Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Trypanosoma brucei metabolism is under circadian control


The Earth's rotation forced life to evolve under cyclic day and night environmental changes. To anticipate such daily cycles, prokaryote and eukaryote free-living organisms evolved intrinsic clocks that regulate physiological and behavioural processes. Daily rhythms have been observed in organisms living within hosts, such as parasites. Whether parasites have intrinsic molecular clocks or whether they simply respond to host rhythmic physiological cues remains unknown. Here, we show that Trypanosoma brucei, the causative agent of human sleeping sickness, has an intrinsic circadian clock that regulates its metabolism in two different stages of the life cycle. We found that, in vitro, 10% of genes in T. brucei are expressed with a circadian rhythm. The maximum expression of these genes occurs at two different phases of the day and may depend on a post-transcriptional mechanism. Circadian genes are enriched in cellular metabolic pathways and coincide with two peaks of intracellular adenosine triphosphate concentration. Moreover, daily changes in the parasite population lead to differences in suramin sensitivity, a drug commonly used to treat this infection. These results demonstrate that parasites have an intrinsic circadian clock that is independent of the host, and which regulates parasite biology throughout the day.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: T. brucei has a circadian transcriptome in two stages of the life cycle, mammalian bloodstream and insect procyclic forms.
Figure 2: Circadian expression is temperature-compensated and detected in vivo during a mouse infection.
Figure 3: T. brucei cycling gene expression is post-transcriptionally regulated.
Figure 4: The T. brucei circadian transcriptome regulates metabolism-related genes.
Figure 5: The T. brucei circadian transcriptome affects the sensitivity of the parasite to stresses.


  1. Young, M. W. & Kay, S. A. Time zones: a comparative genetics of circadian clocks. Nat. Rev. Genet. 2, 702–715 (2001).

    Article  CAS  Google Scholar 

  2. Rosbash, M. The implications of multiple circadian clock origins. PLoS Biol. 7, e1000062 (2009).

    Article  Google Scholar 

  3. Bell-Pedersen, D. et al. Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat. Rev. Genet. 6, 544–556 (2005).

    Article  CAS  Google Scholar 

  4. Welsh, D. K., Yoo, S. H., Liu, A. C., Takahashi, J. S. & Kay, S. A. Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Curr. Biol. 14, 2289–2295 (2004).

    Article  CAS  Google Scholar 

  5. Balsalobre, A., Damiola, F. & Schibler, U. A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell 93, 929–937 (1998).

    Article  CAS  Google Scholar 

  6. Buhr, E. D., Yoo, S. H. & Takahashi, J. S. Temperature as a universal resetting cue for mammalian circadian oscillators. Science 330, 379–385 (2010).

    Article  CAS  Google Scholar 

  7. Refinetti, R. & Menaker, M. The circadian rhythm of body temperature. Physiol. Behav. 51, 613–637 (1992).

    Article  CAS  Google Scholar 

  8. Zhang, R., Lahens, N. F., Ballance, H. I., Hughes, M. E. & Hogenesch, J. B. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc. Natl Acad. Sci. USA 111, 16219–16224 (2014).

    Article  CAS  Google Scholar 

  9. van der Linden, A. M. et al. Genome-wide analysis of light- and temperature-entrained circadian transcripts in Caenorhabditis elegans. PLoS Biol. 8, e1000503 (2010).

    Article  Google Scholar 

  10. Hughes, M. E., Grant, G. R., Paquin, C., Qian, J. & Nitabach, M. N. Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res. 22, 1266–1281 (2012).

    Article  CAS  Google Scholar 

  11. Mony, B. M. et al. Genome-wide dissection of the quorum sensing signalling pathway in Trypanosoma brucei. Nature 505, 681–685 (2013).

    Article  Google Scholar 

  12. Dejung, M. et al. Quantitative proteomics uncovers novel factors involved in developmental differentiation of Trypanosoma brucei. PLoS Pathog. 12, e1005439 (2016).

    Article  Google Scholar 

  13. Kabani, S. et al. Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei. BMC Genomics 10, 427 (2009).

    Article  Google Scholar 

  14. Trindade, S. et al. Trypanosoma brucei parasites occupy and functionally adapt to the adipose tissue in mice. Cell Host Microbe 19, 837–848 (2016).

