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Park, Ohkmae K. 한국생화학분자생물학회 2004 BMB Reports Vol.37 No.1
Proteomics is a leading technology for the high-throughput analysis of proteins on a genome-wide scale. With the completion of genome sequencing projects and the development of analytical methods for protein characterization, proteomics has become a major field of functional genomics. The initial objective of proteomics was the large-scale identification of all protein species in a cell or tissue. The applications are currently being extended to analyze various functional aspects of proteins such as post-translational modifications, protein-protein interactions, activities and structures. Whereas the proteomics research is quite advanced in animals and yeast as well as Escherichia coli, plant proteomics is only at the initial phase. Major studies of plant proteomics have been reported on subcellular protemomes and protein complexes (e.g. proteins in the plasma membranes, chloroplasts, mitochondria and nuclei). Here several plant proteomics studies will be presented, followed by a recent work using multidimensional protein identification technology (MudPIT).
Lipases associated with plant defense against pathogens
Lee, Hye-Jung,Park, Ohkmae K. Elsevier 2019 Plant science Vol.279 No.-
<P><B>Abstract</B></P> <P>When facing microbe invaders, plants activate genetic and metabolic defense mechanisms and undergo extracellular and intracellular changes to obtain a certain level of host resistance. Dynamic adjustment and adaptation occur in structures containing lipophilic compounds and cellular metabolites. Lipids encompassing fatty acids, fatty acid-based polymers, and fatty acid derivatives are part of the fundamental architecture of cells and tissues and are essential compounds in numerous biological processes. Lipid-associated plant defense responses are mostly facilitated by the activation of lipases (lipid hydrolyzing proteins), which cleave or transform lipid substrates in various subcellular compartments. In this review, several types of plant defense-associated lipases are described, including their molecular aspects, enzymatic actions, cellular functions, and possible functional relevance in plant defense. Defensive roles are discussed considering enzyme properties, lipid metabolism, downstream regulation, and phenotypic traits in loss-of-function mutants.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Lipases belonging to the α/β-hydrolase superfamily are structurally diverse. </LI> <LI> Lipases are expressed and activated in plant cells upon pathogen infection. </LI> <LI> Lipases play distinct roles in plant-microbe interactions. </LI> <LI> Plant immunity involves the regulation of defense-associated lipases. </LI> </UL> </P>
Munch, David,Rodriguez, Eleazar,Bressendorff, Simon,Park, Ohkmae K,Hofius, Daniel,Petersen, Morten Landes Bioscience 2014 AUTOPHAGY Vol.10 No.9
<P>Autophagy is a homeostatic degradation and recycling process that is also involved in defense against microbial pathogens and in certain forms of cellular suicide. Autophagy has been proposed to negatively regulate plant immunity-associated cell death related to the hypersensitive response (HR), as older autophagy-deficient mutants are unable to contain this type of cell death 5 to 10 d after infection. Such spreading cell death was found to require NPR1 (nonexpressor of PR genes 1), but surprisingly did not occur in younger atg mutants. In contrast, we find that npr1 mutants are not impaired in rapid programmed cell death activation upon pathogen recognition. Furthermore, our molecular evidence suggests that the NPR1-dependent spreading cell death in older atg mutants may originate from an inability to cope with excessive accumulation of ubiquitinated proteins and ER stress which derive from salicylic acid (SA)-dependent signaling (e.g., systemic acquired resistance). We also demonstrate that both senescence and immunity-related cell death seen in older atg mutants can be recapitulated in younger atg mutants primed with ER stress. We therefore propose that the reduction in SA signaling caused by npr1 loss-of-function is sufficient to alleviate the stress levels accumulated during aging in autophagy deficient cells which would otherwise become insurmountable and lead to uncontrolled cell death.</P>
Lee, Jeong Hwan,Hong, Sung Myun,Yoo, Seong Jeon,Park, Ohkmae K.,Lee, Jong Seob,Ahn, Ji Hoon Blackwell Publishing Ltd 2006 Physiologia plantarum Vol.126 No.4
<P>Genetic analyses have identified four major genetic pathways which control the timing of floral transitions in <I>Arabidopsis</I>. The floral promotion or inhibitory signals from these distinct pathways ultimately converge into a subset of genes, commonly known as the floral integrators, such that the plants are compelled either to switch into a flowering phase or to remain in the vegetative stage. In this review, we have discussed the recent findings regarding cross-talk between floral promotion pathways and flowering locus T and suppressor of overexpression of <I>Constans 1</I>, the major floral integrators within <I>Arabidopsis</I>. The spatial regulation of these integrators has also been discussed, as these spatial patterns may help us to understand the manner in which floral inductive signals are transmitted. We have also discussed conservation and divergence with regard to the regulation of floral integrators between <I>Arabidopsis</I> and rice. Finally, we have provided a series of insights into the complex signaling network which coordinates plant development.</P>
Isolation of the Arabidopsis phosphoproteome using a biotin-tagging approach.
