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Madi N, Cato ET, Abu Sayeed M, Creasy-Marrazzo A, Cuénod A, Islam K, Khabir MIU, Bhuiyan MTR, Begum YA, Freeman E, Vustepalli A, Brinkley L, Kamat M, Bailey LS, Basso KB, Qadri F, Khan AI, Shapiro BJ, Nelson EJ. Phage predation, disease severity, and pathogen genetic diversity in cholera patients. Science 2024; 384:eadj3166. [PMID: 38669570 DOI: 10.1126/science.adj3166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/12/2024] [Indexed: 04/28/2024]
Abstract
Despite an increasingly detailed picture of the molecular mechanisms of bacteriophage (phage)-bacterial interactions, we lack an understanding of how these interactions evolve and impact disease within patients. In this work, we report a year-long, nationwide study of diarrheal disease patients in Bangladesh. Among cholera patients, we quantified Vibrio cholerae (prey) and its virulent phages (predators) using metagenomics and quantitative polymerase chain reaction while accounting for antibiotic exposure using quantitative mass spectrometry. Virulent phage (ICP1) and antibiotics suppressed V. cholerae to varying degrees and were inversely associated with severe dehydration depending on resistance mechanisms. In the absence of antiphage defenses, predation was "effective," with a high predator:prey ratio that correlated with increased genetic diversity among the prey. In the presence of antiphage defenses, predation was "ineffective," with a lower predator:prey ratio that correlated with increased genetic diversity among the predators. Phage-bacteria coevolution within patients should therefore be considered in the deployment of phage-based therapies and diagnostics.
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Affiliation(s)
- Naïma Madi
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Emilee T Cato
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Md Abu Sayeed
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Ashton Creasy-Marrazzo
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Aline Cuénod
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Kamrul Islam
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Imam Ul Khabir
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Taufiqur R Bhuiyan
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Yasmin A Begum
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Emma Freeman
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Anirudh Vustepalli
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Lindsey Brinkley
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Manasi Kamat
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Firdausi Qadri
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful I Khan
- Infectious Diseases Division (IDD) & Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - B Jesse Shapiro
- Department of Microbiology & Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- McGill Centre for Microbiome Research, McGill University, Montréal, QC, Canada
| | - Eric J Nelson
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, FL, USA
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Madi N, Cato ET, Sayeed MA, Creasy-Marrazzo A, Cuénod A, Islam K, Khabir MIU, Bhuiyan MTR, Begum YA, Freeman E, Vustepalli A, Brinkley L, Kamat M, Bailey LS, Basso KB, Qadri F, Khan AI, Shapiro BJ, Nelson EJ. Phage predation, disease severity and pathogen genetic diversity in cholera patients. bioRxiv 2024:2023.06.14.544933. [PMID: 37398242 PMCID: PMC10312676 DOI: 10.1101/2023.06.14.544933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Despite an increasingly detailed picture of the molecular mechanisms of phage-bacterial interactions, we lack an understanding of how these interactions evolve and impact disease within patients. Here we report a year-long, nation-wide study of diarrheal disease patients in Bangladesh. Among cholera patients, we quantified Vibrio cholerae (prey) and its virulent phages (predators) using metagenomics and quantitative PCR, while accounting for antibiotic exposure using quantitative mass spectrometry. Virulent phage (ICP1) and antibiotics suppressed V. cholerae to varying degrees and were inversely associated with severe dehydration depending on resistance mechanisms. In the absence of anti-phage defenses, predation was 'effective,' with a high predator:prey ratio that correlated with increased genetic diversity among the prey. In the presence of anti-phage defenses, predation was 'ineffective,' with a lower predator:prey ratio that correlated with increased genetic diversity among the predators. Phage-bacteria coevolution within patients should therefore be considered in the deployment of phage-based therapies and diagnostics. One Sentence Summary A survey of cholera patients in Bangladesh identifies phage predation as a biomarker of disease severity and driver of coevolution within patients.
