Nam-Soo Jwa

Plant secretome: Unlocking secrets of the secreted proteins

Plant secretomics is a newly emerging area of the plant proteomics field. It basically describes the global study of secreted proteins into the extracellular space of plant cell or tissue at any given time and under certain conditions through various secretory mechanisms. A combination of biochemical, proteomics and bioinformatics approaches has been developed to isolate, identify and profile secreted proteins using complementary in vitro suspension‐cultured cells and in planta systems. Developed inventories of secreted proteins under normal, biotic and abiotic conditions revealed several different types of novel secreted proteins, including the leaderless secretory proteins (LSPs). On average, LSPs can account for more than 50% of the total identified secretome, supporting, as in other eukaryotes, the existence of novel secretory mechanisms independent of the classical endoplasmic reticulum‐Golgi secretory pathway, and suggesting that this non‐classical mechanism of protein expression is, for as yet unknown reasons, more massively used than in other eukaryotic systems. Plants LSPs, which seem to be potentially involved in the defense/stress responses, might have dual (extracellular and/or intracellular) roles as most of them have established intracellular functions, yet presently unknown extracellular functions. Evidence is emerging on the role of glycosylation in the apical sorting and trafficking of secretory proteins. These initial secretome studies in plants have considerably advanced our understanding on secretion of different types of proteins and their underlying mechanisms, and opened a door for comparative analyses of plant secretomes with those of other organisms. In this first review on plant secretomics, we summarize and discuss the secretome definition, the applied approaches for unlocking secrets of the secreted proteins in the extracellular fluid, the possible functional significance and secretory mechanisms of LSPs, as well as glycosylation of secreted proteins and challenges involved ahead. Further improvements in existing and developing strategies and techniques will continue to drive forward plant secretomics research to building comprehensive and confident data sets of secreted proteins. This will lead to an increased understanding on how cells couple the concerted action of secreted protein networks to their internal and external environments.

Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling.

Ozone (O(3)), a serious air pollutant, is known to significantly reduce photosynthesis, growth, and yield and to cause foliar injury and senescence. Here, integrated transcriptomics, proteomics, and metabolomics approaches were applied to investigate the molecular responses of O(3) in the leaves of 2-week-old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O(3) for a period of 24 h. On the basis of the morphological alteration of O(3)-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12, and 24 h using rice DNA microarray chip. A total of 1535 nonredundant genes showed altered expression of more than 5-fold over the control, representing 8 main functional categories. Genes involved in information storage and processing (10%) and cellular processing and signaling categories (24%) were highly represented within 1 h of O(3) treatment; transcriptional factor and signal transduction, respectively, were the main subcategories. Genes categorized into information storage and processing (17, 23%), cellular processing and signaling (20, 16%) and metabolism (18, 19%) were mainly regulated at 12 and 24 h; their main subcategories were ribosomal protein, post-translational modification, and signal transduction and secondary metabolites biosynthesis, respectively. Two-dimensional gel electrophoresis-based proteomics analyses in combination with tandem mass spectrometer identified 23 differentially expressed protein spots (21 nonredundant proteins) in leaves exposed to O(3) for 24 h compared to respective control. Identified proteins were found to be involved in cellular processing and signaling (32%), photosynthesis (19%), and defense (14%). Capillary electrophoresis-mass spectrometry-based metabolomic profiling revealed accumulation of amino acids, gamma-aminobutyric acid, and glutathione in O(3) exposed leaves until 24 h over control. This systematic survey showed that O(3) triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice.

