Type IV Secretion Systems Diversity in the Acidithiobacillus Genus

Abstract:

Dispersal between genomes of certain mobile genetic elements and their gene cargo depends on conjugative type IV secretion systems. In this work, variants of these nanomachines, tra and trb, have been profiled in publicly available genomes of the genus Acidithiobacillus and in a set of relevant strains. Our analyses show that the trb system is of broad distribution, being present in most of the strains analyzed. In turn, the tra type is present in fewer strains of A. ferrooxidans, A. ferrivorans, A. ferriphilus and A. thiooxidans, and generally correlates with the presence of larger ICE in the respective genomes. Herein, sequence conservation, genomic context, integration site and synteny analyses are performed to infer functionality of the T4SS systems of the acidithiobacilli.

• Periodical: Solid State Phenomena (Volume 262)
• Pages: 429-433
• DOI: https://doi.org/10.4028/www.scientific.net/SSP.262.429
• Online since: August 2017
• Authors: Rodrigo Flores-Ríos, Ana Moya-Beltrán, Paulo C. Covarrubias, Lillian G. Acuña, Omar Orellana, Raquel Quatrini*
• Keywords: Acidithiobacillus spp., Conjugation, Conjugative Element, Integrative Element, Type 4 Secretion System

References

[1] D.E. Rawlings, Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microb. Cell Fact. 4 (2005) 13.

DOI: 10.1186/1475-2859-4-13

[2] D.B. Johnson, Biomining-biotechnologies for extracting and recovering metals from ores and waste materials, Curr. Opin. Biotechnol. 30 (2014) 24-31.

DOI: 10.1016/j.copbio.2014.04.008

[3] H. Nuñez, P.C. Covarrubias, A. Moya-Beltrán, F. Issotta, J. Atavales, L.G. Acuña, D.B. Johnson, R. Quatrini, Detection, identification and typing of Acidithiobacillus species and strains: a review, Res. Microbiol. 167 (2016) 555–567.

DOI: 10.1016/j.resmic.2016.05.006

[4] H. Nuñez, A. Moya-Beltrán, P.C. Covarrubias, F. Issotta, J.P. Cardenas, M. Gonzalez, J. Atavales, L.G. Acuña, D.B. Johnson, R. Quatrini, Molecular systematics of the genus Acidithiobacillus: insights into the phylogenetic structure and diversification of the taxon, Front. Microbiol. 8 (2017).

DOI: 10.3389/fmicb.2017.00030

[5] R. Quatrini, F.J. Ossandon, D.E. Rawlings, The flexible genome of acidophilic prokaryotes, in: R. Quatrini, D.B. Johnson (Eds. ), Acidophiles: Life in extremely acidic environments, Caister Academic Press, UK, 2016, pp.199-220.

DOI: 10.21775/9781910190333.12

[6] M. Juhas, D.W. Crook, D.W. Hood, Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence, Cell Microbiol. 10c (2008) 2377-2386.

DOI: 10.1111/j.1462-5822.2008.01187.x

[7] T.D. Lawley, W.A. Klimke, M.J. Gubbins, L.S. Frost, F factor conjugation is a true type IV secretion system, FEMS Microbiol. Lett. 224 (2003) 1–15.

DOI: 10.1016/s0378-1097(03)00430-0

[8] P.J. Christie, K. Atmakuri, V. Krishnamoorthy, S. Jakubowski, E. Cascales, Biogenesis, architecture, and function of bacterial type IV secretion systems, Annu. Rev. Microbiol. 59 (2005) 451–485.

DOI: 10.1146/annurev.micro.58.030603.123630

[9] M. Juhas, D.W. Crook, I.D. Dimopoulou, G. Lunter, R.M. Harding, D.J. Ferguson, D.W. Hood, Novel type IV secretion system involved in propagation of genomic islands, J. Bacteriol. 189 (2007) 761–771.

DOI: 10.1128/jb.01327-06

[10] K. Katoh, D.M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol. 30 (2013) 772–80.

DOI: 10.1093/molbev/mst010

[11] R.C. Souza, G. del Rosario Quispe Saji, M.O. Costa, D.S. Netto, N.C. Lima, C.C. Klein, A.T. Vasconcelos, M.F. Nicolás, AtlasT4SS: a curated database for type IV secretion systems, BMC Microbiol. 12 (2012) 172.

DOI: 10.1186/1471-2180-12-172

[12] M.G. Langille, W. Hsiao, F.S. Brinkman, Detecting genomic islands using bioinformatics approaches, Nat. Rev. Microbiol. 8 (2010) 373-382.

DOI: 10.1038/nrmicro2350

[13] P. Bustamante, M. Tello, O. Orellana, Toxin-antitoxin systems in the mobile genome of Acidithiobacillus ferrooxidans. PLoS One 9 (2014) e112226.

DOI: 10.1371/journal.pone.0112226

[14] L.G. Acuña, J.P. Cardenas, P.C. Covarrubias, J.J. Haristoy, R. Flores, H. Nunez, G. Riadi, A. Shmaryahu, J. Valdes, M. Dopson, D.E. Rawlings, J.F. Banfield, D.S. Holmes, R. Quatrini, Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus, PLoS One 8 (2013).

DOI: 10.1371/journal.pone.0078237

[15] P. Bustamante, P.C. Covarrubias, G. Levicán, A. Katz, P. Tapia, D.S. Holmes, R. Quatrini, O. Orellana, ICE Afe 1, an actively excising genetic element from the biomining bacterium Acidithiobacillus ferrooxidans, J. Mol. Microbiol. Biotechnol. 22(2012).

DOI: 10.1159/000346669

[16] G. Levicán, A. Katz, J. Valdés, R. Quatrini, D.S. Holmes, O. Orellana, A 300 kb genome segment, including a complete set of tRNA genes, is dispensable for Acidithiobacillus ferrooxidans, Adv. Mat. Res. 71-73 (2009) 187-190.

DOI: 10.4028/www.scientific.net/amr.71-73.187

[17] Y. Cui, X. Chen, H. Luo, Z. Fan, J. Luo, S. He, H. Yue, P. Zhang, R. Chen, BioCircos. js: an interactive Circos JavaScript library for biological data visualization on web applications, Bioinformatics. 32 (2016) 11: 1740-2.

DOI: 10.1093/bioinformatics/btw041