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Quetglas-Llabrés MM, Monserrat-Mesquida M, Bouzas C, García S, Argelich E, Casares M, Ugarriza L, Llompart I, Tur JA, Sureda A. Impact of Adherence to the Mediterranean Diet on Antioxidant Status and Metabolic Parameters in NAFLD Patients: A 24-Month Lifestyle Intervention Study. Antioxidants (Basel) 2024; 13:480. [PMID: 38671927 PMCID: PMC11047536 DOI: 10.3390/antiox13040480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The Mediterranean Diet (MedDiet) is recognized as a healthy dietary pattern. Non-alcoholic fatty liver disease (NAFLD) is characterized by the excessive accumulation of fat in the liver. OBJECTIVES To assess the antioxidant status in erythrocytes, plasma, and peripheral blood mononuclear cells (PBMCs) of NAFLD patients following a 24-month lifestyle intervention based on the MedDiet. Adult patients (n = 40; aged 40-60 years) diagnosed with NAFLD by magnetic resonance imaging were divided into two groups based on their adherence to the MedDiet. Consumption was assessed using a validated 143-item semiquantitative Food Frequency Questionnaire. Anthropometrics, biochemistry parameters, intrahepatic fat contents (IFC), antioxidants, and inflammatory biomarkers were measured in plasma and erythrocytes before and after the intervention. RESULTS After the intervention, body mass index (BMI) and plasma levels of total cholesterol, low-density lipoprotein cholesterol (LDL-chol), triglycerides, malondialdehyde (MDA), and cytokeratin-18 (CK18) decreased, and high-density lipoprotein cholesterol (HDL-chol) increased. Participants with high adherence to MedDiet showed lower IFC, hepatic enzyme (AST, ALT, and GGT), glycemia, oxidase LDL (oxLDL) plasma levels, and erythrocyte MDA levels. Higher antioxidant activity (erythrocyte catalase-CAT, superoxide dismutase-SOD, glutathione peroxidase-GPx, glutathione reductase-GRd, and total glutathione-GSH as well as PBMCs-CAT gene expression) was observed in these patients, along with a reduction of PBMCs reactive oxygen species production and Toll-like receptor 4 (TLR4) expression. Inverse associations were observed between adherence to the MedDiet and BMI, glycemia, AST, IFC, and CK18 plasma levels and oxLDL, CAT, SOD, and GRd activities in erythrocytes. A significant linear regression was observed between adherence to the MedDiet and antioxidant score. CONCLUSIONS Adherence to the MedDiet is associated with improved plasma and PBMC antioxidant and inflammatory biomarker profiles and high antioxidant defences in erythrocytes.
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Affiliation(s)
- Maria Magdalena Quetglas-Llabrés
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Margalida Monserrat-Mesquida
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Cristina Bouzas
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Silvia García
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Emma Argelich
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Miguel Casares
- Radiodiagnosis Service, Red Asistencial Juaneda, 07011 Palma de Mallorca, Spain
| | - Lucía Ugarriza
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- C.S. Camp Redó, IBSalut, 07010 Palma de Mallorca, Spain
| | - Isabel Llompart
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Clinical Analysis Service, University Hospital Son Espases, 07198 Palma de Mallorca, Spain
| | - Josep A. Tur
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Antoni Sureda
- Research Group on Community Nutrition & Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain (M.M.-M.); (I.L.); (A.S.)
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
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2
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Novikova PV, Bhanu Busi S, Probst AJ, May P, Wilmes P. Functional prediction of proteins from the human gut archaeome. ISME COMMUNICATIONS 2024; 4:ycad014. [PMID: 38486809 PMCID: PMC10939349 DOI: 10.1093/ismeco/ycad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 03/17/2024]
Abstract
The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.
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Affiliation(s)
- Polina V Novikova
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- UK Centre for Ecology and Hydrology, Wallingford, OX10 8 BB, United Kingdom
| | - Alexander J Probst
- Environmental Metagenomics, Department of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, for Environmental Microbiology and Biotechnology, University Duisburg-Essen, Duisburg 47057, Germany
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Paul Wilmes
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
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3
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Meerovich GA, Akhlyustina EV, Romanishkin ID, Makarova EA, Tiganova IG, Zhukhovitsky VG, Kholina EG, Kovalenko IB, Romanova YM, Loschenov VB, Strakhovskaya MG. Photodynamic inactivation of bacteria: Why it is not enough to excite a photosensitizer. Photodiagnosis Photodyn Ther 2023; 44:103853. [PMID: 37863377 DOI: 10.1016/j.pdpdt.2023.103853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
BACKGROUND The development of multidrug resistance (MDR) in infectious agents is one of the most serious global problems facing humanity. Antimicrobial photodynamic therapy (APDT) shows encouraging results in the fight against MDR pathogens, including those in biofilms. METHODS Photosensitizers (PS), monocationic methylene blue, polycationic and polyanionic derivatives of phthalocyanines, electroneutral and polycationic derivatives of bacteriochlorin were used to study photodynamic inactivation of Gram-positive and Gram-negative planktonic bacteria and biofilms under LED irradiation. Zeta potential measurements, confocal fluorescence imaging, and coarse-grained modeling were used to evaluate the interactions of PS with bacteria. PS aggregation and photobleaching were studied using absorption and fluorescence spectroscopy. RESULTS The main approaches to ensure high efficiency of bacteria photosensitization are analyzed. CONCLUSIONS PS must maintain a delicate balance between binding to exocellular and external structures of bacterial cells and penetration through the cell wall so as not to get stuck on the way to photooxidation-sensitive structures of the bacterial cell.
