Systems Biology of Plant Senescence and Death: How do plants know when to die and how to die?

Hong Gil Nam
Hong Gil Nam
DGIST, Korea
16:10~17:00,November 22nd, 2013


As we see from the death of whole rice field in autumn and of autumn leaves, plants and their organs age, senesce and die. Plant senescence is one of the most magnificent developmental events that we encounter in nature and is regarded as an evolutionarily acquired process critical for plants’ fitness. One of our main research interests is to understand how plants know when to die and how to die. We, thus, have isolated many key molecular components involved in this process and have been trying to understand the process at the systems level. As an example, we identified the trifurcate feed forward pathway for age-dependent cell death involving EIN2, ORE1, and miR164 (Science, 2009), which revealed a fundamental characteristics of aging andsenescence control in plant. We found that in young stage of Arabidopsisleaves, miR164 suppress ORE1 which functions positively in aging-induced cell death. However, in old stage, EIN2 suppresses miR164 and induces ORE1 expression, which leads to age-dependent cell death in leaves. We are further extending this network module through combination of computational and experimental analysis.

Reactive oxygen species (ROS) have been implicated in age-dependent cell death, but the underlying mechanisms remain largely elusive due to its involvement in many cellular processes. Previously, we reported that a receptor kinase, RPK1, functions as a positive regulator in death process. We have now found that RPK1 facilitated the age-dependent, transient production of superoxide vesicles at the plasma membrane through its kinase activity. The action of RPK1 involves activation of calmodulin and a specific NADPH oxidase to lead to activation of senescence genes.

Another question we are asking is how the biological complexity evolved into a computing network to process such diverse biological information. Complex biological networks are composed of recurring regulatory building blocks, referred to as network motifs. Network motifs, such as feedback and feed-forward loops, serve as basic regulatory units that collectively confer computational capability of biological networks. We previously reported that a plant hormone, cytokinin, defies age-dependent cell death through two component signaling system. The signaling network of cytokinin involves 11 type B ARRs and 10 type A ARRs in Arabidopsis, which are positive and negative components in the signaling pathway, respectively. We have uncovered emergent systems properties of the ARR regulatory network composed of the entanglednegative feedback loops of the B and A type ARRs using transgenic approach as well as computationalmodeling.

Senescence can be better understood by examining the shift of functional and regulatory molecular networks throughout life history. We recently initiated examination of the life history of Arabidopsisleaf by performing next generation sequencing (NGS) for several stages of a leaf from an early age to death. We used directional total RNA-seq, mRNA-seq, and smRNA-seq to provide comprehensive multi-dimensional transcriptomes of Arabidopsisleaf during the entire lifespan. Leaf lifespan programs were accompanied by global changes of coding and non-coding RNAs, and also distinct, yet coordinated age-dependent changes in the nucleus, mitochondria, and chloroplasts. Through this study, we aim to understand age-dependent change of molecular network, its integration into aging and death, and evolution of aging and death and to provide a plausible clue to reprogram aging process.

With these experiences, we have recently launched the academy of new biology for plant life

history research in Arabidopsisand crop plants. One of our new technological challenges is establishment of phenome facility and integration of phenome data (all the aspects of morphological and physiological phenomena of growth and development) with genomic, proteomic, and metabolomic data to interlink the genetic and environmental inputs to growth and development with the understanding of the controlling mechanisms from birth to death of plants.


Research Interests:

  • Plant senescence and death
  • Animal aging 

Awards and Honors:

  • 2012:Nominated as one of “the 100 most influential Koreans for the next decade -the dreaming pioneers”, DongA Daily, Korea
  • 2011: Best Broadcast Award in Life Science (BRIC), Korean Society of Biochemistry and Molecular Biology
  • 2011: Guest Scholar ofHonor, Rural Development Administration, Korea
  • 2011: Storer Lecturer, University of California, Davis, USA
  • 2010: The National Scholar, Ministry of Education, Science & Technology and National Research Foundation of Korea
  • 2009: The 54thNational Academy ofScience Award in the field of Basic Science, National Academy of Sciences, Korea
  • 2009: POSCO TJ Park Prize in the field of Science, POSCO TJ Park Foundation, Korea