    Article  CAS  Google Scholar 

  15. Nilsson, D. et al. Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei. PLoS Pathog. 6, e1001037 (2010).

    Article  Google Scholar 

  16. Koike, N. et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338, 349–354 (2012).

    Article  CAS  Google Scholar 

  17. Hoffmann, J. et al. Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells. PLoS ONE 9, e102238 (2014).

    Article  Google Scholar 

  18. Hughes, M. E. et al. Harmonics of circadian gene transcription in mammals. PLoS Genet. 5, e1000442 (2009).

    Article  Google Scholar 

  19. Izumo, M. et al. Differential effects of light and feeding on circadian organization of peripheral clocks in a forebrain Bmal1 mutant. eLife 3, e04617 (2014).

    Article  Google Scholar 

  20. Reddy, A. B. & Rey, G. Metabolic and nontranscriptional circadian clocks: eukaryotes. Annu. Rev. Biochem. 83, 165–189 (2014).

    Article  CAS  Google Scholar 

  21. Figueiredo, L. M., Cross, G. A. & Janzen, C. J. Epigenetic regulation in African trypanosomes: a new kid on the block. Nat. Rev. Microbiol. 7, 504–513 (2009).

    Article  CAS  Google Scholar 

  22. Clayton, C. E. Life without transcriptional control? From fly to man and back again. EMBO J. 21, 1881–1888 (2002).

    Article  CAS  Google Scholar 

  23. Asio, S. M., Simonsen, P. E. & Onapa, A. W. Analysis of the 24-h microfilarial periodicity of Mansonella perstans. Parasitol. Res. 104, 945–948 (2009).

    Article  Google Scholar 

  24. Lindstrom, K. M. et al. Feather mites and internal parasites in small ground finches (Geospiza fuliginosa, Emberizidae) from the Galapagos Islands (Equador). J. Parasitol. 95, 39–45 (2009).

    Article  Google Scholar 

  25. Gryczynska, A., Dolnik, O. & Mazgajski, T. D. Parasites of chaffinch (Fringilla coelebs) population. Part I. Coccidia (Protozoa, Apicomplexa). Wiad. Parazytol. 45, 495–500 (1999).

    CAS  PubMed  Google Scholar 

  26. Dolnik, O. V., Metzger, B. J. & Loonen, M. J. Keeping the clock set under the midnight sun: diurnal periodicity and synchrony of avian Isospora parasites cycle in the high Arctic. Parasitology 138, 1077–1081 (2011).

    Article  Google Scholar 

  27. Hawking, F. The clock of the malaria parasite. Sci. Am. 222, 123–131 (1970).

    Article  CAS  Google Scholar 

  28. Thaiss, C. A. et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 159, 514–529 (2014).

    Article  CAS  Google Scholar 

  29. Zarrinpar, A., Chaix, A., Yooseph, S. & Panda, S. Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metab. 20, 1006–1017 (2014).

    Article  CAS  Google Scholar 

  30. Curtis, A. M., Bellet, M. M., Sassone-Corsi, P. & O'Neill, L. A. Circadian clock proteins and immunity. Immunity 40, 178–186 (2014).

    Article  CAS  Google Scholar 

  31. Brady, J. & Crump, A. J. The control of circadian activity rhythms in tsetse flies: environment or physiological clock? Physiol. Entomol. 3, 177–190 (1978).

    Article  Google Scholar 

  32. MacGregor, P., Savill, N. J., Hall, D. & Matthews, K. R. Transmission stages dominate trypanosome within-host dynamics during chronic infections. Cell Host Microbe. 9, 310–318 (2011).

    Article  CAS  Google Scholar 

  33. Bass, J. & Takahashi, J. S. Circadian integration of metabolism and energetics. Science 330, 1349–1354 (2010).

    Article  CAS  Google Scholar 

  34. Engstler, M. & Boshart, M. Cold shock and regulation of surface protein trafficking convey sensitization to inducers of stage differentiation in Trypanosoma brucei. Genes Dev. 18, 2798–2811 (2004).

    Article  CAS  Google Scholar 

  35. Hirumi, H. & Hirumi, K. Continuous cultivation of Trypanosoma brucei blood stream forms in a medium containing a low concentration of serum protein without feeder cell layers. J. Parasitol. 75, 985–989 (1989).

    Article  CAS  Google Scholar 

  36. Knusel, S. & Roditi, I. Insights into the regulation of GPEET procyclin during differentiation from early to late procyclic forms of Trypanosoma brucei. Mol. Biochem. Parasitol. 191, 66–74 (2013).

