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Zhang Y, Yu J, Han R, Ma Z, Zhang M, Li Y, Tang Y, Nie G, Zhou C. Genome-wide identification and structural analysis of the BMP gene family in Triplophysa dalaica. BMC Genomics 2024; 25:194. [PMID: 38373886 PMCID: PMC10875767 DOI: 10.1186/s12864-024-10049-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Bone morphogenetic proteins (BMPs) are part of the transforming growth factor beta (TGF-β) superfamily and play crucial roles in bone development, as well as in the formation and maintenance of various organs. Triplophysa dalaica, a small loach fish that primarily inhabits relatively high elevations and cooler water bodies, was the focus of this study. Understanding the function of BMP genes during the morphogenesis of T. dalaica helps to clarify the mechanisms of its evolution and serves as a reference for the study of BMP genes in other bony fishes. The data for the T. dalaica transcriptome and genome used in this investigation were derived from the outcomes of our laboratory sequencing. RESULTS This study identified a total of 26 BMP genes, all of which, except for BMP1, possess similar TGF-β structural domains. We conducted an analysis of these 26 BMP genes, examining their physicochemical properties, subcellular localization, phylogenetic relationships, covariance within and among species, chromosomal localization, gene structure, conserved motifs, conserved structural domains, and expression patterns. Our findings indicated that three BMP genes were associated with unstable proteins, while 11 BMP genes were located within the extracellular matrix. Furthermore, some BMP genes were duplicated, with the majority being enriched in the GO:0008083 pathway, which is related to growth factor activity. It was hypothesized that genes within the BMP1/3/11/15 subgroup (Group I) play a significant role in the growth and development of T. dalaica. By analyzing the expression patterns of proteins in nine tissues (gonad, kidney, gill, spleen, brain, liver, fin, heart, and muscle), we found that BMP genes play diverse regulatory roles during different stages of growth and development and exhibit characteristics of division of labor. CONCLUSIONS This study contributes to a deeper understanding of BMP gene family member expression patterns in high-altitude, high-salinity environments and provides valuable insights for future research on the BMP gene family in bony fishes.
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Affiliation(s)
- Yizheng Zhang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Jinhui Yu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Rui Han
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Zhigang Ma
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Meng Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Yikai Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Yongtao Tang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Guoxing Nie
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China.
| | - Chuanjiang Zhou
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, People's Republic of China.
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Riaz Z, Hussain M, Parveen S, Sultana M, Saeed S, Ishaque U, Faiz Z, Tayyab M. In Silico Analysis: Genome-Wide Identification, Characterization and Evolutionary Adaptations of Bone Morphogenetic Protein (BMP) Gene Family in Homo sapiens. Mol Biotechnol 2023:10.1007/s12033-023-00944-3. [PMID: 37914865 DOI: 10.1007/s12033-023-00944-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
We systematically analyzed BMP gene family in H. sapiens to elucidate genetic structure, phylogenetic relationships, adaptive evolution and tissue-specific expression pattern. Total of 13 BMPs genes were identified in the H. sapiens genome. Bone morphogenetic proteins (BMPs) are composed of a variable number of exons ranging from 2 to 21. They exhibit a molecular weight ranging from 31,081.81 to 82,899.61 Da. These proteins possess hydrophilic characteristics, display thermostability, and exhibit a pH range from acidic to basic. We identified four segmental and two tandem duplication events in BMP gene family of H. sapiens. All of the vertebrate species that were studied show the presence of BMPs 1, 2, 3, 4, 5, 6, 7, 8A, and 15, however only Homo sapiens demonstrated the presence of BMP9 and BMP11. The pathway and process enrichment analysis of BMPs genes showed that these were considerably enriched in positive regulation of pathway-restricted SMAD protein phosphorylation (92%) and cartilage development (77%) biological processes. These genes exhibited positive selection signals that were shown to be conserved across vertebrate lineages. The results showed that BMP2/3/5/6/8a/15 proteins underwent adaptive selection at many amino acid locations and increased positive selection was detected in TGF-β propeptide and TGF-β super family domains which were involved in dorso-ventral patterning, limb bud development. More over the expression pattern of BMP genes revealed that BMP1 and BMP5; BMP4 and BMP6 exhibited substantially identical expression patterns in all tissues while BMP10, BMP15, and BMP3 showed tissue-specific expression.
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Affiliation(s)
- Zainab Riaz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Hussain
- Department of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Punjab, Pakistan.
| | - Mehwish Sultana
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Saba Saeed
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
- Institue of Zoology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Urwah Ishaque
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Zunaira Faiz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
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Sun X, Li M, Huang S, Zhang H, Li K. Protective effect of bone morphogenetic protein-7 induced differentiation of bone marrow mesenchymal stem cells in rat with acute spinal cord injury. Funct Integr Genomics 2023; 23:68. [PMID: 36849554 DOI: 10.1007/s10142-023-00994-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/08/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
The principal aim of present study was to assess the therapeutic efficacy of bone morphogenetic protein-7 (BMP-7) induced differentiation of bone marrow mesenchymal stem cells (BMSCs) in a rat acute spinal cord injury (SCI) model. BMSCs were isolated from rats, and then divided into a control and a BMP-7 induction groups. The proliferation ability of BMSCs and glial cell markers were determined. Forty Sprague-Dawley (SD) rats were randomly divided into sham, SCI, BMSC, and BMP7 + BMSC groups (n = 10). Among these rats, the recovery of hind limb motor function, the pathological related markers, and motor evoked potentials (MEP) were identified. BMSCs differentiated into neuron-like cells after the introduction of exogenous BMP-7. Interestingly, the expression levels of MAP-2 and Nestin increased, whereas the expression level of GFAP decreased after the treatment with exogenous BMP-7. Furthermore, the Basso, Beattie, and Bresnahan (BBB) score reached 19.33 ± 0.58 in the BMP-7 + BMSC group at day 42. Nissl bodies in the model group were reduced compared to the sham group. After 42 days, in both the BMSC and BMP-7 + BMSC groups, the number of Nissl bodies increased. This is especially so for the number of Nissl bodies in the BMP-7 + BMSC group, which was more than that in the BMSC group. The expression of Tuj-1 and MBP in BMP-7 + BMSC group increased, whereas the expression of GFAP decreased. Moreover, the MEP waveform decreased significantly after surgery. Furthermore, the waveform was wider and the amplitude was higher in BMP-7 + BMSC group than that in BMSC group. BMP-7 promotes BMSC proliferation, induces the differentiation of BMSCsinto neuron-like cells, and inhibits the formation of glial scar. BMP-7 plays a confident role in the recovery of SCI rats.
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Affiliation(s)
- Xudong Sun
- The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, No.280, Changhuai Road, Longzihu Distract, Bengbu, 233044, Anhui Province, China
| | - Maoyong Li
- The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, No.280, Changhuai Road, Longzihu Distract, Bengbu, 233044, Anhui Province, China
| | - Shiyuan Huang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, No.280, Changhuai Road, Longzihu Distract, Bengbu, 233044, Anhui Province, China
| | - Heng Zhang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, No.280, Changhuai Road, Longzihu Distract, Bengbu, 233044, Anhui Province, China.
| | - Kuanxin Li
- The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, No.280, Changhuai Road, Longzihu Distract, Bengbu, 233044, Anhui Province, China.
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