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Kundu S, Jaiswal M, Babu Mullapudi V, Guo J, Kamat M, Basso KB, Guo Z. Investigation of Glycosylphosphatidylinositol (GPI)-Plasma Membrane Interaction in Live Cells and the Influence of GPI Glycan Structure on the Interaction. Chemistry 2024; 30:e202303047. [PMID: 37966101 PMCID: PMC10922586 DOI: 10.1002/chem.202303047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/05/2023] [Accepted: 11/15/2023] [Indexed: 11/16/2023]
Abstract
Glycosylphosphatidylinositols (GPIs) need to interact with other components in the cell membrane to transduce transmembrane signals. A bifunctional GPI probe was employed for photoaffinity-based proximity labelling and identification of GPI-interacting proteins in the cell membrane. This probe contained the entire core structure of GPIs and was functionalized with photoreactive diazirine and clickable alkyne to facilitate its crosslinking with proteins and attachment of an affinity tag. It was disclosed that this probe was more selective than our previously reported probe containing only a part structure of the GPI core for cell membrane incorporation and an improved probe for studying GPI-cell membrane interaction. Eighty-eight unique membrane proteins, many of which are related to GPIs/GPI-anchored proteins, were identified utilizing this probe. The proteomics dataset is a valuable resource for further analyses and data mining to find new GPI-related proteins and signalling pathways. A comparison of these results with those of our previous probe provided direct evidence for the profound impact of GPI glycan structure on its interaction with the cell membrane.
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Affiliation(s)
- Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Mohit Jaiswal
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | | | - Jiatong Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Manasi Kamat
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- UF Health Cancer Centre, University of Florida, Gainesville, FL 32611, USA
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Bhar S, Yoon CS, Mai K, Han J, Prajapati DV, Wang Y, Steffen CL, Bailey LS, Basso KB, Butcher RA. An acyl-CoA thioesterase is essential for the biosynthesis of a key dauer pheromone in C. elegans. Cell Chem Biol 2024:S2451-9456(23)00437-3. [PMID: 38183989 DOI: 10.1016/j.chembiol.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/02/2023] [Accepted: 12/10/2023] [Indexed: 01/08/2024]
Abstract
Methyl ketone (MK)-ascarosides represent essential components of several pheromones in Caenorhabditis elegans, including the dauer pheromone, which triggers the stress-resistant dauer larval stage, and the male-attracting sex pheromone. Here, we identify an acyl-CoA thioesterase, ACOT-15, that is required for the biosynthesis of MK-ascarosides. We propose a model in which ACOT-15 hydrolyzes the β-keto acyl-CoA side chain of an ascaroside intermediate during β-oxidation, leading to decarboxylation and formation of the MK. Using comparative metabolomics, we identify additional ACOT-15-dependent metabolites, including an unusual piperidyl-modified ascaroside, reminiscent of the alkaloid pelletierine. The β-keto acid generated by ACOT-15 likely couples to 1-piperideine to produce the piperidyl ascaroside, which is much less dauer-inducing than the dauer pheromone, asc-C6-MK (ascr#2, 1). The bacterial food provided influences production of the piperidyl ascaroside by the worm. Our work shows how the biosynthesis of MK- and piperidyl ascarosides intersect and how bacterial food may impact chemical signaling in the worm.
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Affiliation(s)
- Subhradeep Bhar
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Chi-Su Yoon
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Kevin Mai
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Jungsoo Han
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Dilip V Prajapati
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Yuting Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Candy L Steffen
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
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Dill MN, Tabatabaei M, Kamat M, Basso KB, Moore E, Simmons CS. Generation and characterization of two immortalized dermal fibroblast cell lines from the spiny mouse (Acomys). PLoS One 2023; 18:e0280169. [PMID: 37418364 PMCID: PMC10328323 DOI: 10.1371/journal.pone.0280169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/14/2023] [Indexed: 07/09/2023] Open
Abstract
The spiny mouse (Acomys) is gaining popularity as a research organism due to its phenomenal regenerative capabilities. Acomys recovers from injuries to several organs without fibrosis. For example, Acomys heals full thickness skin injuries with rapid re-epithelialization of the wound and regeneration of hair follicles, sebaceous glands, erector pili muscles, adipocytes, and dermis without scarring. Understanding mechanisms of Acomys regeneration may uncover potential therapeutics for wound healing in humans. However, access to Acomys colonies is limited and primary fibroblasts can only be maintained in culture for a limited time. To address these obstacles, we generated immortalized Acomys dermal fibroblast cell lines using two methods: transfection with the SV40 large T antigen and spontaneous immortalization. The two cell lines (AcoSV40 and AcoSI-1) maintained the morphological and functional characteristics of primary Acomys fibroblasts, including maintenance of key fibroblast markers and ECM deposition. The availability of these cells will lower the barrier to working with Acomys as a model research organism, increasing the pace at which new discoveries to promote regeneration in humans can be made.
