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Eukaryotic Cell, November 2008, p. 2012-2016, Vol. 7, No. 11
1535-9778/08/$08.00+0     doi:10.1128/EC.00198-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

African Trypanosomes Contain 5-Methylcytosine in Nuclear DNA ^,

Kevin T. Militello,^1* Ping Wang,² Sangeeta K. Jayakar,¹ Rebecca L. Pietrasik,¹ Christopher D. Dupont,^1, Kristi Dodd,¹ Anthony M. King,¹ and Paul R. Valenti^1,

State University of New York at Geneseo, Department of Biology, Geneseo, New York,¹ Roswell Park Cancer Institute, Pharmacokinetics/Pharmacodynamics Facility, Buffalo, New York²

Received 17 June 2008/ Accepted 2 September 2008

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It is currently unclear if there are modified DNA bases in Trypanosoma brucei other than J-base. We identify herein a cytosine-5 DNA methyltransferase gene and report the presence and location of 5-methylcytosine in genomic DNA. Our data demonstrate that African trypanosomes contain a functional cytosine DNA methylation pathway.

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Experiments from the early 1980s demonstrated that inactive Trypanosoma brucei variant surface glycoprotein (VSG) genes were resistant to digestion by certain restriction enzymes, suggesting the presence of modified DNA bases (2, 18). Searches for the presence of modified DNA bases in T. brucei uncovered J-base and its precursor, 5-hydroxymethyluracil (11, 12). It generally has been assumed that no other modified DNA bases exist in T. brucei.

Since the modified DNA base 5-methylcytosine (5MC) is widespread in prokaryotes and higher eukaryotes, we searched for genes capable of encoding a cytosine-5 DNA methyltransferase (C5-DNA MTase) in T. brucei. TBLASTN was used to search the T. brucei TREU927 nuclear genome sequence, using the Escherichia coli Dcm C5-DNA MTase protein as a query (4, 16). A significant match (E = 1.2 x 10^–20) was found on T. brucei chromosome 3, and we named the locus the TbDMT gene. The TbDMT gene codes for a protein with a predicted molecular mass of 69 kDa, and it is now listed as a putative C5-DNA MTase in GeneDB (www.genedb.org). No other T. brucei C5-DNA MTase homologs were identified by BLAST analyses with the Dcm protein or other queries, suggesting but not proving that T. brucei has a single C5-DNA MTase. The alignment of the predicted TbDMT protein sequence with experimentally validated prokaryotic C5-DNA MTases indicates that TbDMT contains the 10 conserved domains found in all C5-DNA MTases, including the catalytic cysteine residue of domain IV (Fig. 1) (19). The predicted TbDMT protein is more homologous to prokaryotic enzymes than to eukaryotic enzymes with respect to the 10 conserved domains (data not shown). However, TbDMT contains an N-terminal extension that is longer than that of most prokaryotic enzymes, which is a characteristic of the human DNMT1 and DNMT3A/B enzymes (10). Quantitative PCR analysis of RNA from T. brucei bloodstream-form (BF) and procyclic-form (PF) parasites indicates that the TbDMT gene is expressed in both stages. BF parasites have 2.3 (±0.3, which is one standard deviation) times more TbDMT RNA using β-tubulin as a loading control and 1.5 (±0.2) times more TbDMT RNA using 18S rRNA as a loading control, indicating that there is little stage-specific regulation.

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FIG. 1. Multiple-sequence alignment of TbDMT with bacterial C5-DNA MTases. Proteins homologous to TbDMT in the Swiss-Prot database were identified using BLASTP. A multiple-sequence alignment was created with T-Coffee. The sequences (abbreviations and Swiss-Prot/GenBank accession numbers are listed in parentheses) are from Dactylococcopsis salina (Da; P50185 [GenBank] ), a Moraxella species (Msp; P11408 [GenBank] ), Neisseria lactamica (Nl; P50182 [GenBank] ), Haemophilus parainfluenza (Hp; P15446 [GenBank] ), and Escherichia coli (Ec; P0AED9), all of which are experimentally validated C5-DNA MTases. Tb, T. brucei. (A) Domain structure of aligned C5-DNA MTases. Roman numerals above black boxes represent the 10 conserved domains found in all C5-DNA MTases. N represents nonconserved N-terminal extensions, and C represents short, nonconserved C-terminal extensions. (B) Sequence of the 10 conserved domains of the C5-DNA MTases (indicated by Roman numerals). Black shading indicates residues that are identical in all sequences, and gray shading indicates residues that are structurally similar in all sequences. The putative catalytic cysteine residue in domain IV is indicated with an asterisk.

