Deep Proteome Profiling of Semen of Indian Indigenous Malnad Gidda (Bos indicus) Cattle

A proteomic approach to identifying spermatozoa proteins in Indonesian native Madura bulls

Proteins assist sperm mature, transit the female reproductive tract, and recognise sperm oocytes. Indigenous Indonesian bulls, Madura bulls, have not been studied for reproductive proteomics. As local Indonesian beef livestock, Madura cattle assist in achieving food security; hence, their number must be improved. Thus, the identification of molecular proteomics-based bull fertility biomarkers is needed. This study aimed to characterise the sperm fertility function of the superior Madura bull (Bos indicus × Bos Javanicus) spermatozoa proteome. Frozen semen from eight Madura superior bulls (Bos indicus × Bos javanicus) aged 4-8 years was obtained from the artificial insemination centre (AIC) in Singosari and Lembang. Madura superior bulls are those that have passed the bull breeding soundness evaluation. Frozen sperm were thawed and centrifuged at 3000 × g for 30 min. Proteins in sperm were characterised through proteomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The resulting gene symbols for each protein were then subjected to bioinformatics tools, including UniProt, DAVID, and STRING databases. Regarding sperm fertility, the analysis revealed that 15 proteins were identified in the sperm of Madura bulls. Amongst the identified proteins, the superior Madura bull sperm contained several motilities, energy-related proteins, and chaperone proteins. A substantial portion of characterised proteins are linked to metabolic pathways and the tricarboxylic acid (TCA) cycle, contributing to sperm energy production. In conclusion, the first in-depth proteome identification of sperm related to sperm quality and bull fertility of a unique indigenous Madura breed of Indonesia was performed using the LC-MS/MS proteomic method. These findings may serve as a reference point for further studies related to the functions of bovine sperm and biomarkers of fertility and sperm quality.

Identification of heat shock protein70-2 and protamine-1 mRNA, proteins, and analyses of their association with fertility using frozen-thawed sperm in Madura bulls

OBJECTIVE

This study aims to identify heat shock protein70-2 (HSP70-2) and protamine-1 (PRM1) mRNA and protein in Madura bull sperm and demonstrate their relation as bull fertility biomarkers.

METHODS

The Madura bull fertility rates were grouped based on the percentage of first service conception rate (%FSCR) as high fertility (HF) (79.04%; n = 4), and low fertility (LF) (65.84%; n = 4). mRNA of HSP70-2 and PRM1 with peptidylprolyl isomerase A (PPIA) as a housekeeping gene were determined by quantitative real-time polymerase chain reaction, while enzyme-linked immunoassay was used to measure protein abundance. In the post-thawed semen samples, sperm motility, viability, acrosome integrity, and sperm DNA fragmentation index were analyzed. Data analysis was performed on the measured parameters of semen quality, relative mRNA expression, and protein abundance of HSP70-2 and PRM1, among the bulls with various fertility levels (HF and LF) in a one-way analysis of variance analysis. The Pearson correlation was used to analyze the relationship between semen quality, mRNA, proteins, and fertility rate.

RESULTS

Relative mRNA expression and protein abundance of HSP70-2 and PRM1 were detected and were found to be highly expressed in bulls with HF (p<0.05) and were associated with several parameters of semen quality.

CONCLUSION

HSP70-2 and PRM1 mRNA and protein molecules have great potential to serve as molecular markers for determining bull fertility.

Relative Abundance of Spermadhesin-1 in the Seminal Plasma of Young Nellore Bulls Is in Agreement with Reproductive Parameters

