Enzymes and other agents that enhance cell wall extensibility

Regulation of cell wall remodeling in grapevine (Vitis vinifera L.) callus under individual mineral stress deficiency

Cell wall (CW) is a dynamic structure that determines the plant form, growth and response to environmental conditions. Vitis vinifera callus grown under nitrogen (-N), phosphorous (-P) and sulfur (-S) deficiency were used as a model system to address the influence of mineral stress in CW remodeling. Callus cells morphology was altered, mostly under -N, resulting in changes in cell length and width compared with the control. CW composition ascertained with specific staining and immuno-detection showed a decrease in cellulose and altered pattern of pectin methylesterification. Under mineral stress genes expression from candidate families disclosed mainly a downregulation of a glycosyl hydrolase family 9C (GH9C), xyloglucan transglycosylase/hydrolases (XTHs) with predicted hydrolytic activity and pectin methylesterases (PMEs). Conversely, upregulation of PMEs inhibitors (PMEIs) was observed. While methylesterification patterns can be associated to PME/PMEI gene expression, the lower cellulose content cannot be attributed to altered cellulose synthase (CesA) gene expression suggesting the involvement of other gene families. Salt extracts from -N and -P callus tissues increased plastic deformation in cucumber hypocotyls while no effect was observed with -S extracts. The lower endo-acting glycosyl hydrolase activity of -N callus extracts pinpoints a more expressive impact of -N on CW-remodeling.

Good and bad protons: genetic aspects of acidity stress responses in plants

Physiological aspects of acidity stress in plants (synonymous with H(+) rhizotoxicity or low-pH stress) have long been a focus of research, in particular with respect to acidic soils where aluminium and H(+) rhizotoxicities often co-occur. However, toxic H(+) and Al(3+) elicit different response mechanisms in plants, and it is important to consider their effects separately. The primary aim of this review was to provide the current state of knowledge regarding the genetics of the specific reactions to low-pH stress in growing plants. A comparison of the results gleaned from quantitative trait loci analysis and global transcriptome profiling of plants in response to high proton concentrations revealed a two-stage genetic response: (i) in the short-term, proton pump H(+)-ATPases present the first barrier in root cells, allocating an excess of H(+) into either the apoplast or vacuole; the ensuing defence signaling system involves auxin, salicylic acid, and methyl jasmonate, which subsequently initiate expression of STOP and DREB transcription factors as well as chaperone ROF; (2) the long-term response includes other genes, such as alternative oxidase and type II NAD(P)H dehydrogenase, which act to detoxify dangerous reactive oxygen species in mitochondria, and help plants better manage the stress. A range of transporter genes including those for nitrate (NTR1), malate (ALMT1), and heavy metals are often up-regulated by H(+) rhizotoxicity. Expansins, cell-wall-related genes, the γ-aminobutyric acid shunt and biochemical pH-stat genes also reflect changes in cell metabolism and biochemistry in acidic conditions. However, the genetics underlying the acidity stress response of plants is complicated and only fragmentally understood.

Nitrogen Source and External Medium pH Interaction Differentially Affects Root and Shoot Metabolism in Arabidopsis

Ammonium nutrition often represents an important growth-limiting stress in plants. Some of the symptoms that plants present under ammonium nutrition have been associated with pH deregulation, in fact external medium pH control is known to improve plants ammonium tolerance. However, the way plant cell metabolism adjusts to these changes is not completely understood. Thus, in this work we focused on how Arabidopsis thaliana shoot and root respond to different nutritional regimes by varying the nitrogen source ([Formula: see text] and [Formula: see text]), concentration (2 and 10 mM) and pH of the external medium (5.7 and 6.7) to gain a deeper understanding of cell metabolic adaptation upon altering these environmental factors. The results obtained evidence changes in the response of ammonium assimilation machinery and of the anaplerotic enzymes associated to Tricarboxylic Acids (TCA) cycle in function of the plant organ, the nitrogen source and the degree of ammonium stress. A greater stress severity at pH 5.7 was related to [Formula: see text] accumulation; this could not be circumvented in spite of the stimulation of glutamine synthetase, glutamate dehydrogenase, and TCA cycle anaplerotic enzymes. Moreover, this study suggests specific functions for different gln and gdh isoforms based on the nutritional regime. Overall, [Formula: see text] accumulation triggering ammonium stress appears to bear no relation to nitrogen assimilation impairment.

Analysis of Stress-Responsive Gene Expression in Cultivated and Weedy Rice Differing in Cold Stress Tolerance

Rice (Oryza sativa L.) cultivars show impairment of growth in response to environmental stresses such as cold at the early seedling stage. Locally adapted weedy rice is able to survive under adverse environmental conditions, and can emerge in fields from greater soil depth. Cold-tolerant weedy rice can be a good genetic source for developing cold-tolerant, weed-competitive rice cultivars. An in-depth analysis is presented here of diverse indica and japonica rice genotypes, mostly weedy rice, for cold stress response to provide an understanding of different stress adaptive mechanisms towards improvement of the rice crop performance in the field. We have tested a collection of weedy rice genotypes to: 1) classify the subspecies (ssp.) grouping (japonica or indica) of 21 accessions; 2) evaluate their sensitivity to cold stress; and 3) analyze the expression of stress-responsive genes under cold stress and a combination of cold and depth stress. Seeds were germinated at 25°C at 1.5- and 10-cm sowing depth for 10d. Seedlings were then exposed to cold stress at 10°C for 6, 24 and 96h, and the expression of cold-, anoxia-, and submergence-inducible genes was analyzed. Control plants were seeded at 1.5cm depth and kept at 25°C. The analysis revealed that cold stress signaling in indica genotypes is more complex than that of japonica as it operates via both the CBF-dependent and CBF-independent pathways, implicated through induction of transcription factors including OsNAC2, OsMYB46 and OsF-BOX28. When plants were exposed to cold + sowing depth stress, a complex signaling network was induced that involved cross talk between stresses mediated by CBF-dependent and CBF-independent pathways to circumvent the detrimental effects of stresses. The experiments revealed the importance of the CBF regulon for tolerance to both stresses in japonica and indica ssp. The mechanisms for cold tolerance differed among weedy indica genotypes and also between weedy indica and cultivated japonica ssp. as indicated by the up/downregulation of various stress-responsive pathways identified from gene expression analysis. The cold-stress response is described in relation to the stress signaling pathways, showing complex adaptive mechanisms in different genotypes.

