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Graboski AL, Kowalewski ME, Simpson JB, Cao X, Ha M, Zhang J, Walton WG, Flaherty DP, Redinbo MR. Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate. Cell Chem Biol 2023; 30:1402-1413.e7. [PMID: 37633277 DOI: 10.1016/j.chembiol.2023.07.015] [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: 05/02/2023] [Revised: 06/27/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
Indoxyl sulfate is a microbially derived uremic toxin that accumulates in late-stage chronic kidney disease and contributes to both renal and cardiovascular toxicity. Indoxyl sulfate is generated by the metabolism of indole, a compound created solely by gut microbial tryptophanases. Here, we characterize the landscape of tryptophanase enzymes in the human gut microbiome and find remarkable structural and functional similarities across diverse taxa. We leverage this homology through a medicinal chemistry campaign to create a potent pan-inhibitor, (3S) ALG-05, and validate its action as a transition-state analog. (3S) ALG-05 successfully reduces indole production in microbial culture and displays minimal toxicity against microbial and mammalian cells. Mice treated with (3S) ALG-05 show reduced cecal indole and serum indoxyl sulfate levels with minimal changes in other tryptophan-metabolizing pathways. These studies present a non-bactericidal pan-inhibitor of gut microbial tryptophanases with potential promise for reducing indoxyl sulfate in chronic kidney disease.
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Affiliation(s)
- Amanda L Graboski
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark E Kowalewski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua B Simpson
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xufeng Cao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Mary Ha
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jianan Zhang
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Matthew R Redinbo
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
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2
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Sarosh A, Kwong SM, Jensen SO, Northern F, Walton WG, Eakes TC, Redinbo MR, Firth N, McLaughlin KJ. pSK41/pGO1-family conjugative plasmids of Staphylococcus aureus encode a cryptic repressor of replication. Plasmid 2023; 128:102708. [PMID: 37967733 DOI: 10.1016/j.plasmid.2023.102708] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
The majority of large multiresistance plasmids of Staphylococcus aureus utilise a RepA_N-type replication initiation protein, the expression of which is regulated by a small antisense RNA (RNAI) that overlaps the rep mRNA leader. The pSK41/pGO1-family of conjugative plasmids additionally possess a small (86 codon) divergently transcribed ORF (orf86) located upstream of the rep locus. The product of pSK41 orf86 was predicted to have a helix-turn-helix motif suggestive of a likely function in transcriptional repression. In this study, we investigated the effect of Orf86 on transcription of thirteen pSK41 backbone promoters. We found that Orf86 only repressed transcription from the rep promoter, and hence now redesignate the product as Cop. Over-expression of Cop in trans reduced the copy number of pSK41 mini-replicons, both in the presence and absence of rnaI. in vitro protein-DNA binding experiments with purified 6 × His-Cop demonstrated specific DNA binding, adjacent to, and partially overlapping the -35 hexamer of the rep promoter. The crystal structure of Cop revealed a dimeric structure similar to other known transcriptional regulators. Cop mRNA was found to result from "read-through" transcription from the strong RNAI promoter that escapes the rnaI terminator. Thus, PrnaI is responsible for transcription of two distinct negative regulators of plasmid copy number; the antisense RNAI that primarily represses Rep translation, and Cop protein that can repress rep transcription. Deletion of cop in a native plasmid did not appear to impact copy number, indicating a cryptic auxiliary role.
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Affiliation(s)
- Alvina Sarosh
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales 2751, Australia; Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales 2170, Australia
| | - Faith Northern
- Chemistry Department, Vassar College, Poughkeepsie, NY 12604, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas C Eakes
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry, Microbiology and Genomics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
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3
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Lietzan AD, Simpson JB, Walton WG, Jariwala PB, Xu Y, Boynton MH, Liu J, Redinbo MR. Microbial β-glucuronidases drive human periodontal disease etiology. Sci Adv 2023; 9:eadg3390. [PMID: 37146137 PMCID: PMC10162664 DOI: 10.1126/sciadv.adg3390] [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] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Periodontitis is a chronic inflammatory disease associated with persistent oral microbial dysbiosis. The human β-glucuronidase (GUS) degrades constituents of the periodontium and is used as a biomarker for periodontitis severity. However, the human microbiome also encodes GUS enzymes, and the role of these factors in periodontal disease is poorly understood. Here, we define the 53 unique GUSs in the human oral microbiome and examine diverse GUS orthologs from periodontitis-associated pathogens. Oral bacterial GUS enzymes are more efficient polysaccharide degraders and processers of biomarker substrates than the human enzyme, particularly at pHs associated with disease progression. Using a microbial GUS-selective inhibitor, we show that GUS activity is reduced in clinical samples obtained from individuals with untreated periodontitis and that the degree of inhibition correlates with disease severity. Together, these results establish oral GUS activity as a biomarker that captures both host and microbial contributions to periodontitis, facilitating more efficient clinical monitoring and treatment paradigms for this common inflammatory disease.
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Affiliation(s)
- Adam D. Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G. Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Parth B. Jariwala
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yongmei Xu
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marcella H. Boynton
- Division of General Medicine and Clinical Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jian Liu
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrated Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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4
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Conway JM, Walton WG, Salas-González I, Law TF, Lindberg CA, Crook LE, Kosina SM, Fitzpatrick CR, Lietzan AD, Northen TR, Jones CD, Finkel OM, Redinbo MR, Dangl JL. Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome. Nat Microbiol 2022; 7:1817-1833. [PMID: 36266335 PMCID: PMC9613470 DOI: 10.1038/s41564-022-01244-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 09/26/2021] [Accepted: 09/02/2022] [Indexed: 11/13/2022]
Abstract
Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon's MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
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Affiliation(s)
- Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Theresa F Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chloe A Lindberg
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura E Crook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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5
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Jacob P, Kim NH, Wu F, El-Kasmi F, Chi Y, Walton WG, Furzer OJ, Lietzan AD, Sunil S, Kempthorn K, Redinbo MR, Pei ZM, Wan L, Dangl JL. Plant "helper" immune receptors are Ca 2+-permeable nonselective cation channels. Science 2021; 373:420-425. [PMID: 34140391 PMCID: PMC8939002 DOI: 10.1126/science.abg7917] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [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: 01/28/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022]
Abstract
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) regulate immunity and cell death. In Arabidopsis, a subfamily of "helper" NLRs is required by many "sensor" NLRs. Active NRG1.1 oligomerized, was enriched in plasma membrane puncta, and conferred cytoplasmic calcium ion (Ca2+) influx in plant and human cells. NRG1.1-dependent Ca2+ influx and cell death were sensitive to Ca2+ channel blockers and were suppressed by mutations affecting oligomerization or plasma membrane enrichment. Ca2+ influx and cell death mediated by NRG1.1 and ACTIVATED DISEASE RESISTANCE 1 (ADR1), another helper NLR, required conserved negatively charged N-terminal residues. Whole-cell voltage-clamp recordings demonstrated that Arabidopsis helper NLRs form Ca2+-permeable cation channels to directly regulate cytoplasmic Ca2+ levels and consequent cell death. Thus, helper NLRs transduce cell death signals directly.
