Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution

Missense genetic variants in major bitter taste receptors are associated with diet quality and food intake in a highly admixed underrepresented population

BACKGROUND AND AIMS

To investigate associations between Single Nucleotide Polymorphisms (SNPs) in the TAS1R and TAS2R taste receptors and diet quality, intake of alcohol, added sugar, and fat, using linear regression and machine learning techniques in a highly admixed population.

METHODS

In the ISA-Capital health survey, 901 individuals were interviewed and had socioeconomic, demographic, health characteristics, along with dietary information obtained through two 24-h recalls. Data on 12 components related to food groups, nutrients, and calories was combined into a diet quality score (BHEI-R). BHEI-R, SoFAAs (calories from added sugar, saturated fat, and alcohol) and Alcohol use were tested for associations with 255 TAS2R SNPs and 73 TAS1R SNPs for 637 individuals with regression analysis and Random Forest. Significant SNPs were combined into Genetic taste scores (GTSs).

RESULTS

Among 23 SNPs significantly associated either by stepwise linear/logistic regression or random forest with any possible biological functionality, the missense variants rs149217752 in TAS2R40, for SoFAAs, and rs2233997 in TAS2R4, were associated with both BHEI-R (under 4% increase in Mean Squared Error) and SoFAAs. GTSs increased the variance explanation of quantitative phenotypes and there was a moderately high AUC for alcohol use.

CONCLUSIONS

The study provides insights into the genetic basis of human taste perception through the identification of missense variants in the TAS2R gene family. These findings may contribute to future strategies in precision nutrition aimed at improving food quality by reducing added sugar, saturated fat, and alcohol intake.

Generalised Periodontitis: Examining TAS2R16 Serum Levels and Common Gene Polymorphisms (rs860170, rs978739, rs1357949)

The objective of this study was to evaluate and compare the associations between TAS2R16 serum levels and common gene rs860170, rs978739, and rs1357949 polymorphisms in patients affected by generalized periodontitis. The study enrolled 590 patients: 280 patients with periodontitis and 310 healthy controls as a reference group. Patients underwent periodontal examination and radiographic analysis to confirm the periodontitis diagnosis. Blood samples were collected, and the DNA salting-out method was used for DNA extraction from peripheral venous blood. Genotyping of TAS2R16 (rs860170, rs978739, and rs1357949) was performed using real-time polymerase chain reaction (RT-PCR), and serum level analysis was performed for both periodontitis-affected patients and reference group subjects. The analysis of TAS2R16 rs860170 (TT, CT, and CC) showed a statistically significant difference between generalized periodontitis and the reference group (41.8%, 58.2%, and 0% vs. 38.7%, 56.1%, and 5.2%, p < 0.001). TAS2R16 rs860170 (TT, CT, and CC) showed a statistically significant difference between males in generalized periodontitis and reference groups (38.4%, 61.6%, and 0% vs. 32.9%, 56.6%, and 10.5%, p = 0.002). Female-specific analysis showed that the TAS2R16 rs978739 C allele was more frequent in generalized periodontitis compared to the reference group (37.5% vs. 28.7%, p = 0.016). Subjects aged 70 years and older demonstrated a statistically significant difference in TAS2R16 rs860170 (TT, CT, and CC) between generalized periodontitis and the reference group (42.8%, 57.2%, and 0% vs. 38.6%, 53.8%, and 7.6%, p = 0.003). TAS2R16 serum levels were elevated in generalized periodontitis compared to the reference group (0.112 (0.06) ng/mL vs. 0.075 (0.03) ng/mL, p = 0.002). Females carrying the TAS2R16 rs978739 C allele were more prone to generalized periodontitis development. Associations were found between TAS2R16 rs860170 polymorphisms, elevated TAS2R16 serum levels, and generalized periodontitis development.

