Stem-loop-induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control
Anna M. Smirnova,
Vladislava Hronová,
Mahabub Pasha Mohammad,
Anna Herrmannová,
Stanislava Gunišová,
Denisa Petráčková,
Petr Halada,
Štěpán Coufal,
Michał Świrski,
Justin Rendleman,
Kristína Jendruchová,
Maria Hatzoglou,
Petra Beznosková,
Christine Vogel,
Leoš Shivaya Valášek
Affiliations
Anna M. Smirnova
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Vladislava Hronová
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Mahabub Pasha Mohammad
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Anna Herrmannová
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Stanislava Gunišová
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Denisa Petráčková
Laboratory of Post-transcriptional Control of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Petr Halada
Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
Štěpán Coufal
Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Michał Świrski
Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
Justin Rendleman
Department of Biology, New York University, New York, NY, USA
Kristína Jendruchová
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Maria Hatzoglou
Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
Petra Beznosková
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
Christine Vogel
Department of Biology, New York University, New York, NY, USA; Corresponding author
Leoš Shivaya Valášek
Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Corresponding author
Summary: Activating transcription factor 4 (ATF4) is a master transcriptional regulator of the integrated stress response, leading cells toward adaptation or death. ATF4’s induction under stress was thought to be due to delayed translation reinitiation, where the reinitiation-permissive upstream open reading frame 1 (uORF1) plays a key role. Accumulating evidence challenging this mechanism as the sole source of ATF4 translation control prompted us to investigate additional regulatory routes. We identified a highly conserved stem-loop in the uORF2/ATF4 overlap, immediately preceded by a near-cognate CUG, which introduces another layer of regulation in the form of ribosome queuing. These elements explain how the inhibitory uORF2 can be translated under stress, confirming prior observations but contradicting the original regulatory model. We also identified two highly conserved, potentially modified adenines performing antagonistic roles. Finally, we demonstrated that the canonical ATF4 translation start site is substantially leaky scanned. Thus, ATF4’s translational control is more complex than originally described, underpinning its key role in diverse biological processes.
