1
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Mock MB, Summers RM. Microbial metabolism of caffeine and potential applications in bioremediation. J Appl Microbiol 2024; 135:lxae080. [PMID: 38549434 DOI: 10.1093/jambio/lxae080] [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: 09/08/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
With increasing global consumption of caffeine-rich products, such as coffee, tea, and energy drinks, there is also an increase in urban and processing waste full of residual caffeine with limited disposal options. This waste caffeine has been found to leach into the surrounding environment where it poses a threat to microorganisms, insects, small animals, and entire ecosystems. Growing interest in harnessing this environmental contaminant has led to the discovery of 79 bacterial strains, eight yeast strains, and 32 fungal strains capable of metabolizing caffeine by N-demethylation and/or C-8 oxidation. Recently observed promiscuity of caffeine-degrading enzymes in vivo has opened up the possibility of engineering bacterial strains capable of producing a wide variety of caffeine derivatives from a renewable resource. These engineered strains can be used to reduce the negative environmental impact of leached caffeine-rich waste through bioremediation efforts supplemented by our increasing understanding of new techniques such as cell immobilization. Here, we compile all of the known caffeine-degrading microbial strains, discuss their metabolism and related enzymology, and investigate their potential application in bioremediation.
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Affiliation(s)
- Meredith B Mock
- Department of Chemical and Biological Engineering, The University of Alabama, Box 870203, Tuscaloosa, AL 35487, United States
| | - Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Box 870203, Tuscaloosa, AL 35487, United States
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2
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Zimmerman JAO, Fang M, Pufall MA. PI3Kδ Inhibition Potentiates Glucocorticoids in B-lymphoblastic Leukemia by Decreasing Receptor Phosphorylation and Enhancing Gene Regulation. Cancers (Basel) 2023; 16:143. [PMID: 38201570 PMCID: PMC10778422 DOI: 10.3390/cancers16010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Glucocorticoids are the cornerstone of B-lymphoblastic leukemia (B-ALL) therapy. Because response to glucocorticoids alone predicts overall outcomes for B-ALL, enhancing glucocorticoid potency should improve treatment. We previously showed that inhibition of the lymphoid-restricted PI3Kδ with idelalisib enhances glucocorticoid activity in B-ALL cells. Here, we show that idelalisib enhances glucocorticoid potency in 90% of primary B-ALL specimens and is most pronounced at sub-saturating doses of glucocorticoids near the EC50. Potentiation is associated with enhanced regulation of all glucocorticoid-regulated genes, including genes that drive B-ALL cell death. Idelalisib reduces phosphorylation of the glucocorticoid receptor (GR) at PI3Kδ/MAPK1 (ERK2) targets S203 and S226. Ablation of these phospho-acceptor sites enhances sensitivity to glucocorticoids with ablation of S226 in particular reducing synergy. We also show that phosphorylation of S226 reduces the affinity of GR for DNA in vitro. We propose that PI3Kδ inhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation, increasing DNA binding affinity, and enhancing downstream gene regulation. This mechanism and the response of patient specimens suggest that idelalisib will benefit most patients with B-ALL, but particularly patients with less responsive, including high-risk, disease. This combination is also promising for the development of less toxic glucocorticoid-sparing therapies.
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Affiliation(s)
- Jessica A. O. Zimmerman
- Division of Pediatric Hematology/Oncology, Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
| | - Mimi Fang
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Miles A. Pufall
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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3
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Hao J, Yu J, Yorek MS, Yu CL, Pope RM, Chimenti MS, Xiong Y, Klingelhutz A, Jabbari A, Li B. Keratinocyte FABP5-VCP complex mediates recruitment of neutrophils in psoriasis. Cell Rep 2023; 42:113449. [PMID: 37967009 PMCID: PMC10729729 DOI: 10.1016/j.celrep.2023.113449] [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: 04/28/2023] [Revised: 10/03/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023] Open
Abstract
One of the hallmarks of intractable psoriasis is neutrophil infiltration in skin lesions. However, detailed molecular mechanisms of neutrophil chemotaxis and activation remain unclear. Here, we demonstrate a significant upregulation of epidermal fatty acid binding protein (E-FABP, FABP5) in the skin of human psoriasis and psoriatic mouse models. Genetic deletion of FABP5 in mice by global knockout and keratinocyte conditional (Krt6a-Cre) knockout, but not myeloid cell conditional (LysM-Cre) knockout, attenuates psoriatic symptoms. Immunophenotypic analysis shows that FABP5 deficiency specifically reduces skin recruitment of Ly6G+ neutrophils. Mechanistically, activated keratinocytes produce chemokines and cytokines that trigger neutrophil chemotaxis and activation in an FABP5-dependent manner. Proteomic analysis further identifies that FABP5 interacts with valosin-containing protein (VCP), a key player in NF-κB signaling activation. Silencing of FABP5, VCP, or both inhibits NF-κB/neutrophil chemotaxis signaling. Collectively, these data demonstrate dysregulated FABP5 as a molecular mechanism promoting NF-κB signaling and neutrophil infiltration in psoriasis pathogenesis.
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Affiliation(s)
- Jiaqing Hao
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Jianyu Yu
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Matthew S Yorek
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Chi-Li Yu
- Proteomics Facility, University of Iowa, Iowa City, IA, USA
| | | | - Michael S Chimenti
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Yiqin Xiong
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Aloysius Klingelhutz
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Ali Jabbari
- Department of Dermatology, University of Iowa, Iowa City, IA, USA; Iowa City VA Medical Center, Iowa City, IA, USA
| | - Bing Li
- Department of Pathology, University of Iowa, Iowa City, IA, USA.
