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Hou M, Akhtar MS, Hayashi M, Ashino R, Matsumoto-Oda A, Hayakawa T, Ishida T, Melin AD, Imai H, Kawamura S. Reduction of bitter taste receptor gene family in folivorous colobine primates relative to omnivorous cercopithecine primates. Primates 2024:10.1007/s10329-024-01124-w. [PMID: 38605281 DOI: 10.1007/s10329-024-01124-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/26/2024] [Indexed: 04/13/2024]
Abstract
Bitter taste perception is important in preventing animals from ingesting potentially toxic compounds. Whole-genome assembly (WGA) data have revealed that bitter taste receptor genes (TAS2Rs) comprise a multigene family with dozens of intact and disrupted genes in primates. However, publicly available WGA data are often incomplete, especially for multigene families. In this study, we employed a targeted capture (TC) approach specifically probing TAS2Rs for ten species of cercopithecid primates with diverse diets, including eight omnivorous cercopithecine species and two folivorous colobine species. We designed RNA probes for all TAS2Rs that we modeled to be intact in the common ancestor of cercopithecids ("ancestral-cercopithecid TAS2R gene set"). The TC was followed by short-read and high-depth massive-parallel sequencing. TC retrieved more intact TAS2R genes than found in WGA databases. We confirmed a large number of gene "births" at the common ancestor of cercopithecids and found that the colobine common ancestor and the cercopithecine common ancestor had contrasting trajectories: four gene "deaths" and three gene births, respectively. The number of intact TAS2R genes was markedly reduced in colobines (25-28 detected via TC and 20-26 detected via WGA analysis) as compared with cercopithecines (27-36 via TC and 19-30 via WGA). Birth or death events occurred at almost every phylogenetic-tree branch, making the composition of intact genes variable among species. These results show that evolutionary change in intact TAS2R genes is a complex process, refute a simple general prediction that herbivory favors more TAS2R genes, and have implications for understanding dietary adaptations and the evolution of detoxification abilities.
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Affiliation(s)
- Min Hou
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Muhammad Shoaib Akhtar
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Masahiro Hayashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Ryuichi Ashino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Akiko Matsumoto-Oda
- Graduate School of Tourism Sciences, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Japan Monkey Centre, Inuyama, Aichi, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Alberta, Canada
| | - Hiroo Imai
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Kyoto, Aichi, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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Veilleux CC, Dominy NJ, Melin AD. The sensory ecology of primate food perception, revisited. Evol Anthropol 2022; 31:281-301. [PMID: 36519416 DOI: 10.1002/evan.21967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 09/06/2022] [Accepted: 10/23/2022] [Indexed: 12/23/2022]
Abstract
Twenty years ago, Dominy and colleagues published "The sensory ecology of primate food perception," an impactful review that brought new perspectives to understanding primate foraging adaptations. Their review synthesized information on primate senses and explored how senses informed feeding behavior. Research on primate sensory ecology has seen explosive growth in the last two decades. Here, we revisit this important topic, focusing on the numerous new discoveries and lines of innovative research. We begin by reviewing each of the five traditionally recognized senses involved in foraging: audition, olfaction, vision, touch, and taste. For each sense, we provide an overview of sensory function and comparative ecology, comment on the state of knowledge at the time of the original review, and highlight advancements and lingering gaps in knowledge. Next, we provide an outline for creative, multidisciplinary, and innovative future research programs that we anticipate will generate exciting new discoveries in the next two decades.