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Affiliation(s)
- Pierre Jacob
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nak Hyun Kim
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feihua Wu
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Horticulture, Foshan University, Foshan, China
| | - Farid El-Kasmi
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Yuan Chi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oliver J Furzer
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sruthi Sunil
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Korina Kempthorn
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhen-Ming Pei
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | - Li Wan
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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6
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Ervin SM, Simpson JB, Gibbs ME, Creekmore BC, Lim L, Walton WG, Gharaibeh RZ, Redinbo MR. Structural Insights into Endobiotic Reactivation by Human Gut Microbiome-Encoded Sulfatases. Biochemistry 2020; 59:3939-3950. [PMID: 32993284 DOI: 10.1021/acs.biochem.0c00711] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Phase II drug metabolism inactivates xenobiotics and endobiotics through the addition of either a glucuronic acid or sulfate moiety prior to excretion, often via the gastrointestinal tract. While the human gut microbial β-glucuronidase enzymes that reactivate glucuronide conjugates in the intestines are becoming well characterized and even controlled by targeted inhibitors, the sulfatases encoded by the human gut microbiome have not been comprehensively examined. Gut microbial sulfatases are poised to reactivate xenobiotics and endobiotics, which are then capable of undergoing enterohepatic recirculation or exerting local effects on the gut epithelium. Here, using protein structure-guided methods, we identify 728 distinct microbiome-encoded sulfatase proteins from the 4.8 million unique proteins present in the Human Microbiome Project Stool Sample database and 1766 gut microbial sulfatases from the 9.9 million sequences in the Integrated Gene Catalogue. We purify a representative set of these sulfatases, elucidate crystal structures, and pinpoint unique structural motifs essential to endobiotic sulfate processing. Gut microbial sulfatases differentially process sulfated forms of the neurotransmitters serotonin and dopamine, and the hormones melatonin, estrone, dehydroepiandrosterone, and thyroxine in a manner dependent both on variabilities in active site architecture and on markedly distinct oligomeric states. Taken together, these data provide initial insights into the structural and functional diversity of gut microbial sulfatases, providing a path toward defining the roles these enzymes play in health and disease.
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Affiliation(s)
- Samantha M Ervin
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joshua B Simpson
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Morgan E Gibbs
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Benjamin C Creekmore
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lauren Lim
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G Walton
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida 32603, United States
| | - Matthew R Redinbo
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Integrated Program for Biological and Genome Sciences and Departments of Biochemistry and Microbiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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7
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Dvořák Z, Kopp F, Costello CM, Kemp JS, Li H, Vrzalová A, Štěpánková M, Bartoňková I, Jiskrová E, Poulíková K, Vyhlídalová B, Nordstroem LU, Karunaratne CV, Ranhotra HS, Mun KS, Naren AP, Murray IA, Perdew GH, Brtko J, Toporova L, Schön A, Wallace BD, Walton WG, Redinbo MR, Sun K, Beck A, Kortagere S, Neary MC, Chandran A, Vishveshwara S, Cavalluzzi MM, Lentini G, Cui JY, Gu H, March JC, Chatterjee S, Matson A, Wright D, Flannigan KL, Hirota SA, Sartor RB, Mani S. Targeting the pregnane X receptor using microbial metabolite mimicry. EMBO Mol Med 2020; 12:e11621. [PMID: 32153125 PMCID: PMC7136958 DOI: 10.15252/emmm.201911621] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 10/16/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/18/2022] Open
Abstract
The human PXR (pregnane X receptor), a master regulator of drug metabolism, has essential roles in intestinal homeostasis and abrogating inflammation. Existing PXR ligands have substantial off-target toxicity. Based on prior work that established microbial (indole) metabolites as PXR ligands, we proposed microbial metabolite mimicry as a novel strategy for drug discovery that allows exploiting previously unexplored parts of chemical space. Here, we report functionalized indole derivatives as first-in-class non-cytotoxic PXR agonists as a proof of concept for microbial metabolite mimicry. The lead compound, FKK6 (Felix Kopp Kortagere 6), binds directly to PXR protein in solution, induces PXR-specific target gene expression in cells, human organoids, and mice. FKK6 significantly represses pro-inflammatory cytokine production cells and abrogates inflammation in mice expressing the human PXR gene. The development of FKK6 demonstrates for the first time that microbial metabolite mimicry is a viable strategy for drug discovery and opens the door to underexploited regions of chemical space.
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8
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Bhatt AP, Pellock SJ, Biernat KA, Walton WG, Wallace BD, Creekmore BC, Letertre MM, Swann JR, Wilson ID, Roques JR, Darr DB, Bailey ST, Montgomery SA, Roach JM, Azcarate-Peril MA, Sartor RB, Gharaibeh RZ, Bultman SJ, Redinbo MR. Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy. Proc Natl Acad Sci U S A 2020; 117:7374-7381. [PMID: 32170007 PMCID: PMC7132129 DOI: 10.1073/pnas.1918095117] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [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] [Indexed: 12/14/2022] Open
Abstract
Irinotecan treats a range of solid tumors, but its effectiveness is severely limited by gastrointestinal (GI) tract toxicity caused by gut bacterial β-glucuronidase (GUS) enzymes. Targeted bacterial GUS inhibitors have been shown to partially alleviate irinotecan-induced GI tract damage and resultant diarrhea in mice. Here, we unravel the mechanistic basis for GI protection by gut microbial GUS inhibitors using in vivo models. We use in vitro, in fimo, and in vivo models to determine whether GUS inhibition alters the anticancer efficacy of irinotecan. We demonstrate that a single dose of irinotecan increases GI bacterial GUS activity in 1 d and reduces intestinal epithelial cell proliferation in 5 d, both blocked by a single dose of a GUS inhibitor. In a tumor xenograft model, GUS inhibition prevents intestinal toxicity and maintains the antitumor efficacy of irinotecan. Remarkably, GUS inhibitor also effectively blocks the striking irinotecan-induced bloom of Enterobacteriaceae in immune-deficient mice. In a genetically engineered mouse model of cancer, GUS inhibition alleviates gut damage, improves survival, and does not alter gut microbial composition; however, by allowing dose intensification, it dramatically improves irinotecan's effectiveness, reducing tumors to a fraction of that achieved by irinotecan alone, while simultaneously promoting epithelial regeneration. These results indicate that targeted gut microbial enzyme inhibitors can improve cancer chemotherapeutic outcomes by protecting the gut epithelium from microbial dysbiosis and proliferative crypt damage.
