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

Omics studies reveal the response mechanisms of Corynebacterium glutamicum to l-homoserine osmotic stress

To investigate the mechanism of osmotic stress produced by Corynebacterium glutamicum (C. glutamicum) in the production of l-homoserine. The present study employed genomic and transcriptomic analyses of both evolved strains and the parental strain grown under l-homoserine osmotic stress to investigate the response mechanisms and identify specific tolerance targets. The results indicated that the evolved strain enhanced its tolerance to l-homoserine stress by inactivating aspartokinase, thereby interrupting the intracellular synthesis pathway of l-homoserine. Early in stress exposure, C. glutamicum suppressed the synthesis of l -homoserine and instead enhanced its catabolic activity. In response to osmotic stress, C. glutamicum also relied on a variety of energy metabolism and ion transport pathways, including ABC transporters and ATP metabolism, which are essential for high-osmolarity tolerance. Given the gradual accumulation of l-homoserine within the cell, this study focused on the transcriptional expression patterns during the adaptation phase, excluding cellular responses during the high-concentration stress phase. These findings provide valuable insights for improving C. glutamicum's tolerance to l-homoserine stress during amino-acid fermentation and highlight potential targets for metabolic engineering strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04304-7.

Bioconversion of Fe3O4 Nanoparticles by Probiotics

Background/Objectives: Iron deficiency anemia remains a primary global health concern, affecting millions worldwide. Despite the widespread availability of iron supplements, their efficacy is often hindered by poor bioavailability and adverse gastrointestinal effects. This study explores the potential of probiotics to enhance the bioavailability of Fe3O4 NPs through probiotic-mediated mechanisms. Methods: Lactobacillus fermentum, Lactobacillus rhamnosus, and Lactobacillus plantarum were utilized to investigate their interactions with Fe3O4 NPs, synthesized via co-precipitation and characterized using transmission electron microscopy, scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. Results: The results indicated that probiotics adhere to the nanoparticle surface, with L. fermentum exhibiting the highest adhesion and internalization capacity, leading to a significant increase in 4-hydroxyphenylacetic acid (4-HPLA) production (11.73 ± 0.09 mg/mL at 24 h, p < 0.05). Spectroscopic analyses further revealed that probiotic metabolism facilitates the oxidation of Fe3O4 to Fe2O3. Additionally, Fe3O4 nanoparticle-treated cultures demonstrated enhanced bacterial viability and metabolic activity, highlighting a synergistic effect between probiotics and iron nanoparticles. Conclusions: These findings provide compelling evidence for probiotic-assisted iron supplementation as a promising strategy to enhance iron bioavailability while mitigating the gastrointestinal side effects of conventional iron supplements.

Mechanisms on salt tolerant of Paenibacillus polymyxa SC2 and its growth-promoting effects on maize seedlings under saline conditions

Soil salinity negatively affects microbial communities, soil fertility, and agricultural productivity and has become a major agricultural problem worldwide. Plant growth-promoting rhizobacteria (PGPR) with salt tolerance can benefit plant growth under saline conditions and diminish the negative effects of salt stress on plants. In this study, we aimed to understand the salt-tolerance mechanism of Paenibacillus polymyxa at the genetic and metabolic levels and elucidate the mechanism of strain SC2 in promoting maize growth under saline conditions. Under salt stress, we found that strain SC2 promoted maize seedling growth, which was accompanied by a significant upregulation of genes encoding for the biosynthesis of peptidoglycan, polysaccharide, and fatty acid, the metabolism of purine and pyrimidine, and the transport of osmoprotectants such as trehalose, glycine betaine, and K+ in strain SC2. To further enhance the salt resistance of strain SC2, three mutants (SC2-11, SC2-13, and SC2-14) with higher capacities for salt resistance and exopolysaccharide synthesis were obtained via atmospheric and room-temperature plasma mutagenesis. In saline-alkaline soil, the mutants showed better promoting effect on maize seedlings than wild-type SC2. The fresh weight of maize seedlings was increased by 68.10% after treatment with SC2-11 compared with that of the control group. The transcriptome analysis of maize roots demonstrated that SC2 and SC2-11 could induce the upregulation of genes related to the plant hormone signal transduction, starch and sucrose metabolism, reactive oxygen species scavenging, and auxin and ethylene signaling under saline-alkaline stress. In addition, various transcription factors, such as zinc finger proteins, ethylene-responsive-element-binding protein, WRKY, myeloblastosis proteins, basic helix-loop-helix proteins, and NAC proteins, were up-regulated in response to abiotic stress. Moreover, the microbial community composition of maize rhizosphere soil after inoculating with strain SC2 was varied from the one after inoculating with mutant SC2-11. Our results provide new insights into the various genes involved in the salt resistance of strain SC2 and a theoretical basis for utilizing P. polymyxa in saline-alkaline environments.

Lactobacillus Persisters Formation and Resuscitation

Lactobacillus is a commonly used probiotic, and many researchers have focused on its stress response to improve its functionality and survival. However, studies on persister cells, dormant cells that aid bacteria in surviving general stress, have focused on pathogenic bacteria that cause infection, not Lactobacillus. Thus, understanding Lactobacillus persister cells will provide essential clues for understanding how Lactobacillus survives and maintains its function under various environmental conditions. We treated Lactobacillus strains with various antibiotics to determine the conditions required for persister formation using kill curves and transmission electron microscopy. In addition, we observed the resuscitation patterns of persister cells using single-cell analysis. Our results show that Lactobacillus creates a small population of persister cells (0.0001-1% of the bacterial population) in response to beta-lactam antibiotics such as ampicillin and amoxicillin. Moreover, only around 0.5-1% of persister cells are heterogeneously resuscitated by adding fresh media; the characteristics are typical of persister cells. This study provides a method for forming and verifying the persistence of Lactobacillus and demonstrates that antibiotic-induced Lactobacillus persister cells show characteristics of dormancy, sensitivity of antibiotics, same as exponential cells, multi-drug tolerance, and resuscitation, which are characteristics of general persister cells. This study suggests that the mechanisms of formation and resuscitation may vary depending on the characteristics, such as the membrane structure of the bacterial species.

