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Wang H, Liu S, Cui J, Li C, Hu Y, Zhou W, Chang Y, Qiu X, Liu Z, Wang X. Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing. PLoS One 2015; 10:e0134899. [PMID: 26244987 PMCID: PMC4526669 DOI: 10.1371/journal.pone.0134899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 07/15/2015] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs), as a family of non-coding small RNAs, play important roles in the post-transcriptional regulation of gene expression. Sea cucumber (Apostichopus japonicus) is an important economic species which is widely cultured in East Asia. The longitudinal muscle (LTM) and respiratory tree (RPT) are two important tissues in sea cucumber, playing important roles such as respiration and movement. In this study, we identified and characterized miRNAs in the LTM and RPT of sea cucumber (Apostichopus japonicus) using Illumina HiSeq 2000 platform. A total of 314 and 221 conserved miRNAs were identified in LTM and RPT, respectively. In addition, 27 and 34 novel miRNAs were identified in the LTM and RPT, respectively. A set of 58 miRNAs were identified to be differentially expressed between LTM and RPT. Among them, 9 miRNAs (miR-31a-3p, miR-738, miR-1692, let-7a, miR-72a, miR-100b-5p, miR-31b-5p, miR-429-3p, and miR-2008) in RPT and 7 miRNAs (miR-127, miR-340, miR-381, miR-3543, miR-434-5p, miR-136-3p, and miR-300-3p) in LTM were differentially expressed with foldchange value being greater than 10. A total of 14,207 and 12,174 target genes of these miRNAs were predicted, respectively. Functional analysis of these target genes of miRNAs were performed by GO analysis and pathway analysis. This result provided in this work will be useful for understanding biological characteristics of the LTM and RPT of sea cucumber and assisting molecular breeding of sea cucumber for aquaculture.
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Affiliation(s)
- Hongdi Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, United States of America
| | - Jun Cui
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Chengze Li
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Yucai Hu
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
- School of Science, Dalian Ocean University, Dalian 116023, China
| | - Wei Zhou
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Xuemei Qiu
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, United States of America
| | - Xiuli Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
- * E-mail:
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da Costa DCF, Landeira-Fernandez AM. Thermogenic activity of the Ca2+-ATPase from blue marlin heater organ: regulation by KCl and temperature. Am J Physiol Regul Integr Comp Physiol 2009; 297:R1460-8. [PMID: 19710387 DOI: 10.1152/ajpregu.90993.2008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This work shows that vesicles derived from the blue marlin heater organ retain a sarcoplasmic reticulum (SR) Ca(2+)-ATPase that can interconvert different forms of energy. During the hydrolysis of ATP part of the energy is always converted into heat, and the other part can be converted into work (Ca(2+) transport) or heat, depending on the temperature and the presence of KCl in the reaction medium. At 15 degrees C, where KCl stimulates the activity approximately threefold, measurements of the amount of heat released per mole of ATP hydrolyzed (DeltaH(cal)) show similar values (approximately -11 kcal/mol) in the presence or absence of a Ca(2+) gradient. At 25 degrees C, KCl activates the enzyme to the same extent as at 15 degrees C, but inhibits the production of extra heat by SR Ca(2+)-ATPase when a Ca(2+) gradient is built up across the membrane. The DeltaH(cal) values found in the presence of a Ca(2+)-gradient were -26.2 +/- 2.9 kcal/mol (n = 7) in control experiments and -16.1 +/- 1.5 (n = 14) in the presence of 100 mM KCl. At 35 degrees C, KCl has a smaller effect ( approximately 1.5-fold) on activating the enzyme. Similar to SR Ca(2+)-ATPase from mammals, at this temperature the enzyme produces almost twice the amount of heat per mole of ATP hydrolyzed in the presence of a Ca(2+) gradient and KCl has no effect at all on this increment. These data suggest that the marlin SR Ca(2+)-ATPase may play an important role in heater organ thermogenesis and that KCl has the potential for regulating the heat production catalyzed by the enzyme.
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Affiliation(s)
- Danielly Cristiny Ferraz da Costa
- Instituto de Bioquímica Médica, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil.
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Nigro M, Arruda AP, de Meis L. Ca2+ transport and heat production in vesicles derived from the sarcoplasmic reticulum terminal cisternae: Regulation by K+. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1517-22. [DOI: 10.1016/j.bbamem.2009.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 03/24/2009] [Accepted: 04/08/2009] [Indexed: 10/20/2022]
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Abstract
Purines appear to be the most primitive and widespread chemical messengers in the animal and plant kingdoms. The evidence for purinergic signalling in plants, invertebrates and lower vertebrates is reviewed. Much is based on pharmacological studies, but important recent studies have utilized the techniques of molecular biology and receptors have been cloned and characterized in primitive invertebrates, including the social amoeba Dictyostelium and the platyhelminth Schistosoma, as well as the green algae Ostreococcus, which resemble P2X receptors identified in mammals. This suggests that contrary to earlier speculations, P2X ion channel receptors appeared early in evolution, while G protein-coupled P1 and P2Y receptors were introduced either at the same time or perhaps even later. The absence of gene coding for P2X receptors in some animal groups [e.g. in some insects, roundworms (Caenorhabditis elegans) and the plant Arabidopsis] in contrast to the potent pharmacological actions of nucleotides in the same species, suggests that novel receptors are still to be discovered.
