Hepatic mitochondrial function in Hereford steers with divergent residual feed intake phenotypes

An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle

BACKGROUND

Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network.

RESULTS

Of the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts.

CONCLUSIONS

Although similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.

The mRNA-lncRNA landscape of multiple tissues uncovers key regulators and molecular pathways that underlie heterosis for feed intake and efficiency in laying chickens

BACKGROUND

Heterosis is routinely exploited to improve animal performance. However, heterosis and its underlying molecular mechanism for feed intake and efficiency have been rarely explored in chickens. Feed efficiency continues to be an important breeding goal trait since feed accounts for 60 to 70% of the total production costs in poultry. Here, we profiled the mRNA-lncRNA landscape of 96 samples of the hypothalamus, liver and duodenum mucosa from White Leghorn (WL), Beijing-You chicken (YY), and their reciprocal crosses (WY and YW) to elucidate the regulatory mechanisms of heterosis.

RESULTS

We observed negative heterosis for both feed intake and residual feed intake (RFI) in YW during the laying period from 43 to 46 weeks of age. Analysis of the global expression pattern showed that non-additivity was a major component of the inheritance of gene expression in the three tissues for YW but not for WY. The YW-specific non-additively expressed genes (YWG) and lncRNA (YWL) dominated the total number of non-additively expressed genes and lncRNA in the hypothalamus and duodenum mucosa. Enrichment analysis of YWG showed that mitochondria components and oxidation phosphorylation (OXPHOS) pathways were shared among the three tissues. The OXPHOS pathway was enriched by target genes for YWL with non-additive inheritance of expression in the liver and duodenum mucosa. Weighted gene co-expression network analysis revealed divergent co-expression modules associated with feed intake and RFI in the three tissues from WL, YW, and YY. Among the negatively related modules, the OXPHOS pathway was enriched by hub genes in the three tissues, which supports the critical role of oxidative phosphorylation. Furthermore, protein quantification of ATP5I was highly consistent with ATP5I expression in the liver, which suggests that, in crossbred YW, non-additive gene expression is down-regulated and decreases ATP production through oxidative phosphorylation, resulting in negative heterosis for feed intake and efficiency.

CONCLUSIONS

Our results demonstrate that non-additively expressed genes and lncRNA involved in oxidative phosphorylation in the hypothalamus, liver, and duodenum mucosa are key regulators of the negative heterosis for feed intake and RFI in layer chickens. These findings should facilitate the rational choice of suitable parents for producing crossbred chickens.

Residual Feed Intake in Beef Cattle Is Associated With Differences in Hepatic mRNA Expression of Fatty Acid, Amino Acid, and Mitochondrial Energy Metabolism Genes

We evaluated the mRNA expression of genes involved in hepatic fatty acid, amino acid, and mitochondrial energy metabolism in crossbred beef steers with divergent low and high residual feed intake (RFI). Low-RFI beef steers (n = 8; RFI = - 1.93 kg/d) and high-RFI beef steers (n = 8; RFI = + 2.01kg/d) were selected from a group of 56 growing crossbred beef steers (average BW = 261 ± 18.5 kg) fed a high-forage total mixed ration after a 49-d performance testing period. At the end of the 49-d performance testing period, liver biopsies were collected from the low-RFI and high-RFI beef steers for RNA extraction and cDNA synthesis. The mRNA expression of 84 genes each related to fatty acid metabolism, amino acid metabolism, and mitochondrial energy metabolism were analyzed using pathway-focused PCR-based arrays. The mRNA expression of 8 genes (CRAT, SLC27A5, SLC27A2, ACSBG2, ACADL, ACADSB, ACAA1, and ACAA2) involved fatty acid transport and β-oxidation were upregulated (FC ≥ 2.0, FDR ≤ 0.05) in low-RFI, compared to high-RFI steers. Among those involved in amino acid metabolism, hepatic mRNA expression of a gene encoding for aminoadipate aminotransferase, an enzyme related to lysine degradation, was downregulated (FC = -5.45, FDR = 0.01) in low-RFI steers, whereas those of methionine adenosyltransferase I and aspartate aminotransferase 2, which both link amino acid and lipid metabolism, were upregulated (FC ≥ 2.0, FDR ≤ 0.05). Two mitochondrial energy metabolism genes (UQCRC1 and ATP5G1) involved in ATP synthesis via oxidative phosphorylation were upregulated (FC ≥ 2.0, FDR ≤ 0.05) in low-RFI beef steers, compared to high-RFI beef steers. The results of this study demonstrated that low-RFI beef steers exhibit upregulation of molecular mechanisms related to fatty acid transport, fatty acid β-oxidation, and mitochondrial ATP synthesis, which suggest that low-RFI beef steers have enhanced metabolic capacity to maximize capture of energy and nutrients from feeds consumed.