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Affiliation(s)
- Michele N. Dill
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Mohammad Tabatabaei
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Manasi Kamat
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Erika Moore
- Department of Materials Science and Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Chelsey S. Simmons
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, United States of America
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, Florida, United States of America
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Pei J, Xiao Y, Liu X, Hu W, Sobh A, Yuan Y, Zhou S, Hua N, Mackintosh SG, Zhang X, Basso KB, Kamat M, Yang Q, Licht JD, Zheng G, Zhou D, Lv D. Piperlongumine conjugates induce targeted protein degradation. Cell Chem Biol 2023; 30:203-213.e17. [PMID: 36750097 PMCID: PMC10074544 DOI: 10.1016/j.chembiol.2023.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 02/09/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. In this study, we identified piperlongumine (PL), a natural product, as a covalent E3 ligase recruiter, which induces CDK9 degradation when it is conjugated with SNS-032, a CDK9 inhibitor. The lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome-dependent manner and is much more potent than SNS-032 against various tumor cells in vitro. Mechanistically, we identified KEAP1 as the E3 ligase recruited by 955 to degrade CDK9 through a TurboID-based proteomics study, which was further confirmed by KEAP1 knockout and the nanoBRET ternary complex formation assay. In addition, PL-ceritinib conjugate can degrade EML4-ALK fusion oncoprotein, suggesting that PL may have a broader application as a covalent E3 ligase ligand in targeted protein degradation.
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Affiliation(s)
- Jing Pei
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Xingui Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Wanyi Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, 2033 Mowry Road, Suite 145, Gainesville, FL 32610, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Shuo Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Nan Hua
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 803, Little Rock, AR 72205, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Manasi Kamat
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Qingping Yang
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, 2033 Mowry Road, Suite 145, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA.
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA; Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA; Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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Walker MK, Bailey LS, Basso KB, Redfern RR. Nonpolar Lipids Contribute to Midday Fogging During Scleral Lens Wear. Invest Ophthalmol Vis Sci 2023; 64:7. [PMID: 36630141 PMCID: PMC9840443 DOI: 10.1167/iovs.64.1.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Purpose To determine correlations between lipids in the fluid reservoir (FR) and the severity of midday fogging (MDF) in scleral lens (SL) wear. Methods SL neophytes were recruited to wear custom SL for 4 days, examined after 8 hours on days 1 and 4. Lens vault and MDF were quantified from anterior segment optical coherence tomography (AS-OCT), and the FR was collected and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Relative abundance of lipids was compared to MDF scores using nonparametric correlation testing (Spearman rank). Ocular surface and SL fitting characteristics (lens vault, fitting curves) were likewise compared to MDF. Results Thirteen participants (26 eyes, 69% female, 28 ± 9 years old) were included in this study. MDF severity after 8 hours of SL wear was 33 ± 29 units on day 1 and 28 ± 24 units on day 4 (r = .94; P < 0.01). Twelve samples were analyzed using LC-MS/MS, and a total of 170 distinct lipid species were detected. The lipid classes with greatest correlation to MDF were the wax esters (r = .73, P = 0.01), cholesteryl esters (r = .59; P = 0.049), and triacylglycerols (r = .64, P = 0.03). Polar lipids were observed abundantly in all samples. None of the measured ocular surface or fitting outcomes were correlated to MDF. Conclusions Nonpolar lipids were the greatest contributors to MDF among these normal participants. Polar lipids may be due to cellular debris, although they do not appear contributory to MDF.
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Affiliation(s)
- Maria K. Walker
- College of Optometry, The Ocular Surface Institute, University of Houston, Houston, Texas, United States
| | - Laura S. Bailey
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Rachel R. Redfern
- College of Optometry, The Ocular Surface Institute, University of Houston, Houston, Texas, United States
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Pastore AJ, Montoya A, Kamat M, Basso KB, Italia JS, Chatterjee A, Drosou M, Pantazis DA, Angerhofer A. Selective incorporation of 5-hydroxytryptophan blocks long range electron transfer in oxalate decarboxylase. Protein Sci 2023; 32:e4537. [PMID: 36482787 PMCID: PMC9801070 DOI: 10.1002/pro.4537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Oxalate decarboxylase from Bacillus subtilis is a binuclear Mn-dependent acid stress response enzyme that converts the mono-anion of oxalic acid into formate and carbon dioxide in a redox neutral unimolecular disproportionation reaction. A π-stacked tryptophan dimer, W96 and W274, at the interface between two monomer subunits facilitates long-range electron transfer between the two Mn ions and plays an important role in the catalytic mechanism. Substitution of W96 with the unnatural amino acid 5-hydroxytryptophan leads to a persistent EPR signal which can be traced back to the neutral radical of 5-hydroxytryptophan with its hydroxyl proton removed. 5-Hydroxytryptophan acts as a hole sink preventing the formation of Mn(III) at the N-terminal active site and strongly suppresses enzymatic activity. The lower boundary of the standard reduction potential for the active site Mn(II)/Mn(III) couple can therefore be estimated as 740 mV against the normal hydrogen electrode at pH 4, the pH of maximum catalytic efficiency. Our results support the catalytic importance of long-range electron transfer in oxalate decarboxylase while at the same time highlighting the utility of unnatural amino acid incorporation and specifically the use of 5-hydroxytryptophan as an energetic sink for hole hopping to probe electron transfer in redox proteins.
