Hashem Lab

Publications

  • Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine

Wang C, Kassem S, Rocha REO, Sun P, Nguyen TT, Kloehn J, Liu X, Brusini L, Bonavoglia A, Barua S, Boissier F, Lucia Del Cistia M, Peng H, Tang X, Xie F, Wang Z, Vadas O, Suo X, Hashem Y, Soldati-Favre D, Jia Y (2024). Nature Commun. 15:10689. DOI: 10.1038/s41467-024-55033-z.

  • A rapid, facile, and economical method for the isolation of ribosomes and translational machinery for structural and functional studies

Erath J, Kemper D, Mugo E, Jacoby A, Valenzuela E, Jungers CF, Beatty WL, Hashem Y, Jovanovic M, Djuranovic S, Djuranovic SP (2024). BioRxiv. 22:2024.10.21.619433. doi: 10.1101/2024.10.21.619433.

  • N6-methyladenosine in 5′ UTR does not promote translation initiation

Guca E, Alarcon R, Palo MZ, Santos L, Alonso-Gil S, Davyt M, de Lima LHF, Boissier F, Das S, Zagrovic B, Puglisi JD, Hashem Y, Ignatova Z (2024). Mol Cell. 15:S1097-2765(23)01074-2. DOI: 10.1016/j.molcel.2023.12.028.

  • Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering

De S, Zhou M, Brown ZP, Burton-Smith RN, Hashem Y, Pestova T, Hellen CUT, Frank J (2024). BioRxiv. 18:2024.10.11.617640. doi: 10.1101/2024.10.11.617640.

  • Regulation of the macrolide resistance ABC-F translation factor MsrD

Fostier CR, Ousalem F, Leroy EC, Ngo S, Soufari H, Innis CA, Hashem Y, Boël G (2023). Nat Commun. 14: 3891. DOI: https://doi.org/10.1038/s41467-023-39553-8

  • Purification of Mitochondrial Ribosomal Complexes from Trypanosoma cruzi and Leishmania tarentolae for Cryo-EM Analysis

Durrieu-Gaillard S, Sissler M, Hashem Y (2022). Bio Protoc. Volume 12. DOI: 10.21769/BioProtoc.4425. Free postprint here.

  • Purification of Mitochondrial Ribosomal Complexes from Trypanosoma cruzi and Leishmania tarentolae for Cryo-EM Analysis

Durrieu-Gaillard S, Sissler M, Hashem Y (2022). Bio Protoc. Volume 12. DOI: 10.21769/BioProtoc.4425. Free postprint here.

  • Mitoribosome assembly comes into view

Sissler M, Hashem Y (2021). Nat Struct Mol Biol. 28, pages 631–633. DOI: 10.1038/s41594-021-00640-3.

  • How to build a ribosome from RNA fragments in Chlamydomonas mitochondria

Waltz F, Salinas-Giegé T, Englmeier R, Meichel H, Soufari H, Kuhn L, Pfeffer S, Förster F, Engel B D, Giegé P, Drouard L, Hashem Y(2021). Nat Commun 7176. DOI: doi.org/10.1038/s41467-021-27200-z.

  • Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs

Sweeney T R, Dhote V, Guca E, Hellen C U T, Hashem Y, Pestova T V (2021). Nucleic Acids Res Volume 49, 12955–12969. DOI: 10.1093/nar/gkab1192.

  • Purification and Cryo-electron Microscopy Analysis of Plant Mitochondrial Ribosomes

Waltz F, Giegé P, Hashem Y (2021). Bio Protoc. Volume 11. DOI: 10.21769/BioProtoc.4111.

  • Peculiarities of aminoacyl-tRNA synthetases from trypanosomatids

Parrot C, Moulinier L, Bernard F, Hashem Y, Dupuy D, Sissler M (2021). J Biol Chem Volume 297, 100913. DOI: 10.1016/j.jbc.2021.100913.

  • Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus

Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y (2021). Front Mol Biosci. Volume 8. DOI: 10.3389/fmolb.2021.738752.

