The Role of Proteomics in Identification of Key Proteins of Bacterial Cells with Focus on Probiotic Bacteria
Abstract
:1. Introduction
2. Proteomic Methods, Including MS-Based Approaches
3. Proteins of Probiotic Bacterial Cells and the Examples Studied by Proteomics
3.1. Whole Cell Lysates and Intracellular Proteins Identification
3.2. Surface Proteins Identification
3.3. Extracellular/Secreted Proteins Identification
3.4. The Proteins of EVs
4. Health-Related Functions of Probiotic Bacteria Examined by Proteomics
5. Concluding Remarks and Future Perspectives
Funding
Data Availability Statement
Conflicts of Interest
References
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Probiotics | Type of Proteins Examined | Findings | Ref./ Year |
---|---|---|---|
Pediococcus pentosaceus 1101 | intracellular proteins and whole-cell lysates | A total of 100 proteins were differentially expressed under exposure of the probiotic strain to 0.5% bile salts and acidity; two kinases and N-acetylmuramoyl-L-alanine amidase were identified as having crucial roles in adaptation of probiotic strain to conditions in the gastrointestinal tract. | [10]/ 2022 |
Lactococcus lactis subsp. lactis NCDO2118; lactis IL1403; cremoris NZ9000; cremoris MG1363 | intracellular proteins and whole-cell lysates | The core proteome for L. lactis strains was determined (586 proteins) as responsible for strains stress resistance; strain-unique proteins were identified in three strains; 19 and 3 novel proteins to IL1403 and MG1363 strain, respectively, were found. | [56]/ 2019 |
Lactococcus lactis subsp. lactis IL1403 | intracellular proteins and whole-cell lysates | Over 400 proteins were altered in the probiotic strain under ethanol-induced stress; stress-related proteins increased the activity of alcohol dehydrogenase. | [57]/ 2023 |
Lactococcus lactis subsp. lactis IL1403 | intracellular proteins and whole-cell lysates | The molecular mechanism of ethanol-induced stress on the probiotic strain was determined using both in silico prediction and in vivo validation in a mice model. The FAPEG peptide exhibited the strongest ability to enhance alcohol dehydrogenase activity and prevent alcoholic liver injury. | [58]/ 2024 |
Levilactobacillus brevis strains PA6; A4; A7; M4; DSMZ 20054 | surface proteins | Ten different S-layer proteins (Slps) were identified on these probiotic strains; simultaneous detection of eight Slps were found on the S-layer of A7 strain; 40 S-layer-associated proteins (SLAPs) were detected as common to all strains, however, with different quantities. | [67]/ 2022 |
Lactobacillus crispatus Lv25; Lactobacillus reuteri RC14 | surface proteins | The presence of surface oligopeptide-binding proteins (OppA-like proteins) was confirmed in these strains; OppA proteins participated in the binding of diverse lactobacilli to the surface of human epithelial cells. | [75]/ 2019 |
Pediococcus pentosaceus GS4 | surface proteins | The probiotic strain produced 98 kDa surface layer protein Slp that contributed to its adherence to epithelial cells in vitro. | [76]/ 2020 |
Bifidobacterium longum BBMN68 | surface proteins | Out of 829 proteins identified with altered expression, 56 proteins were upregulated in the probiotic strain under a bile stress; the crucial role of pili (Pil1) was recognized in increased B. longum BBMN68 adhesion to HT-29 cells under bile stress conditions. | [77]/ 2024 |
Lactobacillus casei ATCC 393 | surface proteins | Probiotic strain under sodium selenite treatment synthesized Se nanoparticles (SeNPs) by decreasing toxic sodium selenite into elemental selenium; SeNPs were coated by proteins in range 11–17 kDa with the most abundant 50S ribosomal protein L7/L12. | [78]/ 2023 |
Limosilactobacillus reuteri ZJ625; Ligilactobacillus salivarius ZJ614 | extracellular/secreted proteins | Differentially expressed proteins were identified in co-culture of these two strains as compared to the cultures of each individual strain; the crosstalk between two strains in their co-culture was mediated by S-ribosylhomocysteine lyase. | [62]/ 2023 |
Lactobacillus mucosae LM1 | extracellular/secreted proteins | The differences in exoproteome composition of probiotic strain under treatment by various bile concentrations indicated that this bacterium regulated its exoproteome by secretion of various intracellular proteins. | [81]/ 2021 |
Lactobacillus plantarum; Lactobacillus fermentum; Lactobacillus gasseri | proteins of EVs | As the most abundant protein, GAPDH was identified in the EVs of L. plantarum, the enolase in EVs of L. gasseri, and the citrate lyase alpha chain in the EVs of L. fermentum; EVs from L. fermentum and L. gasseri were composed of plasma membrane proteins, the EVs from L. plantarum contained more cytosolic proteins. | [91]/ 2023 |
Lactobacillus salivarius SNK-6 | proteins of EVs | In total, 320 proteins were identified (10–38 kDa) in the spherical EVs with diameters in the range of 100–256 nm; various anti-inflammatory proteins were detected. | [92]/ 2024 |
Propionibacterium freudenreichii CIRM-BIA129 | proteins of EVs | EVs from probiotics were prepared by two purification methods and from two different culture media; the differences in protein content were related rather to EVs purification methods than to the type of culture media used. | [93]/ 2023 |
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Stastna, M. The Role of Proteomics in Identification of Key Proteins of Bacterial Cells with Focus on Probiotic Bacteria. Int. J. Mol. Sci. 2024, 25, 8564. https://doi.org/10.3390/ijms25168564
Stastna M. The Role of Proteomics in Identification of Key Proteins of Bacterial Cells with Focus on Probiotic Bacteria. International Journal of Molecular Sciences. 2024; 25(16):8564. https://doi.org/10.3390/ijms25168564
Chicago/Turabian StyleStastna, Miroslava. 2024. "The Role of Proteomics in Identification of Key Proteins of Bacterial Cells with Focus on Probiotic Bacteria" International Journal of Molecular Sciences 25, no. 16: 8564. https://doi.org/10.3390/ijms25168564