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Affiliation(s)
- G Burnstock
- Autonomic Neuroscience Centre, Royal Free and University College Medical School, London, UK.
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Vieira VP, Rocha JB, Stefanello FM, Balz D, Morsch VM, Schetinger MR. Heparin and chondroitin sulfate inhibit adenine nucleotide hydrolysis in liver and kidney membrane enriched fractions. Int J Biochem Cell Biol 2001; 33:1193-201. [PMID: 11606255 DOI: 10.1016/s1357-2725(01)00083-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inhibition of adenine nucleotide hydrolysis by heparin and chondroitin sulfate (sulfated polysaccharides) was studied in membrane preparations from liver and kidney of adult rats. Hydrolysis was measured by the activity of NTPDase and 5'-nucleotidase. The inhibition of NTPDase by heparin was observed at three different pH values (6.0, 8.0 and 10.0). In liver, the maximal inhibition observed for ATP and ADP hydrolysis was about 80% at pH 8.0 and 70% at pH 6.0 and 10.0. Similarly to the effect observed in liver, heparin caused inhibition of ATP and ADP hydrolysis that reached a maximum of 70% in kidney (pH 8.0). Na(+), K(+) and Rb(+) changed the inhibitory potency of heparin, suggesting that its effects may be related to charge interaction. In addition to heparin, chondroitin sulfate also caused a dose-dependent inhibition in liver and kidney membranes. The maximal inhibition observed for ATP and ADP hydrolysis was about 60 and 50%, respectively. In addition, the hepatic and renal activity of 5'-nucleotidase was inhibited by heparin and chondroitin sulfate, except for kidney membranes where chondroitin sulfate did not alter AMP hydrolysis. On this basis, the findings indicate that glycosaminoglycans have a potential role as inhibitors of adenine nucleotide hydrolysis on the surface of liver and kidney cell membranes in vitro.
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Affiliation(s)
- V P Vieira
- Departamento de Química, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS, Brazil
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Landeira-Fernandez A. Ca(2+)transport by the sarcoplasmic reticulum Ca(2+)-ATPase in sea cucumber (Ludwigothurea grisea) muscle. J Exp Biol 2001; 204:909-21. [PMID: 11171414 DOI: 10.1242/jeb.204.5.909] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In muscle cells, the excitation-contraction cycle is triggered by an increase in the concentration of free cytoplasmic Ca(2+). The Ca(2+)-ATPase present in the membrane of the sarcoplasmic reticulum (SR) pumps Ca(2+) from the cytosol into this intracellular compartment, thus promoting muscle relaxation. The microsomal fraction derived from the longitudinal smooth muscle of the body wall from the sea cucumber Ludwigothurea grisea retains a membrane-bound Ca(2+)-ATPase that is able to transport Ca(2+) mediated by ATP hydrolysis. Immunological analyses reveal that monoclonal antibodies against sarco-endoplasmic reticulum Ca(2+)-ATPase (SERCA1 and SERCA2a) cross-react with a 110 kDa band, indicating that the sea cucumber Ca(2+)-ATPase is a SERCA-type ATPase. Like the mammalian Ca(2+)-ATPase isoforms so far described, the enzyme also shows a high affinity for Ca(2+) and ATP, has an optimum pH of approximately 7.0 and is sensitive to thapsigargin and cyclopiazonic acid, specific inhibitors of the SERCA pumps. However, unlike the mammalian SERCA isoforms, concentrations of ATP above 2 mmol l(−1) inhibit Ca(2+) transport, but not ATP hydrolysis, in sea cucumber vesicles, suggesting that high ATP concentrations uncouple the Ca(2+)-ATPase. Another unique feature observed with the sea cucumber Ca(2+)-ATPase is the high dependence of maximal activity on K(+) or Na(+). Similar activation promoted by these cations was observed with various mammalian Ca(2+)-ATPase preparations when they were incubated in the presence of low concentrations of sulphated polysaccharides. In control experiments, K(+) and Na(+) have almost no effect on Ca(2+) transport, but in the presence of heparin or fucosylated chondroitin sulphate, the activity of the different mammalian Ca(2+)-ATPases is inhibited and they are activated by either K(+) or Na(+) in a manner similar to the native sea cucumber ATPase. These results led us to investigate the possible occurrence of a highly sulphated polysaccharide on vesicles from the SR of sea cucumber smooth muscle that could act as an ‘endogenous’ Ca(2+)-ATPase inhibitor. In fact, SR vesicles derived from the sea cucumber, but not from rabbit muscle, contain a highly sulphated polysaccharide. After extraction and purification of these polysaccharide molecules, their effect was tested on vesicles obtained from rabbit muscle. This compound inhibited Ca(2+) uptake in rabbit SR vesicles, at concentrations lower than heparin, and restored the dependence on monovalent cations. These results strongly suggest that the sea cucumber Ca(2+)-ATPase is activated by monovalent cations because of the presence of endogenous sulphated polysaccharides.
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Affiliation(s)
- A Landeira-Fernandez
- Instituto de Ciências Biomédicas, Departamento de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Cidade Universitária, RJ, Rio de Janeiro, Brasil 21941-590.
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