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Liao X, Liu Y, Han T, Yang M, Liu W, Wang Y, He C, Lu Z. Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove Clam Geloina erosa. Front Physiol 2022; 13:851957. [PMID: 35514334 PMCID: PMC9065350 DOI: 10.3389/fphys.2022.851957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. Geloina erosa, a species of Corbiculidae, plays an important role in mangrove ecology. It is highly adaptable and can withstand environmental pollution and microbial infections. However, there is no reference genome or full-length transcriptome available for G. erosa. This impedes the study of the biological functions of its different tissues because transcriptome research requires reference genome or full-length transcriptome as a reference to improve accuracy. In this study, we applied a combination of Illumina and PacBio single-molecule real-time sequencing technologies to sequence the full-length transcriptomes of G. erosa tissues. Transcriptomes of nine samples obtained from three tissues (hepatopancreas, gill, and muscle) were sequenced using Illumina. Furthermore, we obtained 87,310 full-length reads non-chimeric sequences. After removing redundancy, 22,749 transcripts were obtained. The average Q score of 30 was 94.48%. In total, 271 alternative splicing events were predicted. There were 14,496 complete regions and 3,870 lncRNAs. Differential expression analysis revealed tissue-specific physiological functions. The gills mainly express functions related to filtration, metabolism, identifying pathogens and activating immunity, and neural activity. The hepatopancreas is the main tissue related to metabolism, it also involved in the immune response. The muscle mainly express functions related to muscle movement and control, it contains more energy metabolites that gill and hepatopancreas. Our research provides an important reference for studying the gene expression of G. erosa under various environmental stresses. Moreover, we present a reliable sequence that will provide an excellent foundation for further research on G. erosa.
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Affiliation(s)
- Xin Liao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China
| | - Yunqing Liu
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China
| | - Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Mingliu Yang
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China
| | - Wenai Liu
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China
| | - Yadi Wang
- Henan Key Laboratory of Big Data Analysis and Processing, Institute of Data and Knowledge Engineering, School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Matusovsky OS, Dobrzhanskaya AV, Pankova VV, Kiselev KV, Girich UV, Shelud'ko NS. Crenomytilus grayanus 40kDa calponin-like protein: cDNA cloning, sequence analysis, tissue expression, and post-translational modifications. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2017; 22:98-108. [PMID: 28288367 DOI: 10.1016/j.cbd.2017.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/18/2017] [Accepted: 02/24/2017] [Indexed: 01/22/2023]
Abstract
Calponin-like protein (CaP-40), a third major protein after actin and tropomyosin, has recently been identified by us in the Ca2+-regulated thin filaments of mussel Crenomytilus grayanus. It contains calponin homology domain, five calponin family repeats and possesses similar biochemical properties as vertebrate smooth muscle calponin. In this paper, we report a full-length cDNA sequence of CaP-40, study its expression pattern on mRNA and protein levels, evaluate CaP-40 post-translational modifications and perform protein-protein interaction analysis. The full-length sequence of CaP-40 consists of 398 amino acids and has high similarity to calponins among molluscan species. CaP-40 gene is widely expressed in mussel tissues, with the highest expression in adductor and mantle. Comparison of these data with protein content established by mass-spectrometry analysis revealed that the high mRNA content is mirrored by high protein levels for adductor smooth muscles. To provide unbiased insight into the function of CaP-40 and effect of its over-expression in adductor smooth muscle, we built protein-protein interaction network of identified Crenomytilus grayanus proteome. In addition, we showed that CaP-40 is subjected to post-translational N- and C-terminal acetylation at N127, G229 and G349 sites which potentially regulates its function in vivo.
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Affiliation(s)
- Oleg S Matusovsky
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia; School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia.
| | - Anna V Dobrzhanskaya
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Victoria V Pankova
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia; Far Eastern Federal University, Vladivostok, Russia
| | - Konstantin V Kiselev
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia; Department of Biotechnology and Microbiology, The School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russia
| | - Ulyana V Girich
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Nikolay S Shelud'ko
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
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Wang J, Gao J, Xie J, Zheng X, Yan Y, Li S, Xie L, Zhang R. Cloning and mineralization-related functions of the calponin gene in Chlamys farreri. Comp Biochem Physiol B Biochem Mol Biol 2016; 201:53-8. [PMID: 27378404 DOI: 10.1016/j.cbpb.2016.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 10/21/2022]
Abstract
Calponin is a widely distributed protein which is associated with the bio-mineralization process in vertebrates. Recently, a new type of calponin has been found in shellfish; the present study aimed to determine if this gene in shellfish functions in bio-mineralization, one of the most important processes in a mollusk's growth. We chose Chlamys farreri, a seashell species with great economic value, as the object of the study and obtained its full-length cDNA to study the function of calponin by gene expression analysis, shell notching experiment and RNA interference assays. Calponin in C. farreri is a basic protein that is highly conserved among mollusk species. Except for high expression in the adductor muscle and foot, which correlated with its function of regulating muscle contraction, the calponin gene was expressed more in the mantle than in other tissues. The expression of the gene was induced by shell notching and an RNA interference assay showed that inhibition of calponin expression caused the growth of irregular mineral crystals on the shell. Further analysis indicated that calponin might function by regulating the expression of other mineralization-related genes. Calponin is a mineralization-related protein in C. farreri that might influence mineral crystal growth by affecting the expressions of other proteins, such as matrix proteins and mineralization-regulating proteins.
