Strategies in herbivory by mammals revisited: The role of liver metabolism in a juniper specialist (Neotoma stephensi) and a generalist (Neotoma albigula)

Impact of DNA methylation on digestive and metabolic gene expression in red pandas (Ailurus fulgens) during the transition from milk to bamboo diet

BACKGROUND

DNA methylation plays a crucial role in species development and environmental adaptation. In mammals, there are significant dietary changes from infancy to adulthood. Notably, the red panda transitions from milk consumption as juveniles to a bamboo-based diet as adults, with significant alterations in food characteristics and nutritional content. However, the regulatory role of DNA methylation in this process remains unclear. In this study, we investigate the regulatory role of DNA methylation on the expression of digestive and metabolic genes in the liver and pancreas during the red panda's dietary transition from suckling stage to adulthood.

RESULTS

Our findings reveal significant differences in DNA methylation patterns before and after dietary transition, highlighting the specific alterations in the methylation profiles of genes involved in lipid, carbohydrate, and amino acid metabolism. We found that perilipin-4 (PLIN4) is hypomethylated and highly expressed in the liver of adult red pandas, facilitating lipid droplet formation and storage, crucial for adapting to the low-fat content in bamboo. In contrast, genes like lipoprotein lipase (LPL), crucial for lipid breakdown, exhibited hypermethylated with low-expression patterns, reflecting a reduced lipid metabolism capacity in adults. Carbohydrate metabolism-related genes like ADH4 and FAM3C are hypomethylated and highly expressed in adults, enhancing glycogen production and glucose utilization. Genes involved in protein metabolism like CTSZ and GLDC, exhibit hypomethylated with high-expression and hypermethylated with low-expression patterns in the pancreas of adults, respectively, contributing to protein metabolism balance post-weaning.

CONCLUSION

This study reveals the regulatory role of DNA methylation in the dietary transition of red pandas from milk to bamboo and provides methylation evidence for the molecular regulation of adaptive expression of digestive and metabolic genes in red pandas with specialized diets.

Turning Over an Old Leaf- do Mammalian Herbivores Retain the Ability to Biotransform Toxic Ancestral Diets?

Herbivores are frequently exposed to potentially toxic doses of plant secondary metabolites (PSMs). Furthermore, the plant species available and their associated PSMs may change over extended time periods. To understand the ability of herbivores to biotransform novel PSMs, we investigated populations of one species of mammalian herbivore that had undergone a radical diet shift, i.e., the desert woodrat's (Neotoma lepida) switch juniper (Juniperus spp) to creosote bush (Larrea tridentata). To determine whether woodrats currently feeding on creosote also retain the ability to consume and biotransform the PSMs in their ancestral diet of juniper, we compared various metrics of hepatic biotransformation in a population that ingests creosote bush (Mojave woodrats) to one that specializes on the ancestral diet of juniper (Great Basin woodrats). We investigated PSM biotransformation capabilities by quantifying the hepatic metabolism of α-pinene, a common terpene in juniper. We also measured total cytochrome P450 content, cytochrome P450 2B (CYP2B) and glutathione S-transferase (GST) concentrations, and the activity of GST in the livers of both populations consuming control (rabbit chow) and juniper diets. There were no differences in hepatic metabolism of α-pinene, total P450 content, or CYP2B concentration between woodrat populations when feeding on juniper. The only difference found was that the Mojave woodrats had higher GST activity compared to the Great Basin woodrats when feeding on juniper. Our results suggest that despite the change to a novel toxic diet, the Mojave woodrats maintain the capacity to metabolize their ancestral diet of juniper.

Bioinformatics analysis of miRNAs germacrone protection on diabetic nephropathy

Diabetes nephropathy (DN) is a prevalent and severe microvascular diabetic complication. Despite the recent developments in germacrone-based therapies for DN, the underlying mechanisms of germacrone in DN remain poorly understood. This study used comprehensive bioinformatics analysis to identify critical microRNAs (miRNAs) and the potential underlying pathways related to germacrone activities. Additionally, we established a DN mice model, which was treated with germacrone, to investigate how it altered the miRNA transcriptome in mice kidneys. RNA sequencing was also performed on the DN mice model with and without germacrone pre-treatment. Based on our results, we found 23 miRNAs were differentially expressed in the DN group compared to the controls, and a total of 14 miRNAs were differentially expressed between the DN group and the germacrone-treated group. In addition, we identified three miRNAs (mmu-miR-542-5p, mmu-miR-149-5p and mmu-miR-196a-2-3p) that were upregulated with the DN group and downregulated in the germacrone-treated group. Bioinformatics analysis suggested that autophagy and apoptosis were related to the pathogenesis of DN and germacrone treatment. Subsequently, the expression level of mmu-miR-542-5p, mmu-miR-149-5p and mmu-miR-196a-2-3p were validated in a validation dataset. Altogether, these findings add important knowledge on the pathogenesis of DN and the impacts of germacrone.

