Pseudomonas fluorescens N21.4 metabolites enhance secondary metabolism isoflavones in soybean (Glycine max) calli cultures

Phytopharmaceuticals are plant secondary metabolites that are strongly inducible and especially sensitive to biotic changes. Plant cell cultures are a good alternative to obtain secondary metabolites, in case effective stimulation can be achieved. In this study, metabolic elicitors from two rhizobacteria able to enhance isoflavone content in soybean seedlings were tested on three different soybean calli cell lines. Results show that metabolic elicitors from Chryseobacterium balustinum Aur9 were not effective. However, there are at least two different metabolic elicitors from Pseudomonas fluorescens N21.4, one under 10 kDa and another over 10 kDa, that trigger isoflavone metabolism in the three cell lines with different isoflavone content. Elicitors from N21.4 achieved total isoflavone increases up to 29.7% (0.205 mg/g), 64.5% (0.487 mg/g), and 23.4% (0.726 mg/g) in the low-, intermediate-, and high-yield lines, respectively. Therefore, these elicitors have a great potential to enhance isoflavone production in cell cultures for development of functional ingredients.

Soybean ureide transporters play a critical role in nodule development, function and nitrogen export

Legumes can access atmospheric nitrogen through a symbiotic relationship with nitrogen-fixing bacteroids that reside in root nodules. In soybean, the products of fixation are the ureides allantoin and allantoic acid, which are also the dominant long-distance transport forms of nitrogen from nodules to the shoot. Movement of nitrogen assimilates out of the nodules occurs via the nodule vasculature; however, the molecular mechanisms for ureide export and the importance of nitrogen transport processes for nodule physiology have not been resolved. Here, we demonstrate the function of two soybean proteins - GmUPS1-1 (XP_003516366) and GmUPS1-2 (XP_003518768) - in allantoin and allantoic acid transport out of the nodule. Localization studies revealed the presence of both transporters in the plasma membrane, and expression in nodule cortex cells and vascular endodermis. Functional analysis in soybean showed that repression of GmUPS1-1 and GmUPS1-2 in nodules leads to an accumulation of ureides and decreased nitrogen partitioning to roots and shoot. It was further demonstrated that nodule development, nitrogen fixation and nodule metabolism were negatively affected in RNAi UPS1 plants. Together, we conclude that export of ureides from nodules is mediated by UPS1 proteins, and that activity of the transporters is not only essential for shoot nitrogen supply but also for nodule development and function.

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

BACKGROUND

Current experimental evidence indicates that functionally related genes show coordinated expression in order to perform their cellular functions. In this way, the cell transcriptional machinery can respond optimally to internal or external stimuli. This provides a research opportunity to identify and study co-expressed gene modules whose transcription is controlled by shared gene regulatory networks.

RESULTS

We developed and integrated a set of computational methods of differential gene expression analysis, gene clustering, gene network inference, gene function prediction, and DNA motif identification to automatically identify differentially co-expressed gene modules, reconstruct their regulatory networks, and validate their correctness. We tested the methods using microarray data derived from soybean cells grown under various stress conditions. Our methods were able to identify 42 coherent gene modules within which average gene expression correlation coefficients are greater than 0.8 and reconstruct their putative regulatory networks. A total of 32 modules and their regulatory networks were further validated by the coherence of predicted gene functions and the consistency of putative transcription factor binding motifs. Approximately half of the 32 modules were partially supported by the literature, which demonstrates that the bioinformatic methods used can help elucidate the molecular responses of soybean cells upon various environmental stresses.

CONCLUSIONS

The bioinformatics methods and genome-wide data sources for gene expression, clustering, regulation, and function analysis were integrated seamlessly into one modular protocol to systematically analyze and infer modules and networks from only differential expression genes in soybean cells grown under stress conditions. Our approach appears to effectively reduce the complexity of the problem, and is sufficiently robust and accurate to generate a rather complete and detailed view of putative soybean gene transcription logic potentially underlying the responses to the various environmental challenges. The same automated method can also be applied to reconstruct differentially co-expressed gene modules and their regulatory networks from gene expression data of any other transcriptome.

14-3-3 proteins act as scaffolds for GmMYB62 and GmMYB176 and regulate their intracellular localization in soybean

Isoflavonoids are plant natural compounds predominantly found in leguminous plant. They play important functions in both nitrogen fixation and stress resistance. Many clinical studies have linked dietary intake of isoflavonoids to human health benefits. Binding of 14-3-3 proteins to GmMYB176, an isoflavonoid regulator, modulates expression of key isoflavonoids gene expression and its biosynthesis. We have recently demonstrated that the interaction of 14-3-3 proteins with GmMYB176 regulates nuclear-cytoplasmic localization of GmMYB176 thereby affecting target gene expression. Here, we report GmMYB62 as a new R1 MYB client protein of soybean 14-3-3s that may function together with GmMYB176 for gene regulation in soybean.

Immunofluorescent localization of ubiquitin and proteasomes in nucleolar vacuoles of soybean root meristematic cells

In this study, using the immunofluorescent method, the immunopositive signals to ubiquitin and proteasomes in nucleoli of root meristematic cells of soybean seedlings have been observed. In fact, those signals were present exclusively in nucleolar vacuoles. No signals were observed in the nucleolar territory out of the nucleolar vacuoles or in the nucleoli without vacuoles. The ubiquitin-proteasome system (UPS) may act within the nucleoli of plants with high metabolic activities and may provide an additional level of regulation of intracellular proteolysis via compartment-specific activities of their components. It is suggested that the presence of the UPS solely in vacuolated nucleoli serves as a mechanism that enhances the speed of ribosome subunit production in very actively transcribing nucleoli. On the other hand, nucleolar vacuoles in a cell/nucleus could play additional roles associated with temporary sequestration or storage of some cellular factors, including components of the ubiquitin-proteasome system.

Proteomics techniques for the development of flood tolerant crops

Proteomics is a useful analytical approach for investigating crop responses to stress. Recent remarkable advances in proteomic techniques allow for the identification of a wider range of proteins than was previously possible. The application of proteomic techniques to clarify the molecular mechanisms underlying crop responses to flooding stress may facilitate the development of flood tolerant crops. Flooding is an environmental stress found worldwide and may increase in frequency due to changes in global climate. Waterlogging resulting from flooding causes significant reductions in the growth and yield of several crops. Transient flooding displaces gases in soil pores and often causes hypoxia in plants grown on land with poor drainage. Changes in protein expression and post-translational modification of proteins occur as plants activate their defense system in response to flooding stress. In this review, we discuss the contributions that proteomic studies have made toward increasing our understanding of the well-organized cellular response to flooding in soybean and other crops. The biological relevance of the proteins identified using proteomic techniques in regard to crop stress tolerance will be discussed as well.

Differential responses of microsomal proteins and metabolites in two contrasting cadmium (Cd)-accumulating soybean cultivars under Cd stress

While there are significant genotypic differences in cadmium (Cd) uptake and distribution in soybean cultivars, little attention has been paid to the underlying molecular mechanisms. We adopted a comparative proteomic approach coupled with metabolite analysis to examine Cd uptake and translocation in two contrasting Cd-accumulating soybean cultivars, Enrei and Harosoy, which accumulate higher amount of Cd in the roots and aerial parts, respectively. Proteins extracted from the root microsomal fraction were evaluated by immunoblot analysis using different subcellular marker proteins. Analysis of control and Cd-exposed samples by two-dimensional gel electrophoresis coupled with mass spectrometry revealed a total of 13 and 11 differentially expressed proteins in the Enrei and Harosoy cultivars, respectively. Metabolome profiling identified a total of 32 metabolites, the expression of 18 of which was significantly altered in at least in one cultivar in response to Cd stress. Analysis of the combined proteomic and metabolomic results revealed that proteins and amino acids associate with Cd-chelating pathways are highly active in the Enrei cultivar. In addition, proteins associated with lignin biosynthesis are significantly upregulated in the Enrei cultivar under Cd stress. Our results indicate that in the Enrei cultivar, Cd-chelating agents may bind excess free Cd ion and that translocation of Cd from the roots to the aerial parts might be prevented by increased xylem lignification.

