Comparative proteomics of matrix fractions between pimpled and normal chicken eggshells

Integrating proteomics and metabolomics to elucidate the regulatory mechanisms of pimpled egg production in chickens: Multi-omics analysis of the mechanism of pimpled egg formation

Eggshells not only protect the contents of the egg from external damage but are also a key factor influencing consumer choice, second only to price. In the later stages of egg production, the incidence of pimpled eggs significantly increases, severely affecting the hatchability and food safety of the eggs. This study compares the differences in the uterine proteomes and metabolomes of hens producing pimpled eggs and those producing normal eggs, aiming to identify the proteins and metabolites that may play a crucial role in the formation of pimpled eggs. A total of 242 differentially expressed proteins (DEPs) were identified in uterine tissue, of which 116 were upregulated and 126 were downregulated. Enrichment analysis revealed that the DEPs were enriched in pathways related to ion transport, energy metabolism, and immune responses. The study found that in the normal eggs (NE) group, HCO₃⁻ was predominantly transported via SLC4A1, although other transport pathways may also play a role. In contrast, in the pimpled eggs (PE) group, bicarbonate ions (HCO₃⁻) was primarily transported through SLC4A4. Additionally, a total of 44 differentially metabolites (DMs) were identified in the uterus, with 5'-Adenylic acid (ATP) being significantly downregulated in the PE group. The ions and matrix proteins required for eggshell formation are transported from uterine cells to the uterine fluid against a concentration gradient, a process that consumes a substantial amount of energy. The decrease in ATP concentration in the PE group may be a significant factor influencing the formation of pimpled eggs. Subsequently, we found that the DEPs and DMs were jointly enriched in several signaling pathways, including the FoxO signaling pathway related to energy metabolism, nicotinate and nicotinamide metabolism, and tryptophan metabolism associated with immune response. Notably, the DMs involved in these signaling pathways were all downregulated in the PE group. Our research findings indicate that SLC4A1, SLC4A2, and ATP2B4 (DEPs), along with 5'-adenylic acid and trigonelline (DMs), influence the formation of eggshells through mechanisms related to energy metabolism, ion transport, and immune response. These DEPs and DMs may serve as potential biomarkers for the genetic improvement of eggshell quality.

TMT-Based quantitative proteomic analysis reveals age-related changes in eggshell matrix proteins and their correlation with eggshell quality in Xinyang blue-shelled laying hens

The decline in eggshell quality with increasing hen age may be related to changes in ultrastructure and chemical composition, with matrix proteins playing key roles in these changes. However, research on blue-shelled eggs remains limited. This study investigated the effects of hen age (35, 55, 75, and 85 weeks) on the physical, mechanical, and chemical properties of eggshells in the Xinyang blue-shelled laying hens, as well as their ultrastructural and nanostructural characteristics. Subsequently, a comparative proteomic analysis was performed to elucidate the differential protein profiles in eggshells from hens at 35 and 85 weeks of age. Results showed that egg weight, eggshell weight, and eggshell surface area increased with hen age, whereas eggshell stiffness decreased (p < 0.05). As the age advanced, the eggshell organic matter content declined (p < 0.05). The effective layer ratio, mammillae density, as well as the porosity and total pore area in the mammillary layer also decreased with age, whereas the ratio of the mammillary layer increased (p < 0.05). Compared to eggshells collected from 35-week-old hens, those from 85-week-old hens showed increases in egg weight, eggshell weight, surface area, and both the ratio and thickness of the mammillary layer (p < 0.05). However, significant decreases were observed in eggshell stiffness, organic matter content, phosphorus content, effective layer ratio, mammillae density, as well as the porosity and total pore area in the mammillary layer (p < 0.05). Additionally, eggshell stiffness, phosphorus content, and organic matter content were significantly correlated with each other (p < 0.05). Proteomic analysis identified 37 downregulated and 68 upregulated differentially expressed proteins (DEPs, FC > 1.2 or < 0.83, with a p-value < 0.05) in eggshells from 85-week-old hens compared to those from 35-week-old hens. These DEPs are associated with functions such as biomineralization, calcium transport, immunity, and proteases and protease inhibitors. Mantel and Pearson correlations suggest that these functions may be involved in regulating eggshell stiffness, phosphorus content, and organic matter content. Overall, the eggshell stiffness decreased from 35 to 85 weeks of age, which may be attributed to the reductions in eggshell organic matter and phosphorus contents, as well as the deteriorations in eggshell ultrastructure. The proteins associated with biomineralization, calcium transport, immunity, and proteases and protease inhibitors may contribute to these changes.

