Selective translation by alternative bacterial ribosomes

Chen, Yuxiang; Xu, Zhiyu; Ge, Xueliang; Sanyal, Suparna; Lu, Zhi John; Javid, Babak

doi:10.1101/605931

Cited by 5 publications

(5 citation statements)

References 64 publications

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“…This technique enables very precise identification of specific mRNA strands being actively translated at any given moment in time. Ribosome profiling experiments performed in the non-pathogenic Mycobacterium smegmatis have uncovered important new details about translation, including the translation of hundreds of small, previously unannotated proteins at the 5' ends of transcripts (Shell et al, 2015), the translation by alternative ribosomes that have distinct functionality compared with their canonical counterparts (Chen et al, 2019) as well as cysteine-responsive attenuation of translation (Canestrari et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Ribosome profiling inMycobacterium tuberculosisreveals robust leaderless translation

Sawyer¹,

Phelan²,

Clark³

et al. 2020

Preprint

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Mycobacterium tuberculosis, which causes tuberculosis, expresses a large proportion of leaderless transcripts lacking the canonical bacterial translation initiation signals. The role leaderless genes play in the physiology of this pathogen, which can undergo prolonged periods of non-replicating persistence in the host, is currently unknown. We have previously demonstrated that levels of leaderless transcription increase under conditions of nutrient starvation. However, little is known about the implications of this for persistent infection. Here, we performed ribosome profiling to characterise the translational landscape of M. tuberculosis in vitro. Our data reveals robust leaderless translation in the pathogen and points towards different mechanisms for their initiation of translation compared to canonical Shine-Dalgarno genes. Furthermore, under conditions of nutrient starvation, we found a significant global up-regulation of leaderless genes in the translatome. Our data represents a rich resource for others seeking to understand translational regulation not only in M. tuberculosis but in bacterial pathogens.

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Section: Introductionmentioning

confidence: 99%

Ribosome profiling inMycobacterium tuberculosisreveals robust leaderless translation

Sawyer¹,

Phelan²,

Clark³

et al. 2020

Preprint

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“…This allows taking a snapshot of translation, hence the "translatome," as compared with the transcriptome obtained in typical RNA-Seq (1)(2)(3). New discoveries from this approach include previously undetected "intergenic" (4) and overlapping genes (5), a deeper understanding of translational regulation (6,7), and the finding that different ribosome types may be used in translating different genes (8). Important experimental steps include RNA digestion, monosome purification, RNA extraction, and footprint size selection (1,9) (Fig.…”

mentioning

confidence: 99%

Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data

Glaub

Huptas

Neuhaus

et al. 2020

Journal of Biological Chemistry

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Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a “one-size-fits-all” ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.

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“…Embryonic development is a highly regulated process that depends on the synthesis of the correct proteins at the correct time, place, and quantities in order to shape an organism. Translational control has been increasingly recognized as an important layer of regulation in gene expression during key stem cell fate decisions [1][2][3] , responses to stimuli [4][5][6] , and within developing embryos 7,8 . Recently, the ribosome itself has emerged as a direct regulator of gene expression.…”

Section: Introductionmentioning

confidence: 99%

RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages

Susanto,

Hung,

Levine

et al. 2023

Preprint

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Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translational control. However, a lack of technologies to enrich RAPs across many sample types has prevented systematic analysis of RAP number, dynamics, and functions. Here, we have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development that is linked to the translation of genes with long coding sequences. Finally, we characterized ribosome composition remodeling during immune activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs ranging from those with neuroregulatory functions to those activated by immune stimuli, thereby providing critical insights into how ribosomes are remodeled.

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Selective translation by alternative bacterial ribosomes

Abstract: 21Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species but 22our study suggests that alternative ribosomes may represent a further layer of regulation of gene 44 translation. 45

Cited by 5 publications

References 64 publications

Ribosome profiling inMycobacterium tuberculosisreveals robust leaderless translation

Ribosome profiling inMycobacterium tuberculosisreveals robust leaderless translation

Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data

RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages

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