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Wei, Lei; Wang, Qing; Ning, Xuanxuan; Mu, Changkao; Wang, Chunlin; Cao, Ruiwen; Wu, Huifeng; Cong, Ming; Li, Fei; Ji, Chenglong; Zhao, Jianmin (2015): Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2 [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.846883, Supplement to: Wei, L et al. (2015): Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2. Comparative Biochemistry and Physiology Part D: Genomics & Proteomics, 13, 16-23, https://doi.org/10.1016/j.cbd.2014.12.001

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Abstract:
Ocean acidification (OA) has been found to affect an array of normal physiological processes in mollusks, especially posing a significant threat to the fabrication process of mollusk shell. In the current study, the impact of exposure to elevated pCO2 condition was investigated in mantle tissue of Crassostrea gigas by an integrated metabolomic and proteomic approach. Analysis of metabolome and proteome revealed that elevated pCO2 could affect energy metabolism in oyster C. gigas, marked by differentially altered ATP, succinate, MDH, PEPCK and ALDH levels. Moreover, the up-regulated calponin-2, tropomyosins and myosin light chains indicated that elevated pCO2 probably caused disturbances in cytoskeleton structure in mantle tissue of oyster C. gigas. This work demonstrated that a combination of proteomics and metabolomics could provide important insights into the effects of OA at molecular levels.
Keyword(s):
Animalia; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Crassostrea gigas; Gene expression (incl. proteomics); Laboratory experiment; Mollusca; Single species; South Pacific; Temperate
Further details:
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse (2015): seacarb: seawater carbonate chemistry with R. R package version 3.0.6. https://cran.r-project.org/package=seacarb
Project(s):
Ocean Acidification International Coordination Centre (OA-ICC)
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2015) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation is 2015-06-01.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1 SpeciesSpeciesWu, Huifeng
2 TreatmentTreatWu, Huifeng
3 Gene nameGeneWu, Huifeng
4 mRNA gene expression, relativemRNA expressWu, Huifeng
5 mRNA gene expression, relative, standard deviationmRNA express std dev±Wu, Huifeng
6 Temperature, waterTemp°CWu, Huifeng
7 Temperature, water, standard deviationTemp std dev±Wu, Huifeng
8 SalinitySalWu, Huifeng
9 Salinity, standard deviationSal std dev±Wu, Huifeng
10 pHpHWu, HuifengNBS scale
11 pH, standard deviationpH std dev±Wu, HuifengNBS scale
12 Carbon, inorganic, dissolvedDICµmol/kgWu, Huifeng
13 Carbon, inorganic, dissolved, standard deviationDIC std dev±Wu, Huifeng
14 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetppmvWu, HuifengCalculated using CO2SYS
15 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Wu, HuifengCalculated using CO2SYS
16 Alkalinity, totalATµmol/kgWu, HuifengCalculated using CO2SYS
17 Alkalinity, total, standard deviationAT std dev±Wu, HuifengCalculated using CO2SYS
18 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
19 pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
20 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
21 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
22 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
23 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
24 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25 Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
26 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
27 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
540 data points

Data

Download dataset as tab-delimited text — use the following character encoding:

1 
Species		2 
Treat		3 
Gene		4 
mRNA express		5 
mRNA express std dev [±]		6 
Temp [°C]		7 
Temp std dev [±]		8 
Sal		9 
Sal std dev [±]		10 
pH
(NBS scale)		11 
pH std dev [±]
(NBS scale)		12 
DIC [µmol/kg]		13 
DIC std dev [±]		14 
pCO2water_SST_wet [ppmv]
(Calculated using CO2SYS)		15 
pCO2 std dev [±]
(Calculated using CO2SYS)		16 
AT [µmol/kg]
(Calculated using CO2SYS)		17 
AT std dev [±]
(Calculated using CO2SYS)		18 
CSC flag
(Calculated using seacarb afte...)		19 
pH
(total scale, Calculated using...)		20 
CO2 [µmol/kg]
(Calculated using seacarb afte...)		21 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		22 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		23 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)		24 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)		25 
AT [µmol/kg]
(Calculated using seacarb afte...)		26 
Omega Arg
(Calculated using seacarb afte...)		27 
Omega Cal
(Calculated using seacarb afte...)
Crassostrea gigas (mollusk)ControlMyosin essential light chain1.180.6617.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlCalponin-21.110.6017.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlTropomyosin1.070.4317.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlMalate dehydrogenase, cytoplasmic, partial1.010.2017.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlAldehyde dehydrogenase, mitochondrial1.020.2717.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)OA stressMyosin essential light chain1.460.6818.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressCalponin-20.740.2018.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressTropomyosin1.050.3018.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressMalate dehydrogenase, cytoplasmic, partial0.760.0918.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressAldehyde dehydrogenase, mitochondrial1.440.5718.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)ControlcgPif971.010.2617.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlCgigas-IMSP-21.160.6317.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlCgigas-IMSP-31.000.5317.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlHypothetical protein CGI_100074581.120.6817.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)ControlCarbonic anhydrase 61.110.5417.980.9729.250.168.180.012143.1326.21427.5310.142352.3629.65278.0515.00423.51424.991967.57160.572353.992.543.99
Crassostrea gigas (mollusk)OA stresscgPif971.140.3218.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressCgigas-IMSP-21.240.4018.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressCgigas-IMSP-30.610.2918.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressHypothetical protein CGI_100074580.950.3818.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13
Crassostrea gigas (mollusk)OA stressCarbonic anhydrase 64.681.0318.140.5029.410.087.570.022377.3025.202013.4171.222369.2428.92277.4469.941986.091993.032261.6545.712371.630.721.13