Signalling molecules and blast pathogen attack activates rice OsPR1a and OsPR1b genes: A model illustrating components participating during defence/stress response

Abstract Recently the rice (Oryza sativa L.) OsPR1a and OsPR1b genes were primarily characterized against jasmonic acid, ethylene and protein phosphatase 2A inhibitors. The dicot PR1 are recognized as reliable marker genes in defence/stress responses, and we also propose OsPR1 as marker genes in rice, a model monocot crop genus. Therefore, to gain further insight into the expression/regulation of OsPR1 genes, we characterized their activation against signalling molecules such as salicylic acid (SA), abscisic acid (ABA) and hydrogen peroxide (H2O2), and the blast pathogen Magnaporthe grisea. Here, we report that SA and H2O2 strongly induced the mRNA level of both OsPR1 genes, whereas ABA was found to be moderately effective. These inductions were specific in nature and required a de novo synthesized protein factor. A potential interaction amongst the signalling molecules in modulating the expression of OsPR1 genes was observed. Moreover, a specific induction of OsPR1 expression in an incompatible versus compatible host-pathogen interaction was also found. Finally, based on our present and previous results, a model of OsPR1 expression/regulation has been proposed, which reveals their essential role in defence/stress responses in rice and use as potent gene markers.

Characterization of a rice (Oryza sativa L.) Bowman-Birk proteinase inhibitor: tightly light regulated induction in response to cut, jasmonic acid, ethylene and protein phosphatase 2A inhibitors.

The Bowman-Birk (BB) family of proteinase inhibitors (PI), initially reported from legume seeds, and thereafter also from wounded alfalfa and maize leaves appear to be regulated in similar ways as the extensively characterized PI I and PI II family from dicots. Here, we report a first characterization of the expression profiles of a rice (Oryza sativa L. cv. Nipponbare) BBPI gene, OsBBPI, which is part of a multigene family as demonstrated by genomic Southern hybridization. OsBBPI was found to be rapidly induced in rice seedling leaf in response to cut, exogenous jasmonic acid (JA), and two potent protein phosphatase 2A (PP2A) inhibitors, cantharidin (CN) and endothall (EN), in a light/dark-, time- and dose-dependent manner; this induction was completely inhibited by cycloheximide (CHX), indicating a requirement for de novo protein synthesis in its induction. Surprisingly, dark strongly up regulated cut-, JA-, CN-, and EN-induced OsBBPI expression, with the strongest enhancement observed with JA. A simultaneous application of a serine/threonine protein kinase inhibitor staurosporine (ST) did not affect significantly the JA-, CN-, and EN-induced OsBBPI transcript. Besides JA, it was found that the ethylene generator ethephon (ET) also had an enhancing effect on OsBBPI transcript, suggesting a direct effect of ethylene on OsBBPI expression. However, a simultaneous application of salicylic acid (SA) and abscisic acid (ABA), with JA, respectively, completely blocked OsBBPI gene expression, whereas kinetin (KN) was only partially effective. To the best of our knowledge, complete inhibition of JA-induced OsBBPI expression by SA is the first report in monocots, and with ABA in plants. Taken together, these results suggest that among the phytohormones tested here, JA and ethylene play important role(s) in regulating OsBBPI expression, with an intimate interaction with light signals. Finally, that the induced OsBBPI expression follows a kinase-signaling cascade is implied by the use of PP2A inhibitors.

Molecular cloning and mRNA expression analysis of a novel rice (Oryzasativa L.) MAPK kinase kinase, OsEDR1, an ortholog of ArabidopsisAtEDR1, reveal its role in defense/stress signalling pathways and development

Mitogen-activated protein kinase (MAPK) cascade(s) is important for plant defense/stress responses. Though MAPKs have been identified and characterized in rice (Oryza sativa L.), a monocot cereal crop research model, the first upstream component of the kinase cascade, namely MAPK kinase kinase (MAPKKK) has not yet been identified. Here we report the cloning of a novel rice gene encoding a MAPKKK, OsEDR1, designated based on its homology with the Arabidopsis MAPKKK, AtEDR1. OsEDR1, a single copy gene in the genome of rice, encodes a predicted protein with molecular mass of 113046.13 and a pI of 9.03. Using our established two-week-old rice seedling in vitro model system, we show that OsEDR1 has a constitutive expression in seedling leaves and is further up-regulated within 15 min upon wounding by cut, treatment with the global signals jasmonic acid (JA), salicylic acid (SA), ethylene (ethephon, ET), abscisic acid, and hydrogen peroxide. In addition, protein phosphatase inhibitors, fungal elicitor chitosan, drought, high salt and sugar, and heavy metals also dramatically induce its expression. Moreover, OsEDR1 expression was altered by co-application of JA, SA, and ET, and required de novo synthesized protein factor(s) in its transient regulation. Furthermore, using an in vivo system we also show that OsEDR1 responds to changes in temperature and environmental pollutants-ozone and sulfur dioxide. Finally, OsEDR1 expression varied significantly in vegetative and reproductive tissues. These results suggest a role for OsEDR1 in defense/stress signalling pathways and development.