Differential hepatic mitochondrial function and gluconeogenic gene expression in 2 Holstein strains in a pasture-based system

The objective of this study was to assess hepatic ATP synthesis in Holstein cows of North American and New Zealand origins and the gluconeogenic pathway, one of the pathways with the highest ATP demands in the ruminant liver. Autumn-calving Holstein cows of New Zealand and North American origins were managed in a pasture-based system with supplementation of concentrate that represented approximately 33% of the predicted dry matter intake during 2017, 2018, and 2019, and hepatic biopsies were taken during mid-lactation at 174 ± 23 days in milk. Cows of both strains produced similar levels of solids-corrected milk, and no differences in body condition score were found. Plasma glucose concentrations were higher for cows of New Zealand versus North American origin. Hepatic mitochondrial function evaluated measuring oxygen consumption rates showed that mitochondrial parameters related to ATP synthesis and maximum respiratory rate were increased for cows of New Zealand compared with North American origin. However, hepatic gene expression of pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate dehydrogenase kinase was increased in North American compared with New Zealand cows. These results altogether suggest an increased activity of the tricarboxylic cycle in New Zealand cows, leading to increased ATP synthesis, whereas North American cows pull tricarboxylic cycle intermediates toward gluconeogenesis. The fact that this occurs during mid-lactation could account for the increased persistency of North American cows, especially in a pasture-based system. In addition, we observed an augmented mitochondrial density in New Zealand cows, which could be related to feed efficiency mechanisms. In sum, our results contribute to the elucidation of hepatic molecular mechanisms in dairy cows in production systems with higher inclusion of pastures.

Identification of Key Genes Associated With Early Calf-Hood Nutrition in Subcutaneous and Visceral Adipose Tissues by Co-Expression Analysis

Background

Substantive evidence has confirmed that nutrition state is associated with health risk and the onset of pubertal and metabolic profile. Due to heterogeneity, adipose tissues in different anatomical positions tend to show various metabolic mechanisms for nutrition. To date, the complicated molecular mechanisms of early calf-hood nutrition on bovine adipose tissue are still largely unknown. This study aimed to identify key genes and functionally enriched pathways associated with early calf-hood nutrition in visceral and subcutaneous adipose tissue.

Results

The RNA-seq data of visceral and subcutaneous adipose tissues of calves feeding on low and high dietary nutrition for more than 100 days were downloaded and analyzed by weighted gene co-expression network analysis (WGCNA). Two modules that positively associated with a low plane of nutrition diet and two modules with a high plane of nutrition diet were identified in the subcutaneous adipose tissue. The blue and yellow modules, most closely associated with low and high nutrition, were selected for the functional enrichment analysis and exploration of hub genes. The results showed that genes in the blue module were significantly enriched in pathways that related to fat metabolism, reproduction, and cell communication. Genes in the yellow module were enriched in pathways related to fat metabolism, reproduction, cell proliferation, and senescence. Meanwhile, the blue and brown modules in visceral adipose tissue were most closely associated with low and high nutrition, respectively. Notably, genes of the blue module were significantly enriched in pathways related to substance metabolism, and genes in the brown module were significantly enriched in energy metabolism and disease pathways. Finally, key genes in subcutaneous adipose tissue for low nutrition (PLCG1, GNA11, and ANXA5) and high nutrition (BUB1B, ASPM, RRM2, PBK, NCAPG, and MKI67), and visceral adipose tissue for low nutrition (RPS5, RPL4, RPL14, and RPLP0) and high nutrition (SDHA and AKT1) were obtained and verified.

Conclusion

The study applied WGCNA to identify hub genes and functionally enriched pathways in subcutaneous and visceral adipose tissue and provided a basis for studying the effect of early calf-hood nutrition on the two adipose tissue types.

Association of Residual Feed Intake With Blood Metabolites and Reproduction in Holstein Cows