Kwon, Sun Jae,Choi, Eun Young,Seo, Jong Bok,Park, Ohkmae K Korean Society for Molecular Biology 2007 Molecules and cells Vol.24 No.2
<P>Protein phosphorylation plays a key role in signal transduction in cells. Since phosphoproteins are present in low abundance, enrichment methods are required for their purification and analysis. Chemical derivatization strategies have been devised for enriching phosphoproteins and phosphopeptides. In this report, we employed a strategy that replaces the phosphate moieties on serine and threonine residues with a biotin-containing tag via a series of chemical reactions. Ribulose 1,5-bis-phosphate carboxylase/oxygenase (RUBISCO)-depleted protein extracts prepared from Arabidopsis seedlings were chemically modified for 'biotin-tagging'. The biotinylated (previously phosphorylated) proteins were then selectively isolated by avidin-biotin affinity chromatography, followed by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). This led to the identification of 31 protein spots, representing 18 different proteins, which are implicated in a variety of cellular processes. Despite its current technical limitations, with further improvements in tools and techniques this strategy may be developed into a useful approach.</P>
Kwon, Soon Il,Cho, Hong Joo,Kim, Sung Ryul,Park, Ohkmae K. American Society of Plant Biologists 2013 PLANT PHYSIOLOGY - Vol.161 No.4
<P><I>A Rab GTPase protein connects autophagy with plant immunity-triggered hypersensitive response and programmed cell death.</I></P>
Sakuraba, Yasuhito,Lee, Sang-Hwa,Kim, Ye-Sol,Park, Ohkmae K.,Hö,rtensteiner, Stefan,Paek, Nam-Chon Oxford University Press 2014 Journal of experimental botany Vol.65 No.14
<P>Plant autophagy, one of the essential proteolysis systems, balances proteome and nutrient levels in cells of the whole plant. Autophagy has been studied by analysing <I>Arabidopsis thaliana</I> autophagy-defective <I>atg</I> mutants, but the relationship between autophagy and chlorophyll (Chl) breakdown during stress-induced leaf yellowing remains unclear. During natural senescence or under abiotic-stress conditions, extensive cell death and early yellowing occurs in the leaves of <I>atg</I> mutants. A new finding is revealed that <I>atg5</I> and <I>atg7</I> mutants exhibit a functional stay-green phenotype under mild abiotic-stress conditions, but leaf yellowing proceeds normally in wild-type leaves under these conditions. Under mild salt stress, <I>atg5</I> leaves retained high levels of Chls and all photosystem proteins and maintained a normal chloroplast structure. Furthermore, a double mutant of <I>atg5</I> and non-functional stay-green <I>nonyellowing1-1</I> (<I>atg5 nye1-1</I>) showed a much stronger stay-green phenotype than either single mutant. Taking these results together, it is proposed that autophagy functions in the non-selective catabolism of Chls and photosynthetic proteins during stress-induced leaf yellowing, in addition to the selective degradation of Chl–apoprotein complexes in the chloroplasts through the senescence-induced STAY-GREEN1/NYE1 and Chl catabolic enzymes.</P>