This study aimed to evaluate the proteomic profile of seminal plasma from young Nellore bulls. We used 20 bulls aged between 19.8 and 22.7 months, divided into two groups according to the results of the Breeding Soundness Evaluation (BSE): approved (FIT n = 10) and not approved (UNFIT n = 10). The scrotal perimeter was measured and a semen collection was performed through electroejaculation. The percentage of sperm motility, mass motility, and sperm vigor were calculated using conventional microscopy, and the percentage of sperm abnormalities was calculated using phase-contrast microscopy of all ejaculates. Seminal plasma was separated from spermatozoa using centrifugation and processed for proteomic analysis by LC-MS/MS. Seminal plasma proteins were identified using MASCOT Daemon software v.2.4.0 and label-free quantification analysis was carried out by SCAFFOLD Q+ software v.4.0 using the Exponentially Modified Protein Abundance Index (emPAI) method. Functional classification of proteins was performed based on their genetic ontology terms using KOG. Functional cluster analysis was performed on DAVID. There were no differences in scrotal perimeter and physical semen characteristics between FIT and UNFIT groups of bulls. The percentage of sperm abnormalities was higher (p < 0.05) in the UNFIT group of bulls. A total of 297 proteins were identified for the two groups. There were a total of 11 differentially abundant proteins (p < 0.05), two of them more abundant in FIT bulls (Spermadhesin-1 and Ig gamma-1 chain C region) and nine in UNFIT bulls (Vasoactive intestinal peptide, Metalloproteinase inhibitor 2, Ig lambda-1 chain C regions, Protein FAM3C, Hemoglobin beta, Seminal ribonuclease, Spermadhesin 2, Seminal plasma protein BSP-30kDa, and Spermadhesin Z13). Spermadhesin-1 was the protein with the highest relative abundance (36.7%) in the seminal plasma among all bulls, corresponding to 47.7% for the FIT bulls and 25,7% for the UNFIT bulls. Posttranslational modification, protein turnover, and chaperones were the functional categories with the highest number of classified proteins. Protein functional annotation clusters were related to Phospholipid efflux, ATP binding, and chaperonin-containing T-complex. The differentially abundant proteins in the group of FIT bulls were related to sperm capacitation and protection against reactive species of oxygen. In contrast, differentially expressed proteins in the group of UNFIT bulls were related to motility inhibition, intramembrane cholesterol removal and oxidative stress. In conclusion, the proteomic profile of the seminal plasma of FIT bulls presents proteins with participation in several biological processes favorable to fertilization, while the proteins of the seminal plasma of UNFIT bulls indicate a series of alterations that can compromise the fertilizing capacity of the spermatozoa. In addition, the relative abundance of spermadhesin-1 found in the seminal plasma of young Nellore bulls could be studied as a reproductive parameter for selection.

Exploring molecular dynamic indicators associated with reproductive performance of Bos indicus cattle in blood plasma samples through data-independent acquisition mass spectrometry

Improving reproductive performance of cattle is of paramount importance for sustainable dairy farming. Poor reproduction performance (RP) hinders the genetic improvement of important Bos indicus cattle breeds. It is well known that incorporation of molecular information along with conventional breeding method is far better than use of conventional method alone for the genetic improvement of reproductive performance traits in cattle. Therefore, the present study sought to investigate the plasma proteome of the Deoni cows in cyclical (n = 6) and pregnant (n = 6) reproductive phases with varying reproductive performance (high and low). High-throughput data independent acquisition (DIA) based proteomics was performed to understand corresponding proteome. We identified a total of 430 plasma proteins. Among cyclic cows, twenty proteins were differentially regulated in low RP as compared to high RP. BARD1 and AFP proteins were observed upregulated in cyclical cows whose upregulation reported to affect reproductive performance in cattle. Among the pregnant cows, thirty-five proteins were differentially regulated, including the downregulation of FGL2 and ZNFX1 that modulates the maternal immune response mechanism which is required for successful implantation of the embryo. Also, proteins such as AHSG, CLU and SERPINA6 were upregulated in the pregnant cows whose upregulation reported to reduced reproductive performance. The results of this study will be helpful in establishing a framework for future research on the aspect of improving reproductive performance in Bos indicus cattle breeds. SIGNIFICANCE: The Indian subcontinent is the center of domestication for Bos indicus cattle breeds and they are known for their disease resistance, heat tolerance, ability to survive in low input regime and harsh climatic conditions. In recent times, population of many important Bos indicus breeds including Deoni cattle is declining due to various factors, especially due to reproductive performance. Traditional breeding methods are not sufficient enough to understand and improve the reproductive performance traits in important Bos indicus cattle breeds. Proteomics approach is a promising technology to understand the complex biological factors which leads to poor reproductive performance in cattle. The present study utilized DIA based LC- MS/MS analysis to identify the plasma proteins associated with reproductive performance in cyclical and pregnant cows. This study if improved further, can be used to develop potential protein markers associated with reproductive performance which is useful for the selection and genetic improvement of important Bos indicus breeds.

