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Arciola CR, Ravaioli S, Mirzaei R, Dolzani P, Montanaro L, Daglia M, Campoccia D. Biofilms in Periprosthetic Orthopedic Infections Seen through the Eyes of Neutrophils: How Can We Help Neutrophils? Int J Mol Sci 2023; 24:16669. [PMID: 38068991 PMCID: PMC10706149 DOI: 10.3390/ijms242316669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Despite advancements in our knowledge of neutrophil responses to planktonic bacteria during acute inflammation, much remains to be elucidated on how neutrophils deal with bacterial biofilms in implant infections. Further complexity transpires from the emerging findings on the role that biomaterials play in conditioning bacterial adhesion, the variety of biofilm matrices, and the insidious measures that biofilm bacteria devise against neutrophils. Thus, grasping the entirety of neutrophil-biofilm interactions occurring in periprosthetic tissues is a difficult goal. The bactericidal weapons of neutrophils consist of the following: ready-to-use antibacterial proteins and enzymes stored in granules; NADPH oxidase-derived reactive oxygen species (ROS); and net-like structures of DNA, histones, and granule proteins, which neutrophils extrude to extracellularly trap pathogens (the so-called NETs: an allusive acronym for "neutrophil extracellular traps"). Neutrophils are bactericidal (and therefore defensive) cells endowed with a rich offensive armamentarium through which, if frustrated in their attempts to engulf and phagocytose biofilms, they can trigger the destruction of periprosthetic bone. This study speculates on how neutrophils interact with biofilms in the dramatic scenario of implant infections, also considering the implications of this interaction in view of the design of new therapeutic strategies and functionalized biomaterials, to help neutrophils in their arduous task of managing biofilms.
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Affiliation(s)
- Carla Renata Arciola
- Laboratory of Immunorheumatology and Tissue Regeneration, Laboratory of Pathology of Implant Infections, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy;
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| | - Stefano Ravaioli
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (S.R.); (D.C.)
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Laboratory, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Paolo Dolzani
- Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy;
| | - Lucio Montanaro
- Laboratory of Immunorheumatology and Tissue Regeneration, Laboratory of Pathology of Implant Infections, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy;
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| | - Maria Daglia
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy;
| | - Davide Campoccia
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (S.R.); (D.C.)
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Gonçalves LG, Santos S, Gomes LP, Armengaud J, Miragaia M, Coelho AV. Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis. Front Microbiol 2022; 13:1000737. [PMID: 36246270 PMCID: PMC9554481 DOI: 10.3389/fmicb.2022.1000737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus epidermidis is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, S. epidermidis has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials. Thus new preventive and therapeutic strategies are urgently needed. However, the molecular mechanisms associated with S. epidermidis colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis commensal strain by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring during a sudden pH change, simulating the skin barrier break produced by a catheter. We found that exposure of S. epidermidis to skin pH induced oxidative phosphorylation and biosynthesis of peptidoglycan, lipoteichoic acids and betaine. In contrast, at blood pH, the bacterial assimilation of monosaccharides and its oxidation by glycolysis and fermentation was promoted. Additionally, several proteins related to virulence and immune evasion, namely extracellular proteases and membrane iron transporters were more abundant at blood pH. In the situation of an abrupt skin-to-blood pH shift we observed the decrease in the osmolyte betaine and changes in the levels of several metabolites and proteins involved in cellular redoxl homeostasis. Our results suggest that at the skin pH S. epidermidis cells are metabolically more active and adhesion is promoted, while at blood pH, metabolism is tuned down and cells have a more virulent profile. pH increase during commensal-to-pathogen conversion appears to be a critical environmental signal to the remodelling of the S. epidermidis metabolism toward a more pathogenic state. Targeting S. epidermidis proteins induced by pH 7.4 and promoting the acidification of the medical device surface or surrounding environment might be new strategies to treat and prevent S. epidermidis infections.
