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Campli G, Volovych O, Kim K, Veldsman WP, Drage HB, Sheizaf I, Lynch S, Chipman AD, Daley AC, Robinson-Rechavi M, Waterhouse RM. The moulting arthropod: a complete genetic toolkit review. Biol Rev Camb Philos Soc 2024. [PMID: 39039636 DOI: 10.1111/brv.13123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Exoskeletons are a defining character of all arthropods that provide physical support for their segmented bodies and appendages as well as protection from the environment and predation. This ubiquitous yet evolutionarily variable feature has been instrumental in facilitating the adoption of a variety of lifestyles and the exploitation of ecological niches across all environments. Throughout the radiation that produced the more than one million described modern species, adaptability afforded by segmentation and exoskeletons has led to a diversity that is unrivalled amongst animals. However, because of the limited extensibility of exoskeleton chitin and cuticle components, they must be periodically shed and replaced with new larger ones, notably to accommodate the growing individuals encased within. Therefore, arthropods grow discontinuously by undergoing periodic moulting events, which follow a series of steps from the preparatory pre-moult phase to ecdysis itself and post-moult maturation of new exoskeletons. Each event represents a particularly vulnerable period in an arthropod's life cycle, so processes must be tightly regulated and meticulously executed to ensure successful transitions for normal growth and development. Decades of research in representative arthropods provide a foundation of understanding of the mechanisms involved. Building on this, studies continue to develop and test hypotheses on the presence and function of molecular components, including neuropeptides, hormones, and receptors, as well as the so-called early, late, and fate genes, across arthropod diversity. Here, we review the literature to develop a comprehensive overview of the status of accumulated knowledge of the genetic toolkit governing arthropod moulting. From biosynthesis and regulation of ecdysteroid and sesquiterpenoid hormones, to factors involved in hormonal stimulation responses and exoskeleton remodelling, we identify commonalities and differences, as well as highlighting major knowledge gaps, across arthropod groups. We examine the available evidence supporting current models of how components operate together to prepare for, execute, and recover from ecdysis, comparing reports from Chelicerata, Myriapoda, Crustacea, and Hexapoda. Evidence is generally highly taxonomically imbalanced, with most reports based on insect study systems. Biases are also evident in research on different moulting phases and processes, with the early triggers and late effectors generally being the least well explored. Our synthesis contrasts knowledge based on reported observations with reasonably plausible assumptions given current taxonomic sampling, and exposes weak assumptions or major gaps that need addressing. Encouragingly, advances in genomics are driving a diversification of tractable study systems by facilitating the cataloguing of putative genetic toolkits in previously under-explored taxa. Analysis of genome and transcriptome data supported by experimental investigations have validated the presence of an "ultra-conserved" core of arthropod genes involved in moulting processes. The molecular machinery has likely evolved with elaborations on this conserved pathway backbone, but more taxonomic exploration is needed to characterise lineage-specific changes and novelties. Furthermore, linking these to transformative innovations in moulting processes across Arthropoda remains hampered by knowledge gaps and hypotheses based on untested assumptions. Promisingly however, emerging from the synthesis is a framework that highlights research avenues from the underlying genetics to the dynamic molecular biology through to the complex physiology of moulting.
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Affiliation(s)
- Giulia Campli
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Olga Volovych
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Kenneth Kim
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Werner P Veldsman
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Harriet B Drage
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Idan Sheizaf
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Sinéad Lynch
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Ariel D Chipman
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Allison C Daley
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
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Wang X, Tan J, Zou H, Wang F, Xu J. Cloning and Characterization of Chitin Deacetylase from Euphausia superba. Int J Mol Sci 2024; 25:2075. [PMID: 38396751 PMCID: PMC10889134 DOI: 10.3390/ijms25042075] [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: 01/05/2024] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Chitin deacetylase (CDA) can catalyze the deacetylation of chitin to produce chitosan. In this study, we identified and characterized a chitin deacetylase gene from Euphausia superba (EsCDA-9k), and a soluble recombinant protein chitin deacetylase from Euphausia superba of molecular weight 45 kDa was cloned, expressed, and purified. The full-length cDNA sequence of EsCDA-9k was 1068 bp long and encoded 355 amino acid residues that contained the typical domain structure of carbohydrate esterase family 4. The predicted three-dimensional structure of EsCDA-9k showed a 67.32% homology with Penaeus monodon. Recombinant chitin deacetylase had the highest activity at 40 °C and pH 8.0 in Tris-HCl buffer. The enzyme activity was enhanced by metal ions Co2+, Fe3+, Ca2+, and Na+, while it was inhibited by Zn2+, Ba2+, Mg2+, and EDTA. Molecular simulation of EsCDA-9k was conducted based on sequence alignment and homology modeling. The EsCDA-9k F18G mutant showed a 1.6-fold higher activity than the wild-type enzyme. In summary, this is the first report of the cloning and heterologous expression of the chitin deacetylase gene in Euphausia superba. The characterization and function study of EsCDA-9k will serve as an important reference point for future application.
