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Mizoguchi E, Sadanaga T, Nanni L, Wang S, Mizoguchi A. Recently Updated Role of Chitinase 3-like 1 on Various Cell Types as a Major Influencer of Chronic Inflammation. Cells 2024; 13:678. [PMID: 38667293 PMCID: PMC11049018 DOI: 10.3390/cells13080678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Chitinase 3-like 1 (also known as CHI3L1 or YKL-40) is a mammalian chitinase that has no enzymatic activity, but has the ability to bind to chitin, the polymer of N-acetylglucosamine (GlcNAc). Chitin is a component of fungi, crustaceans, arthropods including insects and mites, and parasites, but it is completely absent from mammals, including humans and mice. In general, chitin-containing organisms produce mammalian chitinases, such as CHI3L1, to protect the body from exogenous pathogens as well as hostile environments, and it was thought that it had a similar effect in mammals. However, recent studies have revealed that CHI3L1 plays a pathophysiological role by inducing anti-apoptotic activity in epithelial cells and macrophages. Under chronic inflammatory conditions such as inflammatory bowel disease and chronic obstructive pulmonary disease, many groups already confirmed that the expression of CHI3L1 is significantly induced on the apical side of epithelial cells, and activates many downstream pathways involved in inflammation and carcinogenesis. In this review article, we summarize the expression of CHI3L1 under chronic inflammatory conditions in various disorders and discuss the potential roles of CHI3L1 in those disorders on various cell types.
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Affiliation(s)
- Emiko Mizoguchi
- Department of Immunology, Kurume University School of Medicine, Kurume 830-0011, Japan; (T.S.); (S.W.); (A.M.)
- Department of Molecular Microbiology and Immunology, Brown University Alpert Medical School, Providence, RI 02912, USA
| | - Takayuki Sadanaga
- Department of Immunology, Kurume University School of Medicine, Kurume 830-0011, Japan; (T.S.); (S.W.); (A.M.)
- Department of Molecular Microbiology and Immunology, Brown University Alpert Medical School, Providence, RI 02912, USA
| | - Linda Nanni
- Catholic University of the Sacred Heart, 00168 Rome, Italy;
| | - Siyuan Wang
- Department of Immunology, Kurume University School of Medicine, Kurume 830-0011, Japan; (T.S.); (S.W.); (A.M.)
| | - Atsushi Mizoguchi
- Department of Immunology, Kurume University School of Medicine, Kurume 830-0011, Japan; (T.S.); (S.W.); (A.M.)
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Silva SG, Nabhan Homsi M, Keller-Costa T, Rocha U, Costa R. Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon. mSystems 2023; 8:e0064323. [PMID: 38018967 PMCID: PMC10734526 DOI: 10.1128/msystems.00643-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE This is the most comprehensive study performed thus far on the biosynthetic potential within the Flavobacteriaceae family. Our findings reveal intertwined taxonomic and natural product biosynthesis diversification within the family. We posit that the carbohydrate, peptide, and secondary metabolism triad synergistically shaped the evolution of this keystone bacterial taxon, acting as major forces underpinning the broad host range and opportunistic-to-pathogenic behavior encompassed by species in the family. This study further breaks new ground for future research on select Flavobacteriaceae spp. as reservoirs of novel drug leads.
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Affiliation(s)
- Sandra Godinho Silva
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Masun Nabhan Homsi
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Tina Keller-Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Ulisses Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Rodrigo Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
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3
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Abstract
It has been widely appreciated that numerous bacterial species express chitinases for the purpose of degrading environmental chitin. However, chitinases and chitin-binding proteins are also expressed by pathogenic bacterial species during infection even though mammals do not produce chitin. Alternative molecular targets are therefore likely present within the host. Here, we will describe our current understanding of chitinase/chitin-binding proteins as virulence factors that promote bacterial colonization and infection. The targets of these chitinases in the host have been shown to include immune system components, mucins, and surface glycans. Bacterial chitinases have also been shown to interact with other microorganisms, targeting the peptidoglycan or chitin in the bacterial and fungal cell wall, respectively. This review highlights that even though the name "chitinase" implies activity toward chitin, chitinases can have a wide diversity of targets, including ones relevant to host infection. Chitinases may therefore be useful as a target of future anti-infective therapeutics.
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Affiliation(s)
- Jason R. Devlin
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
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Phaengphairee P, Boontiam W, Wealleans A, Hong J, Kim YY. Dietary supplementation with full-fat Hermetia illucens larvae and multi-probiotics, as a substitute for antibiotics, improves the growth performance, gut health, and antioxidative capacity of weaned pigs. BMC Vet Res 2023; 19:7. [PMID: 36631776 PMCID: PMC9832753 DOI: 10.1186/s12917-022-03550-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/12/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Dietary supplementation of full-fat black soldier fly larvae (BSFL full-fat meal; alone or in combination with multi-probiotics) was tested as an alternative to dietary antibiotics in weaning piglets. We also tested the effects of these diets on growth performance, nutrient digestibility coefficients, immune status, oxidative stress, intestinal histomorphology, and rectal microbial modulations in weaned pigs. A total of 80 piglets [(Landrace × Large White) × Duroc] of both sexes (a ratio of gilts and barrows; 1:1), were randomly allotted to four diet groups: positive control (PC) diet supplemented with 0.02% amoxicillin; negative control (NC) diet without supplement addition; BSFL12 diet (NC + 12% BSFL full-fat meal); and BSFL + Pro diet (BSFL full-fat meal + 0.1% multi-probiotics, including Bacillus subtilis, B. licheniformis, and Saccharomyces cerevisiae). All groups had five replicates, with four piglets per replicate. RESULTS Dietary BSFL + Pro improved the overall average daily gain (P = 0.013), and gain-to-feed ratio (P = 0.032). The BSFL12 and BSFL + Pro diets improved nutrient digestibility and increased the serum levels of immunoglobulin A and glutathione peroxidase, while reducing the levels of pro-inflammatory cytokines. The spleen weight was higher and caecal pH was lower in pigs fed the BSFL + Pro diet than in those fed the NC diet (P = 0.011 and P = 0.021, respectively). Pigs fed the BSFL diets had longer duodenal villi, a higher villus height-to-crypt depth ratio (P = 0.004), and shorter crypt depth (P = 0.017) than those fed NC. The BSFL + Pro diet also increased faecal Lactobacillus spp. count (P = 0.008) and reduced Escherichia coli (P = 0.021) counts compared with that seen with PC and NC diets, respectively. CONCLUSIONS Dietary supplementation with BSFL or BSFL + multi-probiotics can improve the growth performance and intestinal health of pigs and may be an effective strategy to replace antibiotics for weaned pigs.
