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Niu M, Whang H, Wu Z, Jiang S, Chen L. Deletion of Asb15b gene can lead to a significant decrease in zebrafish intermuscular bone. Gene 2024; 923:148561. [PMID: 38754570 DOI: 10.1016/j.gene.2024.148561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Intermuscular bones, which are present in numerous economically significant fish species, have a negative impact on the development of aquaculture. The Asb15b gene, primarily expressed in skeletal muscle, plays a crucial role in regulating protein turnover and the development of muscle fibers. It stimulates protein synthesis and controls the differentiation of muscle fibers. In this study, we employed CRISPR/Cas9 technology to generate homozygous zebrafish strains with 7 bp and 49 bp deletions in the Asb15b gene. Subsequent analyses using skeleton staining demonstrated a substantial reduction in the number of intermuscular bones in adult Asb15b-/- -7 bp and Asb15b-/- -49 bp mutants compared to the wild-type zebrafish, with decreases of 30 % (P < 0.001) and 40 % (P < 0.0001), respectively. Histological experiments further revealed that the diameter and number of muscle fibers in adult Asb15b-/- mutants did not exhibit significant changes when compared to wild-type zebrafish. Moreover, qRT-PCR experiments demonstrated significant differences in the expression of bmp6 and runx2b genes, which are key regulators of intermuscular bone development, during different stages of intermuscular bone development in Asb15b-/- mutants. This study strongly suggests that the Asb15b gene plays a crucial role in regulating intermuscular bone development in fish and lays the groundwork for further exploration of the role of the Asb15b gene in zebrafish intermuscular bone development.
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Affiliation(s)
- Minghui Niu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Huamin Whang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Zhichao Wu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Shouwen Jiang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Liangbiao Chen
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China.
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Xiao Z, Chen Y, Wang X, Sun Q, Tu T, Liu J, Nie C, Gao Z. Effect of runx2b deficiency in intermuscular bones on the regulatory network of lncRNA-miRNA-mRNA. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101171. [PMID: 38103500 DOI: 10.1016/j.cbd.2023.101171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/10/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Intermuscular bones (IBs) are mineralized spicules that negatively impact the quality and value of fish products. Runx2b is a crucial modulator in promoting bone formation through regulating osteoblast differentiation. Previous studies suggested that loss of runx2b gene completely inhibited IBs formation in zebrafish. However, how the whole transcriptome, including mRNA and non-coding RNA (ncRNA), affects the IBs development in runx2b-/- zebrafish are not known. The aim of this study was to identify the regulatory networks of differentially expressed (DE) lncRNAs, miRNAs, and mRNAs in zebrafish with and without IBs (runx2b+/+ fish and runx2b-/- fish) utilizing high-throughput sequencing techniques. All together there are 1051 mRNAs, 456 lncRNAs, and 18 miRNAs differentially expressed were found between these two strains. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) has highlighted significant pathways linked to the development of IBs, specifically the TGF-beta and Wnt signaling pathways, and a number of genes concentrated on these two signaling pathways related to the formation of IBs. Further, 1989 competing endogenous RNA (ceRNA) networks were created according to the correlation among mRNAs, miRNAs and lncRNAs. The ceRNA networks results revealed 52 ceRNA pairs related to the IBs formation, consisting of 52 mRNAs, 37 lncRNAs, and 6 miRNAs. Of these, we found that dre-miR-2189 was the key element of ceRNA pairs, interacting with 19 mRNAs and 11 lncRNAs, and MSTRG.13175.1 could regulate sp7 expression by interacting with dre-miR-2189 to function in osteogenic differentiation. Subsequent experiments at the cellular level also revealed the interaction mechanism. The outcomes indicated a crucial role of miRNAs and lncRNAs in the development of fish IBs, which offer new views into the functions of ncRNAs involved in IBs formation.