Quantitative proteomics profiling of spermatozoa and seminal plasma reveals proteins associated with semen quality in Bos indicus bulls

Cattle breeding approaches are an evolving field of research in veterinary science. Certain factors such as Ejaculate Rejection Rate (ERR) pose a limitation to such approaches. In this regard, we sought to investigate the spermatozoa and seminal plasma proteome of Hallikar bulls with low (n = 3) and high (n = 3) ERR. Through the Tandem mass spectrometry approach, we identified a total of 2409 proteins, in which 828 proteins were common in both the semen components, whereas 375 and 378 proteins were unique to spermatozoa and seminal plasma respectively. Tandem mass tags (TMT) based protein quantification resulted in 75 spermatozoal, and 42 seminal plasma proteins being differentially regulated between high and low ERR bulls. Proteins such as SPADH2, TIMP-2, and PLA2G7 which are negative regulators of motility were upregulated in the seminal plasma of high ERR bulls. Proteins such as OAZ3, GPx4, and GSTM3 whose upregulation leads to reduced motility were upregulated in the spermatozoa of high ERR bulls. Caltrin and ADM proteins that enhance sperm motility were downregulated in the seminal plasma of high ERR bulls. The regulation of ACE, a negative regulator of sperm motility was upregulated in both the spermatozoa and seminal plasma of high ERR bulls. SIGNIFICANCE: The saying "Bull is more than half of the herd" signifies the importance of bull in the genetic improvement of the herd. Traditionally used semen quality tests will provide limited information about the potential fertility of bulls. The proteomics approach is a promising omics technology to understand the factors involved in male fertility. The present study identified the spermatozoal and seminal plasma proteins that are differentially regulated between high and low ERR bulls. Sperm motility-associated proteins are differentially regulated. This study if improved further, can be used to develop markers associated with semen quality which is useful for the selection of bulls.

High-throughput proteomic characterization of seminal plasma from bulls with contrasting semen quality

Seminal plasma proteins are the major extrinsic factors that can modulate the sperm quality and functions. The present study was carried out to compare the proteomic profiles of seminal plasma from breeding bulls producing good and poor quality semen in an effort to understand the possible proteins associated with semen quality. A total of 910 and 715 proteins were detected in the seminal plasma of poor and good quality semen producing bulls, respectively. A total of 705 proteins were common to both the groups, in which 380 proteins were upregulated and 89 proteins were downregulated in the seminal plasma of poor quality semen, while 236 proteins were co-expressed. The proteins negatively influencing sperm functions such as CCL2, UQCRC2, and SAA1 were among the top ten upregulated proteins in the seminal plasma of poor quality semen. Proteins having a positive role in sperm functions (NGF, EEF1A2, COL1A2, IZUMO4, PRSS1, COL1A1, WFDC2) were among the top ten downregulated proteins in the seminal plasma of poor quality semen. The upregulation of oxidation-reduction process-related proteins, histone proteins (HIST3H2A, H2AFJ, H2AFZ, H2AFX, HIST2H2AB, H2AFV, HIST1H2AC, HIST2H2AC, LOC104975684, LOC524236, LOC614970, LOC529277), and ubiquinol-cytochrome-c reductase proteins (UQCRB, UQCRFS1, UQCRQ, UQCRC1, UQCRC2) indicate deranged oxidation-reduction equilibrium, chromatin condensation and spermatogenesis in poor quality semen producing bulls. The expression of proteins essential for motile cilium (CCDC114, CFAP206, TEKT4), chromatin integrity (PRM2), gamete fusion (IZUMO4, EQTN), hyperactivation, tyrosine phosphorylation, and capacitation [PI3K-Akt signalling pathway-related proteins (COL1A1, COL2A1, COL1A2, SPP1, PDGFA, NGF)] were down regulated in poor quality semen producing bulls.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03474-6.

Testis-enriched ferlin, FER1L5, is required for Ca2+-activated acrosome reaction and male fertility

Spermatozoa need to undergo an exocytotic event called the acrosome reaction before fusing with eggs. Although calcium ion (Ca2+) is essential for the acrosome reaction, its molecular mechanism remains unknown. Ferlin is a single transmembrane protein with multiple Ca2+-binding C2 domains, and there are six ferlins, dysferlin (DYSF), otoferlin (OTOF), myoferlin (MYOF), fer-1-like 4 (FER1L4), FER1L5, and FER1L6, in mammals. Dysf, Otof, and Myof knockout mice have been generated, and each knockout mouse line exhibited membrane fusion disorders such as muscular dystrophy in Dysf, deafness in Otof, and abnormal myogenesis in Myof. Here, by generating mutant mice of Fer1l4, Fer1l5, and Fer1l6, we found that only Fer1l5 is required for male fertility. Fer1l5 mutant spermatozoa could migrate in the female reproductive tract and reach eggs, but no acrosome reaction took place. Even a Ca2+ ionophore cannot induce the acrosome reaction in Fer1l5 mutant spermatozoa. These results suggest that FER1L5 is the missing link between Ca2+ and the acrosome reaction.