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Affiliation(s)
- Luis Gafeira Gonçalves
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana Santos
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Laidson Paes Gomes
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé, SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- *Correspondence: Maria Miragaia,
| | - Ana Varela Coelho
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Enhanced Biosynthesis of Fatty Acids Is Associated with the Acquisition of Ciprofloxacin Resistance in Edwardsiella tarda. mSystems 2021; 6:e0069421. [PMID: 34427511 PMCID: PMC8407472 DOI: 10.1128/msystems.00694-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Misuse and overuse of antibiotics drive the selection and spread of antibiotic-resistant bacteria. Although genetic mutations have been well defined for different types of antibiotic resistance, ways to revert antibiotic resistance are largely unexplored. Here, we adopted a proteomics approach to investigate the mechanism underlying ciprofloxacin resistance in Edwardsiella tarda, a representative pathogen that infects both economic animal species and human beings. By comparing the protein expression profiles of ciprofloxacin-sensitive and -resistant E. tarda, a total of 233 proteins of differential abundance were identified, where 53 proteins belong to the functional categories of metabolism, featuring a disrupted pyruvate cycle and decreased energy metabolism but increased fatty acid biosynthesis. The altered pyruvate cycle and energy metabolism were confirmed by gene expression and biochemical assays. Furthermore, the role of fatty acid biosynthesis and quinolone resistance were explored. The expression level and enzymatic activity of acetyl coenzyme A (acetyl-CoA) carboxylase, the first step of fatty acid biosynthesis, were increased in ciprofloxacin-resistant E. tarda. Treatment of ciprofloxacin-resistant E. tarda with acetyl-CoA carboxylase and 3-oxoacyl-[acyl carrier protein] synthase II inhibitors, 2-aminooxazole and triclosan, respectively, reduced the expression of fatty acid biosynthesis and promoted quinolone-mediated killing efficacy to antibiotic-resistant bacteria. Similar results were obtained in clinically isolated E. tarda strains. Our study suggests that energy metabolism has been reprogramed in ciprofloxacin-resistant bacteria that favor the biosynthesis of fatty acid, presenting a novel target to tackle antibiotic-resistant bacteria. IMPORTANCEEdwardsiella tarda is the causative agent of edwardsiellosis, which imposes huge challenges on clinics and aquaculture. Due to the overuse of antibiotics, the emergence and spread of antibiotic-resistant E. tarda threaten human health and animal farming. However, the mechanism of ciprofloxacin resistance in E. tarda is still lacking. Here, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomics was performed to identify a differential proteome between ciprofloxacin-sensitive and -resistant E. tarda. The fluctuated pyruvate cycle and reduced energy metabolism and elevated fatty acid biosynthesis are metabolic signatures of ciprofloxacin resistance. Moreover, inhibition of biosynthesis of fatty acids promotes quinolone-mediated killing efficacy in both lab-evolved and clinically isolated strains. This study reveals that a ciprofloxacin resistance mechanism is mediated by the elevated biosynthesis of fatty acids and the depressed pyruvate metabolism and energy metabolism in E. tarda. These findings provide a novel understanding for the ciprofloxacin resistance mechanism in E. tarda.
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Jiang R, Li Y, Wang H, Kong D, Wu X, Xu J. A study on the degradation efficiency of fluoranthene and the transmembrane protein mechanism of Rhodococcus sp. BAP-1 based on iTRAQ. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:140208. [PMID: 32783839 DOI: 10.1016/j.scitotenv.2020.140208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/20/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Based on previous studies that examined the whole proteome of Rhodococcus sp. BAP-1 during the degradation of polycyclic aromatic hydrocarbons (PAHs), transmembrane proteins have a large role in the degradation of fluoranthene. To further study the specific functions and mechanisms of transmembrane proteins from Rhodococcus sp. BAP-1 involved in the degradation process of fluoranthene, the degradation of PAHs and the membrane permeability were determined. In addition, the isobaric tags for relative and absolute quantization (iTRAQ) method were used to conduct a proteomics analysis of Rhodococcus sp. BAP-1 after exposure to fluoranthene for 1 d, 3 d, and 6 d. The results showed that the degradation rate was the highest on the first and sixth days, and the membrane permeability was also the highest on the sixth day. The iTRAQ analysis results showed 18, 29, and 48 upregulated proteins and 111, 97, and 21 downregulated proteins in the 1 d group vs control group, 3 d group vs control group, and 6 d group vs control group samples respectively. According to a Clusters of Orthologous Groups of proteins (COG) analysis, amino acid transport and metabolism are the most important functions. According to functional analysis from the gene ontology (GO) database, the oxidation-reduction process is the most important biological process; transporter activity is the main molecular function; and transmembrane proteins are the most important in the cell composition. This study combined the degradation rate, membrane permeability and transmembrane protein functions to analyze the functions and mechanisms of transmembrane proteins from Rhodococcus sp. BAP-1, which are involved in the degradation of fluoranthene at the protein level, and this study provides a solid foundation for further research on the metabolic processes of bacteria.