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Affiliation(s)
- Zhengyu Xiao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yulong Chen
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xudong Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiujie Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Tan Tu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Junqi Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunhong Nie
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Yu J, Guo L, Zhang SH, Zhu QY, Chen RY, Wong BH, Ding GH, Chen J. Transcriptomic analysis of intermuscular bone development in barbel steed (Hemibarbus labeo). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101030. [PMID: 36343604 DOI: 10.1016/j.cbd.2022.101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
Intermuscular bones (IBs), which are little, bony spicules in muscle, are embedded in lower teleosts' myosepta. Despite the importance of studying IB development in freshwater aquaculture species, the genes associated with IB development need to be further explored. In the present study, we identified four stages of IB development in barbel steed (Hemibarbus labeo), namely stage 1: IBs have not emerged, stage 2: a few small IBs have emerged in the tail, stage 3: longer IBs gradually emerged in the tail and stage 4: all of the IBs in the tail are mature and long, via Alizarin red staining. Subsequently, we used the HiseqXTen platform to sequence and de novo assemble the transcriptome of epaxial muscle (between 35th and 40th myomere) of barbel steed at 29 days (stage 1) and 42 days (stage 3) after hatching. A total of 190,814 unigenes were obtained with an average length and N50 of 648 bp and 1027 bp, respectively. We found 2174 differentially expressed genes (DEGs) between stages 1 and 3, of which 378 and 1796 were up- and down-regulated, respectively. Functional enrichment analysis showed that several DEGs functioned in ossification, positive regulation of osteoblast differentiation, osteoblast differentiation, and BMP signaling pathway, and were further enriched in signal pathway, including osteoclast differentiation, TGF-β signaling pathway, cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and other KEEG pathways. In conclusion, we identified genes that may be related to IB development, such as kazal type serine peptidase inhibitor domain 1 (KAZALD1), extracellular matrix protein 1 (ECM1), tetranectin, bone morphogenetic protein 1 (bmp1), acid phosphatase 5 (ACP5), collagen type XI alpha 1 chain (COL11A1), matrix metallopeptidase 9 (MMP9), pannexin-3 (PANX3), sp7 transcription factor (Sp7), and c-x-c motif chemokine ligand 8 (CXCL8), by comparing the transcriptomes of epaxial muscle before and after IB ossification. This study provided a theoretical basis for identifying the molecular mechanisms underlying IB development in fish.
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Affiliation(s)
- Jing Yu
- College of Ecology, Lishui University, Lishui 323000, China
| | - Ling Guo
- College of Ecology, Lishui University, Lishui 323000, China
| | - Si-Hai Zhang
- College of Ecology, Lishui University, Lishui 323000, China
| | - Qun-Yin Zhu
- College of Ecology, Lishui University, Lishui 323000, China
| | - Ru-Yi Chen
- College of Ecology, Lishui University, Lishui 323000, China
| | - Boon Hui Wong
- Department of Biological Science, National University of Singapore, Singapore 117558, Singapore
| | - Guo-Hua Ding
- College of Ecology, Lishui University, Lishui 323000, China
| | - Jie Chen
- College of Ecology, Lishui University, Lishui 323000, China.
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Comparison of Myosepta Development and Transcriptome Profiling between Blunt Snout Bream with and Tilapia without Intermuscular Bones. BIOLOGY 2021; 10:biology10121311. [PMID: 34943226 PMCID: PMC8698383 DOI: 10.3390/biology10121311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023]
Abstract
Simple Summary The presence or absence of intermuscular bones (IBs) is directly related to the economic and edible value of fish. The specific regulatory mechanism of IB formation is not completely known yet. Here, we explored the molecular mechanisms that regulate the formation of IBs based on histological analysis, transcriptome profiling, and gene expression quantification using M. amblycephala (with IBs) and O. niloticus (without IBs) as models. As a result, we identified several bone-related genes and elucidated their regulatory roles in the development of IBs. Abstract Intermuscular bones (IBs) are small spicule-like bones located in the myosepta of basal teleosts, which negatively affect the edibleness and economic value of fish. Blunt snout bream (Megalobrama amblycephala, with epineural and epipleural IBs) and tilapia (Oreochromis niloticus, without epineural and epipleural IBs) are two major aquaculture species and ideal models for studying the formation mechanisms of fish IBs. Here, we compared myosepta development between M. amblycephala and O. niloticus, based on histological analysis, transcriptome profiling, and expression analysis of bone-related genes. The histological results showed that dye condensation began to appear in the myosepta 20 days post hatching (dph) in M. amblycephala, and IBs could be clearly observed 50 dph in the myosepta, based on different staining methods. However, in O. niloticus, dye condensation was not observed in the myosepta from 10 to 60 dph. Differentially expressed genes (DEGs) at different developmental stages were screened by comparing the transcriptomes of M. amblycephala and O. niloticus, and KEGG analysis demonstrated that these DEGs were enriched in many bone-related pathways, such as focal adhesion, calcium, and Wnt signaling pathways. Quantitative PCR was performed to further compare the expression levels of some bone-related genes (scxa, scxb, runx2a, runx2b, bgp, sp7, col1a2, entpd5a, entpd5b, phex, alpl, and fgf23). All the tested genes (except for alpl) exhibited higher expression levels in M. amblycephala than in O. niloticus. A comparison of the dorsal and abdominal muscle tissues between the two species also revealed significant expression differences for most of the tested genes. The results suggest that scxa, scxb, runx2a, runx2b, entpd5a, col1a2, and bgp may play important roles in IB development. Our findings provide some insights into the molecular mechanisms of IB formation, as well as clues for further functional analysis of the identified genes to better understand the development of IBs.
