Structure and function of chicken interleukin-1 beta mutants: uncoupling of receptor binding and in vivo biological activity

Prediction of the most deleterious non-synonymous SNPs in the human IL1B gene: evidence from bioinformatics analyses

BACKGROUND

Polymorphisms in IL1B play a significant role in depression, multiple inflammatory-associated disorders, and susceptibility to infection. Functional non-synonymous SNPs (nsSNPs) result in changes in the encoded amino acids, potentially leading to structural and functional alterations in the mutant proteins. So far, most genetic studies have concentrated on SNPs located in the IL1B promoter region, without addressing nsSNPs and their association with multifactorial diseases. Therefore, this study aimed to explore the impact of deleterious nsSNPs retrieved from the dbSNP database on the structure and functions of the IL1B protein.

RESULTS

Six web servers (SIFT, PolyPhen-2, PROVEAN, SNPs&GO, PHD-SNP, PANTHER) were used to analyze the impact of 222 missense SNPs on the function and structure of IL1B protein. Five novel nsSNPs (E100K, T240I, S53Y, D128Y, and F228S) were found to be deleterious and had a mutational impact on the structure and function of the IL1B protein. The I-mutant v2.0 and MUPro servers predicted that these mutations decreased the stability of the IL1B protein. Additionally, these five mutations were found to be conserved, underscoring their significance in protein structure and function. Three of them (T240I, D128Y, and F228S) were predicted to be cancer-causing nsSNPs. To analyze the behavior of the mutant structures under physiological conditions, we conducted a 50 ns molecular dynamics simulation using the WebGro online tool. Our findings indicate that the mutant values differ from those of the IL1B wild type in terms of RMSD, RMSF, Rg, SASA, and the number of hydrogen bonds.

CONCLUSIONS

This study provides valuable insights into nsSNPs located in the coding regions of IL1B, which lead to direct deleterious effects on the functional and structural aspects of the IL1B protein. Thus, these nsSNPs could be considered significant candidates in the pathogenesis of disorders caused by IL1B dysfunction, contributing to effective drug discovery and the development of precision medications. Thorough research and wet lab experiments are required to verify our findings. Moreover, bioinformatic tools were found valuable in the prediction of deleterious nsSNPs.

Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats

Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds

During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.

Comparing effects of natural betaine and betaine hydrochloride on gut physiology in broiler chickens

Betaine is a well-known component of poultry diets with various effects on nutritional physiology. For example, increased water retention due to the osmolytic effect of betaine increases the volume of the cell, thereby accelerating the anabolic activity, integrity of cell membrane, and overall performance of the bird. Betaine is a multifunctional component (trimethyl derivative) acting as the most efficient methyl group donor and as an organic osmolyte, which can directly influence the gastrointestinal tract integrity, functionality, and health. So far, nothing is known about the effect of betaine on the intestinal barrier in chickens. In addition, little is known about comparing natural betaine with its synthetic form. Therefore, an animal study was conducted to ascertain the effects of betaine supplementation (natural and synthetic) on performance and intestinal physiological responses of broilers. One hundred and five 1-day-old broiler chicks were randomly assigned into 3 groups with 35 birds each: control, natural betaine (1 kg active natural (n)-betaine/ton of feed) and synthetic (syn)-betaine‐HCL (1 kg active betaine /ton of feed). Histological assessment showed lower jejunal crypt depth and villi height/crypt depth ratio in syn-betaine-HCL group compared with natural n-betaine fed birds. Furthermore, it was found that syn-betaine-HCL negatively affects the integrity of the intestine by increasing the intestinal paracellular permeability in both jejunum and cecum as evidenced by a higher mannitol flux. Additionally, syn-betaine-HCl significantly upregulated the IFN-γ mRNA expression at certain time points, which could promote intestinal permeability, as it plays an important role in intestinal barrier dysfunction. Body weight (BW) and body weight gain (BWG) did not differ (P > 0.05) between the control birds and birds supplemented with syn-betaine‐HCL. However, the BW and BWG were significantly (P < 0.05) improved by the dietary inclusion of n-betaine compared with other treatments. Altogether, the dietary inclusion of n-betaine had a positive effect on performance and did not negatively affect gut paracellular permeability. Furthermore, our results show that syn-betaine-HCl induces changes in the intestine, indicating an alteration of the intestinal histology and permeability. Thus, natural or synthetic betaine has different effects, which needs to be considered when using them as a feed supplement.

