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Xie J, Sun Y, Cao Y, Han L, Li Y, Ding B, Gao C, Hao P, Jin X, Chang Y, Song J, Yin D, Ding J. Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:151-162. [PMID: 35122573 PMCID: PMC8940865 DOI: 10.1007/s10126-022-10093-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Polyploid breeding is widely used in aquaculture as an important area of new research. We have previously grown Apostichopus japonicus triploids with a growth advantage. The body length, body weight, and aestivation time of triploid and diploid A. japonicus were measured in this study, and the transcriptome and metabolome were used to examine the growth advantage of triploids A. japonicus. The results showed that the proportion of triploid A. japonicus with a body length of 6-12 cm and 12-18 cm was significantly higher than that of diploid A. japonicus, and triploid A. japonicus had a shorter aestivation time (39 days) than diploid (63 days). We discovered 3296 differentially expressed genes (DEGs); 13 DEGs (for example, cyclin-dependent kinase 2) related to growth advantage, immune regulation, and energy storage were screened as potential candidates. According to Gene Ontology (GO) enrichment analysis, DEGs were significantly enriched in the cytoplasm (cellular component), ATP binding process (molecular function), oxidation-reduction process (biological process), and other pathways. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment data, DEGs were significantly enriched in ribosome production and other areas. We discovered 414 significant differential metabolites (SDMs), with 11 important SDMs (for example, nocodazole) linked to a growth advantage. SDMs are significantly enriched in metabolic pathways, as well as other pathways, according to the KEGG enrichment results. According to a combined transcriptome and metabolome analysis, 6 DEGs have regulatory relationships with 11 SDMs, which act on 11 metabolic pathways together. Our results further enrich the biological data of triploid A. japonicus and provide useful resources for genetic improvement of this species.
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Affiliation(s)
- Jiahui Xie
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yi Sun
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yue Cao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Lingshu Han
- Ningbo University, Ningbo, Zhejiang, People's Republic of China, 315211
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Beichen Ding
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Donghong Yin
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023.
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Dolmatov IY. Molecular Aspects of Regeneration Mechanisms in Holothurians. Genes (Basel) 2021; 12:250. [PMID: 33578707 PMCID: PMC7916379 DOI: 10.3390/genes12020250] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023] Open
Abstract
Holothurians, or sea cucumbers, belong to the phylum Echinodermata. They show good regenerative abilities. The present review provides an analysis of available data on the molecular aspects of regeneration mechanisms in holothurians. The genes and signaling pathways activated during the asexual reproduction and the formation of the anterior and posterior parts of the body, as well as the molecular mechanisms that provide regeneration of the nervous and digestive systems, are considered here. Damage causes a strong stress response, the signs of which are recorded even at late regeneration stages. In holothurian tissues, the concentrations of reactive oxygen species and antioxidant enzymes increase. Furthermore, the cellular and humoral components of the immune system are activated. Extracellular matrix remodeling and Wnt signaling play a major role in the regeneration in holothurians. All available morphological and molecular data show that the dedifferentiation of specialized cells in the remnant of the organ and the epithelial morphogenesis constitute the basis of regeneration in holothurians. However, depending on the type of damage, the mechanisms of regeneration may differ significantly in the spatial organization of regeneration process, the involvement of different cell types, and the depth of reprogramming of their genome (dedifferentiation or transdifferentiation).