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Affiliation(s)
- Gennady A Meerovich
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia; National Research Nuclear University "MEPhI", Moscow 115409, Russia
| | | | - Igor D Romanishkin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia.
| | | | - Irina G Tiganova
- Gamaleya National Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia
| | - Vladimir G Zhukhovitsky
- Gamaleya National Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia; Ministry of Public Health of the Russian Federation, Russian Medical Academy of Continuing Professional Education (RMANPO), Moscow 125993, Russia
| | | | - Ilya B Kovalenko
- Lomonosov Moscow State University, Moscow 119234, Russia; Federal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies of the Federal Medical and Biological Agency of Russia, Moscow 115682, Russia
| | - Yulia M Romanova
- Gamaleya National Research Centre for Epidemiology and Microbiology, Moscow 123098, Russia
| | - Victor B Loschenov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia; National Research Nuclear University "MEPhI", Moscow 115409, Russia
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4
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Gauba A, Rahman KM. Evaluation of Antibiotic Resistance Mechanisms in Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:1590. [PMID: 37998792 PMCID: PMC10668847 DOI: 10.3390/antibiotics12111590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Multidrug-resistant Gram-negative bacterial infections are exponentially increasing, posing one of the most urgent global healthcare and economic threats. Due to the lack of new therapies, the World Health Organization classified these bacterial species as priority pathogens in 2017, known as ESKAPE pathogens. This classification emphasizes the need for urgent research and development of novel targeted therapies. The majority of these priority pathogens are Gram-negative species, which possess a structurally dynamic cell envelope enabling them to resist multiple antibiotics, thereby leading to increased mortality rates. Despite 6 years having passed since the WHO classification, the progress in generating new treatment ideas has not been sufficient, and antimicrobial resistance continues to escalate, acting as a global ticking time bomb. Numerous efforts and strategies have been employed to combat the rising levels of antibiotic resistance by targeting specific resistance mechanisms. These mechanisms include antibiotic inactivating/modifying enzymes, outer membrane porin remodelling, enhanced efflux pump action, and alteration of antibiotic target sites. Some strategies have demonstrated clinical promise, such as the utilization of beta-lactamase inhibitors as antibiotic adjuvants, as well as recent advancements in machine-based learning employing artificial intelligence to facilitate the production of novel narrow-spectrum antibiotics. However, further research into an enhanced understanding of the precise mechanisms by which antibiotic resistance occurs, specifically tailored to each bacterial species, could pave the way for exploring narrow-spectrum targeted therapies. This review aims to introduce the key features of Gram-negative bacteria and their current treatment approaches, summarizing the major antibiotic resistance mechanisms with a focus on Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Additionally, potential directions for alternative therapies will be discussed, along with their relative modes of action, providing a future perspective and insight into the discipline of antimicrobial resistance.
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Affiliation(s)
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, London SE1 9NH, UK;
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5
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Nabil-Adam A, Ashour ML, Shreadah MA. Modulation of MAPK/NF-κB Pathway and NLRP3 Inflammasome by Secondary Metabolites from Red Algae: A Mechanistic Study. ACS OMEGA 2023; 8:37971-37990. [PMID: 37867644 PMCID: PMC10586274 DOI: 10.1021/acsomega.3c03480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/21/2023] [Indexed: 10/24/2023]
Abstract
The pharmacological properties of seaweeds are diverse. No studies have been conducted on the protective effect of Galaxaura oblongata (GOE) against lippopolysaccharide (LPS)-induced inflammation in the brain. This study is divided into three phases, the first of which is the initial phase. In vitro study includes antioxidant, radical scavenging, and anti-inflammatory activities, including cyclooxygenase-1 (COX1), COX2, NO, acetylcholine inhibition, sphingosine kinase 1, tumor necrosis factor α (TNF-α), and interleukin-6, as well as antioxidant and radical-scavenging activities, including 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid. Using LPS-induced acute inflammation, the second phase was conducted in vivo. Antioxidant and anti-inflammatory assays were performed to investigate the protective role of GOE. In addition to the phytochemical analysis, the bioactive content of GOE was also investigated. In vitro results demonstrated the potential of GOE as an antioxidant, anti-inflammatory, and neuroprotective agent. A study using LPS as an induced lung injury and neuroinflammation model confirmed the in vitro results. The GOE significantly reduced inflammatory, oxidative, and neurodegenerative biomarkers based on histopathological and immuno-histochemistry results. Based on computational drug design, four target proteins were approved: nuclear factor κB, mitogen-activated protein kinases, TNF-α, and NLRP3. Using polyphenolic compounds in GOE as ligands demonstrated good alignment and affinity against the three proteins. Finally, the current study offers a new approach to developing drug leads considering GOE's protective and curative roles.