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Affiliation(s)
- Ruhan Jiang
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China, Guangxi Normal University, 541004 Guilin, Guangxi, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, Guangxi, China.
| | - Hongqi Wang
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China.
| | - Dekang Kong
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Xiaoxiong Wu
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Jie Xu
- Shunyi District Ecological Protection Bureau, 101300 Beijing, China
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5
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Chang TT, Ho CH. Plasma proteome atlas for differentiating tumor stage and post-surgical prognosis of hepatocellular carcinoma and cholangiocarcinoma. PLoS One 2020; 15:e0238251. [PMID: 32845921 PMCID: PMC7449477 DOI: 10.1371/journal.pone.0238251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022] Open
Abstract
Although mass spectrometry-based plasma proteomics enables sensitive and large-scale discovery and validation of biomarkers for various diseases, its integrative application to hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) is not well investigated. Therefore, we analyzed albumin- and immunoglobulin G-depleted plasma samples from 148 and 60 patients with HCC and CCA, respectively, using liquid chromatography-tandem mass spectrometry. The algorithm used to measure the content of each protein was the percentage of exponentially modified protein abundance index. From 5320 proteins assayed in plasma, 53 and 25 biomarker candidates were identified for HCC and CCA, respectively. The abundance of six and two HCC markers particularly protruded in stage II and III, respectively, whereas plasma serine protease inhibitor was the sole marker the level of which steadily decreased with CCA progression. From a prognostic facet, we showed candidate markers and their cutoff levels for evaluating probability of tumor recurrence and patient survival period. Combination Kaplan-Meier models showed that HCC stage III or IV and both the content of alpha-2-HS-glycoprotein and apolipoprotein CIII <0.2% exhibited the poorest post-surgical recurrence-free and overall survivals. Furthermore, the content of afamin ≥0.2% played a significant role on the poor prognosis in patients with CCA. Our findings, taken together, characterized novel plasma biomarker signatures in dissecting tumor stages and post-surgical outcomes of HCC and CCA.
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Affiliation(s)
- Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Hsun Ho
- Department of Medical Laboratory Science, College of Medicine, I-Shou University, Kaohsiung City, Taiwan
- * E-mail:
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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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Zhang P, Zhu J, Xu XY, Qing TP, Dai YZ, Feng B. Identification and function of extracellular protein in wastewater treatment using proteomic approaches: A minireview. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 233:24-29. [PMID: 30553123 DOI: 10.1016/j.jenvman.2018.12.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/04/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
Microbial extracellular proteins serve as important functions in wastewater treatment process. Analysis of their compositions and properties is crucial to probe their specific functions. However, conventional analytical techniques cannot obtain interest protein information from complex proteins. Recently, the extracellular proteomics method has been applied to resolve the composition of extracellular proteins. In order to better understand the roles of extracellular protein in wastewater treatment process, this review provides the information on the proteomics methods and their application in investigating extracellular proteins involved in microbial attachment/aggregation, biodegradation of pollutants, and response to environmental stresses. Future work needs to exploit the full capability of the proteome.
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Affiliation(s)
- Peng Zhang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China.
| | - Jing Zhu
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Xiao-Yan Xu
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Tai-Ping Qing
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - You-Zhi Dai
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Bo Feng
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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Chignell JF, Schlegel C, Ulber R, Reardon KF. Quantitative proteomic analysis of
Lactobacillus delbrueckii
ssp.