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4
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Zimmerman JA, Fang M, Pufall MA. PI3Kδ inhibition potentiates glucocorticoids in B-lymphoblastic leukemia by decreasing receptor phosphorylation and enhancing gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.527869. [PMID: 36798391 PMCID: PMC9934697 DOI: 10.1101/2023.02.10.527869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Glucocorticoids, including dexamethasone and prednisone, are the cornerstone of B-lymphoblastic leukemia (B-ALL) therapy. Because response to glucocorticoids alone predicts overall outcomes for B-ALL, enhancing glucocorticoid potency is a route to improving outcomes. However, systematic toxicities prevent the use of higher dose and more potent glucocorticoids. We therefore took a functional genomic approach to identify targets to enhance glucocorticoid activity specifically in B-ALL cells. Here we show that inhibition of the lymphoid-restricted PI3Kδ, signaling through the RAS/MAPK pathway, enhances both prednisone and dexamethasone activity in almost all ex vivo B-ALL specimens tested. This potentiation is most synergistic at sub-saturating doses of glucocorticoids, approaching the EC50. Potentiation correlates with global enhancement of glucocorticoid-induced gene regulation, including regulation of effector genes that drive B-ALL cell death. Idelalisib reduces phosphorylation of the glucocorticoid receptor (GR) at MAPK1/ERK2 targets S203 and S226, and ablation of these phospho-acceptor sites enhances glucocorticoid potency. We further show that phosphorylation of S226 reduces the affinity of GR for DNA in vitro, which impairs DNA binding. We therefore propose that PI3Kδ inhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation, increasing DNA binding affinity, and enhancing downstream gene regulation. The overall enhancement of GR function suggests that idelalisib will provide benefit to most patients with B-ALL by improving outcomes for patients whose disease is less responsive to glucocorticoid-based therapy, including high-risk disease, and allowing less toxic glucocorticoid-sparing strategies for patients with standard-risk disease.
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Affiliation(s)
- Jessica A.O. Zimmerman
- Division of Pediatric Hematology/Oncology, Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Mimi Fang
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Miles A. Pufall
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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5
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Srivastava D, Yadav RP, Singh S, Boyd K, Artemyev NO. Unique interface and dynamics of the complex of HSP90 with a specialized cochaperone AIPL1. Structure 2023; 31:309-317.e5. [PMID: 36657440 PMCID: PMC9992320 DOI: 10.1016/j.str.2022.12.014] [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: 10/17/2022] [Revised: 12/06/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023]
Abstract
Photoreceptor phosphodiesterase PDE6 is central for visual signal transduction. Maturation of PDE6 depends on a specialized chaperone complex of HSP90 with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1). Disruption of PDE6 maturation underlies a severe form of retina degeneration. Here, we report a 3.9 Å cryoelectron microscopy (cryo-EM) structure of the complex of HSP90 with AIPL1. This structure reveals a unique interaction of the FK506-binding protein (FKBP)-like domain of AIPL1 with HSP90 at its dimer interface. Unusually, the N terminus AIPL1 inserts into the HSP90 lumen in a manner that was observed previously for HSP90 clients. Deletion of the 7 N-terminal residues of AIPL1 decreased its ability to cochaperone PDE6. Multi-body refinement of the cryo-EM data indicated large swing-like movements of AIPL1-FKBP. Modeling the complex of HSP90 with AIPL1 using crosslinking constraints indicated proximity of the mobile tetratricopeptide repeat (TPR) domain with the C-terminal domain of HSP90. Our study establishes a framework for future structural studies of PDE6 maturation.
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Affiliation(s)
- Dhiraj Srivastava
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Ravi P Yadav
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Sneha Singh
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kimberly Boyd
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
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6
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Tang J, Xiao Y, Lin G, Guo H, Deng HX, Tu S, Langdon WY, Yang H, Tao L, Li Y, Pope RM, Gupta N, Zhang J. Tyrosine phosphorylation of NLRP3 by the Src family kinase Lyn suppresses the activity of the NLRP3 inflammasome. Sci Signal 2021; 14:eabe3410. [PMID: 34699250 DOI: 10.1126/scisignal.abe3410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Juan Tang
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH 43210, USA.,Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China.,Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yizhi Xiao
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA.,Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Guoxin Lin
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH 43210, USA.,Department of Pathology, University of Iowa, Iowa City, IA 52242, USA.,Department of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Hui Guo
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH 43210, USA.,Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Han-Xiang Deng
- Department of Neurology, Northwestern University, Chicago, IL 60611, USA
| | - Sha Tu
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA.,Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Wallace Y Langdon
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Huixiang Yang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Lijian Tao
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yalan Li
- Proteomics Facility, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - R Marshall Pope
- Proteomics Facility, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Neetu Gupta
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jian Zhang
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH 43210, USA.,Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
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7
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Thathola P, Agnihotri V, Pandey A. Microbial Degradation of Caffeine Using Himalayan Psychrotolerant Pseudomonas sp.GBPI_Hb5 (MCC 3295). Curr Microbiol 2021; 78:3924-3935. [PMID: 34522981 DOI: 10.1007/s00284-021-02644-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Caffeine, a xenobiotic compound, is continuously released into the environment. Fifteen psychrotolerant bacterial strains, isolated from the Indian Himalayan region, were screened for their caffeine degradation capacity. The medium for the growth of bacteria was optimized using Box-Behnken method. Among these bacteria, Pseudomonassp. (GBPI_Hb5), showing the best response, was further used for caffeine degradation in batch mode. The culture medium, having caffeine as a sole source of carbon, was used for analyzing the effect of pH, agitation speed, temperature, inoculum volume, and caffeine concentration on bacterial growth and its caffeine degradation potential. The bacterium GBPI_Hb5 showed approx. 93% caffeine degradation up to 96 h under controlled conditions. The compounds produced during the degradation of caffeine were also studied. The study is likely to have implications in the bioremediation of caffeine from polluted environments.
