1
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Bartosik K, Micura R. Access to capped RNAs by chemical ligation. RSC Chem Biol 2024:d4cb00165f. [PMID: 39279877 PMCID: PMC11393730 DOI: 10.1039/d4cb00165f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 09/04/2024] [Indexed: 09/18/2024] Open
Abstract
A distinctive feature of eukaryotic mRNAs is the presence of a cap structure at the 5' end. The typical cap consists of 7-methylguanosine linked to the first transcribed nucleotide through a 5',5'-triphosphate bridge. It plays a key role in many processes in eukaryotic cells, including splicing, intracellular transport, initiation of translation and turnover. Synthetic capped oligonucleotides have served as useful tools for elucidating these physiological processes. In addition, cap mimics with artificial modifications are of interest for the design of mRNA-based therapeutics and vaccines. While the short cap mimics can be obtained by chemical synthesis, the preparation of capped analogs of mRNA length is still challenging and requires templated enzymatic ligation of synthetic RNA fragments. To increase the availability of capped mRNA analogs, we present here a practical and non-templated approach based on the use of click ligation resulting in RNAs bearing a single triazole linkage within the oligo-phosphate backbone. Capped RNA fragments with up to 81 nucleotides in length have thus been obtained in nanomolar yields and are in demand for biochemical, spectroscopic or structural studies.
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Affiliation(s)
- Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82 6020 Innsbruck Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82 6020 Innsbruck Austria
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2
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Penteado RF, da Silva RS, Moura DMN, de Lima GB, Malvezzi AM, Monteiro TTDS, Xavier CC, Vichier-Guerre S, Dugué L, Pochet S, Zanchin NIT, Reis CRDS, de Melo Neto OP, Guimarães BG. Structural analysis of the Trypanosoma brucei EIF4E6/EIF4G5 complex reveals details of the interaction between unusual eIF4F subunits. Sci Rep 2024; 14:2178. [PMID: 38272944 PMCID: PMC10810786 DOI: 10.1038/s41598-024-52364-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Recognition of the mRNA 5' end is a critical step needed for translation initiation. This step is performed by the cap binding protein eIF4E, which joins the larger eIF4G subunit to form the eIF4F complex. Trypanosomatids have a minimum of five different eIF4F-like complexes formed through specific but not well-defined interactions between four different eIF4E and five eIF4G homologues. The EIF4E6/EIF4G5 complex has been linked with the stage-specific translation of mRNAs encoding the major Trypanosoma brucei virulence factors. Here, to better define the molecular basis for the TbEIF4E6/TbEIF4G5 interaction, we describe the identification of the peptide interacting with TbEIF4E6 in the region comprising residues 79-166 of TbEIF4G5. The TbEIF4E6-TbEIF4G5_79-116 complex reconstituted with recombinant proteins is highly stable even in the absence of cap-4. The crystal structure of the complex was subsequently solved, revealing extensive interacting surfaces. Comparative analyses highlight the conservation of the overall structural arrangement of different eIF4E/eIF4G complexes. However, highly different interacting surfaces are formed with distinct binding contacts occurring both in the canonical and noncanonical elements within eIF4G and the respective eIF4E counterpart. These specific pairs of complementary interacting surfaces are likely responsible for the selective association needed for the formation of distinct eIF4F complexes in trypanosomatids.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Laurence Dugué
- Epigenetic Chemical Biology, Institut Pasteur, Paris, France
| | - Sylvie Pochet
- Epigenetic Chemical Biology, Institut Pasteur, Paris, France
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3
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Bose P, Baron N, Pullaiahgari D, Ben-Zvi A, Shapira M. LeishIF3d is a non-canonical cap-binding protein in Leishmania. Front Mol Biosci 2023; 10:1191934. [PMID: 37325473 PMCID: PMC10266417 DOI: 10.3389/fmolb.2023.1191934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Translation of most cellular mRNAs in eukaryotes proceeds through a cap-dependent pathway, whereby the cap-binding complex, eIF4F, anchors the pre-initiation complex at the 5' end of mRNAs driving translation initiation. The genome of Leishmania encodes a large repertoire of cap-binding complexes that fulfill a variety of functions possibly involved in survival along the life cycle. However, most of these complexes function in the promastigote life form that resides in the sand fly vector and decrease their activity in amastigotes, the mammalian life form. Here we examined the possibility that LeishIF3d drives translation in Leishmania using alternative pathways. We describe a non-canonical cap-binding activity of LeishIF3d and examine its potential role in driving translation. LeishIF3d is required for translation, as reducing its expression by a hemizygous deletion reduces the translation activity of the LeishIF3d(+/-) mutant cells. Proteomic analysis of the mutant cells highlights the reduced expression of flagellar and cytoskeletal proteins, as reflected in the morphological changes observed in the mutant cells. Targeted mutations in two predicted alpha helices diminish the cap-binding activity of LeishIF3d. Overall, LeishIF3d could serve as a driving force for alternative translation pathways, although it does not seem to offer an alternative pathway for translation in amastigotes.