The objectives of this study were to evaluate the associations between residual dry matter (DM) intake or residual feed intake (RFI) from 1 to 15 weeks postpartum and concentrations of metabolites in plasma in early lactation and reproduction in Holstein cows. Data from 9 experiments, including 851 cows, were used. Intake of DM, milk yield, and body weight were evaluated daily, whereas milk composition and body condition were evaluated twice weekly for the first 105 days postpartum. Blood was sampled on the day of calving and again on days 7, 14, and 21 postpartum and analyzed for concentrations of non-esterified fatty acids (FA), β-hydroxybutyrate (BHB), and glucose. Reproduction was evaluated for the first 300 days postpartum. Residual DM intake was calculated as the observed minus the predicted intake, with intake predicted based on a model that accounted for major energy sinks. Cows were ranked and categorized into RFI quartiles, from the smallest (Q1) to the largest (Q4) RFI (−1.87, −0.46, 0.39, and 1.90 kg/day). Increasing efficiency (i.e., from Q4 to Q1) resulted in linear decreases in DM intake (Q1 to Q4; 18.9, 20.4, 21.3, and 22.7 kg/day), and median days open (132, 125, 135, and 147 d). Conversely, improving efficiency was associated with a linear increase in pregnancy per artificial insemination (AI, 31.4, 30.6, 31.2, and 24.5%) and quadratic increases in the 21-day cycle pregnancy rate (21.2, 21.1, 22.0, and 16.6%) and the proportion of pregnant cows (79.0, 80.7, 82.4, and 71.5%). The estimated net energy for lactation (NEL) content of diets increased linearly with improved RFI (1.88, 1.76, 1.71, and 1.58 Mcal/kg), resulting in no association between RFI and energy-corrected milk yield or body energy change. Nevertheless, increased feed efficiency was associated with a linear increase in concentrations of blood FA (0.68, 0.63, 0.60, and 0.59 mM), but a quadratic association with BHB (0.75, 0.64, 0.64, and 0.65 mM), with no association with glucose. Collectively, the most feed efficient cows ate 3.8 kg/day less DM, produced the same amount of energy-corrected milk, and had improved reproductive performance compared with the least efficient cows, thus suggesting that the underlying mechanisms responsible for improved feed efficiency might also be linked with improvements in reproduction.

Proteomic Analysis of Liver from Finishing Beef Cattle Supplemented with a Rumen-Protected B-Vitamin Blend and Hydroxy Trace Minerals

Simple Summary

Greater metabolic needs in high-producing beef cattle might lead to mineral and vitamin deficiency. Previous studies have shown the benefits of B-vitamin and trace mineral supplementation in animal performance of ruminants; however, little is known about the effects of supplementing finishing beef cattle with rumen-protected forms on the liver metabolism. Therefore, the aim of the present study was to determinate the impact of rumen-protected B-vitamin blend and hydroxy trace mineral supplementation on the hepatic proteome of finishing steers. This study reports the first evidence indicating that the supplementation of these micronutrients induces protein changes concerning oxidative metabolism and responses to oxidative stress in the liver tissue.

Abstract

Vitamin B and trace minerals are crucial molecular signals involved in many biological pathways; however, their bioavailability is compromised in high-producing ruminant animals. So far, studies have mainly focused on the effects of these micronutrients on animal performance, but their use in a rumen-protected form and their impact on liver metabolism in finishing beef cattle is poorly known. We used a shotgun proteomic approach combined with biological network analyses to assess the effects of a rumen-protected B-vitamin blend, as well as those of hydroxy trace minerals, on the hepatic proteome. A total of 20 non-castrated Nellore males with 353 ± 43 kg of initial body weight were randomly assigned to one of the following treatments: CTRL—inorganic trace minerals without supplementation of a protected vitamin B blend, or SUP—supplementation of hydroxy trace minerals and a protected vitamin B blend. All animals were fed the same amount of the experimental diet for 106 days, and liver biopsies were performed at the end of the experimental period. Supplemented animals showed 37 up-regulated proteins (p < 0.10), and the enrichment analysis revealed that these proteins were involved in protein folding (p = 0.04), mitochondrial respiratory chain complex I (p = 0.01) and IV (p = 0.01), chaperonin-containing T-complex 2 (p = 0.01), glutathione metabolism (p < 0.01), and other aspects linked to oxidative-stress responses. These results indicate that rumen-protected vitamin B and hydroxy trace mineral supplementation during the finishing phase alters the abundance of proteins associated with the electron transport chain and other oxidation–reduction pathways, boosting the production of reactive oxygen species, which appear to modulate proteins linked to oxidative-damage responses to maintain cellular homeostasis.

