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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. [PMID: 39201251 PMCID: PMC11354107 DOI: 10.3390/ijms25168564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 09/02/2024] Open
Abstract
Probiotics can affect human health, keep the balance between beneficial and pathogenic bacteria, and their colonizing abilities enable the enhancement of the epithelial barrier, preventing the invasion of pathogens. Health benefits of probiotics were related to allergy, depression, eczema, cancer, obesity, inflammatory diseases, viral infections, and immune regulation. Probiotic bacterial cells contain various proteins that function as effector molecules, and explaining their roles in probiotic actions is a key to developing efficient and targeted treatments for various disorders. Systematic proteomic studies of probiotic proteins (probioproteomics) can provide information about the type of proteins involved, their expression levels, and the pathological changes. Advanced proteomic methods with mass spectrometry instrumentation and bioinformatics can point out potential candidates of next-generation probiotics that are regulated under pharmaceutical frameworks. In addition, the application of proteomics with other omics methods creates a powerful tool that can expand our understanding about diverse probiotic functionality. In this review, proteomic strategies for identification/quantitation of the proteins in probiotic bacteria were overviewed. The types of probiotic proteins investigated by proteomics were described, such as intracellular proteins, surface proteins, secreted proteins, and the proteins of extracellular vesicles. Examples of pathological conditions in which probiotic bacteria played crucial roles were discussed.
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Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Veveri 97, 602 00 Brno, Czech Republic
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2
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Surface Layer Protein Pattern of Levilactobacillus brevis Strains Investigated by Proteomics. Nutrients 2022; 14:nu14183679. [PMID: 36145058 PMCID: PMC9504196 DOI: 10.3390/nu14183679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
The outermost constituent of many bacterial cells is represented by an S-layer, i.e., a semiporous lattice-like layer composed of self-assembling protein subunits called S-layer proteins (Slps). These proteins are involved in several processes, such as protecting against environmental stresses, mediating bacterial adhesion to host cells, and modulating gut immune response. Slps may also act as a scaffold for the external display of additional cell surface proteins also named S-layer associated proteins (SLAPs). Levilactobacillus brevis is an S-layer forming lactic acid bacterium present in many different environments, such as sourdough, milk, cheese, and the intestinal tract of humans and animals. This microorganism exhibits probiotic features including the inhibition of bacterial infection and the improvement of human immune function. The potential role of Slps in its probiotic and biotechnological features was documented. A shotgun proteomic approach was applied to identify in a single experiment both the Slps and the SLAPs pattern of five different L. brevis strains isolated from traditional sourdoughs of the Southern Italian region. This study reveals that these closely related strains expressed a specific pattern of surface proteins, possibly affecting their peculiar properties.
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3
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Heavey MK, Durmusoglu D, Crook N, Anselmo AC. Discovery and delivery strategies for engineered live biotherapeutic products. Trends Biotechnol 2022; 40:354-369. [PMID: 34481657 PMCID: PMC8831446 DOI: 10.1016/j.tibtech.2021.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
Genetically engineered microbes that secrete therapeutics, sense and respond to external environments, and/or target specific sites in the gut fall under an emergent class of therapeutics, called live biotherapeutic products (LBPs). As live organisms that require symbiotic host interactions, LBPs offer unique therapeutic opportunities, but also face distinct challenges in the gut microenvironment. In this review, we describe recent approaches (often demonstrated using traditional probiotic microorganisms) to discover LBP chassis and genetic parts utilizing omics-based methods and highlight LBP delivery strategies, with a focus on addressing physiological challenges that LBPs encounter after oral administration. Finally, we share our perspective on the opportunity to apply an integrated approach, wherein discovery and delivery strategies are utilized synergistically, towards tailoring and optimizing LBP efficacy.