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Affiliation(s)
- Priyanka Bose
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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4
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Characterization of an Atypical eIF4E Ortholog in Leishmania, LeishIF4E-6. Int J Mol Sci 2021; 22:ijms222312720. [PMID: 34884522 PMCID: PMC8657474 DOI: 10.3390/ijms222312720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 01/11/2023] Open
Abstract
Leishmania parasites are digenetic protists that shuffle between sand fly vectors and mammalian hosts, transforming from flagellated extracellular promastigotes that reside within the intestinal tract of female sand flies to the obligatory intracellular and non-motile amastigotes within mammalian macrophages. Stage differentiation is regulated mainly by post-transcriptional mechanisms, including translation regulation. Leishmania parasites encode six different cap-binding proteins, LeishIF4E1-6, that show poor conservation with their counterparts from higher eukaryotes and among themselves. In view of the changing host milieu encountered throughout their life cycle, we propose that each LeishIF4E has a unique role, although these functions may be difficult to determine. Here we characterize LeishIF4E-6, a unique eIF4E ortholog that does not readily associate with m7GTP cap in either of the tested life forms of the parasite. We discuss the potential effect of substituting two essential tryptophan residues in the cap-binding pocket, expected to be involved in the cap-binding activity, as judged from structural studies in the mammalian eIF4E. LeishIF4E-6 binds to LeishIF4G-5, one of the five eIF4G candidates in Leishmania. However, despite this binding, LeishIF4E-6 does not appear to function as a translation factor. Its episomal overexpression causes a general reduction in the global activity of protein synthesis, which was not observed in the hemizygous deletion mutant generated by CRISPR-Cas9. This genetic profile suggests that LeishIF4E-6 has a repressive role. The interactome of LeishIF4E-6 highlights proteins involved in RNA metabolism such as the P-body marker DHH1, PUF1 and an mRNA-decapping enzyme that is homologous to the TbALPH1.
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5
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Falk F, Kamanyi Marucha K, Clayton C. The EIF4E1-4EIP cap-binding complex of Trypanosoma brucei interacts with the terminal uridylyl transferase TUT3. PLoS One 2021; 16:e0258903. [PMID: 34807934 PMCID: PMC8608314 DOI: 10.1371/journal.pone.0258903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Most transcription in Trypanosoma brucei is constitutive and polycistronic. Consequently, the parasite relies on post-transcriptional mechanisms, especially affecting translation initiation and mRNA decay, to control gene expression both at steady-state and for adaptation to different environments. The parasite has six isoforms of the cap-binding protein EIF4E as well as five EIF4Gs. EIF4E1 does not bind to any EIF4G, instead being associated with a 4E-binding protein, 4EIP. 4EIP represses translation and reduces the stability of a reporter mRNA when artificially tethered to the 3’-UTR, whether or not EIF4E1 is present. 4EIP is essential during the transition from the mammalian bloodstream form to the procyclic form that lives in the Tsetse vector. In contrast, EIF4E1 is dispensable during differentiation, but is required for establishment of growing procyclic forms. In Leishmania, there is some evidence that EIF4E1 might be active in translation initiation, via direct recruitment of EIF3. However in T. brucei, EIF4E1 showed no detectable association with other translation initiation factors, even in the complete absence of 4EIP. There was some evidence for interactions with NOT complex components, but if these occur they must be weak and transient. We found that EIF4E1is less abundant in the absence of 4EIP, and RNA pull-down results suggested this might occur through co-translational complex assembly. We also report that 4EIP directly recruits the cytosolic terminal uridylyl transferase TUT3 to EIF4E1/4EIP complexes. There was, however, no evidence that TUT3 is essential for 4EIP function.
