The accumulation of abundant soluble proteins changes early in the development of the primary roots of maize (Zea mays L.)

Proteomics of Maize Root Development

Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding

Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

Transcriptomic complexity in young maize primary roots in response to low water potentials

BACKGROUND

Widespread and more frequently occurring drought conditions are a consequence of global warming and increase the demand for tolerant crop varieties to feed the growing world population. A better understanding of the molecular mechanisms underlying the water deficit response of crops will enable targeted breeding strategies to develop robust cultivars.

RESULTS

In the present study, the transcriptional response of maize (Zea mays L.) primary roots to low water potentials was monitored by RNA sequencing (RNA-Seq) experiments. After 6 h and 24 h of mild (-0.2 MPa) and severe (-0.8 MPa) water deficit conditions, the primary root transcriptomes of seedlings grown under water deficit and control conditions were compared. The number of responsive genes was dependent on and increased with intensification of water deficit treatment. After short-term mild and severe water deficit 249 and 3,000 genes were differentially expressed, respectively. After a 24 h treatment the number of affected genes increased to 7,267 and 12,838 for mild and severe water deficit, respectively, including more than 80% of the short-term responsive genes. About half of the differentially expressed genes were up-regulated and maximal fold-changes increased with treatment intensity to more than 300-fold. A consensus set of 53 genes was differentially regulated independently of the nature of deficit treatment. Characterization revealed an overrepresentation of the Gene Ontology (GO) categories "oxidoreductase activity" and "heme binding" among regulated genes connecting the water deficit response to ROS metabolism.

CONCLUSION

This study gives a comprehensive insight in water deficit responsive genes in young maize primary roots and provides a set of candidate genes that merit further genetic analyses in the future.

Root architecture and root and tuber crop productivity

It is becoming increasingly evident that optimization of root architecture for resource capture is vital for enabling the next green revolution. Although cereals provide half of the calories consumed by humans, root and tuber crops are the second major source of carbohydrates globally. Yet, knowledge of root architecture in root and tuber species is limited. In this opinion article, we highlight what is known about the root system in root and tuber crops, and mark new research directions towards a better understanding of the relation between root architecture and yield. We believe that unraveling the role of root architecture in root and tuber crop productivity will improve global food security, especially in regions with marginal soil fertility and low-input agricultural systems.

A systematic proteomic analysis of NaCl-stressed germinating maize seeds

Salt (NaCl) is a common physiological stressor of plants. To better understand how germinating seeds respond to salt stress, we examined the changes that occurred in the proteome of maize seeds during NaCl-treated germination. Phenotypically, salt concentrations less than 0.2 M appear to delay germination, while higher concentrations disrupt development completely, leading to seed death. The identities of 96 proteins with expression levels altered by NaCl-incubation were established using 2-DE-MALDI-TOF-MS and 2-DE-MALDI-TOF-MS/MS. Of these 96 proteins, 79 were altered greater than twofold when incubated with a 0.2 M salt solution, while 51 were altered when incubated with a 0.1 M salt solution. According to their functional annotations in the Swiss-Prot protein-sequence databases, these proteins are mainly involved in seed storage, energy metabolism, stress response, and protein metabolism. Notably, the expression of proteins that respond to abscisic acid signals increased in response to salt stress. The results of this study provide important clues as to how NaCl stresses the physiology of germinating maize seeds.

Root morphological and proteomic responses to growth restriction in maize plants supplied with sufficient N

The primary objective of this study was to better understand how root morphological alteration stimulates N uptake in maize plants after root growth restriction, by investigating the changes in length and number of lateral roots, (15)NO(3)(-) influx, the expression level of the low-affinity Nitrate transporter ZmNrt1.1, and proteomic composition of primary roots. Maize seedlings were hydroponically cultured with three different types of root systems: an intact root system, embryonic roots only, or primary roots only. In spite of sufficient N supply, root growth restriction stimulated compensatory growth of remaining roots, as indicated by the increased lateral root number and root density. On the other hand, there was no significant difference in (15)NO(3)(-) influx between control and primary root plants; neither in ZmNrt1.1 expression levels in primary roots of different treatments. Our data suggested that increased N uptake by maize seedlings experiencing root growth restriction is attributed to root morphological adaptation, rather than explained by the variation in N uptake activity. Eight proteins were differentially accumulated in embryonic and primary root plants compared to control plants. These differentially accumulated proteins were closely related to signal transduction and increased root growth.