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Affiliation(s)
- Pheeraphong Phaengphairee
- grid.9786.00000 0004 0470 0856Division of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002 Thailand
| | - Waewaree Boontiam
- grid.9786.00000 0004 0470 0856Division of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002 Thailand
| | - Alexandra Wealleans
- Kemin Europa N.V., Animal Nutrition and Health EMENA, Toekomstlaan 42, 2200 Herentals, Belgium
| | - Jinsu Hong
- grid.263791.80000 0001 2167 853XDepartment of Animal Science, South Dakota State University, Brookings, SD 57007 USA
| | - Yoo Yong Kim
- grid.31501.360000 0004 0470 5905School of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Gangnam-ru, Seoul, 135-754 South Korea
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5
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Devlin JR, Santus W, Mendez J, Peng W, Yu A, Wang J, Alejandro-Navarreto X, Kiernan K, Singh M, Jiang P, Mechref Y, Behnsen J. Salmonella enterica serovar Typhimurium chitinases modulate the intestinal glycome and promote small intestinal invasion. PLoS Pathog 2022; 18:e1010167. [PMID: 35482787 PMCID: PMC9049507 DOI: 10.1371/journal.ppat.1010167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/23/2022] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the leading causes of food-borne illnesses worldwide. To colonize the gastrointestinal tract, S. Typhimurium produces multiple virulence factors that facilitate cellular invasion. Chitinases have been recently emerging as virulence factors for various pathogenic bacterial species, and the S. Typhimurium genome contains two annotated chitinases: STM0018 (chiA) and STM0233. However, the role of these chitinases during S. Typhimurium pathogenesis is unknown. The putative chitinase STM0233 has not been studied previously, and only limited data exists on ChiA. Chitinases typically hydrolyze chitin polymers, which are absent in vertebrates. However, chiA expression was detected in infection models and purified ChiA cleaved carbohydrate subunits present on mammalian surface glycoproteins, indicating a role during pathogenesis. Here, we demonstrate that expression of chiA and STM0233 is upregulated in the mouse gut and that both chitinases facilitate epithelial cell adhesion and invasion. S. Typhimurium lacking both chitinases showed a 70% reduction in invasion of small intestinal epithelial cells in vitro. In a gastroenteritis mouse model, chitinase-deficient S. Typhimurium strains were also significantly attenuated in the invasion of small intestinal tissue. This reduced invasion resulted in significantly delayed S. Typhimurium dissemination to the spleen and the liver, but chitinases were not required for systemic survival. The invasion defect of the chitinase-deficient strain was rescued by the presence of wild-type S. Typhimurium, suggesting that chitinases are secreted. By analyzing N-linked glycans of small intestinal cells, we identified specific N-acetylglucosamine-containing glycans as potential extracellular targets of S. Typhimurium chitinases. This analysis also revealed a differential abundance of Lewis X/A-containing glycans that is likely a result of host cell modulation due to the detection of S. Typhimurium chitinases. Similar glycomic changes elicited by chitinase deficient strains indicate functional redundancy of the chitinases. Overall, our results demonstrate that S. Typhimurium chitinases contribute to intestinal adhesion and invasion through modulation of the host glycome.
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Affiliation(s)
- Jason R. Devlin
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - William Santus
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Jorge Mendez
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Xiomarie Alejandro-Navarreto
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Kaitlyn Kiernan
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Manmeet Singh
- Department of Pathology, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, United States of America
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Neiers F, Saliou JM, Briand L, Robichon A. Adaptive Variation of Buchnera Endosymbiont Density in Aphid Host Acyrthosiphon pisum Controlled by Environmental Conditions. ACS OMEGA 2021; 6:17902-17914. [PMID: 34308025 PMCID: PMC8296009 DOI: 10.1021/acsomega.1c01465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The scarcity of transcriptional regulatory genes in Buchnera aphidicola, an obligate endosymbiont in aphids, suggests the stability of expressed gene patterns and metabolic pathways. This observation argues in favor of the hypothesis that this endosymbiont bacteria might contribute little to the host adaptation when aphid hosts are facing challenging fluctuating environment. Finding evidence for the increased expression or silenced genes involved in metabolic pathways under the pressure of stress conditions and/or a given environment has been challenging for experimenters with this bacterial symbiotic model. Transcriptomic data have shown that Buchnera gene expression changes are confined to a narrow range when the aphids face brutal environmental variations. In this report, we demonstrate that instead of manipulating individual genes, the conditions may act on the relative mass of endosymbiont corresponding to the needs of the host. The control of the fluctuating number of endosymbiont cells per individual host appears to be an unexpected regulatory modality that contributes to the adaptation of aphids to their environment. This feature may account for the success of the symbiotic advantages in overcoming the drastic changes in temperature and food supplies during evolution.
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Affiliation(s)
- Fabrice Neiers
- Centre des Sciences
du Goût et de l’Alimentation (CSGA), Université de Bourgogne-Franche Comté, CNRS, INRA, 21000 Dijon, France
| | - Jean-Michel Saliou
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, US 41—UMS 2014—PLBS, F-59000 Lille, France
| | - Loïc Briand
- Centre des Sciences
du Goût et de l’Alimentation (CSGA), Université de Bourgogne-Franche Comté, CNRS, INRA, 21000 Dijon, France
| | - Alain Robichon
- ISA, Université Côte
dʼAzur, INRA, CNRS, 06903 Sophia Antipolis, France
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Chitinases and Chitinase-Like Proteins as Therapeutic Targets in Inflammatory Diseases, with a Special Focus on Inflammatory Bowel Diseases. Int J Mol Sci 2021; 22:ijms22136966. [PMID: 34203467 PMCID: PMC8268069 DOI: 10.3390/ijms22136966] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 11/17/2022] Open
Abstract
Chitinases belong to the evolutionarily conserved glycosyl hydrolase family 18 (GH18). They catalyze degradation of chitin to N-acetylglucosamine by hydrolysis of the β-(1-4)-glycosidic bonds. Although mammals do not synthesize chitin, they possess two enzymatically active chitinases, i.e., chitotriosidase (CHIT1) and acidic mammalian chitinase (AMCase), as well as several chitinase-like proteins (YKL-40, YKL-39, oviductin, and stabilin-interacting protein). The latter lack enzymatic activity but still display oligosaccharides-binding ability. The physiologic functions of chitinases are still unclear, but they have been shown to be involved in the pathogenesis of various human fibrotic and inflammatory disorders, particularly those of the lung (idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, sarcoidosis, and asthma) and the gastrointestinal tract (inflammatory bowel diseases (IBDs) and colon cancer). In this review, we summarize the current knowledge about chitinases, particularly in IBDs, and demonstrate that chitinases can serve as prognostic biomarkers of disease progression. Moreover, we suggest that the inhibition of chitinase activity may be considered as a novel therapeutic strategy for the treatment of IBDs.
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Li QM, Zhou YL, Wei ZF, Wang Y. Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters. Microorganisms 2021; 9:757. [PMID: 33916768 PMCID: PMC8067016 DOI: 10.3390/microorganisms9040757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.
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Affiliation(s)
- Qing-Mei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan-Fei Wei
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
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Kretsch AM, Morgan GL, Acken KA, Barr SA, Li B. Pseudomonas Virulence Factor Pathway Synthesizes Autoinducers That Regulate the Secretome of a Pathogen. ACS Chem Biol 2021; 16:501-509. [PMID: 33595276 DOI: 10.1021/acschembio.0c00901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cell-to-cell communication via chemical signals is an essential mechanism that pathogenic bacteria use to coordinate group behaviors and promote virulence. The Pseudomonas virulence factor (pvf) gene cluster is distributed in more than 500 strains of proteobacteria including both plant and human pathogens. The pvf cluster has been implicated in the production of signaling molecules important for virulence; however, the regulatory impact of these signaling molecules on virulence had not been elucidated. Using the insect pathogen Pseudomonas entomophila L48 as a model, we demonstrated that pvf-encoded biosynthetic enzymes produce PVF autoinducers that regulate the expression of pvf genes and a gene encoding the toxin monalysin via quorum sensing. In addition, PVF autoinducers regulate the expression of nearly 200 secreted and membrane proteins, including toxins, motility proteins, and components of the type VI secretion system, which play key roles in bacterial virulence, colonization, and competition with other microbes. Deletion of pvf also altered the secondary metabolome. Six major compounds upregulated by PVF autoinducers were isolated and structurally characterized, including three insecticidal 3-indolyl oxazoles, the labradorins, and three antimicrobial pyrrolizidine alkaloids, the pyreudiones. The signaling properties of PVF autoinducers and their wide-ranging regulatory effects indicate multifaceted roles of PVF in controlling cell physiology and promoting virulence. The broad genome distribution of pvf suggests that PVF-mediated signaling is relevant to many bacteria of agricultural and biomedical significance.