TAT-mediated aequorin transduction: an alternative approach for effective calcium measurements in plant cells

Cell-penetrating peptides are short cationic peptides with the property of translocating across the plasma membrane and transferring macromolecules otherwise unable to permeate cell membranes. We investigated the potential ability of the protein transduction domain derived from amino acids 47-57 of the human immunodeficiency virus type 1 (HIV-1) TAT (transactivator of transcription) protein to be used as a nanocarrier for the delivery of aequorin, a Ca(2+)-sensitive photoprotein widely used as a reliable Ca(2+) reporter in cell populations. The TAT peptide, either covalently linked to apoaequorin or ionically bound to plasmids encoding differentially targeted aequorin, was supplied to plant suspension-cultured cells. The TAT-aequorin fusion protein was found to be rapidly and effectively translocated into plant cells. The chimeric molecule was internalized in fully active biological form and at levels suitable to monitor intracellular Ca(2+) concentrations. Plant cells incubated for just 5 min with TAT-aequorin responded to different environmental stimuli with the expected Ca(2+) signatures. On the other hand, TAT-mediated plasmid internalization did not provide the necessary level of transformation efficiency to allow calibration of luminescence signals into Ca(2+) concentration values. These results indicate that TAT-mediated aequorin transduction is a promising alternative to traditional plant transformation methods to monitor intracellular Ca(2+) dynamics rapidly and effectively in plant cells.

Mapping cell fate decisions that occur during soybean defense responses

The soybean defense response to the soybean cyst nematode was used as a model to map at cellular resolution its genotype-defined cell fate decisions occurring during its resistant reactions. The defense responses occur at the site of infection, a nurse cell known as the syncytium. Two major genotype-defined defense responses exist, the G. max ([Peking])- and G. max ([PI 88788])-types. Resistance in G. max ([Peking]) is potent and rapid, accompanied by the formation of cell wall appositions (CWAs), structures known to perform important defense roles. In contrast, defense occurs by a potent but more prolonged reaction in G. max ([PI 88788]), lacking CWAs. Comparative transcriptomic analyses with confirmation by Illumina® deep sequencing were organized through a custom-developed application, Pathway Analysis and Integrated Coloring of Experiments (PAICE) that presents gene expression of these cytologically and developmentally distinct defense responses using the Kyoto Encyclopedia of Genes and Genomes (KEGG) framework. The analyses resulted in the generation of 1,643 PAICE pathways, allowing better understanding of gene activity across all chromosomes. Analyses of the rhg1 resistance locus, defined within a 67 kb region of DNA demonstrate expression of an amino acid transporter and an α soluble NSF attachment protein gene specifically in syncytia undergoing their defense responses.

The substrate specificities of sunflower and soybean phospholipases D using transphosphatidylation reaction

BACKGROUND

Phospholipase D (PLD) belongs to a lipolytic enzyme subclass which catalyzes the hydrolysis and transesterification of glycerophospholipids at the terminal phosphodiester bond.

RESULTS

In this work, we have studied the substrate specificity of PLDs from germinating sunflower seeds and cultured-soybean cells, using their capacity of transphosphatidylation. In the presence of a nucleophilic acceptor, such as [¹⁴C]ethanol, PLD catalyzes the production of phosphatidyl-[¹⁴C]-ethanol. The resulting product is easily identified since it is well separated from the other lipids by thin-layer chromatography. The main advantage of this assay is that the phospholipid used as substrate does not need to be radiolabelled and thus allow us a large choice of polar heads and fatty acids. In vitro, we observed that sunflower and soybean cell PLD show the following decreasing order of specificity: phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol; while phosphatidylserine and phosphatidylinositol are utilized much less efficiently.

CONCLUSIONS

The substrate specificity is modulated by the fatty acid composition of the phosphatidylcholine used as well as by the presence of other charged phospholipids.

The NAC domain-containing protein, GmNAC6, is a downstream component of the ER stress- and osmotic stress-induced NRP-mediated cell-death signaling pathway

BACKGROUND

The endoplasmic reticulum (ER) is a major signaling organelle, which integrates a variety of responses against physiological stresses. In plants, one such stress-integrating response is the N-rich protein (NRP)-mediated cell death signaling pathway, which is synergistically activated by combined ER stress and osmotic stress signals. Despite the potential of this integrated signaling to protect plant cells against different stress conditions, mechanistic knowledge of the pathway is lacking, and downstream components have yet to be identified.

RESULTS

In the present investigation, we discovered an NAC domain-containing protein from soybean, GmNAC6 (Glycine max NAC6), to be a downstream component of the integrated pathway. Similar to NRP-A and NRP-B, GmNAC6 is induced by ER stress and osmotic stress individually, but requires both signals for full activation. Transient expression of GmNAC6 promoted cell death and hypersensitive-like responses in planta. GmNAC6 and NRPs also share overlapping responses to biotic signals, but the induction of NRPs peaked before the increased accumulation of GmNAC6 transcripts. Consistent with the delayed kinetics of GmNAC6 induction, increased levels of NRP-A and NRP-B transcripts induced promoter activation and the expression of the GmNAC6 gene.

CONCLUSIONS

Collectively, our results biochemically link GmNAC6 to the ER stress- and osmotic stress-integrating cell death response and show that GmNAC6 may act downstream of the NRPs.

A cell-type-specific defect in border cell formation in the Acacia mangium root cap developing an extraordinary sheath of sloughed-off cells

BACKGROUND AND AIMS

Root caps release border cells, which play central roles in microbe interaction and root protection against soil stresses. However, the number and connectivity of border cells differ widely among plant species. Better understanding of key border-cell phenotype across species will help define the total function of border cells and associated genes.

METHODS

The spatio-temporal detachment of border cells in the leguminous tree Acacia mangium was investigated by using light and fluorescent microscopy with fluorescein diacetate, and their number and structural connectivity compared with that in soybean (Glycine max).

KEY RESULTS

Border-like cells with a sheet structure peeled bilaterally from the lateral root cap of A. mangium. Hydroponic root elongation partially facilitated acropetal peeling of border-like cells, which accumulate as a sheath that covers the 0- to 4-mm tip within 1 week. Although root elongation under friction caused basipetal peeling, lateral root caps were minimally trimmed as compared with hydroponic roots. In the meantime, A. mangium columella caps simultaneously released single border cells with a number similar to those in soybean.

CONCLUSIONS

These results suggest that cell type-specific inhibitory factors induce a distinct defective phenotype in single border-cell formation in A. mangium lateral root caps.

Response and tolerance of root border cells to aluminum toxicity in soybean seedlings

Root border cells (RBCs) and their secreted mucilage are suggested to participate in the resistance against toxic metal cations, including aluminum (Al), in the rhizosphere. However, the mechanisms by which the individual cell populations respond to Al and their role in Al resistance still remain unclear. In this research, the response and tolerance of RBCs to Al toxicity were investigated in the root tips of two soybean cultivars [Zhechun No. 2 (Al-tolerant cultivar) and Huachun No. 18 (Al-sensitive cultivar)]. Al inhibited root elongation and increased pectin methylesterase (PME) activity in the root tip. Removal of RBCs from the root tips resulted in a more severe inhibition of root elongation, especially in Huachun No. 18. Increasing Al levels and treatment time decreased the relative percent viability of RBCs in situ and in vitro in both soybean cultivars. Al application significantly increased mucilage layer thickness around the detached RBCs of both cultivars. Additionally, a significantly higher relative percent cell viability of attached and detached RBCs and thicker mucilage layers were observed in Zhechun No. 2. The higher viability of attached and detached RBCs, as well as the thickening of the mucilage layer in separated RBCs, suggest that RBCs play an important role in protecting root apices from Al toxicity.

Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways

BACKGROUND

Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plant cells. The expression of some plant genes is altered by the nematode as it establishes its feeding site.

RESULTS

We examined the expression of soybean (Glycine max) genes in galls formed in roots by the root-knot nematode, Meloidogyne incognita, 12 days and 10 weeks after infection to understand the effects of infection of roots by M. incognita. Gene expression was monitored using the Affymetrix Soybean GeneChip containing 37,500 G. max probe sets. Gene expression patterns were integrated with biochemical pathways from the Kyoto Encyclopedia of Genes and Genomes using PAICE software. Genes encoding enzymes involved in carbohydrate and cell wall metabolism, cell cycle control and plant defense were altered.

CONCLUSIONS

A number of different soybean genes were identified that were differentially expressed which provided insights into the interaction between M. incognita and soybean and into the formation and maintenance of giant cells. Some of these genes may be candidates for broadening plants resistance to root-knot nematode through over-expression or silencing and require further examination.

pHairyRed: a novel binary vector containing the DsRed2 reporter gene for visual selection of transgenic hairy roots

We developed a new plant transformation vector, pHairyRed, for enabling high throughput, non-destructive selection of Agrobacterium rhizogenes-mediated 'hairy-root' transformation. pHairyRed allows easy in planta visualization of transgenic tissue with minimal disturbance to the plant. The DsRed2 reporter gene, encoding a red fluorescent protein, was cloned to yield pHairyRed (harbouring a multiple cloning site), which was used with the highly efficient K599 A. rhizogenes strain to infect soybean (Glycine max L. Merrill) plants. DsRed2 fluorescence was easily detected in planta for the duration of a 5-week study with negligible levels of background autofluorescence. This enabled visual selection of transformed roots and subsequent excission of non-transformed roots. pHairyRed-transformed roots nodulated normally when inoculated with Bradyrhizobium japonicum. Within the nodule, DsRed2 fluorescence was plant-specific, being absent in the bacteroid-dominated nodule infected zone. To test the reliability of pHairyRed as a high-fidelity binary vector reporter system, the gene encoding the soybean Nod factor receptor, GmNFR1α, was cloned into the vector for use in a complementation study with a non-nodulating nfr1α mutant of soybean. Complementation was achieved and, without exception, DsRed2 fluorescence was detected in all hairy roots that successfully formed nodules (100%, n = 34). We anticipate broad application of this reporter system for the further analysis of root-related events in soybean and related legumes.

Search for nodulation-related CLE genes in the genome of Glycine max

CLE peptides are potentially involved in nodule organ development and in the autoregulation of nodulation (AON), a systemic process that restricts nodule number. A genome-wide survey of CLE peptide genes in the soybean glycine max genome resulted in the identification of 39 GmCLE genes, the majority of which have not yet been annotated. qRT-PCR analysis indicated two different nodulation-related CLE expression patterns, one linked with nodule primordium development and a new one linked with nodule maturation. Moreover, two GmCLE gene pairs, encoding group-III CLE peptides that were previously shown to be involved in AON, had a transient expression pattern during nodule development, were induced by the essential nodulation hormone cytokinin, and one pair was also slightly induced by the addition of nitrate. Hence, our data support the hypothesis that group-III CLE peptides produced in the nodules are involved in primordium homeostasis and intertwined in activating AON, but not in sustaining it.

A soybean β-expansin gene GmEXPB2 intrinsically involved in root system architecture responses to abiotic stresses

Root system architecture responds plastically to some abiotic stresses, including phosphorus (P), iron (Fe) and water deficiency, but its response mechanism is still unclear. We cloned and characterized a vegetative β-expansin gene, GmEXPB2, from a Pi starvation-induced soybean cDNA library. Transient expression of 35S::GmEXPB2-GFP in onion epidermal cells verified that GmEXPB2 is a secretory protein located on the cell wall. GmEXPB2 was found to be primarily expressed in roots, and was highly induced by Pi starvation, and the induction pattern was confirmed by GUS staining in transgenic soybean hairy roots. Results from intact soybean composite plants either over-expressing GmEXPB2 or containing knockdown constructs, showed that GmEXPB2 is involved in hairy root elongation, and subsequently affects plant growth and P uptake, especially at low P levels. The results from a heterogeneous transformation system indicated that over-expressing GmEXPB2 in Arabidopsis increased root cell division and elongation, and enhanced plant growth and P uptake at both low and high P levels. Furthermore, we found that, in addition to Pi starvation, GmEXPB2 was also induced by Fe and mild water deficiencies. Taken together, our results suggest that GmEXPB2 is a critical root β-expansin gene that is intrinsically involved in root system architecture responses to some abiotic stresses, including P, Fe and water deficiency. In the case of Pi starvation responses, GmEXPB2 may enhance both P efficiency and P responsiveness by regulating adaptive changes of the root system architecture. This finding has great agricultural potential for improving crop P uptake on both low-P and P-fertilized soils.

Evolutionary duplication of lipo-oligochitin-like receptor genes in soybean differentiates their function in cell division and cell invasion

Gene duplication in evolution has long been viewed as a mechanism for functional divergence. We recently cloned two related lipo-oligo-chitin receptor genes (GmNFR1α and GmNFR1β) in Glycine max(soybean) that allowed the distinction of two nodulation factor (NF) responses during early legume nodule ontogeny, namely invasion of the root hair and concomitant cortical cell divisions. Root-controlled GmNFR1αmutants nod49 and rj1 failed to form curled root hairs, infection threads and nodules but develop subepidermal cortical cell divisions (CCD) and mycorrhizal associations. In contrast GmNFR1β mutant PI437.654 had full symbiotic abilities. However, GmNFR1α mutants formed normal nodules at reduced frequency when inoculated with high Bradyrhizobium titers. The mutation was complemented in Agrobacterium rhizogenes K599 transformed roots using both CaMV 35S and the native GmNFR1promoters. GmNFR1α may encode a high affinity NF receptor responsible for the entire nodulation cascade while GmNFR1β with lower affinity to NF suffices to induce cell divisions but not early infection events.

Novel spatial expression of soybean WUSCHEL in the incipient floral primordia

The homeobox transcription factor WUSCHEL (WUS) is known to play a critical role in the maintenance of the stem cell population in shoot and floral meristems of Arabidopsis thaliana. The corresponding gene is yet to be characterized in soybean, a vital legume crop. In this study, we isolated the soybean ortholog of WUS (GmWUS) and explored its possible conserved function by in situ hybridization analysis and ectopic expression in Arabidopsis. GmWUS is expressed in the centre of soybean vegetative shoot apical meristem and floral meristem. Intriguingly, GmWUS is also found to be expressed in the incipient floral primordia before the formation of distinct floral meristem. This novel spatial expression pattern implicates GmWUS playing a role in the floral initiation process; it also raises the question of the molecular mechanism underlying the activation of GmWUS in these cells that have adopted the floral fate. Meanwhile, ectopic expression of GmWUS in Arabidopsis results in adventitious shoot and floral meristems' formation, and the disruption in floral organ patterning. These phenotypic alterations are largely consistent with the ectopic expression of Arabidopsis WUS, indicating similar function of GmWUS with its Arabidopsis counterpart. Nevertheless, our in situ hybridization analysis has revealed its spatial expression in the incipient floral primordia indicating an additional role of GmWUS in the floral initiation process.

