The Ribosome as a Switchboard for Bacterial Stress Response

He, Cheng-Guang; Gualerzi, Claudio O.

doi:10.3389/fmicb.2020.619038

Cited by 25 publications

(11 citation statements)

References 143 publications

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“…This is a finding in line with a hypothesis that rRNAs play a central role in sensing stress. 38 The Helicase Sensor Identifies the Methyl Group Lost from m 4 C m during Stress. The hypermodified RNA m 4 C m stands out as one for further investigation because its levels decrease with both forms of stress studied.…”

Section: Acs Chemical Biologymentioning

confidence: 99%

Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes

et al. 2023

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The bacterium Escherichia coli possesses 16S and 23S rRNA strands that have 36 chemical modification sites with 17 different structures. Nanopore direct RNA sequencing using a protein nanopore sensor and helicase brake, which is also a sensor, was applied to the rRNAs. Nanopore current levels, base calling profile, and helicase dwell times for the modifications relative to unmodified synthetic rRNA controls found signatures for nearly all modifications. Signatures for clustered modifications were determined by selective sequencing of writer knockout E. coli and sequencing of synthetic RNAs utilizing some custom-synthesized nucleotide triphosphates for their preparation. The knowledge of each modification's signature, apart from 5-methylcytidine, was used to determine how metabolic and cold-shock stress impact rRNA modifications. Metabolic stress resulted in either no change or a decrease, and one site increased in modification occupancy, while cold-shock stress led to either no change or a decrease. The double modification m 4 C m 1402 resides in 16S rRNA, and it decreased with both stressors. Using the helicase dwell time, it was determined that the N 4 methyl group is lost during both stressors, and the 2′-OMe group remained. In the ribosome, this modification stabilizes binding to the mRNA codon at the P-site resulting in increased translational fidelity that is lost during stress. The E. coli genome has seven rRNA operons (rrn), and the earlier studies aligned the nanopore reads to a single operon (rrnA). Here, the reads were aligned to all seven operons to identify operon-specific changes in the 11 pseudouridines. This study demonstrates that direct sequencing for >16 different RNA modifications in a strand is achievable.

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Section: Acs Chemical Biologymentioning

confidence: 99%

Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes

et al. 2023

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“…Also, a significant loss of 30S/50S ribosomal proteins was observed at cold conditions. Numerous studies report that loss of ribosomal proteins in bacteria is the reaction to stress and is necessary for survival under nutrient- or energy-limited conditions 48,49,50,51 . GO analysis revealed that translation, gene expression, and protein folding were significantly affected at cold conditions (Figure 5a).…”

Section: Resultsmentioning

confidence: 99%

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

Kazakova,

Ivanov,

Kusainova

et al. 2024

Preprint

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Microbial proteomics and metaproteomic studies rely heavily on mass spectrometry. Standard liquid chromatography/tandem mass spectrometry-based methods for protein identification and quantitation exhibit lengthy analysis time. Here, we report on the implementation of the previously developed DirectMS1 approach for metaproteomics studies that provides a unique combination of accurate protein quantitation and rapid analysis time. We validated our method using a series of proteome-wide analyses of bacterial samples including strain isolates, mock microbiomes composed of bacteria spiked at known concentrations and human fecal microbiomes. We demonstrated that the developed two-stage search algorithm identifies the bacterial isolate species with an accuracy of 95%, when no prior information on the sample is available. Microbiome composition was resolved at the genus level with the mean difference between the actual and identified microbiome components of 12%. Pearson coefficient of up to 0.97 was achieved in estimates of strain biomass change in mock microbiome samples. By the example of Rhodococcus biodegradation of n-alkanes, phenols and its derivatives, we showed that our approach effectively characterizes changes in the activity of metabolic pathways of strain isolates. For the benchmarking, the changes in biodegradation activity were also assessed using the standard label-free and TMT DDA approaches.

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“…When bacteria are exposed to environmental stress, their ribosomes may act as either sensors, targets or responders to the change in conditions. A full discussion of the mechanisms underlying these processes is beyond the scope of this review and has already been described by Starosta et al (2014) and Cheng-Guang and Gualerzi (2021) so here we will focus on how ribosome profiling has contributed to understanding the interplay between ribosomes and cellular stress.…”

Section: Insights From Ribosome Profiling In Mycobacteriamentioning

confidence: 99%

Ribosome profiling enhances understanding of mycobacterial translation

Sawyer

Cortes²

2022

Front. Microbiol.

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A recent addition to the -omics toolkit, ribosome profiling, enables researchers to gain insight into the process and regulation of translation by mapping fragments of mRNA protected from nuclease digestion by ribosome binding. In this review, we discuss how ribosome profiling applied to mycobacteria has led to discoveries about translational regulation. Using case studies, we show that the traditional view of “canonical” translation mechanisms needs expanding to encompass features of mycobacterial translation that are more widespread than previously recognized. We also discuss the limitations of the method and potential future developments that could yield further insight into the fundamental biology of this important human pathogen.

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The Ribosome as a Switchboard for Bacterial Stress Response

Cited by 25 publications

References 143 publications

Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes

Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

Ribosome profiling enhances understanding of mycobacterial translation

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