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Affiliation(s)
- Aadra P Bhatt
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - Samuel J Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Bret D Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Benjamin C Creekmore
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Marine M Letertre
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Jonathan R Swann
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Ian D Wilson
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Jose R Roques
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sean T Bailey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7525
| | - Jeffrey M Roach
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - R Balfour Sartor
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Raad Z Gharaibeh
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32610
| | - Scott J Bultman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264
| | - Matthew R Redinbo
- Department of Biochemistry, Integrated Program for Biological and Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290;
- Department of Biophysics, Integrated Program for Biological and Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
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9
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Bartolini D, De Franco F, Torquato P, Marinelli R, Cerra B, Ronchetti R, Schon A, Fallarino F, De Luca A, Bellezza G, Ferri I, Sidoni A, Walton WG, Pellock SJ, Redinbo MR, Mani S, Pellicciari R, Gioiello A, Galli F. Garcinoic Acid Is a Natural and Selective Agonist of Pregnane X Receptor. J Med Chem 2020; 63:3701-3712. [PMID: 32160459 PMCID: PMC7901650 DOI: 10.1021/acs.jmedchem.0c00012] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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Pregnane X receptor (PXR) is a master xenobiotic-sensing transcription factor and a
validated target for immune and inflammatory diseases. The identification of chemical
probes to investigate the therapeutic relevance of the receptor is still highly desired.
In fact, currently available PXR ligands are not highly selective and can exhibit
toxicity and/or potential off-target effects. In this study, we have identified
garcinoic acid as a selective and efficient PXR agonist. The properties of this natural
molecule as a specific PXR agonist were demonstrated by the screening on a panel of
nuclear receptors, the assessment of the physical and thermodynamic binding affinity,
and the determination of the PXR-garcinoic acid complex crystal structure. Cytotoxicity,
transcriptional, and functional properties were investigated in human liver cells, and
compound activity and target engagement were confirmed in vivo in mouse liver and gut
tissue. In conclusion, garcinoic acid is a selective natural agonist of PXR and a
promising lead compound toward the development of new PXR-regulating modulators.
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Affiliation(s)
- Desirée Bartolini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy
| | | | - Pierangelo Torquato
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy
| | - Rita Marinelli
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy
| | - Bruno Cerra
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy
| | - Riccardo Ronchetti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy
| | - Arne Schon
- The Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Francesca Fallarino
- Department of Experimental Medicine, University of Perugia, Perugia 06129, Italy
| | - Antonella De Luca
- Section of Anatomic Pathology and Histology, Department of Experimental Medicine, University of Perugia, Perugia 06129, Italy
| | - Guido Bellezza
- Section of Anatomic Pathology and Histology, Department of Experimental Medicine, University of Perugia, Perugia 06129, Italy
| | - Ivana Ferri
- Section of Anatomic Pathology and Histology, Department of Experimental Medicine, University of Perugia, Perugia 06129, Italy
| | - Angelo Sidoni
- Section of Anatomic Pathology and Histology, Department of Experimental Medicine, University of Perugia, Perugia 06129, Italy
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Samuel J Pellock
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Sridhar Mani
- The Departments of Biochemistry, Medicine, Genetics, and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | | | - Antimo Gioiello
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy
| | - Francesco Galli
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy
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10
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Jariwala PB, Pellock SJ, Goldfarb D, Cloer EW, Artola M, Simpson JB, Bhatt AP, Walton WG, Roberts LR, Major MB, Davies GJ, Overkleeft HS, Redinbo MR. Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling. ACS Chem Biol 2020; 15:217-225. [PMID: 31774274 PMCID: PMC7321802 DOI: 10.1021/acschembio.9b00788] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [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] [Indexed: 02/06/2023]
Abstract
It is increasingly clear that interindividual variability in human gut microbial composition contributes to differential drug responses. For example, gastrointestinal (GI) toxicity is not observed in all patients treated with the anticancer drug irinotecan, and it has been suggested that this variability is a result of differences in the types and levels of gut bacterial β-glucuronidases (GUSs). GUS enzymes promote drug toxicity by hydrolyzing the inactive drug-glucuronide conjugate back to the active drug, which damages the GI epithelium. Proteomics-based identification of the exact GUS enzymes responsible for drug reactivation from the complexity of the human microbiota has not been accomplished, however. Here, we discover the specific bacterial GUS enzymes that generate SN-38, the active and toxic metabolite of irinotecan, from human fecal samples using a unique activity-based protein profiling (ABPP) platform. We identify and quantify gut bacterial GUS enzymes from human feces with an ABPP-enabled proteomics pipeline and then integrate this information with ex vivo kinetics to pinpoint the specific GUS enzymes responsible for SN-38 reactivation. Furthermore, the same approach also reveals the molecular basis for differential gut bacterial GUS inhibition observed between human fecal samples. Taken together, this work provides an unprecedented technical and bioinformatics pipeline to discover the microbial enzymes responsible for specific reactions from the complexity of human feces. Identifying such microbial enzymes may lead to precision biomarkers and novel drug targets to advance the promise of personalized medicine.
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Affiliation(s)
- Parth B. Jariwala
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samuel J. Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dennis Goldfarb
- Institute for Informatics, Washington University, St. Louis, Missouri 63130, United States
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63130, United States
| | - Erica W. Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Marta Artola
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2311, The Netherlands
| | - Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aadra P. Bhatt
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G. Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lee R. Roberts
- Exploratory Science Center, Merck & Company Inc., Cambridge, Massachusetts 02141, United States
| | - Michael B. Major
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63130, United States
- Department of Otolaryngology, Washington University, St. Louis, Missouri 63130, United States
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Herman S. Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2311, The Netherlands
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Integrated Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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11
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Ervin SM, Hanley RP, Lim L, Walton WG, Pearce KH, Bhatt AP, James LI, Redinbo MR. Targeting Regorafenib-Induced Toxicity through Inhibition of Gut Microbial β-Glucuronidases. ACS Chem Biol 2019; 14:2737-2744. [PMID: 31663730 DOI: 10.1021/acschembio.9b00663] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Regorafenib (Stivarga) is an oral small molecule kinase inhibitor used to treat metastatic colorectal cancer, hepatocellular carcinomas, and gastrointestinal stromal tumors. Diarrhea is one of the most frequently observed adverse reactions associated with regorafenib. This toxicity may arise from the reactivation of the inactive regorafenib-glucuronide to regorafenib by gut microbial β-glucuronidase (GUS) enzymes in the gastrointestinal tract. We sought to unravel the molecular basis of regorafenib-glucuronide processing by human intestinal GUS enzymes and to examine the potential inhibition of these enzymes. Using a panel of 31 unique gut microbial GUS enzymes derived from the 279 mapped from the human gut microbiome, we found that only four were capable of regorafenib-glucuronide processing. Using crystal structures as a guide, we pinpointed the molecular features unique to these enzymes that confer regorafenib-glucuronide processing activity. Furthermore, a pilot screen identified the FDA-approved drug raloxifene as an inhibitor of regorafenib reactivation by the GUS proteins discovered. Novel synthetic raloxifene analogs exhibited improved potency in both in vitro and ex vivo studies. Taken together, these data establish that regorafenib reactivation is exclusively catalyzed by gut microbial enzymes and that these enzymes are amenable to targeted inhibition. Our results unravel key molecular details of regorafenib reactivation in the GI tract and provide a potential pathway to improve clinical outcomes with regorafenib.