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10
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Proteomic profiling of clinical and environmental strains of Pseudomonas aeruginosa. Mol Biol Rep 2021; 48:2325-2333. [PMID: 33728559 DOI: 10.1007/s11033-021-06262-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
Pseudomonas aeruginosa is a ubiquitous bacterium, which is able to change its physiological characteristics in response to different habitats. Environmental strains are presumably less pathogenic than clinical strains and whether or not the clinical strains originate from the environment or through inter-host transmission remains poorly understood. To minimize the risk of infection, a better understanding of proteomic profiling of P. aeruginosa is necessary for elucidating the correlation between environmental and clinical strains. Based on antimicrobial susceptibility and patterns of virulence, we selected 12 clinical and environmental strains: (i) environmental, (ii) multidrug resistant (MDR) clinical and (iii) susceptible clinical strains. Whole-cell protein was extracted from each strain and subjected to two-dimensional differential gel electrophoresis (2-D DIGE) and liquid chromatography tandem mass spectrometry quadrupole time-of-flight (LC-MS QTOF). All 12 strains were clustered into 3 distinct groups based on their variance in protein expression. A total of 526 matched spots were detected and four differentially expressed protein spots (p < 0.05) were identified and all differential spots were downregulated in MDR strain J3. Upregulation of chitin binding and BON domain proteins was present in the environmental and some MDR strains, whereas the clinical strains exhibited distinct proteomic profiles with increased expression of serine protein kinase and arginine/ornithine transport ATP-binding proteins. Significant difference in expression was observed between susceptible clinical and MDR strains, as well as susceptible clinical and environmental strains. Transition from an environmental saprophyte to a clinical strain could alter its physiological characteristics to further increase its adaptation.
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Yao L, Li X, Zhou Z, Shi D, Li Z, Li S, Yao H, Yang J, Yu H, Xiao Y. Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey ( Rhinopithecus roxellana hubeiensis). BIOMED RESEARCH INTERNATIONAL 2021; 2021:6667715. [PMID: 33778078 PMCID: PMC7979289 DOI: 10.1155/2021/6667715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/08/2021] [Accepted: 02/28/2021] [Indexed: 11/18/2022]
Abstract
The gut microbiota represents a source of genetic and metabolic diversity of a complex polymicrobial ecosystem within its host. To investigate age-based variations of the gut microbiota among Shennongjia golden snub-nosed monkeys (Rhinopithecus roxellana hubeiensis), we characterized the microbial species in fecal samples from 18 Shennongjia golden snub-nosed monkeys evenly pooled into 3 aged groups (Group 1, 1-3 years; Group 2, 5-8 years; Group 3, above 12 years) in Shennongjia, Hubei Province, China. Genomic DNA was extracted from fecal samples, and the 16S rRNA gene V4 region was sequenced using the Illumina high-throughput MiSeq platform PE250. A total of 28 microbial phyla were identified in the gut microbiome of these monkeys with the ten most abundant phyla (i.e., Firmicutes, Bacteroidetes, Verrucomicrobia, Spirochaetes, Tenericutes, Proteobacteria, Planctomycetes, Fibrobacteres, Cyanobacteria, and Euryarchaeota). A total of 1,469 (of 16 phyla and 166 genera), 1,381 (of 16 phyla and 157 genera), and 1,931 (of 19 phyla and 190 genera) operational taxonomic units (OTUs) were revealed in Groups 1, 2, and 3, respectively, with Group 3 containing the most diverse groups of OTUs as revealed by the species relative abundance clustering analysis. These results suggest that the gut microbiota in these monkeys maintain a dynamic status, starting from the early developmental stages of life with the species relative abundance increasing with age. This is the first study to comprehensively characterize the gut microbiota and provide valuable information for monitoring the health and nutritional needs of this endangered primate at different ages.
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Affiliation(s)
- Lijuan Yao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zutao Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Deshi Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Zili Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Shangfei Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Hui Yao
- Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Hubei Conservation and Research Center for the Golden Monkey, Muyu, Shennongjia, 442411 Hubei, China
| | - Jingyuan Yang
- Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Hubei Conservation and Research Center for the Golden Monkey, Muyu, Shennongjia, 442411 Hubei, China
| | - Huiliang Yu
- Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Hubei Conservation and Research Center for the Golden Monkey, Muyu, Shennongjia, 442411 Hubei, China
| | - Yuncai Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
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12
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Sanders M, Lawlor JMJ, Li X, Schuen JN, Millard SL, Zhang X, Buck L, Grysko B, Uhl KL, Hinds D, Stenger CL, Morris M, Lamb N, Levy H, Bupp C, Prokop JW. Genomic, transcriptomic, and protein landscape profile of CFTR and cystic fibrosis. Hum Genet 2021; 140:423-439. [PMID: 32734384 PMCID: PMC7855842 DOI: 10.1007/s00439-020-02211-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/25/2020] [Indexed: 01/18/2023]
Abstract
Cystic Fibrosis (CF) is caused most often by removal of amino acid 508 (Phe508del, deltaF508) within CFTR, yet dozens of additional CFTR variants are known to give rise to CF and many variants in the genome are known to contribute to CF pathology. To address CFTR coding variants, we developed a sequence-to-structure-to-dynamic matrix for all amino acids of CFTR using 233 vertebrate species, CFTR structure within a lipid membrane, and 20 ns of molecular dynamic simulation to assess known variants from the CFTR1, CFTR2, ClinVar, TOPmed, gnomAD, and COSMIC databases. Surprisingly, we identify 18 variants of uncertain significance within CFTR from diverse populations that are heritable and a likely cause of CF that have been understudied due to nonexistence in Caucasian populations. In addition, 15 sites within the genome are known to modulate CF pathology, where we have identified one genome region (chr11:34754985-34836401) that contributes to CF through modulation of expression of a noncoding RNA in epithelial cells. These 15 sites are just the beginning of understanding comodifiers of CF, where utilization of eQTLs suggests many additional genomics of CFTR expressing cells that can be influenced by genomic background of CFTR variants. This work highlights that many additional insights of CF genetics are needed, particularly as pharmaceutical interventions increase in the coming years.
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Affiliation(s)
- Morgan Sanders
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - John N Schuen
- Pediatric Pulmonology, Helen DeVos Children's Hospital, Grand Rapids, MI, 49503, USA
| | - Susan L Millard
- Pediatric Pulmonology, Helen DeVos Children's Hospital, Grand Rapids, MI, 49503, USA
| | - Xi Zhang
- Department of Pediatrics, Division of Pulmonary Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Leah Buck
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
- Department of Mathematics, University of North Alabama, Florence, AL, 35632, USA
| | - Bethany Grysko
- Spectrum Health Medical Genetics, Grand Rapids, MI, 49503, USA
| | - Katie L Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, AL, 35632, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Hara Levy
- Department of Pediatrics, Division of Pulmonary Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Caleb Bupp
- Spectrum Health Medical Genetics, Grand Rapids, MI, 49503, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA.
