Characterization of porcine MMP-2 and its association with immune traits

Identification of the matrix metalloproteinase (MMP) gene family in Japanese flounder (Paralichthys olivaceus): Involved in immune response regulation to temperature stress and Edwardsiella tarda infection

The Matrix metalloproteinase (MMP) gene family is responsible for regulating the degradation of Extra Cellular Matrix (ECM) proteins, which are important for physiological processes such as wound healing, tissue remodeling, and stress response. Although MMPs have been studied in many species, their role in immune response in Japanese flounder (Paralichthys olivaceus) is still not fully understood. This study conducted a comprehensive analysis of MMPs in flounder, including gene structures, evolutionary relationships, conserved domains, molecular evolution, and expression patterns. Analysis revealed that MMP genes could be grouped into 17 subfamilies and were evolutionarily conserved and functionally-constrained. Meanwhile, MMP genes were found to express in different embryonic and larval stages and might play the role of sentinel in healthy tissues. Furthermore, expression profiling showed that MMPs had diverse functions in environmental stress, with 60% (9/15) and 73% (11/15) of MMPs showing differential expression patterns under temperature stress and Edwardsiella tarda (E. tarda) infection, respectively. These findings provide a useful resource for understanding the immune functions of MMP genes in Japanese flounder.

Alterations of mRNA and lncRNA profiles associated with the extracellular matrix and spermatogenesis in goats

Objective

Spermatozoa are produced within the seminiferous tubules after sexual maturity. The expression levels of mRNAs and lncRNAs in testicular tissues are different at each stage of testicular development and are closely related to formation of the extracellular matrix (ECM) and spermatogenesis. Therefore, we set out to study the expression of lncRNAs and mRNAs during the different developmental stages of the goat testis.

Methods

We constructed 12 RNA libraries using testicular tissues from goats aged 3, 6, and 12 months, and studied the functions of mRNAs and lncRNAs using the gene ontogeny (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. Relationships between differentially expressed genes (DEGs) were analyzed by lncRNA-mRNA co-expression network and protein-protein interaction network (PPI). Finally, the protein expression levels of matrix metalloproteinase 2 (MMP2), insulin-like growth factor 2 (IGF2), and insulin-like growth factor-binding protein 6 (IGFBP6) were detected by western blotting.

Results

We found 23, 8, and 135 differentially expressed lncRNAs and 161, 12, and 665 differentially expressed mRNAs that were identified between 3 vs 6, 6 vs 12, and 3 vs 12 months, respectively. GO, KEGG, and PPI analyses showed that the differential genes were mainly related to the ECM. Moreover, MMP2 was a hub gene and co-expressed with the lncRNA TCONS-0002139 and TCONS-00093342. The results of quantitative reverse-transcription polymerase chain reaction verification were consistent with those of RNA-seq sequencing. The expression trends of MMP2, IGF2, and IGFBP6 protein were the same as that of mRNA, which all decreased with age. IGF2 and MMP2 were significantly different in the 3 vs 6-month-old group (p<0.05).

Conclusion

These results improve our understanding of the molecular mechanisms involved in sexual maturation of the goat testis.

Expression pattern and association analysis of porcine matrix metallopeptidase 9 (MMP9) with diarrhea and performance traits in piglets

Matrix metalloproteinase 9 (MMP9) plays critical roles in multiple biological processes, such as reproduction, cell proliferation and differentiation, and host defenses. The aim of this study was to evaluate whether MMP9 is a candidate gene for resistance to diarrhea in piglets. In this study, quantitative real-time PCR was used to analyze the expression of MMP9 mRNA in different tissues of specific pathogen-free piglets. MMP9 was expressed in all the tissues (heart, liver, spleen, lung, kidney, stomach, duodenum, jejunum, ileum, and colon) analyzed. An association analysis between MMP9 polymorphisms and piglet diarrhea score and performance traits were performed in Min (Chinese indigenous breed) and Landrace populations. In the statistical analysis, at the g.48178429 G>A locus, AA piglets had a lower diarrhea score than that of GA in the Min population (P < .05), whereas GG had higher day-35 body weight and average daily gain (ADG) than AA in the Landrace breed (P < .05). At the rs336583561 locus, Min piglets with the GG genotype have a lower diarrhea score than AG piglets (P < .05). At g.48184777C>T, CC animals have higher body weight than TC Landrace piglets (P < .05 or P < .01). A 5' flanking deletion assay indicated that g.48178429 G>A was not located in the MMP9 promoter region. Our results suggest that the A allele at the g.48178429 G>A locus and the G allele at rs336583561 are resistance alleles in Min pigs. Before these markers are used in pig breeding programs, more studies in larger populations are needed.

