N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum
Abstract Background Plasmodium falciparum exhibits high translational plasticity during its development in RBCs, yet the regulation at the post-transcriptional level is not well understood. The N6-methyl adenosine (m6A) is an important epigenetic modification primarily present on mRNA that controls...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-08-01
|
| Series: | Epigenetics & Chromatin |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13072-020-00355-7 |
| _version_ | 1819091729602576384 |
|---|---|
| author | Gayathri Govindaraju Rajashekar Varma Kadumuri Devadathan Valiyamangalath Sethumadhavan C. A. Jabeena Sreenivas Chavali Arumugam Rajavelu |
| author_facet | Gayathri Govindaraju Rajashekar Varma Kadumuri Devadathan Valiyamangalath Sethumadhavan C. A. Jabeena Sreenivas Chavali Arumugam Rajavelu |
| author_sort | Gayathri Govindaraju |
| collection | DOAJ |
| description | Abstract Background Plasmodium falciparum exhibits high translational plasticity during its development in RBCs, yet the regulation at the post-transcriptional level is not well understood. The N6-methyl adenosine (m6A) is an important epigenetic modification primarily present on mRNA that controls the levels of transcripts and efficiency of translation in eukaryotes. Recently, the dynamics of m6A on mRNAs at all three developmental stages of P. falciparum in RBCs have been profiled; however, the proteins that regulate the m6A containing mRNAs in the parasites are unknown. Results Using sequence analysis, we computationally identified that the P. falciparum genome encodes two putative YTH (YT521-B Homology) domain-containing proteins, which could potentially bind to m6A containing mRNA. We developed a modified methylated RNA immunoprecipitation (MeRIP) assay using PfYTH2 and find that it binds selectively to m6A containing transcripts. The PfYTH2 has a conserved aromatic amino acid cage that forms the methyl-binding pocket. Through site-directed mutagenesis experiments and molecular dynamics simulations, we show that F98 residue is important for m6A binding on mRNA. Fluorescence depolarization assay confirmed that PfYTH2 binds to methylated RNA oligos with high affinity. Further, MeRIP sequencing data revealed that PfYTH2 has more permissive sequence specificity on target m6A containing mRNA than other known eukaryotic YTH proteins. Taken together, here we identify and characterize PfYTH2 as the major protein that could regulate m6A containing transcripts in P. falciparum. Conclusion Plasmodium spp. lost the canonical m6A-specific demethylases in their genomes, however, the YTH domain-containing proteins seem to be retained. This study presents a possibility that the YTH proteins are involved in post-transcriptional control in P. falciparum, and might orchestrate the translation of mRNA in various developmental stages of P. falciparum. This is perhaps the first characterization of the methyl-reading function of YTH protein in any parasites. |
| first_indexed | 2024-12-21T22:44:21Z |
| format | Article |
| id | doaj.art-8c90492991fd48a4915bd9cafe180174 |
| institution | Directory Open Access Journal |
| issn | 1756-8935 |
| language | English |
| last_indexed | 2024-12-21T22:44:21Z |
| publishDate | 2020-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Epigenetics & Chromatin |
| spelling | doaj.art-8c90492991fd48a4915bd9cafe1801742022-12-21T18:47:45ZengBMCEpigenetics & Chromatin1756-89352020-08-0113111510.1186/s13072-020-00355-7N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparumGayathri Govindaraju0Rajashekar Varma Kadumuri1Devadathan Valiyamangalath Sethumadhavan2C. A. Jabeena3Sreenivas Chavali4Arumugam Rajavelu5Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB)Department of Biology, Indian Institute of Science Education and Research (IISER) TirupatiPathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB)Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB)Department of Biology, Indian Institute of Science Education and Research (IISER) TirupatiPathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB)Abstract Background Plasmodium falciparum exhibits high translational plasticity during its development in RBCs, yet the regulation at the post-transcriptional level is not well understood. The N6-methyl adenosine (m6A) is an important epigenetic modification primarily present on mRNA that controls the levels of transcripts and efficiency of translation in eukaryotes. Recently, the dynamics of m6A on mRNAs at all three developmental stages of P. falciparum in RBCs have been profiled; however, the proteins that regulate the m6A containing mRNAs in the parasites are unknown. Results Using sequence analysis, we computationally identified that the P. falciparum genome encodes two putative YTH (YT521-B Homology) domain-containing proteins, which could potentially bind to m6A containing mRNA. We developed a modified methylated RNA immunoprecipitation (MeRIP) assay using PfYTH2 and find that it binds selectively to m6A containing transcripts. The PfYTH2 has a conserved aromatic amino acid cage that forms the methyl-binding pocket. Through site-directed mutagenesis experiments and molecular dynamics simulations, we show that F98 residue is important for m6A binding on mRNA. Fluorescence depolarization assay confirmed that PfYTH2 binds to methylated RNA oligos with high affinity. Further, MeRIP sequencing data revealed that PfYTH2 has more permissive sequence specificity on target m6A containing mRNA than other known eukaryotic YTH proteins. Taken together, here we identify and characterize PfYTH2 as the major protein that could regulate m6A containing transcripts in P. falciparum. Conclusion Plasmodium spp. lost the canonical m6A-specific demethylases in their genomes, however, the YTH domain-containing proteins seem to be retained. This study presents a possibility that the YTH proteins are involved in post-transcriptional control in P. falciparum, and might orchestrate the translation of mRNA in various developmental stages of P. falciparum. This is perhaps the first characterization of the methyl-reading function of YTH protein in any parasites.http://link.springer.com/article/10.1186/s13072-020-00355-7RNA methylationN6-adenosine methylationMethyl readingPost-transcriptional regulationPlasmodiumEpigenetics |
| spellingShingle | Gayathri Govindaraju Rajashekar Varma Kadumuri Devadathan Valiyamangalath Sethumadhavan C. A. Jabeena Sreenivas Chavali Arumugam Rajavelu N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum Epigenetics & Chromatin RNA methylation N6-adenosine methylation Methyl reading Post-transcriptional regulation Plasmodium Epigenetics |
| title | N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum |
| title_full | N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum |
| title_fullStr | N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum |
| title_full_unstemmed | N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum |
| title_short | N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum |
| title_sort | n6 adenosine methylation on mrna is recognized by yth2 domain protein of human malaria parasite plasmodium falciparum |
| topic | RNA methylation N6-adenosine methylation Methyl reading Post-transcriptional regulation Plasmodium Epigenetics |
| url | http://link.springer.com/article/10.1186/s13072-020-00355-7 |
| work_keys_str_mv | AT gayathrigovindaraju n6adenosinemethylationonmrnaisrecognizedbyyth2domainproteinofhumanmalariaparasiteplasmodiumfalciparum AT rajashekarvarmakadumuri n6adenosinemethylationonmrnaisrecognizedbyyth2domainproteinofhumanmalariaparasiteplasmodiumfalciparum AT devadathanvaliyamangalathsethumadhavan n6adenosinemethylationonmrnaisrecognizedbyyth2domainproteinofhumanmalariaparasiteplasmodiumfalciparum AT cajabeena n6adenosinemethylationonmrnaisrecognizedbyyth2domainproteinofhumanmalariaparasiteplasmodiumfalciparum AT sreenivaschavali n6adenosinemethylationonmrnaisrecognizedbyyth2domainproteinofhumanmalariaparasiteplasmodiumfalciparum AT arumugamrajavelu n6adenosinemethylationonmrnaisrecognizedbyyth2domainproteinofhumanmalariaparasiteplasmodiumfalciparum |