1
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Greenhalgh R, Klure DM, Orr TJ, Armstrong NM, Shapiro MD, Dearing MD. The desert woodrat (Neotoma lepida) induces a diversity of biotransformation genes in response to creosote bush resin. Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109870. [PMID: 38428625 PMCID: PMC11006593 DOI: 10.1016/j.cbpc.2024.109870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/03/2024]
Abstract
Liver biotransformation enzymes have long been thought to enable animals to feed on diets rich in xenobiotic compounds. However, despite decades of pharmacological research in humans and rodents, little is known about hepatic gene expression in specialized mammalian herbivores feeding on toxic diets. Leveraging a recently identified population of the desert woodrat (Neotoma lepida) found to be highly tolerant to toxic creosote bush (Larrea tridentata), we explored the expression changes of suites of biotransformation genes in response to diets enriched with varying amounts of creosote resin. Analysis of hepatic RNA-seq data indicated a dose-dependent response to these compounds, including the upregulation of several genes encoding transcription factors and numerous phase I, II, and III biotransformation families. Notably, elevated expression of five biotransformation families - carboxylesterases, cytochromes P450, aldo-keto reductases, epoxide hydrolases, and UDP-glucuronosyltransferases - corresponded to species-specific duplication events in the genome, suggesting that these genes play a prominent role in N. lepida's adaptation to creosote bush. Building on pharmaceutical studies in model rodents, we propose a hypothesis for how the differentially expressed genes are involved in the biotransformation of creosote xenobiotics. Our results provide some of the first details about how these processes likely operate in the liver of a specialized mammalian herbivore.
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Affiliation(s)
- Robert Greenhalgh
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Dylan M Klure
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Teri J Orr
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Noah M Armstrong
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
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2
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Dearing MD, Orr TJ, Klure DM, Greenhalgh R, Weinstein SB, Stapleton T, Yamada KY, Nelson MD, Doolin ML, Nielsen DP, Matocq MD, Shapiro MD. Toxin tolerance across landscapes: Ecological exposure not a prerequisite. Funct Ecol 2022; 36:2119-2131. [PMID: 37727272 PMCID: PMC10508905 DOI: 10.1111/1365-2435.14093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/27/2022] [Indexed: 09/21/2023]
Abstract
Little is known about the tolerances of mammalian herbivores to plant specialized metabolites across landscapes.We investigated the tolerances of two species of herbivorous woodrats, Neotoma lepida (desert woodrat) and Neotoma bryanti (Bryant's woodrat) to creosote bush (Larrea tridentata), a widely distributed shrub with a highly toxic resin. Woodrats were sampled from 13 locations both with and without creosote bush across a 900 km transect in the US southwest. We tested whether these woodrat populations consume creosote bush using plant metabarcoding of feces and quantified their tolerance to creosote bush through feeding trials using chow amended with creosote resin.Toxin tolerance was analyzed in the context of population structure across collection sites with microsatellite analyses. Genetic differentiation among woodrats collected from different locations was minimal within either species. Tolerance differed substantially between the two species, with N. lepida persisting 20% longer than N. bryanti in feeding trials with creosote resin. Furthermore, in both species, tolerance to creosote resin was similar among woodrats near or within creosote bush habitat. In both species, woodrats collected greater than 25 km from creosote had markedly lower tolerances to creosote resin compared to animals from within the range of creosote bush.The results imply that mammalian herbivores are adapted to the specialized metabolites of plants in their diet, and that this tolerance can extend several kilometers outside of the range of dietary items. That is, direct ecological exposure to the specialized chemistry of particular plant species is not a prerequisite for tolerance to these compounds. These findings lay the groundwork for additional studies to investigate the genetic mechanisms underlying toxin tolerance and to identify how these mechanisms are maintained across landscape-level scales in mammalian herbivores.