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Affiliation(s)
- Samantha M. Ervin
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ronan P. Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lauren Lim
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G. Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aadra P. Bhatt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Integrated Program for Biological and Genome Sciences and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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12
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Creekmore BC, Gray JH, Walton WG, Biernat KA, Little MS, Xu Y, Liu J, Gharaibeh RZ, Redinbo MR. Mouse Gut Microbiome-Encoded β-Glucuronidases Identified Using Metagenome Analysis Guided by Protein Structure. mSystems 2019; 4:e00452-19. [PMID: 31455640 PMCID: PMC6712278 DOI: 10.1128/msystems.00452-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 07/23/2019] [Accepted: 08/09/2019] [Indexed: 11/25/2022] Open
Abstract
Gut microbial β-glucuronidase (GUS) enzymes play important roles in drug efficacy and toxicity, intestinal carcinogenesis, and mammalian-microbial symbiosis. Recently, the first catalog of human gut GUS proteins was provided for the Human Microbiome Project stool sample database and revealed 279 unique GUS enzymes organized into six categories based on active-site structural features. Because mice represent a model biomedical research organism, here we provide an analogous catalog of mouse intestinal microbial GUS proteins-a mouse gut GUSome. Using metagenome analysis guided by protein structure, we examined 2.5 million unique proteins from a comprehensive mouse gut metagenome created from several mouse strains, providers, housing conditions, and diets. We identified 444 unique GUS proteins and organized them into six categories based on active-site features, similarly to the human GUSome analysis. GUS enzymes were encoded by the major gut microbial phyla, including Firmicutes (60%) and Bacteroidetes (21%), and there were nearly 20% for which taxonomy could not be assigned. No differences in gut microbial gus gene composition were observed for mice based on sex. However, mice exhibited gus differences based on active-site features associated with provider, location, strain, and diet. Furthermore, diet yielded the largest differences in gus composition. Biochemical analysis of two low-fat-associated GUS enzymes revealed that they are variable with respect to their efficacy of processing both sulfated and nonsulfated heparan nonasaccharides containing terminal glucuronides.IMPORTANCE Mice are commonly employed as model organisms of mammalian disease; as such, our understanding of the compositions of their gut microbiomes is critical to appreciating how the mouse and human gastrointestinal tracts mirror one another. GUS enzymes, with importance in normal physiology and disease, are an attractive set of proteins to use for such analyses. Here we show that while the specific GUS enzymes differ at the sequence level, a core GUSome functionality appears conserved between mouse and human gastrointestinal bacteria. Mouse strain, provider, housing location, and diet exhibit distinct GUSomes and gus gene compositions, but sex seems not to affect the GUSome. These data provide a basis for understanding the gut microbial GUS enzymes present in commonly used laboratory mice. Further, they demonstrate the utility of metagenome analysis guided by protein structure to provide specific sets of functionally related proteins from whole-genome metagenome sequencing data.
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Affiliation(s)
- Benjamin C Creekmore
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Josh H Gray
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael S Little
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yongmei Xu
- Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jian Liu
- Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Integrated Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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13
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Pellock SJ, Walton WG, Redinbo MR. Selecting a Single Stereocenter: The Molecular Nuances That Differentiate β-Hexuronidases in the Human Gut Microbiome. Biochemistry 2019; 58:1311-1317. [PMID: 30729778 DOI: 10.1021/acs.biochem.8b01285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human gut microbiome is a ripe space for the discovery of new proteins and novel functions. Many genes in the gut microbiome encode glycoside hydrolases that help bacteria scavenge sugars present in the human gut. Glycoside hydrolase family 2 (GH2) is one group of sugar-scavenging proteins, which includes β-glucuronidases (GUS) and β-galacturonidases (GalAses), enzymes that cleave the sugar conjugates of the epimers glucuronate and galacturonate. Here we structurally and functionally characterize a GH2 GalAse and a hybrid GUS/GalAse, which reveal the molecular details that enable these GHs to differentiate a single stereocenter. First, we characterized a previously annotated GUS from Eisenbergiella tayi and demonstrated that it is, in fact, a GalAse. We determined the crystal structure of this GalAse, identified the key residue that confers GalAse activity, and convert this GalAse into a GUS by mutating a single residue. We performed bioinformatic analysis of 279 putative GUS enzymes from the human gut microbiome and identified 12 additional putative GH2 GalAses, one of which we characterized and confirmed is a GalAse. Lastly, we report the structure of a hybrid GUS/GalAse from Fusicatenibacter saccharivorans, which revealed a unique hexamer that positions the N-terminus of adjacent protomers in the aglycone binding site. Taken together, these data reveal a new class of bacterial GalAses in the human gut microbiome and unravel the structural details that differentiate GH2 GUSs and GalAses.
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14
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Biernat KA, Pellock SJ, Bhatt AP, Bivins MM, Walton WG, Tran BNT, Wei L, Snider MC, Cesmat AP, Tripathy A, Erie DA, Redinbo MR. Structure, function, and inhibition of drug reactivating human gut microbial β-glucuronidases. Sci Rep 2019; 9:825. [PMID: 30696850 PMCID: PMC6351562 DOI: 10.1038/s41598-018-36069-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/14/2018] [Indexed: 01/15/2023] Open
Abstract
Bacterial β-glucuronidase (GUS) enzymes cause drug toxicity by reversing Phase II glucuronidation in the gastrointestinal tract. While many human gut microbial GUS enzymes have been examined with model glucuronide substrates like p-nitrophenol-β-D-glucuronide (pNPG), the GUS orthologs that are most efficient at processing drug-glucuronides remain unclear. Here we present the crystal structures of GUS enzymes from human gut commensals Lactobacillus rhamnosus, Ruminococcus gnavus, and Faecalibacterium prausnitzii that possess an active site loop (Loop 1; L1) analogous to that found in E. coli GUS, which processes drug substrates. We also resolve the structure of the No Loop GUS from Bacteroides dorei. We then compare the pNPG and diclofenac glucuronide processing abilities of a panel of twelve structurally diverse GUS proteins, and find that the new L1 GUS enzymes presented here process small glucuronide substrates inefficiently compared to previously characterized L1 GUS enzymes like E. coli GUS. We further demonstrate that our GUS inhibitors, which are effective against some L1 enzymes, are not potent towards all. Our findings pinpoint active site structural features necessary for the processing of drug-glucuronide substrates and the inhibition of such processing.
