Ribosome Profiling and RNA Sequencing Reveal Genome-Wide Cellular Translation and Transcription Regulation Under Osmotic Stress in Lactobacillus rhamnosus ATCC 53103

Abstract

To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.

Development and study of the functional properties of marshmallow enriched with bee (Apis mellifera) honey and encapsulated probiotics (Lactobacillus rhamnosus)

“…High concentrations of sugars in marshmallows could trigger the osmosis process in probiotics, causing water loss from bacterial cells and affecting bacterial growth ( 52 ). Additionally, the survival of probiotics can be affected by the characteristics of the packaging material, such as thickness and gas permeability ( 53 ).…”

Lactobacillus Persisters Formation and Resuscitation

“…The ubiquitous formation mechanism of persister cells depends on stress-induced inactivation of ribosomes, which ultimately leads to dormancy [ 20 ]. A previous study reported that Lactobacillus ribosomes are inactivated when exposed to stress [ 31 ]. This indicates that Lactobacillus is present in the persister cells because of the consequent inactivation of ribosomes.…”

Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium

“…Nonetheless, mRNA level is only an approximate proxy for protein abundance, with a coefficient of determination in the range of ∼0.4–0.6 (Schwanhäusser et al , 2011 ; Wilhelm et al , 2014 ), suggesting that protein synthesis and decay rates are important layers of gene expression regulation. Translational control has been shown to play an important role in shaping the cellular proteome in bacteria (Li et al , 2014 ; Samatova et al , 2020 ; Tollerson & Ibba, 2020 ; Fan et al , 2021 ), eukaryotes (Leppek et al , 2018 ), human cells (Gingold et al , 2014 ; Jang et al , 2015 ), cancer cells (Gonzalez et al , 2014 ; Truitt & Ruggero, 2016 ; Robichaud et al , 2019 ), and virus‐infected cells (Stern‐Ginossar et al , 2019 ; Hernandez‐Alias et al , 2021 ). In Escherichia coli , proteins that are members of multiprotein complexes are produced in precise proportion to their stoichiometry mostly by tuning translation rates (Li et al , 2014 ).…”