Human subsistence and signatures of selection on chemosensory genes

Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. The transition from hunting and gathering to agriculture dramatically altered how humans acquire food. Recent genetic and linguistic studies suggest agriculture may have precipitated olfactory degeneration. Here, we explore the effects of subsistence behaviors on olfactory (OR) and taste (TASR) receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia. We analyze 378 functional OR and 26 functional TASR genes in 133 individuals across populations in Uganda (Twa, Sua, BaKiga) and the Philippines (Agta, Mamanwa, Manobo) with differing subsistence histories. We find no evidence of relaxed selection on chemosensory genes in agricultural populations. However, we identify subsistence-related signatures of local adaptation on chemosensory genes within each geographic region. Our results highlight the importance of culture, subsistence economy, and drift in human chemosensory perception.

The Ile191Val Variant of the TAS1R2 Subunit of Sweet Taste Receptors Is Associated With Reduced HbA1c in a Human Cohort With Variable Levels of Glucose Homeostasis

The Ile191Val variant of the TAS1R2 gene of sweet taste receptors causes a partial loss-of-function and is associated with reduced glucose excursions in a healthy lean cohort. However, it is unclear whether this polymorphism contributes to the regulation of glucose homeostasis in metabolically unhealthy individuals. Thus, we used participants with variable glycemic profiles and obesity to assess the effects of the TAS1R2-Ile191Val variant. We found that the Val minor allele carriers had lower HbA1c at all levels of fasting glucose and glucose tolerance. These effects were not due to differences in beta-cell function or insulin sensitivity assessed with a frequently sampled intravenous glucose tolerance test. This study extends our previous findings and provides further evidence that sweet taste receptor function may contribute to glucose regulation in humans.

Role of Leu72Met of GHRL and Gln223Arg of LEPR Variants on Food Intake, Subjective Appetite, and Hunger-Satiety Hormones

Appetite regulation has been recognized as a promising target for the prevention of obesity, which has become a worldwide health issue. Polymorphisms in the genes of hormones or receptors including Leu72Met for ghrelin and Gln223Arg for the leptin receptor could play a role in dietary intake, hunger, and satiety process. The aim of this study was to analyze subjective appetite assessments, dietary intake, and appetite hormones in relationship to these polymorphisms. Subjects (n = 132) with normal BMIs were enrolled. Dietary intake was analyzed with 3-day diet records. Subjective appetite was measured by visual analogue scales. Biochemical parameters were measured after 12 h of fasting and 120′ following ingestion of a test meal. Ghrelin and leptin levels were measured by ELISA assay (enzyme-linked immunosorbent assay) and insulin by chemiluminescence assay. The polymorphisms were determined by allelic discrimination using TaqMan^® probes. Fasting ghrelin levels differed significantly between men and women. The consumption of fruit and bread/starch with added sugar servings, as indicated by dietary records, and measured ghrelin levels were higher in carriers of Leu72Met/Met72Met compared to Leu72Leu carriers; total sugar intake was higher in Gln223Gln carriers than in Gln223Arg/Arg223Arg carriers. In conclusion, the Leu72Met and Gln223Arg polymorphism in ghrelin and LEPR may contribute to differential responses to a standardized meal as evidenced by higher postprandial levels of ghrelin and may also contribute to a higher dietary sugar intake.

Demographic history was a formative mechanism of the genetic structure for the taste receptor TAS2R16 in human populations inhabiting Africa's Sahel/Savannah Belt

OBJECTIVES

Mode of subsistence is an important factor influencing dietary habits and the genetic structure of various populations through differential intensity of gene flow and selection pressures. Previous studies suggest that in Africa Taste 2 Receptor Member 16 (TAS2R16), which encodes the 7-transmembrane receptor protein for bitterness, might also be under positive selection pressure.

METHODS

However, since sampling coverage of populations was limited, we created a new TAS2R16 population dataset from across the African Sahel/Savannah belt representing various local populations of differing subsistence modes, linguistic affiliations, and geographic provenience. We sequenced the TAS2R16 exon gene and analyzed 2250 haplotypes among 19 populations.