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Affiliation(s)
- Asmaa Nabil-Adam
- Marine
Biotechnology and Natural Products Laboratory, National Institute of Oceanography & Fisheries, Alexandria 21556, Egypt
| | - Mohamed L. Ashour
- Department
of Pharmacognosy, Faculty of Pharmacy, Ain-Shams
University, Abbasia, Cairo 11566, Egypt
- Department
of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P. O. Box
6231, Jeddah 21442, Saudi Arabia
| | - Mohamed Attia Shreadah
- Marine
Biotechnology and Natural Products Laboratory, National Institute of Oceanography & Fisheries, Alexandria 21556, Egypt
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6
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Kyomuhimbo HD, Feleni U, Haneklaus NH, Brink H. Recent Advances in Applications of Oxidases and Peroxidases Polymer-Based Enzyme Biocatalysts in Sensing and Wastewater Treatment: A Review. Polymers (Basel) 2023; 15:3492. [PMID: 37631549 PMCID: PMC10460086 DOI: 10.3390/polym15163492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Oxidase and peroxidase enzymes have attracted attention in various biotechnological industries due to their ease of synthesis, wide range of applications, and operation under mild conditions. Their applicability, however, is limited by their poor stability in harsher conditions and their non-reusability. As a result, several approaches such as enzyme engineering, medium engineering, and enzyme immobilization have been used to improve the enzyme properties. Several materials have been used as supports for these enzymes to increase their stability and reusability. This review focusses on the immobilization of oxidase and peroxidase enzymes on metal and metal oxide nanoparticle-polymer composite supports and the different methods used to achieve the immobilization. The application of the enzyme-metal/metal oxide-polymer biocatalysts in biosensing of hydrogen peroxide, glucose, pesticides, and herbicides as well as blood components such as cholesterol, urea, dopamine, and xanthine have been extensively reviewed. The application of the biocatalysts in wastewater treatment through degradation of dyes, pesticides, and other organic compounds has also been discussed.
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Affiliation(s)
- Hilda Dinah Kyomuhimbo
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
| | - Usisipho Feleni
- Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Florida Campus, Roodepoort, Johannesburg 1710, South Africa;
| | - Nils H. Haneklaus
- Transdisciplinarity Laboratory Sustainable Mineral Resources, University for Continuing Education Krems, 3500 Krems, Austria;
| | - Hendrik Brink
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
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7
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Quetglas-Llabrés MM, Monserrat-Mesquida M, Bouzas C, Mateos D, Ugarriza L, Gómez C, Tur JA, Sureda A. Oxidative Stress and Inflammatory Biomarkers Are Related to High Intake of Ultra-Processed Food in Old Adults with Metabolic Syndrome. Antioxidants (Basel) 2023; 12:1532. [PMID: 37627527 PMCID: PMC10451674 DOI: 10.3390/antiox12081532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
In the last few decades the consumption of ultra-processed foods (UPFs) worldwide has substantially augmented. Increasing evidence suggests that high UPF consumption is associated with an increase in non-communicable diseases, being overweight, and obesity. The aim of this study was to assess how UPF consumption affects oxidative and inflammatory status in the plasma, neutrophils, and urine of old adults with metabolic syndrome. Participants (n = 92) were classified into two groups according to UPF consumption. Dietary intakes were measured by a validated semi-quantitative 143-item food frequency questionnaire and UPF consumption was determined according to the NOVA classification system. Low UPF consumers showed higher adherence to the Mediterranean diet than high UPF consumers. A high intake of fiber and a high concentration of polyphenols in urine were also observed in subjects with low UPF consumption. Despite the absence of differences in biochemical profile, oxidative and inflammatory biomarkers showed some significant changes. Catalase and superoxide dismutase activities were lower in high UPF consumers, whereas myeloperoxidase activity was higher. ROS production in neutrophils stimulated with zymosan was higher in high UPF consumers than in low UPF consumers. Biomarkers such as xanthine oxidase, tumor necrosis factor α (TNFα), interleukin (IL)-6, IL-15, and leptin levels were higher in participants with high intake of UPF. No differences were found in malondialdehyde and other inflammatory cytokines. The current study evidenced that MetS participants with high UPF consumption have a more pro-oxidant and inflammatory profile than those with low UPF consumption, despite showing similar blood biochemical profiles.
