Expression of Phospholipase D Family Member 6 in Bovine Testes and Its Molecular Characteristics
Abstract
:1. Introduction
2. Results
2.1. Expression of PLD6 in Bovine Testes
2.2. Phylogenetic and Structural Features of Bovine PLD6
2.3. Molecular Dynamics Simulation and Binding Mode Analysis
2.4. Protein-Protein Interaction (PPI) Network
2.5. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Analysis
2.6. Multi-Sequence Alignment and Expression Analysis of PLD6 by GEO Mining
3. Discussion
4. Materials and Methods
4.1. Animal Tissues
4.2. RT-PCR and qRT-PCR
4.3. Immunostaining
4.4. Bioinformatics
4.4.1. Phylogenetic Analysis
4.4.2. Protein Structure Analysis
4.4.3. Molecular Docking
4.4.4. Molecular Dynamics Simulation
4.4.5. Protein-Protein Interaction (PPI) Network
4.4.6. GO and KEGG Analysis
4.4.7. Multiple Sequence Alignment and GEO Database Mining
4.5. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Importance Score | Number | Trace Residues |
---|---|---|
<25% | 34 | 44, 45, 69, 71, 72, 83, 86, 93, 95, 97, 106, 109, 112, 113, 114, 116, 121, 151, 152, 154, 155, 159, 166, 167, 169, 170, 171, 174, 178, 180, 181, 194, 198, 202 |
<5% | 17 | 86, 93, 95, 112, 121, 152, 154, 159, 166, 167, 169, 170, 174, 178, 180, 198, 202 |
Mnemonic Name | Species | Common Name | Accession Number |
---|---|---|---|
DANRE | Danio rerio | Zebrafish | A3KNW0 |
XENLA | Xenopus laevis | African clawed frog | A1L1C2 |
XENTR | Xenopus tropicalis | Western clawed frog | Q28DT3 |
CRIGR | Cricetulus griseus | Chinese hamster | A0A3L7GMU4 |
MOUSE | Mus musculus | Mouse | Q5SWZ9 |
BOVINE | Bos taurus | Bovine | NP_001258919.1 |
BOVINE | Bos taurus | Bovine | E1BE10 |
PANTR | Pan troglodytes | Chimpanzee | G2HE65 |
HUMAN | Homo sapiens | Human | Q8N2A8 |
PONAB | Pongo abelii | Sumatran orangutan | A0A2J8RII7 |
PONAB | Cercocebus atys | Sooty mangabey | A0A2K5LCM4 |
Potential Biomarker | Proteins Involved (%) | KEGG Pathway ID | Description |
---|---|---|---|
PLD6 | 61.08 | map 00564 | Glycerophospholipid metabolism |
14.77 | map 00440 | Aminophosphonate metabolism | |
9.55 | map 00260 | Glycine, serine and threonine metabolism | |
7.03 | map 00565 | Ether lipid metabolism | |
7.03 | map 04912 | GnRH signaling pathway | |
0.18 | map 00623 | 2,4-Dichlorobenzoate degradation | |
0.18 | map 00960 | Alkaloid biosynthesis II | |
0.18 | map 00650 | Butanoate metabolism |
Gene | Primer Sequence (5′→3′) | Fragment Size (bp) | Gene ID | Accession Number |
---|---|---|---|---|
GAPDH | F: TGACCCCTTCATTGACCTTC | 250 | 281181 | NM_001034034 |
R: TACTCAGCACCAGCATCACC | ||||
VASA | F: TTGGGACTTGTGTAAGAGCTGT | 98 | 493725 | NM_001278643 |
R: CTTGACTTGTTTGAGGC | ||||
UCHL1 | F: CCTTCCCTGGGCAGGTGCGCGC | 280 | 514394 | NM_001046172 |
R: GGCTGTAGAACGCAAGAA | ||||
PLD6 | F: GTGGACAGGAAGGTGCTGAT | 108 | 526651 | NM_001271990 |
R: TACTCCTCGTCCTCCACGAT |
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Yang, R.; Zhang, B.; Zhu, W.; Zhu, C.; Chen, L.; Zhao, Y.; Wang, Y.; Zhang, Y.; Riaz, A.; Tang, B.; et al. Expression of Phospholipase D Family Member 6 in Bovine Testes and Its Molecular Characteristics. Int. J. Mol. Sci. 2023, 24, 12172. https://doi.org/10.3390/ijms241512172
Yang R, Zhang B, Zhu W, Zhu C, Chen L, Zhao Y, Wang Y, Zhang Y, Riaz A, Tang B, et al. Expression of Phospholipase D Family Member 6 in Bovine Testes and Its Molecular Characteristics. International Journal of Molecular Sciences. 2023; 24(15):12172. https://doi.org/10.3390/ijms241512172
Chicago/Turabian StyleYang, Rui, Boyang Zhang, Wenqian Zhu, Chunling Zhu, Lanxin Chen, Yansen Zhao, Yueqi Wang, Yan Zhang, Amjad Riaz, Bo Tang, and et al. 2023. "Expression of Phospholipase D Family Member 6 in Bovine Testes and Its Molecular Characteristics" International Journal of Molecular Sciences 24, no. 15: 12172. https://doi.org/10.3390/ijms241512172