Comparative proteomic profiles of the soybean (Glycine max) root apex and differentiated root zone

The root apical meristem (RAM) is responsible for the growth of the plant root system. Because of the importance of root architecture in the performance of crop plants, we established a proteome reference map of the soybean root apex and compared this with the proteome of the differentiated root zone. The root apex samples contained the apical 1 mm of the root, comprising the RAM, quiescent center and root cap. We identified 342 protein spots from 550 excised proteins (∼62%) of root apex samples by MALDI-TOF MS/MS analysis. All these proteins were also present in the differentiated root, but differed in abundance. Functional classification showed that the most numerous protein categories represented in the root were those of stress response, glycolysis, redox homeostasis and protein processing. Using DIGE, we identified 73 differentially accumulated proteins between root apex and differentiated root. Proteins overrepresented in the root apex belonged primarily to the pathways for protein synthesis and processing, cell redox homeostasis and flavonoid biosynthesis. Proteins underrepresented in the root apex were those of glycolysis, tricarboxylic acid metabolism and stress response. Our results highlight the importance of stress and defense response, redox control and flavonoid metabolism in the root apex.

Proteome profile of the developing maize (Zea mays L.) rachis

In this study, we performed the first high-throughput proteomic analysis of developing rachis (cob) from maize genotype Mp313E. Using two proteomic approaches, 2-DE and 2-D LC, we identified 967 proteins. A 2-D proteome reference map was established. Functional classification of identified proteins revealed that proteins involved in various cellular metabolisms, response to stimulus and transport, were the most abundant.

Nonadditive protein accumulation patterns in Maize (Zea mays L.) hybrids during embryo development

Heterosis describes the superior performance of heterozygous F(1)-hybrid plants compared to their homozygous parental inbred lines. In the present study, heterosis was detected for length, weight, and the time point of seminal root primordia initiation in maize (Zea mays L.) embryos of the reciprocal F(1)-hybrids UH005xUH250 and UH250xUH005. A two-dimensional gel electrophoresis (2-DE) proteome survey of the most abundant proteins of the reciprocal hybrids and their parental inbred lines 25 and 35 days after pollination revealed that 141 of 597 detected proteins (24%) exhibited nonadditive accumulation in at least one hybrid. Approximately 44% of all nonadditively accumulated proteins displayed an expression pattern that was not distinguishable from the low parent value. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analyses and subsequent functional classification of the 141 proteins revealed that development, protein metabolism, redox-regulation, glycolysis, and amino acid metabolism were the most prominent functional classes among nonadditively accumulated proteins. In 35-day-old embryos of the hybrid UH250xUH005, a significant up-regulation of enzymes related to glucose metabolism which often exceeded the best parent values was observed. A comparison of nonadditive protein accumulation between rice and maize embryo data sets revealed a significant overlap of nonadditively accumulated proteins suggesting conserved organ- or tissue-specific regulatory mechanisms in monocots related to heterosis.

Specification of cortical parenchyma and stele of maize primary roots by asymmetric levels of auxin, cytokinin, and cytokinin-regulated proteins

In transverse orientation, maize (Zea mays) roots are composed of a central stele that is embedded in multiple layers of cortical parenchyma. The stele functions in the transport of water, nutrients, and photosynthates, while the cortical parenchyma fulfills metabolic functions that are not very well characterized. To better understand the molecular functions of these root tissues, protein- and phytohormone-profiling experiments were conducted. Two-dimensional gel electrophoresis combined with electrospray ionization tandem mass spectrometry identified 59 proteins that were preferentially accumulated in the cortical parenchyma and 11 stele-specific proteins. Hormone profiling revealed preferential accumulation of indole acetic acid and its conjugate indole acetic acid-aspartate in the stele and predominant localization of the cytokinin cis-zeatin, its precursor cis-zeatin riboside, and its conjugate cis-zeatin O-glucoside in the cortical parenchyma. A root-specific beta-glucosidase that functions in the hydrolysis of cis-zeatin O-glucoside was preferentially accumulated in the cortical parenchyma. Similarly, four enzymes involved in ammonium assimilation that are regulated by cytokinin were preferentially accumulated in the cortical parenchyma. The antagonistic distribution of auxin and cytokinin in the stele and cortical parenchyma, together with the cortical parenchyma-specific accumulation of cytokinin-regulated proteins, suggest a molecular framework that specifies the function of these root tissues that also play a role in the formation of lateral roots from pericycle and endodermis cells.