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Affiliation(s)
- Pooja Thathola
- Centre for Land and Water Resource Management, G. B. Pant National Institute of Himalayan Environment, Kosi-Katarmal, Almora, Uttarakhand, 263643, India
| | - Vasudha Agnihotri
- Centre for Land and Water Resource Management, G. B. Pant National Institute of Himalayan Environment, Kosi-Katarmal, Almora, Uttarakhand, 263643, India.
| | - Anita Pandey
- Department of Biotechnology, Graphic Era University, Bell Road, Clement Town, Dehradun, Uttarakhand, 248002, India
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8
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Santos MF, Rappa G, Karbanová J, Fontana S, Bella MAD, Pope MR, Parrino B, Cascioferro SM, Vistoli G, Diana P, Cirrincione G, Arena GO, Woo G, Huang K, Huynh T, Moschetti M, Alessandro R, Corbeil D, Lorico A. Itraconazole inhibits nuclear delivery of extracellular vesicle cargo by disrupting the entry of late endosomes into the nucleoplasmic reticulum. J Extracell Vesicles 2021; 10:e12132. [PMID: 34429859 PMCID: PMC8363911 DOI: 10.1002/jev2.12132] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
Extracellular vesicles (EVs) are mediators of intercellular communication under both healthy and pathological conditions, including the induction of pro-metastatic traits, but it is not yet known how and where functional cargoes of EVs are delivered to their targets in host cell compartments. We have described that after endocytosis, EVs reach Rab7+ late endosomes and a fraction of these enter the nucleoplasmic reticulum and transport EV biomaterials to the host cell nucleoplasm. Their entry therein and docking to outer nuclear membrane occur through a tripartite complex formed by the proteins VAP-A, ORP3 and Rab7 (VOR complex). Here, we report that the antifungal compound itraconazole (ICZ), but not its main metabolite hydroxy-ICZ or ketoconazole, disrupts the binding of Rab7 to ORP3-VAP-A complexes, leading to inhibition of EV-mediated pro-metastatic morphological changes including cell migration behaviour of colon cancer cells. With novel, smaller chemical drugs, inhibition of the VOR complex was maintained, although the ICZ moieties responsible for antifungal activity and interference with intracellular cholesterol distribution were removed. Knowing that cancer cells hijack their microenvironment and that EVs derived from them determine the pre-metastatic niche, small-sized inhibitors of nuclear transfer of EV cargo into host cells could find cancer therapeutic applications, particularly in combination with direct targeting of cancer cells.
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Affiliation(s)
- Mark F. Santos
- College of MedicineTouro University NevadaHendersonNevadaUSA
| | - Germana Rappa
- College of MedicineTouro University NevadaHendersonNevadaUSA
| | - Jana Karbanová
- Biotechnology Centre and Centre for Molecular and Cellular BioengineeringTechnische Universität DresdenDresdenGermany
| | - Simona Fontana
- Department of Biomedicine, Neurosciences and Advanced DiagnosticsUniversity of PalermoPalermoItaly
| | | | | | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie BiologicheChimiche e FarmaceuticheUniversità degli Studi di PalermoPalermoItaly
| | - Stella Maria Cascioferro
- Dipartimento di Scienze e Tecnologie BiologicheChimiche e FarmaceuticheUniversità degli Studi di PalermoPalermoItaly
| | - Giulio Vistoli
- Dipartimento di Scienze FarmaceuticheUniversità degli Studi di MilanoMilanItaly
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie BiologicheChimiche e FarmaceuticheUniversità degli Studi di PalermoPalermoItaly
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie BiologicheChimiche e FarmaceuticheUniversità degli Studi di PalermoPalermoItaly
| | - Goffredo O. Arena
- Department of SurgeryMcGill UniversityMontréalQuébecCanada
- Fondazione Istituto G. GiglioCefalùItaly
| | - Gyunghwi Woo
- College of MedicineTouro University NevadaHendersonNevadaUSA
| | - Kevin Huang
- College of MedicineTouro University NevadaHendersonNevadaUSA
| | - Tony Huynh
- College of MedicineTouro University NevadaHendersonNevadaUSA
| | - Marta Moschetti
- Department of Biomedicine, Neurosciences and Advanced DiagnosticsUniversity of PalermoPalermoItaly
| | - Riccardo Alessandro
- Department of Biomedicine, Neurosciences and Advanced DiagnosticsUniversity of PalermoPalermoItaly
- Institute for Biomedical Research and Innovation (IRIB)National Research Council (CNR)PalermoItaly
| | - Denis Corbeil
- Biotechnology Centre and Centre for Molecular and Cellular BioengineeringTechnische Universität DresdenDresdenGermany
| | - Aurelio Lorico
- College of MedicineTouro University NevadaHendersonNevadaUSA
- Mediterranean Institute of OncologyViagrandeItaly
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9
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Cruz-O'Byrne R, Piraneque-Gambasica N, Aguirre-Forero S. Microbial diversity associated with spontaneous coffee bean fermentation process and specialty coffee production in northern Colombia. Int J Food Microbiol 2021; 354:109282. [PMID: 34140187 DOI: 10.1016/j.ijfoodmicro.2021.109282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/15/2021] [Accepted: 05/30/2021] [Indexed: 01/16/2023]
Abstract
Coffee fermentation involves the action of microorganisms, whose metabolism has a significant influence on the composition of the beans and, consequently, on the beverage's sensory characteristics. In this study, the microbial diversity during the wet fermentation of Coffea arabica L. in the Sierra Nevada of Santa Marta (SNSM) in Colombia was explored by high-throughput sequencing and the resulting cup quality through the standards of the Specialty Coffee Association. The taxonomic assignment of sequence reads showed a high microbial diversity comprised of 695 bacterial and 156 fungal genera. The microbial community was dominated by the Lactic Acid Bacteria (LAB) Leuconostoc, the yeast Kazachstania, and the Acetic Acid Bacteria (AAB) Acetobacter. Co-occurrence relationships suggested synergistic patterns between populations of LAB-AAB, yeasts-AAB, Leuconostoc-Prevotella, LAB-ABB-Selenomonas, and yeasts-fungi-nonLAB-nonAAB, which may result in the production of metabolites that positively impact the sensory attributes of coffee. The beverages produced were classified as specialty coffees, and their score was positively influenced by the fungal richness and the abundance of unclassified Lactobacillales, Pichia, and Pseudomonas. The findings show the richness and microbial diversity of the SNSM and serve as input for future research such as the analysis of microbial-derived metabolites and the establishment of starter cultures in coffee processing that guarantee the generation of high-quality beverages, the standardization of processes, the reduction of economic losses, and the production of value-added products that allow taking advantage of specialty coffee market.