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Affiliation(s)
- M. Denise Dearing
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Teri J. Orr
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
- Department of Biology, New Mexico State University, 1780 East University Avenue, Las Cruces, New Mexico 88003, USA
| | - Dylan M. Klure
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Robert Greenhalgh
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Sara B. Weinstein
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Tess Stapleton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
| | - KayLene Y.H. Yamada
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences, Auburn, Alabama 36849, USA
| | - Madeleine D. Nelson
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Margaret. L. Doolin
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Danny P. Nielsen
- Department of Natural Resources & Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89775, USA
| | - Marjorie D. Matocq
- Department of Natural Resources & Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89775, USA
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
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3
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Skopec MM, Halpert JR, Dearing MD. Mammalian cytochrome P450 biodiversity: Physiological importance, function, and protein and genomic structures of cytochromes P4502B in multiple species of woodrats with different dietary preferences. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:107-129. [PMID: 35953153 DOI: 10.1016/bs.apha.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The vast diversity of cytochrome P450 enzymes in mammals has been proposed to result in large measure from plant-animal warfare, whereby evolution of chemical defenses such as phenolics and terpenoids in plants led to duplication and divergence of P450 genes in herbivores. Over evolutionary time, natural selection is predicted to have produced P450s with high affinity and enhanced metabolism of substrates that are ingested regularly by herbivores. Interestingly, however, almost all knowledge of the interactions of mammalian P450 enzymes with substrates stems from studies of the metabolism of drugs and model compounds rather than studies on wild mammalian herbivores and their respective PSMs. A question of particular interest centers on the role of individual P450 enzymes in the ability of certain herbivores to specialize on plants that are lethal to most other species, including those from the same genus as the specialists. We tackled this intricate problem using a tractable natural system (herbivorous woodrats, genus Neotoma) focusing on comparisons of the specialist N. stephensi, the facultative specialist N. lepida, and the generalist N. albigula, and employing a cross-disciplinary approach involving ecology, biochemistry, pharmacology, structural biology, and genomics. Based on multiple findings suggesting the importance of CYP2B enzymes for ingestion of juniper and a major constituent, α-pinene, we characterized the structure, function and activity of several CYP2B enzymes in woodrats with different dietary habits. Results to date suggest that differences in CYP2B gene copy number may contribute to differential tolerance of PSMs among woodrat species, although additional work is warranted to firmly link gene copy number to juniper tolerance.
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Affiliation(s)
- Michele M Skopec
- Department of Zoology, Weber State University, Ogden, UT, United States
| | - James R Halpert
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, United States.
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States.
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4
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Greenhalgh R, Holding ML, Orr TJ, Henderson JB, Parchman TL, Matocq MD, Shapiro MD, Dearing MD. Trio‐binned genomes of the woodrats
Neotoma bryanti
and
Neotoma lepida
reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing genes. Mol Ecol Resour 2022; 22:2713-2731. [DOI: 10.1111/1755-0998.13650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Robert Greenhalgh
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
| | - Matthew L. Holding
- Department of Natural Resources & Environmental ScienceUniversity of Nevada1664 North Virginia StreetRenoNevada89775USA
- Present address: Life Sciences InstituteUniversity of Michigan210 Washtenaw AvenueAnn ArborMichigan48109USA
| | - Teri J. Orr
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
- Department of BiologyNew Mexico State University1780 East University AvenueLas CrucesNew Mexico88003USA
| | - James B. Henderson
- Center for Comparative GenomicsCalifornia Academy of Sciences55 Music Concourse DriveSan FranciscoCalifornia94118USA
| | - Thomas L. Parchman
- Department of BiologyUniversity of NevadaReno1664 North Virginia StreetNevada89775USA
| | - Marjorie D. Matocq