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Bones of teleost fish demonstrate high fracture strain. J Biomech 2021; 120:110341. [PMID: 33743397 DOI: 10.1016/j.jbiomech.2021.110341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/04/2021] [Accepted: 02/12/2021] [Indexed: 11/22/2022]
Abstract
The endoskeleton of teleosts (bony fish) includes a vertebral spine with articulating rib bones (RBs) similar to humans and further encompasses mineralized tissues that are not found in mammals, including intermuscular bones (IBs). RBs form through endochondral ossification and protect the inner organs, and IBs form through intramembranous ossification within the myosepta and play a role in force transmission and propulsion during locomotion. Based on previous findings suggesting that IBs show a much higher ability for fracture strain compared to mammalian bones, this study aims to investigate whether this ability is general to teleost bones or specific to IBs. We analyzed RBs and IBs of 25 North Atlantic Herring fish. RBs were analyzed using micro-mechanical tensile testing and micro-computed tomography, and both RB and IB were additionally analyzed with Raman spectroscopy. Based on our previous results from IB, we found that RBs are more elastically deformable (on average, 50% higher yield strain and 115% higher elastic work) and stronger (55% higher fracture stress) than values reported for IBs. However, these differences were neither associated with a higher Young's modulus nor a higher degree of mineralization in RBs. Astonishingly, RBs and IBs showed similar fracture strains (12-15% on average, reaching up to 20%), reflecting a much higher ability for tensile deformation than reported for mammalian bone, and further highlighting the biomimetic potential of teleost fish bones for inspiring innovative biomaterials.
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Nie C, Wan S, Chen Y, Zhu D, Wang X, Dong X, Gao ZX. Loss of scleraxis leads to distinct reduction of mineralized intermuscular bone in zebrafish. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Nunes JRS, Pértille F, Andrade SCS, Perazza CA, Villela PMS, Almeida-Val VMF, Gao ZX, Coutinho LL, Hilsdorf AWS. Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum). Anim Genet 2020; 51:899-909. [PMID: 33006182 DOI: 10.1111/age.13001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/21/2023]
Abstract
The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (Padj < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.
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Affiliation(s)
- J R S Nunes
- Nature and Culture Institute, Federal University of Amazon (UFAM), Benjamin Constant, Amazonas, 69630-000, Brazil.,Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.,Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58 183, Sweden
| | - S C S Andrade
- Genetics and Evolutionary Biology Department, University of São Paulo (USP)/Bioscience Institute (IB), São Paulo, São Paulo, 05508-090, Brazil
| | - C A Perazza
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
| | - P M S Villela
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - V M F Almeida-Val
- Brazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, Amazonas, 69067-375, Brazil
| | - Z-X Gao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, China
| | - L L Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - A W S Hilsdorf
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
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Yang G, Qin Z, Kou H, Liang R, Zhao L, Jiang S, Lin L, Zhang K. A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 ( bmp2) in Fishes. Int J Mol Sci 2019; 20:E6137. [PMID: 31817477 PMCID: PMC6940749 DOI: 10.3390/ijms20246137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Intermuscular bones (IBs) are only found in the muscles of fish. Bone morphogenetic protein 2 (bmp2) is considered to be the most active single osteogenesis factor. It promotes cell proliferation and differentiation during bone repair, as well as inducing the formation of bones and cartilages in vivo. However, detailed investigations of this family in fish are incredibly limited. Here, we have used a variety of published and unpublished bmp2 sequences for teleosts and cartilage fish in order to explore and expand our understanding of bmp2 genes in fish. Our results confirmed that teleost genomes contain two or more bmp2 genes, and the diversity of bmp2 genes in vertebrates appears to be as a result of a combination of whole genome duplication (WGD) and gene loss. Differences were also observed in tissue distribution and relative transcription abundance of the bmp2s through a transcriptomic analysis. Our data also indicated that bmp2b may play an important role in the formation of IBs in teleosts. In addition, protein sequence alignments and 3D structural predictions of bmp2a and bmp2b supported their similar roles in fishes. To summarize, our existing work provided novel insights into the bmp2 family genes in fishes through a mixture of comparative genomic and transcriptomic analysis.
