Genome-wide transcription profiles reveal genotype-dependent responses of biological pathways and gene-families in Daphnia exposed to single and mixed stressors.
Genome-wide transcription profiles reveal genotype-dependent responses of biological pathways and gene-families in Daphnia exposed to single and mixed stressors.
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DOI：
10.1021/es4053363
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发表时间：
2014-03-18
影响因子：
11.4
通讯作者：
De Schamphelaere, Karel A. C.
中科院分区：
文献类型：
--
作者：
De Coninck, Dieter I. M.;Asselman, Jana;Glaholt, Stephen;Janssen, Colin R.;Colhourne, John K.;Shaw, Joseph R.;De Schamphelaere, Karel A. C.
本研究调查了实现基于全基因组转录的方法的可能性和局限性，该方法考虑了遗传和环境变异，以更好地了解自然种群对应激源的反应。当将两种不同的水蚤基因型（镉敏感型和耐镉型）暴露于镉、有毒蓝藻绿微囊藻及其混合物时，我们发现转录组水平的观察结果并不总是解释更高水平（生长、繁殖）的观察结果。例如，虽然镉在机体水平上引起了不利影响，但镉暴露后几乎没有基因的差异表达。此外，我们确定了氧化应激和多不饱和脂肪酸代谢相关途径，以及胰蛋白酶和神经rexin IV基因家族，作为微囊藻耐受性基因型差异的潜在原因。此外，应激源混合物的全基因组转录组学数据通过评估两个应激源在基因表达水平上与独立作用基线模型之间的相互作用，可以更好地理解混合反应。该方法表明，泛醌途径、MAPK丝氨酸-苏氨酸蛋白激酶和胶原基因家族中富集了在应激源混合物下表达反应中具有交互作用的基因，而转录和翻译相关途径和基因家族在应激源混合物下的交互反应中大多与基因型差异有关。总的来说，我们的研究结果表明，我们采用的方法可以进一步改善转录组学方法在不良结果途径框架中的可能性和局限性的表征，并预测自然种群的多应激源效应。
The present study investigated the possibilities and limitations of implementing a genome-wide transcription-based approach that takes into account genetic and environmental variation to better understand the response of natural populations to stressors. When exposing two different Daphnia pulex genotypes (a cadmium-sensitive and a cadmium-tolerant one) to cadmium, the toxic cyanobacteria Microcystis aeruginosa, and their mixture, we found that observations at the transcriptomic level do not always explain observations at a higher level (growth, reproduction). For example, although cadmium elicited an adverse effect at the organismal level, almost no genes were differentially expressed after cadmium exposure. In addition, we identified oxidative stress and polyunsaturated fatty acid metabolism-related pathways, as well as trypsin and neurexin IV gene-families as candidates for the underlying causes of genotypic differences in tolerance to Microcystis. Furthermore, the whole-genome transcriptomic data of a stressor mixture allowed a better understanding of mixture responses by evaluating interactions between two stressors at the gene-expression level against the independent action baseline model. This approach has indicated that ubiquinone pathway and the MAPK serine-threonine protein kinase and collagens gene-families were enriched with genes showing an interactive effect in expression response to exposure to the mixture of the stressors, while transcription and translation-related pathways and gene-families were mostly related with genotypic differences in interactive responses to this mixture. Collectively, our results indicate that the methods we employed may improve further characterization of the possibilities and limitations of transcriptomics approaches in the adverse outcome pathway framework and in predictions of multistressor effects on natural populations.
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影响因子：
4.5
作者：
David, Rhiannon M.;Dakic, Vanja;Chipman, J. Kevin
通讯作者：
Chipman, J. Kevin
影响因子：
11.4
作者：
Connon, Richard;Hooper, Helen L.;Callaghan, Amanda
通讯作者：
Callaghan, Amanda
影响因子：
2.7
作者：
DeMott, WR;Muller-Navarra, DC
通讯作者：
Muller-Navarra, DC
影响因子：
11.4
作者：
Asselman, Jana;De Coninck, Dieter I. M.;Glaholt, Stephen;Colbourne, John K.;Janssen, Cohn R.;Shaw, Joseph R.;De Schamphelaere, Karel A. C.
通讯作者：
De Schamphelaere, Karel A. C.
DOI：
10.1126/science.1197761
发表时间：
2011-02-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Colbourne JK;Pfrender ME;Gilbert D;Thomas WK;Tucker A;Oakley TH;Tokishita S;Aerts A;Arnold GJ;Basu MK;Bauer DJ;Cáceres CE;Carmel L;Casola C;Choi JH;Detter JC;Dong Q;Dusheyko S;Eads BD;Fröhlich T;Geiler-Samerotte KA;Gerlach D;Hatcher P;Jogdeo S;Krijgsveld J;Kriventseva EV;Kültz D;Laforsch C;Lindquist E;Lopez J;Manak JR;Muller J;Pangilinan J;Patwardhan RP;Pitluck S;Pritham EJ;Rechtsteiner A;Rho M;Rogozin IB;Sakarya O;Salamov A;Schaack S;Shapiro H;Shiga Y;Skalitzky C;Smith Z;Souvorov A;Sung W;Tang Z;Tsuchiya D;Tu H;Vos H;Wang M;Wolf YI;Yamagata H;Yamada T;Ye Y;Shaw JR;Andrews J;Crease TJ;Tang H;Lucas SM;Robertson HM;Bork P;Koonin EV;Zdobnov EM;Grigoriev IV;Lynch M;Boore JL
通讯作者：
Boore JL