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Affiliation(s)
- Franziska Falk
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Kevin Kamanyi Marucha
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- * E-mail:
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6
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de Lima GB, de Lima Cavalcanti TYV, de Brito ANALM, de Assis LA, Andrade-Vieira RP, Freire ER, da Silva Assunção TR, de Souza Reis CR, Zanchin NIT, Guimarães BG, de-Melo-Neto OP. The translation initiation factor EIF4E5 from Leishmania: crystal structure and interacting partners. RNA Biol 2021; 18:2433-2449. [PMID: 33945405 DOI: 10.1080/15476286.2021.1918919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The mRNA cap-binding protein, eIF4E, mediates the recognition of the mRNA 5' end and, as part of the heterotrimeric eIF4F complex, facilitates the recruitment of the ribosomal subunits to initiate eukaryotic translation. Various regulatory events involving eIF4E and a second eIF4F subunit, eIF4G, are required for proper control of translation initiation. In pathogenic trypanosomatids, six eIF4Es and five eIF4Gs have been described, several forming different eIF4F-like complexes with yet unresolved roles. EIF4E5 is one of the least known of the trypanosomatid eIF4Es and has not been characterized in Leishmania species. Here, we used immunoprecipitation assays, combined with mass-spectrometry, to identify major EIF4E5 interacting proteins in L. infantum. A constitutively expressed, HA-tagged, EIF4E5 co-precipitated mainly with EIF4G1 and binding partners previously described in Trypanosoma brucei, EIF4G1-IP, RBP43 and the 14-3-3 proteins. In contrast, no clear co-precipitation with EIF4G2, also previously reported, was observed. EIF4E5 also co-precipitated with protein kinases, possibly associated with cell-cycle regulation, selected RNA binding proteins and histones. Phosphorylated residues were identified and mapped to the Leishmania-specific C-terminal end. Mutagenesis of the tryptophan residue (W53) postulated to mediate interactions with protein partners or of a neighbouring tryptophan conserved in Leishmania (W45) did not substantially impair the identified interactions. Finally, the crystal structure of Leishmania EIF4E5 evidences remarkable differences in the eIF4G interfacing region, when compared with human eIF4E-1 and with its Trypanosoma orthologue. Mapping of its C-terminal end near the cap-binding site also imply relevant differences in cap-binding function and/or regulation.
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Affiliation(s)
- Gustavo Barbosa de Lima
- Departamento de Microbiologia, Instituto Aggeu Magalhães, FIOCRUZ-PE, Av. Moraes Rego s/n, Recife-PE, Brazil
| | - Thaíse Yasmine Vasconcelos de Lima Cavalcanti
- Departamento de Microbiologia, Instituto Aggeu Magalhães, FIOCRUZ-PE, Av. Moraes Rego s/n, Recife-PE, Brazil.,Programa de Pós-Graduação em Genética, Universidade Federal de Pernambuco, Recife-PE, Brazil
| | - Adriana Neuman Albuquerque Lins Moura de Brito
- Departamento de Microbiologia, Instituto Aggeu Magalhães, FIOCRUZ-PE, Av. Moraes Rego s/n, Recife-PE, Brazil.,Programa de Pós-Graduação em Genética, Universidade Federal de Pernambuco, Recife-PE, Brazil
| | - Ludmilla Arruda de Assis
- Departamento de Microbiologia, Instituto Aggeu Magalhães, FIOCRUZ-PE, Av. Moraes Rego s/n, Recife-PE, Brazil
| | | | - Eden Ribeiro Freire
- Departamento de Microbiologia, Instituto Aggeu Magalhães, FIOCRUZ-PE, Av. Moraes Rego s/n, Recife-PE, Brazil.,Laboratório de Biologia Estrutural e Engenharia de Proteínas, Instituto Carlos Chagas, FIOCRUZ-PR, Curitiba-PR, Brazil
| | | | | | - Nilson Ivo Tonin Zanchin
- Laboratório de Biologia Estrutural e Engenharia de Proteínas, Instituto Carlos Chagas, FIOCRUZ-PR, Curitiba-PR, Brazil
| | - Beatriz Gomes Guimarães
- Laboratório de Biologia Estrutural e Engenharia de Proteínas, Instituto Carlos Chagas, FIOCRUZ-PR, Curitiba-PR, Brazil
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7
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Mabille D, Cardoso Santos C, Hendrickx R, Claes M, Takac P, Clayton C, Hendrickx S, Hulpia F, Maes L, Van Calenbergh S, Caljon G. 4E Interacting Protein as a Potential Novel Drug Target for Nucleoside Analogues in Trypanosoma brucei. Microorganisms 2021; 9:microorganisms9040826. [PMID: 33924674 PMCID: PMC8069773 DOI: 10.3390/microorganisms9040826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 12/22/2022] Open
Abstract
Human African trypanosomiasis is a neglected parasitic disease for which the current treatment options are quite limited. Trypanosomes are not able to synthesize purines de novo and thus solely depend on purine salvage from the host environment. This characteristic makes players of the purine salvage pathway putative drug targets. The activity of known nucleoside analogues such as tubercidin and cordycepin led to the development of a series of C7-substituted nucleoside analogues. Here, we use RNA interference (RNAi) libraries to gain insight into the mode-of-action of these novel nucleoside analogues. Whole-genome RNAi screening revealed the involvement of adenosine kinase and 4E interacting protein into the mode-of-action of certain antitrypanosomal nucleoside analogues. Using RNAi lines and gene-deficient parasites, 4E interacting protein was found to be essential for parasite growth and infectivity in the vertebrate host. The essential nature of this gene product and involvement in the activity of certain nucleoside analogues indicates that it represents a potential novel drug target.
