The Mechanism of Recoding in Pro‐ and Eukaryotes

Poole, Elizabeth S.; Major, Louise L.; Cridge, Andrew G.; Tate, Warren P.

doi:10.1002/3527603433.ch10

Cited by 3 publications

(2 citation statements)

References 63 publications

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“…Furthermore, while ribosome assembly is closely coupled to cell growth, how these two processes are coordinated is unclear (Asato, 2005). Likewise, while translational error rates are known to vary dramatically among different physiological, mutant, and transcript sequence contexts (e.g., Poole et al, 2004), the factors governing fidelity are not fully understood.…”

Section: Introductionmentioning

confidence: 99%

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery

et al. 2016

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Bacterial protein synthesis is an essential, conserved, and environmentally responsive process. Yet, many of its components and dependencies remain unidentified. To address this gap, we used quantitative synthetic genetic arrays to map functional relationships among >48,000 gene pairs in Escherichia coli under four culture conditions differing in temperature and nutrient availability. The resulting data provide global functional insights into the roles and associations of genes, pathways, and processes important for efficient translation, growth, and environmental adaptation. We predict and independently verify the requirement of unannotated genes for normal translation, including a previously unappreciated role of YhbY in 30S biogenesis. Dynamic changes in the patterns of genetic dependencies across the four growth conditions and data projections onto other species reveal overarching functional and evolutionary pressures impacting the translation system and bacterial fitness, underscoring the utility of systematic screens for investigating protein synthesis, adaptation, and evolution.

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Section: Introductionmentioning

confidence: 99%

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery

et al. 2016

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“…While bioinformatic analyses suggest that frameshift sites are not uncommon in the eukaryotic genome (Jacobs et al 2007), the mechanism is likely to be rare in the expression of cellular genes. It is, however, relatively common in viruses (Poole et al 2004). In HIV frameshifting facilitates a precise ratio of structural Gag proteins to enzymatic Pol proteins (Shehu-Xhilaga et al 2001).…”

Section: Introductionmentioning

confidence: 99%

A homogeneous cell-based bicistronic fluorescence assay for high-throughput identification of drugs that perturb viral gene recoding and read-through of nonsense stop codons

Cardno¹,

Poole²,

Mathew³

et al. 2009

RNA

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Recoding mechanisms are programmed protein synthesis events used commonly by viruses but only very rarely in cells for cellular gene expression. For example, HIV-1 has an absolute reliance on frameshifting to produce the correct ratio of key proteins critical for infectivity. To exploit such recoding sites as therapeutic targets, a simple homogeneous assay capable of detecting small perturbations in these low-frequency (<5%) events is required. Current assays based on dual luciferase reporters use expensive substrates and are labor-intensive, both impediments for high-throughput screening. We have developed a cellbased bifluorophore assay able to measure accurately small recoding changes (<0.1%) with a high Z9-factor in 24-or 96-well formats that could be extended to 384 wells. In cases of nonsense mutations arising within coding regions of genes, the assay is suitable for assessing the potential of screened compounds to increase read-through at these nonprogrammed stop signals of variable termination efficiency.

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Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing–activated transfer of a mobile genetic element

Ramsay

Tester²,

Major³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSym R7A is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show that a +1 programmed ribosomal frameshift (PRF) fuses the coding sequences of two TraR-activated genes, msi172 and msi171, producing an activator of rdfS expression named Frameshifted excision activator (FseA). Mass-spectrometry and mutational analyses indicated that the PRF occurred through +1 slippage of the tRNA phe from UUU to UUC within a conserved msi172-encoded motif. FseA activated rdfS expression in the absence of ICEMlSym R7A , suggesting that it directly activated rdfS transcription, despite being unrelated to any characterized DNA-binding proteins. Bacterial two-hybrid and gene-reporter assays demonstrated that FseA was also bound and inhibited by the ICEMlSym R7A -encoded quorum-sensing antiactivator QseM. Thus, activation of ICEMlSym R7A excision is counteracted by TraR antiactivation, ribosomal frameshifting, and FseA antiactivation. This robust suppression likely dampens the inherent biological noise present in the quorum-sensing autoinduction circuit and ensures that ICEMlSym R7A transfer only occurs in a subpopulation of cells in which both qseM expression is repressed and FseA is translated. The architecture of the ICEMlSym R7A transfer regulatory system provides an example of how a set of modular components have assembled through evolution to form a robust genetic toggle that regulates gene transcription and translation at both single-cell and cell-population levels.quorum sensing | antiactivator | ribosomal frameshift | ICE | horizontal gene transfer

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The Mechanism of Recoding in Pro‐ and Eukaryotes

Cited by 3 publications

References 63 publications

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery

A homogeneous cell-based bicistronic fluorescence assay for high-throughput identification of drugs that perturb viral gene recoding and read-through of nonsense stop codons

Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing–activated transfer of a mobile genetic element

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