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Affiliation(s)
- Igor Yu Dolmatov
- A.V. Zhirmunsky National Scientifc Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevsky 17, 690041 Vladivostok, Russia
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3
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Ding K, Zhang L, Fan X, Guo X, Liu X, Yang H. The Effect of Pedal Peptide-Type Neuropeptide on Locomotor Behavior and Muscle Physiology in the Sea Cucumber Apostichopus japonicus. Front Physiol 2020; 11:559348. [PMID: 33192555 PMCID: PMC7642236 DOI: 10.3389/fphys.2020.559348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Neuropeptides are endogenous active substances that are present in nervous tissues and participate in behavioral and physiological processes of the animal system. Locomotor behavior is basic to predation, escape, reproduction in animals, and neuropeptides play an important role in locomotion. In this study, the function of pedal peptide-type neuropeptide (PDP) in the process of locomotor behavior of the sea cucumber Apostichopus japonicus was evaluated. The locomotor behavior of A. japonicus was recorded by infrared camera before and after PDP administration, and muscle physiology was studied by ultra performance liquid chromatography and quadrupole time-off-light mass spectrometry (UPLC-Q-TOF-MS) to clarify the potential physiological mechanisms. The results showed that PDP enhanced the cumulative duration of moving significantly at the 7th h after injection, and reduced the mean and maximum velocity by 16.90 and 14.22% in A. japonicus. The data of muscle metabolomics suggested that some significantly changed metabolites were related to locomotor behavior of sea cucumbers. The decreases of phosphatidylethanolamine (PE) and phosphatidylcholine (PC) might result in the increases of lysophosphatidylcholines (lysoPC) and lysophosphatidylethanolamine (lysoPE), and suggested the change of fluidity and permeability in the muscle cell membrane, which would affect the physiology and function of muscle cells, and finally alter the locomotor behavior. In addition, the increased level of arachidonic acid (ARA) might activate K+ ion channels and then affect the signaling of muscle cells, or promote the sensitivity of muscle cells to Ca2+ and then result in the contractility of longitudinal muscles in sea cucumbers. ARA was also involved in the linoleic acid metabolism which was the only pathway that disturbed significantly after PDP administration. In conclusion, PDP participated in the regulation of locomotor behavior in the sea cucumber, and the decreased PE and PC, increased lysoPC, lysoPE and ARA might be the potential physiological mechanisms that responsible for behavioral effects of PDP in A. japonicus.
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Affiliation(s)
- Kui Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xinhao Fan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xueying Guo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xiang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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4
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Ding K, Zhang L, Zhang T, Yang H, Brinkman R. The Effect of Melatonin on Locomotor Behavior and Muscle Physiology in the Sea Cucumber Apostichopus japonicus. Front Physiol 2019; 10:221. [PMID: 30941049 PMCID: PMC6433841 DOI: 10.3389/fphys.2019.00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
Melatonin is a highly conserved hormone in evolutionary history. It occurs in numerous organisms and plays a role in the endocrine and immune systems. Locomotor behavior is a basic behavior in animals and is an important indicator of circadian rhythms, which are coordinated by the nervous and endocrine systems. To date, the effect of melatonin on locomotor behavior has been studied in vertebrates, including syrian hamsters, sparrows, rats, zebrafish, goldfish, and flatworms. However, there have been few studies of the effects of melatonin on locomotor behavior in marine invertebrates. The goals of present study were to show the existence of melatonin in the sea cucumber Apostichopus japonicus and to evaluate its effect on locomotor activity. In addition, muscle tissues from control and melatonin-treated sea cucumbers were tested using ultra performance liquid chromatography and quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) to determine the changes of metabolic activity in muscle. Melatonin was present in the coelomic fluid of A. japonicus at a concentration of ∼135.0 ng/L. The total distance traveled and number steps taken over 9 h after melatonin administration decreased with increasing concentration of the melatonin dose. Mean and maximum velocity of movement and stride length and stride frequency also decreased, but their differences were not statistically significant. Overall, these results suggest that melatonin administration had a sedative effect on A. japonicus. The levels of 22 different metabolites were altered in the muscle tissues of melatonin-treated sea cucumbers. Serotonin, 9-cis retinoic acid, all-trans retinoic acid, flavin mononucleotide in muscles were downregulated after melatonin administration. Moreover, a high free fatty acid (FFA) concentration and a decrease in the adenosine 5′-triphosphate (ATP) concentration in the muscle tissues of the melatonin-treated group were detected as well. These results suggest that the sedative effect of melatonin involves some other metabolic pathways, and the reduced locomotor modulator—serotonin, inhibited fatty acid oxidation and disturbed oxidative phosphorylation are potential physiological mechanisms that result in the inhibitory effect of melatonin on locomotion in sea cucumbers.
