Elucidating Sequence and Structural Variations Present in RNase P RNA Ribozyme for the Taxonomy of Leptospira spp.
Main Article Content
Abstract
RNase P RNA (RPR) gene responsible for transcribing tRNA processing ribozyme is an essential single-copy gene present in the genome of all organisms and has been proven to be a reliable genetic marker for the differentiation of species. In the present study, phylogenetic analysis was performed by exploiting sequence and structural variations present in the RPRs to determine the taxa of unidentified leptospires. RPR gene-based phylogeny revealed that serovars of Leptospira borgpetersenii could be bifurcated into distinct subgroups A and B. The saprophytic leptospiral strains were classified into three groups namely saprophytic group I, saprophytic group II and saprophytic group III. The presumed taxonomic positions of leptospiral strains Hampton, LT 2116, M4, 18R, Pond 2020, ZV016, ICFT and L. alexanderi were investigated for the phylogeny using both RPR and secY genes. The strains of L. alexanderi branched out as a separate clade between strains of L. santarosai and L. borgpetersenii. Furthermore, a simple restriction digestion assay was performed for the RPR gene-based differentiation of leptospires. PCR amplification and subsequent restriction digestion of the RPR gene amplified helped to distinguish Leptospira sp. The present research contributes to our understanding of leptospiral taxonomy and provides a valuable tool for species identification in diagnostic applications.
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Copyright Transfer Statement
The copyright of this article is transferred to Current Applied Science and Technology journal with effect if and when the article is accepted for publication. The copyright transfer covers the exclusive right to reproduce and distribute the article, including reprints, translations, photographic reproductions, electronic form (offline, online) or any other reproductions of similar nature.
The author warrants that this contribution is original and that he/she has full power to make this grant. The author signs for and accepts responsibility for releasing this material on behalf of any and all co-authors.
Here is the link for download: Copyright transfer form.pdf
References
Hartskeerl, R.A., Collares-Pereira, M. and Ellis, W.A., 2011. Emergence, control and re-emerging leptospirosis: dynamics of infection in the changing world. Clinical Microbiology and Infectious Diseases, 17(4), 494-501, https://doi.org/10.1111/j.1469-0691.2011.03474.x.
Andre-Fontaine, G., Aviat, F. and Thorin, C., 2015. Waterborne Leptospirosis: Survival and preservation of the virulence of pathogenic Leptospira spp. in fresh water. Current Microbiology, 71(1), 136-142, https://doi.org/10.1007/s00284-015-0836-4.
Casanovas-Massana, A., Pedra, G.G., Wunder Jr., E.A., Diggle, P.J., Begon, M. and Ko, A.I., 2018. Quantification of Leptospira interrogans survival in soil and water microcosms. Applied and Environmental Microbiology, 84(13), https://doi.org/10.1128/AEM.00507-18.
Levett, P.N., 2001. Leptospirosis. Clinical Microbiology Reviews, 14(2), 296-326, https://doi.org/10.1128/CMR.14.2.296-326.2001.
Jiménez, J.I.S., Marroquin, J.L.H., Richards, G.A. and Amin, P., 2018. Leptospirosis: Report from the task force on tropical diseases by the World Federation of Societies of Intensive and Critical Care Medicine. Journal of Critical Care, 43 361-365, https://doi.org/10.1016/j.jcrc.2017.11.005.
Mendoza, M.V. and Rivera, W.L., 2019. Identification of Leptospira spp. from environmental sources in areas with high human leptospirosis incidence in the Philippines. Pathogens and Global Health, 113(3), 109-116, https://doi.org/10.1080/20477724.2019.1607460.
Vincent, A.T., Schiettekatte, O., Goarant, C., Neela, V.K., Bernet, E., Thibeaux, R., Ismail, N., Khalid, M.K.N.M., Amran, F., Masuzawa, T., Nakao, R., Korba, A.A., Bourhy, P., Veyrier, F.J. and Picardeau, M., 2019. Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. PLoS Neglected Tropical Diseases, 13(5), https://doi.org/10.1371/journal.pntd.0007270.