Two host cytoplasmic effectors are required for pathogenesis of Phytophthora sojae by suppression of host defenses

Phytophthora sojae encodes hundreds of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling- and necrosis-inducing proteins (CRN) or Crinkler. Their functions and mechanisms in pathogenesis are mostly unknown. Here, we identify a group of five P. sojae-specific CRN-like genes with high levels of sequence similarity, of which three are putative pseudogenes. Functional analysis shows that the two functional genes encode proteins with predicted nuclear localization signals that induce contrasting responses when expressed in Nicotiana benthamiana and soybean (Glycine max). PsCRN63 induces cell death, while PsCRN115 suppresses cell death elicited by the P. sojae necrosis-inducing protein (PsojNIP) or PsCRN63. Expression of CRN fragments with deleted signal peptides and FLAK motifs demonstrates that the carboxyl-terminal portions of PsCRN63 or PsCRN115 are sufficient for their activities. However, the predicted nuclear localization signal is required for PsCRN63 to induce cell death but not for PsCRN115 to suppress cell death. Furthermore, silencing of the PsCRN63 and PsCRN115 genes in P. sojae stable transformants leads to a reduction of virulence on soybean. Intriguingly, the silenced transformants lose the ability to suppress host cell death and callose deposition on inoculated plants. These results suggest a role for CRN effectors in the suppression of host defense responses.

Difference in chilling-induced flavonoid profiles, antioxidant activity and chilling tolerance between soybean near-isogenic lines for the pubescence color gene

Chilling tolerance is an important trait of soybeans [Glycine max (L.) Merr.] produced in cool climates. We previously isolated a soybean flavonoid 3' hydroxylase (F3'H) gene corresponding to the T locus, which controls pubescence and seed coat color. A genetic link between the T gene and chilling tolerance has been reported, although the exact underlying mechanisms remain unclear. Using the soybean near-isogenic lines (NILs) To7B (TT) and To7G (tt), we examined the relationship between chilling injury, antioxidant activity and flavonoid profiles associated with chilling treatment (15°C). Chilling injury was more severe in the second trifoliate leaves of To7G than in those of To7B. Hydrogen peroxide accumulation and lipid peroxidation were enhanced by chilling in To7G. Chilling-induced enhancement of antioxidant activity was more prominent in To7B than in To7G. High performance liquid chromatography analysis indicated that the contents of quercetin glycosides and isorhamnetin glycosides (3',4'-dihydroxylated flavonol derivatives) increase in the second trifoliate leaves of To7B after chilling treatment, whereas the same treatment increased kaempferol glycoside (4'-monohydroxylated flavonol derivatives) content in the corresponding leaves of To7G. Histochemical staining also demonstrated chilling-induced flavonoid accumulation. Microarray analysis and real-time reverse transcription-PCR demonstrated that the transcript levels of soybean F3'H are upregulated by chilling. The differences in chilling injury, antioxidant activity and flavonoid species between the two NILs support the notion that soybean F3'H affects chilling tolerance by increasing antioxidant activity via production of 3',4'-dihydroxylated flavonol derivatives.

Differences in gene expression amplitude overlie a conserved transcriptomic program occurring between the rapid and potent localized resistant reaction at the syncytium of the Glycine max genotype Peking (PI 548402) as compared to the prolonged and potent resistant reaction of PI 88788

Glycine max L. Merr. (soybean) resistance to Heterodera glycines Ichinohe occurs at the site of infection, a nurse cell known as the syncytium. Resistance is classified into two cytologically-defined responses, the G. max ([Peking])- and G. max ([PI 88788])-types. Each type represents a cohort of G. max genotypes. Resistance in G. max ([Peking]) occurs by a potent and rapid localized response, affecting parasitic second stage juveniles (p-J2). In contrast, resistance occurs by a potent but more prolonged reaction in the genotype G. max ([PI 88788]) that affects nematode development at the J3 and J4 stages. Microarray analyses comparing these cytologically and developmentally distinct resistant reactions reveal differences in gene expression in pericycle and surrounding cells even before infection. The differences include higher relative levels of the differentially expressed in response to arachidonic acid 1 gene (DEA1 [Gm-DEA1]) (+224.19-fold) and a protease inhibitor (+68.28-fold) in G. max ([Peking/PI 548402]) as compared to G. max ([PI 88788]). Gene pathway analyses compare the two genotypes (1) before, (2) at various times during, (3) constitutively throughout the resistant reaction and (4) at all time points prior to and during the resistant reaction. The amplified levels of transcriptional activity of defense genes may explain the rapid and potent reaction in G. max ([Peking/PI 548402]) as compared to G. max ([PI 88788]). In contrast, the shared differential expression levels of genes in G. max ([Peking/PI 548402]) and G. max ([PI 88788]) may indicate a conserved genomic program underlying the G. max resistance on which the genotype-specific gene expression programs are built off.

Transient proliferation of proanthocyanidin-accumulating cells on the epidermal apex contributes to highly aluminum-resistant root elongation in camphor tree

Aluminum (Al) is a harmful element that rapidly inhibits the elongation of plant roots in acidic soils. The release of organic anions explains Al resistance in annual crops, but the mechanisms that are responsible for superior Al resistance in some woody plants remain unclear. We examined cell properties at the surface layer of the root apex in the camphor tree (Cinnamomum camphora) to understand its high Al resistance mechanism. Exposure to 500 μm Al for 8 d, more than 20-fold higher concentration and longer duration than what soybean (Glycine max) can tolerate, only reduced root elongation in the camphor tree to 64% of the control despite the slight induction of citrate release. In addition, Al content in the root apices was maintained at low levels. Histochemical profiling revealed that proanthocyanidin (PA)-accumulating cells were present at the adjacent outer layer of epidermis cells at the root apex, having distinctive zones for cell division and the early phase of cell expansion. Then the PA cells were gradually detached off the root, leaving thin debris behind, and the root surface was replaced with the elongating epidermis cells at the 3- to 4-mm region behind the tip. Al did not affect the proliferation of PA cells or epidermis cells, except for the delay in the start of expansion and the accelerated detachment of the former. In soybean roots, the innermost lateral root cap cells were absent in both PA accumulation and active cell division and failed to protect the epidermal cell expansion at 25 μm Al. These results suggest that transient proliferation and detachment of PA cells may facilitate the expansion of epidermis cells away from Al during root elongation in camphor tree.

Plant cell-wall cross-links by REDOR NMR spectroscopy

We present a new method that integrates selective biosynthetic labeling and solid-state NMR detection to identify in situ important protein cross-links in plant cell walls. We have labeled soybean cells by growth in media containing l-[ring-d(4)]tyrosine and l-[ring-4-(13)C]tyrosine, compared whole-cell and cell-wall (13)C CPMAS spectra, and examined intact cell walls using (13)C{(2)H} rotational echo double-resonance (REDOR) solid-state NMR. The proximity of (13)C and (2)H labels shows that 25% of the tyrosines in soybean cell walls are part of isodityrosine cross-links between protein chains. We also used (15)N{(13)C} REDOR of intact cell walls labeled by l-[ε-(15)N,6-(13)C]lysine and depleted in natural-abundance (15)N to establish that the side chains of lysine are not significantly involved in covalent cross-links to proteins or sugars.

Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress

Flooding is a major problem for soybean crop as it reduces the growth and grain yield. To investigate the function of the soybean cell wall in the response to flooding stress, cell wall proteins were analyzed. Cell wall proteins from roots and hypocotyls of soybeans, which were germinated for 2 days and subjected to 2 days of flooding, were purified, separated by two-dimensional polyacrylamide gel electrophoresis and stained with Coomassie brilliant blue. Sixteen out of 204 cell wall proteins showed responses to flooding stress. Of these, two lipoxygenases, four germin-like protein precursors, three stem 28/31 kDa glycoprotein precursors, and one superoxide dismutase [Cu-Zn] were downregulated. A copper amine oxidase was found to have shifted from the basic to acidic zone following flooding stress. Based on these results, it was confirmed by the lignin staining that the lignification was suppressed in the root of soybean under the flooding stress. These results suggest that the roots and hypocotyls of soybean caused the suppression of lignification through decrease of these proteins by downregulation of reactive oxygen species and jasmonate biosynthesis under flooding stress.