Comparative high-throughput analysis of sperm membrane proteins from crossbred bulls with contrasting fertility

The aim of the present study was to identify fertility associated sperm membrane proteins in crossbred bulls. Sperm membrane proteins from high- and low-fertile Holstein Friesian crossbred bulls (n = 3 each) were subjected to high-throughput liquid chromatography-mass spectrometry (LC-MS/MS) for comparative proteomic analysis. Proteomic profiling identified a total of 456 proteins in crossbred bull spermatozoa; it was found that 108 proteins were up regulated while 26 proteins were down regulated (>1.5-folds) in spermatozoa from low- compared to high-fertile bulls. Gene ontology classification revealed that upregulated proteins in low-fertile bulls were involved in biological process such as oxidation-reduction process (p = 3.14E-06), fusion of sperm to egg plasma membrane (p = 7.51E-04), sperm motility (p = 0.03), and capacitation (p = 0.09), while down regulated proteins were associated with transport (p = 6.94E-04), superoxide metabolic process (p = 0.02), and tricarboxylic acid cycle (p = 0.04). KEGG pathway analysis revealed that oxidative phosphorylation and tricarboxylic acid cycle pathways are the most significantly affected pathway in low-fertile bulls. It was concluded that expression of proteins associated with oxidative phosphorylation and tricarboxylic acid cycle pathways were altered in low-fertile crossbred bulls, and expression levels of SPATA19, ELSPBP1, ACRBP, CLU, SUCLA2, and SPATC1 could aid in assessing potential fertility of crossbred bulls.

Identification of biomarkers for bull fertility using functional genomics

Prediction of bull fertility is critical for the sustainability of both dairy and beef cattle production. Even though bulls produce ample amounts of sperm with normal parameters, some bulls may still suffer from subpar fertility. This causes major economic losses in the cattle industry because using artificial insemination, semen from one single bull can be used to inseminate hundreds of thousands of cows. Although there are several traditional methods to estimate bull fertility, such methods are not sufficient to explain and accurately predict the subfertility of individual bulls. Since fertility is a complex trait influenced by a number of factors including genetics, epigenetics, and environment, there is an urgent need for a comprehensive methodological approach to clarify uncertainty in male subfertility. The present review focuses on molecular and functional signatures of bull sperm associated with fertility. Potential roles of functional genomics (proteome, small noncoding RNAs, lipidome, metabolome) on determining male fertility and its potential as a fertility biomarker are discussed. This review provides a better understanding of the molecular signatures of viable and fertile sperm cells and their potential to be used as fertility biomarkers. This information will help uncover the underlying reasons for idiopathic subfertility.

Induction of antiviral and cell mediated immune responses significantly reduce viral load in an acute foot-and-mouth disease virus infection in cattle

Foot-and-mouth disease virus (FMDV) causes a severe infection in ruminant animals. Here we present an in-depth transcriptional analysis of soft-palate tissue from cattle experimentally infected with FMDV. The differentially expressed genes from two Indian cattle (Bos indicus) breeds (Malnad Gidda and Hallikar) and Holstein Friesian (HF) crossbred calves, highlighted the activation of metabolic processes, mitochondrial functions and significant enrichment of innate antiviral immune response pathways in the indigenous calves. The results of RT-qPCR based validation of 12 genes was in alignment with the transcriptome data. The indigenous calves showing lesser virus load, elicited early neutralizing antibodies and IFN-γ immune responses. This study revealed that induction of potent innate antiviral response and cell mediated immunity in indigenous cattle, especially Malnad Gidda, significantly restricted FMDV replication during acute infection. These data highlighting the molecular processes associated with host-pathogen interactions, could aid in the conception of novel strategies to prevent and control FMDV infection in cattle.

Bioinformatics analysis of structures and ligand-bindings of predicted zymogen granule protein observed on Bali cattle (Bos javanicus) saliva

Objective

Previously, we have shown that predicted zymogen granule protein 16 homolog B (P-G3MZ19) existed in Bali cattle (Bos javanicus) saliva. It was suggested that P-G3MZ19 is a member of the mannose-binding lectin family that plays an essential role in innate immunity. In the present study, we aimed to analyze the structure and ligand-binding of P-3MZ19 in Bali cattle saliva.

