Characterization of proteins responsive to gibberellin in the leaf-sheath of rice (Oryza sativa L.) seedling using proteome analysis

CRISPR/Cas9 Directed Mutagenesis of OsGA20ox2 in High Yielding Basmati Rice (Oryza sativa L.) Line and Comparative Proteome Profiling of Unveiled Changes Triggered by Mutations

In rice, semi-dwarfism is among the most required characteristics, as it facilitates better yields and offers lodging resistance. Here, semi-dwarf rice lines lacking any residual transgene-DNA and off-target effects were generated through CRISPR/Cas9-guided mutagenesis of the OsGA20ox2 gene in a high yielding Basmati rice line, and the isobaric tags for relative and absolute quantification (iTRAQ) strategy was utilized to elucidate the proteomic changes in mutants. The results indicated the reduced gibberellins (GA₁ and GA₄) levels, plant height (28.72%), and flag leaf length, while all the other traits remained unchanged. The OsGA20ox2 expression was highly suppressed, and the mutants exhibited decreased cell length, width, and restored their plant height by exogenous GA₃ treatment. Comparative proteomics of the wild-type and homozygous mutant line (GXU43_9) showed an altered level of 588 proteins, 273 upregulated and 315 downregulated, respectively. The identified differentially expressed proteins (DEPs) were mainly enriched in the carbon metabolism and fixation, glycolysis/gluconeogenesis, photosynthesis, and oxidative phosphorylation pathways. The proteins (Q6AWY7, Q6AWY2, Q9FRG8, Q6EPP9, Q6AWX8) associated with growth-regulating factors (GRF2, GRF7, GRF9, GRF10, and GRF11) and GA (Q8RZ73, Q9AS97, Q69VG1, Q8LNJ6, Q0JH50, and Q5MQ85) were downregulated, while the abscisic stress-ripening protein 5 (ASR5) and abscisic acid receptor (PYL5) were upregulated in mutant lines. We integrated CRISPR/Cas9 with proteomic screening as the most reliable strategy for rapid assessment of the CRISPR experiments outcomes.

Functional analysis of the HD-Zip transcription factor genes Oshox12 and Oshox14 in rice

The homeodomain-leucine zipper (HD-Zip) transcription factor family plays vital roles in plant development and morphogenesis as well as responses to biotic and abiotic stresses. In barley, a recessive mutation in Vrs1 (HvHox1) changes two-rowed barley to six-rowed barley, which improves yield considerably. The Vrs1 gene encodes an HD-Zip subfamily I transcription factor. Phylogenetic analysis has shown that the rice HD-Zip I genes Oshox12 and Oshox14 are the closest homologues of Vrs1. Here, we show that Oshox12 and Oshox14 are ubiquitously expressed with higher levels in developing panicles. Trans-activation assays in yeast and rice protoplasts demonstrated that Oshox12 and Oshox14 can bind to a specific DNA sequence, AH1 (CAAT(A/T)ATTG), and activate reporter gene expression. Overexpression of Oshox12 and Oshox14 in rice resulted in reduced panicle length and a dwarf phenotype. In addition, Oshox14 overexpression lines showed a deficiency in panicle exsertion. Our findings suggest that Oshox12 and Oshox14 may be involved in the regulation of panicle development. This study provides a significant advancement in understanding the functions of HD-Zip transcription factors in rice.

Comparative proteomics illustrates the molecular mechanism of potato (Solanum tuberosum L.) tuberization inhibited by exogenous gibberellins in vitro

Among the multiple environmental signals and hormonal factors regulating potato tuberization, gibberellins (GAs) are important components of the signaling pathways in these processes. To understand the GAs-signaling response mechanism of potato tuberization, a comparative proteomics approach was applied to analyze proteome change of potato tuberization in vitro subjected to a range of exogenous GA₃ treatments (0, 0.01, 0.1 and 1.0 μM) using two-dimensional gel electrophoresis. Quantitative image analyses showed that a total of 37 protein spots have their abundance significantly altered more than 2-fold. Among these proteins, 13 proteins were up-regulated, 13 proteins were down-regulated, one protein was absent and 10 proteins were induced after treatment by exogenous GA₃ . The MALDI-TOF/TOF MS analyses led to the identification of differentially abundant proteins that are mainly involved in bioenergy and metabolism, storage, signaling, cell defense and rescue, transcription, chaperones, transport. Furthermore, the comparative analysis of GA₃ -responsive proteome allowed for general elucidation of underlying molecular mechanisms of potato tuberization inhibited by exogenous GA₃ . Most of these cellular processes were not conducive to the transition from stolon elongation to tuber formation, including a blockage of starch and storage protein accumulation, the accelerated carbohydrate catabolism, a blockage of JA biosynthesis but an elevated endogenous GAs level, the amplification of GA₃ signal transduction by other signaling pathways, and the regulation of cellular RNA metabolism for controlling tuberization. Our results firstly integrated physiology and proteome data to provide new insights into GA₃ -signaling response mechanisms of potato tuberization in vitro.