- Department of Natural Resources & Environmental ScienceUniversity of Nevada1664 North Virginia StreetRenoNevada89775USA
| | - Michael D. Shapiro
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
| | - M. Denise Dearing
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
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5
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Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
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Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
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6
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Nielsen DP, Matocq MD. Differences in dietary composition and preference maintained despite gene flow across a woodrat hybrid zone. Ecol Evol 2021; 11:4909-4919. [PMID: 33976858 PMCID: PMC8093690 DOI: 10.1002/ece3.7399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/16/2021] [Accepted: 02/28/2021] [Indexed: 12/16/2022] Open
Abstract
Ecotones, characterized by adjacent yet distinct biotic communities, provide natural laboratories in which to investigate how environmental selection influences the ecology and evolution of organisms. For wild herbivores, differential plant availability across sharp ecotones may be an important source of dietary-based selection.We studied small herbivore diet composition across a sharp ecotone where two species of woodrat, Neotoma bryanti and N. lepida, come into secondary contact with one another and hybridize. We quantified woodrat dietary preference through trnL metabarcoding of field-collected fecal pellets and experimental choice trials. Despite gene flow, parental N. bryanti and N. lepida maintain distinct diets across this fine spatial scale, and across temporal scales that span both wet and dry conditions. Neotoma bryanti maintained a more diverse diet, with Frangula californica (California coffeeberry) making up a large portion of its diet. Neotoma lepida maintains a less diverse diet, with Prunus fasciculata (desert almond) comprising more than half of its diet. Both F. californica and P. fasciculata are known to produce potentially toxic plant secondary compounds (PSCs), which should deter herbivory, yet these plants have relatively high nutritional value as measured by crude protein content. Neotoma bryanti and N. lepida consumed F. californica and P. fasciculata, respectively, in greater abundance than these plants are available on the landscape-indicating dietary selection. Finally, experimental preference trials revealed that N. bryanti exhibited a preference for F. californica, while N. lepida exhibited a relatively stronger preference for P. fasciculata. We find that N. bryanti exhibit a generalist herbivore strategy relative to N. lepida, which exhibit a more specialized feeding strategy in this study system.Our results suggest that woodrats respond to fine-scale environmental differences in plant availability that may require different metabolic strategies in order to balance nutrient acquisition while minimizing exposure to potentially toxic PSCs.
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Affiliation(s)
- Danny P. Nielsen
- Department of Natural Resources and Environmental ScienceUniversity of NevadaRenoNVUSA
- Graduate Program in EECBUniversity of NevadaRenoNVUSA
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental ScienceUniversity of NevadaRenoNVUSA
- Graduate Program in EECBUniversity of NevadaRenoNVUSA
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7
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Kitanovic S, Marks-Fife CA, Parkes QA, Wilderman PR, Halpert JR, Dearing MD. Cytochrome P450 2B diversity in a dietary specialist—the red tree vole (Arborimus longicaudus). J Mammal 2018. [DOI: 10.1093/jmammal/gyy039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AbstractAlthough herbivores rely on liver enzymes to biotransform plant secondary metabolites ingested in plant-based diets, only a few enzymes from a handful of species have been characterized at the genomic level. In this study, we examined cytochrome P450 2B (CYP2B) sequence diversity and gene copy number in a conifer specialist, the red tree vole (Arborimus longicaudus). We fed captive individuals exclusively Douglas-fir (Pseudotsuga menziesii) foliage, cloned and sequenced their liver CYP2B cDNA, and estimated CYP2B gene copy number. We identified 21 unique CYP2B nucleotide sequences, and 20 unique CYP2B amino acid sequences. Gene copy number of CYP2B was estimated at 7.7 copies per haploid genome. We compared red tree vole CYP2B with CYP2B sequences of a generalist, the prairie vole (Microtus ochrogaster), found in GenBank. Our study revealed that the CYP2B enzymes of red tree voles possess unique sequences compared to CYP2B enzymes of other herbivorous species. The unique combination of amino acid residues at key substrate recognition sites of CYP2B enzymes may underlie the ability of the red tree vole to specialize on a highly toxic diet of Douglas-fir.