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Affiliation(s)
- Dorien Mabille
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (D.M.); (C.C.S.); (R.H.); (M.C.); (S.H.); (L.M.)
| | - Camila Cardoso Santos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (D.M.); (C.C.S.); (R.H.); (M.C.); (S.H.); (L.M.)
- Laboratório de Biologia Celular (LBC), Instituto Oswaldo Cruz (IOC/Fiocruz), Rio de Janeiro 21040-900, Brazil
| | - Rik Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (D.M.); (C.C.S.); (R.H.); (M.C.); (S.H.); (L.M.)
| | - Mathieu Claes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (D.M.); (C.C.S.); (R.H.); (M.C.); (S.H.); (L.M.)
| | - Peter Takac
- Institute of Zoology, Slovak Academy of Sciences, 84506 Bratislava, Slovakia;
- Scientica, Ltd., 83106 Bratislava, Slovakia
| | - Christine Clayton
- DKFZ-ZMBH Alliance, Zentrum für Molekulare Biologie der Universität Heidelberg, 69120 Heidelberg, Germany;
| | - Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (D.M.); (C.C.S.); (R.H.); (M.C.); (S.H.); (L.M.)
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry, Campus Heymans, Ghent University, 9000 Gent, Belgium; (F.H.); (S.V.C.)
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (D.M.); (C.C.S.); (R.H.); (M.C.); (S.H.); (L.M.)
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Campus Heymans, Ghent University, 9000 Gent, Belgium; (F.H.); (S.V.C.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (D.M.); (C.C.S.); (R.H.); (M.C.); (S.H.); (L.M.)
- Correspondence:
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8
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Shrivastava R, Tupperwar N, Schwartz B, Baron N, Shapira M. LeishIF4E-5 Is a Promastigote-Specific Cap-Binding Protein in Leishmania. Int J Mol Sci 2021; 22:3979. [PMID: 33921489 PMCID: PMC8069130 DOI: 10.3390/ijms22083979] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Leishmania parasites cycle between sand fly vectors and mammalian hosts, transforming from extracellular promastigotes that reside in the vectors' alimentary canal to obligatory intracellular non-motile amastigotes that are harbored by macrophages of the mammalian hosts. The transition between vector and host exposes them to a broad range of environmental conditions that induces a developmental program of gene expression, with translation regulation playing a key role. The Leishmania genome encodes six paralogs of the cap-binding protein eIF4E. All six isoforms show a relatively low degree of conservation with eIF4Es of other eukaryotes, as well as among themselves. This variability could suggest that they have been assigned discrete roles that could contribute to their survival under the changing environmental conditions. Here, we describe LeishIF4E-5, a LeishIF4E paralog. Despite the low sequence conservation observed between LeishIF4E-5 and other LeishIF4Es, the three aromatic residues in its cap-binding pocket are conserved, in accordance with its cap-binding activity. However, the cap-binding activity of LeishIF4E-5 is restricted to the promastigote life form and not observed in amastigotes. The overexpression of LeishIF4E-5 shows a decline in cell proliferation and an overall reduction in global translation. Immuno-cytochemical analysis shows that LeishIF4E-5 is localized in the cytoplasm, with a non-uniform distribution. Mass spectrometry analysis of proteins that co-purify with LeishIF4E-5 highlighted proteins involved in RNA metabolism, along with two LeishIF4G paralogs, LeishIF4G-1 and LeishIF4G-2. These vary in their conserved eIF4E binding motif, possibly suggesting that they can form different complexes.