Gibberellin-Stimulation of Rhizome Elongation and Differential GA-Responsive Proteomic Changes in Two Grass Species

Rapid and extensive rhizome development is a desirable trait for perennial grass growth and adaptation to environmental stresses. The objective of this study was to determine proteomic changes and associated metabolic pathways of gibberellin (GA) -regulation of rhizome elongation in two perennial grass species differing in rhizome development. Plants of a short-rhizome bunch-type tall fescue (TF; Festuca arundinacea; 'BR') and an extensive rhizomatous Kentucky bluegrass (KB; Poa pratensis; 'Baron') were treated with 10 μM GA3 in hydroponic culture in growth chambers. The average rhizome length in KB was significantly longer than that in TF regardless of GA3 treatment, and increased significantly with GA3 treatment, to a greater extent than that in TF. Comparative proteomic analysis using two-dimensional electrophoresis and mass spectrometry was performed to further investigate proteins and associated metabolic pathways imparting increased rhizome elongation by GA. A total of 37 and 38 differentially expressed proteins in response to GA3 treatment were identified in TF and KB plants, respectively, which were mainly involved in photosynthesis, energy and amino acid metabolism, protein synthesis, defense and cell development processes. Accelerated rhizome elongation in KB by GA could be mainly associated with the increased abundance of proteins involved in energy metabolism (glyceraldehyde-3-phosphate dehydrogenase, fructose-bisphosphate aldolase, and ATP synthase), amino acid metabolism (S-adenosylmethionine and adenosylhomocysteinase), protein synthesis (HSP90, elongation factor Tu and eukaryotic translation initiation factor 5A), cell-wall development (cell dividion cycle protein, alpha tubulin-2A and actin), and signal transduction (calreticulin). These proteins could be used as candidate proteins for further analysis of molecular mechanisms controlling rhizome growth.

Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics

Plants are considered as a simple structured organism when compared to humans and other vertebrates. The number of organs and tissue types is very limited. Instead the origin of the complexity comes from the high number and variety of plant species that exist, with >300,000 compared to 5000 in mammals. Proteomics, defined as the large-scale study of the proteins present in a tissue, cell or cellular compartment at a defined time point, was introduced in 1994. However, the first publications reported in the plant proteomics field only appeared at the beginning of the twenty-first century. Since these early years, the increase of proteomic studies in plants has only followed a linear trend. The main reason for this stems from the challenges specific to studying plants, those of protein extraction from cells with variously strengthened cellulosic cell walls, and a high abundance of interfering compounds, such as phenolic compounds and pigments located in plastids throughout the plant. Indeed, the heterogeneity between different organs and tissue types, between species and different developmental stages, requires the use of optimized plant protein extraction methods as described in this section. The second bottleneck of plant proteomics, which will not be discussed or reviewed here, is the lack of genomic information. Without sequence databases of the >300,000 species, proteomic studies of plants, especially of those that are not considered economically relevant, are impossible to accomplish.

Role of the proteome in phytohormonal signaling

Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Proteomic analysis in nitrogen-deprived Isochrysis galbana during lipid accumulation

The differentially co-expressed proteins in N-deprived and N-enriched I. galbana were comparatively analyzed by using two dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight-mass spectrometry (MALDI-TOF/TOF-MS) with the aim of better understanding lipid metabolism in this oleaginous microalga. Forty-five of the 900 protein spots showed dramatic changes in N-deprived I. galbana compared with the N-enriched cells. Of these, 36 protein spots were analyzed and 27 proteins were successfully identified. The identified proteins were classified into seven groups by their molecular functions, including the proteins related to energy production and transformation, substance metabolism, signal transduction, molecular chaperone, transcription and translation, immune defense and cytoskeleton. These altered proteins slowed cell growth and photosynthesis of I. galbana directly or indirectly, but at the same time increased lipid accumulation. Eight key enzymes involved in lipid metabolism via different pathways were identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), enolase, aspartate aminotransferase (AST), fumarate hydratase (FH), citrate synthase (CS), O-acetyl-serine lyase (OAS-L) and ATP sulfurylase (ATPS). The results suggested that the glycolytic pathway and citrate transport system might be the main routes for lipid anabolism in N-deprived I. galbana, and that the tricarboxylic acid (TCA) cycle, glyoxylate cycle and sulfur assimilation system might be the major pathways involved in lipid catabolism.

Comparative proteomic and transcriptomic approaches to address the active role of GA4 in Japanese apricot flower bud dormancy release

Hormones are closely associated with dormancy in deciduous fruit trees, and gibberellins (GAs) are known to be particularly important. In this study, we observed that GA4 treatment led to earlier bud break in Japanese apricot. To understand better the promoting effect of GA4 on the dormancy release of Japanese apricot flower buds, proteomic and transcriptomic approaches were used to analyse the mechanisms of dormancy release following GA4 treatment, based on two-dimensional gel electrophoresis (2-DE) and digital gene expression (DGE) profiling, respectively. More than 600 highly reproducible protein spots (P<0.05) were detected and, following GA4 treatment, 38 protein spots showed more than a 2-fold difference in expression, and 32 protein spots were confidently identified according to the databases. Compared with water treatment, many proteins that were associated with energy metabolism and oxidation-reduction showed significant changes after GA4 treatment, which might promote dormancy release. We observed that genes at the mRNA level associated with energy metabolism and oxidation-reduction also played an important role in this process. Analysis of the functions of the identified proteins and genes and the related metabolic pathways would provide a comprehensive proteomic and transcriptomic view of the coordination of dormancy release after GA4 treatment in Japanese apricot flower buds.

Exploring the response of rice (Oryza sativa) leaf to gibberellins: a proteomic strategy

BACKGROUND

Gibberellins (GAs) are plant-specific hormones that play a central role in the regulation of growth and development with respect to environmental variability. Plants respond to GAs signal through various biochemical and physiological processes. To better understand the response for GA signal, we carried out a proteomic study in rice (Oryza sativa L. spp. japonica) leaf.