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Affiliation(s)
- Maria Magdalena Quetglas-Llabrés
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Margalida Monserrat-Mesquida
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Bouzas
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - David Mateos
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lucía Ugarriza
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Gómez
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Clinical Analysis Service, University Hospital Son Espases, 07198 Palma de Mallorca, Spain
| | - Josep A. Tur
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Antoni Sureda
- Research Group on Community Nutrition and Oxidative Stress, University of the Balearic Islands-IUNICS, 07122 Palma de Mallorca, Spain
- Health Research Institute of Balearic Islands (IdISBa), 07120 Palma, Spain
- Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
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8
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Gaballa A, Wiedmann M, Carroll LM. More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases. Front Cell Infect Microbiol 2023; 13:1060519. [PMID: 37360531 PMCID: PMC10285318 DOI: 10.3389/fcimb.2023.1060519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Laura M. Carroll
- Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Integrated Science Lab, Umeå University, Umeå, Sweden
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Abstract
Metabolites produced by commensal gut microbes impact host health through their recognition by the immune system and their influence on numerous metabolic pathways. Notably, the gut microbiota can both transform and synthesize lipids as well as break down dietary lipids to generate secondary metabolites with host modulatory properties. Although lipids have largely been consigned to structural roles, particularly in cell membranes, recent research has led to an increased appreciation of their signaling activities, with potential impacts on host health and physiology. This review focuses on studies that highlight the functions of bioactive lipids in mammalian physiology, with a special emphasis on immunity and metabolism.
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Affiliation(s)
- Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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10
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Ge Y, Sun F, Zhao B, Kong F, Li Z, Kong X. Bacteria derived extracellular vesicles in the pathogenesis and treatment of gastrointestinal tumours. Front Oncol 2023; 12:1103446. [PMID: 36776356 PMCID: PMC9910087 DOI: 10.3389/fonc.2022.1103446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023] Open
Abstract
Extracellular vesicles are fundamentally significant in the communication between cells. Outer Membrane Vesicles(OMVs) are a special kind of EVs produced by Gram-negative bacteria, which are minute exosome-like particles budding from the outer membrane, which have been found to play essential roles in diverse bacterial life events, including regulation of microbial interactions, pathogenesis promotion, stress responses and biofilm formation. Recently, and more researches have explored the substantial potentials of EVs as natural functional nanoparticles in the bioengineering applications in infectious diseases, cardiovascular diseases, autoimmune diseases and neurological diseases, such as antibacterial therapy, cancer drugs and immunoadjuvants, with several candidates in clinical trials showing promising efficacy. However, due to the poor understanding of sources, membrane structures and biogenesis mechanisms of EVs, progress in clinical applications still remains timid. In this review, we summarize the latest findings of EVs, especially in gastrointestinal tract tumours, to provide a comprehensive introduction of EVs in tumorigenesis and therapeutics.
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Affiliation(s)
- Yang Ge
- Changhai Clinical Research Unit, Changhai Hospital, Naval Military Medical University, Shanghai, China,Department of Gastroenterology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Fengyuan Sun
- Changhai Clinical Research Unit, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Bo Zhao
- Changhai Clinical Research Unit, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Fanyang Kong
- Changhai Clinical Research Unit, Changhai Hospital, Naval Military Medical University, Shanghai, China,Department of Gastroenterology, Changhai Hospital, Naval Military Medical University, Shanghai, China,*Correspondence: Xiangyu Kong, ; Zhaoshen Li, ; Fanyang Kong,
| | - Zhaoshen Li
- Changhai Clinical Research Unit, Changhai Hospital, Naval Military Medical University, Shanghai, China,*Correspondence: Xiangyu Kong, ; Zhaoshen Li, ; Fanyang Kong,
| | - Xiangyu Kong
- Changhai Clinical Research Unit, Changhai Hospital, Naval Military Medical University, Shanghai, China,Department of Gastroenterology, Changhai Hospital, Naval Military Medical University, Shanghai, China,National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai, China,*Correspondence: Xiangyu Kong, ; Zhaoshen Li, ; Fanyang Kong,
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11
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Yang M, Su Y, Jiang Y, Huang X, Liu Q, Kong Q. Reducing the endotoxic activity or enhancing the vaccine immunogenicity by altering the length of lipid A acyl chain in Salmonella. Int Immunopharmacol 2023; 114:109575. [PMID: 36700768 DOI: 10.1016/j.intimp.2022.109575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
The balance of the attenuation and reactogenicity is an issue in the development of recombinant attenuated Salmonella vaccines (RASV). Some reactogenic strains produced side effects are partially induced by lipid A. As reported, the number of lipid A acyl chains influence the strength and outcome of immune responses. However, there is rarely any study to investigate the modifications of acyl chain length on the effect of the toxicity and immunogenicity in Salmonella. In this study, foreign acyltransferase genes lpxA and lpxD were introduced into S. Typhimurium, which produced the S006 (ΔaraBAD::PlppCtlpxAC10) or S007 (ΔproBA::PlppSslpxDC16) strains with C10 or C16 acyl chains respectively. The results showed that the increased polymyxin B susceptibility, reduced swimming and invasion capabilities were observed in the S006. In addition, it also exhibited a lower endotoxicity and colonization ability compared to the parent strain. The result indicated the introduction of C10 acyl chains could be as a candidate choice for lipid A detoxifying strategy in engineering bacteria. However, the longer acyl chain modification didn't obviously change these abilities. Parallelly, these modifications were introduced into a Salmonella vaccine strain to determine their influences on the immune responses against Pneumonia. After inoculation by the strain V003 (ΔaraBAD ΔproBA::PlppSslpxDC16 χ9241), the mice produced robust levels of anti-PspA IgG, and a balanced Th1/Th2 immunity, which resulted in a significant survival improvement of mice with challenging against Streptococcus pneumonia. Therefore, the combination of lipid A modification with C16 acyl chain may be a better strategy for the development of ideal RASVs.