Molecular dissection of heterosis manifestation during early maize root development

Heterosis is of paramount agronomic importance and has been successfully exploited in maize hybrid breeding for decades. Nevertheless, the molecular basis of heterosis remains elusive. Heterosis is not only observed in adult traits like yield or plant height, but is already detected during embryo and seedling development. Hence, the maize (Zea mays L.) primary root which is the first organ that emerges after germination is a suitable model to study heterosis manifestation. Various seedling root traits including primary root length and lateral root density display heterosis. Microarray studies suggest organ specific patterns of nonadditive gene expression in maize hybrids. Moreover, such experiments support the notion that global expression trends in maize primary roots are conserved between different hybrids. Furthermore, nonadditive expression patterns of specific genes such as a SUPEROXIDE DISMUTASE 2 might contribute to the early manifestation of heterosis. Proteome profiling experiments of maize hybrid primary roots revealed nonadditive accumulation patterns that were distinct from the corresponding RNA profiles underscoring the importance of posttranscriptional processes such as protein modifications that might be related to heterosis. Finally, analysis of selected metabolites imply that a subtle regulation of particular biochemical pathways such as the phenylpropanoid pathway in hybrids might contribute to the manifestation of heterosis in maize primary roots. In the future, recently developed molecular tools will facilitate the analysis of the molecular principles underlying heterosis in maize roots.

New changes in the plasma-membrane-associated proteome of rice roots under salt stress

To gain a better understanding of salt stress responses in plants, we used a proteomic approach to investigate changes in rice (Oryza sativa) root plasma-membrane-associated proteins following treatment with 150 mmol/L NaCl. With or without a 48 h salt treatment, plasma membrane fractions from root tip cells of a salt-sensitive rice cultivar, Wuyunjing 8, were purified by PEG aqueous two-phase partitioning, and plasma-membrane-associated proteins were separated by IEF/SDS-PAGE using an optimized rehydration buffer. Comparative analysis of three independent biological replicates revealed that the expressions of 18 proteins changed by more than 1.5-fold in response to salt stress. Of these proteins, nine were up-regulated and nine were down-regulated. MS analysis indicated that most of these membrane-associated proteins are involved in important physiological processes such as membrane stabilization, ion homeostasis, and signal transduction. In addition, a new leucine-rich-repeat type receptor-like protein kinase, OsRPK1, was identified as a salt-responding protein. Immuno-blots indicated that OsRPK1 is also induced by cold, drought, and abscisic acid. Using immuno-histochemical techniques, we determined that the expression of OsRPK1 was localized in the plasma membrane of cortex cells in roots. The results suggest that different rice cultivars might have different salt stress response mechanisms.

Heme-independent soluble and membrane-associated peroxidase activity of a Zea mays annexin preparation

Annexins are cytosolic proteins capable of reversible, Ca(2+)-dependent membrane binding or insertion. Animal annexins form and regulate Ca(2+)-permeable ion channels and may therefore participate in signaling. Zea mays (maize) annexins (ZmANN33 and ZmANN35) have recently been shown to form a Ca(2+)-permeable conductance in planar lipid bilayers and also exhibit in vitro peroxidase activity. Peroxidases form a superfamily of intra- or extracellular heme-containing enzymes that use H(2)O(2) as the electron acceptor in a number of oxidative reactions. Maize annexin peroxidase activity appears independent of heme and persists after membrane association, the latter suggesting a role in reactive oxygen species signaling.

Genetic and genomic dissection of maize root development and architecture

The complex architecture and plasticity of the maize root system is controlled by a plethora of genes. Mutant analyses have identified genes regulating shoot-borne root initiation (RTCS) and root hair elongation (RTH1 and RTH3). Quantitative trait locus (QTL) studies have highlighted the importance of seminal roots, lateral roots, and root hairs in phosphorus acquisition. Additionally, QTLs that influence root features were shown to affect yield under different water regimes and under flooding conditions. Finally, proteome and transcriptome analyses provided insights into maize root development and identified candidate genes associated with cell specification, and lateral root initiation in pericycle cells. The targeted application of forward-genetics and reverse-genetics approaches will accelerate the unraveling of the functional basis of root development and architecture.