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA.
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13
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Transcriptomics Reveal the Survival Strategies of Enterococcus mundtii in the Gut of Spodoptera littoralis. J Chem Ecol 2021; 47:227-241. [PMID: 33459999 DOI: 10.1007/s10886-021-01246-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/22/2020] [Accepted: 01/04/2021] [Indexed: 12/25/2022]
Abstract
The complex interaction between a higher organism and its resident gut flora is a subject of immense interest in the field of symbiosis. Many insects harbor a complex community of microorganisms in their gut. Larvae of Spodoptera littoralis, a lepidopteran pest, house a bacterial community that varies both spatially (along the length of the gut) and temporally (during the insect's life cycle). To monitor the rapid adaptation of microbes to conditions in the gut, a GFP-tagged reporter strain of E. mundtii, a major player in the gut community, was constructed. After early-instar S. littoralis larvae were fed with the tagged microbes, these were recovered from the larval fore- and hindgut by flow cytometry. The fluorescent reporter confirmed the persistence of E. mundtii in the gut. RNA-sequencing of the sorted bacteria highlighted various strategies of the symbiont's survival, including upregulated pathways for tolerating alkaline stress, forming biofilms and two-component signaling systems for quorum sensing, and resisting oxidative stress. Although these symbionts depend on the host for amino acid and fatty acids, differential regulation among various metabolic pathways points to an enriched lysine synthesis pathway of E. mundtii in the hindgut of the larvae.
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14
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Barger PC, Liles MR, Beck BH, Newton JC. Differential production and secretion of potentially toxigenic extracellular proteins from hypervirulent Aeromonas hydrophila under biofilm and planktonic culture. BMC Microbiol 2021; 21:8. [PMID: 33407117 PMCID: PMC7788984 DOI: 10.1186/s12866-020-02065-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022] Open
Abstract
Background Hypervirulent Aeromonas hydrophila (vAh) is an emerging pathogen in freshwater aquaculture that results in the loss of over 3 million pounds of marketable channel catfish, Ictalurus punctatus, and channel catfish hybrids (I. punctatus, ♀ x blue catfish, I. furcatus, ♂) each year from freshwater catfish production systems in Alabama, U.S.A. vAh isolates are clonal in nature and are genetically unique from, and significantly more virulent than, traditional A. hydrophila isolates from fish. Even with the increased virulence, natural infections cannot be reproduced in aquaria challenges making it difficult to determine modes of infection and the pathophysiology behind the devastating mortalities that are commonly observed. Despite the intimate connection between environmental adaptation and plastic response, the role of environmental adaption on vAh pathogenicity and virulence has not been previously explored. In this study, secreted proteins of vAh cultured as free-living planktonic cells and within a biofilm were compared to elucidate the role of biofilm growth on virulence. Results Functional proteolytic assays found significantly increased degradative activity in biofilm secretomes; in contrast, planktonic secretomes had significantly increased hemolytic activity, suggesting higher toxigenic potential. Intramuscular injection challenges in a channel catfish model showed that in vitro degradative activity translated into in vivo tissue destruction. Identification of secreted proteins by HPLC-MS/MS revealed the presence of many putative virulence proteins under both growth conditions. Biofilm grown vAh produced higher levels of proteolytic enzymes and adhesins, whereas planktonically grown cells secreted higher levels of toxins, porins, and fimbrial proteins. Conclusions This study is the first comparison of the secreted proteomes of vAh when grown in two distinct ecological niches. These data on the adaptive physiological response of vAh based on growth condition increase our understanding of how environmental niche partitioning could affect vAh pathogenicity and virulence. Increased secretion of colonization factors and degradative enzymes during biofilm growth and residency may increase bacterial attachment and host invasiveness, while increased secretion of hemolysins, porins, and other potential toxins under planktonic growth (or after host invasion) could result in increased host mortality. The results of this research underscore the need to use culture methods that more closely mimic natural ecological habitat growth to improve our understanding of vAh pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02065-2.
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Affiliation(s)
- Priscilla C Barger
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA. .,Biological Sciences, College of Sciences and Math, Auburn University, Auburn, AL, USA.
| | - Mark R Liles
- Biological Sciences, College of Sciences and Math, Auburn University, Auburn, AL, USA
| | - Benjamin H Beck
- USDA ARS Aquatic Animal Health Research Unit, Auburn, AL, USA
| | - Joseph C Newton
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.
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15
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Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, Liu P, Narrowe AB, Rodríguez-Ramos J, Bolduc B, Gazitúa MC, Daly RA, Smith GJ, Vik DR, Pope PB, Sullivan MB, Roux S, Wrighton KC. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res 2020; 48:8883-8900. [PMID: 32766782 PMCID: PMC7498326 DOI: 10.1093/nar/gkaa621] [Citation(s) in RCA: 330] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/29/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
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Affiliation(s)
- Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Bridget B McGivern
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Lindsey M Solden
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Pengfei Liu
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Josué Rodríguez-Ramos
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - M Consuelo Gazitúa
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Garrett J Smith
- Department of Microbiology, Radboud University, Nijmegen 6525, Netherlands
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Phil B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas 1432, Norway
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Simon Roux
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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16
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Halbedel S, Prager R, Banerji S, Kleta S, Trost E, Nishanth G, Alles G, Hölzel C, Schlesiger F, Pietzka A, Schlüter D, Flieger A. A Listeria monocytogenes ST2 clone lacking chitinase ChiB from an outbreak of non-invasive gastroenteritis. Emerg Microbes Infect 2019; 8:17-28. [PMID: 30866756 PMCID: PMC6455121 DOI: 10.1080/22221751.2018.1558960] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/27/2022]
Abstract
An outbreak with a remarkable Listeria monocytogenes clone causing 163 cases of non-invasive listeriosis occurred in Germany in 2015. Core genome multi locus sequence typing grouped non-invasive outbreak isolates and isolates obtained from related food samples into a single cluster, but clearly separated genetically close isolates obtained from invasive listeriosis cases. A comparative genomic approach identified a premature stop codon in the chiB gene, encoding one of the two L. monocytogenes chitinases, which clustered with disease outcome. Correction of this premature stop codon in one representative gastroenteritis outbreak isolate restored chitinase production, but effects in infection experiments were not found. While the exact role of chitinases in virulence of L. monocytogenes is still not fully understood, our results now clearly show that ChiB-derived activity is not required to establish L. monocytogenes gastroenteritis in humans. This limits a possible role of ChiB in human listeriosis to later steps of the infection.
