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Pollet RM, Foley MH, Kumar SS, Elmore A, Jabara NT, Venkatesh S, Vasconcelos Pereira G, Martens EC, Koropatkin NM. Multiple TonB homologs are important for carbohydrate utilization by Bacteroides thetaiotaomicron. J Bacteriol 2023; 205:e0021823. [PMID: 37874167 PMCID: PMC10662123 DOI: 10.1128/jb.00218-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The human gut microbiota, including Bacteroides, is required for the degradation of otherwise undigestible polysaccharides. The gut microbiota uses polysaccharides as an energy source, and fermentation products such as short-chain fatty acids are beneficial to the human host. This use of polysaccharides is dependent on the proper pairing of a TonB protein with polysaccharide-specific TonB-dependent transporters; however, the formation of these protein complexes is poorly understood. In this study, we examine the role of 11 predicted TonB homologs in polysaccharide uptake. We show that two proteins, TonB4 and TonB6, may be functionally redundant. This may allow for the development of drugs targeting Bacteroides species containing only a TonB4 homolog with limited impact on species encoding the redundant TonB6.
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Affiliation(s)
- Rebecca M. Pollet
- Department of Chemistry, Vassar College, Poughkeepsie, New York, USA
- Biochemistry Program, Vassar College, Poughkeepsie, New York, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Matthew H. Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Supriya Suresh Kumar
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amanda Elmore
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Sameeksha Venkatesh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Bader AC, Van Zuylen EM, Handsley-Davis M, Alegado RA, Benezra A, Pollet RM, Ehau-Taumaunu H, Weyrich LS, Anderson MZ. A relational framework for microbiome research with Indigenous communities. Nat Microbiol 2023; 8:1768-1776. [PMID: 37770743 DOI: 10.1038/s41564-023-01471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/26/2023] [Indexed: 09/30/2023]
Abstract
Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.
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Affiliation(s)
- Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada.
| | - Essie M Van Zuylen
- Department of Microbiology and Immunology, University of Otago, Dunedin North, Dunedin, New Zealand
- School of Product Design, University of Canterbury, Christchurch, New Zealand
| | - Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
| | - Rosanna A Alegado
- Department of Oceanography, University of Hawai'i Mānoa, Honolulu, HI, USA
| | - Amber Benezra
- Department of Science and Technology Studies, Stevens Institute of Technology, Hoboken, NJ, USA
| | | | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, USA
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Pollet RM, Foley MH, Kumar SS, Elmore A, Jabara NT, Venkatesh S, Pereira GV, Martens EC, Koropatkin NM. Multiple TonB Homologs are Important for Carbohydrate Utilization by Bacteroides thetaiotaomicron. bioRxiv 2023:2023.07.07.548152. [PMID: 37461508 PMCID: PMC10350073 DOI: 10.1101/2023.07.07.548152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The human gut microbiota is able to degrade otherwise undigestible polysaccharides, largely through the activity of the Bacteroides. Uptake of polysaccharides into Bacteroides is controlled by TonB-dependent transporters (TBDT) whose transport is energized by an inner membrane complex composed of the proteins TonB, ExbB, and ExbD. Bacteroides thetaiotaomicron (B. theta) encodes 11 TonB homologs which are predicted to be able to contact TBDTs to facilitate transport. However, it is not clear which TonBs are important for polysaccharide uptake. Using strains in which each of the 11 predicted tonB genes are deleted, we show that TonB4 (BT2059) is important but not essential for proper growth on starch. In the absence of TonB4, we observed an increase in abundance of TonB6 (BT2762) in the membrane of B. theta, suggesting functional redundancy of these TonB proteins. Growth of the single deletion strains on pectin galactan, chondroitin sulfate, arabinan, and levan suggests a similar functional redundancy of the TonB proteins. A search for highly homologous proteins across other Bacteroides species and recent work in B. fragilis suggests that TonB4 is widely conserved and may play a common role in polysaccharide uptake. However, proteins similar to TonB6 are found only in B. theta and closely related species suggesting that the functional redundancy of TonB4 and TonB6 may be limited across the Bacteroides. This study extends our understanding of the protein network required for polysaccharide utilization in B. theta and highlights differences in TonB complexes across Bacteroides species.