The expression of TbDMT in both PF and BF parasites warranted the examination of DNA from these stages for the presence of 5MC. We began by using a blotting assay with a monoclonal antibody against 5MC (Fig. 2) (9, 15, 17). DNAs from T. brucei and control organisms were treated with sodium hydroxide to remove RNA, spotted onto a nitrocellulose membrane, fixed via baking, and incubated overnight with a 1:5,000 dilution of anti-5MC antibody (Calbiochem). Antibody binding was detected by chemiluminescence after incubation with a 1:10,000 dilution of peroxidase-labeled anti-mouse secondary antibody. The antibody reacted strongly with Homo sapiens DNA from placental tissue and E. coli JM109 DNA (dcm⁺), as they contain 5MC (23, 25). The antibody did not react with DNAs from Saccharomyces cerevisiae or E. coli ER2925 DNA (dcm mutant), as these DNAs lack 5MC (20). These control experiments clearly demonstrate the specificity of the antibody for 5MC. T. brucei PF and BF DNAs both were positive for the presence of 5MC in this assay. The signal intensity for the T. brucei samples was less than that of human and E. coli JM109 DNA in all experiments. The T. brucei DNA signal in this assay is not due to residual RNA, because the DNAs were treated with sodium hydroxide prior to spotting, and purified, DNase-treated T. brucei RNA does not react with the antibody under these conditions (data not shown). These data indicate that 5MC is found in T. brucei genomic DNA.

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FIG. 2. Antibody-mediated detection of 5MC in T. brucei DNA. Various amounts of genomic DNA from S. cerevisiae, H. sapiens, E. coli strain ER2925 (dcm knockout), E. coli strain JM109 (dcm+), T. brucei PF parasites, and T. brucei BF parasites were spotted onto a nitrocellulose membrane. After fixation, the filter was probed with a monoclonal antibody against 5MC. Bound antibody was detected using a horseradish peroxidase-conjugated secondary antibody and chemiluminescence.

The presence of 5MC in T. brucei genomic DNA was confirmed using liquid chromatography-electrospray ionization tandem mass spectrometry analysis according to Song et al. (23). DNA (1 µg) was hydrolyzed to dephosphorylated deoxynucleosides, separated by liquid chromatography, and ionized. Tandem mass spectrometry was utilized to detect the mass/charge ratio of the molecular ion (241.2 atomic mass units) and product ion (126.3 atomic mass units) of 5-methyl-2'-deoxycytidine (5MdC) (Fig. 3). The signal intensity for 5MdC was divided by the intensity of 2'-deoxyguanosine and compared to a standard curve of the same deoxynucleosides. E. coli strain BW25113, a wild-type strain (1), contains 0.99% (±0.33%, which is one standard deviation) 5MdC, which is consistent with previous studies of other E. coli strains (25). DNA from E. coli JW1944-2, a dcm knockout strain (1), displays no detectable 5MdC signal above background. 5MdC was detected in T. brucei PF and BF DNA using this strategy, confirming the detection of 5MC using the blotting assay. The levels of 5MdC in these samples are low and made precise quantification difficult. However, the signal for the two T. brucei samples is at least 0.01% 5MdC, as the limit of detection of the assay is 0.01% 5MdC. Thus, there is a minimum of 1 5MC for every 10,000 cytosines in the T. brucei genome. The mass/charge ratio of the molecular ion and product ion of the modified deoxynucleosides clearly indicates that the base is 5MdC and not 5-methylcytidine (an RNA base) or another modified base that previously has gone undetected.