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Affiliation(s)
| | - Chad A Marks-Fife
- Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Quincy A Parkes
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | | | - James R Halpert
- School of Pharmacy, University of Connecticut, Storrs, CT, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, UT, USA
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8
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Tawe L, Motshoge T, Ramatlho P, Mutukwa N, Muthoga CW, Dongho GBD, Martinelli A, Peloewetse E, Russo G, Quaye IK, Paganotti GM. Human cytochrome P450 2B6 genetic variability in Botswana: a case of haplotype diversity and convergent phenotypes. Sci Rep 2018; 8:4912. [PMID: 29559695 PMCID: PMC5861095 DOI: 10.1038/s41598-018-23350-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 03/09/2018] [Indexed: 01/11/2023] Open
Abstract
Identification of inter-individual variability for drug metabolism through cytochrome P450 2B6 (CYP2B6) enzyme is important for understanding the differences in clinical responses to malaria and HIV. This study evaluates the distribution of CYP2B6 alleles, haplotypes and inferred metabolic phenotypes among subjects with different ethnicity in Botswana. A total of 570 subjects were analyzed for CYP2B6 polymorphisms at position 516 G > T (rs3745274), 785 A > G (rs2279343) and 983 T > C (rs28399499). Samples were collected in three districts of Botswana where the population belongs to Bantu (Serowe/Palapye and Chobe) and San-related (Ghanzi) ethnicity. The three districts showed different haplotype composition according to the ethnic background but similar metabolic inferred phenotypes, with 59.12%, 34.56%, 2.10% and 4.21% of the subjects having, respectively, an extensive, intermediate, slow and rapid metabolic profile. The results hint at the possibility of a convergent adaptation of detoxifying metabolic phenotypes despite a different haplotype structure due to the different genetic background. The main implication is that, while there is substantial homogeneity of metabolic inferred phenotypes among the country, the response to drugs metabolized via CYP2B6 could be individually associated to an increased risk of treatment failure and toxicity. These are important facts since Botswana is facing malaria elimination and a very high HIV prevalence.
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Affiliation(s)
- Leabaneng Tawe
- University of Botswana, Department of Medical Laboratory Sciences, Gaborone, Botswana.,Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Sub-Saharan African Network for TB/HIV Research Excellence at Botswana-Harvard Partnership, Gaborone, Botswana
| | - Thato Motshoge
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Pleasure Ramatlho
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Naledi Mutukwa
- University of Botswana, Department of Pathology, Gaborone, Botswana
| | | | - Ghyslaine Bruna Djeunang Dongho
- Sapienza University of Rome, Department of Infectious Diseases and Public Health, Rome, Italy.,Evangelical University of Cameroon, Department of Biomedical Sciences, Bandjoun, Cameroon
| | - Axel Martinelli
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.,King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Thuwal, Saudi Arabia
| | - Elias Peloewetse
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Gianluca Russo
- Sapienza University of Rome, Department of Infectious Diseases and Public Health, Rome, Italy
| | - Isaac Kweku Quaye
- University of Namibia, Department of Biochemistry, Windhoek, Namibia
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana. .,University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. .,University of Botswana, Department of Biomedical Sciences, Gaborone, Botswana.