Establishment of a protein reference map for soybean root hair cells

Root hairs are single tubular cells formed from the differentiation of epidermal cells on roots. They are involved in water and nutrient uptake and represent the infection site on leguminous roots by rhizobia, soil bacteria that establish a nitrogen-fixing symbiosis. Root hairs develop by polar cell expansion or tip growth, a unique mode of plant growth shared only with pollen tubes. A more complete characterization of root hair cell biology will lead to a better understanding of tip growth, the rhizobial infection process, and also lead to improvements in plant water and nutrient uptake. We analyzed the proteome of isolated soybean (Glycine max) root hair cells using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and shotgun proteomics (1D-PAGE-liquid chromatography and multidimensional protein identification technology) approaches. Soybean was selected for this study due to its agronomic importance and its root size. The resulting soybean root hair proteome reference map identified 1,492 different proteins. 2D-PAGE followed by mass spectrometry identified 527 proteins from total cell contents. A complementary shotgun analysis identified 1,134 total proteins, including 443 proteins that were specific to the microsomal fraction. Only 169 proteins were identified by the 2D-PAGE and shotgun methods, which highlights the advantage of using both methods. The proteins identified are involved not only in basic cell metabolism but also in functions more specific to the single root hair cell, including water and nutrient uptake, vesicle trafficking, and hormone and secondary metabolism. The data presented provide useful insight into the metabolic activities of a single, differentiated plant cell type.

Proteomic analysis of early germs with high-oil and normal inbred lines in maize

High-oil maize as a product of long-term selection provides a unique resource for functional genomics. In this study, the abundant soluble proteins of early developing germs from high-oil and normal lines of maize were compared using two-dimensional gel electrophoresis (2-DGE) in combination with mass spectrometry (MS). More than 1100 protein spots were detected on electrophoresis maps of both high-oil and normal lines by using silver staining method. A total of 83 protein spots showed significant differential expression (>two-fold change; t-test: P < 0.05) between high-oil and normal inbred lines. Twenty-seven protein spots including 25 non-redundant proteins were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS). Functional categorization of these proteins was carbohydrate metabolism, cytoskeleton, protein metabolism, stress response, and lipid metabolism. Three such proteins involved in lipid metabolism, namely putative enoyl-ACP reductase (ENR), putative stearoyl-ACP desaturase (SAD) and putative acetyl-CoA C-acyltransferase (ACA), had more abundant expressions in high-oil lines than in normal. At the mRNA expression level, SAD, ENR and ACA were expressed at significantly higher levels in high-oil lines than in normal. The results demonstrated that high expressions of SAD, ENR and ACA might be associated to increasing oil concentration in high-oil maize. This study represents the first proteomic analysis of high-oil maize and contributes to a better understanding of the molecular basis of oil accumulation in high-oil maize.

Proteomic analysis of reactive oxygen species (ROS)-related proteins in rice roots

To investigate the rice root proteome, we applied the PEG fractionation technique combined with two-dimensional gel electrophoresis which rendered more well-separated protein spots. Out of the 295 chosen proteins, 93 were identified by MALDI-TOF mass spectrometry. The proteins were classified as relating to metabolism (38.7%), reactive oxygen species (ROS)-related proteins (22.5%), protein processing/degradation (8.6%), stress/defense (7.5%), energy (6.5%) and signal transduction (5.4%). The high percentage of ROS-related proteins found in rice root brings us to assess the roles of ROS on rice root growth. Treatment with ROS quenching chemicals such as reduced glutathione (GSH), diphenyleneiodonium (DPI) and ascorbate inhibited root growth dose-dependently. Forty-nine proteins identified were either up- or down-regulated by GSH treatment, of which 14 were ROS-related proteins, such noticeably modulated ones as glutathione-S-transferase (GST), superoxide dismutases (SOD) and L-ascorbate peroxidases. The protein levels of four GSTs (NS4, 8, 56 and 57), three APXs (NS46, 49 and 50) and MnSOD (NS45) were strongly reduced by GSH treatment but slightly reduced by ascorbate and DPI. Ascorbate and DPI strongly inhibited expression levels of a catalase A (NP23) and an APX (NS65) but did not affect APXs (NS46, 49 and 50) protein levels. Northern analysis demonstrated that changes in transcript levels of five genes--GST (NS4), GST (NS43), Mn-SOD (NS45), APX (NS50) and APX (NS46/49) in response to ROS quenching chemicals were coherent with patterns shown in two-dimensional electrophoresis analyses. Taken together, we suggest that these proteins may take part in an important role in maintaining cellular redox homeostasis during rice root growth.