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Affiliation(s)
- Xutong Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Jiahao Tan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Huaying Zou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Fang Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Jiakun Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
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Cheng M, Shao Z, Wang X, Lu C, Li S, Duan D. Novel Chitin Deacetylase from Thalassiosira weissflogii Highlights the Potential for Chitin Derivative Production. Metabolites 2023; 13:metabo13030429. [PMID: 36984869 PMCID: PMC10057020 DOI: 10.3390/metabo13030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
β-Chitin is an important carbon fixation product of diatoms, and is the most abundant nitrogen-containing polysaccharide in the ocean. It has potential for widespread application, but the characterization of chitin-related enzymes from β-chitin producers has rarely been reported. In this study, a chitin deacetylase (TwCDA) was retrieved from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) database and was heterologously expressed in vitro for functional analysis. The results showed that both the full-length sequence (TwCDA) and the N-terminal truncated sequence (TwCDA-S) had chitin deacetylase and chitinolytic activities after expression in Escherichia coli. High-performance liquid chromatography (HPLC) and gas chromatography–mass spectrometry (GC-MS) indicated that TwCDA and TwCDA-S could catalyze the deacetylation of oligosaccharide (GlcNAc)5. TwCDA had higher deacetylase activity, and also catalyzed the deacetylation of the β-chitin polymer. A dinitrosalicylic acid (DNS) assay showed that TwCDA-S had high chitinolytic activity for (GlcNAc)5, and the optimal reaction temperature was 35 °C. Liquid chromatography combined with time-of-flight mass spectrometry (LC-coTOF-MS) detected the formation of a N-acetylglucosamine monomer (C8H15NO6) in the reaction mixture. Altogether, we isolated a chitin deacetylase from a marine diatom, which can catalyze the deacetylation and degradation of chitin and chitin oligosaccharides. The relevant results lay a foundation for the internal regulation mechanism of chitin metabolism in diatoms and provide a candidate enzyme for the green industrial preparation of chitosan and chitin oligosaccharides.
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Affiliation(s)
- Mengzhen Cheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xin Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Lu
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai 264005, China
| | - Shuang Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Liang YY, Yan LQ, Tan MH, Li GH, Fang JH, Peng JY, Li KT. Isolation, characterization, and genome sequencing of a novel chitin deacetylase producing Bacillus aryabhattai TCI-16. Front Microbiol 2022; 13:999639. [PMID: 36171752 PMCID: PMC9511218 DOI: 10.3389/fmicb.2022.999639] [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: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022] Open
Abstract
Chitin deacetylase (CDA) is a chitin degradation enzyme that catalyzes the conversion of chitin to chitosan by the deacetylation of N-acetyl-D-glucosamine residues, playing an important role in the high-value utilization of waste chitin. The shells of shrimp and crab are rich in chitin, and mangroves are usually recognized as an active habitat to shrimp and crab. In the present study, a CDA-producing bacterium, strain TCI-16, was isolated and screened from the mangrove soil. Strain TCI-16 was identified and named as Bacillus aryabhattai TCI-16, and the maximum CDA activity in fermentation broth reached 120.35 ± 2.40 U/mL at 36 h of cultivation. Furthermore, the complete genome analysis of B. aryabhattai TCI-16 revealed the chitin-degrading enzyme system at genetic level, in which a total of 13 putative genes were associated with carbohydrate esterase 4 (CE4) family enzymes, including one gene coding CDA, seven genes encoding polysaccharide deacetylases, and five genes encoding peptidoglycan-N-acetyl glucosamine deacetylases. Amino acid sequence analysis showed that the predicted CDA of B. aryabhattai TCI-16 was composed of 236 amino acid residues with a molecular weight of 27.3 kDa, which possessed a conserved CDA active like the known CDAs. However, the CDA of B. aryabhattai TCI-16 showed low homology (approximately 30%) with other microbial CDAs, and its phylogenetic tree belonged to a separate clade in bacteria, suggesting a high probability in structural novelty. In conclusion, the present study indicated that the novel CDA produced by B. aryabhattai TCI-16 might be a promising option for bioconversion of chitin to the value-added chitosan.
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Affiliation(s)
- Ying-yin Liang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Lu-qi Yan
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Ming-hui Tan
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Gang-hui Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Jian-hao Fang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Jie-ying Peng
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Kun-tai Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, College of Food Science and Technology, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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