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9
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Kitanovic S, Orr TJ, Spalink D, Cocke GB, Schramm K, Wilderman PR, Halpert JR, Dearing MD. Role of cytochrome P450 2B sequence variation and gene copy number in facilitating dietary specialization in mammalian herbivores. Mol Ecol 2018; 27:723-736. [DOI: 10.1111/mec.14480] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Teri J. Orr
- Department of Biology University of Utah Salt Lake City UT USA
| | - Daniel Spalink
- Department of Biology University of Utah Salt Lake City UT USA
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10
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Huo L, Liu J, Dearing MD, Szklarz GD, Halpert JR, Wilderman PR. Rational Re-Engineering of the O-Dealkylation of 7-Alkoxycoumarin Derivatives by Cytochromes P450 2B from the Desert Woodrat Neotoma lepida. Biochemistry 2017; 56:2238-2246. [DOI: 10.1021/acs.biochem.7b00097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Lu Huo
- Department
of Pharmaceutical Science, University of Connecticut School of Pharmacy, Storrs, Connecticut 06269-3092, United States
| | - Jingbao Liu
- Department
of Pharmaceutical Science, University of Connecticut School of Pharmacy, Storrs, Connecticut 06269-3092, United States
| | - M. Denise Dearing
- Department
of Biology, University of Utah, Salt Lake City, Utah 84112, United States
| | - Grazyna D. Szklarz
- Department
of Pharmaceutical Sciences, West Virginia University School of Pharmacy, Morgantown, West Virginia 26506, United States
| | - James R. Halpert
- Department
of Pharmaceutical Science, University of Connecticut School of Pharmacy, Storrs, Connecticut 06269-3092, United States
| | - P. Ross Wilderman
- Department
of Pharmaceutical Science, University of Connecticut School of Pharmacy, Storrs, Connecticut 06269-3092, United States
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11
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Okamatsu G, Komatsu T, Ono Y, Inoue H, Uchide T, Onaga T, Endoh D, Kitazawa T, Hiraga T, Uno Y, Teraoka H. Characterization of feline cytochrome P450 2B6. Xenobiotica 2016; 47:93-102. [DOI: 10.3109/00498254.2016.1145754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Gaku Okamatsu
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Tetsuya Komatsu
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Yuka Ono
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Hiroki Inoue
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Tsuyoshi Uchide
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Takenori Onaga
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Takio Kitazawa
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Takeo Hiraga
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
| | - Yasuhiro Uno
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories, Ltd., Kainan, Wakayama, Japan
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan and
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12
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Shah MB, Liu J, Huo L, Zhang Q, Dearing MD, Wilderman PR, Szklarz GD, Stout CD, Halpert JR. Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives as Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism. Mol Pharmacol 2016; 89:435-45. [PMID: 26826176 DOI: 10.1124/mol.115.102111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/20/2016] [Indexed: 01/09/2023] Open
Abstract
Crystal structures of CYP2B35 and CYP2B37 from the desert woodrat were solved in complex with 4-(4-chlorophenyl)imidazole (4-CPI). The closed conformation of CYP2B35 contained two molecules of 4-CPI within the active site, whereas the CYP2B37 structure demonstrated an open conformation with three 4-CPI molecules, one within the active site and the other two in the substrate access channel. To probe structure-function relationships of CYP2B35, CYP2B37, and the related CYP2B36, we tested the O-dealkylation of three series of related substrates-namely, 7-alkoxycoumarins, 7-alkoxy-4-(trifluoromethyl)coumarins, and 7-alkoxy-4-methylcoumarins-with a C1-C7 side chain. CYP2B35 showed the highest catalytic efficiency (kcat/KM) with 7-heptoxycoumarin as a substrate, followed by 7-hexoxycoumarin. In contrast, CYP2B37 showed the highest catalytic efficiency with 7-ethoxy-4-(trifluoromethyl)coumarin (7-EFC), followed by 7-methoxy-4-(trifluoromethyl)coumarin (7-MFC). CYP2B35 had no dealkylation activity with 7-MFC or 7-EFC. Furthermore, the new CYP2B-4-CPI-bound structures were used as templates for docking the 7-substituted coumarin derivatives, which revealed orientations consistent with the functional studies. In addition, the observation of multiple -Cl and -NH-π interactions of 4-CPI with the aromatic side chains in the CYP2B35 and CYP2B37 structures provides insight into the influence of such functional groups on CYP2B ligand binding affinity and specificity. To conclude, structural, computational, and functional analysis revealed striking differences between the active sites of CYP2B35 and CYP2B37 that will aid in the elucidation of new structure-activity relationships.