A distinct subfamily of papain-like cystein proteinases regulated by senescence and stresses in Glycine max

GMCP3 encodes a cystein proteinase of Glycine max belonging to the papain-like family (C1A in MEROPS database) that was previously found to be involved in the mobilization of protein reserves during seed germination. Here, we report that GMCP3 is induced by senescence and diverse stresses in non-seed tissues, thus indicating a more general function in plants. Cladistic analysis of papain-like proteins of plants indicated that GMCP3, along with related proteases of other species, belongs to a distinct new group within the C1A family, which can also be distinguished by the four-exon structure of the gene. We also describe the genomic organization of GMCP3 revealing the presence of two closely related copies that are transcriptionally regulated in a similar way, although only one appears to be functional.

A subtilisin-like protein from soybean contains an embedded, cryptic signal that activates defense-related genes

Among the arsenal of plant-derived compounds activated upon attack by herbivores and pathogens are small peptides that initiate and amplify defense responses. However, only a handful of plant signaling peptides have been reported. Here, we have isolated a 12-aa peptide from soybean (Glycine max) leaves that causes a pH increase of soybean suspension-cultured cell media within 10 min at low nanomolar concentrations, a response that is typical of other endogenous peptide elicitors and pathogen-derived elicitors. The amino acid sequence was determined and was found to be derived from a member of the subtilisin-like protease (subtilase) family. The sequence of the peptide was located within a region of the protein that is unique to subtilases in legume plants and not found within any other plant subtilases thus far identified. We have named this peptide signal Glycine max Subtilase Peptide (GmSubPep). The gene (Glyma18g48580) was expressed in all actively growing tissues of the soybean plant. Although transcription of Glyma18g48580 was not induced by wounding, methyl jasmonate, methyl salicylate, or ethephon, synthetic GmSubPep peptide, when supplied to soybean cultures, induced the expression of known defense-related genes, such as Cyp93A1, Chib-1b, PDR12, and achs. GmSubPep is a unique plant defense peptide signal, cryptically embedded within a plant protein with an independent metabolic role, providing insights into plant defense mechanisms.

Hourglass cell development in the soybean seed coat

BACKGROUND AND AIMS

Hourglass cells (HGCs) are prominent cells in the soybean seed coat, and have potential use as 'phytofactories' to produce specific proteins of interest. Previous studies have shown that HGCs initiate differentiation at about 9 d post-anthesis (dpa), assuming their characteristic morphology by 18 dpa. This study aims to document the structural changes in HGCs during this critical period, and to relate these changes to the concurrent development of a specific soybean peroxidase (SBP) encoded by the Ep gene.

METHODS

Pods were collected from plants at specific growth stages. Fresh material was processed for analysis of Ep peroxidase activity. Tissues were processed for scanning and transmission electron microscopy, as well as extracted for western blotting. A null variety lacking expression of Ep peroxidase was grown as a control.

KEY RESULTS AND CONCLUSIONS

At 9 dpa, HGCs are typical undifferentiated plant cells, but from 12-18 dpa they undergo rapid changes in their internal and external structure. By 18 dpa, they have assumed the characteristic hourglass shape with thick cell walls, intercellular air spaces and large central vacuoles. By 45 dpa, all organelles in HGCs have been degraded. Additional observations indicate that plasmodesmata connect all cell types. SBP activity and SBP protein are detectable in the HGC before they are fully differentiated (approx. 18 dpa). In very early stages, SBP activity appears localized in a vacuole as previously predicted. These results increase our understanding of the structure and development of the HGC and will be valuable for future studies aimed at protein targeting to components of the HGC endomembrane systems.

RPG1-B-derived resistance to AvrB-expressing Pseudomonas syringae requires RIN4-like proteins in soybean

Soybean (Glycine max) RPG1-B (for resistance to Pseudomonas syringae pv glycinea) mediates species-specific resistance to P. syringae expressing the avirulence protein AvrB, similar to the nonorthologous RPM1 in Arabidopsis (Arabidopsis thaliana). RPM1-derived signaling is presumably induced upon AvrB-derived modification of the RPM1-interacting protein, RIN4 (for RPM1-interacting 4). We show that, similar to RPM1, RPG1-B does not directly interact with AvrB but associates with RIN4-like proteins from soybean. Unlike Arabidopsis, soybean contains at least four RIN4-like proteins (GmRIN4a to GmRIN4d). GmRIN4b, but not GmRIN4a, complements the Arabidopsis rin4 mutation. Both GmRIN4a and GmRIN4b bind AvrB, but only GmRIN4b binds RPG1-B. Silencing either GmRIN4a or GmRIN4b abrogates RPG1-B-derived resistance to P. syringae expressing AvrB. Binding studies show that GmRIN4b interacts with GmRIN4a as well as with two other AvrB/RPG1-B-interacting isoforms, GmRIN4c and GmRIN4d. The lack of functional redundancy among GmRIN4a and GmRIN4b and their abilities to interact with each other suggest that the two proteins might function as a heteromeric complex in mediating RPG1-B-derived resistance. Silencing GmRIN4a or GmRIN4b in rpg1-b plants enhances basal resistance to virulent strains of P. syringae and the oomycete Phytophthora sojae. Interestingly, GmRIN4a- or GmRIN4b-silenced rpg1-b plants respond differently to AvrB-expressing bacteria. Although both GmRIN4a and GmRIN4b function to monitor AvrB in the presence of RPG1-B, GmRIN4a, but not GmRIN4b, negatively regulates AvrB virulence activity in the absence of RPG1-B.

Genotoxicity effect of nitrobenzene on soybean (Glycine max) root tip cells

Nitrobenzene is a synthetic compound widely used in industry which can lead to environmental pollution. While the toxicity and carcinogenicity of nitrobenzene on humans and animals have been studied, less is known about its genotoxicity to plants. In this study, the genotoxic effects of nitrobenzene were investigated with growing soybean seedlings in solution culture. Compared with the control, the growth of soybean seedlings (taproot length, longest lateral root length and lateral roots number) decreased and showed statistics difference at nitrobenzene test concentration of 50 and 100mg/L. Micronucleus, chromosomal bridge and others chromosomal aberrations were observed in soybean root tip cells exposed to nitrobenzene. Frequency of chromosomal aberrations increased linearly with nitrobenzene test concentration between 5 and 50mg/L and decreased at 100mg/L which showed significant difference between control and 25mg/L or higher test concentration. Results of the present study suggest that nitrobenzene has genotoxicity on soybean root tip cells. The mechanism of genotoxicity of NB needs further study. It is concluded that high environmental levels of nitrobenzene in rivers, lakes and dam waters are hazardous to aquatic species and to irrigated plants.

Metabolic and structural rearrangement during dark-induced autophagy in soybean (Glycine max L.) nodules: an electron microscopy and 31P and 13C nuclear magnetic resonance study

The effects of dark-induced stress on the evolution of the soluble metabolites present in senescent soybean (Glycine max L.) nodules were analysed in vitro using (13)C- and (31)P-NMR spectroscopy. Sucrose and trehalose were the predominant soluble storage carbons. During dark-induced stress, a decline in sugars and some key glycolytic metabolites was observed. Whereas 84% of the sucrose disappeared, only one-half of the trehalose was utilised. This decline coincides with the depletion of Gln, Asn, Ala and with an accumulation of ureides, which reflect a huge reduction of the N(2) fixation. Concomitantly, phosphodiesters and compounds like P-choline, a good marker of membrane phospholipids hydrolysis and cell autophagy, accumulated in the nodules. An autophagic process was confirmed by the decrease in cell fatty acid content. In addition, a slight increase in unsaturated fatty acids (oleic and linoleic acids) was observed, probably as a response to peroxidation reactions. Electron microscopy analysis revealed that, despite membranes dismantling, most of the bacteroids seem to be structurally intact. Taken together, our results show that the carbohydrate starvation induced in soybean by dark stress triggers a profound metabolic and structural rearrangement in the infected cells of soybean nodule which is representative of symbiotic cessation.