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Affiliation(s)
- Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Samuel J Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Aadra P Bhatt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Marissa M Bivins
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bich Ngoc T Tran
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lianjie Wei
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael C Snider
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrew P Cesmat
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Department of Microbiology and Immunology, and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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15
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Pellock SJ, Walton WG, Ervin SM, Torres-Rivera D, Creekmore BC, Bergan G, Dunn ZD, Li B, Tripathy A, Redinbo MR. Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome. J Mol Biol 2019; 431:970-980. [PMID: 30658055 DOI: 10.1016/j.jmb.2019.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/09/2023]
Abstract
The human gut microbiota encodes β-glucuronidases (GUSs) that play key roles in health and disease via the metabolism of glucuronate-containing carbohydrates and drugs. Hundreds of putative bacterial GUS enzymes have been identified by metagenomic analysis of the human gut microbiome, but less than 10% have characterized structures and functions. Here we describe a set of unique gut microbial GUS enzymes that bind flavin mononucleotide (FMN). First, we show using mass spectrometry, isothermal titration calorimetry, and x-ray crystallography that a purified GUS from the gut commensal microbe Faecalibacterium prausnitzii binds to FMN on a surface groove located 30 Å away from the active site. Second, utilizing structural and functional data from this FMN-binding GUS, we analyzed the 279 unique GUS sequences from the Human Microbiome Project database and identified 14 putative FMN-binding GUSs. We characterized four of these hits and solved the structure of two, the GUSs from Ruminococcus gnavus and Roseburia hominis, which confirmed that these are FMN binders. Third, binding and kinetic analysis of the FMN-binding site mutants of these five GUSs show that they utilize a conserved site to bind FMN that is not essential for GUS activity, but can affect KM. Lastly, a comprehensive structural review of the PDB reveals that the FMN-binding site employed by these enzymes is unlike any structurally characterized FMN binders to date. These findings reveal the first instance of an FMN-binding glycoside hydrolase and suggest a potential link between FMN and carbohydrate metabolism in the human gut microbiota.
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Affiliation(s)
- Samuel J Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samantha M Ervin
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dariana Torres-Rivera
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin C Creekmore
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Grace Bergan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary D Dunn
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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16
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Little MS, Ervin SM, Walton WG, Tripathy A, Xu Y, Liu J, Redinbo MR. Active site flexibility revealed in crystal structures of Parabacteroides merdae β-glucuronidase from the human gut microbiome. Protein Sci 2018; 27:2010-2022. [PMID: 30230652 PMCID: PMC6237702 DOI: 10.1002/pro.3507] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 08/15/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
β-Glucuronidase (GUS) enzymes in the gastrointestinal tract are involved in maintaining mammalian-microbial symbiosis and can play key roles in drug efficacy and toxicity. Parabacteroides merdae GUS was identified as an abundant mini-Loop 2 (mL2) type GUS enzyme in the Human Microbiome Project gut metagenomic database. Here, we report the crystal structure of P. merdae GUS and highlight the differences between this enzyme and extant structures of gut microbial GUS proteins. We find that P. merdae GUS exhibits a distinct tetrameric quaternary structure and that the mL2 motif traces a unique path within the active site, which also includes two arginines distinctive to this GUS. We observe two states of the P. merdae GUS active site; a loop repositions itself by more than 50 Å to place a functionally-relevant residue into the enzyme's catalytic site. Finally, we find that P. merdae GUS is able to bind to homo and heteropolymers of the polysaccharide alginic acid. Together, these data broaden our understanding of the structural and functional diversity in the GUS family of enzymes present in the human gut microbiome and point to specialization as an important feature of microbial GUS orthologs.
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Affiliation(s)
- Michael S. Little
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
| | - Samantha M. Ervin
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
| | - William G. Walton
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
| | - Ashutosh Tripathy
- Department of Biochemistry & BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
| | - Yongmei Xu
- Department of Chemical Biology and Medicinal ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
| | - Jian Liu
- Department of Chemical Biology and Medicinal ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
| | - Matthew R. Redinbo
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
- Department of Biochemistry & BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
- Department of Microbiology & ImmunologyUniversity of North CarolinaChapel HillNorth Carolina27599‐3290
- The Integrated Program for Biological and Genome Sciences, University of North CarolinaChapel HillNorth Carolina27599‐3290
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17
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Pellock SJ, Walton WG, Biernat KA, Torres-Rivera D, Creekmore BC, Xu Y, Liu J, Tripathy A, Stewart LJ, Redinbo MR. Three structurally and functionally distinct β-glucuronidases from the human gut microbe Bacteroides uniformis. J Biol Chem 2018; 293:18559-18573. [PMID: 30301767 DOI: 10.1074/jbc.ra118.005414] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [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: 08/17/2018] [Revised: 10/04/2018] [Indexed: 12/16/2022] Open
Abstract
The glycoside hydrolases encoded by the human gut microbiome play an integral role in processing a variety of exogenous and endogenous glycoconjugates. Here we present three structurally and functionally distinct β-glucuronidase (GUS) glycoside hydrolases from a single human gut commensal microbe, Bacteroides uniformis We show using nine crystal structures, biochemical, and biophysical data that whereas these three proteins share similar overall folds, they exhibit different structural features that create three structurally and functionally unique enzyme active sites. Notably, quaternary structure plays an important role in creating distinct active site features that are hard to predict via structural modeling methods. The enzymes display differential processing capabilities toward glucuronic acid-containing polysaccharides and SN-38-glucuronide, a metabolite of the cancer drug irinotecan. We also demonstrate that GUS-specific and nonselective inhibitors exhibit varying potencies toward each enzyme. Together, these data highlight the diversity of GUS enzymes within a single Bacteroides gut commensal and advance our understanding of how structural details impact the specific roles microbial enzymes play in processing drug-glucuronide and glycan substrates.
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Affiliation(s)
| | | | | | | | | | - Yongmei Xu
- Chemical Biology and Medicinal Chemistry, and
| | - Jian Liu
- Chemical Biology and Medicinal Chemistry, and
| | | | - Lance J Stewart
- the Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, Washington 98195
| | - Matthew R Redinbo
- From the Departments of Chemistry, .,Biochemistry and Biophysics, and.,the Departments of Microbiology and Immunology, and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
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18
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Yu Z, Deslouches B, Walton WG, Redinbo MR, Di YP. Enhanced biofilm prevention activity of a SPLUNC1-derived antimicrobial peptide against Staphylococcus aureus. PLoS One 2018; 13:e0203621. [PMID: 30216370 PMCID: PMC6138395 DOI: 10.1371/journal.pone.0203621] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022] Open
Abstract
SPLUNC1 is a multifunctional protein of the airway with antimicrobial properties. We previously reported that it displayed antibiofilm activities against P. aeruginosa. The goal of this study was to determine whether (1) the antibiofilm property is broad (including S. aureus, another prevalent organism in cystic fibrosis); (2) the α4 region is responsible for such activity; and (3), if so, this motif could be structurally optimized as an antimicrobial peptide with enhanced activities. We used S. aureus biofilm-prevention assays to determine bacterial biomass in the presence of SPLUNC1 and SPLUNC1Δα4 recombinant proteins, or SPLUNC1-derived peptides (α4 and α4M1), using the well-established crystal-violet biofilm detection assay. The SPLUNC1Δα4 showed markedly reduced biofilm prevention compared to the parent protein. Surprisingly, the 30-residue long α4 motif alone demonstrated minimal biofilm prevention activities. However, structural optimization of the α4 motif resulted in a modified peptide (α4M1) with significantly enhanced antibiofilm properties against methicillin–sensitive (MSSA) and–resistant (MRSA) S. aureus, including six different clinical strains of MRSA and the well-known USA300. Hemolytic activity was undetectable at up to 100μM for the peptides. The data warrant further investigation of α4-derived AMPs to explore the potential application of antimicrobial peptides to combat bacterial biofilm-related infections.