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

Consumer demand for healthier confectionery products has prompted the confectionery industry to create products that are reduced in sugar content and supplemented with vitamins, antioxidants or biological elements beneficial to health. The aim of this study was to develop marshmallows enriched with Apis mellifera honey and Lactobacillus rhamnosus and to evaluate the effect of honey concentration and gelatin bloom degrees on marshmallow properties. A completely randomized design with a factorial structure was applied with different honey concentrations (0, 50 and 75%) and at different gelatin bloom degrees (265, 300 and 315 bloom degrees); moreover, the physicochemical properties, total phenol content and antioxidant activity of the marshmallow were studied, as well as the viability of the probiotic. The physicochemical properties of the marshmallows were found to be adequate and showed good stability over time. The concentration of honey and gelatin bloom degrees did not significantly affect probiotic viability. The density of the marshmallows decreased as the percentage of honey increased. Additionally, the pH was lower at higher honey concentrations. The marshmallow with 75% honey and 265 bloom degrees had a higher °Brix value. The honey treatments exhibited higher levels of total antioxidant activity and total phenolic compounds than the sugar-only marshmallows. However, the bloom degrees did not have a significant impact on the antioxidant activity and total phenolic compound content. Although the probiotics did not reach the minimum viability needed, their use as paraprobiotics can be considered.

Importance of the ECM-receptor interaction for adaptive response to hypoxia based on integrated transcription and translation analysis

Low dissolved oxygen (LO) conditions represent a major environmental challenge to marine life, especially benthic animals. For these organisms, drastic declines in oxygen availability (hypoxic events) can trigger mass mortality events and thus, act as agents of selection influencing the evolution of adaptations. In sea cucumbers, one of the most successful groups of benthic invertebrates, the exposure to hypoxic conditions triggers adaptive adjustments in metabolic rates and behaviour. It is unclear, however, how these adaptive responses are regulated and the genetic mechanisms underpinning them. Here, we addressed this knowledge gap by assessing the genetic regulation (transcription and translation) of hypoxia exposure in the sea cucumber Apostichopus japonicus. Transcriptional and translational gene expression profiles under short- and long-term exposure to low oxygen conditions are tightly associated with extracellular matrix (ECM)-receptor interaction in which laminin and collagen likely have important functions. Finding revealed that genes with a high translational efficiency (TE) had a relatively short upstream open reading frame (uORF) and a high uORF normalized minimal free energy, suggesting that sea cucumbers may respond to hypoxic stress via altered TE. These results provide valuable insights into the regulatory mechanisms that confer adaptive capacity to holothurians to survive oxygen deficiency conditions and may also be used to inform the development of strategies for mitigating the harmful effects of hypoxia on other marine invertebrates facing similar challenges.

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

Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.

Translatomics and physiological analyses of the detoxification mechanism of green alga Chlamydomonas reinhardtii to cadmium toxicity

Cadmium (Cd) is one of the most toxic pollutants found in aquatic ecosystems. Although gene expression in algae exposed to Cd has been studied at the transcriptional level, little is known about Cd impacts at the translational level. Ribosome profiling is a novel translatomics method that can directly monitor RNA translation in vivo. Here, we analyzed the translatome of the green alga Chlamydomonas reinhardtii following treatment with Cd to identify the cellular and physiological responses to Cd stress. Interestingly, we found that the cell morphology and cell wall structure were altered, and starch and high-electron-density particles accumulated in the cytoplasm. Several ATP-binding cassette transporters that responded to Cd exposure were identified. Redox homeostasis was adjusted to adapt to Cd toxicity, and GDP-L-galactose phosphorylase (VTC2), glutathione peroxidase (GPX5), and ascorbate were found to play important roles in maintaining reactive oxygen species homeostasis. Moreover, we found that the key enzyme of flavonoid metabolism, i.e., hydroxyisoflavone reductase (IFR1), is also involved in the detoxification of Cd. Thus, in this study, translatome and physiological analyses provided a complete picture of the molecular mechanisms of green algae cell responses to Cd.

Ribosome Profiling Reveals Genome-Wide Cellular Translational Regulation in Lacticaseibacillus rhamnosus ATCC 53103 under Acid Stress

During fermentation and food processing, Lacticaseibacillus rhamnosus ATCC 53103 can encounter many adverse conditions, and acid stress is one of them. The purpose of the present study was to investigate the influence of acid stress on the global translational and transcriptional regulation of Lacticaseibacillus rhamnosus ATCC 53103. Two pH values (pH 6.0 vs. pH 5.0) were applied, the effects of which were studied via ribosome profiling and RNA sequencing assay. Under acid stress, many genes showed differential changes at the translational and transcriptional levels. A total of 10 genes showed different expression trends at the two levels. The expression of 337 genes—which mainly participated in the ABC transporters, amino acid metabolism, and ribosome functional group assembly pathways—was shown to be regulated only at the translational level. The translational efficiency of a few genes participating in the pyrimidine and amino acid metabolism pathways were upregulated. Ribosome occupancy data suggested that ribosomes accumulated remarkably in the elongation region of open reading frame regions under acid stress. This study provides new insights into Lacticaseibacillus rhamnosus ATCC 53103 gene expression under acid stress, and demonstrates that the bacterium can respond to acid stress with synergistic translational and transcriptional regulation mechanisms, improving the vitality of cells.