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Affiliation(s)
- Kui Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Richard Brinkman
- Australian Institute of Marine Science, Townsville, QLD, Australia
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5
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Metabolic response of longitudinal muscles to acute hypoxia in sea cucumber Apostichopus japonicus (Selenka): A metabolome integrated analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:235-244. [DOI: 10.1016/j.cbd.2018.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/23/2018] [Accepted: 12/23/2018] [Indexed: 01/16/2023]
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6
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Transcriptome analysis provides insights into the molecular mechanisms responsible for evisceration behavior in the sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:143-157. [PMID: 30851504 DOI: 10.1016/j.cbd.2019.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 01/05/2023]
Abstract
The sea cucumber Apostichopus japonicus (Selenka) is a valuable economic species in Southeast Asia. It has many fascinating behavioral characteristics, such as autolysis, aestivation, regeneration, and evisceration, thus it is a notable species for studies of special behaviors. Evisceration and autotomy are controlled by the neural network and involve a complicated physiological process. The occurrence of evisceration behavior in sea cucumbers is strongly related to their environment, and it negatively impacts their economic value. Evisceration behavior plays a pivotal role in the survival of A. japonicus, and when it is induced by dramatic changes in the coastal ecological environment and the aquaculture setting it can strongly affect the economic performance of this species. Although numerous studies have focused on intestinal regeneration of A. japonicus, less is known about evisceration behavior, especially its underlying molecular mechanisms. Thus, identification of genes that regulate evisceration in the sea cucumber likely will provide a scientific explanation for this significant specific behavior. In this study, Illumina sequencing (RNA-Seq) was performed on A. japonicus specimens in three states: normal (TCQ), eviscerating (TCZ), and 3 h after evisceration (TCH). In total, 129,905 unigenes were generated with an N50 length of 2651 base pairs, and 54,787 unigenes were annotated from seven functional databases (KEGG, KOG, GO, NR, NT, Interpro, and Swiss-Prot). Additionally, 190, 191, and 320 genes were identified as differentially expressed genes (DEGs) in the comparisons of TCQ vs. TCZ, TCZ vs. TCH, and TCQ vs. TCH, respectively. These DEGs mapped to 157, 113, and 190 signaling pathways in the KEGG database, respectively. KEGG analyses also revealed that potential DEGs enriched in the categories of "environmental information processing," "organismal system," "metabolism," and "cellular processes," and they were involved in evisceration behavior in A. japonicus. These DEGs are related to muscle contraction, hormone and neurotransmitter secretion, nerve and muscle damage, energy support, cellular stress, and apoptosis. In conclusion, through our comparative analysis of A. japonicus in different stages, we identified many candidate evisceration-related genes and signaling pathways that likely are involved in evisceration behavior. These results should help further elucidate the mechanisms underlying evisceration behavior in sea cucumbers.
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7
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Huo D, Sun L, Zhang L, Ru X, Liu S, Yang H. Metabolome responses of the sea cucumber Apostichopus japonicus to multiple environmental stresses: Heat and hypoxia. MARINE POLLUTION BULLETIN 2019; 138:407-420. [PMID: 30660290 DOI: 10.1016/j.marpolbul.2018.11.063] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/24/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Economically important marine organisms face severe environmental challenges, such as high temperature and low dissolved oxygen, from global climate change. Adverse environmental factors impact the survival and growth of economically important marine organisms, thereby negatively influencing the aquaculture industry. However, little is known about the responses of sea cucumbers to combined environmental co-stressors till now. In this study, ultra-performance liquid chromatography (UPLC) was utilized to obtain metabolic profiles of sea cucumbers. Changes in the concentrations of 84, 68, and 417 metabolites related to the responses of sea cucumbers to heat (26 °C), hypoxia (2 mg/L) and the combined stress, respectively, were observed and analyzed. Representative biomarkers were discussed in detail, including deltaline, fusarin C, halichondrin B and rapanone. The concentration of metabolites involved in the regulation of energy metabolism, including amino acid, carbohydrate and lipid metabolism were significantly changed, and the tricarboxylic acid (TCA)-cycle was significantly altered under heat plus hypoxia. We interpreted these changes partly as an adaptation mechanism in response to environmental stress. Based on the decreased accumulation of glutamine, we hypothesized that heat stress is the main factor that interferes with the process of glutamic acid-glutamine metabolism. The present study showed that combined environmental stressors have a more extensive impact on the metabolites of the respiratory tree in sea cucumbers than single stress. These results would facilitate further development of the sea cucumber as an echinoderm model to study mechanisms of response to adverse environments, as well as to help advance knowledge of the adaptation of marine organisms to global climate change.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiaoshang Ru