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Affiliation(s)
- Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Rita Prager
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Sangeeta Banerji
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Sylvia Kleta
- German Federal Institute for Risk AssessmentBerlin, Germany
| | - Eva Trost
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Gopala Nishanth
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Georg Alles
- Paderborn District, Health Office, Paderborn, Germany
| | - Christina Hölzel
- Faculty of Agricultural and Nutritional Sciences, CAU Kiel, Kiel, Germany
- Milk Hygiene, Faculty of Veterinary Medicine, LMU Munich, Oberschleißheim, Germany
| | - Friederike Schlesiger
- Chemical and Veterinary Analytical Institute Ostwestfalen-Lippe (CVUA-OWL), Detmold, Germany
| | - Ariane Pietzka
- German-Austrian Binational Consiliary Laboratory for Listeria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Dirk Schlüter
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- Organ-specific Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
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17
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Danger-Associated Molecular Patterns (DAMPs): the Derivatives and Triggers of Inflammation. Curr Allergy Asthma Rep 2018; 18:63. [PMID: 30267163 DOI: 10.1007/s11882-018-0817-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW Allergen is an umbrella term for irritants of diverse origin. Along with other offenders such as pathogens, mutagens, xenobiotics, and pollutants, allergens can be grouped as inflammatory agents. Danger-associated molecular patterns (DAMPs) are altered metabolism products of necrotic or stressed cells, which are deemed as alarm signals by the innate immune system. Like inflammation, DAMPs play a role in correcting the altered physiological state, but in excess, they can be lethal due to their signal transduction roles. In a vicious loop, inflammatory agents are DAMP generators and DAMPs create a pro-inflammatory state. Only a handful of DAMPs such as uric acid, mtDNA, extracellular ATP, HSPs, amyloid β, S100, HMGB1, and ECM proteins have been studied till now. A large number of DAMPs are still obscure, in need to be unveiled. The identification and functional characterization of those DAMPs in inflammation pathways can be insightful. RECENT FINDINGS As inflammation and immune activation have been implicated in almost all pathologies, studies on them have been intensified in recent times. Consequently, the pathologic mechanisms of various DAMPs have emerged. Following PRR ligation, the activation of inflammasome, MAPK, and NF-kB is some of the common pathways. The limited number of recognized DAMPs are only a fraction of the vast array of other DAMPs. In fact, any misplaced or abnormal level of metabolite can be a DAMP. Sophisticated analysis studies can reveal the full profile of the DAMPs. Lowering the level of DAMPs is useful therapeutic intervention but certainly not as effective as avoiding the DAMP generators, i.e., the inflammatory agents. So, rather than mitigating DAMPs, efforts should be focused on the elimination of inflammatory agents.
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18
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De Corte D, Srivastava A, Koski M, Garcia JAL, Takaki Y, Yokokawa T, Nunoura T, Elisabeth NH, Sintes E, Herndl GJ. Metagenomic insights into zooplankton-associated bacterial communities. Environ Microbiol 2018; 20:492-505. [PMID: 28967193 PMCID: PMC5836950 DOI: 10.1111/1462-2920.13944] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Abstract
Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters.
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Affiliation(s)
- Daniele De Corte
- Department of Limnology and OceanographyCenter of Functional Ecology University of Vienna, Althanstrasse 141090 ViennaAustria
- Present address:
Research and Development Center for Marine Biosciences, Japan Agency for Marine‐Earth Science and Technology (JAMSTEC), Natushima 2‐15YokosukaKanagawa 237‐0061Japan
| | - Abhishek Srivastava
- Department of Limnology and OceanographyCenter of Functional Ecology University of Vienna, Althanstrasse 141090 ViennaAustria
| | - Marja Koski
- National Institute for Aquatic Resources, Section for Oceans and ArcticTechnical University of Denmark, Kavalergaarden 62920 CharlottenlundDenmark
| | - Juan Antonio L. Garcia
- Department of Limnology and OceanographyCenter of Functional Ecology University of Vienna, Althanstrasse 141090 ViennaAustria
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and ResearchJapan Agency for Marine‐Earth Science and Technology (JAMSTEC), Natushima 2‐15YokosukaKanagawa 237‐0061Japan
| | - Taichi Yokokawa
- Department of Subsurface Geobiological Analysis and ResearchJapan Agency for Marine‐Earth Science and Technology (JAMSTEC), Natushima 2‐15YokosukaKanagawa 237‐0061Japan
| | - Takuro Nunoura
- Department of Subsurface Geobiological Analysis and ResearchJapan Agency for Marine‐Earth Science and Technology (JAMSTEC), Natushima 2‐15YokosukaKanagawa 237‐0061Japan
| | - Nathalie H. Elisabeth
- Department of Limnology and OceanographyCenter of Functional Ecology University of Vienna, Althanstrasse 141090 ViennaAustria
| | - Eva Sintes
- Department of Limnology and OceanographyCenter of Functional Ecology University of Vienna, Althanstrasse 141090 ViennaAustria
| | - Gerhard J. Herndl
- Department of Limnology and OceanographyCenter of Functional Ecology University of Vienna, Althanstrasse 141090 ViennaAustria
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research Utrecht University, PO Box 59AB Den Burg1790The Netherlands
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Honda S, Kunii T, Nohara K, Wakita S, Sugahara Y, Kawakita M, Oyama F, Sakaguchi M. Characterization of a Bacillus thuringiensis chitinase that binds to cellulose and chitin. AMB Express 2017; 7:51. [PMID: 28244030 PMCID: PMC5328894 DOI: 10.1186/s13568-017-0352-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 02/21/2017] [Indexed: 12/18/2022] Open
Abstract
Bacillus thuringiensis is a Gram-positive soil bacterium that is known to be a bacterial biopesticide that produces insecticidal proteins called crystal proteins (Cry). In the insecticidal process, chitinases are suggested to perforate the peritrophic membrane barrier to facilitate the invasion of the Cry proteins into epithelial membranes. A chitinase gene from B. thuringiensis was successfully expressed in a soluble form in Escherichia coli, and the gene product was purified and characterized. The purified recombinant enzyme, BthChi74, hydrolyzed an artificial substrate, 4-nitrophenyl N,N′-diacetyl-β-d-chitobioside [4NP-(GlcNAc)2], and the natural substrates, colloidal chitin and crystalline α-chitin, but it did not hydrolyze cellulose. BthChi74 exhibited catalytic activity under a weakly acidic to neutral pH range at 50 °C, and it was stable over a wide pH range for 24 h. Differential scanning fluorimetry (DSF) indicated a protein melting temperature (Tm) of 63.6 °C. Kinetic analysis revealed kcat and KM values of 1.5 s−1 and 159 μM, respectively, with 4NP-(GlcNAc)2 as a substrate. BthChi74 produced (GlcNAc)2 and GlcNAc from colloidal chitin and α-chitin as substrates, but the activity toward the latter was lower than that toward the former. BthChi74 could bind similarly to chitin beads, crystalline α-chitin, and cellulose through a unique family 2 carbohydrate-binding module (CBM2). The structure–function relationships of BthChi74 are discussed in relation to other chitinases, such as Listeria chitinase, which possesses a family 5 carbohydrate-binding module (CBM5).
