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Fisher CR, Masters TL, Johnson S, Greenwood-Quaintance KE, Chia N, Abdel MP, Patel R. Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions. Int J Med Microbiol 2024; 315:151620. [PMID: 38579524 PMCID: PMC11214590 DOI: 10.1016/j.ijmm.2024.151620] [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: 08/22/2023] [Revised: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
Staphylococcus epidermidis is part of the commensal microbiota of the skin and mucous membranes, though it can also act as a pathogen in certain scenarios, causing a range of infections, including periprosthetic joint infection (PJI). Transcriptomic profiling may provide insights into mechanisms by which S. epidermidis adapts while in a pathogenic compared to a commensal state. Here, a total RNA-sequencing approach was used to profile and compare the transcriptomes of 19 paired PJI-associated S. epidermidis samples from an in vivo clinical source and grown in in vitro laboratory culture. Genomic comparison of PJI-associated and publicly available commensal-state isolates were also compared. Of the 1919 total transcripts found, 145 were from differentially expressed genes (DEGs) when comparing in vivo or in vitro samples. Forty-two transcripts were upregulated and 103 downregulated in in vivo samples. Of note, metal sequestration-associated genes, specifically those related to staphylopine activity (cntA, cntK, cntL, and cntM), were upregulated in a subset of clinical in vivo compared to laboratory grown in vitro samples. About 70% of the total transcripts and almost 50% of the DEGs identified have not yet been annotated. There were no significant genomic differences between known commensal and PJI-associated S. epidermidis isolates, suggesting that differential genomics may not play a role in S. epidermidis pathogenicity. In conclusion, this study provides insights into phenotypic alterations employed by S epidermidis to adapt to infective and non-infected microenvironments, potentially informing future therapeutic targets for related infections.
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Affiliation(s)
- Cody R Fisher
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Thao L Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Zeng J, Song K, Wang J, Wen H, Zhou J, Ni T, Lu H, Yu Y. Characterization and optimization of 5´ untranslated region containing poly-adenine tracts in Kluyveromyces marxianus using machine-learning model. Microb Cell Fact 2024; 23:7. [PMID: 38172836 PMCID: PMC10763412 DOI: 10.1186/s12934-023-02271-3] [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: 10/15/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The 5´ untranslated region (5´ UTR) plays a key role in regulating translation efficiency and mRNA stability, making it a favored target in genetic engineering and synthetic biology. A common feature found in the 5´ UTR is the poly-adenine (poly(A)) tract. However, the effect of 5´ UTR poly(A) on protein production remains controversial. Machine-learning models are powerful tools for explaining the complex contributions of features, but models incorporating features of 5´ UTR poly(A) are currently lacking. Thus, our goal is to construct such a model, using natural 5´ UTRs from Kluyveromyces marxianus, a promising cell factory for producing heterologous proteins. RESULTS We constructed a mini-library consisting of 207 5´ UTRs harboring poly(A) and 34 5´ UTRs without poly(A) from K. marxianus. The effects of each 5´ UTR on the production of a GFP reporter were evaluated individually in vivo, and the resulting protein abundance spanned an approximately 450-fold range throughout. The data were used to train a multi-layer perceptron neural network (MLP-NN) model that incorporated the length and position of poly(A) as features. The model exhibited good performance in predicting protein abundance (average R2 = 0.7290). The model suggests that the length of poly(A) is negatively correlated with protein production, whereas poly(A) located between 10 and 30 nt upstream of the start codon (AUG) exhibits a weak positive effect on protein abundance. Using the model as guidance, the deletion or reduction of poly(A) upstream of 30 nt preceding AUG tended to improve the production of GFP and a feruloyl esterase. Deletions of poly(A) showed inconsistent effects on mRNA levels, suggesting that poly(A) represses protein production either with or without reducing mRNA levels. CONCLUSION The effects of poly(A) on protein production depend on its length and position. Integrating poly(A) features into machine-learning models improves simulation accuracy. Deleting or reducing poly(A) upstream of 30 nt preceding AUG tends to enhance protein production. This optimization strategy can be applied to enhance the yield of K. marxianus and other microbial cell factories.