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Affiliation(s)
- Zhongjie Yu
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Molecular Genetics, Institute for Translational Medicine, Qingdao University, Qingdao, China
| | - Berthony Deslouches
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - William G. Walton
- Departments of Chemistry, Biochemistry, and Microbiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Matthew R. Redinbo
- Departments of Chemistry, Biochemistry, and Microbiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Y. Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, United States of America
- * E-mail:
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19
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Pellock S, Creekmore BC, Walton WG, Mehta N, Biernat KA, Cesmat AP, Ariyarathna Y, Dunn ZD, Li B, Jin J, James LI, Redinbo MR. Gut Microbial β-Glucuronidase Inhibition via Catalytic Cycle Interception. ACS Cent Sci 2018; 4:868-879. [PMID: 30062115 PMCID: PMC6062831 DOI: 10.1021/acscentsci.8b00239] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 05/10/2023]
Abstract
Microbial β-glucuronidases (GUSs) cause severe gut toxicities that limit the efficacy of cancer drugs and other therapeutics. Selective inhibitors of bacterial GUS have been shown to alleviate these side effects. Using structural and chemical biology, mass spectrometry, and cell-based assays, we establish that piperazine-containing GUS inhibitors intercept the glycosyl-enzyme catalytic intermediate of these retaining glycosyl hydrolases. We demonstrate that piperazine-based compounds are substrate-dependent GUS inhibitors that bind to the GUS-GlcA catalytic intermediate as a piperazine-linked glucuronide (GlcA, glucuronic acid). We confirm the GUS-dependent formation of inhibitor-glucuronide conjugates by LC-MS and show that methylated piperazine analogs display significantly reduced potencies. We further demonstrate that a range of approved piperazine- and piperidine-containing drugs from many classes, including those for the treatment of depression, infection, and cancer, function by the same mechanism, and we confirm through gene editing that these compounds selectively inhibit GUS in living bacterial cells. Together, these data reveal a unique mechanism of GUS inhibition and show that a range of therapeutics may impact GUS activities in the human gut.
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Affiliation(s)
- Samuel
J. Pellock
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Benjamin C. Creekmore
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G. Walton
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Naimee Mehta
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kristen A. Biernat
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Andrew P. Cesmat
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yamuna Ariyarathna
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Zachary D. Dunn
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Jin
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mt. Sinai, New York, New York 10029, United States
| | - Lindsey I. James
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew R. Redinbo
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- E-mail:
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20
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Kim CS, Ahmad S, Wu T, Walton WG, Redinbo MR, Tarran R. SPLUNC1 is an allosteric modulator of the epithelial sodium channel. FASEB J 2018; 32:2478-2491. [PMID: 29295861 PMCID: PMC5901381 DOI: 10.1096/fj.201701126r] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 10/12/2017] [Accepted: 12/04/2017] [Indexed: 01/20/2023]
Abstract
Cystic fibrosis (CF) is a common genetic disease with significantly increased mortality. CF airways exhibit ion transport abnormalities, including hyperactivity of the epithelial Na+ channel (ENaC). Short-palate lung and nasal epithelial clone 1 (SPLUNC1) is a multifunctional innate defense protein that is secreted into the airway lumen. We have previously demonstrated that SPLUNC1 binds to and inhibits ENaC to maintain fluid homeostasis in airway epithelia and that this process fails in CF airways. Despite this, how SPLUNC1 actually regulates ENaC is unknown. Here, we found that SPLUNC1 caused αγ-ENaC to internalize, whereas SPLUNC1 and β-ENaC remained at the plasma membrane. Additional studies revealed that SPLUNC1 increased neural precursor cell-expressed developmentally down-regulated protein 4-2-dependent ubiquitination of α- but not β- or γ-ENaC. We also labeled intracellular ENaC termini with green fluorescent protein and mCherry, and found that extracellular SPLUNC1 altered intracellular ENaC Forster resonance energy transfer. Taken together, our data indicate that SPLUNC1 is an allosteric regulator of ENaC that dissociates αβγ-ENaC to generate a new SPLUNC1-β-ENaC complex. These data indicate a novel mode for regulating ENaC at the plasma membrane.-Kim, C. S., Ahmad, S., Wu, T., Walton, W. G., Redinbo, M. R., Tarran, R. SPLUNC1 is an allosteric modulator of the epithelial sodium channel.
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Affiliation(s)
- Christine Seulki Kim
- Cystic Fibrosis Center, Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Saira Ahmad
- Cystic Fibrosis Center, Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tongde Wu
- Cystic Fibrosis Center, Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William G. Walton
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew R. Redinbo
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Robert Tarran
- Cystic Fibrosis Center, Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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21
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Pollet RM, D'Agostino EH, Walton WG, Xu Y, Little MS, Biernat KA, Pellock SJ, Patterson LM, Creekmore BC, Isenberg HN, Bahethi RR, Bhatt AP, Liu J, Gharaibeh RZ, Redinbo MR. An Atlas of β-Glucuronidases in the Human Intestinal Microbiome. Structure 2017; 25:967-977.e5. [PMID: 28578872 PMCID: PMC5533298 DOI: 10.1016/j.str.2017.05.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [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: 02/02/2017] [Revised: 03/15/2017] [Accepted: 05/05/2017] [Indexed: 01/16/2023]
Abstract
Microbiome-encoded β-glucuronidase (GUS) enzymes play important roles in human health by metabolizing drugs in the gastrointestinal (GI) tract. The numbers, types, and diversity of these proteins in the human GI microbiome, however, remain undefined. We present an atlas of GUS enzymes comprehensive for the Human Microbiome Project GI database. We identify 3,013 total and 279 unique microbiome-encoded GUS proteins clustered into six unique structural categories. We assign their taxonomy, assess cellular localization, reveal the inter-individual variability within the 139 individuals sampled, and discover 112 novel microbial GUS enzymes. A representative in vitro panel of the most common GUS proteins by read abundances highlights structural and functional variabilities within the family, including their differential processing of smaller glucuronides and larger carbohydrates. These data provide a sequencing-to-molecular roadmap for examining microbiome-encoded enzymes essential to human health.