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Affiliation(s)
- Jun Wang
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Jing Gao
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Jun Xie
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Xiangnan Zheng
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Yi Yan
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Shiguo Li
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Liping Xie
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China.
| | - Rongqing Zhang
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China.
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Sirenko VV, Dobrzhanskaya AV, Shelud'ko NS, Borovikov YS. Calponin-Like Protein from Mussel Smooth Muscle Is a Competitive Inhibitor of Actomyosin ATPase. BIOCHEMISTRY. BIOKHIMIIA 2016; 81:28-33. [PMID: 26885580 DOI: 10.1134/s000629791601003x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The goal of this work was to elucidate the mechanism of inhibition of the actin-activated ATPase of myosin subfragment-1 (S1) by the calponin-like protein from mussel bivalve muscle. The calponin-like protein (Cap) is a 40-kDa actin-binding protein from the bivalve muscle of the mussel Crenomytilus grayanus. Kinetic parameters Vmax and KATPase of actomyosin ATPase in the absence and the presence of Cap were determined to investigate the mechanism of inhibition. It was found that Cap mainly causes increase in KATPase value and to a lesser extent the decrease in Vmax, which indicates that it is most likely a competitive inhibitor of actomyosin ATPase. Analysis of Vmax and KATPase parameters in the presence of tropomyosin revealed that the latter is a noncompetitive inhibitor of the actomyosin ATPase.
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Affiliation(s)
- V V Sirenko
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
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Song Q, Zheng P, Qiu L, Jiang X, Zhao H, Zhou H, Han Q, Diao X. Toxic effects of male Perna viridis gonad exposed to BaP, DDT and their mixture: A metabolomic and proteomic study of the underlying mechanism. Toxicol Lett 2016; 240:185-95. [DOI: 10.1016/j.toxlet.2015.10.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/25/2015] [Accepted: 10/31/2015] [Indexed: 12/17/2022]
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Troponin-like regulation in muscle thin filaments of the mussel Crenomytilus grayanus (Bivalvia: Mytiloida). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015. [DOI: 10.1016/j.bbapap.2015.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sirenko VV, Simonyan AO, Dobrzhanskaya AV, Shelud’ko NS, Borovikov YS. Modulation of conformations of myosin subfragment-1 (S-1) and inhibition of S-1 ATPase by mussel calponin. ACTA ACUST UNITED AC 2015. [DOI: 10.1134/s1990519x15010095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Dobrzhanskaya AV, Vyatchin IG, Lazarev SS, Matusovsky OS, Shelud'ko NS. Molluscan smooth catch muscle contains calponin but not caldesmon. J Muscle Res Cell Motil 2013; 34:23-33. [PMID: 23081709 DOI: 10.1007/s10974-012-9329-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
We isolated Ca(2+)-regulated thin filaments from the smooth muscle of the mussel Crenomytilus grayanus and studied the protein composition of different preparations from this muscle: whole muscle, heat-stable extract, fractions from heat-stable extract, thin filaments and intermediate stages of thin filaments purification. Among the protein components of the above-listed preparations, we did not find caldesmon (CaD), although two isoforms of a calponin-like (CaP-like) protein, which along with CaD is characteristic of vertebrate smooth muscle, were present in thin filaments. Thus, CaD is not Ca(2+)-regulator of thin filaments of this muscle. On the other hand, the mussel CaP-like protein is also not such Ca(2+)-regulator since we have shown that this protein can be selectively removed from isolated mussel thin filaments without loss of their Ca(2+)-sensitivity. We suggest that thin filaments in the smooth catch muscle possess other type of Ca(2+)-regulation, different from that in vertebrate smooth muscles.
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Affiliation(s)
- Anna V Dobrzhanskaya
- Laboratory of Cell Biophysics, A.V. Zhirmunsky Institute of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
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Sirenko VV, Simonyan AH, Dobrzhanskaya AV, Shelud’ko NS, Borovikov YS. 40-kDa Actin-binding protein of thin filaments of the mussel Crenomytilus grayanus inhibits the strong bond formation between actin and myosin head during the ATPase cycle. BIOCHEMISTRY (MOSCOW) 2012; 77:889-95. [DOI: 10.1134/s0006297912080093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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