx, s-layer protein, hemolysin, and chitin-binding protein genes. All of which are known to be associated with the toxicity of L. sphaericus to binary toxin resistant population of Culex quinquefasciatus.
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References
Aachmann, F. L., Sørlie, M., Skjåk-Bræk, G., Eijsink, V. G. H., & Vaaje-Kolstad, G. 2012. NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions. Proceedings of the National Academy of Sciences of the United States of America, 109(46): 18779–18784. https://doi.org/10.1073/pnas.1208822109
Allievi, M. C., Palomino, M. M., Acosta, M. P., Lanati, L., Ruzal, S. M., & Sánchez-Rivas, C. 2014. Contribution of S-layer proteins to the mosquitocidal activity of Lysinibacillus sphaericus. PLoS ONE, 9(10). https://doi.org/10.1371/journal.pone.0111114
Andreeva, Z. I., Nesterenko, V. F., Fomkina, M. G., Ternovsky, V. I., Suzina, N. E., Bakulina, A. Y., Solonin, A. S., & Sineva, E. V. 2007. The properties of Bacillus cereus hemolysin II pores depend on environmental conditions. Biochimica et Biophysica Acta - Biomembranes, 1768(2): 253–263. https://doi.org/10.1016/j.bbamem.2006.11.004
Arkin, A. P., Cottingham, R. W., Henry, C. S., Harris, N. L., Stevens, R. L., Maslov, S., Dehal, P., Ware, D., Perez, F., Canon, S., Sneddon, M. W., Henderson, M. L., Riehl, W. J., Murphy-Olson, D., Chan, S. Y., Kamimura, R. T., Kumari, S., Drake, M. M., Brettin, T. S., … Yu, D. 2018. KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36(7): 566–569. https://doi.org/10.1038/nbt.4163
Baida, G. E., & Kuzmin, N. P. 1996. Mechanism of action of hemolysin III from Bacillus cereus. Biochimica et Biophysica Acta - Biomembranes, 1284(2): 122–124. https://doi.org/10.1016/S0005-2736(96)00168-X
Berry, C. 2012. The bacterium, Lysinibacillus sphaericus, as an insect pathogen. Journal of Invertebrate Pathology, 109(1): 1–10. https://doi.org/10.1016/j.jip.2011.11.008
Broadwell, A. H., Baumann, L., & Baumann, P. 1990. The 42- and 51-kilodalton mosquitocidal proteins of Bacillus sphaericus 2362: Construction of recombinants with enhanced expression and in vivo studies of processing and toxicity. Journal of Bacteriology, 172(5): 2217–2223. https://doi.org/10.1128/jb.172.5.2217-2223.1990
Burgos, Y., & Beutin, L. (2010). Common origin of plasmid encoded alpha-hemolysin genes in Escherichia coli. BMC Microbiology, 10. https://doi.org/10.1186/1471-2180-10-193
Charles, J. F., Nielsen-LeRoux, C., & Delécluse, A. 1996. Bacillus sphaericus toxins: Molecular biology and mode of action. Annual Review of Entomology, 41(1): 451–472. https://doi.org/10.1146/annurev.en.41.010196.002315
Clark, M. A., & Baumann, P. 1991. Modification of the Bacillus sphaericus 51- and 42-kilodalton mosquitocidal proteins: Effects of internal deletions, duplications, and formation of hybrid proteins. Applied and Environmental Microbiology, 57(1): 267–271. https://doi.org/10.1128/aem.57.1.267-271.1991
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. 2004. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Research, 14(7): 1394–1403. https://doi.org/10.1101/gr.2289704
Dussán, J., Andrade, D., Lozano, L., & Vanegas, S. 2002. Caracterización fisiológica y genética de cepas nativas de Bacillus sphaericus. Revista Colombiana de Biotecnología, 4(1): 89–99. http://www.revistas.unal.edu.co/index.php/biotecnologia/article/view/30097
