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Molecules
2019 Mar 12;245:. doi: 10.3390/molecules24050998.
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RNA Sequencing Analysis to Capture the Transcriptome Landscape during Tenderization in Sea Cucumber Apostichopus japonicus.
Dong X
,
Qi H
,
He B
,
Jiang D
,
Zhu B
.
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Sea cucumber (Apostichopus japonicus) is an economically significant species in China having great commercial value. It is challenging to maintain the textural properties during thermal processing due to the distinctive physiochemical structure of the A. japonicus body wall (AJBW). In this study, the gene expression profiles associated with tenderization in AJBW were determined at 0 h (CON), 1 h (T_1h), and 3 h (T_3h) after treatment at 37 °C using Illumina HiSeq™ 4000 platform. Seven-hundred-and-twenty-one and 806 differentially expressed genes (DEGs) were identified in comparisons of T_1h vs. CON and T_3h vs. CON, respectively. Among these DEGs, we found that two endogenous proteases-72 kDa type IV collagenase and matrix metalloproteinase 16 precursor-were significantly upregulated that could directly affect the tenderness of AJBW. In addition, 92 genes controlled four types of physiological and biochemical processes such as oxidative stress response (3), immune system process (55), apoptosis (4), and reorganization of the cytoskeleton and extracellular matrix (30). Further, the RT-qPCR results confirmed the accuracy of RNA-sequencing analysis. Our results showed the dynamic changes in global gene expression during tenderization and provided a series of candidate genes that contributed to tenderization in AJBW. This can help further studies on the genetics/molecular mechanisms associated with tenderization.
Figure 1. (a) The differentially-expressed genes (DEGs) of AJBW during tenderization. (b) Upregulated genes of T_1h and T_3h compared to CON. (c) Downregulated genes of T_1h and T_3h compared to CON.
Figure 2. Distribution of gene ontology (GO) terms of DEGs during tenderization. The number of genes with GO-terms in the categories “Molecular function”, “Biological Process”, and “Cellular component” are shown. (a) GO functional classification of DEGs in T_1h vs. CON. (b) GO functional classification of DEGs in T_3h vs. CON.
Figure 3. Scatterplot of the top 20 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Rich factor represents the ratio of the number of DEGs and the number of all genes in the pathways. (a) KEGG pathway enrichment of DEGs in T_1h vs. CON. (b) KEGG pathway enrichment of DEGs in T_3h vs. CON.
Artigaud,
Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics.
2015, Pubmed
Artigaud,
Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics.
2015,
Pubmed
Barat,
Transcriptional response to heat shock in liver of snow trout (Schizothorax richardsonii)--a vulnerable Himalayan Cyprinid fish.
2016,
Pubmed
Barshis,
Genomic basis for coral resilience to climate change.
2013,
Pubmed
Barshis,
Lineage-specific transcriptional profiles of Symbiodinium spp. unaltered by heat stress in a coral host.
2014,
Pubmed
Cao,
TGF-beta1 mediates 70-kDa heat shock protein induction due to ultraviolet irradiation in human skin fibroblasts.
1999,
Pubmed
Chen,
Superoxide is the major reactive oxygen species regulating autophagy.
2009,
Pubmed
Chen,
Effects of ultrasonic processing on caspase-3, calpain expression and myofibrillar structure of chicken during post-mortem ageing.
2015,
Pubmed
Christensen,
Sensory characteristics of meat cooked for prolonged times at low temperature.
2012,
Pubmed
Dong,
Expression analysis of immune related genes identified from the coelomocytes of sea cucumber (Apostichopus japonicus) in response to LPS challenge.
2014,
Pubmed
,
Echinobase
Farah,
Diverse protective roles of the actin cytoskeleton during oxidative stress.
2011,
Pubmed
Gallagher,
Myosin light chain kinases.
1997,
Pubmed
Gleason,
RNA-seq reveals regional differences in transcriptome response to heat stress in the marine snail Chlorostoma funebralis.
2015,
Pubmed
Gullian Klanian,
Effect of pH on temperature controlled degradation of reactive oxygen species, heat shock protein expression, and mucosal immunity in the sea cucumber Isostichopus badionotus.
2017,
Pubmed
,
Echinobase
Habte-Tsion,
Threonine modulates immune response, antioxidant status and gene expressions of antioxidant enzymes and antioxidant-immune-cytokine-related signaling molecules in juvenile blunt snout bream (Megalobrama amblycephala).
2016,
Pubmed
Hoffmann,
Phylogenetic perspectives in innate immunity.
1999,
Pubmed
Huang,
The effect of active caspase-3 on degradation of chicken myofibrillar proteins and structure of myofibrils.
2011,
Pubmed
Huang,
Changes in apoptotic factors and caspase activation pathways during the postmortem aging of beef muscle.
2016,
Pubmed
Lang,
Transcriptome profiling of selectively bred Pacific oyster Crassostrea gigas families that differ in tolerance of heat shock.
2009,
Pubmed
Larsen,
The matrix reorganized: extracellular matrix remodeling and integrin signaling.
2006,
Pubmed
Lee,
Bax inhibitor-1 regulates endoplasmic reticulum stress-associated reactive oxygen species and heme oxygenase-1 expression.
2007,
Pubmed
Li,
Characterization of skin ulceration syndrome associated microRNAs in sea cucumber Apostichopus japonicus by deep sequencing.