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Affiliation(s)
- Rebecca M Pollet
- Department of Chemistry, Vassar College, Poughkeepsie, NY, 12604, USA
- Biochemistry Program, Vassar College, Poughkeepsie, NY, 12604, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Supriya Suresh Kumar
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Amanda Elmore
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nisrine T Jabara
- Biochemistry Program, Vassar College, Poughkeepsie, NY, 12604, USA
| | - Sameeksha Venkatesh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Pollet RM, Martin LM, Koropatkin NM. TonB-dependent transporters in the Bacteroidetes: Unique domain structures and potential functions. Mol Microbiol 2021; 115:490-501. [PMID: 33448497 DOI: 10.1111/mmi.14683] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/26/2022]
Abstract
The human gut microbiota endows the host with a wealth of metabolic functions central to health, one of which is the degradation and fermentation of complex carbohydrates. The Bacteroidetes are one of the dominant bacterial phyla of this community and possess an expanded capacity for glycan utilization. This is mediated via the coordinated expression of discrete polysaccharide utilization loci (PUL) that invariantly encode a TonB-dependent transporter (SusC) that works with a glycan-capturing lipoprotein (SusD). More broadly within Gram-negative bacteria, TonB-dependent transporters (TBDTs) are deployed for the uptake of not only sugars, but also more often for essential nutrients such as iron and vitamins. Here, we provide a comprehensive look at the repertoire of TBDTs found in the model gut symbiont Bacteroides thetaiotaomicron and the range of predicted functional domains associated with these transporters and SusD proteins for the uptake of both glycans and other nutrients. This atlas of the B. thetaiotaomicron TBDTs reveals that there are at least three distinct subtypes of these transporters encoded within its genome that are presumably regulated in different ways to tune nutrient uptake.
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Affiliation(s)
| | - Lauryn M Martin
- Department of Biology, Alcorn State University, Alcorn, MS, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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Hagan AK, Pollet RM, Libertucci J. Suggestions for Improving Invited Speaker Diversity To Reflect Trainee Diversity. J Microbiol Biol Educ 2020; 21:jmbe-21-22. [PMID: 32313591 PMCID: PMC7148143 DOI: 10.1128/jmbe.v21i1.2105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/28/2020] [Indexed: 05/27/2023]
Abstract
Within the field of biomedical research in the United States, the proportion of underrepresented minorities at the Full Professor level has remained consistently low, even though trainee demographics are becoming more diverse. Underrepresented groups face a complex set of barriers to achieving faculty status, including imposter syndrome, increased performance expectations, and patterns of exclusion. Institutionalized racism and sexism have contributed to these barriers and perpetuated policy that excludes underrepresented minorities. These barriers can contribute to decreased feelings of belonging, which may result in decreased retention of underrepresented minorities. Though some universities have altered their hiring practices to increase the number of underrepresented minorities in the applicant pool, these changes have not been sufficient. Here we argue that departmental invited seminar series can be used to provide trainees with scientific role models and increase their sense of belonging while institutions work towards more inclusive policy. In this study, we investigated the demographics (gender and race) of invited seminar speakers over 5 years to the Department of Microbiology and Immunology at the University of Michigan. We also investigated current trainee demographics and compared them to invited speaker demographics to gauge if our trainees were being provided with representation of themselves. We found that invited speaker demographics were skewed towards Caucasian men, and our trainee demographics were not being represented. From these findings, we proposed policy change within the department to address how speakers are being invited with the goal of increasing speaker diversity to better reflect trainee diversity. To facilitate this process, we developed a set of suggestions and a web-based resource that allows scientists, committees, and moderators to identify members of underserved groups. These resources can be easily adapted by other fields or subfields to promote inclusion and diversity at seminar series, conferences, and colloquia.
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Affiliation(s)
- Ada K. Hagan
- Corresponding author. Current address: Alliance SciComm & Consulting, 215 S. Main Street #755, Linden, MI 48451. Phone: 810-266-0591. E-mail:
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Cerqueira FM, Photenhauer AL, Pollet RM, Brown HA, Koropatkin NM. Starch Digestion by Gut Bacteria: Crowdsourcing for Carbs. Trends Microbiol 2020; 28:95-108. [DOI: 10.1016/j.tim.2019.09.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/12/2022]
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Doden HL, Pollet RM, Mythen SM, Wawrzak Z, Devendran S, Cann I, Koropatkin NM, Ridlon JM. Structural and biochemical characterization of 20β-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32. J Biol Chem 2019; 294:12040-12053. [PMID: 31209107 DOI: 10.1074/jbc.ra119.009390] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/11/2019] [Indexed: 01/20/2023] Open
Abstract
Anaerobic bacteria inhabiting the human gastrointestinal tract have evolved various enzymes that modify host-derived steroids. The bacterial steroid-17,20-desmolase pathway cleaves the cortisol side chain, forming pro-androgens predicted to impact host physiology. Bacterial 20β-hydroxysteroid dehydrogenase (20β-HSDH) regulates cortisol side-chain cleavage by reducing the C-20 carboxyl group on cortisol, yielding 20β-dihydrocortisol. Recently, the gene encoding 20β-HSDH in Butyricicoccus desmolans ATCC 43058 was reported, and a nonredundant protein search yielded a candidate 20β-HSDH gene in Bifidobacterium adolescentis strain L2-32. B. adolescentis 20β-HSDH could regulate cortisol side-chain cleavage by limiting pro-androgen formation in bacteria such as Clostridium scindens and 21-dehydroxylation by Eggerthella lenta Here, the putative B. adolescentis 20β-HSDH was cloned, overexpressed, and purified. 20β-HSDH activity was confirmed through whole-cell and pure enzymatic assays, and it is specific for cortisol. Next, we solved the structures of recombinant 20β-HSDH in both the apo- and holo-forms at 2.0-2.2 Å resolutions, revealing close overlap except for rearrangements near the active site. Interestingly, the structures contain a large, flexible N-terminal region that was investigated by gel-filtration chromatography and CD spectroscopy. This extended N terminus is important for protein stability because deletions of varying lengths caused structural changes and reduced enzymatic activity. A nonconserved extended N terminus was also observed in several short-chain dehydrogenase/reductase family members. B. adolescentis strains capable of 20β-HSDH activity could alter glucocorticoid metabolism in the gut and thereby serve as potential probiotics for the management of androgen-dependent diseases.
