BACKGROUND: The haemoflagellate Trypanosoma lewisi is a kinetoplastid parasite which, as it has been recently reported to cause human disease, deserves increased attention. Characteristic features of all kinetoplastid flagellates are a uniquely structured mitochondrial DNA or kinetoplast, comprised of a network of catenated DNA circles, and RNA editing of mitochondrial transcripts. The aim of this study was to describe the kinetoplast DNA of T. lewisi. METHODS/RESULTS: In this study, purified kinetoplast DNA from T. lewisi was sequenced using high-throughput sequencing in combination with sequencing of PCR amplicons. This allowed the assembly of the T. lewisi kinetoplast maxicircle DNA, which is a homologue of the mitochondrial genome in other eukaryotes. The assembly of 23,745 bp comprises the non-coding and coding regions. Comparative analysis of the maxicircle sequence of T. lewisi with Trypanosoma cruzi, Trypanosoma rangeli, Trypanosoma brucei and Leishmania tarentolae revealed that it shares 78%, 77%, 74% and 66% sequence identity with these parasites, respectively. The high GC content in at least 9 maxicircle genes of T. lewisi (ATPase6; NADH dehydrogenase subunits ND3, ND7, ND8 and ND9; G-rich regions GR3 and GR4; cytochrome oxidase subunit COIII and ribosomal protein RPS12) implies that their products may be extensively edited. A detailed analysis of the non-coding region revealed that it contains numerous repeat motifs and palindromes. CONCLUSIONS: We have sequenced and comprehensively annotated the kinetoplast maxicircle of T. lewisi. Our analysis reveals that T. lewisi is closely related to T. cruzi and T. brucei, and may share similar RNA editing patterns with them rather than with L. tarentolae. These findings provide novel insight into the biological features of this emerging human pathogen.

Canadian Institute for Advanced Research Toronto Canada

Center for Parasitic Organisms State Key Laboratory of Biocontrol School of Life Sciences and Key Laboratory of Tropical Diseases and Control of the Ministry of Education Zhongshan School of Medicine Sun Yat Sen University Guangzhou The People's Republic of China

Ecosystems and Environment Research Centre and Biomedical Research Centre School of Environment and Life Sciences University of Salford Salford UK

Institute of Parasitology Biology Centre Czech Academy of Sciences and Faculty of Science University of South Bohemia České Budějovice Czech Republic

Key Laboratory of Gene Engineering of the Ministry of Education State Key Laboratory of Biocontrol School of Life Sciences Sun Yat Sen University Guangzhou 510275 The People's Republic of China

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Parasit Vectors. 2016 Jan 13;9:15. doi: 10.1186/s13071-016-1297-8. PubMed

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Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, et al. The revised classification of eukaryotes. J Eukaryot Microbiol. 2012;59:429–493. doi: 10.1111/j.1550-7408.2012.00644.x. PubMed DOI PMC

Hoare CA. The trypanosomes of mammals: A zoological monograph. Oxford: Blackwell Scientific Publications; 1972.

Lun ZR, Reid SA, Lai DH, Li FJ. Atypical human trypanosomiasis: a neglected disease or just an unlucky accident? Trends Parasitol. 2009;25:107–108. doi: 10.1016/j.pt.2008.12.001. PubMed DOI

Verma A, Manchanda S, Kumar N, Sharma A, Goel M, Banerjee PS, et al. Trypanosoma lewisi or T. lewisi-like infection in a 37-day-old Indian infant. Am J Trop Med Hyg. 2011;85:221–224. doi: 10.4269/ajtmh.2011.11-0002. PubMed DOI PMC

Lun ZR, Wen YZ, Uzureau P, Lecordier L, Lai DH, Lan YG, et al. Resistance to normal human serum reveals Trypanosoma lewisi as an underestimated human pathogen. Mol Biochem Parasitol. 2015;199:58–61. doi: 10.1016/j.molbiopara.2015.03.007. PubMed DOI

de Sousa MA. On opportunist infections by Trypanosoma lewisi in humans and its differential diagnosis from T. cruzi and T. rangeli. Parasitol Res. 2014;113:4471–4475. doi: 10.1007/s00436-014-4132-1. PubMed DOI

