Structural biology of the mRNA interactome and TRIM proteins
Biophysics
Developmental Biology
Final Report Abstract
The two major objectives of this proposal were to investigate the connection between ubiquitination and RNA binding in TRIM proteins and how novel RNA binding proteins/domains recognize their cognate RNA motifs. Both aims have a focus on a mechanistic understanding, obtained by combining a range of structural biology methods, including NMR, X-ray crystallography, small-angle X-ray and neutron scattering. For the second objective, we could reach the goal as described above, which is an essential step to fully understand the involvement of this protein in neuronal development. In this instance we could again demonstrate how powerful integrative structure modelling is. We also demonstrated how useful NMR can be in the validation of potential novel RNA binding proteins identified in mRNA interactome capture studies. Interestingly, we could confirm RNA binding for some but not all newly identified RNA binding proteins. Regarding the first objective, we are on our way towards establishing a general understanding of the TRIM2/3-related connection between RNA binding and ubiquitination. We are not yet at a stage where we can summarize our findings into a coherent article with high impact, but due to recent results, we are very much optimistic that this can be done within the next year. A surprising turn of events occurred during our work on TRIM25. Also here, we expected that RNA binding will initiate ubiquitination of the adjacent mRNP complex to regulate mRNA translation or degradation. However, based on our structural, biophysical and biochemical results we had to revise our hypothesis and now try to proof that RNA binding will actually increase efficiency of TIRM25 mediated ubiquitination.
Publications
- (2015). The crystal structure of the NHL domain in complex with RNA reveals the molecular basis of Drosophila braintumor-mediated gene regulation. Cell Reports 13(6): 1206-1220
Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann JC, Krahn MP, Meister G
(See online at https://doi.org/10.1016/j.celrep.2015.09.068) - (2017). Segmental, domain-selective perdeuteration and small-angle neutron scattering for structural analysis of multi-domain proteins. Angewandte Chemie Int Ed Engl 56(32): 9322-9325
Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M
(See online at https://doi.org/10.1002/anie.201702904) - (2018). A general small-angle X-ray scattering-based screening protocol validated for protein-RNA interactions. ACS Combinatorial Science 20(4): 197-202
Chen PC, Masiewicz P, Rybin V, Svergun D, Hennig J
(See online at https://doi.org/10.1021/acscombsci.8b00007) - (2018). Molecuar mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition. Nature Communcations 9(1): 1820
Koliopoulos MG, Lethier M, van der Veen AG, Haubrich K, Hennig J, Kowalinski E, Stevens RV, Martin SR, Reis E Sousa C, Cusack S, Rittinger K
(See online at https://doi.org/10.1038/s41467-018-04214-8) - (2018). The role of small-angle scattering in structure-based screening applications. Biophys Rev 10(5): 1295-1310
Chen PC, Hennig J
(See online at https://doi.org/10.1007/s12551-018-0464-x) - (2019). Combined Small-Angle X-ray and neutron scattering restrains in molecular dynamics simulations. J Chem Theory Comput 15(8):4687-4698
Chen PC, Shevchuk R, Strnad FM, Lorenz C, Karge L, Gilles R, Stadler AM, Hennig J, Hub JS
(See online at https://doi.org/10.1021/acs.jctc.9b00292) - (2019). Emerging RNA-binding roles in the TRIM family of ubiquitin ligases. Biol Chem 400(11):1443-1464
Williams FP, Haubrich K, Perez-Borrajero C, Hennig J
(See online at https://doi.org/10.1515/hsz-2019-0158) - (2020). Integrative Structural Biology of protein-RNA complexes. Structure 28(1): 6-28
Dimitrova-Paternoga L, Jagtap PKA, Chen PC, Hennig J
(See online at https://doi.org/10.1016/j.str.2019.11.017) - (2020). Structure-based screening of binding affinities via small-angle X-ray scattering. IUCrJ 7: 644-655
Chen PC, Masiewicz P, Perez K, Hennig J
(See online at https://doi.org/10.1107/s2052252520004169) - (2021). Mechanistic insights into RNA binding and RNA-regulated RIG-I ubiquitination by TRIM25
Haubrich K, Augsten S, Alvarez L, Huppertz I, Simon B, Perez K, Masiewicz P, Lethier M, Rittinger K, Gabel F, Hentze MW, Cusack S, Hennig J
(See online at https://doi.org/10.1101/2020.05.04.070177) - (2021). Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 49(15): 8866-8885
Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J
(See online at https://doi.org/10.1093/nar/gkab635) - (2021). Validation and classification of RNA binding protein identified by mRNA interactome capture. RNA 27(10): 1173-1185
Vaishali, Dimitrova-Paternoga L, Haubrich K, Sun M, Ephrussi A, Hennig J
(See online at https://doi.org/10.1261/rna.078700.121)