  • The Halastavi árva virus intergenic region IRES promotes translation by the simplest possible initiation mechanism

Abaeva I S, Vicens Q, Bochler A, Soufari H, Simonetti A, Pestova T V, Hashem Y, Hellen C U T (2020). Cell Reports Volume 33, 108476. DOI: 10.1016/j.celrep.2020.108476. (preprint on bioRxiv)

  • Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis

Soufari H, Waltz F, Parrot C, Durrieu-Gaillard S, Bochler A, Kuhn L, Sissler M, Hashem Y (2020). PNAS volume 117. DOI: 10.1073/pnas.2011301117. (preprint on bioRxiv)

  • Specificities of the plant mitochondrial translation apparatus

Waltz F, Corre N, Hashem Y, Giegé P. (2020).  pii: S1567-7249(20)30013-1. doi: 10.1016/j.mito.2020.04.008.

  • Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts

Bochler A, Brito Querido J, Prilepskaja T, Soufari H, Lucia Del Cistia M, Kuhn L, Rimoldi Ribeiro A, Valasek LS, Hashem Y. (2020). Cell Reports  Volume 33, 108534. DOI: 10.1016/j.celrep.2020.108534. (preprint on bioRxiv)

  • Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM

Soufari H, Parrot C, Kuhn L, Waltz F, Hashem Y. (2020). Nature Communications volume 11, 5195. DOI: 10.1038/s41467-020-18814-w.(preprint on bioRxiv)

  • Escherichia coli NusG links the lead ribosome with the transcription elongation complex

Washburn RS, Zuber PK, Sun M, Hashem Y, Shen B, Li W, Harvey S, Acosta Reyes FJ, Gottesman ME, Knauer SH, Frank J (2020).  iScience. 23, 101352. doi: 10.1016/j.isci.2020.101352. (prepreint on BioRxiv)

  • Cryo-EM structure of the RNA-rich plant mitochondrial ribosome

Waltz F, Soufari H, Bochler A, Giegé P, Hashem Y (2020). Nature plants. 6, 377–383. DOI: 10.1038/s41477-020-0631-5. (free preprint on BioRxiv)

  • Structural insights into the mammalian late-stage initiation complexes

Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y (2020). Cell Reports 31, 107497. DOI: https://doi.org/10.1016/j.celrep.2020.03.061. (preprint on BioRxiv)

  • Small is big in Arabidopsis mitochondrial ribosome

Waltz F, Nguyen TT, Arrivé M, Bochler A, Chicher J, Hammann P, Kuhn L, Quadrado M, Mireau H, Hashem Y, Giegé P (2019). Nature plants. 5, 106-117. doi: 10.1038/s41477-018-0339-y.

  • Major structural rearrangements of the canonical eukaryotic translation initiation complex

Guca E & Hashem Y (2018). Current Opinion in Structural Biology, Issue 53: Protein and nucleic acid interactions, p.151-158.

  • Structural insights into the role of diphthamide on elongation factor 2 in mRNA reading-frame maintenance

Pellegino S, Demeshkina N, Mancera-Martinez E, Melnikov S, Simonetti A, Myasnikov A, Yusupov M, Yusupova G, Hashem Y (2018). J Mol Biol 430,2677-2687.

  • The jigsaw puzzle of mRNA translation initiation in eukaryotes: a decade of structures unraveling the mechanics of the process

Hashem Y, Frank J (2018). Annual review of biophysics 47, 125-151

  • The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein

Querido JB, Mancera-Martínez E, Vicens Q, Bochler A, Chicher J, Simonetti A, Hashem Y (2017).  Structure 25 (12), 1785-1794. e3

  • ABCE1: A special factor that orchestrates translation at the crossroad between recycling and initiation

Mancera-Martínez E, Querido JB, Valasek LS, Simonetti A, Hashem Y (2017). RNA biology 14 (10), 1279-1285

  • Structures and dynamics of hibernating ribosome’s from Staphylococcus aureus mediated by intermolecular interactions of HPF

Khusainov I, Vicens Q, Ayupov R, Usachev K, Myasnikov A, Simonetti A, Validov S, Kieffer B, Yusupova G, Yusupov M, Hashem Y (2017). EMBO J 36,2073-2087.

  • Structure of the 70S ribosome from human pathogen Staphylococcus aureus

Khusainov I, Vicens Q, Bochler A, Grosse F, Myasnikov A, Ménétret JF, Chicher J, Marzi S, Romby P, Yusupova G, Yusupov M, Hashem Y (2017). Nucleic Acids Res 45,1026.

  • Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle

Valasek LS, Zeman J, Wagner S, Beznoskova P, Pavlíkova Z, Mohammad MP, Hronova V, Herrmannova A, Hashem Y, Gunisova S (2017). Nucleic Acids Res 45,10948-10968.

  • A glimpse on Staphylococcus aureus translation machinery and its control

Khusainov I, Marenna A, Cerciat M, Fechter P, Hashem Y, Marzi S, Romby P, Yusupova G, Yusupov M (2016). Molecular Biology, 50:477-488.

  • eIF3 peripheral subunits rearrangement after mRNA binding and start-codon recognition

Simonetti A, Querido JB, Myasnikov AG, Mancera-Martinez E, Renaud A, Kuhn L, Hashem  Y (2016). Molecular Cell 63 (2), 206-217

  • pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei

Chikne V, Doniger T, Rajan KS, Bartok O, Eliaz D, Cohen-Chalamish S, Tschudi C, Unger R, Hashem Y, Kadener S, Michaeli SA (2016). Scientific Reports 6: Article number: 25296.

  • Dynamical features of the Plasmodium falciparum ribosome during translation.

Sun M, Li W, Blomqvist K, Das S, Hashem Y, Dvorin JD, Frank J (2015). Nucleic Acids Res 43:10515-10524.

  • Structure of mammalian eIF3 in the context of the 43S preinitiation complex

des Georges A, Dhote V, Kuhn L, Hellen CUT, Pestova TV, Frank J, Hashem Y (2015). Nature 525,491–495.

  • Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy

Liao HY, Hashem Y, Frank J (2015). Structure 23:1129-37.

  Y. H. Postdoc publications:

  • EttA binds at ribosomal E site and regulates translation by restricting ribosome dynamics

Chen B, Boël G, Hashem Y, Ning W, Fei J, Wang C, Gonzalez RL Jr., Hunt JF, Frank J (2014). NSMB doi:10.1038/nsmb.2741.

  • EttA, an energy-sensing ABC-F protein, gates ribosome entry into the elongation cycle

Boël G, Smith PC, Englander MT, Chen B, Hashem Y, Testa AJ, Fischer JJ, Wieden HJ, Frank J, Gonzalez RL Jr., Hunt JF (2014). NSMB doi:10.1038/nsmb.2740.

  • Structure of the mammalian ribosomal pre-termination complex associated with eRF1•eRF3•GDPNP

des Georges A, Hashem Y, Unbehau A, Grassucci RA, Taylor D, Hellen CUT, Pestova TV, Frank J (2013). Nucleic Acides Res 42:3409–3418.

  • Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit

Hashem Y, Des Georges A, Dhote V, Langlois R, Liao YH, Grassucci RA, Pestova TV, Hellen CUT, Frank J (2013). Nature 503:539-543.

  • RF3 action is regulated by a class-I release factor and L7/L12 during translation termination

Pallesen J, Hashem Y, Koripella RV, Korkmaz G, Huang C, Ehrenberg M, Sanyal S, Frank J (2013;2). eLife:e00411.

  • Structural insight into the mammalian ribosomal 43S preinitiation complex

Hashem Y, Des Georges A, Dhote V, Langlois R, Liao YH, Grassucci RA, Hellen CUT, Pestova TV, Frank J (2013). Cell 153:1108-1119.

  • High-resolution cryo-EM structure of the Trypanosoma bruceieukaryotic ribosome

Hashem Y, Des Georges A, Fu J, Buss SN, Jossinet F, Jobe A, Zhang Q, Liao HY, Grassucci RA, Bajaj C, Westhof E, Madison-Antenucci S, Frank J (2013). Nature 494:385–389.

  •  Integrity of the P-site is probed during maturation of the 60S ribosomal subunit

Bussiere C, Hashem Y, Arora S, Frank J, Johnson AW (2012). JCB 197:747-59.

  •  tmRNA on its way through the ribosome: Two steps of resume, and what next?

Fu J, Hashem Y, Wower J, Frank J (2011). RNA Biol 1;8:586-90.

  • Visualizing the transfer-messenger RNA as the ribosome resumes translation

Fu J, Hashem Y, Wower I, Lei J, Liao HY, Zwieb C, Wower J, Frank J (2010). EMBO J 29:3819-3825.