Review: Mechanism of herbivores synergistically metabolizing toxic plants through liver and intestinal microbiota

Interspecific interactions are central to ecological research. Plants produce toxic plant secondary metabolites (PSMs) as a defense mechanism against herbivore overgrazing, prompting their gradual adaptation to toxic substances for tolerance or detoxification. P450 enzymes in herbivore livers bind to PSMs, whereas UDP-glucuronosyltransferase and glutathione S-transferase increase the hydrophobicity of the bound PSMs for detoxification. Intestinal microorganisms such as Bacteroidetes metabolize cellulase and other macromolecules to break down toxic components. However, detoxification is an overall response of the animal body, necessitating coordination among various organs to detoxify ingested PSMs. PSMs undergo detoxification metabolism through the liver and gut microbiota, evidenced by increased signaling processes of bile acids, inflammatory signaling molecules, and aromatic hydrocarbon receptors. In this context, we offer a succinct overview of how metabolites from the liver and gut microbiota of herbivores contribute to enhancing metabolic PSMs. We focused mainly on elucidating the molecular communication between the liver and gut microbiota involving endocrine, immune, and metabolic processes in detoxification. We have also discussed the potential for future alterations in the gut of herbivores to enhance the metabolic effects of the liver and boost the detoxification and metabolic abilities of PSMs.

The interaction of genes and environment on percent of juniper in the diet of goats divergently selected for high or low juniper consumption

Diet selection and preference by grazing animals are determined by genetic and environmental factors that interact and affect their efficacy for managing vegetation as targeted grazers and developing animals adapted to local grazing environments. The effect of the rearing environments on the consumption of juniper (Juniperus spp.) by goats that for 15 years were divergently selected for high (J+) or low (J-) percent juniper in their diet was investigated. To test the effect of rearing environment, at the end of the breeding season, pregnant does from both selection lines were grazed on either juniper-infested (JIR) or juniper-free (JFR) rangelands until their kids were weaned at about 75 days of age. Fecal samples were analyzed with fecal near-IR spectroscopy to determine the percent juniper in the diet. Fecal samples were collected from does on JIR when their offspring were 30 days of age and at weaning. Then, does that raised kids in both rearing environments grazed a common JIR pasture for a 28-day adaptation period before collecting fecal samples. After weaning, kids from both rearing environments grazed JIR for 22 days before collecting fecal samples. The J+ does always consumed more (P < 0.001) juniper than J- does, demonstrating different maternal role models for kids reared in the JIR environment. There was no effect of rearing environment (P = 0.488) or rearing environment × selection line interaction (P = 0.096) when J- and J+ does grazed a common JIR pasture. The percentage of juniper in J- kid diets (7%) was the same regardless of the rearing environment. However, the rearing environment did affect the percentage of juniper in the diet of J+ kids, resulting in a gene-environment interaction (P = 0.022). The percentage of juniper in the diet of J+ kids reared in JFR (16%) and JIR (24%) were about two and three times higher than J- kids, respectively, indicating that genetics and the rearing environment contributed about equally to the increase in the percentage of juniper in the J+ kid diets. Regardless of the rearing environment, the J+ kids had a higher percentage of juniper in their diets than J- kids (P < 0.001). Compared to males, female kids had a higher percentage of juniper in their diets (12 vs 17%, respectively; P = 0.002). The ability to select animals with specific dietary preferences holds promise for targeted grazing strategies to restore degraded rangelands, with potential applications in conservation and ecosystem management.

The desert woodrat (Neotoma lepida) induces a diversity of biotransformation genes in response to creosote bush resin

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.

Comparative transcriptomes reveal geographic differences in the ability of the liver of plateau zokors (Eospalax baileyi) to respond and adapt to toxic plants

BACKGROUND

Environmental changes are expected to intensify in the future. The invasion of toxic plants under environmental changes may change herbivore feeding environments. Herbivores living long-term in toxic plant-feeding environments will inevitably ingest plant secondary metabolites (PSMs), and under different feeding environments are likely to have unique protection mechanisms that support improved adaptation to PSMs in their habitat. We aimed to compare different subterranean herbivore population responses and adaptations to toxic plants to unveil their feeding challenges.