lactis
biofilms. AIChE J 2018. [DOI: 10.1002/aic.16449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jeremy F. Chignell
- Dept. of Chemical and Biological Engineering Colorado State University Fort Collins CO, 80523
| | - Christin Schlegel
- Institute of Bioprocess Engineering University of Kaiserslautern Kaiserslautern, D‐67663 Germany
| | - Roland Ulber
- Institute of Bioprocess Engineering University of Kaiserslautern Kaiserslautern, D‐67663 Germany
| | - Kenneth F. Reardon
- Dept. of Chemical and Biological Engineering Colorado State University Fort Collins CO, 80523
- Cell and Molecular Biology Graduate Program Colorado State University Fort Collins CO, 80523
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Dou J, Qin W, Ding A, Liu X, Zhu Y. iTRAQ-based proteomic profiling of a Microbacterium sp. strain during benzo(a)pyrene removal under anaerobic conditions. Appl Microbiol Biotechnol 2017; 101:8365-8377. [DOI: 10.1007/s00253-017-8536-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/16/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
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A Proteomic Signature of Dormancy in the Actinobacterium Micrococcus luteus. J Bacteriol 2017; 199:JB.00206-17. [PMID: 28484042 DOI: 10.1128/jb.00206-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
Dormancy is a protective state in which diverse bacteria, including Mycobacterium tuberculosis, Staphylococcus aureus, Treponema pallidum (syphilis), and Borrelia burgdorferi (Lyme disease), curtail metabolic activity to survive external stresses, including antibiotics. Evidence suggests dormancy consists of a continuum of interrelated states, including viable but nonculturable (VBNC) and persistence states. VBNC and persistence contribute to antibiotic tolerance, reemergence from latent infections, and even quorum sensing and biofilm formation. Previous studies indicate that the protein mechanisms regulating persistence and VBNC states are not well understood. We have queried the VBNC state of Micrococcus luteus NCTC 2665 (MI-2665) by quantitative proteomics combining gel electrophoresis, high-performance liquid chromatography, and tandem mass spectrometry to elucidate some of these mechanisms. MI-2665 is a nonpathogenic actinobacterium containing a small (2.5-Mb), high-GC-content genome which exhibits a well-defined VBNC state induced by nutrient deprivation. The MI-2665 VBNC state demonstrated a loss of protein diversity accompanied by increased levels of 18 proteins that are conserved across actinobacteria, 14 of which have not been previously identified in VNBC. These proteins implicate an anaplerotic strategy in the transition to VBNC, including changes in the glyoxylate shunt, redox and amino acid metabolism, and ribosomal regulatory processes. Our data suggest that MI-2665 is a viable model for dissecting the protein mechanisms underlying the VBNC stress response and provide the first protein-level signature of this state. We expect that this protein signature will enable future studies deciphering the protein mechanisms of dormancy and identify novel therapeutic strategies effective against antibiotic-tolerant bacterial infections.IMPORTANCE Dormancy is a protective state enabling bacteria to survive antibiotics, starvation, and the immune system. Dormancy is comprised of different states, including persistent and viable but nonculturable (VBNC) states that contribute to the spread of bacterial infections. Therefore, it is imperative to identify how bacteria utilize these different dormancy states to survive antibiotic treatment. The objective of our research is to eliminate dormancy as a route to antibiotic tolerance by understanding the proteins that control dormancy in Micrococcus luteus NCTC 2665. This bacterium has unique advantages for studying dormancy, including a small genome and a well-defined and reproducible VBNC state. Our experiments implicate four previously identified and 14 novel proteins upregulated in VBNC that may regulate this critical survival mechanism.
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11
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Nogueira-Ferreira R, Ferreira-Pinto MJ, Silva AF, Vitorino R, Justino J, Costa R, Moreira-Gonçalves D, Quignard JF, Ducret T, Savineau JP, Leite-Moreira AF, Ferreira R, Henriques-Coelho T. HMGB1 down-regulation mediates terameprocol vascular anti-proliferative effect in experimental pulmonary hypertension. J Cell Physiol 2017; 232:3128-3138. [PMID: 28036116 DOI: 10.1002/jcp.25763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 11/07/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a progressive disease with a poor prognosis. Pulmonary artery smooth muscle cells (PASMCs) play a crucial role in PAH pathophysiology, displaying a hyperproliferative, and apoptotic-resistant phenotype. In the present study, we evaluated the potential therapeutic role of terameprocol (TMP), an inhibitor of cellular proliferation and promoter of apoptosis, in a well-established pre-clinical model of PAH induced by monocrotaline (MCT) and studied the biological pathways modulated by TMP in PASMCs. Wistar rats injected with MCT or saline (SHAM group) were treated with TMP or vehicle. On day 21 after injection, we assessed bi-ventricular hemodynamics and cardiac and pulmonary morphometry. The effects of TMP on PASMCs were studied in a primary culture isolated from SHAM and MCT-treated rats, using an iTRAQ-based proteomic approach to investigate the molecular pathways modulated by this drug. In vivo, TMP significantly reduced pulmonary and cardiac remodeling and improved cardiac function in PAH. In vitro, TMP inhibited proliferation and induced apoptosis of PASMCs. A total of 65 proteins were differentially expressed in PASMCs from MCT rats treated with TMP, some of which involved in the modulation of transforming growth factor beta pathway and DNA transcription. Anti-proliferative effect of TMP seems to be explained, at least in part, by the down-regulation of the transcription factor HMGB1. Our findings support the beneficial role of TMP in PAH and suggest that it may be an effective therapeutic option to be considered in the clinical management of PAH.