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Affiliation(s)
- Mairead K. Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Aaron C. Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Correspondence: (A.C. Anselmo), (N. Crook)
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Braschi G, D’Alessandro M, Gottardi D, Siroli L, Patrignani F, Lanciotti R. Effects of Sub-Lethal High Pressure Homogenization Treatment on the Adhesion Mechanisms and Stress Response Genes in Lactobacillus acidophilus 08. Front Microbiol 2021; 12:651711. [PMID: 34122365 PMCID: PMC8193580 DOI: 10.3389/fmicb.2021.651711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/22/2021] [Indexed: 11/20/2022] Open
Abstract
Cell surface hydrophobicity (CSH) and adhesion are very important phenotypical traits for probiotics that confer them a competitive advantage for the resilience in the human gastrointestinal tract. This study was aimed to understand the effects over time of a 50 MPa hyperbaric treatment on the surface properties of Lactobacillus acidophilus 08 including CSH, autoaggregation, and in vitro adhesion (mucin layer and Caco-2 cells). Moreover, a link between the hurdle applied and the expression of genes involved in the general stress response (groEL and clpP) and adhesion processes (efTu and slpA) was evaluated. High pressure homogenization (HPH) at 50 MPa significantly increased the CSH percentage (H%), autoaggregation and in vitro adhesion on mucin of L. acidophilus 08 cells compared with the untreated cells. Moreover, the hyperbaric hurdle induced an upregulation of the stress response genes groEL and ef-TU together with a down regulation of the clpP and S-layer slpA genes. Looking at the protein profile, HPH-treatment showed an increase in the number or intensity of protein bands at high and low molecular weights.
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Affiliation(s)
- Giacomo Braschi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | | | - Davide Gottardi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Lorenzo Siroli
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Cesena, Italy
| | - Francesca Patrignani
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Cesena, Italy
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Cesena, Italy
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Martínez B, Rodríguez A, Kulakauskas S, Chapot-Chartier MP. Cell wall homeostasis in lactic acid bacteria: threats and defences. FEMS Microbiol Rev 2021; 44:538-564. [PMID: 32495833 PMCID: PMC7476776 DOI: 10.1093/femsre/fuaa021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB.
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Affiliation(s)
- Beatriz Martínez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Ana Rodríguez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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6
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In Vivo Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene Expression. mBio 2021; 12:mBio.03399-20. [PMID: 33500337 PMCID: PMC7858073 DOI: 10.1128/mbio.03399-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lactobacillus acidophilus NCFM is a probiotic strain commonly used in dairy products and dietary supplements. Postgenome in vitro studies of NCFM thus far have linked potential key genotypes to its probiotic-relevant attributes, including gut survival, prebiotic utilization, host interactions, and immunomodulatory activities. To corroborate and extend beyond previous in vivo and in vitro functional studies, we employed a dual RNA sequencing (RNA-seq) transcriptomic approach to identify genes potentially driving the gut fitness and activities of L. acidophilus NCFM in vivo, and in parallel, examine the ileal transcriptional response of its murine hosts during monocolonization. Spatial expression profiling of NCFM from the ileum through the colon revealed a set of 134 core genes that were consistently overexpressed during gut transit. These in vivo core genes are predominantly involved in the metabolism of carbohydrates, amino acids, and nucleotides, along with mucus-binding proteins and adhesion factors, confirming their functionally important roles in nutrient acquisition and gut retention. Functional characterization of the highly expressed major S-layer-encoding gene established its indispensable role as a cell shape determinant and maintenance of cell surface integrity, essential for viability and probiotic attributes. Host colonization by L. acidophilus resulted in significant downregulation of several proinflammatory cytokines and tight junction proteins. Genes related to redox signaling, mucin glycosylation, and circadian rhythm modulation were induced, suggesting impacts on intestinal development and immune functions. Metagenomic analysis of NCFM populations postcolonization demonstrated the genomic stability of L. acidophilus as a gut transient and further established its safety as a probiotic and biotherapeutic delivery platform.IMPORTANCE To date, our basis for comprehending the probiotic mechanisms of Lactobacillus acidophilus, one of the most widely consumed probiotic microbes, was largely limited to in vitro functional genomic studies. Using a germfree murine colonization model, in vivo-based transcriptional studies provided the first view of how L. acidophilus survives in the mammalian gut environment, including gene expression patterns linked to survival, efficient nutrient acquisition, stress adaptation, and host interactions. Examination of the host ileal transcriptional response, the primary effector site of L. acidophilus, has also shed light into the mechanistic roles of this probiotic microbe in promoting anti-inflammatory responses, maintaining intestinal epithelial homeostasis and modulation of the circadian-metabolic axis in its host.