RESULTS

Through two-dimensional gel electrophoresis (2-DE) and mass spectroscopy analysis, we identified 61 proteins as GA-responsive. These proteins were annotated in various biological functions, such as signal transduction and cell growth/division, photosynthesis and energy metabolism, protein stability and defense. Among these, photosynthetic proteins decreased while many catabolic proteins increased. In addition, GA up-regulated a variety of cell growth/division, protein stability and defense proteins such as cell division cycle protein 48, molecular chaperones, and catalases.

CONCLUSION

This is the first report that cell division cycle protein 48 may be responsible for leaf expansion after leaf sensing GA signal. The results presented here provide new insight into the mechanism of rice leaf in response to GA signal.

Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64

The NAC (NAM, ATAF1/2 and CUC2) genes are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. We describe the rice (Oryza sativa) OsNAC genes expression profiles (GEPs) under normal and water-deficit treatments (WDTs). The GEPs of the OsNAC genes were analyzed in 25 tissues covering the entire life cycle of Minghui 63. High expression levels of 17 genes were demonstrated in certain tissues under normal conditions suggesting that these genes may play important roles in specific organs. We determined that 16 genes were differentially expressed under at least 1 phytohormone (NAA, GA3, KT, SA, ABA, and JA) treatment. To investigate the GEPs in the root, leaf, and panicle of three rice genotypes [e.g., 2 near-isogenic lines (NILs) and IR64], we used two NILs from a common genetic combination backcross developed by Aday Selection and IR64. WDTs were applied using the fraction of transpirable soil water at severe, mild, and control conditions. Transcriptomic analysis using a 44K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from the two NILs under both WDTs, and the majority of the OsNAC genes that were activated were in the drought-tolerant IR77298-14-1-2-B-10 line compared with the drought-susceptible IR77298-14-1-2-B-13 or IR64. In IR77298-14-1-2-B-10, seventeen genes were very specific in their expression levels. Approximately 70 % of the genes from subgroups SNAC and NAM/CUC3 were activated in the leaf, but 37 % genes from subgroup SND were inactivated in the root compared with the control under severe stress conditions. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis.

Comparative proteomic analysis of early salt stress-responsive proteins in roots of SnRK2 transgenic rice

Background

The rice roots are highly salt-sensitive organ and primary root growth is rapidly suppressed by salt stress. Sucrose nonfermenting 1-related protein kinase2 (SnRK2) family is one of the key regulator of hyper-osmotic stress signalling in various plant cells. To understand early salt response of rice roots and identify SnRK2 signaling components, proteome changes of transgenic rice roots over-expressing OSRK1, a rice SnRK2 kinase were investigated.

Results

Proteomes were analyzed by two-dimensional electrophoresis and protein spots were identified by LC-MS/MS from wild type and OSRK1 transgenic rice roots exposed to 150 mM NaCl for either 3 h or 7 h. Fifty two early salt -responsive protein spots were identified from wild type rice roots. The major up-regulated proteins were enzymes related to energy regulation, amino acid metabolism, methylglyoxal detoxification, redox regulation and protein turnover. It is noted that enzymes known to be involved in GA-induced root growth such as fructose bisphosphate aldolase and methylmalonate semialdehyde dehydrogenase were clearly down-regulated. In contrast to wild type rice roots, only a few proteins were changed by salt stress in OSRK1 transgenic rice roots. A comparative quantitative analysis of the proteome level indicated that forty three early salt-responsive proteins were magnified in transgenic rice roots at unstressed condition. These proteins contain single or multiple potential SnRK2 recognition motives. In vitro kinase assay revealed that one of the identified proteome, calreticulin is a good substrate of OSRK1.

Conclusions

Our present data implicate that rice roots rapidly changed broad spectrum of energy metabolism upon challenging salt stress, and suppression of GA signaling by salt stress may be responsible for the rapid arrest of root growth and development. The broad spectrum of functional categories of proteins affected by over-expression of OSRK1 indicates that OSRK1 is an upstream regulator of stress signaling in rice roots. Enzymes involved in glycolysis, branched amino acid catabolism, dnaK-type molecular chaperone, calcium binding protein, Sal T and glyoxalase are potential targets of OSRK1 in rice roots under salt stress that need to be further investigated.

Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64

The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44-K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought tolerant) and IR77298-14-1-2-B-13 (drought susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis.

The differentially-expressed proteome in Zn/Cd hyperaccumulator Arabis paniculata Franch. in response to Zn and Cd

The Zn/Cd hyperaccumulator Arabis paniculata is able to tolerate high level of Zn and Cd. To clarify the molecular basis of Zn and Cd tolerance, proteomic approaches were applied to identify proteins involved in Zn and Cd stress response in A. paniculata. Plants were exposed to both low and high Zn or Cd levels for 10 d. Proteins of leaves in each treatment were separated by 2-DE (two-dimensional electrophoresis). Nineteen differentially-expressed proteins upon Zn treatments and 18 proteins upon Cd treatments were observed. Seventeen out of 19 of Zn-responsive proteins and 16 out of 18 of Cd-responsive proteins were identified using MALDI-TOF/TOF-MS (matrix-assisted laser desorption/ionization time of flight mass spectrometry). The most of identified proteins were known to function in energy metabolism, xenobiotic/antioxidant defense, cellular metabolism, protein metabolism, suggesting the responses of A. paniculata to Zn and Cd share similar pathway to certain extend. However, the different metal defense was also revealed between Zn and Cd treatment in A. paniculata. These results indicated that A. paniculata against to Zn stress mainly by enhancement of energy metabolism including auxin biosynthesis and protein metabolism to maintain plant growth and correct misfolded proteins. In the case of Cd, plants adopted antioxidative/xenobiotic defense and cellular metabolism to keep cellular redox homeostasis and metal-transportation under Cd stress.

