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The translational landscape of HIV-1 infected cells reveals key gene regulatory principles

A study by Kibe et al. of the translational landscape of HIV-1 reveals alternative translation events, including use of upstream and internal open reading frames, an RNA fold regulating gag-pol frameshifting and ribosome collisions, providing new targets for antivirals.

Anuja Kibe
Stefan Buck
Neva Caliskan
ResearchOpen Access15 Jan 2025
Nature Structural & Molecular Biology

Volume: 32, P: 841-852
Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

Many RNA viruses employ programmed –1 ribosomal frameshifting (PRF) to expand their coding capacity and optimize production of viral proteins. Here, the authors report structural and biophysical analysis of protein 2A from a cardiovirus, with insights into the mechanism of its PRF-stimulatory function.

Chris H. Hill
Lukas Pekarek
Ian Brierley
ResearchOpen Access09 Dec 2021
Nature Communications

Volume: 12, P: 1-16
Author Correction: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging

Liqing Ye
Anne-Sophie Gribling-Burrer
Redmond P. Smyth
Amendments and CorrectionsOpen Access24 Feb 2023
Nature Structural & Molecular Biology

Volume: 30, P: 403
Thermodynamic control of −1 programmed ribosomal frameshifting

Programmed ribosomal frameshifting (PRF) is an alternative translation strategy that causes controlled slippage of the ribosome along the mRNA, changing the sequence of the synthesized protein. Here the authors provide a thermodynamic framework that explains how mRNA sequence determines the efficiency of frameshifting.

Lars V. Bock
Neva Caliskan
Helmut Grubmüller
ResearchOpen Access10 Oct 2019
Nature Communications

Volume: 10, P: 1-11
Translon: a single term for translated regions

Michał I. Świrski
Jack A. S. Tierney
Pavel V. Baranov
Correspondence01 Sept 2025
Nature Methods

Volume: 22, P: 2002-2006
The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Programmed ribosomal frameshifting (PRF) occurs in many viruses including SARS-CoV-2 to allow the translation of multiple proteins from a single transcript. Here, the authors identify the human short isoform of the zinc-finger antiviral protein (ZAP-S) as a direct regulator of PRF in SARS-CoV-2 that severely impairs SARS-CoV-2 frameshifting in cells and directly interacts with the SARS-CoV-2 RNA; interfering with the folding of the frameshift RNA element.

Matthias M. Zimmer
Anuja Kibe
Neva Caliskan
ResearchOpen Access10 Dec 2021
Nature Communications

Volume: 12, P: 1-15
Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging

Comprehensive functional and structural probing of the HIV-1 5′ untranslated region reveals novel interactions that regulate RNA dimerization, Pr55Gag binding and genome packaging into virions.

Liqing Ye
Anne-Sophie Gribling-Burrer
Redmond P. Smyth
ResearchOpen Access28 Mar 2022
Nature Structural & Molecular Biology

Volume: 29, P: 306-319
Spacer prioritization in CRISPR–Cas9 immunity is enabled by the leader RNA

To promote expression of the most recently acquired CRISPR spacers, the transcribed leader region upstream of CRISPR arrays interacts with the conserved repeats bordering the newest spacer, with the resulting interaction promoting tracrRNA hybridization with the second repeat and accelerating crRNA processing

Chunyu Liao
Sahil Sharma
Chase L. Beisel
Research21 Mar 2022
Nature Microbiology

Volume: 7, P: 530-541
The SARS-CoV-2 RNA–protein interactome in infected human cells

Interactions between SARS-CoV-2 viral RNAs and host cell proteins during infection are evaluated to improve our understanding of viral RNA functions and the host innate immune response.

Nora Schmidt
Caleb A. Lareau
Mathias Munschauer
ResearchOpen Access21 Dec 2020
Nature Microbiology

Volume: 6, P: 339-353
Choreography of molecular movements during ribosome progression along mRNA

Ensemble kinetics and FRET analyses reveal the sequence of collective motions on the E. coli ribosome during translocation promoted by EF-G and allow identification of a new early forward swiveling of the SSU head.

Riccardo Belardinelli
Heena Sharma
Marina V Rodnina
Research21 Mar 2016
Nature Structural & Molecular Biology

Volume: 23, P: 342-348
Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)

Here, the authors discuss dual-reporter systems and confounding variables that may lead to misinterpretation of results. They propose guidelines for robust design, physiological interpretation and accurate reporting when using dual reporters.

Gary Loughran
Dmitry E. Andreev
Pavel V. Baranov
Reviews03 Mar 2025
Nature Structural & Molecular Biology

Volume: 32, P: 418-430

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