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Affiliation(s)
| | - Alvaro Montoya
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Manasi Kamat
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Kari B. Basso
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - James S. Italia
- Department of ChemistryBoston CollegeChestnut HillMassachusettsUSA
| | | | - Maria Drosou
- Max‐Planck‐Institut für KohlenforschungMülheim an der RuhrGermany
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Bailey LS, Prajapati DV, Basso KB. Optimization of the Sulfo-Phospho-Vanillin Assay for Total Lipid Normalization in Untargeted Quantitative Lipidomic LC-MS/MS Applications. Anal Chem 2022; 94:17810-17818. [PMID: 36520113 DOI: 10.1021/acs.analchem.2c03488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Liquid chromatography (LC)-mass spectrometry (MS)/MS lipidomic normalization is generally performed by equalizing pre-extraction sample materials or via DNA or protein pre-quantitation methods, which have known measurement inaccuracies. We propose the use of the sulfo-phospho-vanillin assay (SPVA), a total lipid colorimetric analysis, as a pre-quantitation method to normalize lipids in lipidomic LC-MS/MS applications. The assay has been applied to a 300 μL well volume in a 96-well plate and tested using Avanti total lipid standards of porcine brain and E. coli. Assay parameters for lipid sample volume, sulfuric acid, vanillin/phosphoric acid, post-reaction incubation time, and wavelength are optimized for robust application to biologically sourced lipid samples. Standard test samples were prepared using three concentrations covering approximately 100 μg/mL range. The optimized assay yielded test sample errors less than 10%, indicating a precise and accurate assay performance. The test samples were then analyzed by LC-MS/MS and normalized using SPVA pre-quantitation and pseudo-mass normalization. The detected lipids showed smaller standard deviations and greater relative concentration differences compared to the pseudo-mass normalized lipids, showing promise as a normalization method.
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Affiliation(s)
- Laura S Bailey
- Mass Spectrometry Research and Education Center, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Dilip V Prajapati
- Mass Spectrometry Research and Education Center, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Kari B Basso
- Mass Spectrometry Research and Education Center, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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Creasy-Marrazzo A, Saber MM, Kamat M, Bailey LS, Brinkley L, Cato E, Begum Y, Rashid MM, Khan AI, Qadri F, Basso KB, Shapiro BJ, Nelson EJ. Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions. Microb Genom 2022; 8:mgen000905. [PMID: 36748512 PMCID: PMC9837564 DOI: 10.1099/mgen.0.000905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
The antibiotic formulary is threatened by high rates of antimicrobial resistance (AMR) among enteropathogens. Enteric bacteria are exposed to anaerobic conditions within the gastrointestinal tract, yet little is known about how oxygen exposure influences AMR. The facultative anaerobe Vibrio cholerae was chosen as a model to address this knowledge gap. We obtained V. cholerae isolates from 66 cholera patients, sequenced their genomes, and grew them under anaerobic and aerobic conditions with and without three clinically relevant antibiotics (ciprofloxacin, azithromycin, doxycycline). For ciprofloxacin and azithromycin, the minimum inhibitory concentration (MIC) increased under anaerobic conditions compared to aerobic conditions. Using standard resistance breakpoints, the odds of classifying isolates as resistant increased over 10 times for ciprofloxacin and 100 times for azithromycin under anaerobic conditions compared to aerobic conditions. For doxycycline, nearly all isolates were sensitive under both conditions. Using genome-wide association studies, we found associations between genetic elements and AMR phenotypes that varied by oxygen exposure and antibiotic concentrations. These AMR phenotypes were more heritable, and the AMR-associated genetic elements were more often discovered, under anaerobic conditions. These AMR-associated genetic elements are promising targets for future mechanistic research. Our findings provide a rationale to determine whether increased MICs under anaerobic conditions are associated with therapeutic failures and/or microbial escape in cholera patients. If so, there may be a need to determine new AMR breakpoints for anaerobic conditions.