Gut Microbiota-Derived Indole-3-Carboxylate Influences Mucosal Integrity and Immunity Through the Activation of the Aryl Hydrocarbon Receptors and Nutrient Transporters in Broiler Chickens Challenged With Eimeria maxima

Two studies were conducted to evaluate the effects of indole-3-carboxylate (ICOOH) as a postbiotic on maintaining intestinal homeostasis against avian coccidiosis. In the first study, an in vitro culture system was used to investigate the effects of ICOOH on the proinflammatory cytokine response of chicken macrophage cells (CMCs), gut integrity of chicken intestinal epithelial cells (IECs), differentiation of quail muscle cells (QMCs), and primary chicken embryonic muscle cells (PMCs) and anti-parasitic effect against Eimeria maxima. Cells to be tested were seeded in the 24-well plates and treated with ICOOH at concentrations of 0.1, 1.0, and 10.0 µg. CMCs were first stimulated by lipopolysaccharide (LPS) to induce an innate immune response, and QMCs and PMCs were treated with 0.5% and 2% fetal bovine serum, respectively, before they were treated with ICOOH. After 18 h of incubation, cells were harvested, and RT-PCR was performed to measure gene expression of proinflammatory cytokines of CMCs, tight junction (TJ) proteins of IECs, and muscle cell growth markers of QMCs and PMCs. In the second study, in vivo trials were carried out to study the effect of dietary ICOOH on disease parameters in broiler chickens infected with E. maxima. One hundred twenty male broiler chickens (0-day-old) were allocated into the following four treatment groups: 1) basal diet without infection (CON), 2) basal diet with E. maxima (NC), 3) ICOOH at 10.0 mg/kg feed with E. maxima (HI), and 4) ICOOH at 1.0 mg/kg feed with E. maxima (LO). Body weights (BWs) were measured on 0, 7, 14, 20, and 22 days. All groups except the CON chickens were orally infected with E. maxima on day 14. Jejunal samples were collected for lesion score and the transcriptomic analysis of cytokines and TJ proteins. In vitro, ICOOH increased the expression of TJ proteins in IECs and decreased IL-1β and IL-8 transcripts in the LPS-stimulated CMCs. In vivo, chickens on the HI diet showed reduced jejunal IL-1β, IFN-γ, and IL-10 expression and increased expression of genes activated by aryl hydrocarbon receptors and nutrient transporters in E. maxima-infected chickens. In conclusion, these results demonstrate the beneficial effects of dietary ICOOH on intestinal immune responses and barrier integrity in broiler chickens challenged with E. maxima. Furthermore, the present finding supports the notion to use microbial metabolites as novel feed additives to enhance resilience in animal agriculture.

Delay of Feed Post-Hatch Causes Changes in Expression of Immune-Related Genes and Their Correlation with Components of Gut Microbiota, but Does Not Affect Protein Expression

Simple Summary

Newly hatched chicks do not have access to feed until between 48 and 72 h post-hatch based on standard practices in the poultry industry. How these practices affect the chicken’s immune system in not well understood. In this study, we investigated the effect of a delay in access to feed for 48 h in newly hatched chicks on the expression of various immune-related genes in the ileum and analyzed the correlation between these genes and the components of the ileal microbiota. The results suggest that several immune-related genes were affected by delayed access to feed and the age of the birds; however, these changes were transient, occurring mostly within 48 h of the return of birds to feed. In the correlation analysis between gene expression and components of the ileal microbiota, an increased number of significant correlations between immune-related genes and the genera Clostridium, Enterococcus, and the species Clostridium perfringens suggests a perturbation of the immune response and ileal microbiota in response to lack of feed immediately post-hatch. These results point out the complexity of the interplay between microbiota and the immune response and will help further explain the negative effects of delay in access to feed on production parameters in chickens.