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Affiliation(s)
- Guang Yang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhendong Qin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Hongyan Kou
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Rishen Liang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Lijuan Zhao
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Shoujia Jiang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China;
| | - Li Lin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Kai Zhang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong 93117, China
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Nie CH, Wan SM, Liu YL, Liu H, Wang WM, Gao ZX. Development of Teleost Intermuscular Bones Undergoing Intramembranous Ossification Based on Histological-Transcriptomic-Proteomic Data. Int J Mol Sci 2019; 20:E4698. [PMID: 31546739 PMCID: PMC6801895 DOI: 10.3390/ijms20194698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022] Open
Abstract
Intermuscular bones (IBs) specially exist in lower teleost fish and the molecular mechanism for its development remains to be clarified. In this study, different staining methods and comparative proteomics were conducted to investigate the histological structure and proteome of IB development in Megalobrama amblycephala, including four key IB developmental stages (S1-IBs have not emerged in the tail part; S2-several small IBs started to ossify in the tail part; S3-IBs appeared rapidly; S4-all the IBs appeared with mature morphology). Alcian blue and alizarin red S stained results indicated that IBs were gradually formed from S2 to S4, undergoing intramembranous ossification without a cartilaginous phase. A total of 3368 proteins were identified by using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. Functional annotation showed that proteins which were differentially expressed among stages were involved in calcium, MAPK, Wnt, TGF-β, and osteoclast pathways which played a critical role in bone formation and differentiation. Three proteins (collagen9α1, stat1, tnc) associated with chondrocytes did not exhibit significant changes through S2 to S4; however, proteins (entpd5, casq1a, pvalb, anxa2a, anxa5) which associated with osteoblasts and bone formation and differentiation showed significantly a higher expression level from S1 to S2, as well as to S3 and S4. These further demonstrated that development of IBs did not go through a cartilaginous phase. The inhibitors of TGF-β and Wnt pathways were tested on zebrafish (sp7/eGFP) and the results indicated that both inhibitors significantly delayed IB development. This study provides a comprehensive understanding of the IB ossification pattern, which will help further elucidate the molecular mechanisms for IB development in teleosts.
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Affiliation(s)
- Chun-Hong Nie
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Shi-Ming Wan
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Yu-Long Liu
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA.
| | - Han Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Wei-Min Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Ze-Xia Gao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
- National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan 430070, China.
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10
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Costa RA, Martins RST, Capilla E, Anjos L, Power DM. Vertebrate SLRP family evolution and the subfunctionalization of osteoglycin gene duplicates in teleost fish. BMC Evol Biol 2018; 18:191. [PMID: 30545285 PMCID: PMC6293640 DOI: 10.1186/s12862-018-1310-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023] Open
Abstract
Background Osteoglycin (OGN, a.k.a. mimecan) belongs to cluster III of the small leucine-rich proteoglycans (SLRP) of the extracellular matrix (ECM). In vertebrates OGN is a characteristic ECM protein of bone. In the present study we explore the evolution of SLRP III and OGN in teleosts that have a skeleton adapted to an aquatic environment. Results The SLRP gene family has been conserved since the separation of chondrichthyes and osteichthyes. Few gene duplicates of the SLRP III family exist even in the teleosts that experienced a specific whole genome duplication. One exception is ogn for which duplicate copies were identified in fish genomes. The ogn promoter sequence and in vitro mesenchymal stem cell (MSC) cultures suggest the duplicate ogn genes acquired divergent functions. In gilthead sea bream (Sparus aurata) ogn1 was up-regulated during osteoblast and myocyte differentiation in vitro, while ogn2 was severely down-regulated during bone-derived MSCs differentiation into adipocytes in vitro. Conclusions Overall, the phylogenetic analysis indicates that the SLRP III family in vertebrates has been under conservative evolutionary pressure. The retention of the ogn gene duplicates in teleosts was linked with the acquisition of different functions. The acquisition by OGN of functions other than that of a bone ECM protein occurred early in the vertebrate lineage. Electronic supplementary material The online version of this article (10.1186/s12862-018-1310-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R A Costa
- Comparative Endocrinology and Integrative Biology Group, Centre of Marine Sciences, University of Algarve, Campus of Gambelas, 8005-139, Faro, Portugal
| | - R S T Martins
- Comparative Endocrinology and Integrative Biology Group, Centre of Marine Sciences, University of Algarve, Campus of Gambelas, 8005-139, Faro, Portugal.
| | - E Capilla
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - L Anjos
- Comparative Endocrinology and Integrative Biology Group, Centre of Marine Sciences, University of Algarve, Campus of Gambelas, 8005-139, Faro, Portugal
| | - D M Power
- Comparative Endocrinology and Integrative Biology Group, Centre of Marine Sciences, University of Algarve, Campus of Gambelas, 8005-139, Faro, Portugal.