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Affiliation(s)
- Ming Yang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province 130021, China
| | - Yingying Su
- Department of Anatomy, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province 130021, China
| | - Yanlong Jiang
- College of Animal Medicine, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Xin Huang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province 130021, China
| | - Qing Liu
- College of Animal Science and technology, Southwest University, Chongqing 400715, China.
| | - Qingke Kong
- College of veterinary medicine, Southwest University, Chongqing 400715, China.
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12
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Remodeling of Lipid A in Pseudomonas syringae pv. phaseolicola In Vitro. Int J Mol Sci 2022; 23:ijms23041996. [PMID: 35216122 PMCID: PMC8876380 DOI: 10.3390/ijms23041996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas species infect a variety of organisms, including mammals and plants. Mammalian pathogens of the Pseudomonas family modify their lipid A during host entry to evade immune responses and to create an effective barrier against different environments, for example by removal of primary acyl chains, addition of phosphoethanolamine (P-EtN) to primary phosphates, and hydroxylation of secondary acyl chains. For Pseudomonas syringae pv. phaseolicola (Pph) 1448A, an economically important pathogen of beans, we observed similar lipid A modifications by mass spectrometric analysis. Therefore, we investigated predicted proteomes of various plant-associated Pseudomonas spp. for putative lipid A-modifying proteins using the well-studied mammalian pathogen Pseudomonas aeruginosa as a reference. We generated isogenic mutant strains of candidate genes and analyzed their lipid A. We show that the function of PagL, LpxO, and EptA is generally conserved in Pph 1448A. PagL-mediated de-acylation occurs at the distal glucosamine, whereas LpxO hydroxylates the secondary acyl chain on the distal glucosamine. The addition of P-EtN catalyzed by EptA occurs at both phosphates of lipid A. Our study characterizes lipid A modifications in vitro and provides a useful set of mutant strains relevant for further functional studies on lipid A modifications in Pph 1448A.
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13
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Garcia-Vello P, Di Lorenzo F, Zucchetta D, Zamyatina A, De Castro C, Molinaro A. Lipopolysaccharide lipid A: A promising molecule for new immunity-based therapies and antibiotics. Pharmacol Ther 2022; 230:107970. [PMID: 34454000 DOI: 10.1016/j.pharmthera.2021.107970] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Lipopolysaccharides (LPS) are the main components of the external leaflet of the Gram-negative outer membrane and consist of three different moieties: lipid A, core oligosaccharide, and O-polysaccharide. The lipid A is a glucosamine disaccharide with different levels of acylation and phosphorylation, beside carrying, in certain cases, additional substituents on the sugar backbone. It is also the main immunostimulatory part of the LPS, as its recognition by the host immune system represents a fundamental event for detection of perilous microorganisms. Moreover, an uncontrolled immune response caused by a large amount of circulating LPS can lead to dramatic outcomes for human health, such as septic shock. The immunostimulant properties of an LPS incredibly vary depending on lipid A chemical structure, and for this reason, natural and synthetic variants of the lipid A are under study to develop new drugs that mimic or antagonise its natural effects. Here, we review past and recent findings on the lipid A as an antibiotic target and immune-therapeutic molecule, with a special attention on the crucial role of the chemical structure and its exploitation for conceiving novel strategies for treatment of several immune-related pathologies.
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Affiliation(s)
- Pilar Garcia-Vello
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Daniele Zucchetta
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.
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14
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Aissa I, Kilár A, Dörnyei Á. Study on the CID Fragmentation Pathways of Deprotonated 4'-Monophosphoryl Lipid A. Molecules 2021; 26:5961. [PMID: 34641505 PMCID: PMC8512036 DOI: 10.3390/molecules26195961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
Lipid A, the membrane-bound phosphoglycolipid component of bacteria, is held responsible for the clinical syndrome of gram-negative sepsis. In this study, the fragmentation behavior of a set of synthetic lipid A derivatives was studied by electrospray ionization multistage mass spectrometry (ESI-MSn), in conjunction with tandem mass spectrometry (MS/MS), using low-energy collision-induced dissociation (CID). Genealogical insight about the fragmentation pathways of the deprotonated 4'-monophosphoryl lipid A structural analogs led to proposals of a number of alternative dissociation routes that have not been reported previously. Each of the fragment ions was interpreted using various possible mechanisms, consistent with the principles of reactions described in organic chemistry. Specifically, the hypothesized mechanisms are: (i) cleavage of the C-3 primary fatty acid leaves behind an epoxide group attached to the reducing sugar; (ii) cleavage of the C-3' primary fatty acid (as an acid) generates a cyclic phosphate connected to the nonreducing sugar; (iii) cleavage of the C-2' secondary fatty acid occurs both in acid and ketene forms; iv) the C-2 and C-2' primary fatty acids are eliminated as an amide and ketene, respectively; (v) the 0,2A2 cross-ring fragment contains a four-membered ring (oxetanose); (vi) the 0,4A2 ion is consecutively formed from the 0,2A2 ion by retro-aldol, retro-cycloaddition, and transesterification; and (vii) formations of H2PO4- and PO3- are associated with the formation of sugar epoxide. An understanding of the relation between 0,2A2 and 0,4A2-type sugar fragments and the different cleavage mechanisms of the two ester-linked primary fatty acids is invaluable for distinguishing lipid A isomers with different locations of a single ester-linked fatty acid (i.e., at C-3 or C-3'). Thus, in addition to a better comprehension of lipid A fragmentation processes in mass spectrometers, our observations can be applied for a more precise elucidation of naturally occurring lipid A structures.