Rice proteomics: ending phase I and the beginning of phase II.

Rice is a critically important food crop plant on our planet. It is also an excellent model plant for cereal crops, and now in position to serve as a reference plant for biofuel production. Proteomics study of rice therefore is crucial to better understand “rice” as a whole. Rice proteomics has moved well beyond the initial proteome analysis in the early to late 1990s. Since the year 2000, numerous proteomic studies have been performed in rice during growth and development and against a wide variety of environmental factors. These proteomic investigations have established the high‐resolution 2‐D reference gels of rice tissues, organs, and organelle under normal and adverse (stressed) conditions by optimizing suitable, reproducible systems for gel, and MS‐based proteomic techniques, which “rejuvenated” the rice proteome field. This constituted the “phase I” in rice proteomics, and resulted in rice being labeled as the “cornerstone” of cereal food crop proteomes. Now, we are in position to state that rice proteomics today marks the “beginning of phase II”. This is due to the fact that rice researchers are capable of digging deeper into the rice proteome, mapping PTMs (in particular reversible protein phosphorylation), performing inter‐ and intra‐species comparisons, integrating proteomics data with other “omic” technologies‐generated data, and probing the functional aspect of individual proteins. These advancements and their impact on the future of rice proteomics are the focus of this review.

Effects of signaling molecules, protein phosphatase inhibitors and blast pathogen (Magnaporthe grisea) on the mRNA level of a rice (Oryza sativa L.) phospholipid hydroperoxide glutathione peroxidase (OsPHGPX) gene in seedling leaves

With a specific focus on rice self-defense response(s), the effects of global signaling molecules, jasmonic acid (JA), salicylic acid (SA), abscisic acid (ABA), and ethylene (using the ethylene generator, ethephon), and protein phosphatase (PP) inhibitors, cantharidin and endothall on expression of a rice phospholipid hydroperoxide glutathione peroxidase (OsPHGPX) gene in rice seedling leaves were investigated. We provide first evidence for a potent up-regulation of the OsPHGPX mRNA accumulation by these signaling molecules and PP inhibitors that strongly suggest its potential role in defense/stress. The OsPHGPX gene also showed a weak constitutive expression and responsiveness to cut. These inductions were influenced by light signal(s), and did not show a requirement for de novo synthesized protein factor(s). A potential interaction amongst these signaling molecules, especially JA, SA, ABA and kinetin, in modulating the OsPHGPX expression was found. The blast pathogen, Magnaporthe grisea also elicited the accumulation of OsPHGPX mRNA in leaves. This is a first systematic report in rice (and in plants) demonstrating the inducible nature (and expression) of the OsPHGPX gene by a variety of defense/stress-related stimuli, and modulation by the PPs of the kinase-signaling cascade(s).

Systematic secretome analyses of rice leaf and seed callus suspension-cultured cells: workflow development and establishment of high-density two-dimensional gel reference maps.