Altered cell wall properties are responsible for ammonium-reduced aluminium accumulation in rice roots

The phytotoxicity of aluminium (Al) ions can be alleviated by ammonium (NH4(+)) in rice and this effect has been attributed to the decreased Al accumulation in the roots. Here, the effects of different nitrogen forms on cell wall properties were compared in two rice cultivars differing in Al tolerance. An in vitro Al-binding assay revealed that neither NH4(+) nor NO3(-) altered the Al-binding capacity of cell walls, which were extracted from plants not previously exposed to N sources. However, cell walls extracted from NH4(+)-supplied roots displayed lower Al-binding capacity than those from NO3(-)-supplied roots when grown in non-buffered solutions. Fourier-transform infrared microspectroscopy analysis revealed that, compared with NO3(-)-supplied roots, NH4(+)-supplied roots possessed fewer Al-binding groups (-OH and COO-) and lower contents of pectin and hemicellulose. However, when grown in pH-buffered solutions, these differences in the cell wall properties were not observed. Further analysis showed that the Al-binding capacity and properties of cell walls were also altered by pHs alone. Taken together, our results indicate that the NH4(+)-reduced Al accumulation was attributed to the altered cell wall properties triggered by pH decrease due to NH4(+) uptake rather than direct competition for the cell wall binding sites between Al(3+) and NH4(+).

The involvement of expansins in response to water stress during leaf development in wheat

Expansins are cell wall proteins that are generally considered to be the key regulator of cell wall extension during plant growth. In this study, we used two different wheat (Triticum aestivum L.) cultivars to demonstrate that expansins are involved in wheat leaf growth and response to water stress, by regulating the expansin activity and cell wall susceptibility to expansins. Expansin activity was associated with the relative elongation rate of leaves during leaf development, suggesting their involvement in leaf elongation. Moreover, cell wall extension characteristics and expansin gene transcription were closely involved in the leaf cell elongation region. Water stress restrains leaf growth, but the growth rate of leaves was changed after rehydration, which is consistent with the response of expansin activity to water stress. Meanwhile, increased cell wall susceptibility to expansin by water deficit played an important role in maintaining cell wall extension. Furthermore, the expansin activity in drought-resistant cultivar HF9703 was always higher than that in drought-sensitive cultivar 921842 under water stress condition, which may be correlated with the higher expansin gene expression in HF9703 versus 921842. These data provide evidence for a role of expansins in the growth and response of wheat leaves to water stress.

Boron deficiency inhibits root cell elongation via an ethylene/auxin/ROS-dependent pathway in Arabidopsis seedlings

One of the earliest symptoms of boron (B) deficiency is the inhibition of root elongation which can reasonably be attributed to the damaging effects of B deprivation on cell wall integrity. It is shown here that exposure of wild-type Arabidopsis thaliana seedlings to B deficiency for 4h led to a drastic inhibition of root cell length in the transition between the elongation and differentiation zones. To investigate the possible mediation of ethylene, auxin, and reactive oxygen species (ROS) in the effect of B deficiency on root cell elongation, B deficiency was applied together with aminoethoxyvinylglycine (AVG, a chemical inhibitor of ethylene biosynthesis), silver ions (Ag(+), an antagonist of ethylene perception), α-(phenylethyl-2-oxo)-indoleacetic acid (PEO-IAA, a synthetic antagonist of TIR1 receptor function), and diphenylene iodonium (DPI, an inhibitor of ROS production). Interestingly, all these chemicals partially or fully restored cell elongation in B-deficient roots. To further explore the possible role of ethylene and auxin in the inhibition of root cell elongation under B deficiency, a genetic approach was performed by using Arabidopsis mutants defective in the ethylene (ein2-1) or auxin (eir1-4 and aux1-22) response. Root cell elongation in these mutants was less sensitive to B-deficient treatment than that in wild-type plants. Altogether, these results demonstrated that a signalling pathway involving ethylene, auxin, and ROS participates in the reduction of root cell elongation when Arabidopsis seedlings are subjected to B deficiency. A similar signalling process has been described to reduce root elongation rapidly under various types of cell wall stress which supports the idea that this signalling pathway is triggered by the impaired cell wall integrity caused by B deficiency.

Limitation of Cell Elongation in Barley (Hordeum vulgare L.) Leaves Through Mechanical and Tissue-Hydraulic Properties

The aim of the present study was to assess the mechanical and hydraulic limitation of growth in leaf epidermal cells of barley (Hordeum vulgare L.) in response to agents which affect cellular water (mercuric chloride, HgCl(2)) and potassium (cesium chloride, CsCl; tetraethylammonium, TEA) transport, pump activity of plasma membrane H(+)-ATPase and wall acidification (fusicoccin, FC). Cell turgor (P) was measured with the cell pressure probe, and cell osmotic pressure (π) was analyzed through picoliter osmometry of single-cell extracts. A wall extensibility coefficient (M) and tissue hydraulic conductance coefficient (L) were derived using the Lockhart equation. There was a significant positive linear relationship between relative elemental growth rate and P, which fit all treatments, with an overall apparent yield threshold of 0.368 MPa. Differences in growth between treatments could be explained through differences in P. A comparison of L and M showed that growth in all except the FC treatment was co-limited through hydraulic and mechanical properties, though to various extents. This was accompanied by significant (0.17-0.24 MPa) differences in water potential (ΔΨ) between xylem and epidermal cells in the leaf elongation zone. In contrast, FC-treated leaves showed ΔΨ close to zero and a 10-fold increase in L.

Metabolic methanol: molecular pathways and physiological roles

Methanol has been historically considered an exogenous product that leads only to pathological changes in the human body when consumed. However, in normal, healthy individuals, methanol and its short-lived oxidized product, formaldehyde, are naturally occurring compounds whose functions and origins have received limited attention. There are several sources of human physiological methanol. Fruits, vegetables, and alcoholic beverages are likely the main sources of exogenous methanol in the healthy human body. Metabolic methanol may occur as a result of fermentation by gut bacteria and metabolic processes involving S-adenosyl methionine. Regardless of its source, low levels of methanol in the body are maintained by physiological and metabolic clearance mechanisms. Although human blood contains small amounts of methanol and formaldehyde, the content of these molecules increases sharply after receiving even methanol-free ethanol, indicating an endogenous source of the metabolic methanol present at low levels in the blood regulated by a cluster of genes. Recent studies of the pathogenesis of neurological disorders indicate metabolic formaldehyde as a putative causative agent. The detection of increased formaldehyde content in the blood of both neurological patients and the elderly indicates the important role of genetic and biochemical mechanisms of maintaining low levels of methanol and formaldehyde.

