Skip to main content
Log in

Phage Display Screening for Alba Superfamily Proteins from the Human Malaria Parasite, Plasmodium falciparum Reveals a High Level of Association with Protein Modification Pathways and Hints at New Drug Targets

  • Original Paper
  • Published:
Acta Parasitologica Aims and scope Submit manuscript

Abstract

Purpose

A 2016 study estimated that over 3 billion people are currently at risk of contracting malaria. Although a wide variety of medications are available to treat malaria, the parasites have started to exhibit resistance to many commonly used therapeutics necessitating a push for new investigations to identify novel drug targets.

Methods

In this study, nucleic acid-binding Alba superfamily proteins of the human malaria parasite, Plasmodium falciparum were investigated to identify interacting protein motifs. A high-throughput molecular screening technique, phage display, coupled with next-generation sequencing was applied to assess large data sets.

Results

Four P. falciparum Alba proteins were used for screening which appear to have distinct roles in parasite biology based on the results of this work. The majority of the peptide motifs identified from phage display were involved in post-translational modification pathways, thus suggesting that parasite-specific gene regulatory mechanisms are involved which could serve as drug targets for novel therapeutics.

Conclusion

This study found 18 peptide motifs which potentially have strong interactions with one or more of the Alba superfamily proteins from P. falciparum. Considering the large fraction of post-translational modification-related peptide motifs identified from this work, one or more of the protein modification pathways could serve as a good target for malaria treatment.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

Availability of data and materials

The datasets generated during the current study are available from the corresponding author upon reasonable request.

References

  1. WHO (2017) World Malaria Report 2017. 2017

  2. Achan J et al (2011) Quinine, an old anti-malarial drug in a modern world: role in the treatment of malaria. Malar J 10:144. https://doi.org/10.1186/1475-2875-10-144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Greenwood B (2014) Treatment of malaria—a continuing challenge. N Engl J Med 371(5):474–475. https://doi.org/10.1056/NEJMe1407026

    Article  CAS  PubMed  Google Scholar 

  4. Winzeler EA (2008) Malaria research in the post-genomic era. Nature 455(7214):751–756. https://doi.org/10.1038/nature07361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Gardner MJ et al (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419(6906):498–511. https://doi.org/10.1038/nature01097

    Article  CAS  PubMed  Google Scholar 

  6. Foth BJ et al (2008) Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites. Genome Biol 9(12):R177. https://doi.org/10.1186/gb-2008-9-12-r177

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Raabe CA et al (2010) A global view of the nonprotein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res 38(2):608–617. https://doi.org/10.1093/nar/gkp895

    Article  CAS  PubMed  Google Scholar 

  8. Horrocks P et al (2009) Control of gene expression in Plasmodium falciparum—ten years on. Mol Biochem Parasitol 164(1):9–25. https://doi.org/10.1016/j.molbiopara.2008.11.010

    Article  CAS  PubMed  Google Scholar 

  9. Chene A et al (2012) PfAlbas constitute a new eukaryotic DNA/RNA-binding protein family in malaria parasites. Nucleic Acids Res 40(7):3066–3077. https://doi.org/10.1093/nar/gkr1215

    Article  CAS  PubMed  Google Scholar 

  10. Mani J et al (2011) Alba-domain proteins of Trypanosoma brucei are cytoplasmic RNA-binding proteins that interact with the translation machinery. PLoS ONE 6(7):e22463. https://doi.org/10.1371/journal.pone.0022463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Reddy BP et al (2015) A bioinformatic survey of RNA-binding proteins in Plasmodium. BMC Genomics 16:890. https://doi.org/10.1186/s12864-015-2092-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Bell SD et al (2002) The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296(5565):148–151. https://doi.org/10.1126/science.1070506

    Article  CAS  PubMed  Google Scholar 

  13. Goyal M et al (2016) The Alba protein family: structure and function. Biochim Biophys Acta 1864(5):570–583. https://doi.org/10.1016/j.bbapap.2016.02.015

    Article  CAS  PubMed  Google Scholar 

  14. Tanaka T, Padavattan S, Kumarevel T (2012) Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1. J Biol Chem 287(13):10394–10402. https://doi.org/10.1074/jbc.M112.343210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wardleworth BN et al (2002) Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J 21(17):4654–4662

    Article  CAS  Google Scholar 

  16. Bell SD, Jackson SP (2001) Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4(2):208–213

    Article  CAS  Google Scholar 

  17. Guo L et al (2014) Biochemical and structural insights into RNA binding by Ssh10b, a member of the highly conserved Sac10b protein family in Archaea. J Biol Chem 289(3):1478–1490. https://doi.org/10.1074/jbc.M113.521351

    Article  CAS  PubMed  Google Scholar 

  18. Goyal M et al (2012) Identification and molecular characterization of an Alba-family protein from human malaria parasite Plasmodium falciparum. Nucleic Acids Res 40(3):1174–1190. https://doi.org/10.1093/nar/gkr821

    Article  CAS  PubMed  Google Scholar 

  19. Duffy MF et al (2012) The role of chromatin in Plasmodium gene expression. Cell Microbiol 14(6):819–828. https://doi.org/10.1111/j.1462-5822.2012.01777.x