Materials and Methods

Saliva of four adult healthy Bali cattle was collected, lyophilized, and subjected to two-dimensional (2-D) gel electrophoresis. The target spot of around 17 kDa related to P-G3MZ19 was excised for matrix-assisted laser desorption ionization time-of-flight mass spectrometer/time-of-flight mass spectrometer mass spectrometry analysis and sequencing. The structure and the ligand-binding of P-3MZ19 were analyzed using bioinformatics software programs published elsewhere.

Results

Based on Iterative Threading ASSEmbly Refinement the 3D model of P-G3MZ19 was suggested to have similarities to exo-alpha-sialidase (EC 3.2.1.18); while its ligand-binding sites consisted of seven residues, i.e., 25aa-26aa (Gly-Gly), 95aa (Phe), 138aa (Tyr), 140aa (Leu), 141aa (Gly), and 143aa (Thr).

Conclusion

The structure of P-G3MZ19 of Bali cattle saliva and its ligand-binding sites have been successfully determined by using bioinformatics techniques. The biological and immunological roles of the peptide are currently under investigation based on P-G3MZ19 synthetic peptides.

Protein Identification of Spermatozoa and Seminal Plasma in Bottlenose Dolphin (Tursiops truncatus)

Proteins play an important role in many reproductive functions such as sperm maturation, sperm transit in the female genital tract or sperm-oocyte interaction. However, in general, little information concerning reproductive features is available in the case of aquatic animals. The present study aims to characterize the proteome of both spermatozoa and seminal plasma of bottlenose dolphins (Tursiops truncatus) as a model organism for cetaceans. Ejaculate samples were obtained from two trained dolphins housed in an aquarium. Spermatozoa and seminal plasma were analyzed by means of proteomic analyses using an LC-MS/MS, and a list with the gene symbols corresponding to each protein was submitted to the DAVID database. Of the 419 proteins identified in spermatozoa and 303 in seminal plasma, 111 proteins were shared by both. Furthermore, 70 proteins were identified as involved in reproductive processes, 39 in spermatozoa, and 31 in seminal plasma. The five most abundant proteins were also identified in these samples: AKAP3, ODF2, TUBB, GSTM3, ROPN1 for spermatozoa and CST11, LTF, ALB, HSP90B1, PIGR for seminal plasma. In conclusion, this study provides the first characterization of the proteome in cetacean sperm and seminal plasma, opening the way to future research into new biomarkers, the analysis of conservation capacity or possible additional applications in the field of assisted reproductive technologies.

Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. SIGNIFICANCE: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the world have used the technology in this specific research field. We address also major international efforts aiming to increase the research output in this area and highlight the importance of international cooperation to address specific problems inherent to domestic animal proteomics.

Preliminary comparative deep metabolomic analysis of spermatozoa from zebu and crossbred cattle suggests associations between metabolites, sperm quality and fertility

Poor semen quality and infertility/subfertility are more frequent in crossbred than zebu bulls. Using a high-throughput liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based approach, we established the preliminary metabolomic profile of crossbred and zebu bull spermatozoa (n=3 bulls each) and identified changes in sperm metabolomics between the two groups. In all, 1732 and 1240 metabolites were detected in zebu and crossbred bull spermatozoa respectively. After excluding exogenous metabolites, 115 and 87 metabolites were found to be unique to zebu and crossbred bull spermatozoa respectively whereas 71 metabolites were common to both. In the normalised data, 49 metabolites were found to be differentially expressed between zebu and crossbred bull spermatozoa. The significantly enriched (P&lt;0.05) pathways in spermatozoa were taurine and hypotaurine metabolism (observed metabolites taurine and hypotaurine) in zebu and glycerophospholipid metabolism (observed metabolites phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine) in crossbred bulls. The abundance of nitroprusside (variable importance in projection (VIP) score &gt;1.5) was downregulated, whereas that of l-cysteine, acetyl coenzyme A and 2′-deoxyribonucleoside 5′-diphosphate (VIP scores &gt;1.0) was upregulated in crossbred bull spermatozoa. In conclusion, this study established the metabolomic profile of zebu and crossbred bull spermatozoa and suggests that aberrations in taurine, hypotaurine and glycerophospholipid metabolism may be associated with the higher incidence of infertility/subfertility in crossbred bulls.