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Affiliation(s)
- Ashton Creasy-Marrazzo
- Departments of Pediatrics, University of Florida, Gainesville, FL, USA,Department of Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Morteza M. Saber
- Department of Microbiology and Immunology, McGill University, Gainesville, FL, USA
| | - Manasi Kamat
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Laura S. Bailey
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Lindsey Brinkley
- Departments of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Emilee Cato
- Departments of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Yasmin Begum
- Infectious Diseases Division (IDD) and Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Md. Mahbubur Rashid
- Infectious Diseases Division (IDD) and Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Ashraful I. Khan
- Infectious Diseases Division (IDD) and Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division (IDD) and Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Gainesville, FL, USA,*Correspondence: B. Jesse Shapiro,
| | - Eric J. Nelson
- Departments of Pediatrics, University of Florida, Gainesville, FL, USA,*Correspondence: Eric J. Nelson,
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11
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Huang F, Bailey LS, Gao T, Jiang W, Yu L, Bennett DA, Zhao J, Basso KB, Guo Z. Analysis and Comparison of Mouse and Human Brain Gangliosides via Two-Stage Matching of MS/MS Spectra. ACS Omega 2022; 7:6403-6411. [PMID: 35224401 PMCID: PMC8867566 DOI: 10.1021/acsomega.1c07070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/28/2022] [Indexed: 05/13/2023]
Abstract
Glycosphingolipids (GSLs), including gangliosides, are essential components of the cell membrane. Because of their vital biological functions, a facile method for the analysis and comparison of GSLs in biological issues is desired. To this end, a new method for GSL analysis was developed based on two-stage matching of the carbohydrate and glycolipid product ions of experimental and reference MS/MS spectra of GSLs. The applicability of this method to the analysis of gangliosides in biological tissues was verified using human plasma and mouse brains spiked with standards. The method was then used to characterize endogenous gangliosides in mouse and human brains. It was shown that each endogenous ganglioside species had varied lipid forms and that mouse and human brains had different compositions of ganglioside species and lipid forms. Moreover, a 36-carbon ceramide is found to represent the major lipid form for mouse brain gangliosides, while the major lipid form for most human brain gangliosides is a 38-carbon ceramide. This study has verified that the two-stage MS/MS spectral matching method could be used to study gangliosides or GSLs and their lipid forms in complex biological samples, thereby having a broad application.
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Affiliation(s)
- Fanran Huang
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Laura S. Bailey
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Tianqi Gao
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Wenjie Jiang
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Lei Yu
- Rush
Alzheimer’s Disease Center, Rush
University Medical Center, Chicago, Illinois 60612, United States
| | - David A. Bennett
- Rush
Alzheimer’s Disease Center, Rush
University Medical Center, Chicago, Illinois 60612, United States
| | - Jinying Zhao
- Department
of Epidemiology, University of Florida, Gainesville, Florida 32611, United States
| | - Kari B. Basso
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Zhongwu Guo
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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12
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Li J, Zhao X, Bailey LS, Kamat MN, Basso KB. Identification and characterization of proteins, lipids, and metabolites in two organic fertilizer products derived from different nutrient sources. Appl Biol Chem 2021; 64:72. [PMID: 34722955 PMCID: PMC8550213 DOI: 10.1186/s13765-021-00625-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED The biochemical composition of organic fertilizers largely determines their nutrient supply characteristics following soil application as well as their potential impact on soil microbial communities. Yet, limited information is available regarding the biochemical composition of organic fertilizers derived from different nutrient sources. Here, we qualitatively analyzed the presence and abundance of proteins, lipids, and metabolites in a liquid fish fertilizer (LFF) product and a type of granular organic fertilizer (GOF) commonly used in organic vegetable production, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our results suggest that the presence and abundance of proteins, lipids, and metabolites differ greatly between GOF and LFF. The qualitative analysis shows LFF as a rich source of metabolites, while complex proteins and long-chain saturated fatty acids are dominant in GOF. The degree of biochemical composition complexity may help explain the varying impacts of different types of organic fertilizers on nutrient availability, soil health, and environmental quality. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s13765-021-00625-2.