Transcriptome analysis of resistant and susceptible genotypes of Glycine tomentella during Phakopsora pachyrhizi infection reveals novel rust resistance genes

Soybean rust, caused by Phakopsora pachyrhizi, is a destructive foliar disease in nearly all soybean-producing countries. To identify genes controlling resistance to soybean rust, transcriptome profiling was conducted in resistant and susceptible Glycine tomentella genotypes triggered by P. pachyrhizi infection. Among 38,400 genes monitored using a soybean microarray, at 5% false discovery rate, 1,342 genes were identified exhibiting significant differential expression between uninfected and P. pachyrhizi-infected leaves at 12, 24, 48, and 72 h post-inoculation (hpi) in both rust-susceptible and rust-resistant genotypes. Differentially expressed genes were grouped into 12 functional categories, and among those, large numbers relate to basic plant metabolism. Transcripts for genes involved in the phenylpropanoid pathway were up-regulated early during rust infection. Similarly, genes coding for proteins related to stress and defense responses such as glutathione-S-transferases, peroxidases, heat shock proteins, and lipoxygenases were consistently up-regulated following infection at all four time points. Whereas, subsets of genes involved in cellular transport, cellular communication, cell cycle, and DNA processing were down-regulated. Quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) on randomly selected genes from the different categories confirmed these findings. Of differentially expressed genes, those associated with the flavonoid biosynthesis pathway as well as those coding for peroxidases and lipoxygenases were likely to be involved in rust resistance in soybean, and would serve as good candidates for functional studies. These findings provided insights into mechanisms underlying resistance and general activation of plant defense pathways in response to rust infection.

Study of the effects of salicylic acid on soybean mitochondrial lipids and respiratory properties using the alternative oxidase as a stress-reporter protein

Biotic and abiotic stresses can lead to modifications in the lipid composition of cell membranes. Although mitochondria appear to be implicated in stress responses, little is known about the membrane lipid changes that occur in these organelles in plants. Besides cytochrome c oxidase, plant mitochondria have an alternative oxidase (AOX) that accepts electrons directly from ubiquinol, dissipating energy as heat. AOX upregulation occurs under a variety of stresses and its induction by salicylic acid (SA) has been observed in different plant species. AOX was also suggested to be used as a functional marker for cell reprogramming under stress. In the present study, we have used etiolated soybean (Glycine max (L.) Merr. cv Cresir) seedlings to study the effects of SA treatment on the lipid composition and the respiratory properties of hypocotyl mitochondria. AOX expression was studied in detail, as a reporter protein, to evaluate whether modifications in mitochondrial energy metabolism were occurring. In mitochondria extracted from SA-treated seedlings, AOX capacity and protein contents increased. Both AOX1 and AOX2b transcripts accumulated in response to SA, but with different kinetics. A reduction in external NADH oxidation capacity was observed, whereas succinate respiration remained unchanged. The phospholipid composition of mitochondria remained similar in control and SA-treated plants, but a reduction in the relative amount of linolenic acid was observed in phosphatidylcholine, phosphatidylethanolamine and cardiolipin. The possible causes of the fatty acid modifications observed, and the implications for mitochondrial metabolism are discussed.

Genome-wide analysis of gene expression in soybean shoot apical meristem

The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs. The nature of genetic programs and the regulatory networks underlying SAM function in a major legume crop, soybean was investigated here. We used soybean GeneChip (containing 37,744 probe sets) to examine the transcript profiles associated with micro-dissected, actively growing SAMs or growth arrested axillary meristems (AMs) experiencing apical dominance, in comparison to that of non-meristem (NM) tissue. A total of 1,090 and 1,523 transcripts were identified to be significantly up- or down-regulated in the SAM in comparison to the NM. RT-PCR and in situ hybridization analysis were also carried out to verify the experimental approach. The resulting gene expression profiles point to the combinatorial role of diverse regulatory pathways including those associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation in meristem function. In situ hybridization analysis on selected transcripts has implicated their roles in SAM maintenance and the establishment of organ polarity. We also identified a gene, ANGUSITFOLIA3 that could potentially serve as a novel marker for differentiating cells in the meristem. Computational analysis on the promoter regions of Arabidopsis thaliana orthologs of genes with high expression in the soybean SAM revealed a conserved over-representation of three cis-acting regulatory motifs. Our data show that plant meristems possess a unique transcriptional profile, with shared "molecular signatures" in apical and axillary meristems providing a rich source of novel target genes for further studies into a fundamental process that impacts plant growth and crop productivity.

An atypical soybean leucine-rich repeat receptor-like kinase, GmLRK1, may be involved in the regulation of cell elongation

A leucine-rich repeat receptor-like kinase (LRR-RLK) encoded by one of the genes highly expressed in a specific stage of soybean seed development, referred to as GmLRK1, was identified and characterized. Examination of its kinase domain indicated that GmLRK1 may be a catalytically inactive atypical receptor kinase. An autophosphorylation assay confirmed that GmLRK1 is incapable of autophosphorylation in vitro. However, the phosphorylation of GmRLK1 could be induced after incubation with plant protein extracts, suggesting that some plant proteins may interact with GmLRK1 and phosphorylate the protein in vivo. Analyses of the expression profiles of GmLRK1 and its Arabidopsis ortholog At2g36570 revealed that they may be involved in regulation of more fundamental metabolic and/or developmental pathways, rather than a specialized developmental program such as seed development. Our results further indicate that the GmLRK1 and At2g36570 may play a role in the regulation of certain cellular processes that lead to cell elongation and expansion.

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.

Establishment of a soybean (Glycine max Merr. L) transposon-based mutagenesis repository

Soybean is a major crop species providing valuable feedstock for food, feed and biofuel. In recent years, considerable progress has been made in developing genomic resources for soybean, including on-going efforts to sequence the genome. These efforts have identified a large number of soybean genes, most with unknown function. Therefore, a major research priority is determining the function of these genes, especially those involved in agronomic performance and seed traits. One means to study gene function is through mutagenesis and the study of the resulting phenotypes. Transposon-tagging has been used successfully in both model and crop plants to support studies of gene function. In this report, we describe efforts to generate a transposon-based mutant collection of soybean. The Ds transposon system was used to create activation-tagging, gene and enhancer trap elements. Currently, the repository houses approximately 900 soybean events, with flanking sequence data derived from 200 of these events. Analysis of the insertions revealed approximately 70% disrupted known genes, with the majority matching sequences derived from either Glycine max or Medicago truncatula sequences. Among the mutants generated, one resulted in male-sterility and was shown to disrupt the strictosidine synthase gene. This example clearly demonstrates that it is possible to disrupt soybean gene function by insertional mutagenesis and to derive useful mutants by this approach in spite of the tetraploid nature of the soybean genome.

Disposable bioreactors for plant micropropagation and mass plant cell culture

Different types of bioreactors are used at Nestlé R&D Centre - Tours for mass propagation of selected plant varieties by somatic embryogenesis and for large scale culture of plants cells to produce metabolites or recombinant proteins. Recent studies have been directed to cut down the production costs of these two processes by developing disposable cell culture systems. Vegetative propagation of elite plant varieties is achieved through somatic embryogenesis in liquid medium. A pilot scale process has recently been set up for the industrial propagation of Coffea canephora (Robusta coffee). The current production capacity is 3.0 million embryos per year. The pre-germination of the embryos was previously conducted by temporary immersion in liquid medium in 10-L glass bioreactors. An improved process has been developed using a 10-L disposable bioreactor consisting of a bag containing a rigid plastic box ('Box-in-Bag' bioreactor), insuring, amongst other advantages, a higher light transmittance to the biomass due to its horizontal design. For large scale cell culture, two novel flexible plastic-based disposable bioreactors have been developed from 10 to 100 L working volumes, validated with several plant species ('Wave and Undertow' and 'Slug Bubble' bioreactors). The advantages and the limits of these new types of bioreactor are discussed, based mainly on our own experience on coffee somatic embryogenesis and mass cell culture of soya and tobacco.