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Affiliation(s)
- Rohit Shrivastava
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (R.S.); (N.T.); (B.S.); (N.B.)
| | - Nitin Tupperwar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (R.S.); (N.T.); (B.S.); (N.B.)
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 50007, India
| | - Bar Schwartz
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (R.S.); (N.T.); (B.S.); (N.B.)
| | - Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (R.S.); (N.T.); (B.S.); (N.B.)
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (R.S.); (N.T.); (B.S.); (N.B.)
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9
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Hernández-Alvarez L, Oliveira AB, Hernández-González JE, Chahine J, Pascutti PG, de Araujo AS, de Souza FP. Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m 7GTP cap recognition. Comput Struct Biotechnol J 2021; 19:2027-2044. [PMID: 33995900 PMCID: PMC8085901 DOI: 10.1016/j.csbj.2021.03.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Atomistic details on perturbations induced by Lm4E-IP1 binding are described. The modulation of LmIF4E-1 affinity for the cap is confirmed by energetic analyses. Signaling paths between the allosteric and othosteric sites of LmIF4E-1 are predicted. Lm4E-IP1 binding increases the side-chain entropy of W83 and R172 of LmIF4E-1. A mechanism of dynamic allostery is proposed for the regulation mediated by Lm4E-IP1.
During their life cycle, Leishmania parasites display a fine-tuned regulation of the mRNA translation through the differential expression of isoforms of eukaryotic translation initiation factor 4E (LeishIF4Es). The interaction between allosteric modulators such as 4E-interacting proteins (4E-IPs) and LeishIF4E affects the affinity of this initiation factor for the mRNA cap. Here, several computational approaches were employed to elucidate the molecular bases of the previously-reported allosteric modulation in L. major exerted by 4E-IP1 (Lm4E-IP1) on eukaryotic translation initiation factor 4E 1 (LmIF4E-1). Molecular dynamics (MD) simulations and accurate binding free energy calculations (ΔGbind) were combined with network-based modeling of residue-residue correlations. We also describe the differences in internal motions of LmIF4E-1 apo form, cap-bound, and Lm4E-IP1-bound systems. Through community network calculations, the differences in the allosteric pathways of allosterically-inhibited and active forms of LmIF4E-1 were revealed. The ΔGbind values show significant differences between the active and inhibited systems, which are in agreement with the available experimental data. Our study thoroughly describes the dynamical perturbations of LmIF4E-1 cap-binding site triggered by Lm4E-IP1. These findings are not only essential for the understanding of a critical process of trypanosomatids’ gene expression but also for gaining insight into the allostery of eukaryotic IF4Es, which could be useful for structure-based design of drugs against this protein family.
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Affiliation(s)
- Lilian Hernández-Alvarez
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Antonio B Oliveira
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Center for Theoretical Biological Physics, Rice University, Huston, TX, United States
| | - Jorge Enrique Hernández-González
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge Chahine
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Pedro Geraldo Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Suman de Araujo
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
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10
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Das S. Taking a re-look at cap-binding signatures of the mRNA cap-binding protein eIF4E orthologues in trypanosomatids. Mol Cell Biochem 2020; 476:1037-1049. [PMID: 33169189 DOI: 10.1007/s11010-020-03970-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/31/2020] [Indexed: 01/04/2023]
Abstract
Protein translation leading to polypeptide synthesis involves three distinct events, namely, initiation, elongation, and termination. Translation initiation is a multi-step process that is carried out by ribosomes on the mRNA with the assistance of a large number of proteins called translation initiation factors. Trypanosomatids are kinetoplastidas (flagellated protozoans), some of which cause acute disease syndromes in humans. Vector-borne transmission of protozoan parasites like Leishmania and Trypanosoma causes diseases that affect a large section of the world population and lead to significant morbidity and mortality. The mechanisms of translation initiation in higher eukaryotes are relatively well understood. However, structural and functional conservation of initiation factors in trypanosomatids are only beginning to be understood. Studies carried out so far suggests that at least in Leishmania and Trypanosoma eIF4E function may not be restricted to canonical translation initiation and some of the homologues may have alternate/non-canonical functions. Nonetheless, all of them bind the cap analogs, albeit with different efficiencies, indicating that this property may play an important role in the functionality of eIF4Es. Here, I give a brief background of trypanosomatid eIF4Es and revisit the cap-binding signatures of eIF4E orthologues in trypanosomatids, whose genome sequences are available, in detail, in comparison to human eIF4E1 and Trypanosoma cruzi eIF4E5, with an expanded list of members of this group in light of newer findings. The group 1 and 2 eIF4Es may use either a variation of heIF4E1 or T. cruzi eIF4E5 cap-4-binding signatures, while eIF4E5 and eIF4E6 use distinct amino acid contacts.
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Affiliation(s)
- Supratik Das
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India.
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11
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Belfetmi A, Léger-Abraham M. 1H, 13C, and 15N backbone chemical shift assignments of m 7GTP cap-bound Leishmania initiation factor 4E-1. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:259-263. [PMID: 32519295 PMCID: PMC7462832 DOI: 10.1007/s12104-020-09958-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Most of the translational control of gene expression in higher eukaryotes occurs during the initiation step of protein synthesis. While this process is well characterized in mammalian cells, it is less defined in parasites, including the ones that cause human Leishmaniasis. The Leishmania cap-binding isoform 1 (LeishIF4E-1) is the only isoform that binds the specific trypanosomatids-specific hypermethylated 5' cap, called cap-4, in the human stage of the parasite life cycle. We report here the extensive NMR resonance assignment of LeishIF4E-1 bound to a cap analog, m7GTP. The chemical shift data constitute a prerequisite to understanding specific translation initiation mechanisms used in Leishmania parasites and to developing antiparasitic drugs targeting their translation initiation factors.
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Affiliation(s)
- Anissa Belfetmi
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Mélissa Léger-Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
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12
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Tupperwar N, Meleppattu S, Shrivastava R, Baron N, Gilad A, Wagner G, Léger-Abraham M, Shapira M. A newly identified Leishmania IF4E-interacting protein, Leish4E-IP2, modulates the activity of cap-binding protein paralogs. Nucleic Acids Res 2020; 48:4405-4417. [PMID: 32232353 PMCID: PMC7192595 DOI: 10.1093/nar/gkaa173] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/04/2020] [Accepted: 03/16/2020] [Indexed: 01/06/2023] Open
Abstract
Translation of most cellular mRNAs in eukaryotes proceeds through a cap-dependent pathway, whereby the cap-binding complex, eIF4F, anchors the preinitiation complex at the 5′ end of mRNAs and regulates translation initiation. The requirement of Leishmania to survive in changing environments can explain why they encode multiple eIF4E (LeishIF4Es) and eIF4G (LeishIF4Gs) paralogs, as each could be assigned a discrete role during their life cycle. Here we show that the expression and activity of different LeishIF4Es change during the growth of cultured promastigotes, urging a search for regulatory proteins. We describe a novel LeishIF4E-interacting protein, Leish4E-IP2, which contains a conserved Y(X)4LΦ IF4E-binding-motif. Despite its capacity to bind several LeishIF4Es, Leish4E-IP2 was not detected in m7GTP-eluted cap-binding complexes, suggesting that it could inhibit the cap-binding activity of LeishIF4Es. Using a functional assay, we show that a recombinant form of Leish4E-IP2 inhibits the cap-binding activity of LeishIF4E-1 and LeishIF4E-3. Furthermore, we show that transgenic parasites expressing a tagged version of Leish4E-IP2 also display reduced cap-binding activities of tested LeishIF4Es, and decreased global translation. Given its ability to bind more than a single LeishIF4E, we suggest that Leish4E-IP2 could serve as a broad-range repressor of Leishmania protein synthesis.
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Affiliation(s)
- Nitin Tupperwar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Shimi Meleppattu
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02138, USA
| | - Rohit Shrivastava
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ayelet Gilad
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02138, USA
| | - Mélissa Léger-Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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13
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eIF4E and Interactors from Unicellular Eukaryotes. Int J Mol Sci 2020; 21:ijms21062170. [PMID: 32245232 PMCID: PMC7139794 DOI: 10.3390/ijms21062170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 12/22/2022] Open
Abstract
eIF4E, the mRNA cap-binding protein, is well known as a general initiation factor allowing for mRNA-ribosome interaction and cap-dependent translation in eukaryotic cells. In this review we focus on eIF4E and its interactors in unicellular organisms such as yeasts and protozoan eukaryotes. In a first part, we describe eIF4Es from yeast species such as Saccharomyces cerevisiae, Candida albicans, and Schizosaccharomyces pombe. In the second part, we will address eIF4E and interactors from parasite unicellular species—trypanosomatids and marine microorganisms—dinoflagellates. We propose that different strategies have evolved during evolution to accommodate cap-dependent translation to differing requirements. These evolutive “adjustments” involve various forms of eIF4E that are not encountered in all microorganismic species. In yeasts, eIF4E interactors, particularly p20 and Eap1 are found exclusively in Saccharomycotina species such as S. cerevisiae and C. albicans. For protozoan parasites of the Trypanosomatidae family beside a unique cap4-structure located at the 5′UTR of all mRNAs, different eIF4Es and eIF4Gs are active depending on the life cycle stage of the parasite. Additionally, an eIF4E-interacting protein has been identified in Leishmania major which is important for switching from promastigote to amastigote stages. For dinoflagellates, little is known about the structure and function of the multiple and diverse eIF4Es that have been identified thanks to widespread sequencing in recent years.
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Reolon LW, Vichier-Guerre S, de Matos BM, Dugué L, Assunção TRDS, Zanchin NIT, Pochet S, Guimarães BG. Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4. Nucleic Acids Res 2019; 47:5973-5987. [PMID: 31066441 PMCID: PMC6582342 DOI: 10.1093/nar/gkz339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022] Open
Abstract
Association of the initiation factor eIF4E with the mRNA cap structure is a key step for translation. Trypanosomatids present six eIF4E homologues, showing a low conservation and also differing significantly from the IF4Es of multicellular eukaryotes. On the mRNA side, while in most eukaryotes the mRNA contains cap-0 (7-methyl-GTP), the trypanosomatid mRNA features a cap-4, which is formed by a cap-0, followed by the AACU sequence containing 2′-O-ribose methylations and base methylations on nucleotides 1 and 4. The studies on eIF4E-cap-4 interaction have been hindered by the difficulty to synthesize this rather elaborated cap-4 sequence. To overcome this problem, we applied a liquid-phase oligonucleotide synthesis strategy and describe for the first time the crystal structure of a trypanosomatid eIF4E (T. cruzi EIF4E5) in complex with cap-4. The TcEIF4E5-cap-4 structure allowed a detailed description of the binding mechanism, revealing the interaction mode for the AACU sequence, with the bases packed in a parallel stacking conformation and involved, together with the methyl groups, in hydrophobic contacts with the protein. This binding mechanism evidences a distinct cap interaction mode in comparison with previously described eIF4E structures and may account for the difference of TcEIF4E5-cap-4 dissociation constant in comparison with other eIF4E homologues.
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Affiliation(s)
- Lidia Watanabe Reolon
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil.,Biochemistry Postgraduate Program, Federal University of Parana, Curitiba, Paraná 81530-000, Brazil
| | | | - Bruno Moisés de Matos
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil.,Biochemistry Postgraduate Program, Federal University of Parana, Curitiba, Paraná 81530-000, Brazil
| | - Laurence Dugué
- Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523 CNRS, Paris 75015, France
| | | | - Nilson Ivo Tonin Zanchin
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523 CNRS, Paris 75015, France
| | - Beatriz Gomes Guimarães
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil.,Biochemistry Postgraduate Program, Federal University of Parana, Curitiba, Paraná 81530-000, Brazil
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Abstract
Leishmania parasites are the causative agents of a broad spectrum of diseases. The parasites migrate between sand-fly vectors and mammalian hosts, adapting to changing environments by driving a regulated program of gene expression, with translation regulation playing a key role. The leishmanias encode six different paralogs of eIF4E, the cap-binding translation initiation factor. Since these vary in function, expression profile, and assemblage, it is assumed that each is assigned a specific role throughout the life cycle. Using the CRISPR-Cas9 system for Leishmania, we generated a null mutant of LeishIF4E1, eliminating both alleles. Although the mutant cells were viable, their morphology was altered and their ability to synthesize the flagellum was impaired. Elimination of LeishIF4E1 affected their protein expression profile and decreased their ability to infect cultured macrophages. Restoring LeishIF4E1 expression restored the affected features. This study highlights the importance of LeishIF4E1 in diverse cellular events during the life cycle of Leishmania. Leishmania parasites cycle between sand-fly vectors and mammalian hosts, adapting to changing environmental conditions by driving a stage-specific program of gene expression, which is tightly regulated by translation processes. Leishmania encodes six eIF4E orthologs (LeishIF4Es) and five eIF4G candidates, forming different cap-binding complexes with potentially varying functions. Most LeishIF4E paralogs display temperature sensitivity in their cap-binding activity, except for LeishIF4E1, which maintains its cap-binding activity under all conditions. We used the CRISPR-Cas9 system to successfully generate a null mutant of LeishIF4E1 and examine how its elimination affected parasite physiology. Although the LeishIF4E1–/– null mutant was viable, its growth was impaired, in line with a reduction in global translation. As a result of the mutation, the null LeishIF4E1–/– mutant had a defective morphology, as the cells were round and unable to grow a normal flagellum. This was further emphasized when the LeishIF4E1–/– cells failed to develop the promastigote morphology once they shifted from conditions that generate axenic amastigotes (33°C, pH 5.5) back to neutral pH and 25°C, and they maintained their short flagellum and circular structure. Finally, the LeishIF4E1–/– null mutant displayed difficulty in infecting cultured macrophages. The morphological changes and reduced infectivity of the mutant may be related to differences in the proteomic profile of LeishIF4E1–/– cells from that of controls. All defects monitored in the LeishIF4E1–/– null mutant were reversed in the add-back strain, in which expression of LeishIF4E1 was reconstituted, establishing a strong link between the cellular defects and the absence of LeishIF4E1 expression. IMPORTANCELeishmania parasites are the causative agents of a broad spectrum of diseases. The parasites migrate between sand-fly vectors and mammalian hosts, adapting to changing environments by driving a regulated program of gene expression, with translation regulation playing a key role. The leishmanias encode six different paralogs of eIF4E, the cap-binding translation initiation factor. Since these vary in function, expression profile, and assemblage, it is assumed that each is assigned a specific role throughout the life cycle. Using the CRISPR-Cas9 system for Leishmania, we generated a null mutant of LeishIF4E1, eliminating both alleles. Although the mutant cells were viable, their morphology was altered and their ability to synthesize the flagellum was impaired. Elimination of LeishIF4E1 affected their protein expression profile and decreased their ability to infect cultured macrophages. Restoring LeishIF4E1 expression restored the affected features. This study highlights the importance of LeishIF4E1 in diverse cellular events during the life cycle of Leishmania.
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16
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Terrao M, Marucha KK, Mugo E, Droll D, Minia I, Egler F, Braun J, Clayton C. The suppressive cap-binding complex factor 4EIP is required for normal differentiation. Nucleic Acids Res 2019; 46:8993-9010. [PMID: 30124912 PMCID: PMC6158607 DOI: 10.1093/nar/gky733] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/01/2018] [Indexed: 12/27/2022] Open
Abstract
Trypanosoma brucei live in mammals as bloodstream forms and in the Tsetse midgut as procyclic forms. Differentiation from one form to the other proceeds via a growth-arrested stumpy form with low messenger RNA (mRNA) content and translation. The parasites have six eIF4Es and five eIF4Gs. EIF4E1 pairs with the mRNA-binding protein 4EIP but not with any EIF4G. EIF4E1 and 4EIP each inhibit expression when tethered to a reporter mRNA, but while tethered EIF4E1 suppresses only when 4EIP is present, suppression by tethered 4EIP does not require the interaction with EIF4E1. In growing bloodstream forms, 4EIP is preferentially associated with unstable mRNAs. Bloodstream- or procyclic-form trypanosomes lacking 4EIP have only a marginal growth disadvantage. Bloodstream forms without 4EIP are, however, defective in translation suppression during stumpy-form differentiation and cannot subsequently convert to growing procyclic forms. Intriguingly, the differentiation defect can be complemented by a truncated 4EIP that does not interact with EIF4E1. In contrast, bloodstream forms lacking EIF4E1 have a growth defect, stumpy formation seems normal, but they appear unable to grow as procyclic forms. We suggest that 4EIP and EIF4E1 fine-tune mRNA levels in growing cells, and that 4EIP contributes to translation suppression during differentiation to the stumpy form.
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Affiliation(s)
- Monica Terrao
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Kevin K Marucha
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Elisha Mugo
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Dorothea Droll
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Igor Minia
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Franziska Egler
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Johanna Braun
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Christine Clayton
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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17
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Abstract
In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
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Affiliation(s)
- Christine Clayton
- University of Heidelberg Center for Molecular Biology (ZMBH), Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
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