Bourhy, P., Storck, C.H., Theodose, R., Olive, C., Nicolas, M., Hochedez, P., Lamaury, I., Zinini, F., Bremont, S., Landier, A., Cassadou, S., Rosine, J. and Picardeau, M., 2013. Serovar diversity of pathogenic Leptospira circulating in the French West Indies. PLoS Neglected Tropical Diseases, 7(3), https://doi.org/10.1371/journal.pntd.0002114.
Ravishankar, V., Ahmed, A., Sivagnanam, U., Muthuraman, K., Karthikaichamy, A., Wilson, H.A., Devendran, A., Hartskeerl, R.A. and Raj, S.M.L., 2014. Evolution of the RNase P RNA structural domain in Leptospira spp. Research in Microbiology, 165(10), 813-825, https://doi.org/10.1016/j.resmic.2014.10.007.
Guerrier-Takada, C. and Altman, S., 1993. A physical assay for and kinetic analysis of the interactions between M1 RNA and tRNA precursor substrates. Biochemistry, 32(28), 7152-7161.
Frank, D.N. and Pace, N.R., 1998. Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annual Review of Biochemistry, 67, 153-180, https://doi.org/10.1146/annurev.biochem.67.1.153.
Innings, A., Krabbe, M., Ullberg, M. and Herrmann, B., 2005. Identification of 43 Streptococcus species by pyrosequencing analysis of the rnpB gene. Journal of Clinical Microbiology, 43(12), 5983-5991, https://doi.org/10.1128/JCM.43.12.5983-5991.2005.
Täpp, J., Thollesson, M. and Herrmann, B., 2003. Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB. International Journal of Systematic and Evolutionary Microbiology, 53(6), 1861-1871, https://doi.org/10.1099/ijs.0.02639-0.
Peters, I.R., Helps, C.R., McAuliffe, L., Neimark, H., Lappin, M.R., Gruffydd-Jones, T.J., Day, M.J., Hoelzle, L.E., Willi, B., Meli, M., Hofmann-Lehmann, R. and Tasker, S., 2008. RNase P RNA gene (rnpB) phylogeny of Hemoplasmas and other Mycoplasma species. Journal of Clinical Microbiology, 46(5), 1873-1877, https://doi.org/10.1128/JCM.01859-07.
Schön, A., Fingerhut, C. and Hess, W.R., 2002. Conserved and variable domains within divergent RNase P RNA gene sequences of Prochlorococcus strains. International Journal of Systematic and Evolutionary Microbiology, 52(4), 1383-1389, https://doi.org/10.1099/00207713-52-4-1383.
Guglielmini, J., Bourhy, P., Schiettekatte, O., Zinini, F., Brisse, S. and Picardeau, M., 2019. Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Neglected Tropical Diseases, 13(4), https://doi.org/10.1371/journal.pntd.0007374.
Cosate, M.R.V., Sakamoto, T., Mendes, T.A.D.O., Moreira, É.C., da Silva, C.G.R., Brasil, B.S.A.F., Oliveira, C.S.F., de Azevedo, V.A., Ortega, J.M., Leite, R.C. and Haddad, J.P., 2017. Molecular typing of Leptospira interrogans serovar Hardjo isolates from leptospirosis outbreaks in Brazilian livestock. BMC Veterinary Research, 13(1), https://doi.org/10.1186/s12917-017-1081-9.
Leon, A., Pronost, S., Fortier, G., Andre-Fontaine, G. and Leclercq, R., 2010. Multilocus sequence analysis for typing Leptospira interrogans and Leptospira kirschneri. Journal of Clinical Microbiology, 48(2), 581-585, https://doi.org/10.1128/JCM.00543-09.
Ahmed, N., Devi, S.M., Valverde, M.D.L., Vijayachari, P., Machang'u, R.S., Ellis, W.A. and Hartskeerl, R.A., 2006. Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species. Annals of Clinical Microbiology and Antimicrobials, 5, https://doi.org/10.1186/1476-0711-5-28.