Proteomic approach to analyze dormancy breaking of tree seeds

In forest broadleaves from the temperate zone, a large number of species exhibit seed dormancy phenomena. Tree seeds show some of the most pronounced and complicated forms of dormancy in the plant kingdom. Many seeds are deeply physiologically dormant whatever their moisture level and age. However, dormancy can usually be overcome by a cold or warm stratification for several months. The transition from seed dormancy to germination is a multi-step process. In combination with the availability of genome sequence data, proteomics has opened up enormous possibilities for identifying the total set of expressed proteins as well as expression changes during dormancy breaking. The proteomic approach used for analysis of dormancy breaking of tree seeds offers new data allowing better understanding of the mechanism of deep physiological dormancy. The results of proteomic studies on dormancy breaking and the presence of abscisic and gibberellic acids in tree seeds (beech Fagus sylvatica L., Norway maple Acer platanoides L. and sycamore Acer pseudoplatanus L.), help to explain this process better. Most of the changes in protein expression were observed at the end of stratification and in the germinated seeds. This is the most active period of dormancy breaking when seeds pass from the quiescent state to germination. The analysis of the proteins' function showed that the mechanism of seed dormancy breaking involves many processes. Energy metabolism, proteasome, transcription, protein synthesis, signal transduction and methionine metabolism proteins have a special importance.

Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor

Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

Sequence and expression analysis of the thioredoxin protein gene family in rice

Thioredoxin (Trx) proteins play important biological functions in cells by changing redox via thioldisulfide exchange. This system is especially widespread in plants. Through database search, we identified 30 potential Trx protein-encoding genes (OsTrx) in rice (Oryza sativa L.). An analysis of the complete set of OsTrx proteins is presented here, including chromosomal location, conserved motifs, domain duplication, and phylogenetic relationships. Our findings suggest that the expansion of the Trx gene family in rice, in large part, occurred due to gene duplication. A comprehensive expression profile of Trx genes family was investigated by analyzing the signal data of this family extracted from the whole genome microarray analysis of Minghui 63 and Zhenshan 97, two indica parents, and their hybrid Shanyou 63, using 27 different tissues representing the entire life cycle of rice. Results revealed specific expression of some members at germination transition as well as the 3-leaf stage during the vegetative growth phase of rice. OsTrx genes were also found to be differentially up- or down-regulated in rice seedlings subjected to treatments of phytohormones and light/dark conditions. The expression levels of the OsTrx genes in the different tissues and under different treatments were also checked by RT-PCR analysis. The identification of OsTrx genes showing differential expression in specific tissues among different genotypes or in response to different environmental cues could provide a new avenue for functional analyses in rice.

Identification and characterization of a gibberellin-regulated protein, which is ASR5, in the basal region of rice leaf sheaths

Gibberellins (GAs) regulate growth and development in higher plants. To identify GA-regulated proteins during rice leaf sheath elongation, a proteomic approach was used. Proteins from the basal region of leaf sheath in rice seedling treated with GA(3) were analyzed by fluorescence two-dimensional difference gel electrophoresis. The levels of abscisic acid-stress-ripening-inducible 5 protein (ASR5), elongation factor-1 beta, translationally controlled tumor protein, fructose-bisphosphate aldolase and a novel protein increased; whereas the level of RuBisCO subunit binding-protein decreased by GA(3) treatment. ASR5 out of these six proteins was significantly regulated by GA(3) at the protein level but not at the mRNA level in the basal region of leaf sheaths. Since this protein is regulated not only by abscisic acid but also by GA(3), these results indicate that ASR5 might be involved in plant growth in addition to stress in the basal regions of leaf sheaths.

Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray

To elucidate the differences in the regulation of water stress tolerance between two genotypes of rice, upland-rice (UR, resistant to water stress) and lowland-rice (LR, susceptible to water stress), we constructed subtracted cDNA libraries from polyethyleneglycol (PEG)-treated and non-treated rice seedlings (IRAT109, an upland-rice variety) by suppression subtractive hybridization (SSH), from which about 2,000 recombinant colonies were picked and amplified. Then, a cDNA microarray containing these expressed sequence tags (ESTs) was used to analyze the gene expression profiles in UR and LR in response to PEG treatment. Microarray data revealed that the majority of genes expressed in UR and LR are almost identical and Student's t test showed that 13% of all the ESTs detected in leaves and 7% of that in roots expressed differentially in transcripts abundance between the two genotypes. After sequencing, it was found that 64 and 79 unique ESTs expressed at higher levels in UR and LR, respectively. Many of the ESTs that showed higher expression in UR upon PEG treatment represented genes for transcription factors, genes playing roles in detoxification or protection against oxidative stress, and genes that help in maintaining cell turgor. In contrast, some ESTs that showed higher expression in LR were genes functioning in the degradation of cellular components. Based on data from this study and previous reports, we suggest that overexpression of some genes that expressed at higher level in UR may improve water stress tolerance in LR and other plant species.