Gga-miR-34b-3p targets calbindin 1 to regulate cellular calcium ion homeostasis during eggshell calcification in chicken uterus

Improving eggshell quality in poultry is a key breeding goal, and identifying genetic markers that regulate eggshell calcification is essential for accelerating genetic advancements. This study focused on identifying the keys genes and molecular mechanisms that regulate eggshell calcification in the chicken uterus. The results showed that rapid eggshell mineralization began approximately 4 h after the egg enters the uterus, corresponding with observed morphological and histological changes in the uterine tissue. This is associated with increased energy demands and the production of ion transport proteins. Transcriptome analysis identified calbindin-1 (CALB1), ATPase plasma membrane Ca2+ transporting 2 (ATP2B2), and gga-miR-34b-3p as differentially expressed during eggshell formation. CALB1 and ATP2B2 were predicted targets of gga-miR-34b-3p, with roles in maintaining cellular calcium ion balance. A dual-luciferase reporter assay confirmed that gga-miR-34b-3p directly targeted inhibited CALB1 expression, although no significant changes in the luciferase activity were observed with the co-transfection of ATP2B2 wild-type and gga-miR-34b-3p mimic. Validation experiments showed significant increases in CALB1 and ATP2B2 mRNA and protein levels of CALB1 and ATP2B2 in the chicken uterus during eggshell calcification, with CALB1 predominantly expressed in the cytoplasm of uterine tubular gland cells. Furthermore, primary uterine tubular gland cells, identified using immunofluorescence for Cytokertin 18, demonstrated that silencing CALB1 and ATP2B2 increased intracellular Ca2+ concentration in these cells. Taken together, these findings suggest that the gga-miR-34b-3p/CALB1 regulatory axis maintains calcium ion homeostasis in the uterine tubular gland cells, to facilitate continuous and efficient eggshell calcification and thereby enhancing eggshell quality in chickens.

Integrating Single-Cell RNA-Seq and ATAC-Seq Analysis Reveals Uterine Cell Heterogeneity and Regulatory Networks Linked to Pimpled Eggs in Chickens

Pimpled eggs have defective shells, which severely impacts hatching rates and transportation safety. In this study, we constructed single-cell resolution transcriptomic and chromatin accessibility maps from uterine tissues of chickens using single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq). We identified 11 major cell types and characterized their marker genes, along with specific transcription factors (TFs) that determine cell fate. CellChat analysis showed that fibroblasts had the most extensive intercellular communication network and that the chickens laying pimpled eggs had amplified immune-related signaling pathways. Differential expression and enrichment analyses indicated that inflammation in pimpled egg-laying chickens may lead to disruptions in their circadian rhythm and changes in the expression of ion transport-related genes, which negatively impacts eggshell quality. We then integrated TF analysis to construct a regulatory network involving TF-target gene-Gene Ontology associations related to pimpled eggs. We found that the transcription factors ATF3, ATF4, JUN, and FOS regulate uterine activities upstream, while the downregulation of ion pumps and genes associated with metal ion binding directly promotes the formation of pimpled eggs. Finally, by integrating the results of scRNA-seq and scATAC-seq, we identified a rare cell type-ionocytes. Our study constructed single-cell resolution transcriptomic and chromatin accessibility maps of chicken uterine tissue and explored the molecular regulatory mechanisms underlying pimpled egg formation. Our findings provide deeper insights into the structure and function of the chicken uterus, as well as the molecular mechanisms of eggshell formation.

Whole transcriptome sequencing reveals key genes and ceRNA regulatory networks associated with pimpled eggs in hens

Eggshell is one of the most important indicators of egg quality, and due to low shell strength, pimple eggs (PE) are more susceptible to breakage, thus causing huge economic losses to the egg industry. At the current time, the molecular mechanisms that regulate the formation of pimple eggs are poorly understood. In this study, uterine tissues of PE-laying hens (n = 8) and normal egg (NE) -laying hens (n = 8) were analyzed by whole transcriptome sequencing, and a total of 619 differentially expressed mRNAs (DE mRNAs), 122 differentially expressed lncRNAs (DE lncRNAs) and 21 differentially expressed miRNAs (DE miRNAs) were obtained. Based on the targeting relationship among DE mRNAs, DE lncRNAs and DE miRNAs, we constructed a competitive endogenous RNA (ceRNA) network including 12 DE miRNAs, 19 DE lncRNAs, and 128 DE mRNAs. Considering the large amount of information contained in the network, we constructed a smaller ceRNA network to better understand the complex mechanisms of pimple egg formation. The smaller ceRNA network network contains 7 DE lncRNAs (LOC107056551, LOC121109367, LOC121108909, LOC121108862, LOC112530033, LOC121113165, LOC107054145), 5 DE miRNAs (gga-miR-6568-3p, gga-miR-31-5p, gga-miR-18b-3p, gga-miR-1759-3p, gga-miR-12240-3p) and 7 DE mRNAs (CABP1, DNAJC5, HCN3, HPCA, IBSP, KCNT1, OTOP3), and these differentially expressed genes may play key regulatory roles in the formation of pimpled eggs in hens. This study provides the overall expression profiles of mRNAs, lncRNAs and miRNAs in the uterine tissues of hens, which provides a theoretical basis for further research on the molecular mechanisms of pimpled egg formation, and has potential applications in improving eggshell quality.