Suppression of soybean oleosin produces micro-oil bodies that aggregate into oil body/ER complexes

Using RNAi, the seed oil body protein 24-kDa oleosin has been suppressed in transgenic soybeans. The endoplasmic reticulum (ER) forms micro-oil bodies about 50 nm in diameter that coalesce with adjacent oil bodies forming a hierarchy of oil body sizes. The oil bodies in the oleosin knockdown form large oil body-ER complexes with the interior dominated by micro-oil bodies and intermediate-sized oil bodies, while the peripheral areas of the complex are dominated by large oil bodies. The complex merges to form giant oil bodies with onset of seed dormancy that disrupts cell structure. The transcriptome of the oleosin knockdown shows few changes compared to wild-type. Proteomic analysis of the isolated oil bodies of the 24-kDa oleosin knockdown shows the absence of the 24-kDa oleosin and the presence of abundant caleosin and lipoxygenase. The formation of the micro-oil bodies in the oleosin knockdown is interpreted to indicate a function of the oleosin as a surfactant.

Isolation of a novel family of genes related to 2-oxoglutarate-dependent dioxygenases from soybean and analysis of their expression during root nodule senescence

A screen for genes involved in root nodule senescence has led to the isolation of the senescence-associated nodulin 1 (SAN1) multigene family from Glycine max (soybean). The three, tandemly repeated SAN1 genes each have three exons and two introns and are highly conserved. SAN1A and SAN1B code for conceptual proteins of 352 and 353 amino acids, respectively, and share over 83% sequence identity, while SAN1C encodes a truncated protein of 126 amino acids and is likely to be a pseudogene. The SAN1-encoded proteins share sequence similarity and highly conserved motifs with plant 2-oxoglutarate-dependent dioxygenases (2-ODDs), suggesting that they encode 2-ODDs. Analyses of the steady-state mRNA levels of SAN1A and SAN1B during senescence induced by treatment with fixed nitrogen or darkness demonstrate that SAN1A is downregulated during induced senescence. In contrast, SAN1B is upregulated by both treatments. The expression of the SAN1 genes is not restricted to nodules, suggesting that in addition to their function(s) in these organs, they play a more general role in plant metabolism.

A new branch of endoplasmic reticulum stress signaling and the osmotic signal converge on plant-specific asparagine-rich proteins to promote cell death

NRPs (N-rich proteins) were identified as targets of a novel adaptive pathway that integrates endoplasmic reticulum (ER) and osmotic stress signals based on coordinate regulation and synergistic up-regulation by tunicamycin and polyethylene glycol treatments. This integrated pathway diverges from the molecular chaperone-inducing branch of the unfolded protein response (UPR) in several ways. While UPR-specific targets were inversely regulated by ER and osmotic stresses, NRPs required both signals for full activation. Furthermore, BiP (binding protein) overexpression in soybean prevented activation of the UPR by ER stress inducers, but did not affect activation of NRPs. We also found that this integrated pathway transduces a PCD signal generated by ER and osmotic stresses that result in the appearance of markers associated with leaf senescence. Overexpression of NRPs in soybean protoplasts induced caspase-3-like activity and promoted extensive DNA fragmentation. Furthermore, transient expression of NRPs in planta caused leaf yellowing, chlorophyll loss, malondialdehyde production, ethylene evolution, and induction of the senescence marker gene CP1. This phenotype was alleviated by the cytokinin zeatin, a potent senescence inhibitor. Collectively, these results indicate that ER stress induces leaf senescence through activation of plant-specific NRPs via a novel branch of the ER stress response.

Anisotropic contraction in forisomes: simple models won't fit

Forisomes are ATP-independent, Ca(2+)-driven contractile protein bodies acting as reversible valves in the phloem of plants of the legume family. Forisome contraction is anisotropic, as shrinkage in length is associated with radial expansion and vice versa. To test the hypothesis that changes in length and width are causally related, we monitored Ca(2+)- and pH-dependent deformations in the exceptionally large forisomes of Canavalia gladiata by high-speed photography, and computed time-courses of derived geometric parameters (including volume and surface area). Soybean forisomes, which in the resting state resemble those of Canavalia geometrically but have less than 2% of the volume, were also studied to identify size effects. Calcium induced sixfold volume increases in forisomes of both species; in soybean, responses were completed in 0.15 s, compared to about 0.5 s required for a rapid response in Canavalia followed by slow swelling for several minutes. This size-dependent behavior supports the idea that forisome contractility might rest on similar mechanisms as those of polyelectrolyte gels, a class of artificial "smart" materials. In both species, time-courses of forisome length and diameter were variable and lacked correlation, arguing against a simple causal relationship between changes in length and width. Moreover, changes in the geometry of soybean forisomes differed qualitatively between Ca(2+)- and pH-responses, suggesting that divalent cations and protons target different sites on the forisome proteins.

A seed-specific AP2-domain transcription factor from soybean plays a certain role in regulation of seed germination

Plant seed development and germination are under strict temporal and spatial regulation, and transcription factors play important roles in this regulation. In the present study we identified an EST expressed specifically in the developing soybean seeds. The full length of the gene was obtained through further RACE analysis and the gene was named GmSGR. Sequence analysis revealed that this gene belonged to the AP2/ERF transcription factor family. Its AP2 domain had the highest similarity with that of the A-3 member AtABI4 of DREB subgroup in the AP2/ERF family in Arabidopsis. GmSGR did not exhibit transcriptional activation activity in the yeast assay system. GmSGR was overexpressed in Arabidopsis and the germination rates of the transgenic seeds were significantly higher than that of the wild type seeds under higher concentrations of ABA and glucose respectively. However, the germination rates of the transgenic seeds were lower than that of control under salt stress. The expression of AtEm6 and AtRD29B was higher in the seedlings of the transgenic plants than that in the wild-type seedlings. These results suggest that GmSGR may confer reduced ABA sensitivity and enhanced salt sensitivity to the transgenic seeds through regulating the expression of AtEm6 and AtRD29B genes.

Allelism and molecular mapping of soybean necrotic root mutants

Mutability of the w4 flower color locus in soybean, Glycine max (L.) Merr., is conditioned by an allele designated w4-m. Germinal revertants recovered among self-pollinated progeny of mutable plants have been associated with the generation of necrotic root mutations, chlorophyll-deficiency mutations, and sterility mutations. A total of 24 necrotic root mutant lines were generated from a total of 24 independent reversion events at the w4-m locus. The initial mutable population included 4 mutable categories for w4-m, designated (1) low frequency of early excisions, (2) low frequency of late excisions, (3) high frequency of early excisions, and (4) high frequency of late excisions. These mutable categories were based upon flower phenotype, i.e., somatic tissue. A total of 22 of 24 necrotic root mutations occurred from germinal reversions classified in the high frequency of excision categories. Of these 22 mutants, 14 came from early excisions and 8 came from late excisions. These necrotic root mutants were allelic to 6 previously identified necrotic root mutants derived from the study of germinal revertants, i.e., gene tagging studies, chemical mutagenesis, and "spontaneous" occurrences from genetic crosses. Thus, all 30 necrotic root mutants in soybean are allelic. An F2 mapping population from the cross of Minsoy (Rn1 Rn1) x T328 (rn1 rn1) was used to map the Rn1 locus using simple sequence repeat (SSR) markers. The Rn1 locus was located between Satt288 and Satt612 on molecular linkage group G.

Isolation of soybean protein P34 from oil bodies using hydrophobic interaction chromatography

BACKGROUND

Soybeans play a prominent role in allergologic research due to the high incidence of allergic reactions. For detailed studies on specific proteins it is necessary to have access to a large amount of pure substance.