2012,
Pubmed
,
Echinobase
Li,
Transcriptome analysis provides insights into hepatic responses to moderate heat stress in the rainbow trout (Oncorhynchus mykiss).
2017,
Pubmed
Lim,
Thermal stress induces a distinct transcriptome profile in the Pacific oyster Crassostrea gigas.
2016,
Pubmed
Liu,
RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish.
2013,
Pubmed
Liu,
Effects of endogenous cysteine proteinases on structures of collagen fibres from dermis of sea cucumber (Stichopus japonicus).
2017,
Pubmed
,
Echinobase
Mastellos,
Complement: more than a 'guard' against invading pathogens?
2002,
Pubmed
Matés,
Effects of antioxidant enzymes in the molecular control of reactive oxygen species toxicology.
2000,
Pubmed
Meistertzheim,
Identification of differentially expressed genes of the Pacific oyster Crassostrea gigas exposed to prolonged thermal stress.
2007,
Pubmed
Nauta,
The membrane attack complex of complement induces caspase activation and apoptosis.
2002,
Pubmed
Nelson,
The translation machinery and 70 kd heat shock protein cooperate in protein synthesis.
1992,
Pubmed
Parks,
Matrix metalloproteinases as modulators of inflammation and innate immunity.
2004,
Pubmed
Polato,
Location-specific responses to thermal stress in larvae of the reef-building coral Montastraea faveolata.
2010,
Pubmed
Prasopdee,
RNA-Seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini.
2014,
Pubmed
Qi,
ROS production in homogenate from the body wall of sea cucumber Stichopus japonicus under UVA irradiation: ESR spin-trapping study.
2016,
Pubmed
,
Echinobase
Qi,
Apoptosis induction is involved in UVA-induced autolysis in sea cucumber Stichopus japonicus.
2016,
Pubmed
,
Echinobase
Qin,
Unfolding/Refolding Study on Collagen from Sea Cucumber Based on 2D Fourier Transform Infrared Spectroscopy.
2016,
Pubmed
,
Echinobase
Ramírez-Gómez,
LPS-induced genes in intestinal tissue of the sea cucumber Holothuria glaberrima.
2009,
Pubmed
,
Echinobase
Reinehr,
Involvement of the Src family kinase yes in bile salt-induced apoptosis.
2004,
Pubmed
Ren,
The first echinoderm poly-U-binding factor 60 kDa (PUF60) from sea cucumber (Stichopus monotuberculatus): Molecular characterization, inducible expression and involvement of apoptosis.
2015,
Pubmed
,
Echinobase
Roberts,
Heat shock proteins (chaperones) in fish and shellfish and their potential role in relation to fish health: a review.
2010,
Pubmed
Shen,
MiR-29b mimics promotes cell apoptosis of smooth muscle cells via targeting on MMP-2.
2018,
Pubmed
Shiel,
De novo characterisation of the greenlip abalone transcriptome (Haliotis laevigata) with a focus on the heat shock protein 70 (HSP70) family.
2015,
Pubmed
Siwik,
Oxidative stress regulates collagen synthesis and matrix metalloproteinase activity in cardiac fibroblasts.
2001,
Pubmed
Soonthornchai,
Differentially expressed transcripts in stomach of Penaeus monodon in response to AHPND infection.
2016,
Pubmed
Sun,
Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus.
2011,
Pubmed
,
Echinobase
Szulgit,
The echinoderm collagen fibril: a hero in the connective tissue research of the 1990s.
2007,
Pubmed
,
Echinobase
Tallant,
Matrix metalloproteinases: fold and function of their catalytic domains.
2010,
Pubmed
Tan,
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.
2013,
Pubmed
Tanguy,
The immune response of Mytilus edulis hemocytes exposed to Vibrio splendidus LGP32 strain: A transcriptomic attempt at identifying molecular actors.
2018,
Pubmed
Volanakis,
Participation of C3 and its ligands in complement activation.
1990,
Pubmed
Wang,
Calpain and caspase: can you tell the difference?
2000,
Pubmed
Wang,
Effect of mitochondrial apoptotic activation through the mitochondrial membrane permeability transition pore on yak meat tenderness during postmortem aging.
2017,
Pubmed
Wu,
Proteolysis of noncollagenous proteins in sea cucumber, Stichopus japonicus, body wall: characterisation and the effects of cysteine protease inhibitors.
2013,
Pubmed
,
Echinobase
Wu,
Cloning and expression analysis of the gene encoding fibrinogen-like protein A, a novel regeneration-related protein from Apostichopus japonicus.
2014,
Pubmed
,
Echinobase
Yang,
Expression of immune-related genes in embryos and larvae of sea cucumber Apostichopus japonicus.
2010,
Pubmed
,
Echinobase
Yang,
RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.
2016,
Pubmed
,
Echinobase
Zhang,
The sea cucumber genome provides insights into morphological evolution and visceral regeneration.
2017,
Pubmed
,
Echinobase
Zhang,
Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions.
2018,
Pubmed
,
Echinobase
Zhao,
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.
2014,
Pubmed
,
Echinobase
Zhou,
Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers.
2014,
Pubmed
,
Echinobase
Zhu,
Purification and characterization of a cathepsin L-like enzyme from the body wall of the sea cucumber Stichopus japonicus.
2008,
Pubmed
,
Echinobase
Zitka,
Matrix metalloproteinases.
2010,
Pubmed