TMT-based quantitative proteomic analysis unveils uterine fluid difference in hens producing normal and pimpled eggs

Eggshell is a crucial indicator of egg quality. Pimpled eggs (PE) a type of eggshell defect are characterized by low eggshell strength, leading to substantial financial losses. Eggshell formation occurs in the uterine fluid (UF), which contains the required ions and matrix proteins However, the underlying mechanisms of PE formation remain poorly understood. In this study, we analyzed the egg quality of PE, and normal eggs (NE) by examining the differences in UF from hens producing PE and NE (n = 6 each). This 2-wk-long assessment involved histomorphological and proteomics analyses. The results showed that NE had better eggshell quality compared to PE, and the uterus structure in PE hens was conducive to the formation of PE. Using quantitative proteomic analysis, we identified 68 differential abundance proteins (DAPs) in the UF of PE hens, including 9 key proteins related to ion transport, protein synthesis and folding, and immunity. Downregulation of CALM1 and SCNN1G proteins in PE hens might have negatively affected the calcium signaling pathway, decreasing the calcium amount in UF. Additionally, the PHB1 and TSN proteins may affect eggshell formation by regulating immune responses. Taken together, our results provide insights into the mechanism of PE production, with potential applications for enhancing eggshell quality.

Research progress on bird eggshell quality defects: a review

The eggshell quality declined with extending of chicken laying cycles. Eggshell quality is a crucial feature that not only affects consumer preference, but also influences producers' economic profitability. The eggshell ultrastructure consists of mammillary, palisade, and vertical crystal layers. Any defect in shell structure results in a reduction in eggshell quality. Speckled, translucent, pimpled, and soft eggshells are common defects that cause significant financial losses for farmers and food security concerns for consumers. Therefore, reducing the faulty eggshells is critical for poultry production. Defective eggshell quality has been attributed to hereditary factors and external environmental stimuli. As such, improvements can be carried out through selective breeding and environmental control of components such as temperature, moisture, and diet formula balance. In this review, the molecular mechanisms of the main eggshell quality defects (speckled, translucent, pimpled, broken, and soft-shell eggs) and the relevant improvement methods are detailed. We hope this review will serve as a useful resource for poultry production management and effectively increasing eggshell quality.

Integrated proteomic, phosphoproteomic and N-glycoproteomic analyses of chicken eggshell matrix

Eggshell matrix (EM) proteins play an important biological role in eggshell mineralization and embryo development. Many studies have demonstrated that some matrix proteins undergo posttranslational modifications, including phosphorylation and glycosylation, which have important regulatory effects on the functional properties of the proteins. Systematic analysis of the proteome, the phosphorylated modified proteome and the glycosylated modified proteome of the chicken EM was performed using a proteomics strategy. A total of 112 phosphorylation sites from 69 phosphoproteins and 297 N-glycosylation sites from 182 N-glycoproteins were identified in the chicken EM. Among all these identified modified proteins, 129 were not identified in the proteome (547 proteins). Therefore, a total of 676 EM proteins were identified in this study. Gene ontology (GO) enrichment analysis indicated that EM proteins and phosphoproteins were mainly enriched in regulation of enzyme activity, while EM N-glycoproteins were enriched in immune response regulation.

Structural and proteomic analyses of vitelline membrane proteins of blackbird (Turdus merula) and song thrush (Turdus philomelos)

In this study, we aimed to perform structural and proteomic analysis of the vitelline membrane (VM) of two species birds belonging to the family Turdidae: blackbird (Turdus merula) and song thrush (Turdus philomelos). We performed structural analyses using scanning electron microscopy. The VM proteins were identified and compared to the best-known chicken VM proteins. According to our results, VM of both species has a typical three-layered structure: the outer layer, inner layer, and the continuous membrane between them. An unusual observation was the finding of “convexity” formed by the inner layer in blackbird. The role of these convex structures is not known, but they can be typical for the species and can be used in their identification. In addition, we identified two proteins in the VM of both species of birds, of which U3KEZ1 FICAL was not previously identified in any other bird species, and the U3JXV8 FICAL protein was confirmed only once in cockatiel parrot VM. The function of these proteins is not exactly known, but their structure shows similarities to the SERPIN proteins that are involved in microbiological defense, i.e., they are immune proteins. This study contributes to the current knowledge about the structure and composition of proteins of VM, especially because similar analyses have never been performed for Turdidae family. Knowledge of the structure and specific proteins of blackbird and song thrush VM can be beneficial in research on ecology and bird biology and also helpful in developing noninvasive and nongenetic identification methods.