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FIG. 3. Detection of 5MdC in T. brucei DNA using liquid chromatography-electrospray ionization tandem mass spectrometry. (A) Chromatograph of a standard containing 5'-methyl-2'-deoxycytidine (5MdC) and 2'-deoxyguanosine (dG) at a 1:10 ratio. Multiple-reaction monitoring was used to detect molecular ion/product ions for 5MdC (m/z 242.1/126.3) and dG (m/z 268.1/152.3). Chromatographs of hydrolyzed (B) E. coli BW25113 DNA (dcm+), (C) E. coli JW1944-2 DNA (dcm knockout), (D) T. brucei PF DNA, and (E) T. brucei BF DNA. The molecular ion/product ion data for dG is not shown. The y axis of each graph has a scale appropriate for the sample.

To identify the location of 5MC within the T. brucei genome, an immunoprecipitation strategy was utilized (9, 21). T. brucei PF and BF DNAs (2 µg) were digested with DpnII, and linkers were added to facilitate PCR amplification. DNA was denatured and immunoprecipitated with either an immunoglobulin G1 (IgG1) monoclonal antibody against 5MC or an IgG1 isotype control antibody. DNA-antibody complexes were captured using magnetic beads coated with sheep anti-mouse IgG (Invitrogen), eluted via proteinase K treatment, and briefly amplified using 15 cycles of PCR. A robust PCR signal was obtained from the anti-5MC immunoprecipitates, whereas no PCR signals were detected from the IgG1 isotype control immunoprecipitates or from reactions with unmodified T. brucei DNA (see Fig. S1 in the supplemental material).

PCR products from the anti-5MC immunoprecipitates were inserted into the pGEM-T Easy plasmid (Promega). Plasmids were isolated from randomly selected colonies and analyzed by DNA sequencing. BLASTN analysis was used to search both the T. brucei database at GeneDB and the nonredundant nucleotide collection (nr/nt) of the National Center for Biotechnology Information (Table 1). All immunoprecipitated DNAs were bona fide T. brucei DNAs, as the lowest E values were matches to known T. brucei sequences. All immunoprecipitated DNAs were from the nuclear T. brucei genome. No sequences from mitochondrial maxicircles or minicircles were immunoprecipitated. Several different nuclear loci were present in the immunoprecipitate, which is consistent with the heterogeneous PCR products produced. This demonstrates that 5MC is not restricted to a single locus in T. brucei.

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TABLE 1. T. brucei DNAs containing 5MC

Nonetheless, it is possible that there are clusters of 5MC, as some of the immunoprecipitated DNA sequences correspond to the same gene category. For example, retrotransposon hot spot (RHS) loci were highly represented in this analysis, as 6/65 sequences correspond to these loci. RHS genes form a family of approximately 280 members and code for nuclear proteins of unknown function (5). Approximately 60% of all RHS genes are pseudogenes that often contain the retrotransposons Ingi or RIME (5, 6). RHS expression is repressed by the RNA interference machinery (7). 5MC at RHS loci may be used in conjunction with or in addition to RNA interference to repress the transcription of unwanted RHS pseudogenes and Ingi/RIME retrotransposons, as 5MC has this function in many other organisms (26). In support of the model of retrotransposon silencing, one sequence representing the site-specific retrotransposon SLACS (splice leader associated conserved sequence) also was immunoprecipitated.

VSG loci also were highly represented, as 4/65 sequences represent VSG pseudogenes and 1/65 sequences represents an intergenic region between two VSG pseudogenes. The T. brucei TREU927 genome contains >1,200 VSG genes, and the majority are pseudogenes (3). Evidence suggests that one VSG is expressed at a time in BF parasites from 1 of 20 bloodstream expression (bES) sites, and the expressed VSG can be switched by multiple mechanisms (24). The remaining bES genes are transcriptionally repressed in each stage. In contrast, no VSGs are expressed in PF parasites (24). The mechanism of VSG transcriptional silencing has remained a key question. Recent evidence suggests that proteins that modify chromatin and its associated histones, TbISW1 and DOT1B, play a role in bES silencing (8, 13). Thus, it is possible that 5MC is used in addition to or in conjunction with these proteins to silence the transcription of some or all bES genes and/or pseudogenes in these stages to ensure that only one functional VSG is expressed at a time. This hypothesis is based on the strong correlation of 5MC and heterochromatin-induced transcriptional repression in other organisms (22). Roles for 5MC other than transcriptional repression in T. brucei require consideration as well, since RHS and VSG loci were not the only methylated loci identified, and the transcriptional regulation of house-keeping genes in T. brucei is not thought to exist. Since modified bases in other organisms affect biological processes including genome stability, DNA replication, and DNA repair (14), it is possible that 5MC could do the same in T. brucei. In the future, we aim to identify the locations of 5MC in the T. brucei genome at the nucleotide level, elucidate the function of 5MC, and determine the role of the TbDMT protein in this pathway.