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Affiliation(s)
- Rita Nogueira-Ferreira
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.,Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - Manuel J Ferreira-Pinto
- Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - Ana Filipa Silva
- Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - Rui Vitorino
- Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal.,iBiMED, Departamento de Ciências Médicas, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Joana Justino
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Raquel Costa
- Departamento de Bioquímica, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - Daniel Moreira-Gonçalves
- Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal.,CIAFEL, Faculdade de Desporto, Universidade do Porto, Porto, Portugal
| | - Jean-François Quignard
- Université Bordeaux Segalen, Bordeaux, France.,Inserm, Centre de Recherche Cardio-Thoracique, Bordeaux, France
| | - Thomas Ducret
- Université Bordeaux Segalen, Bordeaux, France.,Inserm, Centre de Recherche Cardio-Thoracique, Bordeaux, France
| | - Jean-Pierre Savineau
- Université Bordeaux Segalen, Bordeaux, France.,Inserm, Centre de Recherche Cardio-Thoracique, Bordeaux, France
| | - Adelino F Leite-Moreira
- Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - Rita Ferreira
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Tiago Henriques-Coelho
- Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
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12
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Ma C, Cao J, Li J, Zhou B, Tang J, Miao A. Phenotypic, histological and proteomic analyses reveal multiple differences associated with chloroplast development in yellow and variegated variants from Camellia sinensis. Sci Rep 2016; 6:33369. [PMID: 27633059 PMCID: PMC5025893 DOI: 10.1038/srep33369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/26/2016] [Indexed: 11/20/2022] Open
Abstract
Leaf colour variation is observed in several plants. We obtained two types of branches with yellow and variegated leaves from Camellia sinensis. To reveal the mechanisms that underlie the leaf colour variations, combined morphological, histological, ionomic and proteomic analyses were performed using leaves from abnormal branches (variants) and normal branches (CKs). The measurement of the CIE-Lab coordinates showed that the brightness and yellowness of the variants were more intense than the CKs. When chloroplast profiles were analysed, HY1 (branch with yellow leaves) and HY2 (branch with variegated leaves) displayed abnormal chloroplast structures and a reduced number and size compared with the CKs, indicating that the abnormal chloroplast development might be tightly linked to the leaf colour variations. Moreover, the concentration of elemental minerals was different between the variants and the CKs. Furthermore, DEPs (differentially expressed proteins) were identified in the variants and the CKs by a quantitative proteomics analysis using the label-free approach. The DEPs were significantly involved in photosynthesis and included PSI, PSII, cytochrome b6/f complex, photosynthetic electron transport, LHC and F-type ATPase. Our results suggested that a decrease in the abundance of photosynthetic proteins might be associated with the changes of leaf colours in tea plants.
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Affiliation(s)
- Chengying Ma
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Junxi Cao
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Jianke Li
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Bo Zhou
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Jinchi Tang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Aiqing Miao
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
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13
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Dowle AA, Wilson J, Thomas JR. Comparing the Diagnostic Classification Accuracy of iTRAQ, Peak-Area, Spectral-Counting, and emPAI Methods for Relative Quantification in Expression Proteomics. J Proteome Res 2016; 15:3550-3562. [PMID: 27546623 DOI: 10.1021/acs.jproteome.6b00308] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diagnostic classification accuracy is critical in expression proteomics to ensure that as many true differences as possible are identified with acceptable false-positive rates. We present a comparison of the diagnostic accuracy of iTRAQ with three label-free methods, peak area, spectral counting, and emPAI, for relative quantification using a spiked proteome standard. We provide the first validation of emPAI for intersample relative quantification and find clear differences among the four quantification approaches that could be considered when designing an experiment. Spectral counting was observed to perform surprisingly well in all regards. Peak area performed best for smaller fold differences and was shown to be capable of discerning a 1.1-fold difference with acceptable specificity and sensitivity. The performance of iTRAQ was dramatically worse than the label-free methods with low abundance proteins. Using the iTRAQ data set for validation, we also demonstrate a novel iTRAQ analysis regime that avoids the use of ratios in significance testing and outperforms a common commercial alternative.