Mitochondrial abundance and function in muscle from beef steers with divergent residual feed intakes

The objective of this study was to evaluate the relationship between muscle mitochondrial function and residual feed intake (RFI) in growing beef cattle. A 56-day feeding trial was conducted with 81 Angus × Hereford steers (initial BW = 378 ± 43 kg) from the University of California Sierra Foothills Research Station (Browns Valley, CA, USA). All steers were individually fed the same finishing ration (metabolizable energy = 3.28 Mcal/kg DM). Average daily gain (ADG), DM intake (DMI) and RFI were 1.82 ± 0.27, 8.89 ± 1.06 and 0.00 ± 0.55 kg/day, respectively. After the feeding trial, the steers were categorized into high, medium and low RFI groups. Low RFI steers consumed 13.6% less DM (P < 0.05) and had a 14.1% higher G : F ratio (P < 0.05) than the high RFI group. No differences between RFI groups were found in age, ADG or BW (P > 0.10). The most extreme individuals from the low and high RFI groups were selected to assess mitochondrial function (n = 5 low RFI and n = 6 high RFI). Mitochondrial respiration was measured using an oxygraph (Hansatech Instruments Ltd., Norfolk, UK). State 3 and State 4 respiration rates were similar between both groups (P > 0.10). Respiratory control ratios (RCRs, i.e., State 3 : State 4 oxygen uptakes) declined with animal age and were greater in low RFI steers (4.90) as compared to high RFI steers (4.26) when adjusted for age by analysis of covariance (P = 0.003). Mitochondrial complex II activity levels per gram of muscle were 42% greater in low RFI steers than in high RFI steers (P = 0.004). These data suggest that skeletal muscle mitochondria have greater reserve respiratory capacity and show greater coupling between respiration and phosphorylation in low RFI than in high RFI steers.

Differential hepatic oxidative status in steers with divergent residual feed intake phenotype

Oxidative stress occurs when oxidant production exceeds the antioxidant capacity to detoxify the reactive intermediates or to repair the resulting damage. Feed efficiency has been associated with mitochondrial function due to its impact on cell energy metabolism. However, mitochondria are also recognized as a major source of oxidants. The aim of this study was to determine lipid and protein oxidative stress markers, and gene and protein expression as well as activity of antioxidant enzymes in the liver of steers of divergent residual feed intake (RFI) phenotypes. Hereford steers (n = 111) were evaluated in post-weaning 70 days standard test for RFI. Eighteen steers exhibiting the greatest (n = 9; high-RFI) and the lowest (n = 9; low-RFI) RFI values were selected for this study. After the test, steers were managed together under grazing conditions until slaughter when they reached the slaughter body weight. At slaughter, hepatic samples were obtained, were snap-frozen in liquid nitrogen and stored at -80°C until analyses. Hepatic thiobarbituric acid reactive species and protein carbonyls were greater (P = 0.05) and hepatic 4-hydroxynonenal protein adducts tended (P = 0.10) to be greater for high- than low-RFI steers. Hepatic gene expression glutathione peroxidase 4, glutamate-cysteine ligase catalytic subunit and peroxiredoxin 5 mRNA was greater (P ≤ 0.05) and glutathione peroxidase 3 mRNA tended (P = 0.10) to be greater in low- than high-RFI steers. Hepatic protein expression and enzyme activity of manganese superoxide dismutase and glutathione peroxidase enzyme activity tended (P ≤ 0.10) to be greater for low- than high-RFI steers. High-efficiency steers (low-RFI) probably had better hepatic oxidative status which was strongly associated with greater antioxidant ability near to the oxidant production site and, therefore, reduced oxidative stress of the liver. Decreased hepatic oxidative stress would reduce maintenance requirements due to a lower protein and lipid turnover and better efficiency in the use of energy.

Association analysis between feed efficiency and expression of key genes of the avTOR signaling pathway in meat-type ducks

Genes involved in the target of rapamycin (TOR) signaling pathway are implicated in nutrient translation, cell proliferation and differentiation, and anabolism, which can affect both growth and feed intake. However, the role of TOR signaling in the regulation of feed intake and feed efficiency in poultry is not clear. In the present study, a total of 1000 ducks, of similar initial weight, were chosen and transferred to individual cages to determine their residual feed intake (RFI) from the age of 21 to 42 days. Subsequently, 60 ducks, which were divided into high (HRFI) and low (LRFI) groups according to their RFI, were chosen to analyze the TOR signaling activities in the liver. The differential expression level of genes involved in the TOR signaling pathway was assayed by the real-time polymerase chain reaction. In the liver, the expression of AKT, avTOR, avLST8, and S6K1 was significantly higher in LRFI ducks than in HRFI ducks; avTOR and AKT were negatively associated with the feed conversion ratio and RFI. Furthermore, PI3K was moderately positively associated with AKT; AKT was strongly positively associated with PI3K, avTOR, avLST8, and S6K1; and avTOR was strongly positively associated with S6K1. In conclusion, the activation of avTOR signaling in the liver of LRFI ducks might be ascribed to higher energy state or more active nutrient transport (amino acids), or both, than those in the liver of HRFI ducks. The results of the present study indicate that AKT and avTOR of TOR signaling might be used as candidate genes to assess molecular regulation of feed efficiency.