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10
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Fermentative production of xylitol from a newly isolated xylose reductase producing Pseudomonas putida BSX-46. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Tang J, Tu S, Lin G, Guo H, Yan C, Liu Q, Huang L, Tang N, Xiao Y, Pope RM, Rajaram MVS, Amer AO, Ahmer BM, Gunn JS, Wozniak DJ, Tao L, Coppola V, Zhang L, Langdon WY, Torrelles JB, Lipkowitz S, Zhang J. Sequential ubiquitination of NLRP3 by RNF125 and Cbl-b limits inflammasome activation and endotoxemia. J Exp Med 2020; 217:133674. [PMID: 31999304 PMCID: PMC7144527 DOI: 10.1084/jem.20182091] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/26/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Aberrant NLRP3 inflammasome activation contributes to the development of endotoxemia. The importance of negative regulation of NLRP3 inflammasomes remains poorly understood. Here, we show that the E3 ubiquitin ligase Cbl-b is essential for preventing endotoxemia induced by a sub-lethal dose of LPS via a caspase-11/NLRP3-dependent manner. Further studies show that NLRP3 undergoes both K63- and K48-linked polyubiquitination. Cbl-b binds to the K63-ubiquitin chains attached to the NLRP3 leucine-rich repeat domain (LRR) via its ubiquitin-associated region (UBA) and then targets NLRP3 at K496 for K48-linked ubiquitination and proteasome-mediated degradation. We also identify RNF125 as an additional E3 ubiquitin ligase that initiates K63-linked ubiquitination of the NLRP3 LRR domain. Therefore, NLRP3 is sequentially ubiquitinated by K63- and K48-linked ubiquitination, thus keeping the NLRP3 inflammasomes in check and restraining endotoxemia.
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Affiliation(s)
- Juan Tang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH.,Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Sha Tu
- Department of Pathology, University of Iowa, Iowa City, IA.,Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Guoxin Lin
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH.,Department of Pathology, University of Iowa, Iowa City, IA.,Department of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Hui Guo
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH.,Department of Pathology, University of Iowa, Iowa City, IA
| | - Chengkai Yan
- Department of Pathology, University of Iowa, Iowa City, IA
| | - Qingjun Liu
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - Ling Huang
- Department of Pathology, University of Iowa, Iowa City, IA
| | - Na Tang
- Department of Pathology, University of Iowa, Iowa City, IA
| | - Yizhi Xiao
- Department of Pathology, University of Iowa, Iowa City, IA
| | - R Marshall Pope
- Proteomics Facility, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Murugesan V S Rajaram
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - Amal O Amer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - Brian M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - John S Gunn
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - Lijian Tao
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH
| | - Liwen Zhang
- Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH
| | - Wallace Y Langdon
- School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Jordi B Torrelles
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - Stanley Lipkowitz
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jian Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH.,Department of Pathology, University of Iowa, Iowa City, IA
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12
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Zhou B, Ma C, Zheng C, Xia T, Ma B, Liu X. 3-Methylxanthine production through biodegradation of theobromine by Aspergillus sydowii PT-2. BMC Microbiol 2020; 20:269. [PMID: 32854634 PMCID: PMC7453516 DOI: 10.1186/s12866-020-01951-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022] Open
Abstract
Background Methylxanthines, including caffeine, theobromine and theophylline, are natural and synthetic compounds in tea, which could be metabolized by certain kinds of bacteria and fungi. Previous studies confirmed that several microbial isolates from Pu-erh tea could degrade and convert caffeine and theophylline. We speculated that these candidate isolates also could degrade and convert theobromine through N-demethylation and oxidation. In this study, seven tea-derived fungal strains were inoculated into various theobromine agar medias and theobromine liquid mediums to assess their capacity in theobromine utilization. Related metabolites with theobromine degradation were detected by using HPLC in the liquid culture to investigate their potential application in the production of 3-methylxanthine. Results Based on theobromine utilization capacity, Aspergillus niger PT-1, Aspergillus sydowii PT-2, Aspergillus ustus PT-6 and Aspergillus tamarii PT-7 have demonstrated the potential for theobromine biodegradation. Particularly, A. sydowii PT-2 and A. tamarii PT-7 could degrade theobromine significantly (p < 0.05) in all given liquid mediums. 3,7-Dimethyluric acid, 3-methylxanthine, 7-methylxanthine, 3-methyluric acid, xanthine, and uric acid were detected in A. sydowii PT-2 and A. tamarii PT-7 culture, respectively, which confirmed the existence of N-demethylation and oxidation in theobromine catabolism. 3-Methylxanthine was common and main demethylated metabolite of theobromine in the liquid culture. 3-Methylxanthine in A. sydowii PT-2 culture showed a linear relation with initial theobromine concentrations that 177.12 ± 14.06 mg/L 3-methylxanthine was accumulated in TLM-S with 300 mg/L theobromine. Additionally, pH at 5 and metal ion of Fe2+ promoted 3-methylxanthine production significantly (p < 0.05). Conclusions This study is the first to confirm that A. sydowii PT-2 and A. tamarii PT-7 degrade theobromine through N-demethylation and oxidation, respectively. A. sydowii PT-2 showed the potential application in 3-methylxanthine production with theobromine as feedstock through the N-demethylation at N-7 position.
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Affiliation(s)
- Binxing Zhou
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Cunqiang Ma
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China. .,Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, 464000, Henan, China. .,Kunming Dapu Tea Industry Co., Ltd, Kunming, 650224, Yunnan, China.
| | - Chengqin Zheng
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Bingsong Ma
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Xiaohui Liu
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
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Draft Genome Sequence of Pseudomonas sp. Strain CES, Containing the Entire Alkylxanthine Gene Cluster for Caffeine Breakdown. Microbiol Resour Announc 2020; 9:9/28/e00484-20. [PMID: 32646901 PMCID: PMC7348019 DOI: 10.1128/mra.00484-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas strain CES was isolated from caffeine-enriched soil and found to possess the N-demethylation pathway for caffeine breakdown. We report the nucleotide sequence of the draft genome with 5,827,822 bp, 62.6% G+C content, and 5,427 protein-coding regions. Pseudomonas strain CES was isolated from caffeine-enriched soil and found to possess the N-demethylation pathway for caffeine breakdown. We report the nucleotide sequence of the draft genome with 5,827,822 bp, 62.6% G+C content, and 5,427 protein-coding regions.