Eijsink, V. G. H., Petrovic, D., Forsberg, Z., Mekasha, S., Røhr, Å. K., Várnai, A., Bissaro, B., & Vaaje-Kolstad, G. 2019. On the functional characterization of lytic polysaccharide monooxygenases (LPMOs). Biotechnology for Biofuels, 12(1): 1–16. https://doi.org/10.1186/s13068-019-1392-0
Frederiksen, R. F., Paspaliari, D. K., Larsen, T., Storgaard, B. G., Larsen, M. H., Ingmer, H., Palcic, M. M., & Leisner, J. J. 2013. Bacterial chitinases and chitin-binding proteins as virulence factors. Microbiology (United Kingdom), 159(PART 5): 833–847. https://doi.org/10.1099/mic.0.051839-0
Hernández-Santana, A., Gómez-Garzón, C., & Dussán, J. 2016. Complete genome sequence of Lysinibacillus sphaericus WHO reference strain 2362. Genome Announcements, 4(3): 9–10. https://doi.org/10.1128/genomeA.00545-16
Hu, X., Fan, W., Han, B., Liu, H., Zheng, D., Li, Q., Dong, W., Yan, J., Gao, M., Berry, C., & Yuan, Z. 2008. Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related bacillus species. Journal of Bacteriology, 190(8): 2892–2902. https://doi.org/10.1128/JB.01652-07
Illumina Inc. 2017. Illumina sequencing introduction. Illumina Sequencing Introduction, October: 1–8. https://www.illumina.com/documents/products/illumina_sequencing_introduction.pdf
Jeong, H., Jeong, D. E., Sim, Y. M., Park, S. H., & Choi, S. K. 2013. Genome sequence of Lysinibacillus sphaericus strain KCTC 3346T. Genome Announcements, 1(4): 4–5. https://doi.org/10.1128/genomeA.00625-13
Jones, G. W., Nielsen?Leroux, C., Yang, Y., Yuan, Z., Fiúza Dumas, V., Monnerat, R. G., & Berry, C. 2007. A new Cry toxin with a unique two?component dependency from Bacillus sphaericus . The FASEB Journal, 21(14): 4112–4120. https://doi.org/10.1096/fj.07-8913com
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2): 111–120. https://doi.org/10.1007/BF01731581
Krauthammer, M., Rzhetsky, A., Morozov, P., & Friedman, C. 2000. Using BLAST for identifying gene and protein names in journal articles. Gene, 259(1–2): 245–252. https://doi.org/10.1016/S0378-1119(00)00431-5
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
Labourel, A., Frandsen, K. E. H., Zhang, F., Brouilly, N., Grisel, S., Haon, M., Ciano, L., Ropartz, D., Fanuel, M., Martin, F., Navarro, D., Rosso, M. N., Tandrup, T., Bissaro, B., Johansen, K. S., Zerva, A., Walton, P. H., Henrissat, B., Leggio, L. Lo, & Berrin, J. G. (2020). A fungal family of lytic polysaccharide monooxygenase-like copper proteins. Nature Chemical Biology, 16(3): 345–350. https://doi.org/10.1038/s41589-019-0438-8
Langmead, B., & Salzberg, S. L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4): 357–359. https://doi.org/10.1038/nmeth.1923
Lekakarn, H., Promdonkoy, B., & Boonserm, P. 2015. Interaction of Lysinibacillus sphaericus binary toxin with mosquito larval gut cells: Binding and internalization. Journal of Invertebrate Pathology, 132: 125–131. https://doi.org/10.1016/j.jip.2015.09.010
Lozano, L. C., Ayala, J. A., & Dussán, J. 2011. Lysinibacillus sphaericus S-layer protein toxicity against Culex quinquefasciatus. Biotechnology Letters, 33(10): 2037–2041. https://doi.org/10.1007/s10529-011-0666-9
Manjeet, K., Purushotham, P., Neeraja, C., & Podile, A. R. 2013. Bacterial chitin binding proteins show differential substrate binding and synergy with chitinases. Microbiological Research, 168(7): 461–468. https://doi.org/10.1016/j.micres.2013.01.006
MicrobesNg. n.d.. MicrobesNg Methods Document. Microbesng.Com.
MicrobesNg. 2018. Preparing stock tubes for MicrobesNG. 6–7.
