The Universally Conserved ATPase YchF Regulates Translation of Leaderless mRNA in Response to Stress Conditions

Abstract

The universally conserved P-loop GTPases control diverse cellular processes, like signal transduction, ribosome assembly, cell motility, and intracellular transport and translation. YchF belongs to the Obg-family of P-loop GTPases and is one of the least characterized member of this family. It is unique because it preferentially hydrolyses ATP rather than GTP, but its physiological role is largely unknown. Studies in different organisms including humans suggest a possible role of YchF in regulating the cellular adaptation to stress conditions. In the current study, we explored the role of YchF in the model organism Escherichia coli. By western blot and promoter fusion experiments, we demonstrate that YchF levels decrease during stress conditions or when cells enter stationary phase. The decline in YchF levels trigger increased stress resistance and cells lacking YchF are resistant to multiple stress conditions, like oxidative stress, replication stress, or translational stress. By in vivo site directed cross-linking we demonstrate that YchF interacts with the translation initiation factor 3 (IF3) and with multiple ribosomal proteins at the surface of the small ribosomal subunit. The absence of YchF enhances the anti-association activity of IF3, stimulates the translation of leaderless mRNAs, and increases the resistance against the endoribonuclease MazF, which generates leaderless mRNAs during stress conditions. In summary, our data identify YchF as a stress-responsive regulator of leaderless mRNA translation.

Enhanced translation of leaderless mRNAs under oxidative stress in Escherichia coli

“…As the three methods give similar conclusions, further results are only expressed as the ratio of fluorescence at 2 hrs. To our knowledge, this is the first report of increased lmRNA translation in conditions that do not derive from antibiotics stress (Kaberdina et al, 2009) or artificial deletion (Landwehr et al, 2021) or overexpression of proteins (Vesper et al, 2011).…”

“…Also, high levels of aminoacylated initiator tRNA, which probably increase as a consequence of canonical translation inhibition, have been shown to enhance lmRNA translation in vitro and could also be involved in the regulatory process (Udagawa et al, 2004). Recently, the ATPase YchF of E. coli has been shown to bind the ribosomes and apparently inhibit lmRNA translation (Landwehr et al, 2021). Thus, it is possible that (p)ppGpp may inhibit YchF, although it is also possible that YchF somehow prevents (p)ppGpp production or that it controls lmRNA translation by a (p)ppGpp independent mechanism.…”

An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element

“…Regardless, changes in ribosomal protein abundance might provide a mechanism to trigger and/or maintain the R7A* state. Various stress conditions can alter ribosome composition and selectively enhance translation of leaderless mRNAs ( 47 , 48 ). Increased leaderless mRNA translation is at least partly stimulated through downregulation of the redox-regulated ATPase YchF, which normally represses translation from leaderless mRNA through interactions with translation initiation-factor-3 ( 48 ).…”

Quantitative proteomics identifies the universally conserved ATPase Ola1p as a positive regulator of heat shock response in Saccharomyces cerevisiae

“…Different roles of Ola1/YchF in cellular stress response pathways have been reported ( 3 , 5 , 6 , 9 , 42 ). Furthermore, OLA1 is overexpressed in various cancers ( 43 , 44 ), which underscores the interest in better understanding Ola1/YchF functions.…”

“…Converging evidence supports a model in which Ola1/YchF acts as a negative regulator of the oxidative stress response ( 3 , 7 , 8 ). Furthermore, in bacterial cells, Ola1/YchF levels decrease during stress conditions, which promotes the translation of leaderless RNAs encoding stress response proteins for cell survival ( 9 ). In contrast, Ola1 was shown to stabilize HSP70 in human cells during heat and oxidative stress conditions ( 6 , 10 ).…”