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Isolation, characterization and application of theophylline-degrading Aspergillus fungi. Microb Cell Fact 2020; 19:72. [PMID: 32192512 PMCID: PMC7082937 DOI: 10.1186/s12934-020-01333-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/13/2020] [Indexed: 11/10/2022] Open
Abstract
Background Caffeine, theobromine and theophylline are main purine alkaloid in tea. Theophylline is the downstream metabolite and it remains at a very low level in Camellia sinensis. In our previous study, Aspergillus sydowii could convert caffeine into theophylline in solid-state fermentation of pu-erh tea through N-demethylation. In this study, tea-derived fungi caused theophylline degradation in the solid-state fermentation. The purpose of this study is identify and isolate theophylline-degrading fungi and investigate their application in production of methylxanthines with theophylline as feedstock through microbial conversion. Results Seven tea-derived fungi were collected and identified by ITS, β-tubulin and calmodulin gene sequences, Aspergillus ustus, Aspergillus tamarii, Aspergillus niger and A. sydowii associated with solid-state fermentation of pu-erh tea have shown ability to degrade theophylline in liquid culture. Particularly, A. ustus and A. tamarii could degrade theophylline highly significantly (p < 0.01). 1,3-dimethyluric acid, 3-methylxanthine, 3-methyluric acid, xanthine and uric acid were detected consecutively by HPLC in A. ustus and A. tamarii, respectively. The data from absolute quantification analysis suggested that 3-methylxanthine and xanthine were the main degraded metabolites in A. ustus and A. tamarii, respectively. 129.48 ± 5.81 mg/L of 3-methylxanthine and 159.11 ± 10.8 mg/L of xanthine were produced by A. ustus and A. tamarii in 300 mg/L of theophylline liquid medium, respectively. Conclusions For the first time, we confirmed that isolated A. ustus, A. tamarii degrade theophylline through N-demethylation and oxidation. We were able to biologically produce 3-methylxanthine and xanthine efficiently from theophylline through a new microbial synthesis platform with A. ustus and A. tamarii as appropriate starter strains.
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Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor. Nat Commun 2019; 10:3084. [PMID: 31300652 PMCID: PMC6625990 DOI: 10.1038/s41467-019-11088-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/21/2019] [Indexed: 02/03/2023] Open
Abstract
Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal structures of Ric8A, one in the apo form and the other in complex with a tagged C-terminal fragment of Gα. These structures reveal two principal domains of Ric8A: an armadillo-fold core and a flexible C-terminal tail. Additionally, they show that the Gα C-terminus binds to a highly-conserved patch on the concave surface of the Ric8A armadillo-domain, with selectivity determinants residing in the Gα sequence. Biochemical analysis shows that the Ric8A C-terminal tail is critical for its stability and function. A model of the Ric8A/Gα complex derived from crosslinking mass spectrometry and molecular dynamics simulations suggests that the Ric8A C-terminal tail helps organize the GTP-binding site of Gα. This study lays the groundwork for understanding Ric8A function at the molecular level. Ric8A regulates G protein α-subunits (Gα) by acting as a guanine nucleotide exchange factor (GEF) and a Gα chaperone. Here, the authors solve the crystal structures of free and Gα fragment bound Ric8A, and provide insights into the structural basis for Ric8A’s GEF and chaperone functions.
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Leishmania major degrades murine CXCL1 - An immune evasion strategy. PLoS Negl Trop Dis 2019; 13:e0007533. [PMID: 31260451 PMCID: PMC6625741 DOI: 10.1371/journal.pntd.0007533] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/12/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
Leishmaniasis is a global health problem with an estimated report of 2 million new cases every year and more than 1 billion people at risk of contracting this disease in endemic areas. The innate immune system plays a central role in controlling L. major infection by initiating a signaling cascade that results in production of pro-inflammatory cytokines and recruitment of both innate and adaptive immune cells. Upon infection with L. major, CXCL1 is produced locally and plays an important role in the recruitment of neutrophils to the site of infection. Herein, we report that L. major specifically targets murine CXCL1 for degradation. The degradation of CXCL1 is not dependent on host factors as L. major can directly degrade recombinant CXCL1 in a cell-free system. Using mass spectrometry, we discovered that the L. major protease cleaves at the C-terminal end of murine CXCL1. Finally, our data suggest that L. major metalloproteases are involved in the direct cleavage and degradation of CXCL1, and a synthetic peptide spanning the CXCL1 cleavage site can be used to inhibit L. major metalloprotease activity. In conclusion, our study has identified an immune evasion strategy employed by L. major to evade innate immune responses in mice, likely reservoirs in the endemic areas, and further highlights that targeting these L. major metalloproteases may be important in controlling infection within the reservoir population and transmittance of the disease. Our study discovered a highly specific role for L. major metalloprotease in cleaving and degrading murine CXCL1. Indeed, L. major metalloprotease did not cleave murine CXCL2 or human CXCL1, CXCL2 and CXCL8. CXCL1 is a critical chemokine required for neutrophil recruitment to the site of infection; thus, we propose that this metalloprotease may have evolved to evade immune responses specifically in the murine host. We have further identified that the C-terminal end on CXCL1 is targeted for cleavage by the L. major metalloprotease. Finally, this cleavage site information was used to design peptides that are able to inhibit CXCL1 degradation by L. major. Our study highlights an immune evasion strategy utilized by L. major to establish infection within a murine host.