Differential Roles of PIN1 and PIN2 in Root Meristem Maintenance Under Low-B Conditions in Arabidopsis thaliana

Boron (B) is an essential element for plants; its deficiency causes rapid cessation of root elongation. In addition, B influences auxin accumulation in plants. To assess the importance of auxin transport in B-dependent root elongation, Arabidopsis thaliana pin1-pin4 mutants were grown under low-B conditions. Among them, only the pin2/eir1-1 mutant showed a significantly shorter root under low-B conditions than under control conditions. Moreover, the root meristem size of pin2/eir1-1 was reduced under low-B conditions. Among the PIN-FORMED (PIN) family, PIN1 and PIN2 are important for root meristem growth/maintenance under normal conditions. To investigate the differential response of pin1 and pin2 mutants under low-B conditions, the effect of low-B on PIN1-green fluorescent protein (GFP) and PIN2-GFP accumulation and localization was examined. Low-B did not affect PIN2-GFP, while it reduced the accumulation of PIN1-GFP. Moreover, no signal from DII-VENUS, an auxin sensor, was detected under the low-B condition in the stele of wild-type root meristems. Taken together, these results indicate that under low-B conditions PIN1 is down-regulated and PIN2 plays an important role in root meristem maintenance.

Populus endo-β-1,4-glucanases gene family: genomic organization, phylogenetic analysis, expression profiles and association mapping

Extensive characterization of the poplar GH9 gene family provides new insights into GH9 function and evolution in woody species, and may drive novel progress for molecular breeding in trees. In higher plants, endo-β-1,4-glucanases (cellulases) belonging to the glycosyl hydrolase family 9 (GH9) have roles in cell wall synthesis, remodeling and degradation. To increase the understanding of the GH9 family in perennial woody species, we conducted an extensive characterization of the GH9 family in the model tree species, Populus. We characterized 25 putative GH9 members in Populus with three subclasses (A, B, and C), using structures and bioinformatic analysis. Phylogenetic analyses of 114 GH9s from plant (dicot, monocot, and conifer) and bacterial species (outgroup) demonstrated that plant GH9s are monophyletic with respect to bacteria GH9s. Three subclasses, A, B, and C, of plant GH9 are formed before the divergence of angiosperms and gymnosperms. Chromosomal localization and duplications of GH9s in the Populus genome showed that eight paralogous pairs remained in conserved positions on segmental duplicated blocks, suggesting duplication of chromosomal segments has contributed to the family expansion. By examining tissue-specific expression profiles for all 25 members, we found that GH9 members exhibited distinct but partially overlapping expression patterns, while certain members have higher transcript abundance in mature or developing xylem. Based on our understanding of intraspecific variation and linkage disequilibrium of two KORRIGANs (PtoKOR1 and PtoKOR2) in natural population of Populus tomentosa, two non-synonymous SNPs in PtoKOR1 associated with fiber width and holocellulose content were obtained. Characterizations of the poplar GH9 family provide new insights into GH9 function and evolution in woody species, and may drive novel progress for molecular breeding in trees.

Over-expression of TaEXPB23, a wheat expansin gene, improves oxidative stress tolerance in transgenic tobacco plants

Expansins are cell wall proteins inducing cell wall loosening and participate in all plant growth and development processes which are associated with cell wall modifications. Here, TaEXPB23, a wheat expansin gene, was investigated and the tolerance to oxidative stress was strongly enhanced in over-expression tobacco plants. Our results revealed that over-expressing TaEXPB23 influenced the activity of antioxidant enzymes: in particular, the activity of the cell wall-bound peroxidase. The enhanced tolerance to oxidative stress and increased cell wall-bound peroxidase activity were partly inhibited by an anti-expansin antibody. The Arabidopsis expansin mutant atexpb2 showed reduced cell wall-bound peroxidase activity and decreased oxidative stress tolerance. In addition, atexpb2 exhibited lower chlorophyll contents and the germination rate compared to wild type (WT). Taken together, these results provided a new insight on the role of expansin proteins in plant stress tolerance by cell wall bound peroxidase.

Physical forces regulate plant development and morphogenesis

Plant cells in tissues experience mechanical stress not only as a result of high turgor, but also through interaction with their neighbors. Cells can expand at different rates and in different directions from neighbors with which they share a cell wall. This in connection with specific tissue shapes and properties of the cell wall material can lead to intricate stress patterns throughout the tissue. Two cellular responses to mechanical stress are a microtubule cytoskeletal response that directs new wall synthesis so as to resist stress, and a hormone transporter response that regulates transport of the hormone auxin, a regulator of cell expansion. Shape changes in plant tissues affect the pattern of stresses in the tissues, and at the same time, via the cellular stress responses, the pattern of stresses controls cell growth, which in turn changes tissue shape, and stress pattern. This feedback loop controls plant morphogenesis, and explains several previously mysterious aspects of plant growth.

Summarizing and exploring data of a decade of cytokinin-related transcriptomics

The genome-wide transcriptional response of the model organism Arabidopsis thaliana to cytokinin has been investigated by different research groups as soon as large-scale transcriptomic techniques became affordable. Over the last 10 years many transcriptomic datasets related to cytokinin have been generated using different technological platforms, some of which are published only in databases, culminating in an RNA sequencing experiment. Two approaches have been made to establish a core set of cytokinin-regulated transcripts by meta-analysis of these datasets using different preferences regarding their selection. Here we add another meta-analysis derived from an independent microarray platform (CATMA), combine all the meta-analyses available with RNAseq data in order to establish an advanced core set of cytokinin-regulated transcripts, and compare the results with the regulation of orthologous rice genes by cytokinin. We discuss the functions of some of the less known cytokinin-regulated genes indicating areas deserving further research to explore cytokinin function. Finally, we investigate the promoters of the core set of cytokinin-induced genes for the abundance and distribution of known cytokinin-responsive cis elements and identify a set of novel candidate motifs.

Distribution of XTH, expansin, and secondary-wall-related CesA in floral and fruit abscission zones during fruit development in tomato (Solanum lycopersicum)

After fruit development is triggered by pollination, the abscission zone (AZ) in the fruit pedicel strengthens its adhesion to keep the fruit attached. We previously reported that xyloglucan and arabinan accumulation in the AZ accompanies the shedding of unpollinated flowers. After the fruit has developed and is fully ripened, shedding occurs easily in the AZ due to lignin accumulation. Regulation of cell wall metabolism may play an important role in these processes, but it is not well understood. In the present report, we used immunohistochemistry to visualize changes in the distributions of xyloglucan and arabinan metabolism-related enzymes in the AZs of pollinated and unpollinated flowers, and in ripened fruits. During floral abscission, we observed a gradual increase in polyclonal antibody labeling of expansin in the AZ. The intensities of LM6 and LM15 labeling of arabinan and xyloglucan, respectively, also increased. However, during floral abscission, we observed a large 1 day post anthesis (DPA) peak in the polyclonal antibody labeling of XTH in the AZ, which then decreased. These results suggest that expansin and XTH play important, but different roles in the floral abscission process. During fruit abscission, unlike during floral abscission, no AZ-specific expansin and XTH were observed. Although lignification was seen in the AZ of over-ripe fruit pedicels, secondary cell wall-specific cellulose synthase signals were not observed. This suggests that cellulose metabolism-related enzymes do not play important roles in the AZ prior to fruit abscission.