Proteomics of European beech (Fagus sylvatica L.) seed dormancy breaking: Influence of abscisic and gibberellic acids

A proteomic approach was used to analyze mechanisms of dormancy breaking in beech (Fagus sylvatica L.) seeds and the participation of abscisic and gibberellic acids (ABA and GA) in this process. After imbibition in water, ABA, or GA3 solutions, beechnuts were subjected to cold stratification, which breaks their dormancy. ABA delayed, whereas GA3 promoted seed dormancy breaking. Proteome maps for water, ABA, and GA3 were established, which displayed 1544 silver-stained spots. A total of 74 spots, showing significant changes in volume, were identified by MS. Of these, 18, 45, and 16 spots were identified as water-, ABA-, and GA3-responsive, respectively (five were regulated by both hormones). The classification of proteins showed that most of the proteins associated with dormancy breaking in water are involved in energy metabolism and protein destination. Most of the ABA-responsive proteins are involved in protein destination, energy metabolism, and development. Most of the GA3-responsive proteins are involved in energy metabolism (many more than for ABA and water) and plant defense. We conclude that the mechanism of seed dormancy breaking involves the proteins of many processes, beginning with hormone signal initiation, through signal transduction, transcription, protein synthesis, energy metabolism, storage materials, and ending with the cell cycle.

Over-expression of calcium-dependent protein kinase 13 and calreticulin interacting protein 1 confers cold tolerance on rice plants

Calcium is a ubiquitous signaling molecule and changes in cytosolic calcium concentration are involved in plant responses to various stimuli. The rice calcium-dependent protein kinase 13 (CDPK13) and calreticulin interacting protein 1 (CRTintP1) have previously been reported to be involved in cold stress response in rice. In this study, rice lines transformed with sense CDPK13 or CRTintP1 constructs were produced and used to investigate the function of these proteins. When the plants were incubated at 5 degrees C for 3 days, leaf blades of both the sense transgenic and vector control rice plants became wilted and curled. When the plants were transferred back to non-stress conditions after cold treatment, the leaf blades died, but the sheaths remained green in the sense transgenic rice plants. Expression of CDPK13 or CRTintP1 was further examined in several rice varieties including cold-tolerant rice varieties. Accumulation of these proteins in the cold-tolerant rice variety was higher than that in rice varieties that are intermediate in their cold tolerance. To examine whether over-expression of CDPK13 and CRTintP1 would have any effect on the proteins or not, sense transgenic rice plants were analyzed using proteomics. The 2D-PAGE profiles of proteins from the vector control were compared with those of the sense transgenic rice plants. Two of the proteins that differed between these lines were calreticulins. The results suggest that CDPK13, calreticulin and CRTintP1 might be important signaling components for response to cold stress in rice.

The rice OsGAE1 is a novel gibberellin-regulated gene and involved in rice growth

Gibberellins (GAs) are a class of phytohormones that regulate many aspects of plant growth and development processes including stem elongation, flowering, and seed germination. A novel GA-enhanced gene, designated as OsGAE1, was identified using microarray analysis of GA-regulated genes. OsGAE1 expressed in a dose- and time course-dependent manner with minimum expression at 1 microM GA(3) and maximum expression at 50 microM GA(3) starting from 30 min and peaked at 24 h after GA(3) treatment. OsGAE1 expression was up-regulated by GA(3) at transcript level while no significant effect was observed for other hormones. OsGAE1 was expressed in Escherichia coli with N-terminal His(6) tag and the recombinant protein migrated at 38 kDa, slightly larger than the predicted 29 kDa, during SDS-PAGE. Anti-OsGAE1 antibodies immunoreacted with a protein of 40 kDa in rice leaf sheath. OsGAE1 expressed mainly in growing leaf sheath and callus compared to leaf and root. In situ hybridization and OsGAE1 promoter analysis revealed that OsGAE1 expressed in shoot apex meristem and young primary leaves. Northern blot, Western blot, and GUS activities revealed that OsGAE1 is up-regulated by GA(3). Transgenic rice expressing OsGAE1 in antisense orientation exhibited severely affected vegetative and reproductive growth. The transgenic plants were 55-70% short compared to control. These results suggest that OsGAE1 is differentially expressed in rice leaf sheath in relation to GA(3) and it encodes a functional protein which is involved in GA-regulated growth and development of rice.

Functional characterization of gibberellin-regulated genes in rice using microarray system

Gibberellin (GA) is collectively referred to a group of diterpenoid acids, some of which act as plant hormones and are essential for normal plant growth and development. DNA microarray technology has become the standard tool for the parallel quantification of large numbers of messenger RNA transcripts. The power of this approach has been demonstrated in dissecting plant physiology and development, and in unraveling the underlying cellular signaling pathways. To understand the molecular mechanism by which GA regulates the growth and development of plants, with reference to the monocot model plant-rice, it is essential to identify and analyze more genes and their products at the transcription and translation levels that are regulated by GA. With the availability of draft sequences of two major rice types, indica and japonica rice, it has become possible to analyze global expression profiles of genes on a genome scale. In this review, the progress made in finding new genes in rice leaf sheath using microarray system and their characterization is discussed. It is believed that the findings made in this regard have important implications for understanding the mechanism by which GA regulates the growth and development of rice.

Proteomic dissection of plant development

Plant development is controlled by complex endogenous genetic programs and responses to environmental cues. Proteome analyses have recently been introduced to plant biology to identify proteins instrumental in these developmental processes. To date most plant proteome studies have been employed to generate reference maps of the most abundant soluble proteins of plant organs at a defined developmental stage. However, proteomics is now also utilized for genetic studies comparing the proteomes of different plant genotypes, for physiological studies analyzing the influences of exogenous signals on a particular plant organ, and developmental studies investigating proteome changes during development. Technical advances are now beginning to allow a proteomic dissection of individual cell types, thus greatly increasing the information revealed by proteome analyses.