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Affiliation(s)
- Ibrahim Aissa
- Department of Analytical and Environmental Chemistry, Faculty of Sciences, University of Pécs, Ifjúság útja 6, H-7624 Pécs, Hungary;
| | - Anikó Kilár
- Institute of Bioanalysis, Medical School and Szentágothai Research Centre, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary;
| | - Ágnes Dörnyei
- Department of Analytical and Environmental Chemistry, Faculty of Sciences, University of Pécs, Ifjúság útja 6, H-7624 Pécs, Hungary;
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15
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Groisman EA, Duprey A, Choi J. How the PhoP/PhoQ System Controls Virulence and Mg 2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution. Microbiol Mol Biol Rev 2021; 85:e0017620. [PMID: 34191587 PMCID: PMC8483708 DOI: 10.1128/mmbr.00176-20] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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16
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Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
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17
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Mills JP, Rojas LJ, Marshall SH, Rudin SD, Hujer AM, Nayak L, Bachman MA, Bonomo RA, Kaye KS. Risk Factors for and Mechanisms of COlistin Resistance Among Enterobacterales: Getting at the CORE of the Issue. Open Forum Infect Dis 2021; 8:ofab145. [PMID: 34285928 PMCID: PMC8286092 DOI: 10.1093/ofid/ofab145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/31/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Despite the recent emergence of plasmid-mediated colistin resistance, the epidemiology and mechanisms of colistin-resistant Enterobacterales (CORE) infections remain poorly understood. METHODS A case-case-control study was conducted utilizing routine clinical isolates obtained at a single tertiary health system in Ann Arbor, Michigan. Patients with CORE isolates from January 1, 2016, to March 31, 2017, were matched 1:1 with patients with colistin-susceptible Enterobacterales (COSE) and uninfected controls. Multivariable logistic regression was used to compare clinical and microbiologic features of patients with CORE and COSE to controls. A subset of available CORE isolates underwent whole-genome sequencing to identify putative colistin resistance genes. RESULTS Of 16 373 tested clinical isolates, 166 (0.99%) were colistin-resistant, representing 103 unique patients. Among 103 CORE isolates, 103 COSE isolates, and 102 uninfected controls, antibiotic exposure in the antecedent 90 days and age >55 years were predictors of both CORE and COSE. Of 33 isolates that underwent whole-genome sequencing, a large variety of mutations associated with colistin resistance were identified, including 4 mcr-1/mcr-1.1 genes and 4 pmrA/B mutations among 9 Escherichia coli isolates and 5 mgrB and 3 PmrA mutations among 8 Klebsiella pneumoniae isolates. Genetic mutations found in Enterobacter species were not associated with known phenotypic colistin resistance. CONCLUSIONS Increased age and prior antibiotic receipt were associated with increased risk for patients with CORE and for patients with COSE. Mcr-1, pmrA/B, and mgrB were the predominant colistin resistance-associated mutations identified among E. coli and K. pneumoniae, respectively. Mechanisms of colistin resistance among Enterobacter species could not be determined.
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Affiliation(s)
- John P Mills
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura J Rojas
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Steve H Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Luke Nayak
- Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Bachman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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18
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Klenotic PA, Moseng MA, Morgan CE, Yu EW. Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters. Chem Rev 2021; 121:5378-5416. [PMID: 33211490 PMCID: PMC8119314 DOI: 10.1021/acs.chemrev.0c00621] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multidrug resistant (MDR) bacteria are a global threat with many common infections becoming increasingly difficult to eliminate. While significant effort has gone into the development of potent biocides, the effectiveness of many first-line antibiotics has been diminished due to adaptive resistance mechanisms. Bacterial membrane proteins belonging to the resistance-nodulation-cell division (RND) superfamily play significant roles in mediating bacterial resistance to antimicrobials. They participate in multidrug efflux and cell wall biogenesis to transform bacterial pathogens into "superbugs" that are resistant even to last resort antibiotics. In this review, we summarize the RND superfamily of efflux transporters with a primary focus on the assembly and function of the inner membrane pumps. These pumps are critical for extrusion of antibiotics from the cell as well as the transport of lipid moieties to the outer membrane to establish membrane rigidity and stability. We analyze recently solved structures of bacterial inner membrane efflux pumps as to how they bind and transport their substrates. Our cumulative data indicate that these RND membrane proteins are able to utilize different oligomerization states to achieve particular activities, including forming MDR pumps and cell wall remodeling machineries, to ensure bacterial survival. This mechanistic insight, combined with simulated docking techniques, allows for the design and optimization of new efflux pump inhibitors to more effectively treat infections that today are difficult or impossible to cure.