Impacts of groundwater discharge at Myora Springs (North Stradbroke Island, Australia) on the phenolic metabolism of eelgrass, Zostera muelleri, and grazing by the juvenile rabbitfish, Siganus fuscescens

Myora Springs is one of many groundwater discharge sites on North Stradbroke Island (Queensland, Australia). Here spring waters emerge from wetland forests to join Moreton Bay, mixing with seawater over seagrass meadows dominated by eelgrass, Zostera muelleri. We sought to determine how low pH/high CO2 conditions near the spring affect these plants and their interactions with the black rabbitfish (Siganus fuscescens), a co-occurring grazer. In paired-choice feeding trials S. fuscescens preferentially consumed Z. muelleri shoots collected nearest to Myora Springs. Proximity to the spring did not significantly alter the carbon and nitrogen contents of seagrass tissues but did result in the extraordinary loss of soluble phenolics, including Folin-reactive phenolics, condensed tannins, and phenolic acids by ≥87%. Conversely, seagrass lignin contents were, in this and related experiments, unaffected or increased, suggesting a shift in secondary metabolism away from the production of soluble, but not insoluble, (poly)phenolics. We suggest that groundwater discharge sites such as Myora Springs, and other sites characterized by low pH, are likely to be popular feeding grounds for seagrass grazers seeking to reduce their exposure to soluble phenolics.

Patterns of cell elongation in the determination of the final shape in galls of Baccharopelma dracunculifoliae (Psyllidae) on Baccharis dracunculifolia DC (Asteraceae)

Cell redifferentiation, division, and elongation are recurrent processes, which occur during gall development, and are dependent on the cellulose microfibrils reorientation. We hypothesized that changes in the microfibrils orientation from non-galled tissues to galled ones occur and determine the final gall shape. This determination is caused by a new tissue zonation, its hyperplasia, and relative cell hypertrophy. The impact of the insect's activity on these patterns of cell development was herein tested in Baccharopelma dracunculifoliae-Baccharis dracunculifolia system. In this system, the microfibrils are oriented perpendicularly to the longest cell axis in elongated cells and randomly in isodiametric ones, either in non-galled or in galled tissues. The isodiametric cells of the abaxial epidermis in non-galled tissues divided and elongated periclinally, forming the outer gall epidermis. The anticlinally elongated cells of the abaxial palisade layer and the isodiametric cells of the spongy parenchyma originated the gall outer cortex with hypertrophied and periclinally elongated cells. The anticlinally elongated cells of the adaxial palisade layer originated the inner cortex with hypertrophied and periclinally elongated cells in young and mature galls and isodiametric cells in senescent galls. The isodiametric cells of the adaxial epidermis elongated periclinally in the inner gall epidermis. The current investigation demonstrates the role of cellulose microfibril reorientation for gall development. Once many factors other than this reorientation act on gall development, it should be interesting to check the possible relationship of the new cell elongation patterns with the pectic composition of the cell walls.

Arabidopsis thaliana RALF1 opposes brassinosteroid effects on root cell elongation and lateral root formation

Rapid alkalinization factor (RALF) is a peptide signal that plays a basic role in cell biology and most likely regulates cell expansion. In this study, transgenic Arabidopsis thaliana lines with high and low levels of AtRALF1 transcripts were used to investigate this peptide's mechanism of action. Overexpression of the root-specific isoform AtRALF1 resulted in reduced cell size. Conversely, AtRALF1 silencing increased root length by increasing the size of root cells. AtRALF1-silenced plants also showed an increase in the number of lateral roots, whereas AtRALF1 overexpression produced the opposite effect. In addition, four AtRALF1-inducible genes were identified: two genes encoding proline-rich proteins (AtPRP1 and AtPRP3), one encoding a hydroxyproline-rich glycoprotein (AtHRPG2), and one encoding a xyloglucan endotransglucosylase (TCH4). These genes were expressed in roots and involved in cell-wall rearrangement, and their induction was concentration dependent. Furthermore, AtRALF1-overexpressing plants were less sensitive to exogenous brassinolide (BL); upon BL treatment, the plants showed no increase in root length and a compromised increase in hypocotyl elongation. In addition, the treatment had no effect on the number of emerged lateral roots. AtRALF1 also induces two brassinosteroid (BR)-downregulated genes involved in the BR biosynthetic pathway: the cytochrome P450 monooxygenases CONSTITUTIVE PHOTOMORPHISM AND DWARFISM (CPD) and DWARF4 (DWF4). Simultaneous treatment with both AtRALF1 and BL caused a reduction in AtRALF1-inducible gene expression levels, suggesting that these signals may compete for components shared by both pathways. Taken together, these results indicate an opposing effect of AtRALF1 and BL, and suggest that RALF's mechanism of action could be to interfere with the BR signalling pathway.

Extraction of high-quality DNA from ethanol-preserved tropical plant tissues

Background

Proper conservation of plant samples, especially during remote field collection, is essential to assure quality of extracted DNA. Tropical plant species contain considerable amounts of secondary compounds, such as polysaccharides, phenols, and latex, which affect DNA quality during extraction. The suitability of ethanol (96% v/v) as a preservative solution prior to DNA extraction was evaluated using leaves of Jatropha curcas and other tropical species.

Results

Total DNA extracted from leaf samples stored in liquid nitrogen or ethanol from J. curcas and other tropical species (Theobroma cacao, Coffea arabica, Ricinus communis, Saccharum spp., and Solanum lycopersicon) was similar in quality, with high-molecular-weight DNA visualized by gel electrophoresis. DNA quality was confirmed by digestion with EcoRI or HindIII and by amplification of the ribosomal gene internal transcribed spacer region. Leaf tissue of J. curcas was analyzed by light and transmission electron microscopy before and after exposure to ethanol. Our results indicate that leaf samples can be successfully preserved in ethanol for long periods (30 days) as a viable method for fixation and conservation of DNA from leaves. The success of this technique is likely due to reduction or inactivation of secondary metabolites that could contaminate or degrade genomic DNA.

Conclusions

Tissue conservation in 96% ethanol represents an attractive low-cost alternative to commonly used methods for preservation of samples for DNA extraction. This technique yields DNA of equivalent quality to that obtained from fresh or frozen tissue.

Histone acetylation associated up-regulation of the cell wall related genes is involved in salt stress induced maize root swelling

BACKGROUND

Salt stress usually causes crop growth inhibition and yield decrease. Epigenetic regulation is involved in plant responses to environmental stimuli. The epigenetic regulation of the cell wall related genes associated with the salt-induced cellular response is still little known. This study aimed to analyze cell morphological alterations in maize roots as a consequence of excess salinity in relation to the transcriptional and epigenetic regulation of the cell wall related protein genes.