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Affiliation(s)
- Jianyu Li
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611-0690 USA
| | - Xin Zhao
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611-0690 USA
| | - Laura S. Bailey
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200 USA
| | - Manasi N. Kamat
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200 USA
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200 USA
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13
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Olson RA, Levi JS, Scheutz GM, Lessard JJ, Figg CA, Kamat MN, Basso KB, Sumerlin BS. Macromolecular Photocatalyst for Synthesis and Purification of Protein–Polymer Conjugates. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rebecca A. Olson
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Jordan S. Levi
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Georg M. Scheutz
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Jacob J. Lessard
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - C. Adrian Figg
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Manasi N. Kamat
- Mass Spectrometry Research and Education Center, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Kari B. Basso
- Mass Spectrometry Research and Education Center, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Brent S. Sumerlin
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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14
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Lang Y, Shah NR, Tao X, Reeve SM, Zhou J, Moya B, Sayed ARM, Dharuman S, Oyer JL, Copik AJ, Fleischer BA, Shin E, Werkman C, Basso KB, Lucas DD, Sutaria DS, Mégroz M, Kim TH, Loudon-Hossler V, Wright A, Jimenez-Nieves RH, Wallace MJ, Cadet KC, Jiao Y, Boyce JD, LoVullo ED, Schweizer HP, Bonomo RA, Bharatham N, Tsuji BT, Landersdorfer CB, Norris MH, Shin BS, Louie A, Balasubramanian V, Lee RE, Drusano GL, Bulitta JB. Combating Multidrug-Resistant Bacteria by Integrating a Novel Target Site Penetration and Receptor Binding Assay Platform Into Translational Modeling. Clin Pharmacol Ther 2021; 109:1000-1020. [PMID: 33576025 PMCID: PMC10662281 DOI: 10.1002/cpt.2205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/26/2022]
Abstract
Multidrug-resistant bacteria are causing a serious global health crisis. A dramatic decline in antibiotic discovery and development investment by pharmaceutical industry over the last decades has slowed the adoption of new technologies. It is imperative that we create new mechanistic insights based on latest technologies, and use translational strategies to optimize patient therapy. Although drug development has relied on minimal inhibitory concentration testing and established in vitro and mouse infection models, the limited understanding of outer membrane permeability in Gram-negative bacteria presents major challenges. Our team has developed a platform using the latest technologies to characterize target site penetration and receptor binding in intact bacteria that inform translational modeling and guide new discovery. Enhanced assays can quantify the outer membrane permeability of β-lactam antibiotics and β-lactamase inhibitors using multiplex liquid chromatography tandem mass spectrometry. While β-lactam antibiotics are known to bind to multiple different penicillin-binding proteins (PBPs), their binding profiles are almost always studied in lysed bacteria. Novel assays for PBP binding in the periplasm of intact bacteria were developed and proteins identified via proteomics. To characterize bacterial morphology changes in response to PBP binding, high-throughput flow cytometry and time-lapse confocal microscopy with fluorescent probes provide unprecedented mechanistic insights. Moreover, novel assays to quantify cytosolic receptor binding and intracellular drug concentrations inform target site occupancy. These mechanistic data are integrated by quantitative and systems pharmacology modeling to maximize bacterial killing and minimize resistance in in vitro and mouse infection models. This translational approach holds promise to identify antibiotic combination dosing strategies for patients with serious infections.
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Affiliation(s)
- Yinzhi Lang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Nirav R. Shah
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Jansen R&D, Johnson & Johnson, Spring House, Pennsylvania, USA
| | - Xun Tao
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Genentech USA,Inc., South San Francisco, California, USA
| | - Stephanie M. Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jieqiang Zhou
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Bartolome Moya
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Alaa R. M. Sayed
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Department of Chemistry, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jeremiah L. Oyer
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Alicja J. Copik
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Brett A. Fleischer
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Eunjeong Shin
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Carolin Werkman
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Deanna Deveson Lucas
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Dhruvitkumar S. Sutaria
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Genentech USA,Inc., South San Francisco, California, USA
| | - Marianne Mégroz
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Tae Hwan Kim
- College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk, Korea
| | - Victoria Loudon-Hossler
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Amy Wright
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Rossie H. Jimenez-Nieves
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Keisha C. Cadet
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Yuanyuan Jiao
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - John D. Boyce
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Eric D. LoVullo
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P. Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Robert A. Bonomo
- Research Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Nagakumar Bharatham
- BUGWORKS Research India Pvt. Ltd., Centre for Cellular & Molecular Platforms, National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Brian T. Tsuji
- Laboratory for Antimicrobial Pharmacodynamics, University at Buffalo, Buffalo, New York, USA
| | - Cornelia B. Landersdorfer
- Drug Delivery, Disposition, and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael H. Norris
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Beom Soo Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Arnold Louie
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - Venkataraman Balasubramanian
- BUGWORKS Research India Pvt. Ltd., Centre for Cellular & Molecular Platforms, National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - George L. Drusano
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - Jürgen B. Bulitta
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
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15
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Bailey LS, Huang F, Gao T, Zhao J, Basso KB, Guo Z. Characterization of Glycosphingolipids and Their Diverse Lipid Forms through Two-Stage Matching of LC-MS/MS Spectra. Anal Chem 2021; 93:3154-3162. [PMID: 33534538 DOI: 10.1021/acs.analchem.0c04542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosphingolipids (GSLs) play a key role in various biological and pathological events. Thus, determination of the complete GSL compositions in human tissues is essential for comparative and functional studies of GSLs. In this work, a new strategy was developed for GSL characterization and glycolipidomics analysis based on two-stage matching of experimental and reference MS/MS spectra. In the first stage, carbohydrate fragments, which contain only glycans and thus are conserved within a GSL species, are directly matched to yield a species identification. In the second stage, glycolipid fragments from the matched GSL species, which contain both the lipid and glycans and thus shift due to lipid structural changes, are treated according to lipid rule-based matching to characterize the lipid compositions. This new strategy uses the whole spectrum for GSL characterization. Furthermore, simple databases containing only a single lipid form per GSL species can be utilized to identify multiple GSL lipid forms. It is expected that this method will help accelerate glycolipidomics analysis and disclose new and diverse lipid forms of GSLs.
