Limits...
Identification and quantitative mRNA analysis of a novel splice variant of GPIHBP1 in dairy cattle.

Yang J, Liu X, Zhang Q, Jiang L - J Anim Sci Biotechnol (2014)

Bottom Line: However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China.

ABSTRACT

Background: Identification of functional genes affecting milk production traits is very crucial for improving breeding efficiency in dairy cattle. Many potential candidate genes have been identified through our previous genome wide association study (GWAS). Of these, GPIHBP1 is an important novel candidate gene for milk production traits. However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.

Results: In this study, we identified a novel alternatively splice transcript variant (X5) which leads to a 31 bp insertion in exon 3 and also confirmed the other four existed transcripts (X1, X2, X3 and X4) of the bovine GPIHBP1 gene. We showed that transcript X5 with a 31 bp insertion and transcript X1 with an 8 bp deletion might have tremendous effect on the protein function and structure of GPIHBP1, respectively. With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.

Conclusions: Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

No MeSH data available.


Predicted secondary structures of bovine and human GPIHBP1. Residues involved in the N-signal peptide formation are indicated by underline, α-helices are in red, β-sheets are in green, GPI-modification site is in blue, alternative GPI-modification site is in purple. (A) Amino acid sequence alignments of bovine and human GPIHBP1. The predicted secondary structures for bovine-p1 (XP_002692609.2) and bovine-p2 (XP_005215340.1, XP_005215341.1 and XP_005215342.1) are similar for several regions with that of human GPIHBP1. (B) The predicted secondary structures for bovine-p5.1, bovine-p5.2, bovine-p5.3, bovine-p5.4 and bovine-p5.5 of transcript X5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4373091&req=5

Fig3: Predicted secondary structures of bovine and human GPIHBP1. Residues involved in the N-signal peptide formation are indicated by underline, α-helices are in red, β-sheets are in green, GPI-modification site is in blue, alternative GPI-modification site is in purple. (A) Amino acid sequence alignments of bovine and human GPIHBP1. The predicted secondary structures for bovine-p1 (XP_002692609.2) and bovine-p2 (XP_005215340.1, XP_005215341.1 and XP_005215342.1) are similar for several regions with that of human GPIHBP1. (B) The predicted secondary structures for bovine-p5.1, bovine-p5.2, bovine-p5.3, bovine-p5.4 and bovine-p5.5 of transcript X5.

Mentions: The predicted secondary structures of the bovine GPIHBP1 amino acid sequences were compared with that of the human GPIHBP1 protein. The α-Helix and β-sheet structures of bovine GPIHBP1 P1 and P2 were similar to the human GPIHBP1 protein secondary structure (Figure 3A). By using SignalP 4.1[17], we found that only human GPIHBP1, bovine GPIHBP1 P2 and bovine GPIHBP1 P5.5 had N-terminal signal peptide which contained a predicted helical structure (Figure 3A, B). The GPI-modification sites of the human GPIHBP1 protein, bovine GPIHBP1 P1 and bovine GPIHBP1 P2 were also predicted (P < 0.01) using Big-PI Predictor[18, 22] (Additional file1: Table S5). We found that bovine GPIHBP1 P1 and P2 and the human GPIHBP1 protein had similar position for alternative GPI-modification site. The predicted tertiary structures of the bovine GPIHBP1 P1, bovine GPIHBP1 P2 and human GPIHBP1 sequences are shown in Figure 4. It can be seen that these tertiary structures were similar to the reported UPAR-LY6 domain of the human CD59 protein[19]. Their modeling ranges of residues were 62-138aa, 28-104aa and 58-133aa, respectively, which contained four or five β-sheet structures. However, due to the low alignment quality between target and specified template, the tertiary structures of the predicted bovine GPIHBP1 P5.1, P5.2, P5.3, P5.4, and P5.5 could not be constructed.Figure 3


Identification and quantitative mRNA analysis of a novel splice variant of GPIHBP1 in dairy cattle.

Yang J, Liu X, Zhang Q, Jiang L - J Anim Sci Biotechnol (2014)

Predicted secondary structures of bovine and human GPIHBP1. Residues involved in the N-signal peptide formation are indicated by underline, α-helices are in red, β-sheets are in green, GPI-modification site is in blue, alternative GPI-modification site is in purple. (A) Amino acid sequence alignments of bovine and human GPIHBP1. The predicted secondary structures for bovine-p1 (XP_002692609.2) and bovine-p2 (XP_005215340.1, XP_005215341.1 and XP_005215342.1) are similar for several regions with that of human GPIHBP1. (B) The predicted secondary structures for bovine-p5.1, bovine-p5.2, bovine-p5.3, bovine-p5.4 and bovine-p5.5 of transcript X5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373091&req=5

Fig3: Predicted secondary structures of bovine and human GPIHBP1. Residues involved in the N-signal peptide formation are indicated by underline, α-helices are in red, β-sheets are in green, GPI-modification site is in blue, alternative GPI-modification site is in purple. (A) Amino acid sequence alignments of bovine and human GPIHBP1. The predicted secondary structures for bovine-p1 (XP_002692609.2) and bovine-p2 (XP_005215340.1, XP_005215341.1 and XP_005215342.1) are similar for several regions with that of human GPIHBP1. (B) The predicted secondary structures for bovine-p5.1, bovine-p5.2, bovine-p5.3, bovine-p5.4 and bovine-p5.5 of transcript X5.
Mentions: The predicted secondary structures of the bovine GPIHBP1 amino acid sequences were compared with that of the human GPIHBP1 protein. The α-Helix and β-sheet structures of bovine GPIHBP1 P1 and P2 were similar to the human GPIHBP1 protein secondary structure (Figure 3A). By using SignalP 4.1[17], we found that only human GPIHBP1, bovine GPIHBP1 P2 and bovine GPIHBP1 P5.5 had N-terminal signal peptide which contained a predicted helical structure (Figure 3A, B). The GPI-modification sites of the human GPIHBP1 protein, bovine GPIHBP1 P1 and bovine GPIHBP1 P2 were also predicted (P < 0.01) using Big-PI Predictor[18, 22] (Additional file1: Table S5). We found that bovine GPIHBP1 P1 and P2 and the human GPIHBP1 protein had similar position for alternative GPI-modification site. The predicted tertiary structures of the bovine GPIHBP1 P1, bovine GPIHBP1 P2 and human GPIHBP1 sequences are shown in Figure 4. It can be seen that these tertiary structures were similar to the reported UPAR-LY6 domain of the human CD59 protein[19]. Their modeling ranges of residues were 62-138aa, 28-104aa and 58-133aa, respectively, which contained four or five β-sheet structures. However, due to the low alignment quality between target and specified template, the tertiary structures of the predicted bovine GPIHBP1 P5.1, P5.2, P5.3, P5.4, and P5.5 could not be constructed.Figure 3

Bottom Line: However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China.

ABSTRACT

Background: Identification of functional genes affecting milk production traits is very crucial for improving breeding efficiency in dairy cattle. Many potential candidate genes have been identified through our previous genome wide association study (GWAS). Of these, GPIHBP1 is an important novel candidate gene for milk production traits. However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.

Results: In this study, we identified a novel alternatively splice transcript variant (X5) which leads to a 31 bp insertion in exon 3 and also confirmed the other four existed transcripts (X1, X2, X3 and X4) of the bovine GPIHBP1 gene. We showed that transcript X5 with a 31 bp insertion and transcript X1 with an 8 bp deletion might have tremendous effect on the protein function and structure of GPIHBP1, respectively. With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.

Conclusions: Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

No MeSH data available.