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Raslan MA, Raslan SA, Shehata EM, Mahmoud AS, Viana MVC, Barh D, Sabri NA, Azevedo V. Applications of Proteomics in Probiotics Having Anticancer and Chemopreventive Properties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:243-256. [PMID: 38409425 DOI: 10.1007/978-3-031-50624-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Proteomics has grown in importance in molecular sciences because it gives vital information on protein identification, expression levels, and alteration. Cancer is one of the world's major causes of death and is the major focus of much research. Cancer risk is determined by hereditary variables as well as the body's immunological condition. Probiotics have increasing medical importance due to their therapeutic influence on the human body in the prevention and treatment of numerous chronic illnesses, including cancer, with no adverse effects. Several anticancer, anti-inflammatory, and chemopreventive probiotics are studied using different proteomic approaches like two-dimensional gel electrophoresis, liquid chromatography-mass spectrometry, and matrix-assisted laser desorption/ionization mass spectrometry. To gain relevant information about probiotic characteristics, data from the proteomic analysis are evaluated and processed using bioinformatics pipelines. Proteomic studies showed the significance of different proteomic approaches in characterization, comparing strains, and determination of oxidative stress of different probiotics. Moreover, proteomic approaches identified different proteins that are involved in glucose metabolism and the formation of cell walls or cell membranes, and the differences in the expression of critical enzymes in the HIF-1 signaling pathway, starch, and sucrose metabolism, and other critical metabolic pathways.
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Affiliation(s)
| | | | | | - Amr S Mahmoud
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marcus Vinicius Canário Viana
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Nagwa A Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Novel Insights into the Molecular Mechanisms Underlying Robustness and Stability in Probiotic Bifidobacteria. Appl Environ Microbiol 2023; 89:e0008223. [PMID: 36802222 PMCID: PMC10057886 DOI: 10.1128/aem.00082-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Some probiotic bifidobacteria are highly robust and shelf-stable, whereas others are difficult to produce, due to their sensitivity to stressors. This limits their potential use as probiotics. Here, we investigate the molecular mechanisms underlying the variability in stress physiologies of Bifidobacterium animalis subsp. lactis BB-12 and Bifidobacterium longum subsp. longum BB-46, by applying a combination of classical physiological characterization and transcriptome profiling. The growth behavior, metabolite production, and global gene expression profiles differed considerably between the strains. BB-12 consistently showed higher expression levels of multiple stress-associated genes, compared to BB-46. This difference, besides higher cell surface hydrophobicity and a lower ratio of unsaturated to saturated fatty acids in the cell membrane of BB-12, should contribute to its higher robustness and stability. In BB-46, the expression of genes related to DNA repair and fatty acid biosynthesis was higher in the stationary than in the exponential phase, which was associated with enhanced stability of BB-46 cells harvested in the stationary phase. The results presented herein highlight important genomic and physiological features contributing to the stability and robustness of the studied Bifidobacterium strains. IMPORTANCE Probiotics are industrially and clinically important microorganisms. To exert their health-promoting effects, probiotic microorganisms must be administered at high counts, while maintaining their viability at the time of consumption. In addition, intestinal survival and bioactivity are important criteria for probiotics. Although bifidobacteria are among the most well-documented probiotics, the industrial-scale production and commercialization of some Bifidobacterium strains is challenged by their high sensitivity to environmental stressors encountered during manufacturing and storage. Through a comprehensive comparison of the metabolic and physiological characteristics of 2 Bifidobacterium strains, we identify key biological markers that can serve as indicators for robustness and stability in bifidobacteria.
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Abstract
Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies.