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7
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Dadfarma N, Karimi G, Nowroozi J, Nejadi N, Kazemi B, Bandehpour M. Proteomic analysis of Lactobacillus casei in response to different pHs using two-dimensional electrophoresis and MALDI TOF mass spectroscopy. IRANIAN JOURNAL OF MICROBIOLOGY 2020; 12:431-436. [PMID: 33603998 PMCID: PMC7867702 DOI: 10.18502/ijm.v12i5.4604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Lactobacillus casei, an acid-resistant bacterium, has a protective role against the pathogens. So we aimed to determine the proteome of Lactobacillus casei ATCC39392 strain in response to different pHs of 5 and 7 using proteomic analysis. Materials and Methods: Supernatant and bacterial extraction of Lactobacillus casei ATCC39392 adapts at pHs 5 and 7 were isolated using sodium dodecyl sulfate–polyacrylamide gel and two-dimensional gel electrophoresis. The comparison of results showed that 7 protein spots were seen in pH 5 but not in pH 7. Afterward, they were excised and sent for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to be identified. Results: Seven different proteins (four secretory and three structural) with different roles in human body health were identified. Prescribed proteins include putative cell wall associated Hydrolase, Glycoside Hydrolase, beta-N-Acetyl hexosaminidase, Histidine Kinase, Chaperonin, metal dependent Hydrolase and Lysozyme. Conclusion: Seven isolated proteins with anti-cancer and digestive impresses are proper subjects in therapy or drug delivery approaches especially oral drug usage for protection against stomach acidic area.
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Affiliation(s)
- Narges Dadfarma
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Golgis Karimi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamileh Nowroozi
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Naser Nejadi
- Proteomics Research Center, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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8
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Klotz C, Goh YJ, O'Flaherty S, Barrangou R. S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM. BMC Microbiol 2020; 20:248. [PMID: 32787778 PMCID: PMC7425073 DOI: 10.1186/s12866-020-01908-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Surface layers (S-layers) are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost layer of many bacterial cell envelopes. Within the Lactobacillus genus, S-layer presence is frequently associated with probiotic-relevant properties such as improved adherence to host epithelial cells and modulation of the immune response. However, recent studies have demonstrated that certain S-layer functions may be supplemented by a novel subset of proteins embedded within its lattice, termed S-layer associated proteins (SLAPs). In the following study, four Lactobacillus acidophilus NCFM SLAPs (LBA0046, LBA0864, LBA1426, and LBA1539) were selected for in silico and phenotypic assessment. RESULTS Despite lacking any sequence similarity or catalytic domains that may indicate function, the genes encoding the four proteins of interest were shown to be unique to S-layer-forming, host-adapted lactobacilli species. Likewise, their corresponding deletion mutants exhibited broad, host-relevant phenotypes including decreased inflammatory profiles and reduced adherence to Caco-2 intestinal cells, extracellular matrices, and mucin in vitro. CONCLUSIONS Overall, the data presented in this study collectively links several previously uncharacterized extracellular proteins to roles in the underlying host adaptive mechanisms of L. acidophilus.
