Identification of novel proteins and mRNAs differentially bound to the Leishmania Poly(A) Binding Proteins reveals a direct association between PABP1, the RNA-binding protein RBP23 and mRNAs encoding ribosomal proteins

PLoS Negl Trop Dis. 2021 Oct 27;15(10):e0009899. doi: 10.1371/journal.pntd.0009899. eCollection 2021 Oct.

Abstract

Poly(A) Binding Proteins (PABPs) are major eukaryotic RNA-binding proteins (RBPs) with multiple roles associated with mRNA stability and translation and characterized mainly from multicellular organisms and yeasts. A variable number of PABP homologues are seen in different organisms however the biological reasons for multiple PABPs are generally not well understood. In the unicellular Leishmania, dependent on post-transcriptional mechanisms for the control of its gene expression, three distinct PABPs are found, with yet undefined functional distinctions. Here, using RNA-immunoprecipitation sequencing analysis we show that the Leishmania PABP1 preferentially associates with mRNAs encoding ribosomal proteins, while PABP2 and PABP3 bind to an overlapping set of mRNAs distinct to those enriched in PABP1. Immunoprecipitation studies combined to mass-spectrometry analysis identified RBPs differentially associated with PABP1 or PABP2, including RBP23 and DRBD2, respectively, that were investigated further. Both RBP23 and DRBD2 bind directly to the three PABPs in vitro, but reciprocal experiments confirmed preferential co-immunoprecipitation of PABP1, as well as the EIF4E4/EIF4G3 based translation initiation complex, with RBP23. Other RBP23 binding partners also imply a direct role in translation. DRBD2, in contrast, co-immunoprecipitated with PABP2, PABP3 and with RBPs unrelated to translation. Over 90% of the RBP23-bound mRNAs code for ribosomal proteins, mainly absent from the transcripts co-precipitated with DRBD2. These experiments suggest a novel and specific route for translation of the ribosomal protein mRNAs, mediated by RBP23, PABP1 and the associated EIF4E4/EIF4G3 complex. They also highlight the unique roles that different PABP homologues may have in eukaryotic cells associated with mRNA translation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Leishmania / genetics
  • Leishmania / metabolism*
  • Poly(A)-Binding Proteins / genetics
  • Poly(A)-Binding Proteins / metabolism*
  • Protein Binding
  • Protein Biosynthesis
  • Protozoan Proteins / genetics
  • Protozoan Proteins / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Ribosomal Proteins / genetics
  • Ribosomal Proteins / metabolism*

Substances

  • Poly(A)-Binding Proteins
  • Protozoan Proteins
  • RNA, Messenger
  • RNA-Binding Proteins
  • Ribosomal Proteins

Grants and funding

This work was more recently supported by grants provided by FACEPE (APQ-1662-2.02/15) and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) (401282/2014-7; 422726/2016-8; 400789/2019-1; 310032/2019-9) awarded to OPDMN. The early L. major work was supported by a grant from FACEPE (Fundação de Amparo a Ciência e Tecnologia do Estado de Pernambuco) to FBH (DCR 0032-2.13/09; APQ-0090-2.13/09). This study was also financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 (OPDMN). MJRB is a recipient of a CAPES/PNPD grant (APQ-0876-2.02/16). Studentships for the graduate students were provided by CAPES (LAA, MVCSF, JRDCS), CNPq (KCM), and FIOTEC (IRPUCDA). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.