RESULTS

Here, we investigated the adaptive capacity of the liver in two geographically separated populations of plateau zokors (Eospalax baileyi) before and after exposure to the toxic plant Stellera chamaejasme (SC), at the organ, biochemical, and transcriptomic levels. The results showed no significant liver granules or inflammatory reactions in the Tianzhu (TZ) population after the SC treatment. The transaminase level in the TZ population was significantly lower than that in the Luqu population. Transcriptome analysis revealed that the TZ population exhibited interactions with other detoxification metabolic pathways by oxytocin pathway-associated genes, including diacylglycerol lipase alpha (Dagla), calcium/calmodulin dependent protein kinase II Alpha (Camk2a), and CD38 molecule (Cd38). The phase II process of liver drug metabolism increased to promote the rate of metabolism. We found that alternative splicing (AS) and the expression of the cyclin D (Ccnd1) gene interact-a TZ population hallmark-reduced liver inflammatory responses.

CONCLUSION

Our study supports the detoxification limitation hypothesis that differences in liver detoxification metabolism gene expression and AS are potential factors in herbivore adaptation to PSMs and may be a strategy of different herbivore populations to improve toxic plant adaptability.

Plateau zokors (Eospalax baileyi) respond to secondary metabolites from the roots of Stellera chamaejasme by enhancing hepatic inflammatory factors and metabolic pathway genes

Herbivores rarely consume toxic plants. An increase in the proportion of toxic plant secondary metabolites (PSMs) in poisonous plants can promote detoxification and related metabolic capacity of animals. Poisonous plants with thick taproots like Stellera chamaejasme (SC) are important stored food for the plateau zokor (Eospalax baileyi) during the winter and promote the development of detoxification mechanisms in this animal. In this study, plateau zokors were administered gavages of 0.2, 1.05, and 2.10 ml/kg SC water extracts. Serum samples were collected from plateau zokors to measure the levels of transaminases and oxidative stress. Transcriptome analysis was conducted to evaluate the differential genes of multiple metabolic pathways to investigate the relationship between the physiological processes and metabolic adaptation capacity of these animals in response to SC. After SC administration, plateau zokors showed significant hepatic granular degeneration and inflammatory reactions in the liver and aspartate aminotransferase, alanine aminotransferase, and malondialdehyde levels increased in a dose-dependent manner. Further, differential expression was also found in the plateau zokor livers, with most enrichment in inflammation and detoxification metabolism pathways. The metabolic adaptation responses in P450 xenobiotic clearance, bile secretion, and pancreatic secretion (Gusb, Hmgcr, Gstm1, Gstp1, and Eobag004630005095) were verified by mRNA network analysis as key factors related to the mechanism. Plateau zokors respond to SC PSMs through changes in liver physiology, biochemistry, and genes in multiple metabolic pathways, validating our hypothesis that plateau zokors can metabolize PSMs when they ingest toxic plants.

Kinetic Characteristics of Curcumin and Germacrone in Rat and Human Liver Microsomes: Involvement of CYP Enzymes

Curcumin and germacrone, natural products present in the Zingiberaceae family of plants, have several biological properties. Among these properties, the anti-NSCLC cancer action is noteworthy. In this paper, kinetics of the two compounds in rat liver microsomes (RLMs), human liver microsomes (HLMs), and cytochrome P450 (CYP) enzymes (CYP3A4, 1A2, 2E1, and 2C19) in an NADPH-generating system in vitro were evaluated by UP-HPLC–MS/MS (ultrahigh-pressure liquid chromatography–tandem mass spectrometry). The contents of four cytochrome P450 (CYP) enzymes, adjusting by the compounds were detected using Western blotting in vitro and in vivo. The t1/2 of curcumin was 22.35 min in RLMs and 173.28 min in HLMs, while 18.02 and 16.37 min were gained for germacrone. The Vmax of curcumin in RLMs was about 4-fold in HLMs, meanwhile, the Vmax of germacrone in RLMs was similar to that of HLMs. The single enzyme t1/2 of curcumin was 38.51 min in CYP3A4, 301.4 min in 1A2, 69.31 min in 2E1, 63.01 min in 2C19; besides, as to the same enzymes, t1/2 of germacrone was 36.48 min, 86.64 min, 69.31 min, and 57.76 min. The dynamic curves were obtained by reasonable experimental design and the metabolism of curcumin and germacrone were selected in RLMs/HLMs. The selectivities in the two liver microsomes differed in degradation performance. These results meant that we should pay more attention to drugs in clinical medication–drug and drug–enzyme interactions.

Mammalian cytochrome P450 biodiversity: Physiological importance, function, and protein and genomic structures of cytochromes P4502B in multiple species of woodrats with different dietary preferences

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.