Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs
Abstract Background Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown. Methods To iden...
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| Format: | Article |
| Language: | English |
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BMC
2019-11-01
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| Series: | Proteome Science |
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| Online Access: | http://link.springer.com/article/10.1186/s12953-019-0153-0 |
| _version_ | 1819121034135076864 |
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| author | Suxiang Lu Qian Xiong Kang Du Xiaoni Gan Xuzhen Wang Liandong Yang Ying Wang Feng Ge Shunping He |
| author_facet | Suxiang Lu Qian Xiong Kang Du Xiaoni Gan Xuzhen Wang Liandong Yang Ying Wang Feng Ge Shunping He |
| author_sort | Suxiang Lu |
| collection | DOAJ |
| description | Abstract Background Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown. Methods To identify the differentially expressed proteins (DEPs) during the early stages of lobed fin regeneration in P. senegalus, we performed a differential proteomic analysis using isobaric tag for relative and absolute quantitation (iTRAQ) approach based quantitative proteome from the pectoral lobed fins at 3 time points. Furthermore, we validated the changes in protein expression with multiple-reaction monitoring (MRM) analysis. Results The experiment yielded a total of 3177 proteins and 15,091 unique peptides including 1006 non-redundant (nr) DEPs. Of these, 592 were upregulated while 349 were downregulated after lobed fin amputation when compared to the original tissue. Bioinformatics analyses showed that the DEPs were mainly associated with Ribosome and RNA transport, metabolic, ECM-receptor interaction, Golgi and endoplasmic reticulum, DNA replication, and Regulation of actin cytoskeleton. Conclusions To our knowledge, this is the first proteomic research to investigate alterations in protein levels and affected pathways in bichirs’ lobe-fin/limb regeneration. In addition, our study demonstrated a highly dynamic regulation during lobed fin regeneration in P. senegalus. These results not only provide a comprehensive dataset on differentially expressed proteins during the early stages of lobe-fin/limb regeneration but also advance our understanding of the molecular mechanisms underlying lobe-fin/limb regeneration. |
| first_indexed | 2024-12-22T06:30:08Z |
| format | Article |
| id | doaj.art-c88c850ee2ac4abb96768e573780a16d |
| institution | Directory Open Access Journal |
| issn | 1477-5956 |
| language | English |
| last_indexed | 2024-12-22T06:30:08Z |
| publishDate | 2019-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Proteome Science |
| spelling | doaj.art-c88c850ee2ac4abb96768e573780a16d2022-12-21T18:35:44ZengBMCProteome Science1477-59562019-11-0117111010.1186/s12953-019-0153-0Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in BichirsSuxiang Lu0Qian Xiong1Kang Du2Xiaoni Gan3Xuzhen Wang4Liandong Yang5Ying Wang6Feng Ge7Shunping He8Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of SciencesAbstract Background Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown. Methods To identify the differentially expressed proteins (DEPs) during the early stages of lobed fin regeneration in P. senegalus, we performed a differential proteomic analysis using isobaric tag for relative and absolute quantitation (iTRAQ) approach based quantitative proteome from the pectoral lobed fins at 3 time points. Furthermore, we validated the changes in protein expression with multiple-reaction monitoring (MRM) analysis. Results The experiment yielded a total of 3177 proteins and 15,091 unique peptides including 1006 non-redundant (nr) DEPs. Of these, 592 were upregulated while 349 were downregulated after lobed fin amputation when compared to the original tissue. Bioinformatics analyses showed that the DEPs were mainly associated with Ribosome and RNA transport, metabolic, ECM-receptor interaction, Golgi and endoplasmic reticulum, DNA replication, and Regulation of actin cytoskeleton. Conclusions To our knowledge, this is the first proteomic research to investigate alterations in protein levels and affected pathways in bichirs’ lobe-fin/limb regeneration. In addition, our study demonstrated a highly dynamic regulation during lobed fin regeneration in P. senegalus. These results not only provide a comprehensive dataset on differentially expressed proteins during the early stages of lobe-fin/limb regeneration but also advance our understanding of the molecular mechanisms underlying lobe-fin/limb regeneration.http://link.springer.com/article/10.1186/s12953-019-0153-0Quantitative proteomePolypterus senegalusLimbRegrowthBlastema |
| spellingShingle | Suxiang Lu Qian Xiong Kang Du Xiaoni Gan Xuzhen Wang Liandong Yang Ying Wang Feng Ge Shunping He Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs Proteome Science Quantitative proteome Polypterus senegalus Limb Regrowth Blastema |
| title | Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs |
| title_full | Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs |
| title_fullStr | Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs |
| title_full_unstemmed | Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs |
| title_short | Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs |
| title_sort | comparative itraq proteomics revealed proteins associated with lobed fin regeneration in bichirs |
| topic | Quantitative proteome Polypterus senegalus Limb Regrowth Blastema |
| url | http://link.springer.com/article/10.1186/s12953-019-0153-0 |
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