Immunohistochemical localization of low density lipoprotein (LDL) receptor-related protein-1 (LRP1) in the endometrium of cyclic and pregnant pigs

The low density lipoprotein (LDL) receptor-related protein-1 (LRP1), also known as α2macroglobulin receptor or CD 91, is a multifunctional cell surface receptor that plays an important role in the endocytosis of several ligands and regulation of signalling pathways. In human endometrium, LRP1 was shown to be involved in the endocytic clearance of specific matrix metalloproteinases (MMPs) from the stroma during different phases of the cycle. However, in the pig, it is currently not known whether LRP1 is actually expressed in the endometrium and functions in a similar manner, respectively. For that reason, we examined the localization of LRP1 in the porcine endometrium at different stages of the estrous cycle and pregnancy by immunohistochemistry. Our results showed that LRP1 immunostaining is found in all endometrial specimens examined of both cyclic and pregnant animals. Especially in metestrus and estrus, immunoreactivity (IR) of LRP1 was strongly detected in stromal cells underlying the luminal epithelium (LE). Endometrial glands were mostly surrounded by LRP1-positive cells, which showed some concomitant staining with an antibody against porcine macrophages. In pregnant animals, the number of LRP1-positively stained cells was comparable high within the subepithelial stroma of early pregnant pigs. During apposition and implantation, IR of LRP1 remained high in stromal cells of the endometrium and declined markedly during the ongoing pregnancy stages examined. Our data show, that endometrial LRP1 protein expression was specifically high in such cyclic and pregnancy stages which have a high tissue remodelling activity in dependence of differing steroid hormone concentrations.

Matrix metalloproteinase 2 of grass carp Ctenopharyngodon idella (CiMMP2) is involved in the immune response against bacterial infection

The gene encoding matrix metalloproteinase 2 (MMP2) was cloned from grass carp (Ctenopharyngodon idella), and its expression levels during Aeromonas hydrophila infection and embryonic development stages were evaluated. The complete open reading frame of CiMMP2 was 1974 bp in length, encoding a 658-amino acid polypeptide. The deduced MMP2 protein contained four conserved domain structures, including an N-terminal signal sequence, a propeptide domain, three repeats of fibronectin-type II domain inserted in the catalytic domain and a C-terminal hemopexin-like domain. Phylogenetic analysis of MMP2s grouped grass carp with other teleosts. Detected in all fish tissues examined, CiMMP2 expression increased in the spleen and head kidney at 4 h and was significantly downregulated at 1 d after A. hydrophila infection. CiMMP2 transcripts were present in unfertilized eggs, suggesting its maternal origin. These findings implicate an important role for CiMMP2 in A. hydrophila-related diseases and early embryonic developmental stages of grass carp.

Molecular characteristics of the porcine TIMD4 gene and its association analysis

As a member of the T cell immunoglobulin domain and mucin domain (TIM) gene family, TIMD4 plays an important role in the immune response. To understand its function more precisely, we isolated it and analyzed its subcellular localization, expression pattern, and associations. The porcine TIMD4 gene included nine exons and eight introns with an open reading frame of 1086 bp encoding 361 amino acids. It had relatively high levels in liver, lymph, and spleen. The fusion protein was localized mainly in the cytoplasm of pig kidney cells (PK15). The promoter region contained a TATA box and GATA3 consensus sites. A single nucleotide polymorphism was identified in intron 3 of the porcine TIMD4 gene, and analysis indicated that it had significant associations with the 17-day red blood cell count (p = 0.0106), hemoglobin (p = 0.0149), and hematocrit (p = 0.0063) and with 32-day hemoglobin (p = 0.0140).

Characterization of the porcine p65 subunit of NF-κB and its association with virus antibody levels

NF-κB p65 subunit plays important roles in controlling both innate and adaptive immunity. Here we report the characterization of porcine NF-κB p65 subunit (pp65). pp65 shows high similarity to other mammalian counterparts. pp65 mRNA expression was mainly observed in lung, spleen, liver and small intestine. Furthermore, overexpression of pp65 activates NF-κB in porcine endothelial cell line PIEC, porcine alveolar macrophages cell line 3D4/21 and porcine primary fetal fibroblasts. A COOH-terminal truncation derivative of pp65 (pp65RHD) has been identified as a specific transdominant inhibitor of NFκB. Association study was performed on the selected SNP and indel. The results revealed that the SNP BglI was significantly associated (P<0.05) with pig reproduction and respiratory syndrome virus antibody level (PRRSV-AB) (0 day and 17 days), the classical swine fever virus (CSFV) antibody blocking rates (CSFV-AB) (0 day and 17 days) and pseudorabies virus antibody level (PRV-AB) (0 day and 32 days).