RESULTS

We found no evidence for selection as a driving force of genetic variation at this locus; instead, we discovered a highly significant correlation between TAS2R16 genetic and geographical distances based on provenience of the sampled populations, strongly suggesting that genetic drift most likely prevailed over positive selection at this specific locus. We also found significant correlations with other independent loci, mainly in sedentary farmers.

DISCUSSION

Our results do not support the notion that the genetic diversity of TAS2R16 in Sahelian populations was shaped by selective pressures. This could result from several alternative and not mutually exclusive mechanisms, of which the possibility that, due to the pleiotropic nature of TAS2R16, selective pressures on other traits could counterbalance those acting on bitter taste perception, or that the change of diet in the Neolithic generally relaxed selective pressure on this gene.

The Role of the Intestinal Epithelium in the "Weep and Sweep" Response during Gastro-Intestinal Helminth Infections

Simple Summary

The immune system actively combats intruders such as bacteria, viruses, fungi, and protozoan and metazoan parasites using leukocytes. During an infection white blood cells are activated to internalize bacteria or viruses and release a number of molecules to kill pathogens. Unfortunately, those mechanisms are ineffective against larger intruders like helminths, which are too large to be killed by a single immune cell. To eliminate gastro-intestinal helminths an integrated response involving the nervous, endocrine, and immune systems are used to expel the parasites. This is achieved through increased gut hydration and muscle contractions which detach worms from the gut and lead to release outside the body in a “weep and sweep” response. Epithelial cells of the intestine are significant players in this process, being responsible for detecting the presence of helminths in the gut and participating in the regulation of parasite expulsion. This paper describes the role of the gut epithelium in detecting and eliminating helminths from the intestine.

Abstract

Helminths are metazoan parasites infecting around 1.5 billion people all over the world. During coevolution with hosts, worms have developed numerous ways to trick and evade the host immune response, and because of their size, they cannot be internalized and killed by immune cells in the same way as bacteria or viruses. During infection, a substantial Th₂ component to the immune response is evoked which helps restrain Th₁-mediated tissue damage. Although an enhanced Th₂ response is often not enough to kill the parasite and terminate an infection in itself, when tightly coordinated with the nervous, endocrine, and motor systems it can dislodge parasites from tissues and expel them from the gut. A significant role in this “weep and seep” response is attributed to intestinal epithelial cells (IEC). This review highlights the role of various IEC lineages (enterocytes, tuft cells, Paneth cells, microfold cells, goblet cells, and intestine stem cells) during the course of helminth infections and summarizes their roles in regulating gut architecture and permeability, and muscle contractions and interactions with the immune and nervous system.

The Ile191Val is a partial loss-of-function variant of the TAS1R2 sweet-taste receptor and is associated with reduced glucose excursions in humans

OBJECTIVE

Sweet taste receptors (STR) are expressed in the gut and other extra-oral tissues, suggesting that STR-mediated nutrient sensing may contribute to human physiology beyond taste. A common variant (Ile191Val) in the TAS1R2 gene of STR is associated with nutritional and metabolic outcomes independent of changes in taste perception. It is unclear whether this polymorphism directly alters STR function and how it may contribute to metabolic regulation.

METHODS

We implemented a combination of in vitro biochemical approaches to decipher the effects of TAS1R2 polymorphism on STR function. Then, as proof-of-concept, we assessed its effects on glucose homeostasis in apparently healthy lean participants.

RESULTS

The Ile191Val variant causes a partial loss of function of TAS1R2 through reduced receptor availability in the plasma membrane. Val minor allele carriers have reduced glucose excursions during an OGTT, mirroring effects previously seen in mice with genetic loss of function of TAS1R2. These effects were not due to differences in beta-cell function or insulin sensitivity.

CONCLUSIONS

Our pilot studies on a common TAS1R2 polymorphism suggest that STR sensory function in peripheral tissues, such as the intestine, may contribute to the regulation of metabolic control in humans.