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Affiliation(s)
- Rebecca M Pollet
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emma H D'Agostino
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yongmei Xu
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael S Little
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel J Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Loraine M Patterson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin C Creekmore
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hanna N Isenberg
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rohini R Bahethi
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Aadra P Bhatt
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jian Liu
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raad Z Gharaibeh
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Departments of Biochemistry, Microbiology, and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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22
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Bellendir SP, Rognstad DJ, Morris LP, Zapotoczny G, Walton WG, Redinbo MR, Ramsden DA, Sekelsky J, Erie DA. Substrate preference of Gen endonucleases highlights the importance of branched structures as DNA damage repair intermediates. Nucleic Acids Res 2017; 45:5333-5348. [PMID: 28369583 PMCID: PMC5435919 DOI: 10.1093/nar/gkx214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/16/2017] [Accepted: 03/21/2017] [Indexed: 11/20/2022] Open
Abstract
Human GEN1 and yeast Yen1 are endonucleases with the ability to cleave Holliday junctions (HJs), which are proposed intermediates in recombination. In vivo, GEN1 and Yen1 function secondarily to Mus81, which has weak activity on intact HJs. We show that the genetic relationship is reversed in Drosophila, with Gen mutants having more severe defects than mus81 mutants. In vitro, DmGen, like HsGEN1, efficiently cleaves HJs, 5΄ flaps, splayed arms, and replication fork structures. We find that the cleavage rates for 5΄ flaps are significantly higher than those for HJs for both DmGen and HsGEN1, even in vast excess of enzyme over substrate. Kinetic studies suggest that the difference in cleavage rates results from a slow, rate-limiting conformational change prior to HJ cleavage: formation of a productive dimer on the HJ. Despite the stark difference in vivo that Drosophila uses Gen over Mus81 and humans use MUS81 over GEN1, we find the in vitro activities of DmGen and HsGEN1 to be strikingly similar. These findings suggest that simpler branched structures may be more important substrates for Gen orthologs in vivo, and highlight the utility of using the Drosophila model system to further understand these enzymes.
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Affiliation(s)
| | | | - Lydia P. Morris
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | | | | | - Matthew R. Redinbo
- Department of Chemistry, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, Chapel Hill, NC 27599, USA
| | - Dale A. Ramsden
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, Chapel Hill, NC 27599, USA
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dorothy A. Erie
- Department of Chemistry, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, Chapel Hill, NC 27599, USA
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23
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Wu T, Huang J, Moore PJ, Little MS, Walton WG, Fellner RC, Alexis NE, Peter Di Y, Redinbo MR, Tilley SL, Tarran R. Identification of BPIFA1/SPLUNC1 as an epithelium-derived smooth muscle relaxing factor. Nat Commun 2017; 8:14118. [PMID: 28165446 PMCID: PMC5303822 DOI: 10.1038/ncomms14118] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 11/30/2016] [Indexed: 01/02/2023] Open
Abstract
Asthma is a chronic airway disease characterized by inflammation, mucus hypersecretion and abnormal airway smooth muscle (ASM) contraction. Bacterial permeability family member A1, BPIFA1, is a secreted innate defence protein. Here we show that BPIFA1 levels are reduced in sputum samples from asthmatic patients and that BPIFA1 is secreted basolaterally from healthy, but not asthmatic human bronchial epithelial cultures (HBECs), where it suppresses ASM contractility by binding to and inhibiting the Ca2+ influx channel Orai1. We have localized this effect to a specific, C-terminal α-helical region of BPIFA1. Furthermore, tracheas from Bpifa1-/- mice are hypercontractile, and this phenotype is reversed by the addition of recombinant BPIFA1. Our data suggest that BPIFA1 deficiency in asthmatic airways promotes Orai1 hyperactivity, increased ASM contraction and airway hyperresponsiveness. Strategies that target Orai1 or the BPIFA1 deficiency in asthma may lead to novel therapies to treat this disease.
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Affiliation(s)
- Tongde Wu
- Cystic Fibrosis Center/Marsico Lung Institute, Marsico Hall, 125 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Julianne Huang
- Cystic Fibrosis Center/Marsico Lung Institute, Marsico Hall, 125 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA.,Department of Chemistry, Genome Science Building, 250 Bell Tower Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Patrick J Moore
- Cystic Fibrosis Center/Marsico Lung Institute, Marsico Hall, 125 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Michael S Little
- Department of Chemistry, Genome Science Building, 250 Bell Tower Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - William G Walton
- Department of Chemistry, Genome Science Building, 250 Bell Tower Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Robert C Fellner
- Cystic Fibrosis Center/Marsico Lung Institute, Marsico Hall, 125 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Neil E Alexis
- Center for Environmental Medicine, Asthma, and Lung Biology, US EPA Human Studies Facility, 104 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Y Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, 331 Bridgeside Point Building, Pittsburgh, Pennsylvania 15260, USA
| | - Matthew R Redinbo
- Department of Chemistry, Genome Science Building, 250 Bell Tower Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Stephen L Tilley
- Cystic Fibrosis Center/Marsico Lung Institute, Marsico Hall, 125 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA.,Center for Environmental Medicine, Asthma, and Lung Biology, US EPA Human Studies Facility, 104 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
| | - Robert Tarran
- Cystic Fibrosis Center/Marsico Lung Institute, Marsico Hall, 125 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA.,Department of Cell Biology &Physiology, 5200 Medical Biomolecular Research Building, 111 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7248, USA
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24
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Walton WG, Ahmad S, Little MR, Kim CS, Tyrrell J, Lin Q, Di YP, Tarran R, Redinbo MR. Structural Features Essential to the Antimicrobial Functions of Human SPLUNC1. Biochemistry 2016; 55:2979-91. [PMID: 27145151 PMCID: PMC4887393 DOI: 10.1021/acs.biochem.6b00271] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SPLUNC1 is an abundantly secreted innate immune protein in the mammalian respiratory tract that exerts bacteriostatic and antibiofilm effects, binds to lipopolysaccharide (LPS), and acts as a fluid-spreading surfactant. Here, we unravel the structural elements essential for the surfactant and antimicrobial functions of human SPLUNC1 (short palate lung nasal epithelial clone 1). A unique α-helix (α4) that extends from the body of SPLUNC1 is required for the bacteriostatic, surfactant, and LPS binding activities of this protein. Indeed, we find that mutation of just four leucine residues within this helical motif to alanine is sufficient to significantly inhibit the fluid spreading abilities of SPLUNC1, as well as its bacteriostatic actions against Gram-negative pathogens Burkholderia cenocepacia and Pseudomonas aeruginosa. Conformational flexibility in the body of SPLUNC1 is also involved in the bacteriostatic, surfactant, and LPS binding functions of the protein as revealed by disulfide mutants introduced into SPLUNC1. In addition, SPLUNC1 exerts antibiofilm effects against Gram-negative bacteria, although α4 is not involved in this activity. Interestingly, though, the introduction of surface electrostatic mutations away from α4 based on the unique dolphin SPLUNC1 sequence, and confirmed by crystal structure, is shown to impart antibiofilm activity against Staphylococcus aureus, the first SPLUNC1-dependent effect against a Gram-positive bacterium reported to date. Together, these data pinpoint SPLUNC1 structural motifs required for the antimicrobial and surfactant actions of this protective human protein.