Identification of proteins induced or upregulated by Fusarium head blight infection in the spikes of hexaploid wheat (Triticum aestivum)

Fusarium head blight (FHB) caused by Fusarium graminearum is a destructive disease of wheat and barley. It causes economic losses due to reduction in both yield and quality. Although FHB resistance has been well documented and resistant cultivars have been developed to reduce incidence and severity of FHB, there is a limited understanding of the molecular mechanisms involved in plant resistance against the infection and spread of F. graminearum. In the current study, 2-dimensional displays of proteins extracted from wheat spikelets infected with F. graminearum were compared with those from spikelets inoculated with sterile H2O. Fifteen protein spots were detected that were either induced (qualitatively different) or upregulated (quantitatively increased) following F. graminearum infection of spikelets of 'Ning7840', a resistant cultivar. These proteins were identified by LC-MS/MS analysis. Proteins with an antioxidant function such as superoxide dismutase, dehydroascorbate reductase, and glutathione S-transferases (GSTs) were upregulated or induced 5 d after inoculation with F. graminearum, indicating an oxidative burst of H2O2 inside the tissues infected by FHB. An ascorbate-glutathione cycle is likely involved in reduction of H2O2. Expression of proteins with highest similarity to dehydroascorbate reductase and TaGSTF5 (a glutathione S-transferase) differed following FHB infection in susceptible and resistant cultivars. A 14-3-3 protein homolog was also upregulated in FHB-infected spikelets. In addition, a PR-2 protein (beta-1, 3 glucanase) was upregulated in FHB-infected spikes, which is in accord with a previous study that analyzed transcript accumulation.

An evaluation for cross-species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data

With 1383 tandem mass spectra derived from 120 individual protein spots separated by the two-dimensional (2-D) gel electrophoresis of protein samples from three different species, comparative analyses were performed by searching the Expressed Sequence Tag (EST) database (DB) and the NCBI non-redundant (nr) DB of green plants, respectively, which uses the Mascot search engine to establish a statistical basis. It was confirmed that the former could identify more peptides manually validated by de novo sequencing (DNS) from fewer species in more closely phylogenetic relationships than the latter in a statistically significant manner. Our data demonstrated that correct peptide identifications were given low Mascot scores (e.g. 6-14) and incorrect peptide identifications were given high Mascot scores (e.g. 68-83). Our data also showed that the current evaluation approaches to protein assignments are unsatisfactory because a few 'false-positive' proteins are recognized and several 'false-negative' proteins are rescued by manual validation.

Rice proteome database: a step toward functional analysis of the rice genome

The technique of proteome analysis using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this study, the proteins of rice were cataloged, a rice proteome database was constructed, and a functional characterization of some of the identified proteins was undertaken. Proteins extracted from various tissues and subcellular compartments in rice were separated by 2D-PAGE and an image analyzer was used to construct a display of the proteins. The Rice Proteome Database contains 23 reference maps based on 2D-PAGE of proteins from various rice tissues and subcellular compartments. These reference maps comprise 13129 identified proteins, and the amino acid sequences of 5092 proteins are entered in the database. Major proteins involved in growth or stress responses were identified using the proteome approach. Some of these proteins, including a beta-tubulin, calreticulin, and ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have unexpected functions. The information obtained from the Rice Proteome Database will aid in cloning the genes for and predicting the function of unknown proteins.

Comprehensive Phosphoproteome Analysis in Rice and Identification of Phosphoproteins Responsive to Different Hormones/Stresses

Phosphoproteins in rice were detected by in vitro protein phosphorylation followed by two-dimensional polyacrylamide gel electrophoresis. Forty-four phosphoproteins were detected on a 2D-gel after in vitro protein phosphorylation of the crude extract from rice leaf sheath. Among the phosphoproteins detected, 42 were identified through analysis by Q-TOF MS/MS and/or MALDI-TOF MS. The largest percentage of the identified phosphoproteins are involved in signaling (30%), while 18% are involved in metabolism. When rice seedlings were treated with various hormones and stresses, it was observed that the phosphorylation of 13 proteins was enhanced differentially by different hormone and stress treatments. Furthermore, when the hormone/stress regulated phosphoproteins are compared in rice leaf sheath, leaf blade and root, only cytoplasmic malate dehydrogenase was found to be phosphorylated in all the tissues. Results suggest that in the phosphorylation cascade of rice, glycolytic metabolism processes and Ca(2+)-signaling seem to be important targets in response to hormones and stresses. Furthermore, the direct visualization of phosphoproteins by (32)P-labeling and their mass spectrometric identification provides an accurate and reliable method of analyzing the rice phosphoproteome.

Proteomic analysis of cadmium-induced protein profile alterations from marine alga Nannochloropsis oculata

Protein profile alterations following exposure to cadmium were examined in marine alga Nannochloropsis oculata through proteomic analysis. Alterations of the protein expression patterns following 10 muM cadmium treatment were analyzed on 2-dimensional gels. Out of 380 protein spots detected on 2-D gel using Coomassie staining, 11 spots were changed significantly following cadmium treatment. Because of the non-availability of molecular background information on this non-sequenced algal species, cross-species protein identification through ESI-Q-TOF MS/MS was used to identify altered proteins. Two newly induced proteins were identified as malate dehydrogenase orthologue and NADH dehydrogenase orthologue. One suppressed protein was identified to be glyceraldehydes 3-phosphate dehydrogenase A. Protein spot showing a 3-fold increase was identified as mitochondrial NADH: ubiquinone oxidoreductase orthologue. However, we could not find any matches in the database from ESI-Q-TOF MS/MS for the remaining seven proteins, thus only partial peptide sequences of these proteins were found.