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Zhang H, Song C, Xie J, Ge X, Liu B, Zhang Y, Sun C, Zhou Q, Yang Z. Comparative proteomic analysis of hepatic mechanisms of Megalobrama amblycephala infected by Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2018; 82:339-349. [PMID: 30081179 DOI: 10.1016/j.fsi.2018.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
Hemorrhage syndrome is one of the most prevalent and epidemic diseases that is mainly caused by Aeromonas hydrophila invasion in Megalobrama amblycephala. Recent studies have uncovered a number of immune enzymes and transcripts that are differently expressed in this disease, but the molecular mechanism elicited still remain largely unknown. Here, we constructed an in vivo A. hydrophila infection to investigate the immune mechanism in M. amblycephala using comparative proteomic approach at the one day after infection. 30 altered protein spots were found to undergo differential expression against A. hydrophila infection in the hepatopancreas of M. amblycephala based on 2-DE and were all successfully identified using MALDI-TOF/TOF, representing 18 unique proteins. These proteins were functionally classified into metabolism, antioxidant, cofactors and vitamins, chaperone and signal transduction. Network interaction and Gene Ontology annotation indicated 13 unique proteins were closely related to immune response and directly regulated by each other. Compared with the control group, A. hydrophila infection significantly decreased the metabolism-related mRNA expressions of ENO3, APOA1, CAT and FASN, but increased the mRNA expressions of MDH, ALDOB and RSP12, which was consistent with the protein expression. Nevertheless, FAH was down-regulated at both levels but had no significant difference in mRNA level, ALDH8a1 was down-regulated at protein level but non-significantly up-regulated at the mRNA level. GSTm was up-regulated at protein level but down-regulated at the mRNA level. Consequently, these results revealed that A. hydrophila infection altered the related antioxidative proteins via complex regulatory mechanisms and reduced the immune ability of M. amblycephala at the one day after infection.
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Affiliation(s)
- Huimin Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
| | - Changyou Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Jun Xie
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Xianping Ge
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Yuanyuan Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Cunxin Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Qunlan Zhou
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Zhenfei Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
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Wang K, Wang Y, Wang X, Ren Q, Han S, Ding L, Li Z, Zhou X, Li W, Zhang L. Comparative salivary proteomics analysis of children with and without dental caries using the iTRAQ/MRM approach. J Transl Med 2018; 16:11. [PMID: 29351798 PMCID: PMC5775567 DOI: 10.1186/s12967-018-1388-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/15/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Dental caries is a major worldwide oral disease afflicting a large proportion of children. As an important host factor of caries susceptibility, saliva plays a significant role in the occurrence and development of caries. The aim of the present study was to characterize the healthy and cariogenic salivary proteome and determine the changes in salivary protein expression of children with varying degrees of active caries, also to establish salivary proteome profiles with a potential therapeutic use against dental caries. METHODS In this study, unstimulated saliva samples were collected from 30 children (age 10-12 years) with no dental caries (NDC, n = 10), low dental caries (LDC, n = 10), and high dental caries (HDC, n = 10). Salivary proteins were extracted, reduced, alkylated, trypsin digested and labeled with isobaric tags for relative and absolute quantitation, and then they were analyzed with GO annotation, biological pathway analysis, hierarchical clustering analysis, and protein-protein interaction analysis. Targeted verifications were then performed using multiple reaction monitoring mass spectrometry. RESULTS A total of 244 differentially expressed proteins annotated with GO annotation in biological processes, cellular component and molecular function were identified in comparisons among children with varying degrees of active caries. A number of caries-related proteins as well as pathways were identified in this study. As compared with caries-free children, the most significantly enriched pathways involved by the up-regulated proteins in LDC and HDC were the ubiquitin mediated proteolysis pathway and African trypanosomiasis pathway, respectively. Subsequently, we selected 53 target proteins with differential expression in different comparisons, including mucin 7, mucin 5B, histatin 1, cystatin S and cystatin SN, basic salivary proline rich protein 2, for further verification using MRM assays. Protein-protein interaction analysis of these proteins revealed complex protein interaction networks, indicating synergistic action of salivary proteins in caries resistance or cariogenicity. CONCLUSIONS Overall, our results afford new insight into the salivary proteome of children with dental caries. These findings might have bright prospect in future in developing novel biomimetic peptides with preventive and therapeutic benefits for childhood caries.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Yufei Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Xiuqing Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Qian Ren
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Sili Han
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Longjiang Ding
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Zhongcheng Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Wei Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Linglin Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
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