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Affiliation(s)
- Carrie C Veilleux
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, Hanover, New Hampshire, USA
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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3
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Guevara EE, Greene LK, Blanco MB, Farmer C, Ranaivonasy J, Ratsirarson J, Mahefarisoa KL, Rajaonarivelo T, Rakotondrainibe HH, Junge RE, Williams CV, Rambeloson E, Rasoanaivo HA, Rahalinarivo V, Andrianandrianina LH, Clayton JB, Rothman RS, Lawler RR, Bradley BJ, Yoder AD. Molecular Adaptation to Folivory and the Conservation Implications for Madagascar’s Lemurs. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.736741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change in RNASE1, a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genus Propithecus; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change in RNASE1 that could underlie a capacity for efficient folivory. We characterized RNASE1 in 21 lemur species representing all five families and members of the three extant folivorous lineages: (1) bamboo lemurs (family Lemuridae), (2) sportive lemurs (family Lepilemuridae), and (3) indriids (family Indriidae). We found pervasive sequence change in RNASE1 across all indriids, a dN/dS value > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species’ ecology and, in turn, their resilience to habitat change. Moreover, our results support the body of work demonstrating that not all primate folivores are built the same and reiterate the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.
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Dong X, Liang Q, Li J, Feng P. Positive selection drives the evolution of a primate bitter taste receptor gene. Ecol Evol 2021; 11:5459-5467. [PMID: 34026020 PMCID: PMC8131804 DOI: 10.1002/ece3.7440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
Bitter taste perception is important in food choice of animals, and it is mediated by bitter taste receptor (T2R) containing three regions: extracellular regions (ECs), transmembrane regions (TMs), and intracellular regions (ICs). It is hypothesized that ECs, TMs, and ICs are under different selective pressures, with ECs being unstable while TMs and ICs being constrained. To test this hypothesis, we examined the selective pressures on one of the bitter taste receptor genes-T2R1 and its different areas from 35 primates and found that T2R1 was under neutral evolution but with some positively selected sites in it. Further analyses suggested that TMs, ICs, and the concatenated transmembrane region TM1237 were under purifying selection; in contrast, extracellular regions, the first and second extracellular loop (EL1, EL2), were subject to positive selection with several positively selected sites in them. Therefore, this study supported the above-mentioned hypothesis. The reason why EL1 and EL2 of T2R1 have positively selected sites is probably due to their participation in forming the cap-like structure involved in ligand binding. Positive selection acts as a driving force of the T2R1 functional differentiation and confers the ability to discern various bitter substances for primates, which could help them to adapt to the changing environment during the evolutionary course.
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Affiliation(s)
- Xiaoyan Dong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Qiufang Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Jiaping Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
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Structure-Function Analyses of Human Bitter Taste Receptors-Where Do We Stand? Molecules 2020; 25:molecules25194423. [PMID: 32993119 PMCID: PMC7582848 DOI: 10.3390/molecules25194423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The finding that bitter taste receptors are expressed in numerous tissues outside the oral cavity and fulfill important roles in metabolic regulation, innate immunity and respiratory control, have made these receptors important targets for drug discovery. Efficient drug discovery depends heavily on detailed knowledge on structure-function-relationships of the target receptors. Unfortunately, experimental structures of bitter taste receptors are still lacking, and hence, the field relies mostly on structures obtained by molecular modeling combined with functional experiments and point mutageneses. The present article summarizes the current knowledge on the structure–function relationships of human bitter taste receptors. Although these receptors are difficult to express in heterologous systems and their homology with other G protein-coupled receptors is very low, detailed information are available at least for some of these receptors.
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6
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Baldwin MW, Ko MC. Functional evolution of vertebrate sensory receptors. Horm Behav 2020; 124:104771. [PMID: 32437717 DOI: 10.1016/j.yhbeh.2020.104771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Sensory receptors enable animals to perceive their external world, and functional properties of receptors evolve to detect the specific cues relevant for an organism's survival. Changes in sensory receptor function or tuning can directly impact an organism's behavior. Functional tests of receptors from multiple species and the generation of chimeric receptors between orthologs with different properties allow for the dissection of the molecular basis of receptor function and identification of the key residues that impart functional changes in different species. Knowledge of these functionally important sites facilitates investigation into questions regarding the role of epistasis and the extent of convergence, as well as the timing of sensory shifts relative to other phenotypic changes. However, as receptors can also play roles in non-sensory tissues, and receptor responses can be modulated by numerous other factors including varying expression levels, alternative splicing, and morphological features of the sensory cell, behavioral validation can be instrumental in confirming that responses observed in heterologous systems play a sensory role. Expression profiling of sensory cells and comparative genomics approaches can shed light on cell-type specific modifications and identify other proteins that may affect receptor function and can provide insight into the correlated evolution of complex suites of traits. Here we review the evolutionary history and diversity of functional responses of the major classes of sensory receptors in vertebrates, including opsins, chemosensory receptors, and ion channels involved in temperature-sensing, mechanosensation and electroreception.
