Biology subjects

Rahil, H.

Publications and source records attributed to Rahil, H..

3 recordsLinked to original sources

bioRxiv2024

Molecular basis of mRNA delivery to the bacterial ribosome

Protein synthesis begins with the formation of a ribosome-mRNA complex. In bacteria, the 30S ribosomal subunit is recruited to many mRNAs through base pairing with the Shine Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs and RNA polymerase (RNAP) can promote recruitment of the pioneering 30S subunit. Here we examined ribosome recruitment to nascent mRNAs using cryo-EM, single-molecule fluorescence co-localization, and in-cell crosslinking mass spectrometry. We show that bS1 delivers the mRNA to the ribosome for SD duplex formation and 30S subunit activation. Additionally, bS1 mediates the stimulation of translation initiation by RNAP. Together, our work provides a mechanistic framework for how the SD duplex, ribosomal proteins and RNAP cooperate in 30S recruitment to mRNAs and establish transcription-translation coupling.

biochemistry↗

bioRxiv2023

Yeast eukaryotic initiation factor 4B remodels the mRNA entry site on the small ribosomal subunit

Eukaryotic initiation factor 4B (eIF4B) belongs to the eIF4 group of factors that help in mRNA recruitment to the ribosomal preinitiation complex (PIC) in all eukaryotic organisms. eIF4B stimulates the helicase activity of eIF4A and helps in the formation of the 48S PIC by facilitating mRNA recruitment. However, there is no clear understanding of the location of eIF4B on the 40S and how eIF4B helps in the recruitment of mRNAs. In this work using cryo-electron microscopy, we show that yeast eIF4B binds to the 40S ribosomal subunit at the mRNA entry channel making contacts with ribosomal proteins uS10, uS3, and eS10 and ribosomal rRNA helix h16. The yeast eIF4B position on the 40S overlaps with the RRM domain of eIF3g indicating that the binding of eIF4B may trigger the relocation of the eIF3 b-g-i module to the subunit interface. The 40S head is in partially open conformation that may facilitate the release of eIF3j and hence aid mRNA recruitment and scanning. The structural analysis of yeast eIF4B-bound ribosomal complex provides insight into possible events during mRNA recruitment.

biophysics↗

bioRxiv2021

Drug targeting Nsp1-ribosomal complex shows antiviral activity against SARS-CoV-2

The SARS-Cov-2 non-structural protein 1 (Nsp1) contains an N-terminal domain and C-terminal helices connected by a short linker region. The C-terminal helices of Nsp1 (Nsp1-C-ter) from SARS-Cov-2 bind in the mRNA entry channel of the 40S ribosomal subunit and block the entry of mRNAs thereby shutting down host protein synthesis. Nsp1 suppresses the host immune function and is vital for viral replication. Hence, Nsp1 appears to be an attractive target for therapeutics. In this study, we have in silico screened Food and Drug Administration (FDA)-approved drugs against Nsp1-C-ter and find that montelukast sodium hydrate binds to Nsp1-C-ter with a binding affinity (KD) of 10.8{+/-}0.2 M in vitro and forms a stable complex with it in simulation runs with a binding energy of -76.71{+/-}8.95 kJ/mol. The drug also rescues the inhibitory effect of Nsp1 in host protein synthesis as demonstrated by the expression of firefly luciferase reporter gene in cells. Importantly, montelukast sodium hydrate demonstrates antiviral activity against SARS-CoV-2 with reduced viral replication in HEK cells expressing ACE2 and Vero-E6 cells. We therefore propose montelukast sodium hydrate may help in combatting SARS-CoV-2 infection.

biophysics↗