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Affiliation(s)
- Courtney Klotz
- Genomic Sciences Graduate Program North Carolina State University, Raleigh, NC, USA.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Yong Jun Goh
- Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program North Carolina State University, Raleigh, NC, USA. .,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
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9
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Adu KT, Wilson R, Baker AL, Bowman J, Britz ML. Prolonged Heat Stress of Lactobacillus paracasei GCRL163 Improves Binding to Human Colorectal Adenocarcinoma HT-29 Cells and Modulates the Relative Abundance of Secreted and Cell Surface-Located Proteins. J Proteome Res 2020; 19:1824-1846. [PMID: 32108472 DOI: 10.1021/acs.jproteome.0c00107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lactobacillus casei group bacteria improve cheese ripening and may interact with host intestinal cells as probiotics, where surface proteins play a key role. Three complementary methods [trypsin shaving (TS), LiCl-sucrose (LS) extraction, and extracellular culture fluid precipitation] were used to analyze cell surface proteins of Lactobacillus paracasei GCRL163 by label-free quantitative proteomics after culture to the mid-exponential phase in bioreactors at pH 6.5 and temperatures of 30-45 °C. A total of 416 proteins, including 300 with transmembrane, cell wall anchoring, and secretory motifs and 116 cytoplasmic proteins, were quantified as surface proteins. Although LS caused significantly greater cell lysis as growth temperature increased, higher numbers of extracytoplasmic proteins were exclusively obtained by LS treatment. Together with the increased positive surface charge of cells cultured at supra-optimal temperatures, proteins including cell wall hydrolases Msp1/p75 and Msp2/p40, α-fucosidase AlfB, SecA, and a PspC-domain putative adhesin were upregulated in surface or secreted protein fractions, suggesting that cell adhesion may be altered. Prolonged heat stress (PHS) increased binding of L. paracasei GCRL163 to human colorectal adenocarcinoma HT-29 cells, relative to acid-stressed cells. This study demonstrates that PHS influences cell adhesion and relative abundance of proteins located on the surface, which may impact probiotic functionality, and the detected novel surface proteins likely linked to the cell cycle and envelope stress.
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Affiliation(s)
- Kayode T Adu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Anthony L Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - John Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Margaret L Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
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10
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Klotz C, Goh YJ, O'Flaherty S, Johnson B, Barrangou R. Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface. Front Microbiol 2020; 11:345. [PMID: 32256464 PMCID: PMC7090030 DOI: 10.3389/fmicb.2020.00345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/17/2020] [Indexed: 01/18/2023] Open
Abstract
Bacterial surface-layers (S-layers) are crystalline arrays of repeating proteinaceous subunits that coat the exterior of many cell envelopes. S-layers have demonstrated diverse functions in growth and survival, maintenance of cell integrity, and mediation of host interactions. Additionally, S-layers can act as scaffolds for the outward display of auxiliary proteins and glycoproteins. These non-covalently bound S-layer associated proteins (SLAPs) have characterized roles in cell division, adherence to intestinal cells, and modulation of the host immune response. Recently, IgdA (LBA0695), a Lactobacillus acidophilus SLAP that possesses a Group 3 immunoglobulin (Ig)-like domain and GW (Gly-Tryp) dipeptide surface anchor, was recognized for its high conservation among S-layer-forming lactobacilli, constitutive expression, and surface localization. These findings prompted its selection for examination within the present study. Although IgdA and corresponding orthologs were shown to be unique to host-adapted lactobacilli, the Ig domain itself was specific to vertebrate-adapted species suggesting a role in vertebrate adaptation. Using a counterselective gene replacement system, igdA was deleted from the L. acidophilus NCFM chromosome. The resultant mutant, NCK2532, exhibited a visibly disrupted cell surface which likely contributed to its higher salt sensitivity, severely reduced adhesive capacity, and altered immunogenicity profile. Transcriptomic analyses revealed the induction of several stress response genes and secondary surface proteins. Due to the broad impact of IgdA on the cellular physiology and probiotic attributes of L. acidophilus, identification of similar proteins in alternative bacterial species may help pinpoint next-generation host-adapted probiotic candidates.