Newell, P. D., Roco, C. A., Fricker, A. D., Merkel, S. M., & Chandrangsu, P. 2013. A Small-Group Activity Introducing the Use and Interpretation of BLAST. Journal of Microbiology & Biology Education, 14(2): 238–243. https://doi.org/10.1128/jmbe.v14i2.637
Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A. R., Xia, F., & Stevens, R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research, 42(D1): 206–214. https://doi.org/10.1093/nar/gkt1226
Peña-Montenegro, T. D., Lozano, L., & Dussán, J. 2015. Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5. Standards in Genomic Sciences, 10(FEBRUARY). https://doi.org/10.1186/1944-3277-10-2
Quick, V. S., & Sikela, J. n.d.. Percent Identity of Genomic DNA and Amino Acid Sequences. Center for Academic Research and Training in Anthropogeny. Retrieved March 1, 2021, from https://carta.anthropogeny.org/moca/topics/percent-identity-genomic-dna-and-amino-acid-sequences#:~:text=Percent identity refers to a,to a degree reflects relatedness.
Rahman, A., Nahar, N., Jass, J., Olsson, B., & Mandal, A. 2016. Complete genome sequence of Lysinibacillus sphaericus B1-CDA, a bacterium that accumulates arsenic. Genome Announcements, 4(1): 1–3. https://doi.org/10.1128/genomeA.00999-15
Rey, A., Silva-Quintero, L., & Dussán, J. 2016. Complete genome sequence of the larvicidal bacterium Lysinibacillus sphaericus strain OT4b.25. Genome Announcements, 4(3), 10–11. https://doi.org/10.1128/genomeA.00257-16
Rojas-Pinzón, P. A., & Dussán, J. 2017. Contribution of Lysinibacillus sphaericus hemolysin and chitin-binding protein in entomopathogenic activity against insecticide resistant Aedes aegypti. World Journal of Microbiology and Biotechnology, 33(10) https://doi.org/10.1007/s11274-017-2348-9
Rosselló-Mora, R., & Amann, R. 2001. The species concept for prokaryotes. FEMS Microbiology Reviews, 25(1): 39–67. https://doi.org/10.1016/S0168-6445(00)00040-1
Seemann, T. 2014. Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30(14): 2068–2069. https://doi.org/10.1093/bioinformatics/btu153
Sogandi, S. 2018. Biologi Molekuler: Identifikasi Bakteri Secara Molekuler (Issue July). Universitas 17 Agustus 1945. [Indonesia]
Suginta, W., Sirimontree, P., Sritho, N., Ohnuma, T., & Fukamizo, T. 2016. The chitin-binding domain of a GH-18 chitinase from Vibrio harveyi is crucial for chitin-chitinase interactions. International Journal of Biological Macromolecules, 93: 1111–1117. https://doi.org/10.1016/j.ijbiomac.2016.09.066
Wang, X., King Jordan, I., & Mayer, L. W. 2014. A Phylogenetic Perspective on Molecular Epidemiology. In Molecular Medical Microbiology: Second Edition (Vols. 1–3). Elsevier Ltd. https://doi.org/10.1016/B978-0-12-397169-2.00029-9
Woese, C. R. 1987. Bacterial evolution. Microbiological Reviews, 51(2): 221–271. https://doi.org/0146-0749/87/020221-51$02.00/0
Wong, E., Vaaje-Kolstad, G., Ghosh, A., Hurtado-Guerrero, R., Konarev, P. V., Ibrahim, A. F. M., Svergun, D. I., Eijsink, V. G. H., Chatterjee, N. S., & van Aalten, D. M. F. 2012. The Vibrio cholerae colonization factor GbpA possesses a modular structure that governs binding to different host surfaces. PLoS Pathogens, 8(1): 1–13. https://doi.org/10.1371/journal.ppat.1002373
Yan, W., Xiao, X., & Zhang, Y. 2017. Complete genome sequence of Lysinibacillus sphaericus LMG 22257, a strain with ureolytic activity inducing calcium carbonate precipitation. Journal of Biotechnology, 246: 33–35. https://doi.org/10.1016/j.jbiotec.2017.02.016
Yousten, A. A., & Davidson, E. W. 1982. Ultrastructural Analysis of Spores and Parasporal Crystals Formed by Bacillus sphaericus 2297. Microbiology, 44(6): 1449–1455.
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