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20
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Chen S, Blom J, Walker ED. Genomic, Physiologic, and Symbiotic Characterization of Serratia marcescens Strains Isolated from the Mosquito Anopheles stephensi. Front Microbiol 2017; 8:1483. [PMID: 28861046 PMCID: PMC5561391 DOI: 10.3389/fmicb.2017.01483] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/24/2017] [Indexed: 11/14/2022] Open
Abstract
Strains of Serratia marcescens, originally isolated from the gut lumen of adult female Anopheles stephensi mosquitoes, established persistent infection at high rates in adult A. stephensi whether fed to larvae or in the sugar meal to adults. By contrast, the congener S. fonticola originating from Aedes triseriatus had lower infection in A. stephensi, suggesting co-adaptation of Serratia strains in different species of host mosquitoes. Coinfection at high infection rate in adult A. stephensi resulted after feeding S. marcescens and Elizabethkingia anophelis in the sugar meal, but when fed together to larvae, infection rates with E. anophelis were much higher than were S. marcescens in adult A. stephensi, suggesting a suppression effect of coinfection across life stages. A primary isolate of S. marcescens was resistant to all tested antibiotics, showed high survival in the mosquito gut, and produced alpha-hemolysins which contributed to lysis of erythrocytes ingested with the blood meal. Genomes of two primary isolates from A. stephensi, designated S. marcescens ano1 and ano2, were sequenced and compared to other Serratia symbionts associated with insects, nematodes and plants. Serratia marcescens ano1 and ano2 had predicted virulence factors possibly involved in attacking parasites and/or causing opportunistic infection in mosquito hosts. S. marcescens ano1 and ano2 possessed multiple mechanisms for antagonism against other microorganisms, including production of bacteriocins and multi-antibiotic resistance determinants. These genes contributing to potential anti-malaria activity including serralysins, hemolysins and chitinases are only found in some Serratia species. It is interesting that genome sequences in S. marcescens ano1 and ano2 are distinctly different from those in Serratia sp. Ag1 and Ag2 which were isolated from Anopheles gambiae. Compared to Serratia sp. Ag1 and Ag2, S. marcescens ano1 and ano2 have more rRNAs and many important genes involved in commensal and anti-parasite traits.
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Affiliation(s)
- Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State UniversityEast Lansing, MI, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-UniversityGiessen, Germany
| | - Edward D. Walker
- Department of Microbiology and Molecular Genetics, Michigan State UniversityEast Lansing, MI, United States
- Department of Entomology, Michigan State UniversityEast Lansing, MI, United States
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Draft Genome Sequences of Salmonella enterica Serovar Typhimurium LT2 with Deleted Chitinases That Are Emerging Virulence Factors. GENOME ANNOUNCEMENTS 2017; 5:5/31/e00659-17. [PMID: 28774970 PMCID: PMC5543632 DOI: 10.1128/genomea.00659-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chitinases are glycosyl hydrolases that catalyze the hydrolysis of the β-1,4 linkages in complex carbohydrates and those that contain GlcNAc. These enzymes are considered emerging virulence factors during infection because the host glycan changes. This is the release of four single chitinase deletion mutants in Salmonella enterica serovar Typhimurium LT2.
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22
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Physiological and Molecular Understanding of Bacterial Polysaccharide Monooxygenases. Microbiol Mol Biol Rev 2017; 81:81/3/e00015-17. [PMID: 28659491 DOI: 10.1128/mmbr.00015-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria have long been known to secrete enzymes that degrade cellulose and chitin. The degradation of these two polymers predominantly involves two enzyme families that work synergistically with one another: glycoside hydrolases (GHs) and polysaccharide monooxygenases (PMOs). Although bacterial PMOs are a relatively recent addition to the known biopolymer degradation machinery, there is an extensive amount of literature implicating PMO in numerous physiological roles. This review focuses on these diverse and physiological aspects of bacterial PMOs, including facilitating endosymbiosis, conferring a nutritional advantage, and enhancing virulence in pathogenic organisms. We also discuss the correlation between the presence of PMOs and bacterial lifestyle and speculate on the advantages conferred by PMOs under these conditions. In addition, the molecular aspects of bacterial PMOs, as well as the mechanisms regulating PMO expression and the function of additional domains associated with PMOs, are described. We anticipate that increasing research efforts in this field will continue to expand our understanding of the molecular and physiological roles of bacterial PMOs.
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23
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Patel S. Pathogenicity-associated protein domains: The fiercely-conserved evolutionary signatures. GENE REPORTS 2017; 7:127-141. [PMID: 32363241 PMCID: PMC7185390 DOI: 10.1016/j.genrep.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/15/2022]
Abstract
Proteins have highly conserved domains that determine their functionality. Out of the thousands of domains discovered so far across all living forms, some of the predominant clinically-relevant domains include IENR1, HNHc, HELICc, Pro-kuma_activ, Tryp_SPc, Lactamase_B, PbH1, ChtBD3, CBM49, acidPPc, G3P_acyltransf, RPOL8c, KbaA, HAMP, HisKA, Hr1, Dak2, APC2, Citrate_ly_lig, DALR, VKc, YARHG, WR1, PWI, ZnF_BED, TUDOR, MHC_II_beta, Integrin_B_tail, Excalibur, DISIN, Cadherin, ACTIN, PROF, Robl_LC7, MIT, Kelch, GAS2, B41, Cyclin_C, Connexin_CCC, OmpH, Bac_rhodopsin, AAA, Knot1, NH, Galanin, IB, Elicitin, ACTH, Cache_2, CHASE, AgrB, PRP, IGR, and Antimicrobial21. These domains are distributed in nucleases/helicases, proteases, esterases, lipases, glycosylase, GTPases, phosphatases, methyltransferases, acyltransferase, acetyltransferase, polymerase, kinase, ligase, synthetase, oxidoreductase, protease inhibitors, nucleic acid binding proteins, adhesion and immunity-related proteins, cytoskeletal component-manipulating proteins, lipid biosynthesis and metabolism proteins, membrane-associated proteins, hormone-like and signaling proteins, etc. These domains are ubiquitous stretches or folds of the proteins in pathogens and allergens. Pathogenesis alleviation efforts can benefit enormously if the characteristics of these domains are known. Hence, this review catalogs and discusses the role of such pivotal domains, suggesting hypotheses for better understanding of pathogenesis at molecular level. Proteins have highly conserved regions or domains across pathogens and allergens. Knowledge on these critical domains can facilitate our understanding of pathogenesis mechanisms. Such immune manipulation-related domains include IENR1, HNHc, HELICc, ACTIN, PROF, Robl_LC7, OmpH etc. These domains are presnt in enzyme, transcription regulators, adhesion proteins, and hormones. This review discusses and hypothesizes on these domains.
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Key Words
- CARDs, caspase activation and recruitment domains
- CBM, carbohydrate binding module
- CTD, C-terminal domain
- ChtBD, chitin-binding domain
- Diversification
- HNHc, homing endonucleases
- HTH, helix-turn-helix
- IENR1, intron-encoded endonuclease repeat
- Immune manipulation
- PAMPs, pathogen associated molecular patterns
- Pathogenesis
- Phylogenetic conservation
- Protein domains
- SMART, Simple Modular Architecture Research Tool
- Shuffling
- UDG, uracil DNA glycosylase
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA
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24
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Calduch-Giner JA, Sitjà-Bobadilla A, Pérez-Sánchez J. Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax). Front Physiol 2016; 7:359. [PMID: 27610085 PMCID: PMC4997091 DOI: 10.3389/fphys.2016.00359] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/05/2016] [Indexed: 01/23/2023] Open
Abstract
High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts.
