Abstract
Multiple toxin–antitoxin (TA) systems are housed in different locations within the bacterial genome and are known to be associated with various cellular processes and stress-related adaptation. In endosymbionts, although, the TA system has scarce occurrence but studies have highlighted its presence in enhancing host–symbiont interactions. Wolbachia, an obligate endosymbiont, has recently been proposed as a biocontrol agent which may be helpful in controlling vector-borne diseases. There are reports suggesting the role of TA system in inducing cytoplasmic incompatibility in case of Wolbachia, however, the underlying mechanism is still not known. The present study, therefore, aims at exploring the diversity of TA system in four novel (sourced from India) and three reference genomes (NCBI) of Wolbachia strains. Interestingly, we found several putative toxins and antitoxins of RelEB family of Type II TA system in these Wolbachia genomes. The results show wMel genome possessed more number of putative TA loci than wRi genome. In addition, searching through the other sequenced Wolbachia genomes in NCBI, a complete absence of TA system was observed in Wolbachia-infected nematodes. The sequence-wide analysis of all the putative RelEB proteins present amongst the Wolbachia endosymbiont and within the free-living bacterial genomes reveal strain-specific similarities and conserved sequences. However, large amount of sequence diversity was observed between Wolbachia and free-living bacteria. Understanding this sequence variation may help shed light on the differences between these two forms of bacteria and could also explain their niche preferences.
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References
Aakre CD, Phung TN, Huang D, Laub MT (2013) A bacterial toxin inhibits DNA replication elongation through a direct interaction with the β sliding clamp. Mol Cell 52(5):617–628
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. JMB 215(3):403–410
Amuzu HE, McGraw EA (2016) Wolbachia-based dengue virus inhibition is not tissue-specific in Aedes aegypti. PLoS Negl Trop Dis 10(11):e0005145
Audoly G, Vincentelli R, Edouard S, Georgiades K, Mediannikov O (2011) Effect of rickettsial toxin VapC on its eukaryotic host. PLoS One 6(10):e26528
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Meyer F (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9(1):75
Boggild A, Sofos N, Andersen KR, Feddersen A, Easter AD, Passmore LA, Brodersen DE (2012) The crystal structure of the intact E. coli RelBE toxin–antitoxin complex provides the structural basis for conditional cooperativity. Structure 20(10):1641–1648
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120
Bourtzis K (2008) Wolbachia-based technologies for insect pest population control. In: Transgenesis and the management of vector-borne disease. Springer, New York, pp 104–113
Brelsfoard CL, Dobson SL (2009) Wolbachia-based strategies to control insect pests and disease vectors. Asia Pac J Mol Biol Biotechnol 17(3):55–63
Charlat S, Hurst GD, Mercot H (2003) Evolutionary consequences of Wolbachia infections. Trends Genet 19(4):217–223
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
Fenn K, Conlon C, Jones M, Quail MA, Holroyd NE, Parkhill J, Blaxter M (2006) Phylogenetic relationships of the Wolbachiaof nematodes and arthropods. PLoS Pathog 2(10):e94
Fernandez-Garcia L, Blasco L, Lopez M, Bou G, García-Contreras R, Wood T, Tomas M (2016) Toxin–antitoxin systems in clinical pathogens. Toxins 8(7):227
Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G (2010) Abundance of type I toxin–antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res 38(11):3743–3759
Gene Ontology Consortium (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32(suppl_1):D258–D261
Gotfredsen M, Gerdes K (1998) The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family. Mol Microbiol 29(4):1065–1076
Hardin C, Pogorelov TV, Luthey-Schulten Z (2002) Ab initio protein structure prediction. Curr Opin Struct Biol 12(2):176–181
Hoffmann AA, Ross PA, Rasic G (2015) Wolbachiastrains for disease control: ecological and evolutionary considerations. Evol Appl 8(8):751–768
Kedzierska B, Hayes F (2016) Emerging roles of toxin–antitoxin modules in bacterial pathogenesis. Molecules 21(6):790
Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874
Leplae R, Geeraerts D, Hallez R, Guglielmini J, Dreze P, Melderen LV (2011) Diversity of bacterial type II toxin–antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res 39(13):5513–5525
Markovski M, Wickner S (2013) Preventing bacterial suicide: a novel toxin–antitoxin strategy. Mol Cell 52(5):611–612
Melderen LV, De Bast MS (2009) Bacterial toxin–antitoxin systems: more than selfish entities? PLoS Genet 5(3):e1000437
Metcalf JA (2014) Evolutionary and functional studies of Wolbachia pipientis and its phage. Dissertation, Vanderbilt University
Miallau L, Jain P, Arbing MA, Cascio D, Phan T, Ahn CJ, Chan S, Chernishof I, Maxson M, Chiang J, Jacobs WR (2013) Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin–antitoxin complexes. Structure 21(4):627–637
Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25(1):126–127
Moreira LA, Iturbe-Ormaetxe I, Jeffery JA, Lu G, Pyke AT, Hedges LM, Rocha BC, Hall-Mendelin S, Day A, Riegler M, Hugo LE (2009) A Wolbachiasymbiont in Aedes aegypti limits infection with dengue, Chikungunya, and Plasmodium. Cell 139(7):1268–1278
Mruk I, Kobayashi I (2013) To be or not to be: regulation of restriction-modification systems and other toxin–antitoxin systems. Nucleic Acids Res 42(1):70–86
Okonechnikov K, Golosova O, Fursov M (2012) UniproUGENE: a unified bioinformatics toolkit. Bioinformatics 28(8):1166–1167
Pandey DP, Gerdes K (2005) Toxin–antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 33(3):966–976
Rocker A, Meinhart A (2016) Type II toxin: antitoxin systems. More than small selfish entities? Curr Genet 62(2):287–290
Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738
Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425
Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5(1):16
Schuster CF, Bertram R (2013) Toxin–antitoxin systems are ubiquitous and versatile modulators of prokaryotic cell fate. FEMS Microbiol Lett 340(2):73–85
Serbus LR, Casper-Lindley C, Landmann F, Sullivan W (2008) The genetics and cell biology of Wolbachia–host interactions. Annu Rev Genet 42:683–707
Singhal K, Khanna R, Mohanty S (2017) Is Drosophila-microbe association species-specific or region specific? A study undertaken involving six Indian Drosophila species. World J Microbiol Biotechnol 33(6):103
Sinkins SP, O’Neill SL (2000) Wolbachia as a vehicle to modify insect populations. In: James AA (ed) Insect transgenesis: methods and applications. CRC Press, Boca Raton, pp 271–287
Socolovschi C, Audoly G, Raoult D (2013) Connection of toxin–antitoxin modules to inoculation eschar and arthropod vertical transmission in Rickettsiales. Comp Immunol Microbiol Infect Dis 36(2):199–209
Takagi H, Kakuta Y, Okada T, Yao M, Tanaka I, Kimura M (2005) Crystal structure of archaeal toxin–antitoxin RelE–RelB complex with implications for toxin activity and antitoxin effects. Nat Struct Mol Biol 12(4):327
Tamura K, Subramanian S, Kumar S (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21(1):36–44
Tsilibaris V, Maenhaut-Michel G, Mine N, Melderen LV (2007) What is the benefit to Escherichia coli of having multiple toxin–antitoxin systems in its genome? J Bacteriol 189(17):6101–6108
Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30(9):418–426
Van den Hurk AF, Hall-Mendelin S, Pyke AT, Frentiu FD, McElroy K, Higgs S, O’Neill SL (2012) Impact of Wolbachia on infection with chikungunya and yellow fever viruses in the mosquito vector Aedes aegypti. PLoS Negl Trop Dis 6(11):e1892
Venkatasubramanian KV (2017) India to study bacteria’s impact on mosquito-spread disease viruses. News Week 95(15):17
Wang X, Wood TK (2011) Toxin–antitoxin systems influence biofilm and persister cell formation and the general stress response. Appl Environ Microbiol 77(16):5577–5583
Werren JH (1997) Biology of Wolbachia. Annu Rev Entomol 42(1):587–609
Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, Wiegand C (2004) Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2(3):e69
Xi Z, Khoo CC, Dobson SL (2006) Interspecific transfer of Wolbachia into the mosquito disease vector Aedes albopictus. Proc R Soc B Biol Sci 273(1592):1317–1322
Yamaguchi Y, Park JH, Inouye M (2011) Toxin–antitoxin systems in bacteria and archaea. Annu Rev Genet 45:61–79
Yang J, Zhang Y (2015) Protein structure and function prediction using I-TASSER. Curr Protoc Bioinform 52:5–8
Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015) The I-TASSER suite: protein structure and function prediction. Nat Methods 12:7–8
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829
Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinform 9:40
Zhang D, De Souza RF, Anantharaman V, Iyer LM, Aravind L (2012). Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct 7(1):18
Zhou XF, Li ZX (2016) Establishment of the cytoplasmic incompatibility-inducing Wolbachia strain wMel in an important agricultural pest insect. Sci Rep 6:39200
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucleic Acids Res 39(suppl_2):W347–W352
Acknowledgements
The authors thank the Eurofins Genomics India Pvt Ltd. for providing WGS service. SM thanks to DST for bearing the sequencing expense. KS thanks CSIR for providing JRF-Fellowship. The authors would like to thank Dr Santosh Dev for english grammar editing. The authors also thank the Vice Chancellor, JIIT for providing infra-structure facilities for conducting this work.
Data accessibility
WGS of wRi_AMD: Accession Number: MSYL00000000 (BioProject Number: PRJNA344708; Biosample Number: SAMNO5862085).
WGS of wRi_KL: Accession Number: MKIF00000000 (BioProject Number: PRJNA344708; Biosample Number: SAMNO5831929).
WGS of wMel_KL: Accession Number: MLZJ00000000 (BioProject Number: PRJNA349098; Biosample Number: SAMNO592097).
WGS of wMel_AMD: Accession Number: MNCG00000000 (BioProject Number: PRJNA344708; Biosample Number: SAMNO5932998).
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Singhal, K., Mohanty, S. Comparative genomics reveals the presence of putative toxin–antitoxin system in Wolbachia genomes. Mol Genet Genomics 293, 525–540 (2018). https://doi.org/10.1007/s00438-017-1402-5
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DOI: https://doi.org/10.1007/s00438-017-1402-5