The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12

Abstract

Queuosine (Q) is a conserved hypermodification of the wobble base of tRNA containing GUN anticodons but the physiological consequences of Q deficiency are poorly understood in bacteria. This work combines transcriptomic, proteomic and physiological studies to characterize a Q-deficient Escherichia coli K12 MG1655 mutant. The absence of Q led to increased resistance to nickel and cobalt, and to increased sensitivity to cadmium, compared to the wild-type (WT) strain. Transcriptomic analysis of the WT and Q-deficient strains, grown in the presence and absence of nickel, revealed that the nickel transporter genes (nikABCDE) are down-regulated in the Q– mutant, even when nickel is not added. This mutant is therefore primed to resist to high nickel levels. Downstream analysis of the transcriptomic data suggested that the absence of Q triggers an atypical oxidative stress response, confirmed by the detection of slightly elevated ROS levels in the mutant, increased sensitivity to hydrogen peroxide and paraquat, and a subtle growth phenotype in a strain prone to accumulation of ROS.

Synthesis of queuine by colonic gut microbiome via cross‐feeding

“…Que protects the Entamoeba histolytica against oxidative stress but impairs its toxicity by downregulating the expression of genes previously associated with virulence, including cysteine proteases, cytoskeletal proteins, and small GTPases (Nagaraja et al., 2021). In comparison with wild‐type E. coli , Q‐deficient strain presented increased resistance to the transition metal nickel, whereas was more sensitive to the oxidative stressors (Pollo‐Oliveira et al., 2022). The role of Que for microbiome growth is also noteworthy.…”

Aminoglycoside tolerance inVibrio choleraeengages translational reprogramming associated to queuosine tRNA modification

“…Fe-S clusters are found in DNA base excision repair proteins, SoxR(54) and oxidative stress response factors, among others. Perturbation of iron-homeostasis in the Q-deficient strain could also be seen with the higher expression of the Isc machinery genes and lower expression of the suf genes in E. coli Δtgt (28). However, lacZ fusions that allow to monitor levels of Fe-S clusters did not show any differences when Q was absent(28).…”

“…Perturbation of iron-homeostasis in the Q-deficient strain could also be seen with the higher expression of the Isc machinery genes and lower expression of the suf genes in E. coli Δtgt (28). However, lacZ fusions that allow to monitor levels of Fe-S clusters did not show any differences when Q was absent(28). Moreover, ErpA protein levels were reduced by 50% in E. coli Δtgt .…”

Metal retention and replacement in QueD2 protect queuosine-tRNA biosynthesis in metal-starved Acinetobacter baumannii

“…Taken together, the Q incorporation enables rapid decoding of NAU codons while decreasing amino acid misincorporation, impacting both translational speed and fidelity; as a result, the loss of Q results in myriad, diverse physiological defects in eukaryotic systems ( 24 , 25 , 29 – 38 ). In contrast, the impact of Q-tRNA in bacteria is largely unexplored ( 38 – 40 ).…”

“…Proper enzyme metalation is therefore required to sustain Q biosynthesis, and multimetal starvation may well impact flux through the pathway. Indeed the Q-tRNA biosynthesis pathway has been linked to Zn(II) starvation in a bioinformatics analysis in bacteria ( 49 ) and transcriptionally in higher-order eukaryotes ( 50 ), as well as exogenous exposure to other metals ( 40 , 51 – 55 ).…”