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Affiliation(s)
- Junyuan Zeng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Kunfeng Song
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jingqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Haimei Wen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
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Nguyen LT, Lau LY, Fortes MRS. Proteomic Analysis of Hypothalamus and Pituitary Gland in Pre and Postpubertal Brahman Heifers. Front Genet 2022; 13:935433. [PMID: 35774501 PMCID: PMC9237413 DOI: 10.3389/fgene.2022.935433] [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: 05/03/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
The hypothalamus and the pituitary gland are directly involved in the complex systemic changes that drive the onset of puberty in cattle. Here, we applied integrated bioinformatics to elucidate the critical proteins underlying puberty and uncover potential molecular mechanisms from the hypothalamus and pituitary gland of prepubertal (n = 6) and postpubertal (n = 6) cattle. Proteomic analysis in the hypothalamus and pituitary gland revealed 275 and 186 differentially abundant (DA) proteins, respectively (adjusted p-value < 0.01). The proteome profiles found herein were integrated with previously acquired transcriptome profiles. These transcriptomic studies used the same tissues harvested from the same heifers at pre- and post-puberty. This comparison detected a small number of matched transcripts and protein changes at puberty in each tissue, suggesting the need for multiple omics analyses for interpreting complex biological systems. In the hypothalamus, upregulated DA proteins at post-puberty were enriched in pathways related to puberty, including GnRH, calcium and oxytocin signalling pathways, whereas downregulated proteins were observed in the estrogen signalling pathway, axon guidance and GABAergic synapse. Additionally, this study revealed that ribosomal pathway proteins in the pituitary were involved in the pubertal development of mammals. The reported molecules and derived protein-protein networks are a starting point for future experimental approaches that might dissect with more detail the role of each molecule to provide new insights into the mechanisms of puberty onset in cattle.
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Affiliation(s)
- Loan To Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
- *Correspondence: Loan To Nguyen,
| | - Li Yieng Lau
- Agency of Science, Technology and Research, Singapore, Singapore
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Evaluation of the differences between biofilm and planktonic Brucella abortus via metabolomics and proteomics. Funct Integr Genomics 2021; 21:421-433. [PMID: 34009538 DOI: 10.1007/s10142-021-00788-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
This study analyzed the difference between biofilm and planktonic Brucella abortus using metabolomics and proteomics. Brucella abortus was cultured in different media to induce Brucella abortus biofilm formation and planktonic cells, followed by metabolomics and proteomics analyses for these two samples. Significant differential metabolites were identified, followed by KEGG pathway analysis. Differentially expressed proteins were identified, followed by subcellular localization, GO annotation, and KEGG pathway enrichment. Additionally, a correlation analysis of metabolomics and proteomics was performed. Metabolomics analysis showed 7682 positive and 4433 negative metabolites, including 188 positive and 117 negative significant differential metabolites. These differential metabolites were enriched in fatty acid/unsaturated fatty acid biosynthesis and linoleic acid metabolism. Proteomics analysis revealed 1759 proteins, including 486 differentially expressed proteins, which were enriched in various metabolic and degradation-related pathways. Subcellular localization showed that 74.3% of the differential proteins were cytoplasmic proteins. Correlation analysis showed that 1-palmitoyl-2-oleoyl-phosphatidylglycerol had the most significant correlations with proteins, followed by cytosine. Both metabolites correlated with the protein Q57EI7 (RbsB-1, ribose ABC transporter). One common pathway, fatty acid biosynthesis, was identified by both proteomics and metabolomics analyses that involved the metabolites, oleic acid, and protein Q57DK3 (biotin carboxylase). There were metabolomic and proteomic differences between Brucella abortus biofilm and planktonic cells, and these results provide novel insights into the biofilm-forming process of Brucella abortus.