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Jiang Y, Lu Y, Huang Y, Chen S, Ji Z. Bacillus amyloliquefaciens HZ-12 heterologously expressing NdmABCDE with higher ability of caffeine degradation. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.04.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Win YY, Singh M, Sadiq MB, Anal AK. Isolation and identification of caffeine-degrading bacteria from coffee plantation area. FOOD BIOTECHNOL 2019. [DOI: 10.1080/08905436.2019.1570854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yi Yi Win
- Engineering and Bioprocess Technology, Department of Food, Agriculture and Bioresources, Asian Institute of Technology, Klong Luang, Pathumthani, Thailand
| | - Manisha Singh
- Engineering and Bioprocess Technology, Department of Food, Agriculture and Bioresources, Asian Institute of Technology, Klong Luang, Pathumthani, Thailand
| | - Muhammad Bilal Sadiq
- Engineering and Bioprocess Technology, Department of Food, Agriculture and Bioresources, Asian Institute of Technology, Klong Luang, Pathumthani, Thailand
| | - Anil Kumar Anal
- Engineering and Bioprocess Technology, Department of Food, Agriculture and Bioresources, Asian Institute of Technology, Klong Luang, Pathumthani, Thailand
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Ahmad M, Pataczek L, Hilger TH, Zahir ZA, Hussain A, Rasche F, Schafleitner R, Solberg SØ. Perspectives of Microbial Inoculation for Sustainable Development and Environmental Management. Front Microbiol 2018; 9:2992. [PMID: 30568644 PMCID: PMC6289982 DOI: 10.3389/fmicb.2018.02992] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
How to sustainably feed a growing global population is a question still without an answer. Particularly farmers, to increase production, tend to apply more fertilizers and pesticides, a trend especially predominant in developing countries. Another challenge is that industrialization and other human activities produce pollutants, which accumulate in soils or aquatic environments, contaminating them. Not only is human well-being at risk, but also environmental health. Currently, recycling, land-filling, incineration and pyrolysis are being used to reduce the concentration of toxic pollutants from contaminated sites, but too have adverse effects on the environment, producing even more resistant and highly toxic intermediate compounds. Moreover, these methods are expensive, and are difficult to execute for soil, water, and air decontamination. Alternatively, green technologies are currently being developed to degrade toxic pollutants. This review provides an overview of current research on microbial inoculation as a way to either replace or reduce the use of agrochemicals and clean environments heavily affected by pollution. Microorganism-based inoculants that enhance nutrient uptake, promote crop growth, or protect plants from pests and diseases can replace agrochemicals in food production. Several examples of how biofertilizers and biopesticides enhance crop production are discussed. Plant roots can be colonized by a variety of favorable species and genera that promote plant growth. Microbial interventions can also be used to clean contaminated sites from accumulated pesticides, heavy metals, polyaromatic hydrocarbons, and other industrial effluents. The potential of and key processes used by microorganisms for sustainable development and environmental management are discussed in this review, followed by their future prospects.
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Affiliation(s)
- Maqshoof Ahmad
- Department of Soil Science, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Lisa Pataczek
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Thomas H. Hilger
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Zahir Ahmad Zahir
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Azhar Hussain
- Department of Soil Science, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | | | - Svein Ø. Solberg
- World Vegetable Center, Tainan, China
- Inland Norway University of Applied Sciences, Elverum, Norway
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20
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Park S, Lee W. Removal of selected pharmaceuticals and personal care products in reclaimed water during simulated managed aquifer recharge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:671-677. [PMID: 29870943 DOI: 10.1016/j.scitotenv.2018.05.221] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/28/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
This study investigated the removal of selected pharmaceuticals and personal care products (PPCPs) in a simulated managed aquifer recharge (MAR) system. The PPCPs included antibiotic, antiepileptic, antihypertensive, anti-inflammatory, and antilipidemic drugs, contrast media, herbicides, and stimulants. We first monitored the occurrence and fate of 22 PPCPs at a water reclamation facility (WRF) in Korea, and found carbamazepine and primidone were not readily removed (below 25% removal in average) by the WRF. This reclaimed water passed through a laboratory-scale soil column set-up at 0.5 m/d over one year, simulating MAR system. Atenolol, propranolol, and trimethoprim exhibited higher removal rates (>80%) than other PPCPs through the simulated MAR, while atrazine, carbamazepine, lincomycin, primidone, and sulfamethazine were not readily removed, exhibiting removal rates below 20%. It can be efficient to monitor and manage these recalcitrant compounds at MAR systems to improve water quality.
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Affiliation(s)
- Soohyung Park
- Department of Environmental Engineering, Kumoh National Institute of Technology, Gumi, South Korea
| | - Wontae Lee
- Department of Environmental Engineering, Kumoh National Institute of Technology, Gumi, South Korea.
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21
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Tran NH, Gin KYH. Occurrence and removal of pharmaceuticals, hormones, personal care products, and endocrine disrupters in a full-scale water reclamation plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:1503-1516. [PMID: 28531959 DOI: 10.1016/j.scitotenv.2017.05.097] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 05/12/2023]
Abstract
This study provided the first comprehensive data on the occurrence and removal of twenty-five target emerging contaminants (ECs) in a full-scale water reclamation plant (WRP) in the Southeast Asian region. Nineteen out of the twenty-five ECs were ubiquitously detected in raw influent samples. Concentrations of the detected ECs in raw influent samples ranged substantially from 44.3 to 124,966ng/L, depending upon the compound and sampling date. The elimination of ECs in full-scale conventional activated sludge (CAS) and membrane bioreactor (MBR) systems at a local WRP was evaluated and compared. Several ECs, such as acetaminophen, atenolol, fenoprofen, indomethacin, ibuprofen, and oxybenzone, exhibited excellent removal efficiencies (>90%) in biological wastewater treatment processes, while some of the investigated compounds (carbamazepine, crotamiton, diclofenac, and iopamidol) appeared to be persistent in the both CAS and MBR systems. Field-based monitoring results showed that MBR outperformed CAS in the elimination of most target ECs. The relationship between molecular characteristics of ECs (i.e. physicochemical properties and structural features) and their removal efficiencies during biological wastewater treatment was also elucidated. Excellent removal efficiencies (>90%) were often noted for ECs with the sole presence of electron donating groups (i.e. phenolic [OH], amine [NH2], methoxy [OCH3], phenoxy [OC6H5], or alkyl groups). Conversely, ECs with the absence of electron donating groups or the predominance of strong electron withdrawing groups (e.g. halogenated, carbonyl, carboxyl, and sulfonamide) tended to show poor removal efficiencies (<30%) in biological wastewater treatment processes.
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Affiliation(s)
- Ngoc Han Tran
- NUS Environmental Research Institute, National University of Singapore, T-Lab Building, #02-01, 5A Engineering Drive 1, Singapore 117411, Singapore.