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Affiliation(s)
| | - Meng-Ching Ko
- Max Planck Institute for Ornithology, Seewiesen, Germany
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7
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Purba LHPS, Widayati KA, Suzuki-Hashido N, Itoigawa A, Hayakawa T, Nila S, Juliandi B, Suryobroto B, Imai H. Evolution of the bitter taste receptor TAS2R38 in colobines. Primates 2020; 61:485-494. [PMID: 32006126 DOI: 10.1007/s10329-020-00799-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/21/2020] [Indexed: 01/08/2023]
Abstract
Bitter taste perception enables the detection of potentially toxic molecules and thus evokes avoidance behavior in vertebrates. It is mediated by bitter taste receptors, TAS2Rs. One of the best-studied TAS2R is TAS2R38. Phenylthiocarbamide (PTC) perception and TAS2R38 receptors vary across primate species, and this variation may be related to variation in dietary preferences. In particular, we previously found that the low sensitivity of TAS2R38s in Asian colobines likely evolved as an adaptation to their leaf-eating behavior. However, it remains unclear whether this low PTC sensitivity is a general characteristic of the subfamily Colobinae, a primate group that feeds predominantly on leaves. We performed genetic analyses, functional assays with mutant proteins, and behavioral analyses to evaluate the general characteristics of TAS2R38 in colobines. We found that PTC sensitivity is lower in TAS2R38s of African colobines than in TAS2R38s of omnivorous macaques. Furthermore, two amino acids shared between Asian and African colobines were responsible for low sensitivity to PTC, suggesting that the last common ancestor of extant colobines had this phenotype. We also detected amino acid differences between TAS2R38s in Asian and African colobines, indicating that they evolved independently after the separation of these groups.
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Affiliation(s)
| | - Kanthi Arum Widayati
- Department of Biology, Bogor Agricultural University, Kampus IPB Darmaga, Bogor, 16680, Indonesia.
| | - Nami Suzuki-Hashido
- Academy of Emerging Sciences, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan.,Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Akihiro Itoigawa
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.,Molecular Biology Section, Department of Cellular and Molecular Biology, Primates Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, N10W5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.,Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi, 484-8506, Japan.,Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan
| | - Sarah Nila
- Department of Biology, Bogor Agricultural University, Kampus IPB Darmaga, Bogor, 16680, Indonesia
| | - Berry Juliandi
- Department of Biology, Bogor Agricultural University, Kampus IPB Darmaga, Bogor, 16680, Indonesia
| | - Bambang Suryobroto
- Department of Biology, Bogor Agricultural University, Kampus IPB Darmaga, Bogor, 16680, Indonesia
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primates Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan.
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Widayati KA, Yan X, Suzuki‐Hashido N, Itoigawa A, Purba LHPS, Fahri F, Terai Y, Suryobroto B, Imai H. Functional divergence of the bitter receptor TAS2R38 in Sulawesi macaques. Ecol Evol 2019; 9:10387-10403. [PMID: 31624557 PMCID: PMC6787832 DOI: 10.1002/ece3.5557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 01/31/2023] Open
Abstract
ABSTRACT Bitter perception is mediated by G protein-coupled receptors TAS2Rs and plays an important role in avoiding the ingestion of toxins by inducing innate avoidance behavior in mammals. One of the best-studied TAS2Rs is TAS2R38, which mediates the perception of the bitterness of synthetic phenylthiocarbamide (PTC). Previous studies of TAS2R38 have suggested that geographical separation enabled the independent divergence of bitter taste perception. The functional divergence of TAS2R38 in allopatric species has not been evaluated. We characterized the function of TAS2R38 in four allopatric species of Sulawesi macaques on Sulawesi Island. We found variation in PTC taste perception both within and across species. In most cases, TAS2R38 was sensitive to PTC, with functional divergence among species. We observed different truncated TAS2R38s that were not responsive to PTC in each species of Macaca nigra and M. nigrescens due to premature stop codons. Some variants of intact TAS2R38 with an amino acid substitution showed low sensitivity to PTC in M. tonkeana. Similarly, this intact TAS2R38 with PTC-low sensitivity has also been found in humans. We detected a shared haplotype in all four Sulawesi macaques, which may be the ancestral haplotype of Sulawesi macaques. In addition to shared haplotypes among Sulawesi macaques, other TAS2R38 haplotypes were species-specific. These results implied that the variation in TAS2R38 might be shaped by geographical patterns and local adaptation. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.908jf3r.