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Affiliation(s)
- Marie Schöpping
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ahmad A. Zeidan
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
| | - Carl Johan Franzén
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Yang SP, Xie J, Cheng Y, Zhang Z, Zhao Y, Qian YF. Response of Shewanella putrefaciens to low temperature regulated by membrane fluidity and fatty acid metabolism. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108638] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Ahmed F, Kumar G, Soliman FM, Adly MA, Soliman HAM, El-Matbouli M, Saleh M. Proteomics for understanding pathogenesis, immune modulation and host pathogen interactions in aquaculture. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100625. [PMID: 31639560 DOI: 10.1016/j.cbd.2019.100625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
Abstract
Proteomic analyses techniques are considered strong tools for identifying and quantifying the protein contents in different organisms, organs and secretions. In fish biotechnology, the proteomic analyses have been used for wide range of applications such as identification of immune related proteins during infections and stresses. The proteomic approach has a significant role in understanding pathogen surviving strategies, host defence responses and subsequently, the fish pathogen interactions. Proteomic analyses were employed to highlight the virulence related proteins secreted by the pathogens to invade the fish host's defence barriers and to monitor the kinetics of protein contents of different fish organs in response to infections. The immune related proteins of fish and the virulence related proteins of pathogens are up or down regulated according to their functions in defence or pathogenesis. Therefore, the proteomic analyses are useful in understanding the virulence mechanisms of microorganisms and the fish pathogen interactions thereby supporting the development of new effective therapies. In this review, we focus and summarise the recent proteomic profiling studies exploring pathogen virulence activities and fish immune responses to stressors and infections.
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Affiliation(s)
- Fatma Ahmed
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria; Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Faiza M Soliman
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mohamed A Adly
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Hamdy A M Soliman
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Mona Saleh
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria.
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6
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Imrie L, Le Bihan T, O'Toole Á, Hickner PV, Dunn WA, Weise B, Rund SSC. Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics. PLoS One 2019; 14:e0220225. [PMID: 31356616 PMCID: PMC6663012 DOI: 10.1371/journal.pone.0220225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
The malaria mosquito, Anopheles stephensi, and other mosquitoes modulate their biology to match the time-of-day. In the present work, we used a non-hypothesis driven approach (untargeted proteomics) to identify proteins in mosquito tissue, and then quantified the relative abundance of the identified proteins from An. stephensi bodies. Using these quantified protein levels, we then analyzed the data for proteins that were only detectable at certain times-of-the day, highlighting the need to consider time-of-day in experimental design. Further, we extended our time-of-day analysis to look for proteins which cycle in a rhythmic 24-hour ("circadian") manner, identifying 31 rhythmic proteins. Finally, to maximize the utility of our data, we performed a proteogenomic analysis to improve the genome annotation of An. stephensi. We compare peptides that were detected using mass spectrometry but are 'missing' from the An. stephensi predicted proteome, to reference proteomes from 38 other primarily human disease vector species. We found 239 such peptide matches and reveal that genome annotation can be improved using proteogenomic analysis from taxonomically diverse reference proteomes. Examination of 'missing' peptides revealed reading frame errors, errors in gene-calling, overlapping gene models, and suspected gaps in the genome assembly.
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Affiliation(s)
- Lisa Imrie
- SynthSys–Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thierry Le Bihan
- SynthSys–Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Rapid Novor, Kitchener, Ontario, Canada
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul V. Hickner
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - W. Augustine Dunn
- Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Benjamin Weise
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel S. C. Rund
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
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Vinusha KS, Deepika K, Johnson TS, Agrawal GK, Rakwal R. Proteomic studies on lactic acid bacteria: A review. Biochem Biophys Rep 2018; 14:140-148. [PMID: 29872746 PMCID: PMC5986552 DOI: 10.1016/j.bbrep.2018.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/02/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023] Open
Abstract
Probiotics are amongst the most common microbes in the gastro-intestinal tract of humans and other animals. Prominent among probiotics are Lactobacillus and Bifidobacterium. They offer wide-ranging health promoting benefits to the host which include reduction in pathological alterations, stimulation of mucosal immunity and interaction with mediators of inflammation among others. Proteomics plays a vital role in understanding biological functions of a cell. Proteomics is also slowly and steadily adding to the existing knowledge on role of probiotics. In this paper, the proteomics of probiotics, with special reference to lactic acid bacteria is reviewed with a view to understand i) proteome map, ii) mechanism of adaptation to harsh gut environment such as low pH and bile acid, iii) role of cell surface proteins in adhering to intestinal epithelial cells, and iv) as a tool to answer basic cell functions. We have also reviewed various analytical methods used to carry out proteome analysis, in which 2D-MS and LC-MS/MS approaches were found to be versatile methods to perform high-throughput sample analyses even for a complex gut samples. Further, we present future road map of understanding gut microbes combining meta-proteomics, meta-genomics, meta-transcriptomics and -metabolomics.