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, T-Lab Building, #02-01, 5A Engineering Drive 1, Singapore 117411, Singapore; Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore.
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Lian L, Yan S, Yao B, Chan SA, Song W. Photochemical Transformation of Nicotine in Wastewater Effluent. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11718-11730. [PMID: 28942634 DOI: 10.1021/acs.est.7b03223] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nicotine is a highly toxic tobacco alkaloid that is ubiquitous in wastewater effluent. For the first time, we report the identification of the products and the pathways for the photodegradation of nicotine in an effluent matrix under simulated solar irradiation. Nicotine was found to be degraded by triplet-state organic matter (3OM*), thus indicating that electron transfer is a preferred reaction mechanism. Using the multivariate statistical strategies orthogonal projection to latent structures discriminant analysis (OPLS-DA) and hierarchical clustering, 49 potential transformation products (TPs) of nicotine were successfully extracted from the water matrix via high-resolution ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS). Overall, 30 TPs, including 4 groups of nonseparated isomeric photo TPs, were identified with various levels of confidence based on the tandem mass spectrometry information on standard compounds and the isotope-labeling method (using rac-nicotine-2',3',3'-D3, rac-nicotine-13CD3, and rac-nicotine-D4) under air-saturated conditions. The pyrrolidine ring of nicotine was found to be the reactive site under sunlight irradiation. Pseudooxynicotine was the main primary TP from nicotine, with a maximum transformation ratio of 64%. Nicotinic acid, cotinine, 3'-hydroxycotinine, and myosmine were the final stable TPs after 72 h of solar irradiation, with yields of 13%, 3%, 5%, and 5%, respectively.
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Affiliation(s)
- Lushi Lian
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - Shuwen Yan
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - Bo Yao
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - Shen-An Chan
- Agilent Technology, Inc. , 1350 North Sichuan Road, Shanghai 200080, PR China
| | - Weihua Song
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
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Production of theobromine by N-demethylation of caffeine using metabolically engineered E . coli. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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MacDonald C, Winistorfer S, Pope RM, Wright ME, Piper RC. Enzyme reversal to explore the function of yeast E3 ubiquitin-ligases. Traffic 2017; 18:465-484. [PMID: 28382714 DOI: 10.1111/tra.12485] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/31/2017] [Accepted: 03/31/2017] [Indexed: 12/27/2022]
Abstract
The covalent attachment of ubiquitin onto proteins can elicit a variety of downstream consequences. Attachment is mediated by a large array of E3 ubiquitin ligases, each thought be subject to regulatory control and to have a specific repertoire of substrates. Assessing the biological roles of ligases, and in particular, identifying their biologically relevant substrates has been a persistent yet challenging question. In this study, we describe tools that may help achieve both of these goals. We describe a strategy whereby the activity of a ubiquitin ligase has been enzymatically reversed, accomplished by fusing it to a catalytic domain of an exogenous deubiquitinating enzyme. We present a library of 72 "anti-ligases" that appear to work in a dominant-negative fashion to stabilize their cognate substrates against ubiquitin-dependent proteasomal and lysosomal degradation. We then used the ligase-deubiquitinating enzyme (DUb) library to screen for E3 ligases involved in post-Golgi/endosomal trafficking. We identify ligases previously implicated in these pathways (Rsp5 and Tul1), in addition to ligases previously localized to endosomes (Pib1 and Vps8). We also document an optimized workflow for isolating and analyzing the "ubiquitome" of yeast, which can be used with mass spectrometry to identify substrates perturbed by expression of particular ligase-DUb fusions.
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Affiliation(s)
- Chris MacDonald
- Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa
| | | | - Robert M Pope
- Proteomics Facility, University of Iowa, Iowa City, Iowa
| | - Michael E Wright
- Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa
| | - Robert C Piper
- Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa
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Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem. Appl Environ Microbiol 2017; 83:AEM.03321-16. [PMID: 28258138 DOI: 10.1128/aem.03321-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/01/2017] [Indexed: 01/01/2023] Open
Abstract
A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.
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Li D, Han Q. Cloning and co-expression of recombinant N-demethylase B and N-demethylase D genes in Escherichia coli. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1295819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Dengchao Li
- Department of Bioengineering, School of Life Science, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, Jiangsu Province, P.R. China
| | - Qiumin Han
- School of Health, Jiangsu Food and Pharmaceutical Science College, Huai'an, Jiangsu Province, P.R. China
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Algharrawi KHR, Summers RM, Gopishetty S, Subramanian M. Direct conversion of theophylline to 3-methylxanthine by metabolically engineered E. coli. Microb Cell Fact 2015; 14:203. [PMID: 26691652 PMCID: PMC4687300 DOI: 10.1186/s12934-015-0395-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 12/10/2015] [Indexed: 12/03/2022] Open
Abstract
Background Methylxanthines are natural and synthetic compounds found in many foods, drinks, pharmaceuticals, and cosmetics. Aside from caffeine, production of many methylxanthines is currently performed by chemical synthesis. This process utilizes many chemicals, multiple reactions, and different reaction conditions, making it complicated, environmentally dissatisfactory, and expensive, especially for monomethylxanthines and paraxanthine. A microbial platform could provide an economical, environmentally friendly approach to produce these chemicals in large quantities. The recently discovered genes in our laboratory from Pseudomonasputida, ndmA, ndmB, and ndmD, provide an excellent starting point for precisely engineering Escherichia coli with various gene combinations to produce specific high-value paraxanthine and 1-, 3-, and 7-methylxanthines from any of the economical feedstocks including caffeine, theobromine or theophylline. Here, we show the first example of direct conversion of theophylline to 3-methylxanthine by a metabolically engineered strain of E. coli. Results Here we report the construction of E. coli strains with ndmA and ndmD, capable of producing 3-methylxanthine from exogenously fed theophylline. The strains were engineered with various dosages of the ndmA and ndmD genes, screened, and the best strain was selected for large-scale conversion of theophylline to 3-methylxanthine. Strain pDdA grown in super broth was the most efficient strain; 15 mg/mL cells produced 135 mg/L (0.81 mM) 3-methylxanthine from 1 mM theophylline. An additional 21.6 mg/L (0.13 mM) 1-methylxanthine were also produced, attributed to slight activity of NdmA at the N3-position of theophylline. The 1- and 3-methylxanthine products were separated by preparative chromatography with less than 5 % loss during purification and were identical to commercially available standards. Purity of the isolated 3-methylxanthine was comparable to a commercially available standard, with no contaminant peaks as observed by liquid chromatography-mass spectrophotometry or nuclear magnetic resonance. Conclusions We were able to biologically produce and separate 100 mg of highly pure 3-methylxanthine from theophylline (1,3-dimethylxanthine). The N-demethylation reaction was catalyzed by E. coli engineered with N-demethylase genes, ndmA and ndmD. This microbial conversion represents a first step to develop a new biological platform for the production of methylxanthines from economical feedstocks such as caffeine, theobromine, and theophylline. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0395-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Khalid H R Algharrawi
- Department of Chemical and Biochemical Engineering, The University of Iowa, Coralville, IA, 52241, USA. .,Department of Chemical Engineering, University of Baghdad, Baghdad, Iraq.
| | - Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - Sridhar Gopishetty
- Center for Biocatalysis and Bioprocessing, University of Iowa Research Park, The University of Iowa, 2501 Crosspark Road-Suite C100, Coralville, IA, 52241, USA.
| | - Mani Subramanian
- Department of Chemical and Biochemical Engineering, The University of Iowa, Coralville, IA, 52241, USA.
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Vilanova C, Iglesias A, Porcar M. The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach. Sci Rep 2015; 5:17163. [PMID: 26592442 PMCID: PMC4655483 DOI: 10.1038/srep17163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/16/2015] [Indexed: 12/31/2022] Open
Abstract
Microbial communities are ubiquitous in both natural and artificial environments. However, microbial diversity is usually reduced under strong selection pressures, such as those present in habitats rich in recalcitrant or toxic compounds displaying antimicrobial properties. Caffeine is a natural alkaloid present in coffee, tea and soft drinks with well-known antibacterial properties. Here we present the first systematic analysis of coffee machine-associated bacteria. We sampled the coffee waste reservoir of ten different Nespresso machines and conducted a dynamic monitoring of the colonization process in a new machine. Our results reveal the existence of a varied bacterial community in all the machines sampled, and a rapid colonisation process of the coffee leach. The community developed from a pioneering pool of enterobacteria and other opportunistic taxa to a mature but still highly variable microbiome rich in coffee-adapted bacteria. The bacterial communities described here, for the first time, are potential drivers of biotechnologically relevant processes including decaffeination and bioremediation.
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Affiliation(s)
- Cristina Vilanova
- Universitat de València (Cavanilles Institute of Biodiversity and Evolutionary Biology), 46020 Valencia, Spain
| | - Alba Iglesias
- Universitat de València (Cavanilles Institute of Biodiversity and Evolutionary Biology), 46020 Valencia, Spain
| | - Manuel Porcar
- Universitat de València (Cavanilles Institute of Biodiversity and Evolutionary Biology), 46020 Valencia, Spain.,Fundació General de la Universitat de València, Spain
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29
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RIP1 Cleavage in the Kinase Domain Regulates TRAIL-Induced NF-κB Activation and Lymphoma Survival. Mol Cell Biol 2015. [PMID: 26195820 DOI: 10.1128/mcb.00692-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although TRAIL is considered a potential anticancer agent, it enhances tumor progression by activating NF-κB in apoptosis-resistant cells. Cellular FLICE-like inhibitory protein (cFLIP) overexpression and caspase-8 activation have been implicated in TRAIL-induced NF-κB activation; however, the underlying mechanisms are unknown. Here, we report that caspase-8-dependent cleavage of RIP1 in the kinase domain (KD) and intermediate domain (ID) determines the activation state of the NF-κB pathway in response to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) treatment. In apoptosis-sensitive cells, caspase-8 cleaves RIP1 in the KD and ID immediately after the recruitment of RIP1 to the receptor complex, impairing IκB kinase (IKK) recruitment and NF-κB activation. In apoptosis-resistant cells, cFLIP restricts caspase-8 activity, resulting in limited RIP1 cleavage and generation of a KD-cleaved fragment capable of activating NF-κB but not apoptosis. Notably, depletion of the cytoplasmic pool of TRAF2 and cIAP1 in lymphomas by CD40 ligation inhibits basal RIP1 ubiquitination but does not prompt cell death, due to CD40L-induced cFLIP expression and limited RIP1 cleavage. Inhibition of RIP1 cleavage at the KD suppresses NF-κB activation and cell survival even in cFLIP-overexpressing lymphomas. Importantly, RIP1 is constitutively cleaved in human and mouse lymphomas, suggesting that cFLIP-mediated and caspase-8-dependent limited cleavage of RIP1 is a new layer of mechanism that promotes NF-κB activation and lymphoma survival.
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30
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Summers RM, Mohanty SK, Gopishetty S, Subramanian M. Genetic characterization of caffeine degradation by bacteria and its potential applications. Microb Biotechnol 2015; 8:369-78. [PMID: 25678373 PMCID: PMC4408171 DOI: 10.1111/1751-7915.12262] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/10/2014] [Accepted: 12/26/2014] [Indexed: 12/24/2022] Open
Abstract
The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N-demethylation and C-8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N-demethylation and C-8 oxidation. All of the genes for the N-demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2-kb genomic DNA fragment found in Pseudomonas putida CBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C-8 oxidation of caffeine have been located on a 25.2-kb genomic DNA fragment of Pseudomonas sp. CBB1. The C-8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio-decaffeination, remediation of caffeine-contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated.
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Affiliation(s)
- Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA
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31
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Halden RU, Hartmann EM, Denslow ND, Haynes PA, LaBaer J. Recent advances in proteomics applied to elucidate the role of environmental impacts on human health and organismal function. J Proteome Res 2015; 14:1-4. [PMID: 25751307 DOI: 10.1021/pr501224f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Rolf U Halden
- Center for Environmental Security, Biodesign Institute, Arizona State University , 781 East Terrace Mall, Tempe, Arizona 85287, United States
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