Koizumi, N., Muto, M.M., Akachi, S., Okano, S., Yamamoto, S., Horikawa, K., Harada, S., Funatsumaru, S. and Ohnishi, M., 2013. Molecular and serological investigation of Leptospira and leptospirosis in dogs in Japan. Journal of Medical Microbiology, 62(4), 630-636, https://doi.org/10.1099/jmm.0.050039-0.
Goarant, C., Colot, J., Faelchlin, E., Ponchet, M., Soupé-Gilbert, M.-E., Descloux, E. and Gourinat, A.-C., 2014. An exotic case of leptospirosis imported into an endemic area. Travel Medicine and Infectious Disease, 12(2), 198-200, https://doi.org/10.1016/j.tmaid.2013.12.005.
Pagès, F., Kuli, B., Moiton, M.P., Goarant, C. and Jaffar-Bandjee, M.C., 2015. Leptospirosis after a stay in Madagascar. Journal of Travel Medicine, 22(2), 136-139, https://doi.org/10.1111/jtm.12163.
Thibeaux, R., Geroult, S., Benezech, C., Chabaud, S., Soupé-Gilbert, M.-E., Girault, D., Bierque, E. and Goarant, C., 2017. Seeking the environmental source of Leptospirosis reveals durable bacterial viability in river soils. PLoS Neglected Tropical Diseases, 11(2), https://doi.org/10.1371/journal.pntd.0005414.
Han, H.-J., Wen, H.-L., Liu, J.-W., Qin, X.-R., Zhao, M., Wang, L.-J., Luo, L.-M., Zhou, C.-M., Zhu, Y.-L., Qi, R., Li, W.-Q., Yu, H. and Yu, X.-J., 2018. Pathogenic Leptospira species in insectivorous bats, China, 2015. Emerging Infectious Diseases, 24(6), 1123-1126, https://doi.org/10.3201/eid2406.171585.
Mason, M.R., Encina, C., Sreevatsan, S. and Muñoz-Zanzi, C., 2016. Distribution and diversity of pathogenic Leptospira species in peri-domestic surface waters from South Central Chile. PLoS Neglected Tropical Diseases, 10(8), https://doi.org/10.1371/journal.pntd.0004895.
Li, Y. and Altman, S., 2004. In search of RNase P RNA from microbial genomes. RNA, 10(10), 1533-1540, https://doi.org/10.1261/rna.7970404.
Torres-Larios, A., Swinger, K.K., Krasilnikov, A.S., Pan, T. and Mondragón, A., 2005. Crystal structure of the RNA component of bacterial ribonuclease P. Nature, 437, 584-587, https://doi.org/10.1038/nature04074.
Bourhy, P., Collet, L., Lernout, T., Zinini, F., Hartskeerl, R.A., van der Linden, H., Thiberge, J.M., Diancourt, L., Brisse, S., Giry, C., Pettinelli, F. and Picardeau, M., 2012. Human leptospira isolates circulating in Mayotte (Indian Ocean) have unique serological and molecular features. Journal of Clinical Microbiology, 50(2), 307-311, https://doi.org/10.1128/JCM.05931-11.
Bulach, D.M., Zuerner, R.L., Wilson, P., Seemann, T., McGrath, A., Cullen, P.A., Davis, J., Johnson, M., Kuczek, E., Alt, D.P., Peterson-Burch, B., Coppel, R.L., Rood, J.I., Davies, J.K. and Adler, B., 2006. Genome reduction in Leptospira borgpetersenii reflects limited transmission potential. Proceedings of the National Academy of Sciences of the United States of America, 103(39), 14560-14565, https://doi.org/10.1073/pnas.0603979103.
Brenner, D.J., Kaufmann, A.F., Sulzer, K.R., Steigerwalt, A.G., Rogers, F.C. and Weyant, R.S., 1999. Further determination of DNA relatedness between serogroups and serovars in the family Leptospiraceae with a proposal for Leptospira alexanderi sp. nov. and four new Leptospira genomospecies. International Journal of Systematic Bacteriology, 49(2), 839-858, https://doi.org/10.1099/00207713-49-2-839.