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Affiliation(s)
- Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
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19
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Kawahara K. Variation, Modification and Engineering of Lipid A in Endotoxin of Gram-Negative Bacteria. Int J Mol Sci 2021; 22:2281. [PMID: 33668925 PMCID: PMC7956469 DOI: 10.3390/ijms22052281] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
Lipid A of Gram-negative bacteria is known to represent a central role for the immunological activity of endotoxin. Chemical structure and biosynthetic pathways as well as specific receptors on phagocytic cells had been clarified by the beginning of the 21st century. Although the lipid A of enterobacteria including Escherichia coli share a common structure, other Gram-negative bacteria belonging to various classes of the phylum Proteobacteria and other taxonomical groups show wide variety of lipid A structure with relatively decreased endotoxic activity compared to that of E. coli. The structural diversity is produced from the difference of chain length of 3-hydroxy fatty acids and non-hydroxy fatty acids linked to their hydroxyl groups. In some bacteria, glucosamine in the backbone is substituted by another amino sugar, or phosphate groups bound to the backbone are modified. The variation of structure is also introduced by the enzymes that can modify electrostatic charges or acylation profiles of lipid A during or after its synthesis. Furthermore, lipid A structure can be artificially modified or engineered by the disruption and introduction of biosynthetic genes especially those of acyltransferases. These technologies may produce novel vaccine adjuvants or antagonistic drugs derived from endotoxin in the future.
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Affiliation(s)
- Kazuyoshi Kawahara
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University, Yokohama, Kanagawa 236-8501, Japan
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20
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Troudi A, Pagès JM, Brunel JM. Chemical Highlights Supporting the Role of Lipid A in Efficient Biological Adaptation of Gram-Negative Bacteria to External Stresses. J Med Chem 2021; 64:1816-1834. [PMID: 33538159 DOI: 10.1021/acs.jmedchem.0c02185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria provides an efficient barrier against external noxious compounds such as antimicrobial agents. Associated with drug target modification, it contributes to the overall failure of chemotherapy. In the complex OM architecture, Lipid A plays an essential role by anchoring the lipopolysaccharide in the membrane and ensuring the spatial organization between lipids, proteins, and sugars. Currently, the targets of almost all antibiotics are intracellularly located and require translocation across membranes. We report herein an integrated view of Lipid A synthesis, membrane assembly, a structure comparison at the molecular structure level of numerous Gram-negative bacterial species, as well as its recent use as a target for original antibacterial molecules. This review paves the way for a new vision of a key membrane component that acts during bacterial adaptation to environmental stresses and for the development of new weapons against microbial resistance to usual antibiotics.
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Affiliation(s)
- Azza Troudi
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France.,Laboratory of Microorganisms and Active Biomolecules, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1008, Tunisia
| | - Jean Marie Pagès
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| | - Jean Michel Brunel
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
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21
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Ngo G, Centola M, Krasnoselska G, Pogoryelov D, Yildiz Ö, Schleiff E. LptC from Anabaena sp. PCC 7120: Expression, purification and crystallization. Protein Expr Purif 2020; 175:105689. [PMID: 32698044 DOI: 10.1016/j.pep.2020.105689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
Lipopolysaccharides are central elements of the outer leaflet of the outer membrane of Gram-negative bacteria and as such, of cyanobacteria. In the past, the structural analysis of the system in proteobacteria like Escherichia coli has contributed to a deep understanding of the transport of lipopolysaccharides from plasma membrane to the outer membrane. While many components of the transport system are conserved between proteobacteria and cyanobacteria, the periplasmic LptC appears to be distinct. The cyanobacterial proteins are twice as long as the proteobacterial proteins or proteins from firmicutes. This prompted the question whether the structure of the cyanobacterial proteins is comparable the one of the proteobacterial proteins. To address this question, we expressed LptC from Anabaena sp. PCC 7120 in E. coli as truncated protein without the transmembrane segment. We purified the protein utilizing HIS-tag based affinity chromatography and polished the protein after removal of the tag by size exclusion chromatography. The purified recombinant protein was crystallized by the sitting-drop vapor diffusion technique and best crystals, despite being twinned, diffracted to a resolution of 2.6 Å.
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Affiliation(s)
- Giang Ngo
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Martin Centola
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt, Germany
| | - Ganna Krasnoselska
- Institute for Biochemsitry, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Denys Pogoryelov
- Institute for Biochemsitry, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Özkan Yildiz
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany; Cluster of Excellence Macromolecular Complexes, Max von Laue Str. 9, 60438, Frankfurt, Germany; Frankfurt Institute for Advanced Studies, D-60438, Frankfurt, Germany.