RESULTS

In this contribution, a method for purifying soybean (Glycine max) protein P34 (also called Gly m Bd 30 K or Gly m 1) using hydrophobic interaction chromatography is presented. After screening experiments using 1 mL HiTrap columns, Butyl Sepharose 4 FF was selected for further systematic investigations. With this stationary phase, suitable operation conditions for two-step gradient elution using ammonium sulphate were determined experimentally. The separation conditions obtained in a small column could be scaled up successfully to column volumes of 7.5 and 75 mL, allowing for high product purities of almost 100% with a yield of 27% for the chromatographic separation step. Conditions could be simplified further using a onestep gradient, which gave comparable purification in a shorter process time. The identity of the purified protein was verified using in-gel digestion and mass spectrometry as well as immunological techniques.

CONCLUSION

With the technique presented it is possible to produce, within a short timeframe, pure P34, suitable for further studies where an example antigen is needed.

Quantitative conversion of phytate to inorganic phosphorus in soybean seeds expressing a bacterial phytase

Phytic acid (PA) contains the major portion of the phosphorus in the soybean (Glycine max) seed and chelates divalent cations. During germination, both minerals and phosphate are released upon phytase-catalyzed degradation of PA. We generated a soybean line (CAPPA) in which an Escherichia coli periplasmic phytase, the product of the appA gene, was expressed in the cytoplasm of developing cotyledons. CAPPA exhibited high levels of phytase expression, >or=90% reduction in seed PA, and concomitant increases in total free phosphate. These traits were stable, and, although resulted in a trend for reduced emergence and a statistically significant reduction in germination rates, had no effect on the number of seeds per plant or seed weight. Because phytate is not digested by monogastric animals, untreated soymeal does not provide monogastrics with sufficient phosphorus and minerals, and PA in the waste stream leads to phosphorus runoff. The expression of a cytoplasmic phytase in the CAPPA line therefore improves phosphorus availability and surpasses gains achieved by other reported transgenic and mutational strategies by combining in seeds both high phytase expression and significant increases in available phosphorus. Thus, in addition to its value as a high-phosphate meal source, soymeal from CAPPA could be used to convert PA of admixed meals, such as cornmeal, directly to utilizable inorganic phosphorus.

Analysis of the limitations of hepatitis B surface antigen expression in soybean cell suspension cultures

Soybean cell suspension cultures were transformed using Agrobacterium tumefaciens harboring pHBS/pHER constructs to express hepatitis B surface antigen (HBsAg). The transformed colonies were selected and analyzed for the expression of HBsAg by PCR, reverse transcription (RT) PCR, Western blot and ELISA analysis. The maximum expression of 700 ng/g F.W. was noted in pHER transformed cells. The highest expressing colonies were used to initiate the cell suspension cultures and the expression of HBsAg was estimated periodically. The expression levels were reduced drastically in cell suspension cultures compared to the colonies maintained on semi-solid medium. Various parameters were studied to maximize the cell growth and to retain the expression levels. The supplementation of culture medium with a protease inhibitor, leupeptin hemisulfate could restore up to 50% of HBsAg expression in cell suspension cultures. This is the first report to investigate the possible cause and solution to the loss of recombinant protein expression levels in plant cell suspension cultures.

Calcium-mediated perception and defense responses activated in plant cells by metabolite mixtures secreted by the biocontrol fungus Trichoderma atroviride

BACKGROUND

Calcium is commonly involved as intracellular messenger in the transduction by plants of a wide range of biotic stimuli, including signals from pathogenic and symbiotic fungi. Trichoderma spp. are largely used in the biological control of plant diseases caused by fungal phytopathogens and are able to colonize plant roots. Early molecular events underlying their association with plants are relatively unknown.

RESULTS

Here, we investigated the effects on plant cells of metabolite complexes secreted by Trichoderma atroviride wild type P1 and a deletion mutant of this strain on the level of cytosolic free Ca2+ and activation of defense responses. Trichoderma culture filtrates were obtained by growing the fungus alone or in direct antagonism with its fungal host, the necrotrophic pathogen Botrytis cinerea, and then separated in two fractions (>3 and <3 kDa). When applied to aequorin-expressing soybean (Glycine max L.) cell suspension cultures, Trichoderma and Botrytis metabolite mixtures were distinctively perceived and activated transient intracellular Ca2+ elevations with different kinetics, specific patterns of intracellular accumulation of reactive oxygen species and induction of cell death. Both Ca2+ signature and cellular effects were modified by the culture medium from the knock-out mutant of Trichoderma, defective for the production of the secreted 42 kDa endochitinase.

CONCLUSION

New insights are provided into the mechanism of interaction between Trichoderma and plants, indicating that secreted fungal molecules are sensed by plant cells through intracellular Ca2+ changes. Plant cells are able to discriminate signals originating in the single or two-fungal partner interaction and modulate defense responses.

Dinitro-o-cresol induces apoptosis-like cell death but not alternative oxidase expression in soybean cells

In plants, programmed cell death is thought to be activated during differentiation and in response to biotic and abiotic stresses. Although its mechanisms are far less clear, several morphological and biochemical features have been described in different experimental systems, including DNA laddering and cytosolic protease activation. Moreover, plant mitochondria have an alternative terminal oxidase (AOX), which is thought to be involved in protection against increased reactive oxygen species production, perhaps representing a mechanism to prevent programmed cell death. In this study, we analysed cell death induced by the herbicide dinitro-o-cresol (DNOC) in soybean (Glycine max) suspension cell cultures and evaluated biochemical and molecular events associated with programmed cell death. AOX capacity and expression were also determined. DNOC-treated cells showed fragmented nuclear DNA as assessed by an in situ assay that detects 3'-OH ends. In addition, specific colorimetric assays and immunoblot analysis revealed activation of caspase-3-like proteins and release of cytochrome c from mitochondria, respectively, confirming the apoptotic-like phenotype. Surprisingly, AOX capacity and protein levels decreased in DNOC-treated cells, suggesting no association between cell death and AOX under these experimental conditions. In conclusion, the results show that DNOC induces programmed cell death in soybean cells, suggesting that plants and animals might share similar pathways. Further, the role of AOX in cell death has not been confirmed, and may depend on the nature and intensity of stress conditions.

Activation of members of a MAPK module in beta-glucan elicitor-mediated non-host resistance of soybean

Plants recognize microbial pathogens by discriminating pathogen-associated molecular patterns from self-structures. We study the non-host disease resistance of soybean (Glycine max L.) to the oomycete, Phytophthora sojae. Soybean senses a specific molecular pattern consisting of a branched heptaglucoside that is present in the oomycetal cell walls. Recognition of this elicitor may be achieved through a beta-glucan-binding protein, which forms part of a proposed receptor complex. Subsequently, soybean mounts a complex defense response, which includes the increase of the cytosolic calcium concentration, the production of reactive oxygen species, and the activation of genes responsible for the synthesis of phytoalexins. We now report the identification of two mitogen-activated protein kinases (MAPKs) and one MAPK kinase (MAPKK) that may function as signaling elements in triggering the resistance response. The use of specific antisera enabled the identification of GmMPKs 3 and 6 whose activity is enhanced within the signaling pathway leading to defense reactions. Elicitor specificity of MAPK activation as well as the sensitivity against inhibitors suggested these kinases as part of the beta-glucan signal transduction pathway. An upstream GmMKK1 was identified based on sequence similarity to other plant MAPKKs and its interaction with the MAPKs was analyzed. Recombinant GmMKK1 interacted predominantly with GmMPK6, with concomitant phosphorylation of the MAPK protein. Moreover, a preferential physical interaction between GmMKK1 and GmMPK6 was demonstrated in yeast. These results suggest a role of a MAPK cascade in mediating beta-glucan signal transduction in soybean, similar to other triggers that activate MAPKs during innate immune responses in plants.