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Affiliation(s)
- Josep A Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Biology, Culture and Pathology of Marine Species, Institute of Aquaculture Torre de la Sal (IATS-CSIC) Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Biology, Culture and Pathology of Marine Species, Institute of Aquaculture Torre de la Sal (IATS-CSIC) Castellón, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Biology, Culture and Pathology of Marine Species, Institute of Aquaculture Torre de la Sal (IATS-CSIC) Castellón, Spain
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25
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Bohr S, Patel SJ, Vasko R, Shen K, Golberg A, Berthiaume F, Yarmush ML. The Role of CHI3L1 (Chitinase-3-Like-1) in the Pathogenesis of Infections in Burns in a Mouse Model. PLoS One 2015; 10:e0140440. [PMID: 26528713 PMCID: PMC4631332 DOI: 10.1371/journal.pone.0140440] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/25/2015] [Indexed: 01/12/2023] Open
Abstract
In severe burn injury the unique setting of a depleted, dysfunctional immune system along with a loss of barrier function commonly results in opportunistic infections that eventually proof fatal. Unfortunately, the dynamic sequence of bacterial contamination, colonization and eventually septic invasion with bacteria such as Pseudomonas species is still poorly understood although a limiting factor in clinical decision making. Increasing evidence supports the notion that inhibition of bacterial translocation into the wound site may be an effective alternative to prevent infection. In this context we investigated the role of the mammalian Chitinase-3-Like-1 (CHI3L1) non-enyzmatic protein predominately expressed on epithelial as well as innate immune cells as a potential bacterial-translocation-mediating factor. We show a strong trend that a modulation of chitinase expression is likely to be effective in reducing mortality rates in a mouse model of burn injury with superinfection with the opportunistic PA14 Pseudomonas strain, thus demonstrating possible clinical leverage.
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Affiliation(s)
- Stefan Bohr
- Center for Engineering in Medicine, Shriners Hospitals for Children and Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department Plastic and Hand Surgery—Burn Center, UKA University Clinics RWTH, Aachen, Germany
- * E-mail:
| | - Suraj J. Patel
- Center for Engineering in Medicine, Shriners Hospitals for Children and Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Radovan Vasko
- Department of Medicine, New York Medical College, Valhalla, NY, United States of America
- Department of Nephrology & Rheumatology, UMG University Clinics, Goettingen, Germany
| | - Keyue Shen
- Center for Engineering in Medicine, Shriners Hospitals for Children and Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Alexander Golberg
- Center for Engineering in Medicine, Shriners Hospitals for Children and Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Porter School of Environmental Studies, Tel Aviv University, Tel Aviv, Israel
| | - Francois Berthiaume
- Department of Biomedical Engineering, Rutgers University, New Brunswick, NJ, United States of America
| | - Martin L. Yarmush
- Center for Engineering in Medicine, Shriners Hospitals for Children and Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
- Department of Biomedical Engineering, Rutgers University, New Brunswick, NJ, United States of America
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26
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Hamilton JJ, Marlow VL, Owen RA, Costa MDAA, Guo M, Buchanan G, Chandra G, Trost M, Coulthurst SJ, Palmer T, Stanley-Wall NR, Sargent F. A holin and an endopeptidase are essential for chitinolytic protein secretion in Serratia marcescens. ACTA ACUST UNITED AC 2015; 207:615-26. [PMID: 25488919 PMCID: PMC4259817 DOI: 10.1083/jcb.201404127] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pathogenic bacteria adapt to their environment and manipulate the biochemistry of hosts by secretion of effector molecules. Serratia marcescens is an opportunistic pathogen associated with healthcare-acquired infections and is a prolific secretor of proteins, including three chitinases (ChiA, ChiB, and ChiC) and a chitin binding protein (Cbp21). In this work, genetic, biochemical, and proteomic approaches identified genes that were required for secretion of all three chitinases and Cbp21. A genetic screen identified a holin-like protein (ChiW) and a putative l-alanyl-d-glutamate endopeptidase (ChiX), and subsequent biochemical analyses established that both were required for nonlytic secretion of the entire chitinolytic machinery, with chitinase secretion being blocked at a late stage in the mutants. In addition, live-cell imaging experiments demonstrated bimodal and coordinated expression of chiX and chiA and revealed that cells expressing chiA remained viable. It is proposed that ChiW and ChiX operate in tandem as components of a protein secretion system used by gram-negative bacteria.
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Affiliation(s)
- Jaeger J Hamilton
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Victoria L Marlow
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Richard A Owen
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Marília de Assis Alcoforado Costa
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Manman Guo
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Grant Buchanan
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7TJ, England, UK
| | - Matthias Trost
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Tracy Palmer
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Frank Sargent
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Sutherland TE, Logan N, Rückerl D, Humbles AA, Allan SM, Papayannopoulos V, Stockinger B, Maizels RM, Allen JE. Chitinase-like proteins promote IL-17-mediated neutrophilia in a tradeoff between nematode killing and host damage. Nat Immunol 2014; 15:1116-25. [PMID: 25326751 PMCID: PMC4338525 DOI: 10.1038/ni.3023] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 09/26/2014] [Indexed: 12/12/2022]
Abstract
Enzymatically inactive chitinase-like proteins (CLPs) such as BRP-39, Ym1 and Ym2 are established markers of immune activation and pathology, yet their functions are essentially unknown. We found that Ym1 and Ym2 induced the accumulation of neutrophils through the expansion of γδ T cell populations that produced interleukin 17 (IL-17). While BRP-39 did not influence neutrophilia, it was required for IL-17 production in γδ T cells, which suggested that regulation of IL-17 is an inherent feature of mouse CLPs. Analysis of a nematode infection model, in which the parasite migrates through the lungs, revealed that the IL-17 and neutrophilic inflammation induced by Ym1 limited parasite survival but at the cost of enhanced lung injury. Our studies describe effector functions of CLPs consistent with innate host defense traits of the chitinase family.
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Affiliation(s)
- Tara E Sutherland
- Institute of Immunology and Infection Research, Centre for Immunity Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Logan
- Institute of Immunology and Infection Research, Centre for Immunity Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dominik Rückerl
- Institute of Immunology and Infection Research, Centre for Immunity Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison A Humbles
- Department of Respiratory, Inflammation &Autoimmunity, MedImmune, Gaithersburg, Maryland, USA
| | - Stuart M Allan
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Venizelos Papayannopoulos
- Division of Molecular Immunology, Medical Research Council National Institute for Medical Research, London, UK
| | - Brigitta Stockinger
- Division of Molecular Immunology, Medical Research Council National Institute for Medical Research, London, UK
| | - Rick M Maizels
- Institute of Immunology and Infection Research, Centre for Immunity Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Judith E Allen
- Institute of Immunology and Infection Research, Centre for Immunity Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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28
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Mondal M, Nag D, Koley H, Saha DR, Chatterjee NS. The Vibrio cholerae extracellular chitinase ChiA2 is important for survival and pathogenesis in the host intestine. PLoS One 2014; 9:e103119. [PMID: 25244128 PMCID: PMC4170974 DOI: 10.1371/journal.pone.0103119] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/27/2014] [Indexed: 01/11/2023] Open
Abstract
In aquatic environments, Vibrio cholerae colonizes mainly on the chitinous surface of copepods and utilizes chitin as the sole carbon and nitrogen source. Of the two extracellular chitinases essential for chitin utilization, the expression of chiA2 is maximally up-regulated in host intestine. Recent studies indicate that several bacterial chitinases may be involved in host pathogenesis. However, the role of V. cholerae chitinases in host infection is not yet known. In this study, we provide evidence to show that ChiA2 is important for V. cholerae survival in intestine as well as in pathogenesis. We demonstrate that ChiA2 de-glycosylates mucin and releases reducing sugars like GlcNAc and its oligomers. Deglycosylation of mucin corroborated with reduced uptake of alcian blue stain by ChiA2 treated mucin. Next, we show that V. cholerae could utilize mucin as a nutrient source. In comparison to the wild type strain, ΔchiA2 mutant was 60-fold less efficient in growth in mucin supplemented minimal media and was also ∼6-fold less competent to survive when grown in the presence of mucin-secreting human intestinal HT29 epithelial cells. Similar results were also obtained when the strains were infected in mice intestine. Infection with the ΔchiA2 mutant caused ∼50-fold less fluid accumulation in infant mice as well as in rabbit ileal loop compared to the wild type strain. To see if the difference in survival of the ΔchiA2 mutant and wild type V. cholerae was due to reduced adhesion of the mutant, we monitored binding of the strains on HT29 cells. The initial binding of the wild type and mutant strain was similar. Collectively these data suggest that ChiA2 secreted by V. cholerae in the intestine hydrolyzed intestinal mucin to release GlcNAc, and the released sugar is successfully utilized by V. cholerae for growth and survival in the host intestine.