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16
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Morales-Aparicio JC, Lara Vasquez P, Mishra S, Barrán-Berdón AL, Kamat M, Basso KB, Wen ZT, Brady LJ. The Impacts of Sortase A and the 4'-Phosphopantetheinyl Transferase Homolog Sfp on Streptococcus mutans Extracellular Membrane Vesicle Biogenesis. Front Microbiol 2020; 11:570219. [PMID: 33193163 PMCID: PMC7649765 DOI: 10.3389/fmicb.2020.570219] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Extracellular membrane vesicles (EMVs) are produced by many Gram-positive organisms, but information regarding vesiculogenesis is incomplete. We used single gene deletions to evaluate the impacts on Streptococcus mutans EMV biogenesis of Sortase A (SrtA), which affects S. mutans EMV composition, and Sfp, a 4'-phosphopantetheinyl transferase that affects Bacillus subtilis EMV stability. ΔsrtA EMVs were notably larger than Δsfp and wild-type (WT) EMVs. EMV proteins identified from all three strains are known to be involved in cell wall biogenesis and cell architecture, bacterial adhesion, biofilm cell density and matrix development, and microbial competition. Notably, the AtlA autolysin was not processed to its mature active form in the ΔsrtA mutant. Proteomic and lipidomic analyses of all three strains revealed multiple dissimilarities between vesicular and corresponding cytoplasmic membranes (CMs). A higher proportion of EMV proteins are predicted substrates of the general secretion pathway (GSP). Accordingly, the GSP component SecA was identified as a prominent EMV-associated protein. In contrast, CMs contained more multi-pass transmembrane (TM) protein substrates of co-translational transport machineries than EMVs. EMVs from the WT, but not the mutant strains, were enriched in cardiolipin compared to CMs, and all EMVs were over-represented in polyketide flavonoids. EMVs and CMs were rich in long-chain saturated, monounsaturated, and polyunsaturated fatty acids, except for Δsfp EMVs that contained exclusively polyunsaturated fatty acids. Lipoproteins were less prevalent in EMVs of all three strains compared to their CMs. This study provides insight into biophysical characteristics of S. mutans EMVs and indicates discrete partitioning of protein and lipid components between EMVs and corresponding CMs of WT, ΔsrtA, and Δsfp strains.
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Affiliation(s)
| | | | - Surabhi Mishra
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Ana L. Barrán-Berdón
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Manasi Kamat
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Zezhang T. Wen
- Department of Oral and Craniofacial Biology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, United States
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
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17
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Faghih N, Bhar S, Zhou Y, Dar AR, Mai K, Bailey LS, Basso KB, Butcher RA. A Large Family of Enzymes Responsible for the Modular Architecture of Nematode Pheromones. J Am Chem Soc 2020; 142:13645-13650. [PMID: 32702987 DOI: 10.1021/jacs.0c04223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nematode Caenorhabditis elegans produces a broad family of pheromones, known as the ascarosides, that are modified with a variety of groups derived from primary metabolism. These modifications are essential for the diverse activities of the ascarosides in development and various behaviors, including attraction, aggregation, avoidance, and foraging. The mechanism by which these different groups are added to the ascarosides is poorly understood. Here, we identify a family of over 30 enzymes, which are homologous to mammalian carboxylesterase (CES) enzymes, and show that a number of these enzymes are responsible for the selective addition of specific modifications to the ascarosides. Through stable isotope feeding experiments, we demonstrate the in vivo activity of the CES-like enzymes and provide direct evidence that the acyl-CoA synthetase ACS-7, which was previously implicated in the attachment of certain modifications to the ascarosides in C. elegans, instead activates the side chains of certain ascarosides for shortening through β-oxidation. Our data provide a key to the combinatorial logic that gives rise to different modified ascarosides, which should greatly facilitate the exploration of the specific biological functions of these pheromones in the worm.