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Affiliation(s)
- Courtney Klotz
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Brant Johnson
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States.,Microbiology Graduate Program, North Carolina State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States.,Microbiology Graduate Program, North Carolina State University, Raleigh, NC, United States
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Gender-specific changes in energy metabolism and protein degradation as major pathways affected in livers of mice treated with ibuprofen. Sci Rep 2020; 10:3386. [PMID: 32099006 PMCID: PMC7042271 DOI: 10.1038/s41598-020-60053-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
Ibuprofen, an inhibitor of prostanoid biosynthesis, is a common pharmacological agent used for the management of pain, inflammation and fever. However, the chronic use of ibuprofen at high doses is associated with increased risk for cardiovascular, renal, gastrointestinal and liver injuries. The underlying mechanisms of ibuprofen-mediated effects on liver remain unclear. To determine the mechanisms and signaling pathways affected by ibuprofen (100 mg/kg/day for seven days), we performed proteomic profiling of male mice liver with quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) using ten-plex tandem mass tag (TMT) labeling. More than 300 proteins were significantly altered between the control and ibuprofen-treated groups. The data suggests that several major pathways including (1) energy metabolism, (2) protein degradation, (3) fatty acid metabolism and (4) antioxidant system are altered in livers from ibuprofen treated mice. Independent validation of protein changes in energy metabolism and the antioxidant system was carried out by Western blotting and showed sex-related differences. Proteasome and immunoproteasome activity/expression assays showed ibuprofen induced gender-specific proteasome and immunoproteasome dysfunction in liver. The study observed multifactorial gender-specific ibuprofen-mediated effects on mice liver and suggests that males and females are affected differently by ibuprofen.
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12
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Pan M, Barrangou R. Combining omics technologies with CRISPR-based genome editing to study food microbes. Curr Opin Biotechnol 2020; 61:198-208. [DOI: 10.1016/j.copbio.2019.12.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022]
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Siciliano RA, Lippolis R, Mazzeo MF. Proteomics for the Investigation of Surface-Exposed Proteins in Probiotics. Front Nutr 2019; 6:52. [PMID: 31069232 PMCID: PMC6491629 DOI: 10.3389/fnut.2019.00052] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/05/2019] [Indexed: 01/08/2023] Open
Abstract
Probiotics are commensal microorganisms that are present in the intestinal tract and in many fermented foods and positively affect human health, promoting digestion and uptake of dietary nutrients, strengthening intestinal barrier function, modulating immune response, and enhancing antagonism toward pathogens. The proteosurfaceome, i.e., the complex set of proteins present on the bacterial surface, is directly involved as leading actor in the dynamic communication between bacteria and host. In the last decade, the biological relevance of surface-exposed proteins prompted research activities exploiting the potentiality of proteomics to define the complex network of proteins that are involved in the molecular mechanisms at the basis of the adaptation to gastrointestinal environment and the probiotic effects. These studies also took advantages of the recent technological improvements in proteomics, mass spectrometry and bioinformatics that triggered the development of ad hoc designed innovative strategies to characterize the bacterial proteosurfaceome. This mini-review is aimed at describing the key role of proteomics in depicting the cell wall protein architecture and the involvement of surface-exposed proteins in the intimate and dynamic molecular dialogue between probiotics and intestinal epithelial and immune cells.
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Affiliation(s)
- Rosa Anna Siciliano
- Institute of Food Sciences, National Research Council (CNR-ISA), Avellino, Italy
| | - Rosa Lippolis
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Bari, Italy
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14