Abstract

Because the delay of feed post-hatch (PH) has been associated with negative growth parameters, the aim of the current study was to determine the effect of delayed access to feed in broiler chicks on the expression of immune-related genes and select proteins. In addition, an analysis of the correlation between gene expression and components of the gut microbiota was carried out. Ross 708 eggs were incubated and hatched, and hatchlings were divided into FED and NONFED groups. The NONFED birds did not have access to feed until 48 h PH, while FED birds were given feed immediately PH. The ileum from both groups (n = 6 per group) was sampled at embryonic day 19 (e19) and day 0 (wet chicks), and 4, 24, 48, 72, 96, 144, 192, 240, 288, and 336 h PH. Quantitative PCR (qPCR) was carried out to measure the expression of avian interleukin (IL)-1β, IL-4, IL-6, IL-8, IL-18, transforming growth factor (TGF-β), toll-like receptor (TLR)2, TLR4, interferon (IFN)-β, IFN-γ, and avian β-defensins (AvBD) I, 2, 3, 5, 6, 7, 8, 9, and 10. Protein expression of IL-10, IL-1β, IL-8, and IL-18 were measured using ELISAs. A correlation analysis was carried out to determine whether any significant association existed between immune gene expression and components of the ileal luminal and mucosal microbiota. Expression of several immune-related genes (TGF-β, TLR4, IFN-γ, IL-1β, IL-4, IL-6, and AvBDs 8 and 9) were significantly affected by the interaction between feed status and age. The effects were transient and occurred between 48 and 96 h PH. The rest of the genes and four proteins were significantly affected by age, with a decrease in expression noted over time. Correlation analysis indicated that stronger correlations exist among gene expression and microbiota in NONFED birds. The data presented here indicates that delay in feed PH can affect genes encoding components of the immune system. Additionally, the correlation analysis between immune gene expression and microbiota components indicates that a delay in feed has a significant effect on the interaction between the immune system and the microbiota.

Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens

Background

Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved genetic adaptations to their local environmental conditions, such as hot and arid regions. In the present study, we provide a population genome landscape of genetic variations in 72 chickens representing nine Iranian indigenous ecotypes (Creeper, Isfahan, Lari, Marand, Mashhad, Naked neck, Sari, Shiraz and Yazd) and two commercial lines (White Leghorn and Arian). We further performed comparative population genomics to evaluate the genetic basis underlying variation in the adaptation to hot climate and immune response in indigenous chicken ecotypes. To detect genomic signatures of adaptation, we applied nucleotide diversity (θπ) and F_ST statistical measurements, and further analyzed the results to find genomic regions under selection for hot adaptation and immune response-related traits.

Results

By generating whole-genome data, we assessed the relationship between the genetic diversity of indigenous chicken ecotypes and their genetic distances to two different commercial lines. The results of genetic structure analysis revealed clustering of indigenous chickens in agreement with their geographic origin. Among all studied chicken groups, the highest level of linkage disequilibrium (LD) (~ 0.70) was observed in White Leghorn group at marker pairs distance of 1 Kb. The results from admixture analysis demonstrated evidence of shared ancestry between Arian individuals and indigenous chickens, especially those from the north of the country. Our search for potential genomic regions under selection in indigenous chicken ecotypes revealed several immune response and heat shock protein-related genes, such as HSP70, HSPA9, HSPH1, HSP90AB1 and PLCB4 that have been previously unknown to be involved in environmental-adaptive traits. In addition, we found some other candidate loci on different chromosomes probably related with hot adaptation and immune response-related traits.

Conclusions

The work provides crucial insights into the structural variation in the genome of Iranian indigenous chicken ecotypes, which up to now has not been genetically investigated. Several genes were identified as candidates for drought, heat tolerance, immune response and other phenotypic traits. These candidate genes may be helpful targets for understanding of the molecular basis of adaptation to hot environmental climate and as such they should be used in chicken breeding programs to select more efficient breeds for desert climate.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08434-7.