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Affiliation(s)
- Nasser Faghih
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Subhradeep Bhar
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Yue Zhou
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Abdul Rouf Dar
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Kevin Mai
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
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18
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Kim TH, Tao X, Moya B, Jiao Y, Basso KB, Zhou J, Lang Y, Sutaria DS, Zavascki AP, Barth AL, Reeve SM, Schweizer HP, Deveson Lucas D, Boyce JD, Bonomo RA, Lee RE, Shin BS, Louie A, Drusano GL, Bulitta JB. Novel Cassette Assay To Quantify the Outer Membrane Permeability of Five β-Lactams Simultaneously in Carbapenem-Resistant Klebsiella pneumoniae and Enterobacter cloacae. mBio 2020; 11:e03189-19. [PMID: 32047131 PMCID: PMC7018653 DOI: 10.1128/mbio.03189-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 02/05/2023] Open
Abstract
Poor penetration through the outer membrane (OM) of Gram-negative bacteria is a major barrier of antibiotic development. While β-lactam antibiotics are commonly used against Klebsiella pneumoniae and Enterobacter cloacae, there are limited data on OM permeability especially in K. pneumoniae Here, we developed a novel cassette assay, which can simultaneously quantify the OM permeability to five β-lactams in carbapenem-resistant K. pneumoniae and E. cloacae Both clinical isolates harbored a blaKPC-2 and several other β-lactamases. The OM permeability of each antibiotic was studied separately ("discrete assay") and simultaneously ("cassette assay") by determining the degradation of extracellular β-lactam concentrations via multiplex liquid chromatography-tandem mass spectrometry analyses. Our K. pneumoniae isolate was polymyxin resistant, whereas the E. cloacae was polymyxin susceptible. Imipenem penetrated the OM at least 7-fold faster than meropenem for both isolates. Imipenem penetrated E. cloacae at least 258-fold faster and K. pneumoniae 150-fold faster compared to aztreonam, cefepime, and ceftazidime. For our β-lactams, OM permeability was substantially higher in the E. cloacae compared to the K. pneumoniae isolate (except for aztreonam). This correlated with a higher OmpC porin production in E. cloacae, as determined by proteomics. The cassette and discrete assays showed comparable results, suggesting limited or no competition during influx through OM porins. This cassette assay allowed us, for the first time, to efficiently quantify the OM permeability of multiple β-lactams in carbapenem-resistant K. pneumoniae and E. cloacae Characterizing the OM permeability presents a critical contribution to combating the antimicrobial resistance crisis and enables us to rationally optimize the use of β-lactam antibiotics.IMPORTANCE Antimicrobial resistance is causing a global human health crisis and is affecting all antibiotic classes. While β-lactams have been commonly used against susceptible isolates of Klebsiella pneumoniae and Enterobacter cloacae, carbapenem-resistant isolates are spreading worldwide and pose substantial clinical challenges. Rapid penetration of β-lactams leads to high drug concentrations at their periplasmic target sites, allowing β-lactams to more completely inactivate their target receptors. Despite this, there are limited tangible data on the permeability of β-lactams through the outer membranes of many Gram-negative pathogens. This study presents a novel, cassette assay, which can simultaneously characterize the permeability of five β-lactams in multidrug-resistant clinical isolates. We show that carbapenems, and especially imipenem, penetrate the outer membrane of K. pneumoniae and E. cloacae substantially faster than noncarbapenem β-lactams. The ability to efficiently characterize the outer membrane permeability is critical to optimize the use of β-lactams and combat carbapenem-resistant isolates.
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Affiliation(s)
- Tae Hwan Kim
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Xun Tao
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Bartolome Moya
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Yuanyuan Jiao
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Jieqiang Zhou
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Yinzhi Lang
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Dhruvitkumar S Sutaria
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | | | - Afonso L Barth
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Stephanie M Reeve
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Deanna Deveson Lucas
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria, Australia
| | - John D Boyce
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria, Australia
| | - Robert A Bonomo
- Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Beom Soo Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, South Korea
| | - Arnold Louie
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - George L Drusano
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - Jürgen B Bulitta
- Departments of Pharmaceutics and Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
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Dastmalchi F, Karachi A, Allison JR, Basso KB, Mitchell D, Rahman M. IMMU-31. IN VIVO CELLULAR TRACKING WITH 13C LABELING OF ADOPTIVELY TRANSFERRED T CELLS FOR THE TREATMENT OF BRAIN TUMORS. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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