RESULTS

In this study, maize seedling roots got shorter and displayed swelling after exposure to 200 mM NaCl for 48 h and 96 h. Cytological observation showed that the growth inhibition of maize roots was due to the reduction in meristematic zone cell division activity and elongation zone cell production. The enlargement of the stele tissue and cortex cells contributed to root swelling in the elongation zone. The cell wall is thought to be the major control point for cell enlargement. Cell wall related proteins include xyloglucan endotransglucosylase (XET), expansins (EXP), and the plasma membrane proton pump (MHA). RT-PCR results displayed an up-regulation of cell wall related ZmEXPA1, ZmEXPA3, ZmEXPA5, ZmEXPB1, ZmEXPB2 and ZmXET1 genes and the down-regulation of cell wall related ZmEXPB4 and ZmMHA genes as the duration of exposure was increased. Histone acetylation is regulated by HATs, which are often correlated with gene activation. The expression of histone acetyltransferase genes ZmHATB and ZmGCN5 was increased after 200 mM NaCl treatment, accompanied by an increase in the global acetylation levels of histones H3K9 and H4K5. ChIP experiment showed that the up-regulation of the ZmEXPB2 and ZmXET1 genes was associated with the elevated H3K9 acetylation levels on the promoter regions and coding regions of these two genes.

CONCLUSIONS

These data suggested that the up-regulation of some cell wall related genes mediated cell enlargement to possibly mitigate the salinity-induced ionic toxicity, and different genes had specific function in response to salt stress. Histone modification as a mediator may contribute to rapid regulation of cell wall related gene expression, which reduces the damage of excess salinity to plants.

Relationship between pollination and cell wall properties in common fig fruit

Most botanical types in fig Ficus carica require pollination to fulfil their development and ensure quality onset of the fruit. Cell wall behaviour and composition was followed in fig fruit in response to pollination during maturity. Figs, when ripe, soften drastically and lose of their firmness and cell wall cohesion. Pollination increased peel thickness, flesh thickness, fresh weight and dry matter content of the fruit. Alcohol insoluble solids (AIS), more concentrated in the flesh tissue, were not influenced by the lack of pollination. Concentrations in uronic acids were higher in the AIS of the peel than that of the flesh and differences were significant between pollinated and non-pollinated fruits. Pectin polymers in figs were high methylated (DM>50). The methylation degree (DM) increased more with pollination affecting textural properties of the fig receptacle. The major neutral sugars from the AIS were glucose (Glc) from cellulose followed by arabinose (Ara). No significant changes in neutral sugars content could be allocated to pollination. Pollination is essential in fruit enlargement and softening. Minor changes were determined in the cell wall composition of the fruit at maturity. Fertile seeds resulting from pollination may possibly take place in hormonal activity stimulating many related enzymes of the wall matrix depolymerisation in particular polygalacturonase (PG) and pectin methylesterase (PME).

AtEXP2 is involved in seed germination and abiotic stress response in Arabidopsis

Expansins are cell wall proteins that promote cell wall loosening by inducing pH-dependent cell wall extension and stress relaxation. Expansins are required in a series of physiological developmental processes in higher plants such as seed germination. Here we identified an Arabidopsis expansin gene AtEXPA2 that is exclusively expressed in germinating seeds and the mutant shows delayed germination, suggesting that AtEXP2 is involved in controlling seed germination. Exogenous GA application increased the expression level of AtEXP2 during seed germination, while ABA application had no effect on AtEXP2 expression. Furthermore, the analysis of DELLA mutants show that RGL1, RGL2, RGA, GAI are all involved in repressing AtEXP2 expression, and RGL1 plays the most dominant role in controlling AtEXP2 expression. In stress response, exp2 mutant shows higher sensitivity than wild type in seed germination, while overexpression lines of AtEXP2 are less sensitive to salt stress and osmotic stress, exhibiting enhanced tolerance to stress treatment. Collectively, our results suggest that AtEXP2 is involved in the GA-mediated seed germination and confers salt stress and osmotic stress tolerance in Arabidopsis.

Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus

The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass Holcus lanatus genotypes screened from the same habitat. De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide polymorphism (SNP) calling were conducted on RNA extracted from H. lanatus. Roche 454 sequencing data were assembled into c. 22,000 isotigs, and paired-end Illumina reads for phosphorus-starved (P-) and phosphorus-treated (P+) genovars of tolerant (T) and nontolerant (N) phenotypes were mapped to this reference transcriptome. Heatmaps of the gene expression data showed strong clustering of each P+/P- treated genovar, as well as clustering by N/T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and P- treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNA-binding protein and transposable elements. A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP profiles, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se.

Ethylene-induced changes in lignification and cell wall-degrading enzymes in the roots of mungbean (Vigna radiata) sprouts

As an important regulator, ethylene inhibits root growth and development in plants. To determine the mechanism of ethylene on root elongation growth and lateral root formation, ethylene-induced lignification and cell wall-degrading enzymes in the roots of mungbean sprouts were tested. We initially observed that primary root elongation and lateral root numbers were inhibited, while lignin content was enhanced by ethephon (ETH). Cell wall remolding proteins, polygalacturonase (PG) and carboxymethyl cellulose (Cx) activities were reduced, but α-expansins and xyloglucan endotransglucosylases/hydrolases (XTH) were enhanced by ETH. The promotion in lignin production was correlated with changes in activities of key lignin biosynthesis enzymes and hydrogen peroxide (H2O2) content. These actions induced by ETH were altered via treatment with an ethylene perception antagonist (Ag+). We subsequently demonstrated that the role of endogenous ethylene in regulating root elongation growth and lateral root formation were correlated with lignification and cell wall-degrading enzymes, respectively. These results suggested that the ethylene-regulated inhibition of primary root elongation growth was caused by an increase in lignification that reinforced the cell wall and shortened root length, and the suppression of lateral root formation was linked to activities of PG, Cx, α-expansins and XTH.

Two cytosolic aldolases show different expression patterns during shoot elongation in Moso bamboo, Phyllostachys pubescens Mazel

In fast-growing Moso bamboo (Phyllostachys pubescens Mazel), cytosolic fructose 1,6-bisphosphate aldolase (aldolase; EC 4.2.2.13) was more highly active in elongating tissues than in tissues that had already finished elongating. It is well known that the removal of the culm sheath prevents bamboo from elongating. When the sheath was removed from the culm, the aldolase activity was gradually reduced over time. Two isozyme genes for aldolase, PpAldC1 and PpAldC2, were cloned from the elongating tissues of Moso bamboo. Gene expression analysis using a semi-quantitative reverse transcriptase-polymerase chain reaction revealed that PpAldC1 was highly expressed in elongating tissues but was hardly detected in elongated internodes, while PpAldC2 seemed to be expressed constitutively in both elongating and elongated tissues. Promoter analysis revealed that the expression of PpAldC1 was induced by gibberellin. These results indicated that the two genes for cytosolic aldolase in Moso bamboo showed different expression patterns and that one of them was involved in shoot elongation.

