Callister Stephen J, Parnell J Jacob, Pfrender Michael E, Hashsham Syed A
Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
BMC Res Notes. 2009 Mar 19;2:43. doi: 10.1186/1756-0500-2-43.
Most transcriptional activity is a result of environmental variability. This cause (environment) and effect (gene expression) relationship is essential to survival in any changing environment. The specific relationship between environmental perturbation and gene expression - and stability of the response - has yet to be measured in detail. We describe a method to quantitatively relate perturbation magnitude to response at the level of gene expression. We test our method using Saccharomyces cerevisiae as a model organism and osmotic stress as an environmental stress.
Patterns of gene expression were measured in response to increasing sodium chloride concentrations (0, 0.5, 0.7, 1.0, and 1.2 M) for sixty genes impacted by osmotic shock. Expression of these genes was quantified over five time points using reverse transcriptase real-time polymerase chain reaction. Magnitudes of cumulative response for specific pathways, and the set of all genes, were obtained by combining the temporal response envelopes for genes exhibiting significant changes in expression with time. A linear relationship between perturbation magnitude and response was observed for the range of concentrations studied.
This study develops a quantitative approach to describe the stability of gene response and pathways to environmental perturbation and illustrates the utility of this approach. The approach should be applicable to quantitatively evaluate the response of organisms via the magnitude of response and stability of the transcriptome to environmental change.
大多数转录活动是环境变异性的结果。这种原因（环境）与效应（基因表达）的关系对于在任何变化的环境中生存至关重要。环境扰动与基因表达之间的特定关系以及反应的稳定性尚未得到详细测量。我们描述了一种在基因表达水平上定量关联扰动幅度与反应的方法。我们以酿酒酵母作为模式生物，以渗透胁迫作为环境压力来测试我们的方法。
针对受渗透冲击影响的60个基因，测量了其对氯化钠浓度增加（0、0.5、0.7、1.0和1.2 M）的基因表达模式。使用逆转录实时聚合酶链反应在五个时间点对这些基因的表达进行了定量。通过结合随时间表达有显著变化的基因的时间反应包络，获得了特定途径以及所有基因的累积反应幅度。在所研究的浓度范围内，观察到扰动幅度与反应之间存在线性关系。
本研究开发了一种定量方法来描述基因反应和环境扰动途径的稳定性，并说明了该方法的实用性。该方法应适用于通过转录组对环境变化的反应幅度和稳定性来定量评估生物体的反应。