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Ribič U, Polak T, Lušnic Polak M, Klančnik A, Jeršek B. Adaptation Response Mechanisms of Staphylococcus epidermidis Strains Exposed to Increasing Concentrations of Didecyldimethylammonium Chloride. Microb Drug Resist 2020; 26:583-593. [PMID: 31910354 DOI: 10.1089/mdr.2019.0064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Staphylococcus epidermidis is a commensal inhabitant of human skin and mucosa, and a common nosocomial pathogen in immunocompromised patients. S. epidermidis strains were isolated from places with precisely defined and controlled air quality and regular cleaning and disinfection regimes-cleanrooms. These strains were adapted to increasing concentrations of the quaternary ammonium disinfectant didecyldimethylammonium chloride (DDAC). Compared to nonadapted strains, these strains became adapted to up to 180-fold higher concentrations of DDAC, as seen by their increased minimal inhibitory concentrations. Examination of the stability of adaptation showed that three strains became permanently adapted to DDAC and named as resistant strains, and four strains were temporarily adapted to DDAC and named as strains with higher tolerance to DDAC. Some adapted strains showed cross-resistance to benzalkonium chloride and/or antibiotics. The adaptation response mechanisms of these DDAC-adapted strains were also investigated. The majority of adapted strains showed modifications to cell size and fatty acid composition. Some of the adapted strains showed changes in biofilm formation and overexpression of efflux pumps. Three adapted strains also showed altered growth rates. In this first report of adaptation of S. epidermidis strains to DDAC, the fatty acid profiling showed that the majority of strains had reduced ratio of saturated to unsaturated fatty acids and decreased content of straight-chain fatty acids, at the expense of the anteiso-branched fatty acids. We can conclude that S. epidermidis strains can adapt or become resistant to DDAC. We have revealed several adaptive response mechanisms that can be targeted for control and inhibition of S. epidermidis in cleanrooms and other clean processing environments.
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Affiliation(s)
- Urška Ribič
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Polak
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Mateja Lušnic Polak
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Barbara Jeršek
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Bottagisio M, Soggiu A, Piras C, Bidossi A, Greco V, Pieroni L, Bonizzi L, Roncada P, Lovati AB. Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress. Front Microbiol 2019; 10:1909. [PMID: 31551940 PMCID: PMC6743020 DOI: 10.3389/fmicb.2019.01909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/05/2019] [Indexed: 01/14/2023] Open
Abstract
Prosthetic joint replacement failure has a huge impact on quality of life and hospitalization costs. A leading cause of prosthetic joint infection is bacteria-forming biofilm on the surface of orthopedic devices. Staphylococcus epidermidis is an emergent, low-virulence pathogen implicated in chronic infections, barely indistinguishable from aseptic loosening when embedded in a mature matrix. The literature on the behavior of quiescent S. epidermidis in mature biofilms is scarce. To fill this gap, we performed comparative analysis of the whole proteomic profiles of two methicillin-resistant S. epidermidis strains growing in planktonic and in sessile form to investigate the molecular mechanisms underlying biofilm stability. After 72-h culture of biofilm-forming S. epidermidis, overexpression of proteins involved in the synthesis of nucleoside triphosphate and polysaccharides was observed, whereas planktonic bacteria expressed proteins linked to stress and anaerobic growth. Cytological analysis was performed to determine why planktonic bacteria unexpectedly expressed proteins typical of sessile culture. Images evidenced that prolonged culture under vigorous agitation can create a stressful growing environment that triggers microorganism aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. The choice of a unique late time point provided an important clue for future investigations into the biofilm-like behavior of planktonic cells. Our preliminary results may inform comparative proteomic strategies in the study of mature bacterial biofilm. Finally, there is an increasing number of studies on the aggregation of free-floating bacteria embedded in an extracellular matrix, prompting the need to gain further insight into this mode of bacterial growth.
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Affiliation(s)
- Marta Bottagisio
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Alessio Soggiu
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Cristian Piras
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Alessandro Bidossi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore Roma, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Luigi Bonizzi
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Paola Roncada
- Department of Health Sciences, Università degli Studi "Magna Græcia", Catanzaro, Italy
| | - Arianna B Lovati
- IRCCS Istituto Ortopedico Galeazzi, Cell and Tissue Engineering Laboratory, Milan, Italy
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Reynoso E, Ferreyra DD, Durantini EN, Spesia MB. Photodynamic inactivation to prevent and disrupt Staphylococcus aureus biofilm under different media conditions. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2019; 35:322-331. [PMID: 31006166 DOI: 10.1111/phpp.12477] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/25/2019] [Accepted: 04/14/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVE The goal of this work was to investigate the photodynamic activity of 5,10,15,20-tetrakis[4-(3-N,N-dimethylaminopropoxy)phenyl]chlorin (TAPC) and zinc(II) 2,9,16,23-tetrakis[4-(N-methylpyridyloxy)]phthalocyanine iodide (ZnPPc4+ ) as photosensitizers to inactivate Staphylococcus aureus biofilms and prevent their formations in different culture media. METHODS We incubated S aureus biofilms in different culture media: tryptic soy (TS), nutrient (N), Müeller Hinton (MH) broth, TS with glucose 2 and 5% (w/v) with 5 μM ZnPPc4+ or TAPC and irradiated with visible light (350-800 nm). Photodynamic inactivation (PDI) was determined by count of colony forming units (CFU) and crystal violet method. Furthermore, we studied PDI effect on biofilm development in TS broth. Finally, we examined the effects of PDI on the structure of S aureus biofilm. RESULTS Greater inactivation was achieved, using TAPC or ZnPPc4+ , when S aureus biofilm was grown in N or MH broths rather than in TS. Besides, glucose addition to the medium decreases the ability to develop biofilm and increase the photoinactivation capacity. Prevention of 3 log biofilm developments was obtained when S aureus cultures were treated with TAPC (10 μM) and 108 J/cm2 in TS broth and the number of CFU was counted after 24 hours. Moreover, microscopy studies demonstrated modifications in biofilm architecture. CONCLUSIONS These results indicate that TAPC and ZnPPc4+ may be promising photosensitizers for photodynamic inactivation of S aureus biofilms or to prevent their formation.