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Affiliation(s)
- K Sri Vinusha
- Department of Biotechnology, K. L. E. F. deemed University, Guntur District, Vaddeswaram, Andhra Pradesh 522502, India
| | - K Deepika
- Department of Biotechnology, K. L. E. F. deemed University, Guntur District, Vaddeswaram, Andhra Pradesh 522502, India
| | - T Sudhakar Johnson
- Department of Biotechnology, K. L. E. F. deemed University, Guntur District, Vaddeswaram, Andhra Pradesh 522502, India
| | - Ganesh K Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal.,GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal.,GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal.,Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8574, Japan.,Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics 2016; 147:28-39. [DOI: 10.1016/j.jprot.2016.03.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/19/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
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Nguyen HT, Truong DH, Kouhoundé S, Ly S, Razafindralambo H, Delvigne F. Biochemical Engineering Approaches for Increasing Viability and Functionality of Probiotic Bacteria. Int J Mol Sci 2016; 17:E867. [PMID: 27271598 PMCID: PMC4926401 DOI: 10.3390/ijms17060867] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 01/02/2023] Open
Abstract
The literature presents a growing body of evidence demonstrating the positive effect of probiotics on health. Probiotic consumption levels are rising quickly in the world despite the fluctuation of their viability and functionality. Technological methods aiming at improving probiotic characteristics are thus highly wanted. However, microbial metabolic engineering toolbox is not available for this kind of application. On the other hand, basic microbiology teaches us that bacteria are able to exhibit adaptation to external stresses. It is known that adequately applied sub-lethal stress, i.e., controlled in amplitude and frequency at a given stage of the culture, is able to enhance microbial robustness. This property could be potentially used to improve the viability of probiotic bacteria, but some technical challenges still need to be overcome before any industrial implementation. This review paper investigates the different technical tools that can be used in order to define the proper condition for improving viability of probiotic bacteria and their implementation at the industrial scale. Based on the example of Bifidobacterium bifidum, potentialities for simultaneously improving viability, but also functionality of probiotics will be described.
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Affiliation(s)
- Huu-Thanh Nguyen
- Natural Products and Industrial Biochemistry Research Group (NPIB), Faculty of Applied Sciences, Ton Duc Thang University, 19 Nguyen Huu Tho, Tan Phong Ward, District 7, 700000 Ho Chi Minh City, Vietnam.
- Microbial Processes and Interactions (MiPI), Agro-biochem Department, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium.
| | - Dieu-Hien Truong
- Faculty of Applied Sciences, Ton Duc Thang University, 19 Nguyen Huu Tho, Tan Phong Ward, District 7, 700000 Ho Chi Minh City, Vietnam.
| | - Sonagnon Kouhoundé
- Microbial Processes and Interactions (MiPI), Agro-biochem Department, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium.
| | - Sokny Ly
- Microbial Processes and Interactions (MiPI), Agro-biochem Department, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium.
| | - Hary Razafindralambo
- Food technology and Formulation, Agro-Biochem Department, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium.
| | - Frank Delvigne
- Microbial Processes and Interactions (MiPI), Agro-biochem Department, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium.
