Alpha-aminoadipate delta-semialdehyde synthase mRNA knockdown reduces the lysine requirement of a mouse hepatic cell line

Adaptive Expression and ncRNA Regulation of Genes Related to Digestion and Metabolism in Stomach of Red Pandas during Suckling and Adult Periods

Red pandas evolved from carnivores to herbivores and are unique within Carnivora. Red pandas and carnivorous mammals consume milk during the suckling period, while they consume bamboo and meat during the adult period, respectively. Red pandas and carnivorous mammal ferrets have a close phylogenetic relationship. To further investigate the molecular mechanisms of dietary changes and nutrient utilization in red pandas from suckling to adult, comparative analysis of the whole transcriptome was performed on stomach tissues from red pandas and ferrets during the suckling and adult periods. The main results are as follows: (1) we identified ncRNAs for the first time in stomach tissues of both species, and found significant expression changes of 109 lncRNAs and 106 miRNAs in red pandas and 756 lncRNAs and 109 miRNAs in ferrets between the two periods; (2) up-regulated genes related to amino acid transport regulated by lncRNA-miRNA-mRNA networks may efficiently utilize limited bamboo amino acids in adult red pandas, while up-regulated genes related to amino acid degradation regulated by lncRNAs may maintain the balance of amino acid metabolism due to larger daily intakes in adult ferrets; and (3) some up-regulated genes related to lipid digestion may contribute to the utilization of rich nutrients in milk for the rapid growth and development of suckling red pandas, while up-regulated genes associated with linoleic acid metabolism regulated by lncRNA-miRNA-mRNA networks may promote cholesterol decomposition to reduce health risks for carnivorous adult ferrets. Collectively, our study offers evidence of gene expression adaptation and ncRNA regulation in response to specific dietary changes and nutrient utilization in red pandas during suckling and adult periods.

Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution

Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo-eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo-eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo-eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.

Comparative study of the digestion and metabolism related genes' expression changes during the postnatal food change in different dietary mammals

The changes in the expression of genes related to digestion and metabolism may be various in different dietary mammals from juvenile to adult, especially, the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), which were once carnivores but have shifted to being specialized bamboo eaters, are unique features of their changes are more unclear. To elucidate the changing patterns of gene expression related to digestion and metabolism from juvenile to adult in different dietary mammals, we performed transcriptome analysis of the liver or pancreas in giant and red pandas, herbivorous rabbits (Oryctolagus cuniculus) and macaques (Macaca mulatta), carnivorous ferrets (Mustela putorius furo), and omnivorous mice (Mus musculus) from juvenile to adult. During the transition from juvenile to adulthood, giant and red pandas, as well as rabbits and macaques, show significant upregulation of key genes for carbohydrate metabolism, such as starch hydrolysis and sucrose metabolism, and unsaturated fatty acid metabolism, such as linoleic acid, while there is no significant difference in the expression of key genes for fatty acid β-oxidation. A large number of amino acid metabolism related genes were upregulated in adult rabbits and macaques compared to juveniles. While adult giant and red pandas mainly showed upregulation of key genes for arginine synthesis and downregulation of key genes for arginine and lysine degradation. In adult stages, mouse had significantly higher expression patterns in key genes for starch hydrolysis and sucrose metabolism, as well as lipid and protein metabolism. In contrast to general expectations, genes related to lipid, amino acid and protein metabolism were significantly higher expressed in adult group of ferrets, which may be related to their high metabolic levels. Our study elucidates the pattern of changes in the expression of genes related to digestion and metabolism from juvenile to adult in different dietary mammals, with giant and red pandas showing adaptations associated with specific nutritional limitations of bamboo.

Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation

BACKGROUND

It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species.

RESULTS

The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn't exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region.

CONCLUSIONS

Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.

Untargeted Metabolomics Reveals Intestinal Pathogenesis and Self-Repair in Rabbits Fed an Antibiotic-Free Diet

Simple Summary

In recent years, China imposed a total ban on the use of antibiotics in animal husbandry. This caused huge economic losses, one of the main reasons being an increase in the incidence of diseases. In this study, rabbits were used as a model to study the pathogenesis of intestinal diseases in rabbits on an antibiotic-free diet, through non-targeted metabolomics methods. The results showed that 1969 different metabolites were identified. These differential metabolites were involved in five metabolic pathways associated with intestinal inflammation (tryptophan metabolism, pyrimidine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, lysine degradation, and bile secretion). In summary, the use of non-antibiotic feed might cause intestinal inflammation in rabbits and activate intestinal repair.