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Affiliation(s)
- Eugenia Reynoso
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Darío D Ferreyra
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Edgardo N Durantini
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Mariana B Spesia
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
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Oliveira ASD, Rosa IIR, Novaes E, Oliveira LSD, Baeza LC, Borges CL, Marlinghaus L, Soares CMDA, Giambiagi-deMarval M, Parente-Rocha JA. The exoproteome profiles of three Staphylococcus saprophyticus strains reveal diversity in protein secretion contents. Microbiol Res 2018; 216:85-96. [PMID: 30269860 DOI: 10.1016/j.micres.2018.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/07/2018] [Accepted: 08/21/2018] [Indexed: 12/24/2022]
Abstract
Staphylococcus saprophyticus is a gram-positive microorganism responsible for urinary tract infections (UTIs). Although some virulence factors are characterized, such as urease, autolysins, adhesins and hemagglutinins, large-scale proteomic studies have not been performed within this species. We performed the characterization of the exoproteome from three S. saprophyticus strains: the reference strain ATCC 15,305, a non-capsular strain 7108 and the 9325 strain containing a thick capsule which were cultured in BHI medium and culture supernatants were analysed by using mass spectrometry approach. We observed a core of 72 secreted proteins. In addition, it was possible to detect diversity in the protein profiles of the exoproteomes. Interestingly, strain 7108 presented no secretion of three antigenic proteins, including the classical SsaA antigen. In addition, the level of antigenic proteins secreted by strain 9325 was higher than in ATCC 15,305. This result was confirmed by Western blot analysis using anti-SsaA polyclonal antibodies, and no production/ secretion of SsaA was detected in strain 7108. Transcriptional data shows that 7108 strain produces transcripts encoding SsaA, suggesting post-transcriptional regulation occurs in this strain. Moreover, when compared with the other strains that were analyzed, it was possible to detect higher levels of proteases secreted by strain 7108 and higher levels of antigenic proteins and transglycosylases secreted by 9325 strain. The results reveal diversity in protein secretion among strains. This research is an important first step towards understanding the variability in S. saprophyticus exoproteome profile and could be significant in explaining differences among strains.
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Affiliation(s)
- Andrea Santana de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Isabella Inês Rodrigues Rosa
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Evandro Novaes
- Escola de Agronomia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lucas Silva de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lilian Cristiane Baeza
- Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | | | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Marcia Giambiagi-deMarval
- Laboratório de Microbiologia Molecular, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro - Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
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da Costa JP, Carvalhais V, Ferreira R, Amado F, Vilanova M, Cerca N, Vitorino R. Proteome signatures—how are they obtained and what do they teach us? Appl Microbiol Biotechnol 2015. [DOI: 10.1007/s00253-015-6795-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Carvalhais V, Amado F, Cerveira F, Ferreira R, Vilanova M, Cerca N, Vitorino R. Immunoreactive pattern of Staphylococcus epidermidis biofilm against human whole saliva. Electrophoresis 2015; 36:1228-33. [PMID: 25782040 DOI: 10.1002/elps.201500043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 02/21/2015] [Accepted: 02/23/2015] [Indexed: 01/18/2023]
Abstract
Saliva is essential to interact with microorganisms in the oral cavity. Therefore, the interest in saliva antimicrobial properties is on the rise. Here, we used an immunoproteomic approach, based on protein separation of Staphylococcus epidermidis biofilms by 2DE, followed by Western-blotting, to compare human serum and saliva reactivity profile. A total of 17 proteins were identified by MALDI-TOF/TOF. Serum and saliva presented a distinct pattern of immunoreactive proteins. Our results suggest that saliva seems to have higher propensity to react against S. epidermidis proteins with oxidoreductase activity and proteins involved with L-serine metabolic processes. We show that saliva was a powerful tool for the identification of potential S. epidermidis biofilms proteins.