Tang HJ, Lan YG, Wen YZ, Zhang XC, Desquesnes M, Yang TB, et al. Detection of Trypanosoma lewisi from wild rats in Southern China and its genetic diversity based on the ITS1 and ITS2 sequences. Infect Genet Evol. 2012;12:1046–1051. doi: 10.1016/j.meegid.2012.02.018. PubMed DOI

Truc P, Buscher P, Cuny G, Gonzatti MI, Jannin J, Joshi P, et al. Atypical human infections by animal trypanosomes. PLoS Negl Trop Dis. 2013;7 doi: 10.1371/journal.pntd.0002256. PubMed DOI PMC

Benne R. Mitochondrial genes in trypanosomes. Trends Genet. 1985;1:117–121. doi: 10.1016/0168-9525(85)90044-7. DOI

Jensen RE, Englund PT. Network news: the replication of kinetoplast DNA. Ann Rev Microbiol. 2012;66:473–491. doi: 10.1146/annurev-micro-092611-150057. PubMed DOI

Lukeš J, Guilbride DL, Votýpka J, Zíková A, Benne R, Englund PT. Kinetoplast DNA network: evolution of an improbable structure. Eukaryot Cell. 2002;1:495–502. doi: 10.1128/EC.1.4.495-502.2002. PubMed DOI PMC

Simpson L, Neckelmann N, de la Cruz VF, Simpson AM, Feagin JE, Jasmer DP, et al. Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence. J Biol Chem. 1987;262:6182–6196. PubMed

Stuart K. Kinetoplast DNA, mitochondria DNA with a difference. Mol Biochem Parasitol. 1983;9:93–104. doi: 10.1016/0166-6851(83)90103-2. PubMed DOI

Myler PJ, Glick D, Feagin JE, Morales TH, Stuart KD. Structural organization of the maxicircle variable region of Trypanosoma brucei: identification of potential replication origins and topoisomerase II binding sites. Nucl Acids Res. 1993;21:687–694. doi: 10.1093/nar/21.3.687. PubMed DOI PMC

Kannan S, Burger G. Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2. BMC Genomics. 2008;9:455. doi: 10.1186/1471-2164-9-455. PubMed DOI PMC

Ruvalcaba-Trejo LI, Sturm NR. The Trypanosoma cruzi Sylvio X10 strain maxicircle sequence: the third musketeer. BMC Genomics. 2011;12:58. doi: 10.1186/1471-2164-12-58. PubMed DOI PMC

Blum B, Bakalara N, Simpson L. A model for RNA editing in kinetoplastid mitochondria: RNA molecules transcribed from maxicircle DNA provide the edited information. Cell. 1990;60:189–198. doi: 10.1016/0092-8674(90)90735-W. PubMed DOI

Pollard VW, Rohrer SP, Michelotti EF, Hancock K, Hajduk SL. Organization of minicircle genes for guide RNAs in Trypanosoma brucei. Cell. 1990;63:783–790. doi: 10.1016/0092-8674(90)90144-4. PubMed DOI

Sturm NR, Simpson L. Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA. Cell. 1990;61:879–884. doi: 10.1016/0092-8674(90)90198-N. PubMed DOI

Lukeš J, Hashimi H, Zíková A. Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr Genet. 2005;48:277–299. doi: 10.1007/s00294-005-0027-0. PubMed DOI

Simpson L, Sbicego S, Aphasizhev R. Uridine insertion/deletion RNA editing in trypanosome mitochondria: A complex business. RNA. 2003;9:265–276. doi: 10.1261/rna.2178403. PubMed DOI PMC

Verner Z, Basu S, Benz C, Dixit S, Dobáková EFD, Hashimi H, et al. Malleable mitochondrion of Trypanosoma brucei. Int Rev Cell Mol Biol. 2015;315:73–151. doi: 10.1016/bs.ircmb.2014.11.001. PubMed DOI

Alfonzo JD, Thiemann O, Simpson L. The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria. Nucl Acids Res. 1997;25:3571–3759. doi: 10.1093/nar/25.19.3571. PubMed DOI PMC

Messenger LA, Llewellyn MS, Bhattacharyya T, Franzen O, Lewis MD, Ramirez JD, et al. Multiple mitochondrial introgression events and heteroplasmy in Trypanosoma cruzi revealed by maxicircle MLST and next generation sequencing. PLoS Negl Trop Dis. 2012;6 doi: 10.1371/journal.pntd.0001584. PubMed DOI PMC

