TY - JOUR
T1 - ROSMETER
T2 - A bioinformatic tool for the identification of transcriptomic imprints related to reactive oxygen species type and origin provides new insights into stress responses
AU - Rosenwasser, Shilo
AU - Fluhr, Robert
AU - Joshi, Janak Raj
AU - Leviatan, Noam
AU - Sela, Noa
AU - Hetzroni, Amotz
AU - Friedman, Haya
N1 - Binational Agricultural Research and Development Fund-Cornell [CB-9025-05]; Israel Science Foundation [1008/11]This work was supported by the Binational Agricultural Research and Development Fund-Cornell (grant no. CB-9025-05 to H.F.) and by the Israel Science Foundation (grant no. 1008/11 to R.F.). This is contribution no. 639/12 from the Agricultural Research Organization, Bet Dagan, Israel.
PY - 2013/10
Y1 - 2013/10
N2 - The chemical identity of the reactive oxygen species (ROS) and its subcellular origin will leave a specific imprint on the transcriptome response. In order to facilitate the appreciation of ROS signaling, we developed a tool that is tuned to qualify this imprint. Transcriptome data from experiments in Arabidopsis (Arabidopsis thaliana) for which the ROS type and organelle origin are known were compiled into indices and made accessible by a Web-based interface called ROSMETER. The ROSMETER algorithm uses a vector-based algorithm to portray the ROS signature for a given transcriptome. The ROSMETER platform was applied to identify the ROS signatures profiles in transcriptomes of senescing plants and of those exposed to abiotic and biotic stresses. An unexpected highly significant ROS transcriptome signature of mitochondrial stress was detected during the early presymptomatic stages of leaf senescence, which was accompanied by the specific oxidation of mitochondria-targeted redoxsensitive green fluorescent protein probe. The ROSMETER analysis of diverse stresses revealed both commonalties and prominent differences between various abiotic stress conditions, such as salt, cold, ultraviolet light, drought, heat, and pathogens. Interestingly, early responses to the various abiotic stresses clustered together, independent of later responses, and exhibited negative correlations to several ROS indices. In general, the ROS transcriptome signature of abiotic stresses showed limited correlation to a few indices, while biotic stresses showed broad correlation with multiple indices. The ROSMETER platform can assist in formulating hypotheses to delineate the role of ROS in plant acclimation to environmental stress conditions and to elucidate the molecular mechanisms of the oxidative stress response in plants.
AB - The chemical identity of the reactive oxygen species (ROS) and its subcellular origin will leave a specific imprint on the transcriptome response. In order to facilitate the appreciation of ROS signaling, we developed a tool that is tuned to qualify this imprint. Transcriptome data from experiments in Arabidopsis (Arabidopsis thaliana) for which the ROS type and organelle origin are known were compiled into indices and made accessible by a Web-based interface called ROSMETER. The ROSMETER algorithm uses a vector-based algorithm to portray the ROS signature for a given transcriptome. The ROSMETER platform was applied to identify the ROS signatures profiles in transcriptomes of senescing plants and of those exposed to abiotic and biotic stresses. An unexpected highly significant ROS transcriptome signature of mitochondrial stress was detected during the early presymptomatic stages of leaf senescence, which was accompanied by the specific oxidation of mitochondria-targeted redoxsensitive green fluorescent protein probe. The ROSMETER analysis of diverse stresses revealed both commonalties and prominent differences between various abiotic stress conditions, such as salt, cold, ultraviolet light, drought, heat, and pathogens. Interestingly, early responses to the various abiotic stresses clustered together, independent of later responses, and exhibited negative correlations to several ROS indices. In general, the ROS transcriptome signature of abiotic stresses showed limited correlation to a few indices, while biotic stresses showed broad correlation with multiple indices. The ROSMETER platform can assist in formulating hypotheses to delineate the role of ROS in plant acclimation to environmental stress conditions and to elucidate the molecular mechanisms of the oxidative stress response in plants.
UR - http://www.scopus.com/inward/record.url?scp=84885205778&partnerID=8YFLogxK
U2 - https://doi.org/10.1104/pp.113.218206
DO - https://doi.org/10.1104/pp.113.218206
M3 - مقالة
C2 - 23922270
SN - 0032-0889
VL - 163
SP - 1071
EP - 1083
JO - Plant Physiology
JF - Plant Physiology
IS - 2
ER -