ROSMETER: a bioinformatic tool for the identification of transcriptomic imprints related to reactive oxygen species type and origin provides new insights into stress responses.
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 redox-sensitive 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.
Postharvest Science of Fresh Produce , Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel.
Shilo
S
Rosenwasser
Robert
R
Fluhr
Janak Raj
JR
Joshi
Noam
N
Leviatan
Noa
N
Sela
Amotz
A
Hetzroni
Haya
H
Friedman
D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology*; D019295:Computational Biology / Q000379:methods*; D003624:Darkness; D018506:Gene Expression Regulation, Plant; D049452:Green Fluorescent Proteins / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010084:Oxidation-Reduction; D018384:Oxidative Stress / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D017382:Reactive Oxygen Species / Q000378:metabolism*; D012984:Software; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
D017382:Reactive Oxygen Species; D049452:Green Fluorescent Proteins