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Wei X, Wang S, Zhao X, Wang X, Li H, Lin W, Lu J, Zhurina D, Li B, Riedel CU, Sun Y, Yuan J. Proteomic Profiling of Bifidobacterium bifidum S17 Cultivated Under In Vitro Conditions. Front Microbiol 2016; 7:97. [PMID: 26903976 PMCID: PMC4751264 DOI: 10.3389/fmicb.2016.00097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/18/2016] [Indexed: 01/04/2023] Open
Abstract
Bifidobacteria are frequently used in probiotic food and dairy products. Bifidobacterium bifidum S17 is a promising probiotic candidate strain that displays strong adhesion to intestinal epithelial cells and elicits potent anti-inflammatory capacity both in vitro and in murine models of colitis. The recently sequenced genome of B. bifidum S17 has a size of about 2.2 Mb and encodes 1,782 predicted protein-coding genes. In the present study, a comprehensive proteomic profiling was carried out to identify and characterize proteins expressed by B. bifidum S17. A total of 1148 proteins entries were identified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), representing 64.4% of the predicted proteome. 719 proteins could be assigned to functional categories according to cluster of orthologous groups of proteins (COGs). The COG distribution of the detected proteins highly correlates with that of the complete predicted proteome suggesting a good coverage and representation of the genomic content of B. bifidum S17 by the proteome. COGs that were highly present in the proteome of B. bifidum S17 were Translation, Amino Acid Transport and Metabolism, and Carbohydrate Transport and Metabolism. Complete sets of enzymes for both the bifidus shunt and the Embden-Meyerh of pathway were identified. Further bioinformatic analysis yielded 28 proteins with a predicted extracellular localization including 14 proteins with an LPxTG-motif for cell wall anchoring and two proteins (elongation factor Tu and enolase) with a potential moonlighting function in adhesion. Amongst the predicted extracellular proteins were five of six pilin proteins encoded in the B. bifidum S17 genome as well as several other proteins with a potential role in interaction with host structures. The presented results are the first compilation of a proteomic reference profile for a B. bifidum strain and will facilitate analysis of the molecular mechanisms of physiology, host-interactions and beneficial effects of a potential probiotic strain.
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Affiliation(s)
- Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Simiao Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Weishi Lin
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jing Lu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Daria Zhurina
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
| | - Boxing Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
| | - Yansong Sun
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
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Cholewa B, Pellitteri-Hahn MC, Scarlett CO, Ahmad N. Large-scale label-free comparative proteomics analysis of polo-like kinase 1 inhibition via the small-molecule inhibitor BI 6727 (Volasertib) in BRAF(V600E) mutant melanoma cells. J Proteome Res 2014; 13:5041-50. [PMID: 24884503 PMCID: PMC4227549 DOI: 10.1021/pr5002516] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 12/11/2022]
Abstract
Polo-like kinase 1 (Plk1) is a serine/threonine kinase that plays a key role during the cell cycle by regulating mitotic entry, progression, and exit. Plk1 is overexpressed in a variety of human cancers and is essential to sustained oncogenic proliferation, thus making Plk1 an attractive therapeutic target. However, the clinical efficacy of Plk1 inhibition has not emulated the preclinical success, stressing an urgent need for a better understanding of Plk1 signaling. This study addresses that need by utilizing a quantitative proteomics strategy to compare the proteome of BRAF(V600E) mutant melanoma cells following treatment with the Plk1-specific inhibitor BI 6727. Employing label-free nano-LC-MS/MS technology on a Q-exactive followed by SIEVE processing, we identified more than 20 proteins of interest, many of which have not been previously associated with Plk1 signaling. Here we report the down-regulation of multiple metabolic proteins with an associated decrease in cellular metabolism, as assessed by lactate and NAD levels. Furthermore, we have also identified the down-regulation of multiple proteasomal subunits, resulting in a significant decrease in 20S proteasome activity. Additionally, we have identified a novel association between Plk1 and p53 through heterogeneous ribonucleoprotein C1/C2 (hnRNPC), thus providing valuable insight into Plk1's role in cancer cell survival.