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Affiliation(s)
- Manish B Shah
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Jingbao Liu
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Lu Huo
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Qinghai Zhang
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - M Denise Dearing
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - P Ross Wilderman
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Grazyna D Szklarz
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - C David Stout
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - James R Halpert
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
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13
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Skopec MM, Kohl KD, Schramm K, Halpert JR, Dearing MD. Using the Specialization Framework to Determine Degree of Dietary Specialization in a Herbivorous Woodrat. J Chem Ecol 2015; 41:1059-68. [PMID: 26631406 DOI: 10.1007/s10886-015-0654-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/09/2015] [Accepted: 11/19/2015] [Indexed: 12/26/2022]
Abstract
To be considered a dietary specialist, mammalian herbivores must consume large quantities of a plant species considered "difficult" with respect to nutrient or toxin content, and possess specialized adaptations to deal with plant defensive compounds or low nutritional content. Populations of Neotoma lepida in the Great Basin consume Juniperus osteosperma, a plant heavily defended by terpenes, but a detailed dietary analysis of this population is lacking. Therefore, we investigated the extent of dietary specialization in this species in comparison with the better-studied specialist species, N. stephensi. Microhistological analysis of feces from N. lepida revealed that greater than 90% of their diet in nature was comprised of juniper. In laboratory tolerance trials, N. lepida tolerated a diet of 80% J. osteosperma, similar to that observed for N. stephensi. There was no difference in the abilities of N. lepida and N. stephensi to metabolize hexobarbital, a proxy compound for terpene metabolism. In preference tests of native and non-native juniper species, N. lepida did not exhibit a preference for its native or co-occurring juniper, J. osteosperma, over the non-native species, J. monosperma, whereas N. stephensi preferred its native or co-occurring juniper J. monosperma over non-native J. osteosperma. Behavioral and habitat differences between these woodrat species lead to the categorization of N. stephensi as an obligate juniper specialist with a small range that overlaps that of its preferred food, J. monosperma, and N. lepida as a facultative juniper specialist with a large range, and only a portion of its distribution containing populations that feed extensively on J. osteosperma.
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Affiliation(s)
- Michele M Skopec
- Department of Zoology, Weber State University, 1415 Edvalson Dr., Ogden, UT, 84408, USA.
| | - Kevin D Kohl
- Department of Biology, University of Utah, Salt Lake City, 84112, UT, USA
| | - Katharina Schramm
- Department of Zoology, Weber State University, 1415 Edvalson Dr., Ogden, UT, 84408, USA
- Department of Biology, University of Utah, Salt Lake City, 84112, UT, USA
| | - James R Halpert
- School of Pharmacy, University of Connecticut, Storrs, CT, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, 84112, UT, USA
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14
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Wilderman PR, Jang HH, Malenke JR, Salib M, Angermeier E, Lamime S, Dearing MD, Halpert JR. Functional characterization of cytochromes P450 2B from the desert woodrat Neotoma lepida. Toxicol Appl Pharmacol 2013; 274:393-401. [PMID: 24361551 DOI: 10.1016/j.taap.2013.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
Abstract
Mammalian detoxification processes have been the focus of intense research, but little is known about how wild herbivores process plant secondary compounds, many of which have medicinal value or are drugs. cDNA sequences that code for three enzymes of the cytochrome P450 (CYP) 2B subfamily, here termed 2B35, 2B36, and 2B37 have been recently identified from a wild rodent, the desert woodrat (Malenke et al., 2012). Two variant clones of each enzyme were engineered to increase protein solubility and to facilitate purification, as reported for CYP2B enzymes from multiple species. When expressed in Escherichia coli each of the woodrat proteins gave the characteristic maximum at 450nm in a reduced carbon monoxide difference spectrum but generally expressed at lower levels than rat CYP2B1. Two enzymes, 2B36 and 2B37, showed dealkylation activity with the model substrates 7-ethoxy-4-(trifluoromethyl)coumarin and 7-benzyloxyresorufin, whereas 2B35 was inactive. Binding of the monoterpene (+)-α-pinene produced a Type I shift in the absorbance spectrum of each enzyme. Mutation of 2B37 at residues 114, 262, or 480, key residues governing ligand interactions with other CYP2B enzymes, did not significantly change expression levels or produce the expected functional changes. In summary, two catalytic and one ligand-binding assay are sufficient to distinguish among CYP2B35, 2B36, and 2B37. Differences in functional profiles between 2B36 and 2B37 are partially explained by changes in substrate recognition site residue 114, but not 480. The results advance our understanding of the mechanisms of detoxification in wild mammalian herbivores and highlight the complexity of this system.
