Abstract
We present a computational method to identify conjugative systems in plasmids and chromosomes using the CONJscan module of MacSyFinder. The method relies on the identification of the protein components of the system using hidden Markov model profiles and then checking that the composition and genetic organization of the system is consistent with that expected from a conjugative system. The method can be assessed online using the Galaxy workflow or locally using a standalone software. The latter version allows to modify the models of the module (i.e., to change the expected components, their number, and their organization).
CONJscan identifies conjugative systems, but when the mobile genetic element is integrative (ICE), one often also wants to delimit it from the chromosome. We present a method, with a script, to use the results of CONJscan and comparative genomics to delimit ICE in chromosomes. The method provides a visual representation of the ICE location. Together, these methods facilitate the identification of conjugative elements in bacterial genomes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Grohmann E, Muth G, Espinosa M (2003) Conjugative plasmid transfer in gram-positive bacteria. Microbiol Mol Biol Rev 67:277–301
Smillie C, Pilar Garcillan-Barcia M, Victoria Francia M, Rocha EPC, de la Cruz F (2010) Mobility of plasmids. Microbiol Mol Biol Rev 74:434–452
de la Cruz F, Frost LS, Meyer RJ, Zechner E (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 34:18–40
Garcillan-Barcia MP, Francia MV, de la Cruz F (2009) The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 33:657–687
Guglielmini J, de la Cruz F, Rocha EPC (2013) Evolution of conjugation and type IV secretion systems. Mol Biol Evol 30:315–331
Abby SS, Neron B, Menager H, Touchon M, Rocha EP (2014) MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One 9:e110726
Guglielmini J, Neron B, Abby SS, Garcillan-Barcia MP, la Cruz FD, Rocha EP (2014) Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. Nucleic Acids Res 42:5715–5727
Abby SS, Cury J, Guglielmini J, Neron B, Touchon M, Rocha EP (2016) Identification of protein secretion systems in bacterial genomes. Sci Rep 6:23080
Coluzzi C, Guedon G, Devignes MD, Ambroset C, Loux V, Lacroix T, Payot S, Leblond-Bourget N (2017) A glimpse into the world of integrative and mobilizable elements in Streptococci reveals an unexpected diversity and novel families of mobilization proteins. Front Microbiol 8:443
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421
Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195
Katoh K, Toh H (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26:1899–1900
Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224
Miele V, Penel S, Duret L (2011) Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics 12:116
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461
White EP, Baldridge E, Brym ZT, Locey KJ, McGlinn DJ, Supp SR (2013) Nine simple ways to make it easier to (re) use your data. Ideas Ecol Evol 6:1–10
Cury J, Touchon M, Rocha EPC (2017) Integrative and conjugative elements and their hosts: composition, distribution and organization. Nucleic Acids Res 45:8943–8956
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069
Bellanger X, Morel C, Gonot F, Puymege A, Decaris B, Guedon G (2011) Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture. Mol Microbiol 81:912–925
Alvarez-Martinez CE, Christie PJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73:775–808
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF (2016) A new view of the tree of life. Nat Microbiol 1:16048
Abby SS, Rocha EPC (2017) Identification of protein secretion systems in bacterial genomes using MacSyFinder. Methods Mol Biol 1615:1–21
Acknowledgments
This work was supported by the ANR MAGISBAC project [ANR-14-CE10-0007], the CNRS, and the Institut Pasteur. We thank the collaborators who have worked with us on this topic in the last decade, notably Fernando de la Cruz, Chris Smillie, Marie Touchon, Maria Pilar Garcillan-Barcia, and Julien Guglielmini.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Cury, J., Abby, S.S., Doppelt-Azeroual, O., Néron, B., Rocha, E.P.C. (2020). Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan. In: de la Cruz, F. (eds) Horizontal Gene Transfer. Methods in Molecular Biology, vol 2075. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9877-7_19
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9877-7_19
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9876-0
Online ISBN: 978-1-4939-9877-7
eBook Packages: Springer Protocols