Characterization of Vacuolar Membrane Proteins Changed in Rice Root Treated with Gibberellin

Rice vacuolar membrane proteins changed by gibberellin (GA) were analyzed using a proteome approach. Vacuolar membrane fractions were isolated using a discontinuous sucrose/sorbitol system and 10 proteins increased in vacuolar membrane of the root, treated with GA(3) as compared with control. Fructose-1,6-bisphosphate aldolase C-1 and vacuolar H(+)-ATPase (V-ATPase) increased in root vacuolar membrane by GA(3) interacted in rice roots. It suggests that aldolase C-1 regulates the V-ATPase mediated control of cell elongation that determines root growth.

Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice

Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.

Expression and Function of Proteins during Development of the Basal Region in Rice Seedlings

A differential display of proteins with a two-dimensional polyacrylamide gel electrophoresis approach was used to analyze protein expression changes during development of the basal region in rice seedlings (Oryza sativa L. cv. Nipponbare). The proteins were detected as 700 Coomassie Brilliant Blue-stained spots with pI values from around 3.5 to 9.0. A proteome reference map was established for the basal region of two-week-old seedlings. The basal region proteome map was used to analyze quantitative variations in the tissue during development from 2-, 4-, 6-, 8-, and 10-week-old seedlings. During development, 31 proteins were up-regulated, and 30 proteins were down-regulated compared with the 2-week-old basal region proteome map. The main functions of these proteins were primary metabolism and protein synthesis or maintenance. Calreticulin precursor, enolase, and voltage-dependent anion channel were identified among the up- and down-regulated proteins. The twin spots of calreticulin precursor and enolase with different pI values are possibly due to post-translational modifications such as phosphorylation. In addition, seven proteins showed developmental stage-specific expression. All of the developmentally regulated proteins of the basal region were clustered by the S-system, a differential equation that fit to time course of cluster and analyzed for cluster relationships. Proteins with unknown functions were tentatively assigned to functional groups based on cluster relationships. Basal region development proteome data will be valuable for resolving questions in functional genomics. In addition, cluster analysis of the basal region proteome during development will be useful for the assessment of functional proteins.

Identification of phosphoproteins regulated by gibberellin in rice leaf sheath

To identify the gibberellin (GA) signaling components involved in rice leaf sheath elongation process, protein phosphorylation changed by GA3 was analyzed. The protein kinase activities in rice leaf sheath were assessed in an in-gel kinase assay using SDS-polyacrylamide gel containing histone III-S as a substrate. The activity of a putative 54-kDa calcium dependent protein kinase (CDPK) in cytosolic fraction in rice leaf sheath increased significantly by GA3. Further, phosphorylation status of the proteins changed by GA3 in rice leaf sheath were detected by in vitro protein phosphorylation followed by two-dimensional polyacrylamide gel electrophoresis and the phosphoproteins were identified by mass spectrometry. Sixty phosphoproteins was detected after in vitro protein phosphorylation and the phosphorylation of 7 proteins was enhanced by GA3 treatment. The addition of GA3 treated cytosolic fraction of leaf sheath further increased the phosphorylation of 4 proteins, glyoxalase-I, cytoplasmic malate dehydrogenase, glyceraldehydes-3-phosphate dehydrogenase and another unknown protein. The protein kinase inhibitor, staurosporine inhibited the phosphorylation of these proteins in vitro. Other hormones, particularly, indole acetic acid, 6-benzylaminopurine and abscisic acid did not change the phosphorylation status of these proteins. The identified proteins did not show any change by GA3 treatment at transcription level. The abundance of glyoxalase-I and cytoplasmic malate dehydrogenase remained unchanged by GA3 treatment as detected on 2D-gel by silver staining, unlike for glyceraldehydes-3-phosphate dehydrogenase. Results suggest that the phosphoproteins, glyoxalase-I and cytoplasmic malate dehydrogenase in rice leaf sheath could be important signaling components of GA3, downstream to 54-kDa CDPK.

Rice proteome analysis: A step toward functional analysis of the rice genome

The technique of proteome analysis using 2-DE has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this review, we describe construction of the rice proteome database, the cataloging of rice proteins, and the functional characterization of some of the proteins identified. Initially, proteins extracted from various tissues and organelles were separated by 2-DE and an image analyzer was used to construct a display or reference map of the proteins. The rice proteome database currently contains 23 reference maps based on 2-DE of proteins from different rice tissues and subcellular compartments. These reference maps comprise 13 129 rice proteins, and the amino acid sequences of 5092 of these proteins are entered in the database. Major proteins involved in growth or stress responses have been identified by using a proteomics approach and some of these proteins have unique functions. Furthermore, initial work has also begun on analyzing the phosphoproteome and protein-protein interactions in rice. The information obtained from the rice proteome database will aid in the molecular cloning of rice genes and in predicting the function of unknown proteins.