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22
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OMV Vaccines and the Role of TLR Agonists in Immune Response. Int J Mol Sci 2020; 21:ijms21124416. [PMID: 32575921 PMCID: PMC7352230 DOI: 10.3390/ijms21124416] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/26/2022] Open
Abstract
Outer Membrane Vesicles (OMVs) are bacterial nanoparticles that are spontaneously released during growth both in vitro and in vivo by Gram-negative bacteria. They are spherical, bilayered membrane nanostructures that contain many components found within the external surface of the parent bacterium. Naturally, OMVs serve the bacteria as a mechanism to deliver DNA, RNA, proteins, and toxins, as well as to promote biofilm formation and remodel the outer membrane during growth. On the other hand, as OMVs possess the optimal size to be uptaken by immune cells, and present a range of surface-exposed antigens in native conformation and Toll-like receptor (TLR) activating components, they represent an attractive and powerful vaccine platform able to induce both humoral and cell-mediated immune responses. This work reviews the TLR-agonists expressed on OMVs and their capability to trigger individual TLRs expressed on different cell types of the immune system, and then focuses on their impact on the immune responses elicited by OMVs compared to traditional vaccines.
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Ferrand A, Vergalli J, Pagès JM, Davin-Regli A. An Intertwined Network of Regulation Controls Membrane Permeability Including Drug Influx and Efflux in Enterobacteriaceae. Microorganisms 2020; 8:E833. [PMID: 32492979 PMCID: PMC7355843 DOI: 10.3390/microorganisms8060833] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/19/2022] Open
Abstract
The transport of small molecules across membranes is a pivotal step for controlling the drug concentration into the bacterial cell and it efficiently contributes to the antibiotic susceptibility in Enterobacteriaceae. Two types of membrane transports, passive and active, usually represented by porins and efflux pumps, are involved in this process. Importantly, the expression of these transporters and channels are modulated by an armamentarium of tangled regulatory systems. Among them, Helix-turn-Helix (HTH) family regulators (including the AraC/XylS family) and the two-component systems (TCS) play a key role in bacterial adaptation to environmental stresses and can manage a decrease of porin expression associated with an increase of efflux transporters expression. In the present review, we highlight some recent genetic and functional studies that have substantially contributed to our better understanding of the sophisticated mechanisms controlling the transport of small solutes (antibiotics) across the membrane of Enterobacteriaceae. This information is discussed, taking into account the worrying context of clinical antibiotic resistance and fitness of bacterial pathogens. The localization and relevance of mutations identified in the respective regulation cascades in clinical resistant strains are discussed. The possible way to bypass the membrane/transport barriers is described in the perspective of developing new therapeutic targets to combat bacterial resistance.
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Affiliation(s)
| | | | | | - Anne Davin-Regli
- UMR_MD1, U-1261, Aix-Marseille University, INSERM, SSA, IRBA, MCT, Faculté de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille CEDEX 05, France; (A.F.); (J.V.); (J.-M.P.)
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Lo Sciuto A, Cervoni M, Stefanelli R, Spinnato MC, Di Giamberardino A, Mancone C, Imperi F. Genetic Basis and Physiological Effects of Lipid A Hydroxylation in Pseudomonas aeruginosa PAO1. Pathogens 2019; 8:E291. [PMID: 31835493 PMCID: PMC6963906 DOI: 10.3390/pathogens8040291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/03/2019] [Accepted: 12/08/2019] [Indexed: 01/09/2023] Open
Abstract
Modifications of the lipid A moiety of lipopolysaccharide influence the physicochemical properties of the outer membrane of Gram-negative bacteria. Some bacteria produce lipid A with a single hydroxylated secondary acyl chain. This hydroxylation is catalyzed by the dioxygenase LpxO, and is important for resistance to cationic antimicrobial peptides (e.g., polymyxins), survival in human blood, and pathogenicity in animal models. The lipid A of the human pathogen Pseudomonas aeruginosa can be hydroxylated in both secondary acyl chains, but the genetic basis and physiological role of these hydroxylations are still unknown. Through the generation of single and double deletion mutants in the lpxO1 and lpxO2 homologs of P. aeruginosa PAO1 and lipid A analysis by mass spectrometry, we demonstrate that both LpxO1 and LpxO2 are responsible for lipid A hydroxylation, likely acting on different secondary acyl chains. Lipid A hydroxylation does not appear to affect in vitro growth, cell wall stability, and resistance to human blood or antibiotics in P. aeruginosa. In contrast, it is required for infectivity in the Galleria mellonella infection model, without relevantly affecting in vivo persistence. Overall, these findings suggest a role for lipid A hydroxylation in P. aeruginosa virulence that could not be directly related to outer membrane integrity.
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Affiliation(s)
| | - Matteo Cervoni
- Department of Science, Roma Tre University, 00146 Roma, Italy (M.C.S.)
| | - Roberta Stefanelli
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, 00185 Roma, Italy;
| | | | | | - Carmine Mancone
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Roma, Italy; (A.D.G.); (C.M.)
| | - Francesco Imperi
- Department of Science, Roma Tre University, 00146 Roma, Italy (M.C.S.)
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