Secreted proteins control a multitude of biological and physiological processes in multicellular organisms such as plants. Identification of secreted proteins in reference plants like Arabidopsis and rice under normal growth conditions and adverse environmental conditions will help better understand the secretory pathways. Here, we have performed a systematic in planta and in vitro analyses of proteins secreted by rice leaves (in planta) and seed callus suspension-cultured cells (SCCs; in vitro), respectively, using a combination of biochemical and two-dimensional gel electrophoresis (2-DGE) coupled with liquid chromatography mass spectrometry analyses. Secreted proteins prepared from either leaves or SCCs medium were essentially free from contamination of intracellular proteins as judged by biochemical and Western blot analyses. 2-DGE analyses of secreted proteins collectively identified 222 protein spots with only 6 protein spots common to both in planta and in vitro derived data sets. Data were used to establish high-resolution and high-density 2-D gel reference maps for both in planta and in vitro secreted proteins. Identified proteins belonged to 11 (in planta) and 6 (in vitro) functional classes. Proteins involved in carbon metabolism (33%) and cell wall metabolism having plant defense mechanism (18%) were highly represented in the in planta secreted proteins accounting for 51% of total identified proteins, whereas proteins of cell wall metabolism having plant defense mechanism (64%) were predominant in the in vitro secreted proteins. Interestingly, secreted proteins possessing signal peptides were significantly lower in an in planta (27%) prepared secreted protein population than in vitro (76%) as predicted by SignalP prediction tool, implying the notion that plant might possess yet unidentified secretory pathway(s) in addition to the classical endoplasmic reticulum/Golgi pathway. Taken together, this systematic study provides evidence for (i) significant difference in protein population secreted in planta and in vitro suggesting both approaches are complementary, (ii) identification of many novel and previously known secreted proteins, and (iii) the presence of large number of functionally diverse proteins secreted in planta and in vitro.

Rice Mitogen-Activated Protein Kinase Interactome Analysis Using the Yeast Two-Hybrid System

Mitogen-activated protein kinase (MAPK) cascades support the flow of extracellular signals to intracellular target molecules and ultimately drive a diverse array of physiological functions in cells, tissues, and organisms by interacting with other proteins. Yet, our knowledge of the global physical MAPK interactome in plants remains largely fragmented. Here, we utilized the yeast two-hybrid system and coimmunoprecipitation, pull-down, bimolecular fluorescence complementation, subcellular localization, and kinase assay experiments in the model crop rice (Oryza sativa) to systematically map what is to our knowledge the first plant MAPK-interacting proteins. We identified 80 nonredundant interacting protein pairs (74 nonredundant interactors) for rice MAPKs and elucidated the novel proteome-wide network of MAPK interactors. The established interactome contains four membrane-associated proteins, seven MAP2Ks (for MAPK kinase), four MAPKs, and 59 putative substrates, including 18 transcription factors. Several interactors were also validated by experimental approaches (in vivo and in vitro) and literature survey. Our results highlight the importance of OsMPK1, an ortholog of tobacco (Nicotiana benthamiana) salicyclic acid-induced protein kinase and Arabidopsis (Arabidopsis thaliana) AtMPK6, among the rice MAPKs, as it alone interacts with 41 unique proteins (51.2% of the mapped MAPK interaction network). Additionally, Gene Ontology classification of interacting proteins into 34 functional categories suggested MAPK participation in diverse physiological functions. Together, the results obtained essentially enhance our knowledge of the MAPK-interacting protein network and provide a valuable research resource for developing a nearly complete map of the rice MAPK interactome.

Differential induction of three pathogenesis-related genes, PR10, PR1b and PR5 by the ethylene generator ethephon under light and dark in rice (Oryza sativa L.) seedlings

Summary Ethylene has been shown to be involved in triggering pathogenesis-related (PR) gene expression mainly in dicotyledonous species; however, less attention has been devoted identifying and characterizing PR genes in rice ( Oryza sativa L.), a monocot and a model of cereal crop genera. Here, we demonstrate that ethylene induces at least three important rice PR genes, the PR10, PR1 basic ( PR1b ), and PR5 genes in rice (cv. Nipponbare) seedling leaf, upon treatment with the ethylene generator, ethephon (ET), in a light-, time- and dose-dependent manner. Induction of these PR genes was partially blocked by cycloheximide (CHX), a eukaryotic cytoplasmic protein synthesis inhibitor, which indicates an involvement of cytoplasmic de novo protein synthesis in their induction. These results clearly indicate a dynamic role for ethylene in PR genes induction in rice.