Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
BMC Genomics
2020 Jan 21;211:68. doi: 10.1186/s12864-020-6480-9.
Show Gene links
Show Anatomy links
Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures.
Liang L
,
Chen J
,
Li Y
,
Zhang H
.
???displayArticle.abstract???
BACKGROUND: Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood.
RESULTS: In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa.
CONCLUSIONS: Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.
XDA22040502 Strategic Priority Research Program of CAS, 2018YFC0309804 The National Key Research and Development Program of China, 2016YFC0304905 The National Key Research and Development Program of China, ZDKJ2016012 Major scientific and technological projects of Hainan Province
Fig. 1. Venn diagram of DEGs among different combinations (P15 vs. P0.1, P25 vs. P0.1, and P25 vs. P15). P0.1: experimental group incubated at atmospheric pressure; P15: experimental group incubated at 15âMPa; P25: experimental group incubated at 25âMPa; DEGs: differentially expressed genes; LRGs: linearly related DEGs; PSGs: pressure-sensitive DEGs; HPGs: high-pressure-induced DEGs
Fig. 2. Line graphs of the expression patterns of LRGs, PSGs, and HPGs. Points represent the mean of log2 (RFC) of all genes. Error bars represent standard deviation. LRGs: linearly related DEGs; PSGs: pressure-sensitive DEGs; HPGs: high-pressure-induced DEGs; RFC: relative fold change
Fig. 3. Heatmaps of DEGs annotated in Swiss-Prot. a Heatmap of linearly related DEGs. b Heatmap of pressure-sensitive DEGs. c Heatmap of high-pressure-induced DEGs. P0.1: experimental group incubated at atmospheric pressure; P15: experimental group incubated at 15âMPa; P25: experimental group incubated at 25âMPa; DEGs: differentially expressed genes
Fig. 4. Pathway of clathrin-dependent endocytosis. This pathway is a part of KEGG pathway map (map04144). The proteins involved in this pathway are shown in boxes and their descriptions are listed in the Additional file 6: Table S5. The proteins significantly up-regulated at high-pressure condition in our results are highlighted in red boxes
Fig. 5. The statistics of gene family analysis. a Gene family analysis of linearly related DEGs. b Gene family analysis of pressure-sensitive DEGs. c Gene family analysis of high-pressure-induced DEGs. DEGs: differentially expressed genes
Aertsen,
An SOS response induced by high pressure in Escherichia coli.
2004, Pubmed
Aertsen,
An SOS response induced by high pressure in Escherichia coli.
2004,
Pubmed
Ban,
ABCA3 as a lipid transporter in pulmonary surfactant biogenesis.
2007,
Pubmed
Bao,
Human glycogen debranching enzyme gene (AGL): complete structural organization and characterization of the 5' flanking region.
1996,
Pubmed
Brown,
Metabolic costs imposed by hydrostatic pressure constrain bathymetric range in the lithodid crab Lithodes maja.
2017,
Pubmed
Brown,
Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth.
2014,
Pubmed
Brown,
The effects of changing climate on faunal depth distributions determine winners and losers.
2015,
Pubmed
Calligari,
Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6.
2015,
Pubmed
Chen,
Comparative transcriptome analysis of Eogammarus possjeticus at different hydrostatic pressure and temperature exposures.
2019,
Pubmed
Cottin,
Sustained hydrostatic pressure tolerance of the shallow water shrimp Palaemonetes varians at different temperatures: insights into the colonisation of the deep sea.
2012,
Pubmed
Croniger,
Mice with a deletion in the gene for CCAAT/enhancer-binding protein beta have an attenuated response to cAMP and impaired carbohydrate metabolism.
2001,
Pubmed
Davidson,
Corset: enabling differential gene expression analysis for de novo assembled transcriptomes.
2014,
Pubmed
DeLong,
Adaptation of the membrane lipids of a deep-sea bacterium to changes in hydrostatic pressure.
1985,
Pubmed
Denisov,
Structure and chemistry of cytochrome P450.
2005,
Pubmed
Deshaies,
RING domain E3 ubiquitin ligases.
2009,
Pubmed
Feder,
Thermophysiology: tempeature biology of animals.
1988,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Harnik,
Extinctions in ancient and modern seas.
2012,
Pubmed
Kanehisa,
KEGG for linking genomes to life and the environment.
2008,
Pubmed
Lan,
Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas.
2017,
Pubmed
Li,
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
2011,
Pubmed
Li,
Characteristics of the Copper,Zinc Superoxide Dismutase of a Hadal Sea Cucumber (Paelopatides sp.) from the Mariana Trench.
2018,
Pubmed
,
Echinobase
Love,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
2014,
Pubmed
Mellman,
Endocytosis and molecular sorting.
1996,
Pubmed
Miller,
Molecular phylogeny of extant Holothuroidea (Echinodermata).
2017,
Pubmed
,
Echinobase
Morris,
Acute combined pressure and temperature exposures on a shallow-water crustacean: novel insights into the stress response and high pressure neurological syndrome.
2015,
Pubmed
Oger,
The many ways of coping with pressure.
2010,
Pubmed
Oliver,
Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin.
2010,
Pubmed
,
Echinobase
Peck,
Thermal limits of burrowing capacity are linked to oxygen availability and size in the Antarctic clam Laternula elliptica.
2007,
Pubmed
Peralta,
Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence.
2010,
Pubmed
Phadtare,
Cold-shock response and cold-shock proteins.
1999,
Pubmed
Pinsky,
Marine taxa track local climate velocities.
2013,
Pubmed
Qiu,
The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones.
2006,
Pubmed
Raup,
Mass extinctions in the marine fossil record.
1982,
Pubmed
Rossi,
The proteasome inhibitor bortezomib is a potent inducer of zinc finger AN1-type domain 2a gene expression: role of heat shock factor 1 (HSF1)-heat shock factor 2 (HSF2) heterocomplexes.
2014,
Pubmed
Schmid,
Role of cold shock proteins in growth of Listeria monocytogenes under cold and osmotic stress conditions.
2009,
Pubmed
Siebenaller,
The effects of the deep-sea environment on transmembrane signaling.
2002,
Pubmed
Somero,
Adaptations to high hydrostatic pressure.
1992,
Pubmed
Somero,
Biochemical ecology of deep-sea animals.
1992,
Pubmed
Sun,
Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes.
2017,
Pubmed
Thatje,
On the origin of Antarctic marine benthic community structure.
2005,
Pubmed
Winter,
Exploring the temperature-pressure configurational landscape of biomolecules: from lipid membranes to proteins.
2005,
Pubmed
Xie,
Enhancing the Adaptability of the Deep-Sea Bacterium Shewanella piezotolerans WP3 to High Pressure and Low Temperature by Experimental Evolution under H2O2 Stress.
2018,
Pubmed
Yang,
RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.
2016,
Pubmed
,
Echinobase
Yayanos,
A study of the effects of hydrostatic pressure on macromolecular synthesis in Escherichia coli.
1969,
Pubmed
Zhang,
Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species.
2017,
Pubmed
Zhang,
Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent.
2017,
Pubmed
Zheng,
Insights into deep-sea adaptations and host-symbiont interactions: A comparative transcriptome study on Bathymodiolus mussels and their coastal relatives.
2017,
Pubmed