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An Acid Up-Regulated Surface Protein of Lactobacillus paracasei Strain GCRL 46 is Phylogenetically Related to the Secreted Glucan- (GpbB) and Immunoglobulin-Binding (SibA) Protein of Pathogenic Streptococci. Int J Mol Sci 2019; 20:ijms20071610. [PMID: 30935131 PMCID: PMC6479570 DOI: 10.3390/ijms20071610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/22/2019] [Accepted: 03/28/2019] [Indexed: 02/07/2023] Open
Abstract
Bacterial cell wall hydrolases, including amidases and peptidases, play a critical role in peptidoglycan turnover during growth, impacting daughter cell separation, and cell death, through autolysis. When exploring the regulation of protein expression across the growth cycle of an acid-resistant strain of Lactobacillus paracasei, GCRL 46, we observed temporal up-regulation of proteins in the 40⁻45 kDa molecular weight range for whole-cell extracts when culturing in fermenters at a controlled pH of 4.0 versus optimum growth pH of 6.3. Up-regulation of proteins in this size range was not detected in SDS-PAGE gels of the cytosolic fraction, but was routinely detected following growth at low pH in whole cells and cell debris obtained after bead beating and centrifugation, indicating a cell surface location. N-terminal sequencing and in silico analyses showed sequence similarity with proteins in the L. casei group (L. casei, L. paracasei and L. rhamnosus) which were variously annotated as uncharacterized proteins, surface antigens, possible TrsG proteins, CHAP (cysteine, histidine-dependent amidohydrolases/peptidases)-domain proteins or putative peptidoglycan d,l-endopeptidase due to the presence of a CwlO domain. This protein is a homologue of the p40 (Msp2) secreted protein of L. rhamnosus LGG, which is linked to probiotic functionality in this species, and is phylogenetically related to structurally-similar proteins found in Enterococcus, Streptococcus and Bifidobacterium species, including the glucan-binding (GbpB), surface antigen (SagA) proteins detected in pathogenic group A streptococci species as secreted, immunoglobulin-binding (SibA) proteins (also named PcsB). Three-dimensional (3D) modelling predicted structural similarities in the CHAP proteins from the L. casei group and streptococcal species, indicating retention of overall architecture despite sequence divergence, and an implied retention of function during evolution. A phylogenetically-related hydrolase also contained the CwlO domain with a NLPC_P60 domain, and showed similar overall but distinct architecture to the CHAP proteins. We concluded that the surface-located, CHAP protein in L. casei is up-regulated during long-term exposure to acidic conditions during growth but not during acid shock.
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Adu KT, Wilson R, Nichols DS, Baker AL, Bowman JP, Britz ML. Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress. PLoS One 2018; 13:e0206317. [PMID: 30359441 PMCID: PMC6201924 DOI: 10.1371/journal.pone.0206317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Prolonged heat stress is one of the harsh conditions Lactobacillus casei strains encounter as non-starter lactic acid bacteria in dairy product manufacture. To understand the physiological and molecular mechanisms through which Lb. casei GCRL163 adapts to persistent elevated temperature, label-free quantitative proteomics of cell-free extracts was used to characterize the global responses of the strain cultured anaerobically in bioreactors at 30 to 45°C, pH 6.5, together with GC-MS for fatty acid methyl ester analysis at different growth phases. At higher growth temperatures, repression of energy-consuming metabolic pathways, such as fatty acid, nucleotide and amino acid biosynthesis, was observed, while PTS- and ABC-type transporter systems associated with uptake of nitrogen and carbon sources were up-regulated. Alkaline shock protein Asp23_2 was only detected at 45°C, expressed at high abundance, and presumptive α-L-fucosidase only at 40 and 45°C, with highly increased abundance (log2-fold change of 7) at 45°C. We identified a novel SecB homolog as a protein export chaperone putatively involved in posttranslational translocation systems, which was down-regulated as growth temperature increased and where the modelled 3D-structure shared architectural similarities with the Escherichia coli SecB protein. Membrane lipid analyses revealed temporal changes in fatty acid composition, cyclization of oleic acid to cyclopropane and novel cyclopentenyl moieties, and reduced synthesis of vaccenic acid, at higher temperatures. An 18kDa α-crystallin domain, Hsp20 family heat shock protein was more highly up-regulated in response to heat stress compared to other molecular chaperones, suggesting this protein could be a useful biomarker of prolonged heat stress in Lb. casei GCRL163.
