Coping with stress: How bacteria fine-tune protein synthesis and protein transport

Njenga, Robert; Boele, Julian; Öztürk, Yavuz; Koch, Hans-Georg

doi:10.1016/j.jbc.2023.105163

Cited by 14 publications

(8 citation statements)

References 339 publications

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“…For example, the Cas medium induced genes associated with general aerobic metabolism, while Glu medium relied on genes associated with anaerobic respiration at late growth stages. Both media types cause repression of genes associated with the amino acid biosynthesis and translation GO terms during stationary phase, aligned with prior studies of nutrient deprivation (58, 59).…”

Section: Resultssupporting

confidence: 80%

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Ekdahl,

Julien,

Suraj

et al. 2024

Preprint

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Recent research has indicated the presence of heterochromatin-like regions of extended protein occupancy and transcriptional silencing of bacterial genomes. We utilized an integrative approach to track chromatin structure and transcription in E. coli K-12 across a wide range of nutrient conditions. In the process, we identified multiple loci which act similarly to facultative heterochromatin in eukaryotes, normally silenced but permitting expression of genes under specific conditions. We also found a strong enrichment of small regulatory RNAs (sRNAs) among the set of differentially expressed transcripts during nutrient stress. Using a newly developed bioinformatic pipeline, the transcription factors regulating sRNA expression were bioinformatically predicted, with experimental follow-up revealing novel relationships for 36 sRNA-transcription factors candidates. Direct regulation of sRNA expression was confirmed by mutational analysis for five sRNAs of metabolic interest: IsrB, CsrB and CsrC, GcvB, and GadY. Our integrative analysis thus reveals additional layers of complexity in the nutrient stress response in E. coli and provides a framework for revealing similar poorly understood regulatory logic in other organisms.

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Section: Resultssupporting

confidence: 80%

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Ekdahl,

Julien,

Suraj

et al. 2024

Preprint

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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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“…Proteins, integral to bacterial vitality, are involved in maintaining cellular structure, signaling, metabolic regulation, and immune responses. They act as channels or receptors on cell membranes, modulating substance movement, and mediating extracellular interactions with hosts [64] . Polysaccharides, constituting the peptidoglycan layer of cell walls, provide structural integrity and protection, enabling bacteria to withstand various environmental stresses [65] .…”

Section: Resultsmentioning

confidence: 99%

Preparation of protein-stabilized Litsea cubeba essential oil nano-emulsion by ultrasonication: Bioactivity, stability, in vitro digestion, and safety evaluation

Peng,

Huang,

Liang

et al. 2024

Ultrasonics Sonochemistry

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Coping with stress: How bacteria fine-tune protein synthesis and protein transport

Cited by 14 publications

References 339 publications

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

Preparation of protein-stabilized Litsea cubeba essential oil nano-emulsion by ultrasonication: Bioactivity, stability, in vitro digestion, and safety evaluation

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