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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Sun L, Lin C, Li X, Xing L, Huo D, Sun J, Zhang L, Yang H. Comparative Phospho- and Acetyl Proteomics Analysis of Posttranslational Modifications Regulating Intestine Regeneration in Sea Cucumbers. Front Physiol 2018; 9:836. [PMID: 30018572 PMCID: PMC6037860 DOI: 10.3389/fphys.2018.00836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/14/2018] [Indexed: 12/29/2022] Open
Abstract
Sea cucumbers exposed to stressful circumstances eviscerate most internal organs, and then regenerate them rapidly under favorable environments. Reversible protein phosphorylation and acetylation are major modifications regulating protein function. Herein, for the first time, we perform quantitative phospho- and acetyl proteomics analyses of intestine regeneration in a sea cucumber species Apostichopus japonicus. We identified 1,862 phosphorylation sites in 1,169 proteins, and 712 acetylation sites in 470 proteins. Of the 147 and 251 proteins differentially modified by phosphorylation and acetylation, respectively, most were related to cytoskeleton biogenesis, protein synthesis and modification, signal recognition and transduction, energy production and conversion, or substance transport and metabolism. Phosphorylation appears to play a more important role in signal recognition and transduction than acetylation, while acetylation is of greater importance in posttranslational modification, protein turnover, chaperones; energy production and conversion; amino acid and lipid transport and metabolism. These results expanded our understanding of the regulatory mechanisms of posttranslational modifications in intestine regeneration of sea cucumbers after evisceration.
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Affiliation(s)
- Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chenggang Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaoni Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingchun Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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9
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Li Y, Wang R, Xun X, Wang J, Bao L, Thimmappa R, Ding J, Jiang J, Zhang L, Li T, Lv J, Mu C, Hu X, Zhang L, Liu J, Li Y, Yao L, Jiao W, Wang Y, Lian S, Zhao Z, Zhan Y, Huang X, Liao H, Wang J, Sun H, Mi X, Xia Y, Xing Q, Lu W, Osbourn A, Zhou Z, Chang Y, Bao Z, Wang S. Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation. Cell Discov 2018; 4:29. [PMID: 29951224 PMCID: PMC6018497 DOI: 10.1038/s41421-018-0030-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/18/2018] [Accepted: 04/08/2018] [Indexed: 12/27/2022] Open
Abstract
Echinoderms exhibit several fascinating evolutionary innovations that are rarely seen in the animal kingdom, but how these animals attained such features is not well understood. Here we report the sequencing and analysis of the genome and extensive transcriptomes of the sea cucumber Apostichopus japonicus, a species from a special echinoderm group with extraordinary potential for saponin synthesis, aestivation and organ regeneration. The sea cucumber does not possess a reorganized Hox cluster as previously assumed for all echinoderms, and the spatial expression of Hox7 and Hox11/13b potentially guides the embryo-to-larva axial transformation. Contrary to the typical production of lanosterol in animal cholesterol synthesis, the oxidosqualene cyclase of sea cucumber produces parkeol for saponin synthesis and has "plant-like" motifs suggestive of convergent evolution. The transcriptional factors Klf2 and Egr1 are identified as key regulators of aestivation, probably exerting their effects through a clock gene-controlled process. Intestinal hypometabolism during aestivation is driven by the DNA hypermethylation of various metabolic gene pathways, whereas the transcriptional network of intestine regeneration involves diverse signaling pathways, including Wnt, Hippo and FGF. Decoding the sea cucumber genome provides a new avenue for an in-depth understanding of the extraordinary features of sea cucumbers and other echinoderms.
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Affiliation(s)
- Yuli Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Ruijia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Xiaogang Xun
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Lisui Bao
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637 USA
| | - Ramesha Thimmappa
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Jun Ding
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023 China
| | - Liheng Zhang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Tianqi Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Chuang Mu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Yuqiang Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Lijie Yao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Yangfan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Shanshan Lian
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Zelong Zhao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023 China
| | - Yaoyao Zhan
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Jia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Hongzhen Sun
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Xue Mi
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Yu Xia
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Wei Lu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023 China
| | - Yaqing Chang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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