Abstract

The prohibition of the use of growth-promoting drug additives in feeds was implemented in China in 2020. However, rabbits can experience symptoms of intestinal disease, such as diarrhea and flatulence, when switching from standard normal diets with antibiotics to antibiotic-free diets. The molecular mechanisms related to the occurrence of these diseases as well as associated physiological and metabolic changes in the intestine are unclear. Thus, the objectives of this study were to study the pathogenesis of intestinal inflammation using untargeted metabolomics. This was done to identify differential metabolites between a group of antibiotic-free feed Hyplus rabbits (Dia) whose diet was abruptly changed from a standard normal diet with antibiotics to an antibiotic-free diet, and an antibiotic diet group Hyplus rabbits (Con) that was fed a standard normal diet with antibiotics. Morphological damage to the three intestinal tissues was determined through visual microscopic examination of intestinal Dia and Con tissue samples stained with hematoxylin and eosin (HE). A total of 1969 different metabolites were identified in the three intestinal tissues from Dia and Con rabbits. The level of 1280 metabolites was significantly higher and the level of 761 metabolites was significantly lower in the Dia than in the Con group. These differential metabolites were involved in five metabolic pathways associated with intestinal inflammation (tryptophan metabolism, pyrimidine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, lysine degradation, and bile secretion). Rabbits in the Dia group developed metabolic disorders that affected the intestinal microbiota and changed the permeability of the intestinal tract, thereby triggering intestinal inflammation, affecting feed utilization, reducing production performance, and activating the intestinal tract self-repair mechanism. Thus, the abrupt transition from a diet with antibiotics to an antibiotic-free diet affected the structure and metabolism of the intestinal tract in Hyplus rabbits. Consequently, to avoid these problems, the antibiotic content in a rabbit diet should be changed gradually or alternative antibiotics should be found.

Postruminal protein supply upregulates hepatic lysine oxidation and ornithine transcarbamoylase in lactating dairy cattle

Metabolizable protein supply is a limiting factor for milk production in dairy cows, and the availability of AA is a function of the quantity of the metabolizable protein available and of hepatic AA catabolism. This study aimed to evaluate the effect of postruminal protein infusion on key genes for ureagenesis and AA catabolism. Six multiparous Holstein cows in early lactation were used in a replicated crossover design. Cows were fed a TMR and infused postruminally with either 0 or 600 g/d of milk protein isolate. Periods were 21 d long, consisting of 14 d of adjustment to surroundings, followed by 7 d of protein infusion. On the last day of each infusion, liver samples were collected for mRNA analysis and explant culture, milk samples were collected for mRNA analysis, and blood samples were collected for plasma metabolite analysis. Postruminal infusion of protein increased milk yield by 10.5%, milk fat yield by 12.5%, milk protein yield by 20%, milk lactose yield by 11%, and total solids yield by 15.5%. Postruminal infusion of protein increased milk urea N by 23.5%, blood urea N by 18.6%, and the abundance of hepatic ornithine transcarbamoylase mRNA by 52.8%. Postruminal infusion of protein did not alter the mRNA abundance of hepatic argininosuccinate synthase, α-aminoadipate semialdehyde synthase, cysteine sulfinic acid decarboxylase, or cystathionase. The abundance of RNA for milk proteins was unchanged with postruminal protein infusion. Metabolism of l-[U ¹⁴C] Lys to CO₂ was increased by 127% (0.143 vs. 0.063 ± 0.04 nmol product·mg tissue^-1·h^-1), and the metabolism of l-[U ¹⁴C] Ala to CO₂ increased by 40.5% (0.52 vs. 0.37 ± 0.06 nmol product·mg tissue^-1·h^-1) with postruminal protein infusion. The rate of l-[1-¹⁴C] Met oxidation did not differ. These data indicate increased ureagenesis matched by upregulation of nonessential AA catabolism and a disproportional increase in Lys oxidation in response to increased postruminal protein infusion.