    Article  CAS  PubMed  Google Scholar 

  20. Bunnik EM, Le Roch KG (2015) PfAlba1: master regulator of translation in the malaria parasite. Genome Biol 16:221. https://doi.org/10.1186/s13059-015-0795-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Vembar SS et al (2015) The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages. Genome Biol 16:212. https://doi.org/10.1186/s13059-015-0771-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Munoz EE et al (2017) ALBA4 modulates its stage-specific interactions and specific mRNA fates during Plasmodium yoelii growth and transmission. Mol Microbiol 106(2):266–284. https://doi.org/10.1111/mmi.13762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Zhu X-Q et al (2005) On-column refolding of an insoluble his6-tagged recombinant EC-SOD Overexpressed in Escherichia coli. Acta Biochim Biophys Sin 37(4):265–269. https://doi.org/10.1111/j.1745-7270.2005.00035.x

    Article  CAS  PubMed  Google Scholar 

  24. Tajiri M (2019) Comparison of high-throughput sequencing for phage display peptide screening on two commercially available platforms. Int J Pept Res Ther. https://doi.org/10.1007/s10989-019-09858-8

    Article  Google Scholar 

  25. Blankenberg D et al (2010) Manipulation of FASTQ data with Galaxy. Bioinformatics 26(14):1783–1785. https://doi.org/10.1093/bioinformatics/btq281

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Thiel WH, Giangrande PH (2016) Analyzing HT-SELEX data with the Galaxy Project tools—a web based bioinformatics platform for biomedical research. Methods 97:3–10. https://doi.org/10.1016/j.ymeth.2015.10.008

    Article  CAS  PubMed  Google Scholar 

  27. Stafford RL et al (2014) A general sequence processing and analysis program for protein engineering. J Chem Inf Model 54(10):3020–3032. https://doi.org/10.1021/ci500362s

    Article  CAS  PubMed  Google Scholar 

  28. Bailey TL, Machanick P (2012) Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res 40(17):e128. https://doi.org/10.1093/nar/gks433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Dinkel H et al (2016) ELM 2016–data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Res 44(D1):D294-300. https://doi.org/10.1093/nar/gkv1291

    Article  CAS  PubMed  Google Scholar 

  30. Gouw M et al (2018) The eukaryotic linear motif resource—2018 update. Nucleic Acids Res 46(D1):D428–D434. https://doi.org/10.1093/nar/gkx1077

    Article  CAS  PubMed  Google Scholar 

  31. Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3):381–395. https://doi.org/10.1038/cr.2011.22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Doerig C et al (2015) Post-translational protein modifications in malaria parasites. Nat Rev Microbiol 13(3):160–172. https://doi.org/10.1038/nrmicro3402

    Article  CAS  PubMed  Google Scholar 

  33. Hamilton MJ, Lee M, Le Roch KG (2014) The ubiquitin system: an essential component to unlocking the secrets of malaria parasite biology. Mol Biosyst 10(4):715–723. https://doi.org/10.1039/c3mb70506d

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Ponts N et al (2011) Unraveling the ubiquitome of the human malaria parasite. J Biol Chem 286(46):40320–40330. https://doi.org/10.1074/jbc.M111.238790

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Ye H et al (2002) Distinct molecular mechanism for initiating TRAF6 signalling. Nature 418(6896):443–447. https://doi.org/10.1038/nature00888

    Article  CAS  PubMed  Google Scholar 

  36. Fu Y et al (2012) Plasmodium yoelii blood-stage primes macrophage-mediated innate immune response through modulation of toll-like receptor signalling. Malar J 11:104. https://doi.org/10.1186/1475-2875-11-104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Pozhidaeva A, Bezsonova I (2019) USP7: structure, substrate specificity, and inhibition. DNA Repair (Amst) 76:30–39. https://doi.org/10.1016/j.dnarep.2019.02.005

    Article  CAS  Google Scholar 

  38. Deu E (2017) Proteases as antimalarial targets: strategies for genetic, chemical, and therapeutic validation. FEBS J 284(16):2604–2628. https://doi.org/10.1111/febs.14130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ward P et al (2004) Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics 5:79. https://doi.org/10.1186/1471-2164-5-79

    Article  PubMed  PubMed Central  Google Scholar 

  40. Dastidar EG et al (2012) Involvement of Plasmodium falciparum protein kinase CK2 in the chromatin assembly pathway. BMC Biol 10:5. https://doi.org/10.1186/1741-7007-10-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Barro M, Patton JT (2005) Rotavirus nonstructural protein 1 subverts innate immune response by inducing degradation of IFN regulatory factor 3. Proc Natl Acad Sci USA 102(11):4114–4119. https://doi.org/10.1073/pnas.0408376102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Kanyal A et al (2017) Genome-wide survey and phylogenetic analysis of histone acetyltransferases and histone deacetylases of Plasmodium falciparum. FEBS J. https://doi.org/10.1111/febs.14376

    Article  Google Scholar 

Download references

Acknowledgements

I would like to thank Michigan Technological University Research Excellence Fund (R01547) and Portage Health Foundation (R75389). I would also like to thank Dr. Chelsea Nikula (National Physical Laboratory, London UK) for critical reviewing of the manuscript.

Funding

This work was funded by Michigan Technological University Research Excellence Fund (R01547) and Portage Health Foundation (R75389).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Momoko Tajiri.

Ethics declarations

Conflicts of interest

The author declares no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 400 KB)

Supplementary file2 (DOCX 15 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tajiri, M. Phage Display Screening for Alba Superfamily Proteins from the Human Malaria Parasite, Plasmodium falciparum Reveals a High Level of Association with Protein Modification Pathways and Hints at New Drug Targets. Acta Parasit. 66, 844–850 (2021). https://doi.org/10.1007/s11686-021-00339-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11686-021-00339-x

Keywords

Navigation