Baptista CS, Vencio RZ, Abdala S, Carranza JC, Westenberger SJ, Silva MN, et al. Differential transcription profiles in Trypanosoma cruzi associated with clinical forms of Chagas disease: Maxicircle NADH dehydrogenase subunit 7 gene truncation in asymptomatic patient isolates. Mol Biochem Parasitol. 2006;150:236–248. doi: 10.1016/j.molbiopara.2006.08.008. PubMed DOI

Carnes J, Anupama A, Balmer O, Jackson A, Lewis M, Brown R, et al. Genome and phylogenetic analyses of trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty. PLoS Negl Trop Dis. 2015;9:e3404. doi: 10.1371/journal.pntd.0003404. PubMed DOI PMC

Lai DH, Hashimi H, Lun ZR, Ayala FJ, Lukeš J. Adaptations of Trypanosoma brucei to gradual loss of kinetoplast DNA: Trypanosoma equiperdum and Trypanosoma evansi are petite mutants of T. brucei. Proc Natl Acad Sci U S A. 2008;105:1999–2004. doi: 10.1073/pnas.0711799105. PubMed DOI PMC

Lun ZR, Lai DH, Li FJ, Lukeš J, Ayala FJ. Trypanosoma brucei: two steps to spread out from Africa. Trends Parasitol. 2010;26:424–427. doi: 10.1016/j.pt.2010.05.007. PubMed DOI

Bozzola JJ. Conventional specimen preparation techniques for transmission electron microscopy of cultured cells. Meth Mol Biol. 2007;369:1–18. doi: 10.1007/978-1-59745-294-6_1. PubMed DOI

Perez-Morga D, Englund PT. The structure of replicating kinetoplast DNA networks. J Cell Biol. 1993;123:1069–1079. doi: 10.1083/jcb.123.5.1069. PubMed DOI PMC

Lu G, Moriyama EN. Vector NTI, a balanced all-in-one sequence analysis suite. Brief Bioinform. 2004;5:378–388. doi: 10.1093/bib/5.4.378. PubMed DOI

Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–829. doi: 10.1101/gr.074492.107. PubMed DOI PMC

Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008;9:299–306. doi: 10.1093/bib/bbn017. PubMed DOI PMC

Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16:276–277. doi: 10.1016/S0168-9525(00)02024-2. PubMed DOI

Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell BG, et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics. 2008;24:2672–2676. doi: 10.1093/bioinformatics/btn529. PubMed DOI PMC

Hall T. Bioedit, version7.0.0. Distributed by the author. 2004. http://www.mbio.ncsu.edu/BioEdit/bioedit. Accessed 24 December 2015.

Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006;34:W369–373. doi: 10.1093/nar/gkl198. PubMed DOI PMC

Westenberger SJ, Cerqueira GC, El-Sayed NM, Zingales B, Campbell DA, Sturm NR. Trypanosoma cruzi mitochondrial maxicircles display species-and strain-specific variation and a conserved element in the non-coding region. BMC Genomics. 2006;7:60. doi: 10.1186/1471-2164-7-60. PubMed DOI PMC

Maslov DA, Avila HA, Lake JA, Simpson L. Evolution of RNA editing in kinetoplastid protozoa. Nature. 1994;368:345–348. doi: 10.1038/368345a0. PubMed DOI

Simpson L, Wang SH, Thiemann OH, Alfonzo JD, Maslov DA, Avila HA. U-insertion/deletion Edited Sequence Database. Nucl Acids Res. 1998;26:170–176. doi: 10.1093/nar/26.1.170. PubMed DOI PMC

Simpson L. The mitochondrial genome of kinetoplastid protozoa: genomic organization, transcription, replication, and evolution. Ann Rev Microbiol. 1987;41:363–382. doi: 10.1146/annurev.mi.41.100187.002051. PubMed DOI

Hashimi H, Zimmer SL, Ammerman ML, Read LK, Lukeš J. Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex. Trends Parasitol. 2013;29:91–99. doi: 10.1016/j.pt.2012.11.005. PubMed DOI PMC

Stuart KD, Schnaufer A, Ernst NL, Panigrahi AK. Complex management: RNA editing in trypanosomes. Trends Biochem Sci. 2005;30:97–105. doi: 10.1016/j.tibs.2004.12.006. PubMed DOI

Flegontov PN, Strelkova MV, Kolesnikov AA. The Leishmania major maxicircle divergent region is variable in different isolates and cell types. Mol Biochem Parasitol. 2006;146:173–179. doi: 10.1016/j.molbiopara.2005.12.005. PubMed DOI

Borst P, Fase-Fowler F, Hoeijmakers JHJ, Frasch ACC. Variations in maxi-circle and mini-circle sequences in kinetoplast DNAs from different Trypanosoma brucei strains. Biochim Biophys Acta. 1980;610:197–210. doi: 10.1016/0005-2787(80)90001-5. PubMed DOI

Sloof P, de Haan A, Eier W, van Iersel M, Boel E, van Steeg H, Benne R. The nucleotide sequence of the variable region in Trypanosoma brucei completes the sequence analysis of the maxicircle component of mitochondrial kinetoplast DNA. Mol Biochem Parasitol. 1992;56:289–299. doi: 10.1016/0166-6851(92)90178-M. PubMed DOI

Horvath A, Maslov DA, Peters LS, Haviernik P, Wüstenhagen T, Kolesnikov AA. Analysis of the sequence of repeats in divergent regions of maxi-circular DNA from kinetoplasts of Crithidia oncopelti. Mol Biol (Moscow) 1990;24:1539–1548. PubMed

Flegontov PN, Guo Q, Ren L, Strelkova MV, Kolesnikov AA. Conserved repeats in the kinetoplast maxicircle divergent region of Leishmania sp. and Leptomonas seymouri. Mol Genet Genomics. 2006;276:322–333. doi: 10.1007/s00438-006-0145-5. PubMed DOI

Vasil'eva M, Bessolitsina E, Merzlyak E, Kolesnikov A. Identification of the 12S rRNA gene promoter in Leptomonas seymouri mitochondrial DNA. Mol Biol. 2004;38:839–843. doi: 10.1023/B:MBIL.0000049859.42603.47. PubMed DOI

Fuglsang A. Distribution of potential type II restriction sites (palindromes) in prokaryotes. Biochem Biophys Res Commun. 2003;310:280–285. doi: 10.1016/j.bbrc.2003.09.014. PubMed DOI

Wadkins RM. Targeting DNA, secondary structures. Curr Med Chem. 2000;7:1–15. doi: 10.2174/0929867003375461. PubMed DOI

Higgins CF, McLaren RS, Newbury SF. Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review. Gene. 1988;72:3–14. doi: 10.1016/0378-1119(88)90122-9. PubMed DOI

Anez N. Studies on Trypanosoma rangeli Tejera, 1920. IV--A reconsideration of its systematic position. Mem Inst Osw Cruz. 1982;77:405–415. doi: 10.1590/S0074-02761982000400007. PubMed DOI

Stevens JR, Teixeira MM, Bingle LE, Gibson WC. The taxonomic position and evolutionary relationships of Trypanosoma rangeli. Int J Parasitol. 1999;29:749–757. doi: 10.1016/S0020-7519(99)00016-8. PubMed DOI

Ideozu EJ, Whiteoak AM, Tomlinson AJ, Robertson A, Delahay RJ, Hide G. High prevalence of trypanosomes in European badgers detected using ITS-PCR. Parasit & Vect. 2015;8:1–6. doi: 10.1186/s13071-015-1088-7. PubMed DOI PMC

Lizundia R, Newman C, Buesching CD, Ngugi D, Blake D, Sin YW, et al. Evidence for a role of the host-specific flea (Paraceras melis) in the transmission of Trypanosoma (Megatrypanum) pestanai to the European badger. PLoS One. 2011;6 doi: 10.1371/journal.pone.0016977. PubMed DOI PMC

Lun ZR, Lai DH, Wen YZ, Zheng LL, Shen JL, Yang TB, et al. Cancer in the parasitic protozoans Trypanosoma brucei and Toxoplasma gondii. Proc Natl Acad Sci U S A. 2015;112:8835–8842. doi: 10.1073/pnas.1502599112. PubMed DOI PMC

Mitochondrial RNA editing in Trypanoplasma borreli: New tools, new revelations

Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae

Erratum to: Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen

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