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Affiliation(s)
- Kanthi Arum Widayati
- Department of BiologyBogor Agricultural UniversityBogorIndonesia
- Wildlife Research CenterKyoto UniversityKyotoJapan
| | - Xiaochan Yan
- Primate Research InstituteKyoto UniversityInuyamaJapan
| | | | | | | | - Fahri Fahri
- Department of BiologyTadulako UniversityPaluIndonesia
| | - Yohey Terai
- Department of Evolutionary Studies of BiosystemsThe Graduate University for Advanced StudiesHayamaJapan
| | | | - Hiroo Imai
- Primate Research InstituteKyoto UniversityInuyamaJapan
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Itoigawa A, Hayakawa T, Suzuki-Hashido N, Imai H. A natural point mutation in the bitter taste receptor TAS2R16 causes inverse agonism of arbutin in lemur gustation. Proc Biol Sci 2019; 286:20190884. [PMID: 31161904 DOI: 10.1098/rspb.2019.0884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bitter taste enables the detection of potentially harmful substances and is mediated by bitter taste receptors, TAS2Rs, in vertebrates. Few antagonists and inverse agonists of TAS2Rs have been identified, especially natural compounds. TAS2R16s in humans, apes and Old World monkeys (Catarrhini, Anthropoidea) recognize β-glucoside analogues as specific agonists. Here, we investigated responses of TAS2R16 to β-glucosides in non-anthropoid primates, namely lemurs (Lemuriformes, Strepsirrhini). Salicin acted as an agonist on lemur TAS2R16. Arbutin acted as an agonist in the ring-tailed lemur ( Lemur catta) but as an inverse agonist in black lemur ( Eulemur macaco) and black-and-white ruffed lemur ( Varecia variegata). We identified a strepsirrhine-specific amino acid substitution responsible for the inverse agonism of arbutin. In a food preference test, salicin bitterness was inhibited by arbutin in the black lemur. Structural modelling revealed this locus was important for a rearrangement of the intracellular end of transmembrane helix 7 (TM7). Accordingly, arbutin is the first known natural inverse agonist of TAS2Rs, contributing to our understanding of receptor-ligand interactions and the molecular basis of the unique feeding habit diversification in lemurs. Furthermore, the identification of a causal point mutation suggests that TAS2R can acquire functional changes according to feeding habits and environmental conditions.
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Affiliation(s)
- Akihiro Itoigawa
- 1 Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan.,3 Japan Society for the Promotion of Science , Kojimachi, Chiyoda-ku, Tokyo 102-0083 , Japan
| | - Takashi Hayakawa
- 2 Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan.,4 Faculty of Environmental Earth Science, Hokkaido University , N10W5, Kita-ku, Sapporo, Hokkaido 060-0810 , Japan.,5 Japan Monkey Centre , 26 Inuyamakanrin, Inuyama, Aichi 484-0081 , Japan
| | - Nami Suzuki-Hashido
- 3 Japan Society for the Promotion of Science , Kojimachi, Chiyoda-ku, Tokyo 102-0083 , Japan.,6 Chubu University Academy of Emerging Sciences , 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 , Japan
| | - Hiroo Imai
- 1 Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan
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