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Affiliation(s)
- Heidi L Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rebecca M Pollet
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Sean M Mythen
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, Illinois 60439
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Isaac Cann
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Jason M Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Cancer Center of Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
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8
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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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9
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Hughes RM, Freeman DJ, Lamb KN, Pollet RM, Smith WJ, Lawrence DS. Optogenetic apoptosis: light-triggered cell death. Angew Chem Int Ed Engl 2015; 54:12064-8. [PMID: 26418181 PMCID: PMC4819321 DOI: 10.1002/anie.201506346] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [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: 07/09/2015] [Revised: 08/06/2015] [Indexed: 12/11/2022]
Abstract
An optogenetic Bax has been designed that facilitates light-induced apoptosis. We demonstrate that mitochondrial recruitment of a genetically encoded light-responsive Bax results in the release of mitochondrial proteins, downstream caspase-3 cleavage, changes in cellular morphology, and ultimately cell death. Mutagenesis of a key phosphorylatable residue or modification of the C-terminus mitigates background (dark) levels of apoptosis that result from Bax overexpression. The mechanism of optogenetic Bax-mediated apoptosis was explored using a series of small molecules known to interfere with various steps in programmed cell death. Optogenetic Bax appears to form a mitochondrial apoptosis-induced channel analogous to that of endogenous Bax.
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Affiliation(s)
- Robert M Hughes
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA).
| | - David J Freeman
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - Kelsey N Lamb
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - Rebecca M Pollet
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - Weston J Smith
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - David S Lawrence
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA).
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Wallace BD, Roberts AB, Pollet RM, Ingle JD, Biernat KA, Pellock SJ, Venkatesh MK, Guthrie L, O'Neal SK, Robinson SJ, Dollinger M, Figueroa E, McShane SR, Cohen RD, Jin J, Frye SV, Zamboni WC, Pepe-Ranney C, Mani S, Kelly L, Redinbo MR. Structure and Inhibition of Microbiome β-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity. Chem Biol 2015; 22:1238-49. [PMID: 26364932 PMCID: PMC4575908 DOI: 10.1016/j.chembiol.2015.08.005] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/27/2015] [Accepted: 08/08/2015] [Indexed: 02/07/2023]
Abstract
The selective inhibition of bacterial β-glucuronidases was recently shown to alleviate drug-induced gastrointestinal toxicity in mice, including the damage caused by the widely used anticancer drug irinotecan. Here, we report crystal structures of representative β-glucuronidases from the Firmicutes Streptococcus agalactiae and Clostridium perfringens and the Proteobacterium Escherichia coli, and the characterization of a β-glucuronidase from the Bacteroidetes Bacteroides fragilis. While largely similar in structure, these enzymes exhibit marked differences in catalytic properties and propensities for inhibition, indicating that the microbiome maintains functional diversity in orthologous enzymes. Small changes in the structure of designed inhibitors can induce significant conformational changes in the β-glucuronidase active site. Finally, we establish that β-glucuronidase inhibition does not alter the serum pharmacokinetics of irinotecan or its metabolites in mice. Together, the data presented advance our in vitro and in vivo understanding of the microbial β-glucuronidases, a promising new set of targets for controlling drug-induced gastrointestinal toxicity.
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Affiliation(s)
- Bret D Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Adam B Roberts
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Rebecca M Pollet
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - James D Ingle
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Samuel J Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | | | - Leah Guthrie
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sara K O'Neal
- Department of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Sara J Robinson
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Makani Dollinger
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Esteban Figueroa
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Sarah R McShane
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Rachel D Cohen
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Jian Jin
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Stephen V Frye
- Department of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - William C Zamboni
- Department of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, NC 27599-3290, USA
| | - Charles Pepe-Ranney
- Department of Soil and Crop Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Sridhar Mani
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-3290, USA.
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11
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