 
We are indebted to Laurie K. Read (SUNY Buffalo) for help in all aspects of the project. We thank Sarah McEvoy and John Fisk for help in cultivating parasites. We thank Lakshmi Pendyala and Joshua Prey at the Roswell Park Cancer Institute Pharmacokinetics/Pharmacodynamics Facility for help with experimental design. We thank Robert D. Simon, Harold Hoops, Stanley Hattman, Sarita Menon, John Fisk, and Devin Chandler-Militello for useful discussions throughout the course of the project and critical analysis of the manuscript.

This work was supported by National Institutes of Health award R15AI074035-01 (K.T.M.) and the Geneseo Foundation.

 
* Corresponding author. Mailing address: State University of New York at Geneseo, Integrated Science Center 341, 1 College Circle, Geneseo, NY 14454. Phone: (585) 245-5312. Fax: (585) 245-5007. E-mail: militello{at}geneseo.edu

Published ahead of print on 12 September 2008.

Supplemental material for this article may be found at http://ec.asm.org/.

Present address: University of Pennsylvania, Department of Pathobiology, Philadelphia, PA.

Present address: University of Rochester Medical Center, Infectious Disease Unit, Rochester, NY.

Top ABSTRACT TEXT REFERENCES

 

1
1. Baba, T., H. C. Huan, K. Datsenko, B. L. Wanner, and H. Mori. 2008. The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. Methods Mol. Biol. 416:183-194.[CrossRef][Medline]
2
2. Bernards, A., N. van Harten-Loosbroek, and P. Borst. 1984. Modification of telomeric DNA in Trypanosoma brucei; a role in antigenic variation? Nucleic Acids Res. 12:4153-4170.[Abstract/Free Full Text]
3
3. Berriman, M., E. Ghedin, C. Hertz-Fowler, G. Blandin, H. Renauld, D. C. Bartholomeu, N. J. Lennard, E. Caler, N. E. Hamlin, and B. Haas, et al. 2005. The genome of the African trypanosome Trypanosoma brucei. Science 309:416-422.[Abstract/Free Full Text]
4
4. Bhagwat, A. S., A. Sohail, and R. J. Roberts. 1986. Cloning and characterization of the dcm locus of Escherichia coli K-12. J. Bacteriol. 166:751-755.[Abstract/Free Full Text]
5
5. Bringaud, F., N. Biteau, S. E. Melville, S. Hez, N. M. El-Sayed, V. Leech, M. Berriman, N. Hall, J. E. Donelson, and T. Baltz. 2002. A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei. Eukaryot. Cell 1:137-151.[Abstract/Free Full Text]
6
6. Bringaud, F., N. Biteau, E. Zuiderwijk, M. Berriman, N. M. El-Sayed, E. Ghedin, S. E. Melville, N. Hall, and T. Baltz. 2004. The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei. Mol. Biol. Evol. 21:520-528.[Abstract/Free Full Text]
7
7. Durand-Dubief, M., S. Absalon, L. Menzer, S. Ngwabyt, K. Ersfeld, and P. Bastin. 2007. The Argonaute protein TbAGO1 contributes to large and mini-chromosome segregation and is required for control of RIME retroposons and RHS pseudogene-associated transcripts. Mol. Biochem. Parasitol. 156:144-153.[CrossRef][Medline]
8
8. Figueiredo, L. M., C. J. Janzen, and G. A. Cross. 2008. A histone methyltransferase modulates antigenic variation in African trypanosomes. PLoS Biol. 6:e161.[CrossRef][Medline]
9
9. Fisher, O., R. Siman-Tov, and S. Ankri. 2004. Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica. Nucleic Acids Res. 32:287-297.[Abstract/Free Full Text]
10
10. Goll, M. G., and T. H. Bestor. 2005. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74:481-514.[CrossRef][Medline]
11
11. Gommers-Ampt, J., J. Lutgerink, and P. Borst. 1991. A novel DNA nucleotide in Trypanosoma brucei only present in the mammalian phase of the life-cycle. Nucleic Acids Res. 19:1745-1751.[Abstract/Free Full Text]