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Affiliation(s)
- Kayode T. Adu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - Anthony L. Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Margaret L. Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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Albuquerque‐Souza E, Balzarini D, Ando‐Suguimoto ES, Ishikawa KH, Simionato MRL, Holzhausen M, Mayer MPA. Probiotics alter the immune response of gingival epithelial cells challenged byPorphyromonas gingivalis. J Periodontal Res 2018; 54:115-127. [DOI: 10.1111/jre.12608] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/12/2018] [Accepted: 08/08/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Emmanuel Albuquerque‐Souza
- Division of PeriodonticsDepartment of StomatologySchool of DentistryUniversity of São Paulo São Paulo Brazil
- Department of MicrobiologyInstitute of Biomedical SciencesUniversity of São Paulo São Paulo Brazil
| | - Danilo Balzarini
- Division of PeriodonticsDepartment of StomatologySchool of DentistryUniversity of São Paulo São Paulo Brazil
| | - Ellen S. Ando‐Suguimoto
- Department of MicrobiologyInstitute of Biomedical SciencesUniversity of São Paulo São Paulo Brazil
| | - Karin H. Ishikawa
- Department of MicrobiologyInstitute of Biomedical SciencesUniversity of São Paulo São Paulo Brazil
| | - Maria R. L. Simionato
- Department of MicrobiologyInstitute of Biomedical SciencesUniversity of São Paulo São Paulo Brazil
| | - Marinella Holzhausen
- Division of PeriodonticsDepartment of StomatologySchool of DentistryUniversity of São Paulo São Paulo Brazil
| | - Marcia P. A. Mayer
- Division of PeriodonticsDepartment of StomatologySchool of DentistryUniversity of São Paulo São Paulo Brazil
- Department of MicrobiologyInstitute of Biomedical SciencesUniversity of São Paulo São Paulo Brazil
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Klotz C, Barrangou R. Engineering Components of the Lactobacillus S-Layer for Biotherapeutic Applications. Front Microbiol 2018; 9:2264. [PMID: 30333802 PMCID: PMC6176008 DOI: 10.3389/fmicb.2018.02264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023] Open
Abstract
Lactic acid bacteria (LAB) are frequently harnessed for the delivery of biomolecules to mucosal tissues. Several species of Lactobacillus are commonly employed for this task, of which a subset are known to possess surface-layers (S-layers). S-layers are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost coating of many prokaryotic cell envelopes. Their periodicity and abundance have made them a target for numerous biotechnological applications. In the following review, we examine the multi-faceted S-layer protein (Slp), and its use in both heterologous protein expression systems and mucosal vaccine delivery frameworks, through its diverse genetic components: the strong native promoter, capable of synthesizing as many as 500 Slp subunits per second; the signal peptide that stimulates robust secretion of recombinant proteins; and the structural domains, which can be harnessed for both cell surface display of foreign peptides or adhesion enhancement of a host bacterium. Although numerous studies have established vaccine platforms based on one or more components of the Lactobacillus S-layer, this area of research still remains largely in its infancy, thus this review is meant to not only highlight past works, but also advocate for the future usage of Slps in biotherapeutic research.
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Affiliation(s)
- Courtney Klotz
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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Dietary Nutrients, Proteomes, and Adhesion of Probiotic Lactobacilli to Mucin and Host Epithelial Cells. Microorganisms 2018; 6:microorganisms6030090. [PMID: 30134518 PMCID: PMC6163540 DOI: 10.3390/microorganisms6030090] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 01/26/2023] Open
Abstract
The key role of diet and environment in human health receives increasing attention. Thus functional foods, probiotics, prebiotics, and synbiotics with beneficial effects on health and ability to prevent diseases are in focus. The efficacy of probiotic bacteria has been connected with their adherence to the host epithelium and residence in the gut. Several in vitro techniques are available for analyzing bacterial interactions with mucin and intestinal cells, simulating adhesion to the host in vivo. Proteomics has monitored and identified proteins of probiotic bacteria showing differential abundance elicited in vitro by exposure to food components, including potential prebiotics (e.g., certain carbohydrates, and plant polyphenols). While adhesion of probiotic bacteria influenced by various environmental factors relevant to the gastrointestinal tract has been measured previously, this was rarely correlated with changes in the bacterial proteome induced by dietary nutrients. The present mini-review deals with effects of selected emerging prebiotics, food components and ingredients on the adhesion of probiotic lactobacilli to mucin and gut epithelial cells and concomitant abundancy changes of specific bacterial proteins. Applying this in vitro synbiotics-like approach enabled identification of moonlighting and other surface-located proteins of Lactobacillus acidophilus NCFM that are possibly associated with the adhesive mechanism.
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Banić M, Uroić K, Leboš Pavunc A, Novak J, Zorić K, Durgo K, Petković H, Jamnik P, Kazazić S, Kazazić S, Radović S, Scalabrin S, Hynӧnen U, Šušković J, Kos B. Characterization of S-layer proteins of potential probiotic starter culture Lactobacillus brevis SF9B isolated from sauerkraut. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.03.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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