Taste receptor polymorphisms and longevity: a systematic review and meta-analysis

Bitter taste receptors (TAS2R) are involved in a variety of non-tasting physiological processes, including immune-inflammatory ones. Therefore, their genetic variations might influence various traits. In particular, in different populations of South Italy (Calabria, Cilento, and Sardinia), polymorphisms of TAS2R16 and TAS238 have been analysed in association with longevity with inconsistent results. A meta-analytic approach to quantitatively synthesize the possible effect of the previous variants and, possibly, to reconcile the inconsistencies has been used in the present paper. TAS2R38 variants in the Cilento population were also analysed for their possible association with longevity and the obtained data have been included in the relative meta-analysis. In population from Cilento no association was found between TAS2R38 and longevity, and no association was observed as well, performing the meta-analysis with data of the other studies. Concerning TAS2R16 gene, instead, the genotype associated with longevity in the Calabria population maintained its significance in the meta-analysis with data from Cilento population, that, alone, were not significant in the previously published study. In conclusion, our results suggest that TAS2R16 genotype variant is associated with longevity in South Italy.

Contrasting Patterns of Gene Duplication, Relocation, and Selection Among Human Taste Genes

In humans, taste genes are responsible for perceiving at least 5 different taste qualities. Human taste genes’ evolutionary mechanisms need to be explored. We compiled a list of 69 human taste-related genes and divided them into 7 functional groups. We carried out comparative genomic and evolutionary analyses for these taste genes based on 8 vertebrate species. We found that relative to other groups of human taste genes, human TAS2R genes have a higher proportion of tandem duplicates, suggesting that tandem duplications have contributed significantly to the expansion of the human TAS2R gene family. Human TAS2R genes tend to have fewer collinear genes in outgroup species and evolve faster, suggesting that human TAS2R genes have experienced more gene relocations. Moreover, human TAS2R genes tend to be under more relaxed purifying selection than other genes. Our study sheds new insights into diverse and contrasting evolutionary patterns among human taste genes.

Ecological Sensing Through Taste and Chemosensation Mediates Inflammation: A Biological Anthropological Approach

Ecological sensing and inflammation have evolved to ensure optima between organism survival and reproductive success in different and changing environments. At the molecular level, ecological sensing consists of many types of receptors located in different tissues that orchestrate integrated responses (immune, neuroendocrine systems) to external and internal stimuli. This review describes emerging data on taste and chemosensory receptors, proposing them as broad ecological sensors and providing evidence that taste perception is shaped not only according to sense epitopes from nutrients but also in response to highly diverse external and internal stimuli. We apply a biological anthropological approach to examine how ecological sensing has been shaped by these stimuli through human evolution for complex interkingdom communication between a host and pathological and symbiotic bacteria, focusing on population-specific genetic diversity. We then focus on how these sensory receptors play a major role in inflammatory processes that form the basis of many modern common metabolic diseases such as obesity, type 2 diabetes, and aging. The impacts of human niche construction and cultural evolution in shaping environments are described with emphasis on consequent biological responsiveness.

Weighted single-step genome-wide association study and pathway analyses for feed efficiency traits in Nellore cattle

The aim was to conduct a weighted single-step genome-wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein-coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p-value < .05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int-1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE-related traits.

Genetic variants in taste-related genes and risk of pancreatic cancer

Pancreatic ductal adenocarcinoma is an aggressive and relatively rare cancer with a dismal 5-year survival rate and a clear genetic background. Genetic variants in taste receptors and taste-related genes have been associated with a variety of human traits and phenotypes among which several cancer types and pancreatic cancer risk factors. In this study, we analysed 2854 single-nucleotide polymorphisms in 50 taste-related genes, including 37 taste receptors. To cover all the genetic variability of the selected genes and to include also regulatory elements, we added 5000 nucleotides to both ends of each gene. We used a two-phase approach, with the PanScan data set (3314 cases and 3431 controls) as the discovery phase and PanC4 (3893 cases and 3632 controls) as validation phase, for a total of 7207 cases and 7063 controls. The datasets were downloaded from the NCBI database of genotypes and phenotypes (dbGaP). We observed that the taste 1 receptor member 2 (TAS1R2)-rs11261087 variant was associated with pancreatic cancer risk in both phases independently, with a consistent association of the T allele with decreased risk of developing the disease [phase 1 odds ratio (OR) = 0.89, 95% confidence interval (CI) 0.80-0.98; phase 2 OR = 0.91, 95% CI 0.83-0.99; all subjects together OR = 0.90, 95% CI 0.84-0.96, P = 0.002]. However, neither the association observed in the validation phase nor those observed in the joint analysis were statistically significant considering multiple testing. Functional studies are warranted to better understand the impact of the genetic variability of TAS1R2 on PDAC risk.