12
12. Gommers-Ampt, J. H., A. J. Teixeira, G. van de Werken, W. J. van Dijk, and P. Borst. 1993. The identification of hydroxymethyluracil in DNA of Trypanosoma brucei. Nucleic Acids Res. 21:2039-2043.[Abstract/Free Full Text]
13
13. Hughes, K., M. Wand, L. Foulston, R. Young, K. Harley, S. Terry, K. Ersfeld, and G. Rudenko. 2007. A novel ISWI is involved in VSG expression site downregulation in African trypanosomes. EMBO J. 26:2400-2410.[CrossRef][Medline]
14
14. Karpf, A. R., and S. Matsui. 2005. Genetic disruption of cytosine DNA methyltransferase enzymes induces chromosomal instability in human cancer cells. Cancer Res. 65:8635-8639.[Abstract/Free Full Text]
15
15. Katoh, M., T. Curk, Q. Xu, B. Zupan, A. Kuspa, and G. Shaulsky. 2006. Developmentally regulated DNA methylation in Dictyostelium discoideum. Eukaryot. Cell 5:18-25.[Abstract/Free Full Text]
16
16. Marinus, M. G., and N. R. Morris. 1973. Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12. J. Bacteriol. 114:1143-1150.[Abstract/Free Full Text]
17
17. Oakeley, E. J., A. Podesta, and J. P. Jost. 1997. Developmental changes in DNA methylation of the two tobacco pollen nuclei during maturation. Proc. Natl. Acad. Sci. USA 94:11721-11725.[Abstract/Free Full Text]
18
18. Pays, E., M. F. Delauw, M. Laurent, and M. Steinert. 1984. Possible DNA modification in GC dinucleotides of Trypanosoma brucei telomeric sequences; relationship with antigen gene transcription. Nucleic Acids Res. 12:5235-5247.[Abstract/Free Full Text]
19
19. Pósfai, J., A. S. Bhagwat, G. Posfai, and R. J. Roberts. 1989. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res. 17:2421-2435.[Abstract/Free Full Text]
20
20. Proffitt, J. H., J. R. Davie, D. Swinton, and S. Hattman. 1984. 5-Methylcytosine is not detectable in Saccharomyces cerevisiae DNA. Mol. Cell. Biol. 4:985-988.[Abstract/Free Full Text]
21
21. Salzberg, A., O. Fisher, R. Siman-Tov, and S. Ankri. 2004. Identification of methylated sequences in genomic DNA of adult Drosophila melanogaster. Biochem. Biophys. Res. Commun. 322:465-469.[CrossRef][Medline]
22
22. Smith, E., and A. Shilatifard. 2007. The A, B, Gs of silencing. Genes Dev. 21:1141-1144.[Free Full Text]
23
23. Song, L., S. R. James, L. Kazim, and A. R. Karpf. 2005. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal. Chem. 77:504-510.[Medline]
24
24. Taylor, J. E., and G. Rudenko. 2006. Switching trypanosome coats: what's in the wardrobe? Trends Genet. 22:614-620.[CrossRef][Medline]
25
25. Vanyushin, B. F., A. N. Belozersky, N. A. Kokurina, and D. X. Kadirova. 1968. 5-Methylcytosine and 6-methylamino-purine in bacterial DNA. Nature 218:1066-1067.[CrossRef][Medline]
26
26. Yoder, J. A., C. P. Walsh, and T. H. Bestor. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13:335-340.[CrossRef][Medline]

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Eukaryotic Cell, November 2008, p. 2012-2016, Vol. 7, No. 11
1535-9778/08/$08.00+0     doi:10.1128/EC.00198-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

This Article Abstract Full Text (PDF) Supplemental material Alert me when this article is cited Alert me if a correction is posted Citation Map Services E-mail this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Militello, K. T. Articles by Valenti, P. R. Search for Related Content PubMed PubMed Citation Articles by Militello, K. T. Articles by Valenti, P. R.