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Affiliation(s)
- Virginia Carvalhais
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal.,CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Francisco Amado
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Frederico Cerveira
- Anatomia Patológica, Centro Hospitalar Baixo-Vouga, Avenida Artur Ravara, Aveiro, Portugal
| | - Rita Ferreira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manuel Vilanova
- IBMC - Instituto de Biologia Molecular e Celular, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Nuno Cerca
- IBMC - Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Rui Vitorino
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal.,iBiMED - Institute for Biomedical Research, University of Aveiro, Aveiro, Portugal
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11
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Carvalhais V, Cerveira F, Vilanova M, Cerca N, Vitorino R. An immunoproteomic approach for characterization of dormancy within Staphylococcus epidermidis biofilms. Mol Immunol 2015; 65:429-35. [PMID: 25749707 DOI: 10.1016/j.molimm.2015.02.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/19/2015] [Indexed: 01/02/2023]
Abstract
Virulence of Staphylococcus epidermidis is mainly attributed to surface colonization and biofilm formation in indwelling medical devices. Physiological heterogeneity of biofilms may influence host immune response and sensitivity to antibiotics. Dormant cells, among others, contribute to biofilm heterogeneity. The aim of this study was to identify immunogenic proteins of S. epidermidis biofilms associated with dormancy mechanism, by using two-dimensional electrophoresis (2-DE) immunoblotting and mass spectrometry (MS). A total of 19 bacterial proteins, recognized by human serum samples, were identified. These proteins were mainly involved in small molecule metabolic biological processes. Catalytic activity and ion binding were the most representative molecular functions. CodY and GpmA proteins were more reactive to sera when biofilm dormancy was induced, while FtnA and ClpP were more reactive when dormancy was prevented. This is the first work that identifies differences in immunoreactive proteins within bacterial biofilms with induced or prevented dormancy. Considering the importance of dormancy within biofilms, further evaluation of these proteins can provide insights into the mechanisms related to dormancy and help to improve current understanding on how dormancy affects the host immune response.
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Affiliation(s)
- Virginia Carvalhais
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Frederico Cerveira
- Anatomia Patológica, Centro Hospitalar Baixo-Vouga, Avenida Artur Ravara, 3814-501 Aveiro, Portugal
| | - Manuel Vilanova
- IBMC - Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Rua de Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Nuno Cerca
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rui Vitorino
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; iBiMED, Institute for Biomedical Research, University of Aveiro, Aveiro, Portugal.
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Proteomic profile of dormancy within Staphylococcus epidermidis biofilms using iTRAQ and label-free strategies. Appl Microbiol Biotechnol 2015; 99:2751-62. [PMID: 25672847 DOI: 10.1007/s00253-015-6434-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/16/2014] [Accepted: 01/25/2015] [Indexed: 12/12/2022]
Abstract
Staphylococcus epidermidis is an important nosocomial bacterium among carriers of indwelling medical devices, since it has a strong ability to form biofilms. The presence of dormant bacteria within a biofilm is one of the factors that contribute to biofilm antibiotic tolerance and immune evasion. Here, we provide a detailed characterization of the quantitative proteomic profile of S. epidermidis biofilms with different proportions of dormant bacteria. A total of 427 and 409 proteins were identified by label-free and label-based quantitative methodologies, respectively. From these, 29 proteins were found to be differentially expressed between S. epidermidis biofilms with prevented and induced dormancy. Proteins overexpressed in S. epidermidis with prevented dormancy were associated with ribosome synthesis pathway, which reflects the metabolic state of dormant bacteria. In the opposite, underexpressed proteins were related to catalytic activity and ion binding, with involvement in purine, arginine, and proline metabolism. Additionally, GTPase activity seems to be enhanced in S. epidermidis biofilm with induced dormancy. The role of magnesium in dormancy modulation was further investigated with bioinformatics tool based in predicted interactions. The main molecular function of proteins, which strongly interact with magnesium, was nucleic acid binding. Different proteomic strategies allowed to obtain similar results and evidenced that prevented dormancy led to an expression of a markedly different repertoire of proteins in comparison to the one of dormant biofilms.
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