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Affiliation(s)
- Brian
D. Cholewa
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Molly C. Pellitteri-Hahn
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Cameron O. Scarlett
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Nihal Ahmad
- Department of Dermatology, Molecular and Environmental Toxicology
Center, and School of Pharmacy, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706, United States
- William
S. Middleton Memorial VA Hospital, 2500 Overlook Terrace, Madison, Wisconsin 53705, United States
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Growth phase-dependent proteomes of the Malaysian isolated Lactococcus lactis dairy strain M4 using label-free qualitative shotgun proteomics analysis. ScientificWorldJournal 2014; 2014:642891. [PMID: 24982972 PMCID: PMC3984853 DOI: 10.1155/2014/642891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/10/2014] [Indexed: 11/17/2022] Open
Abstract
Lactococcus lactis is the most studied mesophilic fermentative lactic acid bacterium. It is used extensively in the food industry and plays a pivotal role as a cell factory and also as vaccine delivery platforms. The proteome of the Malaysian isolated L. lactis M4 dairy strain, obtained from the milk of locally bred cows, was studied to elucidate the physiological changes occurring between the growth phases of this bacterium. In this study, ultraperformance liquid chromatography nanoflow electrospray ionization tandem mass spectrometry (UPLC- nano-ESI-MSE) approach was used for qualitative proteomic analysis. A total of 100 and 121 proteins were identified from the midexponential and early stationary growth phases, respectively, of the L. lactis strain M4. During the exponential phase, the most important reaction was the generation of sufficient energy, whereas, in the early stationary phase, the metabolic energy pathways decreased and the biosynthesis of proteins became more important. Thus, the metabolism of the cells shifted from energy production in the exponential phase to the synthesis of macromolecules in the stationary phase. The resultant proteomes are essential in providing an improved view of the cellular machinery of L. lactis during the transition of growth phases and hence provide insight into various biotechnological applications.
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Aires J, Butel MJ. Proteomics, human gut microbiota and probiotics. Expert Rev Proteomics 2014; 8:279-88. [DOI: 10.1586/epr.11.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Science and technology for the mastership of probiotic applications in food products. J Biotechnol 2012; 162:356-65. [DOI: 10.1016/j.jbiotec.2012.07.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 07/10/2012] [Accepted: 07/13/2012] [Indexed: 01/07/2023]
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15
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Ruiz L, Ruas-Madiedo P, Gueimonde M, de los Reyes-Gavilán CG, Margolles A, Sánchez B. How do bifidobacteria counteract environmental challenges? Mechanisms involved and physiological consequences. GENES & NUTRITION 2011; 6:307-18. [PMID: 21484166 PMCID: PMC3145062 DOI: 10.1007/s12263-010-0207-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 12/26/2010] [Indexed: 01/04/2023]
Abstract
An effective response to stress is of paramount importance for probiotic bifidobacteria administered in foods, since it determines their performance as beneficial microorganisms. Firstly, bifidobacteria have to be resistant to the stress sources typical in manufacturing, including heating, exposure to low water activities, osmotic shock and presence of oxygen. Secondly, and once they are orally ingested, bifidobacteria have to overcome physiological barriers in order to arrive in the large intestine biologically active. These barriers are mainly the acid pH in the stomach and the presence of high bile salt concentrations in the small intestine. In addition, the large intestine is, in terms of microbial amounts, a densely populated environment in which there is an extreme variability in carbon source availability. For this reason, bifidobacteria harbours a wide molecular machinery allowing the degradation of a wide variety of otherwise non-digestible sugars. In this review, the molecular mechanisms allowing this bacterial group to favourably react to the presence of different stress sources are presented and discussed.
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Affiliation(s)
- Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Ctra. Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Ctra. Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Ctra. Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
| | - Clara G. de los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Ctra. Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Ctra. Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Ctra. Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
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HspR mutations are naturally selected in Bifidobacterium longum when successive heat shock treatments are applied. J Bacteriol 2010; 192:256-63. [PMID: 19880603 DOI: 10.1128/jb.01147-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of molecular tools allowed light to be shed on several widespread genetic mechanisms aiming at limiting the effect of molecular damage on bacterial survival. For some bacterial taxa, there are limited tools in the genetic toolbox, which restricts the possibilities to investigate the molecular basis of their stress response. In that case, an alternative strategy is to study genetic variants of a strain under stress conditions. The comparative study of the genetic determinants responsible for their phenotypes, e.g., an improved tolerance to stress, offers precious clues on the molecular mechanisms effective in this bacterial taxon. We applied this approach and isolated two heat shock-tolerant strains derived from Bifidobacterium longum NCC2705. A global analysis of their transcriptomes revealed that the dnaK operon and the clpB gene were overexpressed in both heat shock-tolerant strains. We sequenced the hspR gene coding for the negative regulator of dnaK and clpB and found point mutations affecting protein domains likely responsible for the binding of the regulators to the promoter DNA. Complementation of the mutant strains by the wild-type regulator hspR restored its heat sensitivity and thus demonstrated that these mutations were responsible for the observed heat tolerance phenotype.
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