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Affiliation(s)
- P Ross Wilderman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Hyun-Hee Jang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jael R Malenke
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Mariam Salib
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Elisabeth Angermeier
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Sonia Lamime
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - James R Halpert
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
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15
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Kurnath P, Dearing MD. Warmer ambient temperatures depress liver function in a mammalian herbivore. Biol Lett 2013; 9:20130562. [PMID: 24046878 DOI: 10.1098/rsbl.2013.0562] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Diet selection in mammalian herbivores is thought to be mainly influenced by intrinsic factors such as nutrients and plant secondary compounds, yet extrinsic factors like ambient temperature may also play a role. In particular, warmer ambient temperatures could enhance the toxicity of plant defence compounds through decreased liver metabolism of herbivores. Temperature-dependent toxicity has been documented in pharmacology and agriculture science but not in wild mammalian herbivores. Here, we investigated how ambient temperature affects liver metabolism in the desert woodrat, Neotoma lepida. Woodrats (n = 21) were acclimated for 30 days to two ambient temperatures (cool = 21°C, warm = 29°C). In a second experiment, the temperature exposure was reduced to 3.5 h. After temperature treatments, animals were given a hypnotic agent and clearance time of the agent was estimated from the duration of the hypnotic state. The average clearance time of the agent in the long acclimation experiment was 45% longer for animals acclimated to 29°C compared with 21°C. Similarly, after the short exposure experiment, woodrats at 29°C had clearance times 26% longer compared with 21°C. Our results are consistent with the hypothesis that liver function is reduced at warmer environmental temperatures and may provide a physiological mechanism through which climate change affects herbivorous mammals.
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Affiliation(s)
- Patrice Kurnath
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
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16
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Skopec MM, Malenke JR, Halpert JR, Denise Dearing M. An in vivo assay for elucidating the importance of cytochromes P450 for the ability of a wild mammalian herbivore (Neotoma lepida) to consume toxic plants. Physiol Biochem Zool 2013; 86:593-601. [PMID: 23995490 DOI: 10.1086/672212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An in vivo assay using the cytochrome P450 (P450) suicide inhibitor 1-aminobenzotriazole (ABT) and 24-h food intake was developed to determine the relative importance of P450s in two populations of Neotoma lepida with respect to biotransformation of plant secondary compounds in the animals' natural diets. The efficacy of ABT as a P450 inhibitor was first validated using hypnotic-state assays with and without pretreatment with ABT. Pretreatment with 100 mg/kg ABT by gavage increased hexobarbital sleep times 3-4-fold in both populations, showing effective inhibition of P450s in woodrats. Next, the Great Basin population was fed a terpene-rich juniper diet, and the Mojave population was fed a phenolic-rich creosote diet, with rabbit chow serving as the control diet in each group. Treatment with ABT inhibited food intake in the Great Basin population fed the juniper diet to a greater extent (35%) than the Great Basin population fed the control diet (19%) or the Mojave population fed the creosote diet (16%). The food intake of the Mojave population fed the control diet was not significantly inhibited by ABT. The findings suggest that the biotransformation of terpenes in juniper relies more heavily on P450s than that of phenolics in creosote. This assay provides an inexpensive and noninvasive method to explore the relative importance of P450s in the biotransformation strategies of wild mammalian herbivores.
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Affiliation(s)
- Michele M Skopec
- Department of Zoology, Weber State University, Ogden, Utah 84408, USA.
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