Comparative microarray analysis of programmed cell death induced by proteasome malfunction and hypersensitive response in plants q Moonil Kim a,1 , Sanghyeob Lee b,1 , Kyoungsook Park a , Eun-Ju Jeong a , Choong-Min Ryu c , Doil Choi b , Hyun-Sook Pai d, * a BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Republic of Korea b Laboratory of Plant Genomics, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Republic of Korea c Laboratory of Microbial Genomics, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Republic of Korea d Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea Received 16 January 2006 Available online 9 February 2006 Abstract Programmed cell death (PCD) plays a pivotal role in the elimination of injured or unwanted cells during diverse physiological and developmental conditions in organisms. However in contrast to the animal system, signaling pathways and molecular mechanism of PCD are largely unknown in plants. We previously reported that silencing of NbPAF encoding the a6 subunit of 20S proteasome by virus-induced gene silencing activated programmed cell death in plants by inactivating proteasome function. In this study, we analyzed global gene expression profile of PCD induced by suppression of NbPAF expression, in comparison with that of hypersensitive response (HR)-induced PCD, using a cDNA microarray representing 4685 hot pepper genes. HR is a well-characterized PCD program in plants, which occurs in response to pathogen infection. The microarray analyses identified 247 genes whose gene expression was differentially modulated during PCD activated by NbPAF depletion or HR. Most of the genes that were up-regulated during the NbPAF-mediated PCD, including the ubiquitin/proteasome pathway-related genes, were down-regulated during HR cell death. In contrast, transcription of many defense-related genes, transcription factor genes, and photosynthesis-related genes remained unchanged or repressed during NbPAF-mediated PCD, while it was highly induced during HR cell death. Only a small number of genes including antioxidant-related genes and proteases were found to be up-regulated during induction of PCD by both proteasome inactivation and HR. Based on these results, these two PCD pathways appear to be differentially regulated, but some overlapping mechanism exists, which involves core regulators of plant PCD. Ó 2006 Elsevier Inc. All rights reserved. Keywords: a6 Subunit of 20S proteasome; cDNA microarray; Gene expression; Hot pepper; Hypersensitive response; Virus-induced gene silencing Programmed cell death (PCD) is a genetically regulated biological process that plays a crucial role in the homeosta- sis of multicellular organisms [1]. PCD is essential for many developmental processes in plants, such as petal senes- cence, xylogenesis, aerenchyma formation, endosperm development, and for response of plants to pathogen infec- tion as well [2]. While cell death pathways in animal cells have been well characterized, relatively little is known about the molecular mechanism of PCD in plants. Particu- larly, plant homologs of the key regulators of animal apop- tosis, such as caspases and Bcl-2 family members, have not been identified yet. The selective degradation or stabilization of intracellular proteins by ubiquitin-proteasome-dependent pathways is essential for the regulation of many cellular processes including development, cell cycle, cell growth, and apoptosis [3]. Studies have demonstrated that ubiquitin-proteasome 0006-291X/$ - see front matter Ó 2006 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2006.01.176 q Abbreviations: HR, hypersensitive response; NbPAF, Nicotiana benth- amiana proteasome a6 subunit; PCD, programmed cell death; ROS, reactive oxygen species; VIGS, virus-induced gene silencing. * Corresponding author. Fax: +82 2 312 5657. E-mail address: hspai@yonsei.ac.kr (H.-S. Pai). 1 These authors contributed equally to this work. www.elsevier.com/locate/ybbrc Biochemical and Biophysical Research Communications 342 (2006) 514–521 BBRC