    Article  CAS  Google Scholar 

  37. Cox, M. P., Peterson, D. A. & Biggs, P. J. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11, 485 (2010).

    Article  Google Scholar 

  38. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  39. Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).

    Article  CAS  Google Scholar 

  40. Pages, H., Aboyoun, P., Gentleman, R. & DebRoy, S. Biostrings: String Objects Representing Biological Sequences, and Matching Algorithms. R package v.2.38.4 (Bioconductor, 2016);

  41. Lawrence, M., Gentleman, R. & Carey, V. Rtracklayer: an R package for interfacing with genome browsers. Bioinformatics 25, 1841–1842 (2009).

    Article  CAS  Google Scholar 

  42. Huber, W. et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods 12, 115–121 (2015).

    Article  CAS  Google Scholar 

  43. Warnes, G. R. et al. gplots: Various R Programming Tools for Plotting Data. R package v.3.0.1 (CRAN, 2016);

  44. Wichert, S., Fokianos, K. & Strimmer, K. Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 20, 5–20 (2004).

    Article  CAS  Google Scholar 

  45. Hughes, M. E., Hogenesch, J. B. & Kornacker, K. JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J. Biol. Rhythms 25, 372–380 (2010).

    Article  Google Scholar 

  46. Yang, R. & Su, Z. Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation. Bioinformatics 26, i168–i174 (2010).

    Article  CAS  Google Scholar 

  47. Kurt Hornik, B. G. movMF: an R package for fitting mixtures of von Mises–Fisher distributions. J. Stat. Softw. 58, 1–31 (2014).

    Google Scholar 

  48. Siepka, S. M. & Takahashi, J. S. Methods to record circadian rhythm wheel running activity in mice. Methods Enzymol. 393, 230–239 (2005).

    Article  CAS  Google Scholar 

  49. Siepka, S. M. et al. Circadian mutant overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression. Cell 129, 1011–1023 (2007).

    Article  CAS  Google Scholar 

  50. Falcon, S. & Gentleman, R. Using GOstats to test gene lists for GO term association. Bioinformatics 23, 257–258 (2007).

    Article  CAS  Google Scholar 

Download references


The authors thank M. Phillips for help with starting parasite cultures at UT Southwestern and advice on the suramin sensitivity experiments, P. Nakashe for the library preparations of the light/dark data sets, M. Broderick for help during the oxidative stress experiment, L. Pinho, I. Kornblum and G. Kilaru for technical support, J. Stubblefield for help during the blood collection, D. Barry, M. Phillips, C. Green and M. Vaz for reading the manuscript and C. Janzen for the GFP-PAD1utr cell line. The work was supported by an HHMI International Early Career Scientist award (55007419, to L.M.F.), EMBO Installation Grant (2151) to L.M.F., Fundação para a Ciência e Tecnologia awards (SFRH/BD/51286/2010 to F.R.-F. and IF/00595/2014 to N.L.B.-M.). J.S.T. is an Investigator in the Howard Hughes Medical Institute.

Author information

Authors and Affiliations



F.R-F., L.M.F. and J.S.T. designed the study. F.R.-F. performed the experiments. D.P.-N., F.R.-F., N.L.B.-M., L.M.F. and J.S.T analysed the data. F.R.-F. wrote the manuscript and all authors contributed to reviewing the manuscript.

Corresponding authors

Correspondence to Joseph S. Takahashi or Luisa M. Figueiredo.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–10 and Supplementary Tables 1 and 2. (PDF 11397 kb)

Supplementary Data 1

List of genes, their RPKM counts and circadian algorithms analyses for bloodstream forms entrained with temperature. (XLSX 1626 kb)

Supplementary Data 2

List of genes, their RPKM counts and circadian algorithms analyses for insect procyclic forms entrained with temperature. (XLSX 1241 kb)

Supplementary Data 3

List of genes, their RPKM counts and circadian algorithms analyses for bloodstream forms entrained with light. (XLSX 382 kb)

Supplementary Data 4

GO term enrichment analysis of bloodstream and procyclic forms throughout the day. (XLSX 39 kb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Rijo-Ferreira, F., Pinto-Neves, D., Barbosa-Morais, N. et al. Trypanosoma brucei metabolism is under circadian control. Nat Microbiol 2, 17032 (2017).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing