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Paz I, Argoetti A, Cohen N, Even N, Mandel-Gutfreund Y. RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment. Methods Mol Biol 2022; 2404:53-65. [PMID: 34694603 DOI: 10.1007/978-1-0716-1851-6_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
RNA-binding proteins (RBPs) play a key role in post-transcriptional regulation via binding to coding and non-coding RNAs. Recent development in experimental technologies, aimed to identify the targets of RBPs, has significantly broadened our knowledge on protein-RNA interactions. However, for many RBPs in many organisms and cell types, experimental RNA-binding data is not available. In this chapter we describe a computational approach, named RBPmap, available as a web service via http://rbpmap.technion.ac.il/ and as a stand-alone version for download. RBPmap was designed for mapping and predicting the binding sites of any RBP within a nucleic acid sequence, given the availability of an experimentally defined binding motif of the RBP. The algorithm searches for a sub-sequence that significantly matches the RBP motif, considering the clustering propensity of other weak matches within the motif environment. Here, we present different applications of RBPmap for discovering the involvement of RBPs and their targets in a variety of cellular processes, in health and disease states. Finally, we demonstrate the performance of RBPmap in predicting the binding targets of RBPs in large-scale RNA-binding data, reinforcing the strength of the tool in distinguishing cognate binding sites from weak motifs.
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Affiliation(s)
- Inbal Paz
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Noa Cohen
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Computer Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Niv Even
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Computer Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
- Department of Computer Sciences, Technion-Israel Institute of Technology, Haifa, Israel.
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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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Etzion-Fuchs A, Todd DA, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res 2021; 49:e78. [PMID: 33999210 PMCID: PMC8287948 DOI: 10.1093/nar/gkab356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/30/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023] Open
Abstract
Domains are instrumental in facilitating protein interactions with DNA, RNA, small molecules, ions and peptides. Identifying ligand-binding domains within sequences is a critical step in protein function annotation, and the ligand-binding properties of proteins are frequently analyzed based upon whether they contain one of these domains. To date, however, knowledge of whether and how protein domains interact with ligands has been limited to domains that have been observed in co-crystal structures; this leaves approximately two-thirds of human protein domain families uncharacterized with respect to whether and how they bind DNA, RNA, small molecules, ions and peptides. To fill this gap, we introduce dSPRINT, a novel ensemble machine learning method for predicting whether a domain binds DNA, RNA, small molecules, ions or peptides, along with the positions within it that participate in these types of interactions. In stringent cross-validation testing, we demonstrate that dSPRINT has an excellent performance in uncovering ligand-binding positions and domains. We also apply dSPRINT to newly characterize the molecular functions of domains of unknown function. dSPRINT's predictions can be transferred from domains to sequences, enabling predictions about the ligand-binding properties of 95% of human genes. The dSPRINT framework and its predictions for 6503 human protein domains are freely available at http://protdomain.princeton.edu/dsprint.
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Affiliation(s)
- Anat Etzion-Fuchs
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ 08544, USA
| | - David A Todd
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ 08544, USA.,Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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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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Palomino‐Hernandez O, Margreiter MA, Rossetti G. Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies. Isr J Chem 2020. [DOI: 10.1002/ijch.202000021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Oscar Palomino‐Hernandez
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
- Computation-based Science and Technology Research CenterThe Cyprus Institute Nicosia 2121 Cyprus
- Institute of Life ScienceThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Michael A. Margreiter
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Jülich Supercomputing Centre (JSC)Forschungszentrum Jülich 52425 Jülich Germany
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation University Hospital AachenRWTH Aachen University Pauwelsstraße 30 52074 Aachen Germany
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Shrivastava R, Drory-Retwitzer M, Shapira M. Nutritional stress targets LeishIF4E-3 to storage granules that contain RNA and ribosome components in Leishmania. PLoS Negl Trop Dis 2019; 13:e0007237. [PMID: 30870425 PMCID: PMC6435199 DOI: 10.1371/journal.pntd.0007237] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 03/26/2019] [Accepted: 02/12/2019] [Indexed: 12/02/2022] Open
Abstract
Leishmania parasites lack pathways for de novo purine biosynthesis. The depletion of purines induces differentiation into virulent metacyclic forms. In vitro, the parasites can survive prolonged periods of purine withdrawal changing their morphology to long and slender cells with an extended flagellum, and decreasing their translation rates. Reduced translation leads to the appearance of discrete granules that contain LeishIF4E-3, one of the six eIF4E paralogs encoded by the Leishmania genome. We hypothesize that each is responsible for a different function during the life cycle. LeishIF4E-3 is a weak cap-binding protein paralog, but its involvement in translation under normal conditions cannot be excluded. However, in response to nutritional stress, LeishIF4E-3 concentrates in specific cytoplasmic granules. LeishIF4E-3 granulation can be induced by the independent elimination of purines, amino acids and glucose. As these granules contain mature mRNAs, we propose that these bodies store inactive transcripts until recovery from stress occurs. In attempt to examine the content of the nutritional stress-induced granules, they were concentrated over sucrose gradients and further pulled-down by targeting in vivo tagged LeishIF4E-3. Proteomic analysis highlighted granule enrichment with multiple ribosomal proteins, suggesting that ribosome particles are abundant in these foci, as expected in case of translation inhibition. RNA-binding proteins, RNA helicases and metabolic enzymes were also enriched in the granules, whereas no degradation enzymes or P-body markers were detected. The starvation-induced LeishIF4E-3-containing granules, therefore, appear to store stalled ribosomes and ribosomal subunits, along with their associated mRNAs. Following nutritional stress, LeishIF4E-3 becomes phosphorylated at position S75, located in its less-conserved N-terminal extension. The ability of the S75A mutant to form granules was reduced, indicating that cellular signaling regulates LeishIF4E-3 function. Cells respond to cellular stress by decreasing protein translation, to prevent the formation of partially folded or misfolded new polypeptides whose accumulation can be detrimental to living cells. Under such conditions, the cells benefit from storing inactive mRNAs and stalled ribosomal particles, to maintain their availability once conditions improve; dedicated granules offer a solution for such storage. Leishmania parasites are exposed to a variety of stress conditions as a natural part of their life cycle, including the nutritional stress that the parasites experience within the gut of the sandfly. Thus, Leishmania and related trypanosomatids serve as a good model system to investigate RNA fate during different stress conditions. Various granules appear in Leishmania and related organisms in response to different stress conditions. Here, we investigated how nutritional stress, in particular elimination of purines, induced the formation of granules that harbor a specific cap-binding protein, LeishIF4E-3. The starvation-induced LeishIF4E-3 containing granules consist of a variety of ribosomal proteins, along with RNA-binding proteins and mature mRNAs. We thus propose that Leishmania modulates the assembly of LeishIF4E-3-containing granules for transient storage of stalled ribosomal particles and inactive mRNAs. Following renewal of nutrient availability, as occurs during the parasite’s life cycle, the granules disappear. Although their fate is yet unclear, they could be recycled in the cell. Unlike other granules described in trypanosomes, the LeishIF4E-3-containing granules did not contain RNA degradation enzymes, suggesting that their function is mainly for storage until conditions improve.
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Affiliation(s)
- Rohit Shrivastava
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Matan Drory-Retwitzer
- Department of Computer 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
- * E-mail:
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