Dose-response of different dietary leucine levels on growth performance and amino acid metabolism in piglets differing for aminoadipate-semialdehyde synthase genotypes

Dose-response studies of dietary leucine (Leu) in weaners are needed for a proper diet formulation. Dietary Leu effect was assessed in a 3-weeks dose-response trial with a 2 (genotype) x 5 (diets) factorial arrangement on one-hundred weaned pigs (9 to 20 kg body weight (BW)). Pigs differed for a polymorphism at the aminoadipate-semialdehyde synthase (AASS) gene, involved in lysine (Lys) metabolism. Pigs received experimental diets (d7 to d28) differing for the standardized ileal digestible (SID) Leu:Lys: 70%, 85%, 100%, 115%, 130%. Daily feed intake (ADFI), daily gain (ADG) and feed:gain (F:G) in all pigs and ADG and F:G in two classes of BW were analyzed using regression analysis with curvilinear-plateau (CLP) and linear quadratic function (LQ) models. Amino acid (AA) concentrations in plasma, liver, muscle and urine were determined. AASS genotype did not affect the parameters. Dietary Leu affected performance parameters, with a maximum response for ADG and F:G between 100.5% and 110.7% SID Leu:Lys, higher than the usually recommended one, and between 110.5% and 115.4% and between 94.9% and 110.2% SID Leu:Lys for ADG for light and heavy pigs respectively. AA variations in tissues highlighted Leu role in protein synthesis and its influence on the other branched chain AAs.

A single transcription factor is sufficient to induce and maintain secretory cell architecture

Here, Lo et al. demonstrate that cell architecture can be controlled by a developmentally regulated transcriptional program independent of the program that specifies cell identity. They show that MIST1 (BHLHA15) is a “scaling factor” that universally establishes secretory morphology in cells that perform regulated secretion, and targeted deletion of MIST1 causes dismantling of the secretory apparatus of diverse exocrine cells.

We hypothesized that basic helix–loop–helix (bHLH) MIST1 (BHLHA15) is a “scaling factor” that universally establishes secretory morphology in cells that perform regulated secretion. Here, we show that targeted deletion of MIST1 caused dismantling of the secretory apparatus of diverse exocrine cells. Parietal cells (PCs), whose function is to pump acid into the stomach, normally lack MIST1 and do not perform regulated secretion. Forced expression of MIST1 in PCs caused them to expand their apical cytoplasm, rearrange mitochondrial/lysosome trafficking, and generate large secretory granules. Mist1 induced a cohort of genes regulated by MIST1 in multiple organs but did not affect PC function. MIST1 bound CATATG/CAGCTG E boxes in the first intron of genes that regulate autophagosome/lysosomal degradation, mitochondrial trafficking, and amino acid metabolism. Similar alterations in cell architecture and gene expression were also caused by ectopically inducing MIST1 in vivo in hepatocytes. Thus, MIST1 is a scaling factor necessary and sufficient by itself to induce and maintain secretory cell architecture. Our results indicate that, whereas mature cell types in each organ may have unique developmental origins, cells performing similar physiological functions throughout the body share similar transcription factor-mediated architectural “blueprints.”

Dietary L-homoserine spares threonine in chicks

Four chick bioassays were conducted to evaluate the threonine (Thr) replacement value of l-homoserine (HS). Growth rate was increased (P < 0.05) by dietary addition of 800 mg l-HS/kg diet to a purified diet severely deficient in Thr or by the addition of 800 or 1000 mg of l-HS/kg diet to a corn-peanut meal diet distinctly deficient in Thr. The addition of an isomolar level of alpha-ketobutyrate, a catabolic product of both Thr and HS, did not elicit a response. Standard-curve methodology predicted a Thr replacement value of 38 +/- 9% for HS. Interactions (P < 0.01) were observed in assays 2 and 4 between dietary Thr adequacy and 800 or 1000 mg l-HS/kg supplementation. Thus, HS improved growth performance when added to a Thr-deficient diet (0.46 g Thr/100 g diet), but it decreased growth performance when added to the same diet containing surfeit Thr (0.80 g Thr/100 g diet). The results indicate that low levels of HS elicit a growth response in young chicks fed Thr-deficient diets.