Molecular cloning, expression and characterization of bovine UQCC and its association with body measurement traits

Ubiquinol-cytochrome c reductase complex chaperone (UQCC) involved in the development and maintenance of bone and cartilage is an important candidate gene for body measurement traits selection through marker-assisted selection (MAS). The expression of UQCC is upregulated in many human and animal models of height as well as other stature indexes. We have cloned the cDNA sequence coding UQCC gene in bovine. Genomic structural analysis indicated that bovine UQCC shares a high similarity with human UQCC. Furthermore, Real-Time PCR analysis show that the expression of bovine UQCC is remarkably different in diverse tissues, including high level expression in the spleen, heart and windpipe, and relatively low expression in other tissues. We also analyzed allele frequencies in different cattle breeds and an association study on the selected SNPs. SNP DraI A2691T in intron 1 and SNP Bsh1236I A3150G in intron 8 are significantly associated with Body Length (BL), Rump Length (RL), Chest Depth (CD) and Pin Bone Width (PBW). For the A2691T SNP marker, there are significant effects on the RL (p = 0.0001), CD (p = 0.0059) and PBW (p < 0.0001) in 679 individuals; with A3150G SNP marker, there are significant effects on the BL (p = 0.0047) and CD (p = 0.0454. Regarding association analysis of combination of the two SNPs, there are significant effects on the BL (p = 0.0215), CD (p = 0.0282) and PBW (p = 0.0329) in the total population. The results suggest that the UQCC gene is a candidate gene of body measurement traits in bovine reproduction and breeding, and provide data for establishing of an animal model using cattle to study big animal body type.

Expression and SNP association analysis of porcine FBXL4 gene

As a kind of E3 ligase, the product of FBXL4 gene belongs to a member of FBLs which is the biggest eukaryotic subfamily of F-BOX proteins, it can recognize some substrate through particular protein-protein interaction domains. To investigate its functions, the polymorphism and association analysis was analyzed. The partial cDNA of porcine FBXL4 with 2384 bp long was first cloned; the deduced protein comprises a conserved F-BOX domain at position from the 277th to 332nd amino acid. The phylogenetic tree indicated porcine FBXL4 has the closest genetic relationship with bovine FBXL4 than other selected animal species. Ten tissue expression level of porcine FBXL4 mRNA fluctuated remarkably in a large range by quantitative RT-PCR analysis. For two identified SNPs, the genotyping analysis of Tail showed TT genotype owned dominance in introduced Landrace pig and miniature Guizhou and Wuzhishan breeds, but CC genotype was more than two other genotypes in miniature Laiwu breed. While in another genotyping analysis of BsaJI, CC genotype was obviously more than other genotypes in two kinds of Chinese miniature pig breeds and introduced Landrace pig breeds. Furthermore, the association analysis with immune traits and blood parameters revealed that SNP Tail was significantly associated with the lymphocyte percentage (P = 0.0166) and the antibody levels for pseudorabies virus vaccination (P = 0.0001) of neonate piglets at 0 day. Meanwhile, SNP BsaJI was significantly associated with lymphocyte percentage of individuals at 32 days (P = 0.0351), neutrophil percentage (P = 0.0005), the absolute lymphocyte count (P = 0.0458), and the mixed cells (P = 0.0010) of neonate piglets at 0 day.

Molecular characterization and association analysis of porcine PANE1 gene

The proliferation associated nuclear element 1 (PANE1) is a novel gene that is involved in immune response besides its primary role in centromere assembly. Different PANE1 transcripts show a distinct expression patterns in resting and activated CD19+ cells. In this study, we cloned and characterized the cDNA sequence of porcine PANE1, which shares high sequence identity with their mammalian counterparts. Chromosome localization by INRA IMpRH panel assigned this gene to SSC 5p14-p15, and it was closely linked to porcine ACO2 and CYP25 genes (61cR, LOD score 4.91). The reverse transcriptase-polymerase chain reaction revealed that porcine PANE1 gene was differently expressed in seven diverse tissues, showed highest expression level in lymph node, but lowest in kidney. A single nucleotide polymorphism (SNP) (C>A) which can be digested by restriction enzyme BssHII was identified in intron 1 of porcine PANE1, allele frequencies determination in different pig breeds and association analysis were performed on this SNP BssHII by PCR-restriction fragment length polymorphism assay. Allele frequencies varied greatly among different pig breeds, and the association results indicated that piglet individuals with the AA genotype had significantly higher levels of lymphocyte percentage (LYMPH%) (17 days) (P = 0.0218), mean corpuscular volume (32 days) (P = 0.0314) and absolute value of lymphocyte (LYMPH#) (32 days) (P = 0.0356), but lower (P < 0.0001) birth weight than those with other two genotypes.