Review: Chemosensing of nutrients and non-nutrients in the human and porcine gastrointestinal tract

The gastrointestinal tract (GIT) is an interface between the external and internal milieus that requires continuous monitoring for nutrients or pathogens and toxic chemicals. The study of the physiological/molecular mechanisms, mediating the responses to the monitoring of the GIT contents, has been referred to as chemosensory science. While most of the progress in this area of research has been obtained in laboratory rodents and humans, significant steps forward have also been reported in pigs. The objective of this review was to update the current knowledge on nutrient chemosensing in pigs in light of recent advances in humans and laboratory rodents. A second objective relates to informing the existence of nutrient sensors with their functionality, particularly linked to the gut peptides relevant to the onset/offset of appetite. Several cell types of the intestinal epithelium such as Paneth, goblet, tuft and enteroendocrine cells (EECs) contain subsets of chemosensory receptors also found on the tongue as part of the taste system. In particular, EECs show specific co-expression patterns between nutrient sensors and/or transceptors (transport proteins with sensing functions) and anorexigenic hormones such as cholecystokinin (CCK), peptide tyrosine tyrosine (PYY) or glucagon-like peptide-1 (GLP-1), amongst others. In addition, the administration of bitter compounds has an inhibitory effect on GIT motility and on appetite through GLP-1-, CCK-, ghrelin- and PYY-labelled EECs in the human small intestine and colon. Furthermore, the mammalian chemosensory system is the target of some bacterial metabolites. Recent studies on the human microbiome have discovered that commensal bacteria have developed strategies to stimulate chemosensory receptors and trigger host cellular functions. Finally, the study of gene polymorphisms related to nutrient sensors explains differences in food choices, food intake and appetite between individuals.

Is there adaptation in the human genome for taste perception and phase I biotransformation?

Background

During the modern human expansion, new environmental pressures may have driven adaptation, especially in genes related to the perception of ingested substances and their detoxification. Consequently, positive (adaptive) selection may have occurred in genes related to taste, and in those related to the CYP450 system due to its role in biotransformation of potentially toxic compounds. A total of 91 genes (taste receptors and CYP450 superfamily) have been studied using Hierarchical Boosting, a powerful combination of different selection tests, to detect signatures of recent positive selection in three continental human populations: Northern Europeans (CEU), East Asians (CHB) and Africans (YRI). Analyses have been refined with selection analyses of the 26 populations of 1000 Genomes Project Phase 3.

Results

Genes related to taste perception have not been positively selected in the three continental human populations. This finding suggests that, contrary to results of previous studies, different allele frequencies among populations in genes such as TAS2R38 and TAS2R16 are not due to positive selection but to genetic drift. CYP1 and CYP2 genes, also previously considered to be under positive selection, did not show signatures of selective sweeps. However, three genes belonging to the CYP450 system have been identified by the Hierarchical Boosting as positively selected: CYP3A4 and CYP3A43 in CEU, and CYP27A1 in CHB.

Conclusions

No main adaptive differences are found in known taste receptor genes among the three continental human populations studied. However, there are important genetic adaptations in the cytochrome P450 system related to the Out of Africa expansion of modern humans. We confirmed that CYP3A4 and CYP3A43 are under selection in CEU, and we report for the first time CYP27A1 to be under positive selection in CHB.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1366-7) contains supplementary material, which is available to authorized users.