Plant micro- and nanomechanics: experimental techniques for plant cell-wall analysis

In the last few decades, micro- and nanomechanical methods have become increasingly important analytical techniques to gain deeper insight into the nanostructure and mechanical design of plant cell walls. The objective of this article is to review the most common micro- and nanomechanical approaches that are utilized to study primary and secondary cell walls from a biomechanics perspective. In light of their quite disparate functions, the common and opposing structural features of primary and secondary cell walls are reviewed briefly. A significant part of the article is devoted to an overview of the methodological aspects of the mechanical characterization techniques with a particular focus on new developments and advancements in the field of nanomechanics. This is followed and complemented by a review of numerous studies on the mechanical role of cellulose fibrils and the various matrix components as well as the polymer interactions in the context of primary and secondary cell-wall function.

Another brick in the cell wall: biosynthesis dependent growth model

Expansive growth of plant cell is conditioned by the cell wall ability to extend irreversibly. This process is possible if (i) a tensile stress is developed in the cell wall due to the coupling effect between turgor pressure and the modulation of its mechanical properties through enzymatic and physicochemical reactions and if (ii) new cell wall elements can be synthesized and assembled to the existing wall. In other words, expansive growth is the result of coupling effects between mechanical, thermal and chemical energy. To have a better understanding of this process, models must describe the interplay between physical or mechanical variable with biological events. In this paper we propose a general unified and theoretical framework to model growth in function of energy forms and their coupling. This framework is based on irreversible thermodynamics. It is then applied to model growth of the internodal cell of Chara corallina modulated by changes in pressure and temperature. The results describe accurately cell growth in term of length increment but also in term of cell pectate biosynthesis and incorporation to the expanding wall. Moreover, the classical growth model based on Lockhart's equation such as the one proposed by Ortega, appears as a particular and restrictive case of the more general growth equation developed in this paper.

The effect of subambient to elevated atmospheric CO₂ concentration on vascular function in Helianthus annuus: implications for plant response to climate change

Plant gas exchange is regulated by stomata, which coordinate leaf-level water loss with xylem transport. Stomatal opening responds to internal concentrations of CO₂ in the leaf, but changing CO₂ can also lead to changes in stomatal density that influence transpiration. Given that stomatal conductance increases under subambient concentrations of CO₂ and, conversely, that plants lose less water at elevated concentrations, can downstream effects of atmospheric CO₂ be observed in xylem tissue? We approached this problem by evaluating leaf stomatal density, xylem transport, xylem anatomy and resistance to cavitation in Helianthus annuus plants grown under three CO₂ regimes ranging from pre-industrial to elevated concentrations. Xylem transport, conduit size and stomatal density all increased at 290 ppm relative to ambient and elevated CO₂ concentrations. The shoots of the 290-ppm-grown plants were most vulnerable to cavitation, whereas xylem cavitation resistance did not differ in 390- and 480-ppm-grown plants. Our data indicate that, even as an indirect driver of water loss, CO₂ can affect xylem structure and water transport by coupling stomatal and xylem hydraulic functions during plant development. This plastic response has implications for plant water use under variable concentrations of CO₂, as well as the evolution of efficient xylem transport.

Control of cell wall extensibility during pollen tube growth

In this review, we address the question of how the tip-growing pollen tube achieves its rapid rate of elongation while maintaining an intact cell wall. Although turgor is essential for growth to occur, the local expansion rate is controlled by local changes in the viscosity of the apical wall. We focus on several different structures and underlying processes that are thought to be major participants including exocytosis, the organization and activity of the actin cytoskeleton, calcium and proton physiology, and cellular energetics. We think that the actin cytoskeleton, in particular the apical cortical actin fringe, directs the flow of vesicles to the apical domain, where they fuse with the plasma membrane and contribute their contents to the expanding cell wall. While pH gradients, as generated by a proton-ATPase located on the plasma membrane along the side of the clear zone, may regulate rapid actin turnover and new polymerization in the fringe, the tip-focused calcium gradient biases secretion towards the polar axis. The recent data showing that exocytosis of new wall material precedes and predicts the process of cell elongation provide support for the idea that the intussusception of newly secreted pectin contributes to decreases in apical wall viscosity and to cell expansion. Other prime factors will be the localization and activity of the enzyme pectin methyl-esterase, and the chelation of calcium by pectic acids. Finally, we acknowledge a role for reactive oxygen species in the control of wall viscosity.

Integrated metabolomics and genomics analysis provides new insights into the fiber elongation process in Ligon lintless-2 mutant cotton (Gossypium hirsutum L.)

BACKGROUND

The length of cotton fiber is an important agronomic trait characteristic that directly affects the quality of yarn and fabric. The cotton (Gossypium hirsutum L.) fiber mutation, Ligon lintless-2, is controlled by a single dominant gene (Li(2)) and results in extremely shortened lint fibers on mature seeds with no visible pleiotropic effects on vegetative growth and development. The Li(2) mutant phenotype provides an ideal model system to study fiber elongation. To understand metabolic processes involved in cotton fiber elongation, changes in metabolites and transcripts in the Li(2) mutant fibers were compared to wild-type fibers during development.

RESULTS

Principal component analysis of metabolites from GC-MS data separated Li(2) mutant fiber samples from WT fiber samples at the WT elongation stage, indicating that the Li(2) mutation altered the metabolome of the mutant fibers. The observed alterations in the Li(2) metabolome included significant reductions in the levels of detected free sugars, sugar alcohols, sugar acids, and sugar phosphates. Biological processes associated with carbohydrate biosynthesis, cell wall loosening, and cytoskeleton were also down-regulated in Li(2) fibers. Gamma-aminobutyric acid, known as a signaling factor in many organisms, was significantly elevated in mutant fibers. Higher accumulation of 2-ketoglutarate, succinate, and malate suggested higher nitrate assimilation in the Li(2) line. Transcriptional activation of genes involved in nitrogen compound metabolism along with changes in the levels of nitrogen transport amino acids suggested re-direction of carbon flow into nitrogen metabolism in Li(2) mutant fibers.

CONCLUSIONS

This report provides the first comprehensive analysis of metabolite and transcript changes in response to the Li(2) mutation in elongating fibers. A number of factors associated with cell elongation found in this study will facilitate further research in understanding metabolic processes of cotton fiber elongation.