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Affiliation(s)
- William G. Walton
- Departments of Chemistry, Biochemistry and Microbiology, 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Saira Ahmad
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Michael R. Little
- Departments of Chemistry, Biochemistry and Microbiology, 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Christine S.K. Kim
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Jean Tyrrell
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Qiao Lin
- Department of Environmental and Occupational Health, 331 Bridgeside Point Building, University of Pittsburgh, Pittsburgh, PA 15260
| | - Y. Peter Di
- Department of Environmental and Occupational Health, 331 Bridgeside Point Building, University of Pittsburgh, Pittsburgh, PA 15260
| | - Robert Tarran
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Matthew R. Redinbo
- Departments of Chemistry, Biochemistry and Microbiology, 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA,Corresponding Author: 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA, 919-962-4581, 919-962-2388 fax,
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25
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Hobbs CA, Blanchard MG, Alijevic O, Tan CD, Kellenberger S, Bencharit S, Cao R, Kesimer M, Walton WG, Henderson AG, Redinbo MR, Stutts MJ, Tarran R. Identification of the SPLUNC1 ENaC-inhibitory domain yields novel strategies to treat sodium hyperabsorption in cystic fibrosis airway epithelial cultures. Am J Physiol Lung Cell Mol Physiol 2013; 305:L990-L1001. [PMID: 24124190 DOI: 10.1152/ajplung.00103.2013] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The epithelial sodium channel (ENaC) is responsible for Na(+) and fluid absorption across colon, kidney, and airway epithelia. Short palate lung and nasal epithelial clone 1 (SPLUNC1) is a secreted, innate defense protein and an autocrine inhibitor of ENaC that is highly expressed in airway epithelia. While SPLUNC1 has a bactericidal permeability-increasing protein (BPI)-type structure, its NH2-terminal region lacks structure. Here we found that an 18 amino acid peptide, S18, which corresponded to residues G22-A39 of the SPLUNC1 NH2 terminus inhibited ENaC activity to a similar degree as full-length SPLUNC1 (∼2.5 fold), while SPLUNC1 protein lacking this region was without effect. S18 did not inhibit the structurally related acid-sensing ion channels, indicating specificity for ENaC. However, S18 preferentially bound to the βENaC subunit in a glycosylation-dependent manner. ENaC hyperactivity is contributory to cystic fibrosis (CF) lung disease. Unlike control, CF human bronchial epithelial cultures (HBECs) where airway surface liquid (ASL) height was abnormally low (4.2 ± 0.6 μm), addition of S18 prevented ENaC-led ASL hyperabsorption and maintained CF ASL height at 7.9 ± 0.6 μm, even in the presence of neutrophil elastase, which is comparable to heights seen in normal HBECs. Our data also indicate that the ENaC inhibitory domain of SPLUNC1 may be cleaved away from the main molecule by neutrophil elastase, suggesting that it may still be active during inflammation or neutrophilia. Furthermore, the robust inhibition of ENaC by the S18 peptide suggests that this peptide may be suitable for treating CF lung disease.
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Affiliation(s)
- Carey A Hobbs
- Cystic Fibrosis/Pulmonary Research and Treatment Center, 7125 Thurston Bowles Bldg., UNC, Chapel Hill, NC 27599-7248.
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26
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Hobbs CA, Blanchard MG, Kellenberger S, Bencharit S, Cao R, Kesimer M, Walton WG, Redinbo MR, Stutts MJ, Tarran R. Identification of SPLUNC1's ENaC-inhibitory domain yields novel strategies to treat sodium hyperabsorption in cystic fibrosis airways. FASEB J 2012; 26:4348-59. [PMID: 22798424 DOI: 10.1096/fj.12-207431] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The epithelial sodium channel (ENaC) is responsible for Na+ and fluid absorption across colon, kidney, and airway epithelia. We have previously identified SPLUNC1 as an autocrine inhibitor of ENaC. We have now located the ENaC inhibitory domain of SPLUNC1 to SPLUNC1's N terminus, and a peptide corresponding to this domain, G22-A39, inhibited ENaC activity to a similar degree as full-length SPLUNC1 (∼2.5 fold). However, G22-A39 had no effect on the structurally related acid-sensing ion channels, indicating specificity for ENaC. G22-A39 preferentially bound to the β-ENaC subunit in a glycosylation-dependent manner. ENaC hyperactivity is contributory to cystic fibrosis (CF) lung disease. Addition of G22-A39 to CF human bronchial epithelial cultures (HBECs) resulted in an increase in airway surface liquid height from 4.2±0.6 to 7.9±0.6 μm, comparable to heights seen in normal HBECs, even in the presence of neutrophil elastase. Our data also indicate that the ENaC inhibitory domain of SPLUNC1 may be cleaved away from the main molecule by neutrophil elastase, which suggests that it may still be active during inflammation or neutrophilia. Furthermore, the robust inhibition of ENaC by the G22-A39 peptide suggests that this peptide may be suitable for treating CF lung disease.
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Affiliation(s)
- Carey A Hobbs
- Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Prosthodontics, University of North Carolina, Chapel Hill, 7125 Thurston Bowles Bldg., Chapel Hill, NC 27599-7248, USA
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Abstract
Hematopoietic stem cells (HSCs) have enormous potential for use in transplantation and gene therapy. However, the frequency of repopulating HSCs is often very low; thus, highly effective techniques for cell enrichment and maintenance are required to obtain sufficient cell numbers for therapeutic use and for studies of HSC physiology. Common methods of HSC enrichment use antibodies recognizing HSC surface marker antigens. Because antibodies are known to alter the physiology of other cell types, we investigated the effect of such enrichment strategies on the physiology and lineage commitment of HSCs. We sorted HSCs using a method that does not require antibodies: exclusion of Hoechst 33342 to isolate side population (SP) cells. To elucidate the effect of antibody binding on this HSC population, we compared untreated SP cells with SP cells treated with the Sca-1(+)c-Kit(+)Lin(-) (SKL) antibody cocktail prior to SP sorting. Our findings revealed that HSCs incubated with the antibody cocktail had decreased expression of the stem cell-associated genes c-Kit, Cd34, Tal-1, and Slamf1 relative to untreated SP cells or to cells treated with polyclonal isotype control antibodies. Moreover, SKL antibodies induced cycling in SP cells and diminished their ability to confer long-term hematopoietic engraftment in lethally irradiated mice. Taken together, these data suggest that antibody-based stem cell isolation procedures can have negative effects on HSC physiology.
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Affiliation(s)
- Jennifer B Gilner
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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