Proteomic changes in rice leaves during development of field-grown rice plants

Of the numerous factors affecting rice yield, how solar radiation is transformed into biomass through rice leaves is the most important. We have analyzed proteomic changes in rice leaves collected from six different developing stages (vegetative to ripening). We studied protein expression profiles of rice leaves by running two-dimensional gel electrophoresis. Differential protein expression among the six phases were analyzed by image analysis, which allowed the identification of 49 significantly different gel spots. The spots were further verified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, in which 89.8% of them were confirmed to be rice proteins. Finally, we confirmed some of the interesting rice proteins by immunoblotting. Three major conclusions can be drawn from these experimental results. (i) Protein expression in rice leaves, at least for high or middle abundance proteins, is attenuated during growth (especially some chloroplast proteins). However, the change is slow and the expression profiles are relatively stable during rice development. (ii) Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), a major protein in rice leaves, is expressed at constant levels at different growth stages. Interestingly, a high ratio of degradation of the RuBisCO large subunit was found in all samples. This was confirmed by two approaches, mass spectrometry and immunoblotting. The degraded fragments are similar to other digested products of RuBisCO mediated by free radials. (iii) The expression of antioxidant proteins such as superoxide dismutase and peroxidase decline at the early ripening stage.

Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments

The genome of several species has now been elucidated; these genomes indicate the proteomic potential of the cell. While identification of genomes has been, and continues to be, a technically and intellectually demanding process, the identification of the proteome contains inherently greater difficulties. The proteome of each living cell is dynamic, altering in response to the individual cell's metabolic state and reception of intracellular and extracellular signal molecules, and many of the proteins which are expressed will be post-translationally altered. Thus if the purpose of the proteome analysis is to aid the understanding of protein function and interaction, then it is identification of the proteins in their final state which is required: for this mass spectrometric identification of individual proteins, indicating site and nature of modifications, is essential. Here we review the principles of the methodologies involved in such analyses, give some indication of current achievements in plant proteomics, and indicate imminent and prospective technical developments.

Technical aspects of functional proteomics in plants

Since the completion of genome sequences of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. This analysis is achieved by separation and identification of proteins, determination of their function and functional network, and construction of an appropriate database. Many improvements in separation and identification of proteins, such as two-dimensional electrophoresis, nano-liquid chromatography and mass spectrometry, have rapidly been achieved. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. These techniques have provided the possibility of high-throughput analysis of function and functional network of proteins in plants. However, to cope with the huge information emerging from proteome analyses, more sophisticated techniques and software are essential. The development and adaptation of such techniques will ease analyses of protein profiling, identification of post-translational modifications and protein-protein interaction, which are vital for elucidation of the protein functions.

Microarray analysis of brassinosteroids- and gibberellin-regulated gene expression in rice seedlings

In order to understand the molecular mechanisms by which two types of phytohormones, brassinosteroids (BRs) and gibberellins (GAs), regulate plant growth and development, a cDNA microarray was made containing 4000 clones randomly selected from a rice cDNA library constructed from RNA isolated from seedlings treated with GA(3) and brassinolide (BL). The array was then probed to identify differences in expression using labelled cDNAs prepared from treated and control seedlings. Nine and 29 unique cDNA clones were up-regulated, while 32 and 42 unique cDNA clones were down-regulated by BL and GA(3), respectively. The predicted products of these BL- and GA-regulated genes fall into such functional categories as signal transduction, transcription, metabolism, cellular organization, and defense or anti-stress responses. Northern analysis of the selected BL- and GA(3)-regulated genes not only confirmed their BL or GA(3) dose dependent expression, but also revealed significant differences in the degree of expression in different organs and in response to other phytohormones. These results demonstrate that BR and GA influence growth and development by coordinately regulating the expression of specific groups of genes.

Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003

The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified proteins showing tissue and subcellular localization, corresponding to 4180 separate protein entries in the database. The Rice Proteome Database contains the calculated properties of each protein such as molecular weight, isoelectric point and expression; experimentally determined properties such as amino acid sequences obtained using protein sequencers and mass spectrometry; and the results of database searches such as sequence homologies. The database is searchable by keyword, accession number, protein name, isoelectric point, molecular weight and amino acid sequence, or by selection of a spot on one of the 2D-PAGE reference maps. Cross-references are provided to tools for proteomics and to other 2D-PAGE databases, which in turn provide many links to other molecular databases. The information in the Rice Proteome Database is updated weekly, and is available on the World Wide Web at http://gene64.dna.affrc.go.jp/RPD/.

Proteome analysis of rice tissues by two-dimensional electrophoresis: an approach to the investigation of gibberellin regulated proteins

Protein databases constructed using high-resolution two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) were used to explore the proteome expressed in various rice tissues. Proteins from leaf sheath, root, and cultured suspension cells were systematically analyzed using 2D-PAGE, mass spectrometry and Edman sequencing, followed by database searching. In all, 79 of the 431 spots detected by 2D-PAGE in the leaf sheath, 73 of the 508 spots in the root and 140 of the 962 spots in the cultured suspension cells could be identified. Protein lists were constructed for each tissue and used to investigate the effects of gibberellin (GA) treatment. In the leaf sheath, root and cultured suspension cells, 8, 21, and 14 of the identified proteins, respectively, were regulated by GA. These proteins included polypeptides involved in general metabolism, energy production, transcriptional regulation and signal transduction in the leaf sheath; in metabolism and defense in the root; and in metabolism, energy production, cell growth, defense and signal transduction in the cultured suspension cells. These results indicate that the proteome databases assembled in these studies will be useful for the rapid assessment of changes in protein content in specific tissues, and that proteins regulated by GA may play a significant role in tissue growth.