Cell Wall Composition, Biosynthesis and Remodeling during Pollen Tube Growth

The pollen tube is a fast tip-growing cell carrying the two sperm cells to the ovule allowing the double fertilization process and seed setting. To succeed in this process, the spatial and temporal controls of pollen tube growth within the female organ are critical. It requires a massive cell wall deposition to promote fast pollen tube elongation and a tight control of the cell wall remodeling to modify the mechanical properties. In addition, during its journey, the pollen tube interacts with the pistil, which plays key roles in pollen tube nutrition, guidance and in the rejection of the self-incompatible pollen. This review focuses on our current knowledge in the biochemistry and localization of the main cell wall polymers including pectin, hemicellulose, cellulose and callose from several pollen tube species. Moreover, based on transcriptomic data and functional genomic studies, the possible enzymes involved in the cell wall remodeling during pollen tube growth and their impact on the cell wall mechanics are also described. Finally, mutant analyses have permitted to gain insight in the function of several genes involved in the pollen tube cell wall biosynthesis and their roles in pollen tube growth are further discussed.

Low oxygen response mechanisms in green organisms

Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. This involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. For a coordinated response to low oxygen, plants exploit various molecular mechanisms to sense when oxygen is either absent or in limited amounts. In Arabidopsis thaliana, a direct oxygen sensing system has recently been discovered, where a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the fate of the protein under normoxia/hypoxia. In Oryza sativa, this same group of ERFs drives physiological and anatomical modifications that vary in relation to the genotype studied. The microalga Chlamydomonas reinhardtii responses to low oxygen seem to have evolved independently of higher plants, posing questions on how the fermentative metabolism is modulated. In this review, we summarize the most recent findings related to these topics, highlighting promising developments for the future.

A tale of two tissues: AtGH9C1 is an endo-β-1,4-glucanase involved in root hair and endosperm development in Arabidopsis

Arabidopsis AtGH9C1 is an endo-β-1,4-glucanase possessing a carbohydrate-binding domain (CBM49). Analysis of AtGH9C1 expression by promoter-reporter GUS, RT-PCR, public transcriptome databases and GFP protein tagging demonstrated a high and selective expression of AtGH9C1 in root hairs and in the endosperm. Expression in root hair cells started prior to bulge formation and continued during hair elongation. AtGH9C1 expression increased with treatments that increase density (ACC) or length (sucrose) of root hairs. Expression in the endosperm extended sequentially to the micropylar, peripheral and chalazal compartments. A mutant with reduced AtGH9C1 expression had a delay in germination and a marked reduction in root hair presence. Complementation of the mutant partially improved both germination and root hair density. Experiments with ectopically expressed AtGH9C1-GFP with and without the CBM49, demonstrated that both forms of the protein are secreted and that CBM49 targets the protein to specific regions of the cell wall, but what makes these regions special is still unknown. The amino acid alignment of angiosperm GH9 genes with C-terminal extensions illustrate that AtGH9C1 belongs to a different clade than its tomato homolog, S1GH9C1. The latter has a CBM49 that was shown to bind crystalline cellulose. We suggest that AtGH9C1 is associated with the weakening of the cell wall during formation and growth of the root hair as well as with the sequential anterior-posterior breakdown of the endosperm cell wall that provides space for the growing embryo. Thus, is likely that the CBM49 of AtGH9C1 recognizes a form of cellulose or glucan polymer that is prevalent in the wall of these specialized tissues and that is different than the one recognized by S1GH9C1.

Cell division and endoreduplication play important roles in stem swelling of tuber mustard (Brassica juncea Coss. var. tumida Tsen et Lee)

We investigated spatio-temporal variations in cell division and the occurrence of endoreduplication in cells of tuber mustard stems during development. Cells in the stem had 8C nuclei (C represents DNA content of a two haploid genome), since it is an allotetraploid species derived from diploid Brassica rapa (AA) and B. nigra (BB), thus indicating the occurrence of endoreduplication. Additionally, we observed a dynamic change of cell ploidy in different regions of the swollen stems, with a decrease in 4C proportion in P4-1 and a sharp increase in 8C cells that became the dominant cell type (86.33% at most) in the inner pith cells. Furthermore, cDNAs of 14 cell cycle genes and four cell expansion genes were cloned and their spatial transcripts analysed in order to understand their roles in stem development. The expression of most cell cycle genes peaked in regions of the outer pith (P2 or P3), some genes regulating S/G2 and G2/M (BjCDKB1;2, BjCYCB1;1 and BjCYCB1;2) significantly decrease in P5 and P6, while G1/S regulators (BjE2Fa, BjE2Fb and BjE2Fc) showed a relative high expression level in the inner pith (P5) where cells were undergoing endoreduplication. Coincidentally, BjXTH1and BjXTH2 were exclusively expressed in the endoreduplicated cells. Our results suggest that cells of outer pith regions (P2 and P3) mainly divide for cell proliferation, while cells of the inner pith expand through endoreduplication. Endoreduplication could trigger expression of BjXTH1 and BjXTH2 and thus function in cell expansion of the pith tissue.

Structural basis for entropy-driven cellulose binding by a type-A cellulose-binding module (CBM) and bacterial expansin

Components of modular cellulases, type-A cellulose-binding modules (CBMs) bind to crystalline cellulose and enhance enzyme effectiveness, but structural details of the interaction are uncertain. We analyzed cellulose binding by EXLX1, a bacterial expansin with ability to loosen plant cell walls and whose domain D2 has type-A CBM characteristics. EXLX1 strongly binds to crystalline cellulose via D2, whereas its affinity for soluble cellooligosaccharides is weak. Calorimetry indicated cellulose binding was largely entropically driven. We solved the crystal structures of EXLX1 complexed with cellulose-like oligosaccharides to find that EXLX1 binds the ligands through hydrophobic interactions of three linearly arranged aromatic residues in D2. The crystal structures revealed a unique form of ligand-mediated dimerization, with the oligosaccharide sandwiched between two D2 domains in opposite polarity. This report clarifies the molecular target of expansin and the specific molecular interactions of a type-A CBM with cellulose.

Arabidopsis GT34 family contains five xyloglucan α-1,6-xylosyltransferases

The Arabidopsis genome includes seven family 34 glycosyltransferase (GT34) encoding genes. XXT1 and XXT2 have previously been shown to encode XyG α-1,6-xylosyltransferases, while knockout mutants of a third, XXT5, exhibit decreased XyG content, suggesting a similar activity. Here, we extend the study to the rest of the Arabidopsis GT34 genes in terms of biochemical activity and their roles in XyG biosynthesis. The enzyme activity of XXTs was investigated using recombinant protein expressed in E. coli. XyG analysis of single and double T-DNA insertion knockouts, together with overexpression of GT34s in selected mutant lines, provided detailed function of each gene. We reveal the activity of the third member of the GT34 gene family (XXT4) that exhibits xylosyltransferase activity. Double mutants for either xxt2 or xxt5 had a large impact on XyG content, structure and size distribution. Overexpression of the remaining member, XXT3, was able to restore XyG epitopes in xxt2, xxt5 and xxt2 xxt5 double knockouts, suggesting that it also encodes a protein with XXT activity. Our work demonstrates that five of the seven Arabidopsis GT34 genes encode XXT enzymes.

