Ornithine capture by a translating ribosome controls bacterial polyamine synthesis

Abstract

Polyamines are essential metabolites that play an important role in cell growth, stress adaptation, and microbial virulence 1-3 . In order to survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues 2 . Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF 4 , via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryo-EM structure of an Escherichia coli (E. coli) ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor RF1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.

Human ribosomal G-quadruplexes regulate heme bioavailability

“…Our results suggest that ribosomes, and G4 containing rRNAs in particular, may regulate heme metabolism, acting to buffer intracellular heme and possibly regulate heme trafficking and cotranslational hemylation. The ribosome as a potential heme buffer is consistent with its role as a general and versatile sink for ions and small molecules, including antibiotics, (57) platinum-based drugs, (58-60) metabolites (61), and metal cations Mg 2+ , Ca 2+ , Mn 2+ , Fe 2+ , and K + (62-67).…”

Human Ribosomal G-Quadruplexes Regulate Heme Bioavailability

“…The ribosome as a hub for heme is consistent with its role as an abundant and versatile sink for ions and small molecules, including antibiotics, (40) platinum-based drugs, (41)(42)(43) certain metabolites (44), and metal cations Mg 2+ , Ca 2+ , Mn 2+ , and Fe 2+ , K + (45-51). Hemin Agarose Binding.…”

A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics

“…Molecules that occupy the ribosome exit tunnel have the potential to directly interact with amino acids in the nascent peptide, and thereby interfere with peptide elongation, leading to translation arrest. This has been shown for L-ornithine, L-tryptophan, and macrolide antibiotics; by binding in the ribosome exit tunnel, these molecules pause the ribosome in a nascent peptide sequence-dependent manner (Arenz et al, 2014b(Arenz et al, , 2014aBischoff et al, 2014;Valle et al, 2019). Macrolides such as erythromycin were suggested to restrict translation elongation of ermBL/ermCL uORFs, to prevent correct positioning of the next charged tRNA in the A-site and thus cause ribosome arrest (Arenz et al, 2014b(Arenz et al, , 2014a.…”

“…Rho termination inside a coding region also requires an accessible Rut; these Ruts are typically cryptic elements within the ORF that become exposed as a consequence of translational repression. Regulators of premature Rho termination events include small RNAs (sRNAs) (Bossi et al, 2012;Sedlyarova et al, 2016;Silva et al, 2019;Wang et al, 2015b), RNA-binding proteins (Baniulyte et al, 2017;Figueroa-Bossi et al, 2014), riboswitches (Bastet et al, 2017;Caron et al, 2012;Hollands et al, 2012), and small upstream ORFs (uORFs) (Ben-Zvi et al, 2019;Kriner and Groisman, 2015;Valle et al, 2019;Yanofsky, 2007).…”