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Affiliation(s)
- Moumita Mondal
- Division of Biochemistry, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Dhrubajyoti Nag
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Hemanta Koley
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Dhira Rani Saha
- Division of Electron Microscopy, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Nabendu Sekhar Chatterjee
- Division of Biochemistry, National Institute of Cholera and Enteric Diseases, Kolkata, India
- * E-mail:
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29
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Beckerman AP, de Roij J, Dennis SR, Little TJ. A shared mechanism of defense against predators and parasites: chitin regulation and its implications for life-history theory. Ecol Evol 2013; 3:5119-26. [PMID: 24455141 PMCID: PMC3892373 DOI: 10.1002/ece3.766] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/07/2013] [Accepted: 08/12/2013] [Indexed: 01/16/2023] Open
Abstract
Defenses against predators and parasites offer excellent illustrations of adaptive phenotypic plasticity. Despite vast knowledge about such induced defenses, they have been studied largely in isolation, which is surprising, given that predation and parasitism are ubiquitous and act simultaneously in the wild. This raises the possibility that victims must trade-off responses to predation versus parasitism. Here, we propose that arthropod responses to predators and parasites will commonly be based on the endocrine regulation of chitin synthesis and degradation. The proposal is compelling because many inducible defenses are centered on temporal or spatial modifications of chitin-rich structures. Moreover, we show how the chitin synthesis pathway ends in a split to carapace or gut chitin, and how this form of molecular regulation can be incorporated into theory on life-history trade-offs, specifically the Y-model. Our hypothesis thus spans several biological scales to address advice from Stearns that “Endocrine mechanisms may prove to be only the tip of an iceberg of physiological mechanisms that modulate the expression of genetic covariance”.
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Affiliation(s)
- Andrew P Beckerman
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank Sheffield, S10 2TN, U.K
| | - Job de Roij
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh Kings Buildings, Edinburgh, EH9 3JT, U.K
| | - Stuart R Dennis
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank Sheffield, S10 2TN, U.K
| | - Tom J Little
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh Kings Buildings, Edinburgh, EH9 3JT, U.K
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30
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Sehar U, Mehmood MA, Hussain K, Nawaz S, Nadeem S, Siddique MH, Nadeem H, Gull M, Ahmad N, Sohail I, Gill SS, Majeed S. Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4. Bioinformation 2013; 9:901-7. [PMID: 24307767 PMCID: PMC3842575 DOI: 10.6026/97320630009901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 10/19/2013] [Indexed: 11/23/2022] Open
Abstract
This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.
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Affiliation(s)
- Ujala Sehar
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University Faisalabad, Faisalabad, Pakistan
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31
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Sehar U, Mehmood MA, Nawaz S, Nadeem S, Hussain K, Sohail I, Tabassum MR, Gill SS, Saqib A. Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis. Bioinformation 2013; 9:725-9. [PMID: 23976829 PMCID: PMC3746096 DOI: 10.6026/97320630009725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 07/25/2013] [Indexed: 12/03/2022] Open
Abstract
Bacillus thuringiensis is an insecticidal bacterium whose chitinolytic system has been exploited to improve insect resistance in crops. In the present study, we studied the CBP24 from B. thuringiensis using homology modeling and molecular docking. The primary and secondary structure analyses showed CBP24 is a positively charged protein and contains single domain that belongs to family CBM33. The 3D model after refinement was used to explore the chitin binding characteristics of CBP24 using AUTODOCK. The docking analyses have shown that the surface exposed hydrophilic amino acid residues Thr-103, Lys-112 and Ser-162 interact with substrate through H-bonding. While, the amino acids resides Glu-39, Tyr-46, Ser-104 and Asn-109 were shown to have polar interactions with the substrate. The binding energy values evaluation of docking depicts a stable intermolecular conformation of the docked complex. The functional characterization of the CBP24 will elucidate the substrate-interaction pathway of the protein in specific and the carbohydrate binding proteins in general leading towards the exploration and exploitation of the prokaryotic substrate utilization pathways.
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Affiliation(s)
- Ujala Sehar
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Salman Nawaz
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Shahid Nadeem
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Khadim Hussain
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Iqra Sohail
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Muhammad Rizwan Tabassum
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Saba Shahid Gill
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Anam Saqib
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
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32
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Johnson CN. Fitness factors in vibrios: a mini-review. MICROBIAL ECOLOGY 2013; 65:826-851. [PMID: 23306394 DOI: 10.1007/s00248-012-0168-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
Vibrios are Gram-negative curved bacilli that occur naturally in marine, estuarine, and freshwater systems. Some species include human and animal pathogens, and some vibrios are necessary for natural systems, including the carbon cycle and osmoregulation. Countless in vivo and in vitro studies have examined the interactions between vibrios and their environment, including molecules, cells, whole animals, and abiotic substrates. Many studies have characterized virulence factors, attachment factors, regulatory factors, and antimicrobial resistance factors, and most of these factors impact the organism's fitness regardless of its external environment. This review aims to identify common attributes among factors that increase fitness in various environments, regardless of whether the environment is an oyster, a rabbit, a flask of immortalized mammalian cells, or a planktonic chitin particle. This review aims to summarize findings published thus far to encapsulate some of the basic similarities among the many vibrio fitness factors and how they frame our understanding of vibrio ecology. Factors representing these similarities include hemolysins, capsular polysaccharides, flagella, proteases, attachment factors, type III secretion systems, chitin binding proteins, iron acquisition systems, and colonization factors.
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Affiliation(s)
- Crystal N Johnson
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, LA, USA.
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33
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Pathogen recognition and activation of the innate immune response in zebrafish. Adv Hematol 2012; 2012:159807. [PMID: 22811714 PMCID: PMC3395205 DOI: 10.1155/2012/159807] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/22/2012] [Indexed: 12/28/2022] Open
Abstract
The zebrafish has proven itself as an excellent model to study vertebrate innate immunity. It presents us with possibilities for in vivo imaging of host-pathogen interactions which are unparalleled in mammalian model systems. In addition, its suitability for genetic approaches is providing new insights on the mechanisms underlying the innate immune response. Here, we review the pattern recognition receptors that identify invading microbes, as well as the innate immune effector mechanisms that they activate in zebrafish embryos. We compare the current knowledge about these processes in mammalian models and zebrafish and discuss recent studies using zebrafish infection models that have advanced our general understanding of the innate immune system. Furthermore, we use transcriptome analysis of zebrafish infected with E. tarda, S. typhimurium, and M. marinum to visualize the gene expression profiles resulting from these infections. Our data illustrate that the two acute disease-causing pathogens, E. tarda and S. typhimurium, elicit a highly similar proinflammatory gene induction profile, while the chronic disease-causing pathogen, M. marinum, induces a weaker and delayed innate immune response.
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