Wheat (Triticum aestivumL.) root proteome and differentially expressed root proteins between hybrid and parents

To better understand the development of wheat roots, a reference map of the major soluble proteins of wheat roots was established using a combination of 2-DE and MALDI TOF MS and MS/MS, and a total of 450 protein spots were detected with silver staining in a pH ranges of 4-7, of which 282 spots corresponding to 240 proteins were identified. These identified proteins were grouped into diverse functional categories. In comparison with a wheat leave proteome, in root, proteins involved in metabolism and transport were over-represented, whereas proteins involved in energy, disease and defense, transcription, and signal transduction were under-represented. To further get an insight into the molecular basis of wheat heterosis, differential proteome analysis between hybrid and parents were performed. A total of 45 differentially expressed protein spots were detected, and both quantitative and qualitative differences could be observed. Moreover, 25 of the 45 differentially expressed protein spots were identified, which were involved in metabolism, signal transduction, energy, cell growth and division, disease and defense, secondary metabolism. These results indicated that hybridization between two parental lines can cause expression differences between wheat hybrid and its parents not only at mRNA levels but also at protein abundances.

Proteomic analysis of roots growth and metabolic changes under phosphorus deficit in maize (Zea mays L.) plants

Phosphorus (P) deficiency is a major limitation for plant growth and development. Plants can respond defensively to this stress, modifying their metabolic pathways and root morphology, and this involves changes in their gene expression. To better understand the low P adaptive mechanism of crops, we conducted the comparative proteome analysis for proteins isolated from maize roots treated with 1000 microM (control) or 5 microM KH2PO4 for 17 days. The results showed that approximately 20% of detected proteins on 2-DE gels were increased or decreased by two-fold or more under phosphate (Pi) stress. We identified 106 differentially expressed proteins by MALDI-TOF MS. Analysis of these P starvation responsive proteins suggested that they were involved in phytohormone biosynthesis, carbon and energy metabolisms, protein synthesis and fate, signal transduction, cell cycle, cellular organization, defense, secondary metabolism, etc. It could be concluded that they may play important roles in sensing the change of external Pi concentration and regulating complex adaptation activities for Pi deprivation to facilitate P homeostasis. Simultaneously, as a basic platform, the results would also be useful for the further characterization of gene function in plant P nutrition.

ZmGrp3: identification of a novel marker for root initiation in maize and development of a robust assay to quantify allele-specific contribution to gene expression in hybrids

This study comprises a comprehensive gene expression analysis of the root tip specific maize gene ZmGrp3. In the first part of this paper expression of ZmGrp3 was studied in maize inbred lines. First, RNA in situ hybridization experiments confined the expression of ZmGrp3 to the columella and the epidermis of all embryonic and postembryonic root types. Second, Northern-blot analyses of the maize root initiation mutants rtcs and lrt1 revealed that the ZmGrp3 gene is not expressed prior to root initiation, thus providing a novel marker for this developmental process. Finally, a comprehensive expression profiling in 42 tissues via the Lynx MPSS system revealed almost exclusive expression of ZmGrp3 in maize roots. In the second part of this survey, ZmGrp3 expression was assayed in maize hybrids. In this context, a novel approach to quantify allele-specific contribution to gene expression in maize hybrids was developed. This assay combines RT-PCR amplification of polymorphisms between two alleles and subsequent quantification of allele-specific gene expression via a combination of didesoxyterminator assays and capillary electrophoresis. Allelic expression of the ZmGrp3 gene in six reciprocal hybrids generated from three ZmGrp3 alleles was analyzed via a new statistical mixed model approach.