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Affiliation(s)
- Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Julie Wilson
- Departments of Mathematics and Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Jerry R Thomas
- Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom
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14
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Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities. Appl Microbiol Biotechnol 2016; 100:7263-79. [PMID: 27102130 DOI: 10.1007/s00253-016-7532-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/28/2016] [Accepted: 04/05/2016] [Indexed: 02/06/2023]
Abstract
We collected several biofilm samples from Japanese rivers and established a reproducible multi-species biofilm model that can be analyzed in laboratories. Bacterial abundance at the generic level was highly similar between the planktonic and biofilm communities, whereas comparative metatranscriptomic analysis revealed many upregulated and downregulated genes in the biofilm. Many genes involved in iron-sulfur metabolism, stress response, and cell envelope function were upregulated; biofilm formation is mediated by an iron-dependent signaling mechanism and the signal is relayed to stress-responsive and cell envelope function genes. Flagella-related gene expression was regulated depending upon the growth phase, indicating different roles of flagella during the adherence, maturation, and dispersal steps of biofilm formation. Downregulation of DNA repair genes was observed, indicating that spontaneous mutation frequency would be elevated within the biofilm and that the biofilm is a cradle for generating novel genetic traits. Although the significance remains unclear, genes for rRNA methyltransferase, chromosome partitioning, aminoacyl-tRNA synthase, and cysteine, methionine, leucine, thiamine, nucleotide, and fatty acid metabolism were found to be differentially regulated. These results indicate that planktonic and biofilm communities are in different dynamic states. Studies on biofilm and sessile cells, which have received less attention, are important for understanding microbial ecology and for designing tailor-made anti-biofilm drugs.
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15
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Semanjski M, Macek B. Shotgun proteomics of bacterial pathogens: advances, challenges and clinical implications. Expert Rev Proteomics 2016; 13:139-56. [PMID: 26653908 DOI: 10.1586/14789450.2016.1132168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry-based proteomics is increasingly used in analysis of bacterial pathogens. Simple experimental set-ups based on high accuracy mass spectrometry and powerful biochemical and bioinformatics tools are capable of reliably quantifying levels of several thousand bacterial proteins in a single experiment, reaching the analytical capacity to completely map whole proteomes. Here the authors present the state-of-the-art in bacterial pathogen proteomics and discuss challenges that the field is facing, especially in analysis of low abundant, modified proteins from organisms that are difficult to culture. Constant improvements in speed and sensitivity of mass spectrometers, as well as in bioinformatic and biochemical workflows will soon allow for comprehensive analysis of regulatory mechanisms of pathogenicity and enable routine application of proteomics in the clinical setting.
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Affiliation(s)
- Maja Semanjski
- a Quantitative Proteomics and Proteome Center Tuebingen, Interfaculty Institute for Cell Biology , University of Tuebingen , Tuebingen , Germany
| | - Boris Macek
- a Quantitative Proteomics and Proteome Center Tuebingen, Interfaculty Institute for Cell Biology , University of Tuebingen , Tuebingen , Germany
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16
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Khemiri A, Jouenne T, Cosette P. Proteomics dedicated to biofilmology: What have we learned from a decade of research? Med Microbiol Immunol 2015; 205:1-19. [PMID: 26068406 DOI: 10.1007/s00430-015-0423-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 06/03/2015] [Indexed: 12/31/2022]
Abstract
Advances in proteomics techniques over the past decade, closely integrated with genomic and physicochemical approach, have played a great role in developing knowledge of the biofilm lifestyle of bacteria. Despite bacterial proteome versatility, many studies have demonstrated the ability of proteomics approaches to elucidating the biofilm phenotype. Though these investigations have been largely used for biofilm studies in the last decades, they represent, however, a very low percentage of proteomics works performed up to now. Such approaches have offered new targets for combating microbial biofilms by providing a comprehensive quantitative and qualitative overview of their protein cell content. Herein, we summarized the state of the art in knowledge about biofilm physiology after one decade of proteomic analysis. In a second part, we highlighted missing research tracks for the next decade, emphasizing the emergence of posttranslational modifications in proteomic studies stemming from recent advances in mass spectrometry-based proteomics.
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Affiliation(s)
- Arbia Khemiri
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France.
- University of Normandy, UR, Mont-Saint-Aignan, France.
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France.
| | - Thierry Jouenne
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
| | - Pascal Cosette
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
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17
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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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18
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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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