Comparative proteome analyses of maize (Zea mays L.) primary roots prior to lateral root initiation reveal differential protein expression in the lateral root initiation mutant rum1

The embryonically preformed primary root is the first root type of maize that emerges after germination. In this study the abundant soluble proteins of 2.5-day-old primary roots of wild-type and lateral root mutant rum1 seedlings were compared before the initiation of lateral roots. In CBB-stained 2-D gels, among 350 detected proteins 14 were identified as differentially accumulated (>twofold change; t-test: 95% significance) in wild-type versus rum1 primary roots. These proteins which were identified via ESI MS/MS are encoded by 12 different genes. Functionally, these proteins are involved in lignin biosynthesis, defense, and the citrate cycle. Nine of these genes were further analyzed at the RNA expression level. This study represents the first comparative proteomic analysis of maize primary roots prior to lateral root initiation and will contribute to a better understanding of the molecular basis of root development in cereals.

Plant proteome analysis: A 2004–2006 update

Since the appearance of the review entitled "Plant Proteome Analysis" in Proteomics in February 2004 (Cánovas, F. M., Dumas-Gaudot, E., Recorbert, G., Jorrín, J. et al., Proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. Although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. These papers concern the proteome of at least 35 plant species but have concentrated mainly on thale cress (Arabidopsis thaliana) and rice (Oryza sativa). The scientific objectives have ranged from a proteomic analysis of organs, tissues, cell suspensions, or subcellular fractions to the study of plant development and response to various stresses. A number of contributions have covered PTMs and protein interactions. The dominant analytical platform has been 2-DE coupled to MS, but "second generation" techniques such as DIGE, multidimensional protein identification technology, isotope-coded affinity tags, and stable isotope labeling by amino acids in cell culture have begun to make an impact. This review aims to provide an update of the contribution of proteomics to plant biology during the period 2004-2006, and is divided into six sections: introduction, subcellular proteomes, plant development, responses to biotic and abiotic stresses, PTMs, and protein interactions. The conclusions summarize a view of the major pitfalls and challenges of plant proteomics.

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.

Branch roots of young maize seedlings, their production, growth, and phloem supply from the primary root

Branch root development on the primary root of maize (Zea mays L.) seedlings was followed for 9 d after planting. This period includes the shift from seedling heterotrophy to autotrophy. Linear density of branches in the basal region ranged from ~38 cm^-1 at the base to ~10 cm^-1 beyond 10 cm. Branch roots in the first ~8 cm were produced before assimilate was available. Branch length decreased from ~26 mm at 1 cm along the primary root to ~8 mm at 10 cm from the base. Without the cotyledon, branch root density in the basal region was ~10 cm^-1 and roots were short (~5 mm). Beyond 8-10 cm both measurements matched those of intact seedlings. Dark-grown seedlings had basal branch root densities higher than those without cotyledons but none beyond 10 cm. There were more and smaller diameter sieve tubes in the basal region of the primary root. These decreased distally in number but had larger diameters where branches formed after assimilate was available. Proliferation of basal branch roots in very young seedlings can have major advantages for successful seedling establishment in the field and could be screened for without difficulty.

Proteomic analysis of shoot-borne root initiation in maize (Zea mays L.)

Postembryonically formed shoot-borne roots make up the major backbone of the adult maize root stock. In this study the abundant soluble proteins of the first node (coleoptilar node) of wild-type and mutant rtcs seedlings, which do not initiate crown roots, were compared at two early stages of crown root formation. In Coomassie Bluestained 2-D gels, representing soluble proteins of coleoptilar nodes 5 and 10 days after germination, 146 and 203 proteins were detected, respectively. Five differentially accumulated proteins (> two-fold change; t-test: 95% significance) were identified in 5-day-old and 14 differentially accumulated proteins in 10-day-old coleoptilar nodes of wild-type versus rtcs. All 19 differentially accumulated proteins were identified via ESI MS/MS mass spectrometry. Five differentially accumulated proteins, including a regulatory G-protein and a putative auxin-binding protein, were further analyzed at the RNA expression level. These experiments confirmed differential gene expression and revealed subtle developmental regulation of these genes during early coleoptilar node development. This study represents the first proteomic analysis of shoot-borne root initiation in cereals and will contribute to a better understanding of the molecular basis of this developmental process unique to cereals.