Analysis of 2,297 expressed sequence tags (ESTs) from a cDNA library of flax (Linum ustitatissimum L.) bark tissue

Bast fibre crops are the second most important natural fibre crops following cotton. Of these, flax (Linum ustitatissimum L.) is the most widely planted in the world, with its fibre used for high quality linen textile. A cDNA library of flax bark tissues was constructed with the purpose of identifying genes involved in the Bast fibre development. A total of 2,297 unigene sequences were obtained from 3,200 randomly selected clones of the cDNA library. These sequences were grouped into 155 clusters and 2,142 singletons, which have been submitted to the GenBank databases. By putative functional annotation, 23.3% of these sequences were similar to known proteins in GenBank, 44.0% of these sequences were similar to unknown proteins, and 32.7% of these sequences showed no significant similarity to any other protein sequences in existing databases. Classified by the Gene Ontology, 24.8, 23.1 and 14.3% were assigned to molecular function, biological process, and cellular component GO terms, respectively. By further bioinformatics approaches, about 110 ESTs matched cell wall related genes in the MAIZEWALL database, representing 16 functional categories of all 19 categories, of which, the most abundant category was protein synthesis. Based on the PlantTFDB database, 39 of the 64 transcription factor families in the Arabidopsis thaliana genome were identified as being involved in flax cell wall formation. The sequences and bioinformatics analysis data generated in this paper will be useful for gene expression, cloning and genetic engineering studies to characterize bast fibre development and improve the properties of the bast fibres.

Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency

BACKGROUND

Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far.

RESULTS

A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism.

CONCLUSIONS

The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.

Analysis of carotenoids and lycopene in tomato (Lycopersicon esculentum Mill.) and their retention in tomato juice

In  this  work  we  investigated  the  effect  of  variety  and  processing  on  the  content  of  carotenoids  and  lycopene  in  fruits  and Tomato  juice  from  the  fruit  after  heat  treatment.  The  experiment  included  four  varieties  are edible  tomato  for  industrial processing (Báb, Žiara PK, Šampion and Roti PK). The concentration of total carotenoids and lycopene were determined spectrophotometrically  on  UV-VIS  spectrophotometer  Jenway  at  a  wavelength  of  445  and  472  nm.  The  highest  average content  of  carotenoids  in  fruits  were  recorded  at  a  variety  Roti  PK  (7.0  mg/100 g-1)  and  lowest  in  variety  Báb (4.8 mg/100 g-1). Heat treatment had a statistically significant positive effect on the lycopene content, changes in carotenoid content were not significant. Effect of genotype (variety) for the content of the endpoint was significantly important.

Convergence and divergence in gene expression profiles induced by leaf senescence and 27 senescence-promoting hormonal, pathological and environmental stress treatments

In addition to age and developmental progress, leaf senescence and senescence-associated genes (SAGs) can be induced by other factors such as plant hormones, pathogen infection and environmental stresses. The relationship is not clear, however, between these induced senescence processes and developmental leaf senescence, and to what extent these senescence-promoting signals mimic age and developmental senescence in terms of gene expression profiles. By analysing microarray expression data from 27 different treatments (that are known to promote senescence) and comparing them with that from developmental leaf senescence, we were able to show that at early stages of treatments, different hormones and stresses showed limited similarity in the induction of gene expression to that of developmental leaf senescence. Once the senescence process is initiated, as evidenced by visible yellowing, generally after a prolonged period of treatments, a great proportion of SAGs of developmental leaf senescence are shared by gene expression profiles in response to different treatments. This indicates that although different signals that lead to initiation of senescence may do so through distinct signal transduction pathways, senescence processes induced either developmentally or by different senescence-promoting treatments may share common execution events.

Manipulating corn germplasm to increase recombinant protein accumulation

Using plants as biofactories for industrial enzymes is a developing technology. The application of this technology to plant biomass conversion for biofuels and biobased products has potential for significantly lowering the cost of these products because of lower enzyme production costs. However, the concentration of the enzymes in plant tissue must be high to realize this goal. We describe the enhancement of the accumulation of cellulases in transgenic maize seed as a part of the process to lower the cost of these dominant enzymes for the bioconversion process. We have used breeding to move these genes into elite and high oil germplasm to enhance protein accumulation in grain. We have also explored processing of the grain to isolate the germ, which preferentially contains the enzymes, to further enhance recovery of enzyme on a dry weight basis of raw materials. The enzymes are active on microcrystalline cellulose to release glucose and cellobiose.

Golgi-mediated synthesis and secretion of matrix polysaccharides of the primary cell wall of higher plants

The Golgi apparatus of eukaryotic cells is known for its central role in the processing, sorting, and transport of proteins to intra- and extra-cellular compartments. In plants, it has the additional task of assembling and exporting the non-cellulosic polysaccharides of the cell wall matrix including pectin and hemicelluloses, which are important for plant development and protection. In this review, we focus on the biosynthesis of complex polysaccharides of the primary cell wall of eudicotyledonous plants. We present and discuss the compartmental organization of the Golgi stacks with regards to complex polysaccharide assembly and secretion using immuno-electron microscopy and specific antibodies recognizing various sugar epitopes. We also discuss the significance of the recently identified Golgi-localized glycosyltransferases responsible for the biosynthesis of xyloglucan (XyG) and pectin.

Identification and Characterization of Cell Wall Proteins of a Toxic Dinoflagellate Alexandrium catenella Using 2-D DIGE and MALDI TOF-TOF Mass Spectrometry

The cell wall is an important subcellular component of dinoflagellate cells with regard to various aspects of cell surface-associated ecophysiology, but the full range of cell wall proteins (CWPs) and their functions remain to be elucidated. This study identified and characterized CWPs of a toxic dinoflagellate, Alexandrium catenella, using a combination of 2D fluorescence difference gel electrophoresis (DIGE) and MALDI TOF-TOF mass spectrometry approaches. Using sequential extraction and temperature shock methods, sequentially extracted CWPs and protoplast proteins, respectively, were separated from A. catenella. From the comparison between sequentially extracted CWPs labeled with Cy3 and protoplast proteins labeled with Cy5, 120 CWPs were confidently identified in the 2D DIGE gel. These proteins gave positive identification of protein orthologues in the protein database using de novo sequence analysis and homology-based search. The majority of the prominent CWPs identified were hypothetical or putative proteins with unknown function or no annotation, while cell wall modification enzymes, cell wall structural proteins, transporter/binding proteins, and signaling and defense proteins were tentatively identified in agreement with the expected role of the extracellular matrix in cell physiology. This work represents the first attempt to investigate dinoflagellate CWPs and provides a potential tool for future comprehensive characterization of dinoflagellate CWPs and elucidation of their physiological functions.

Physiological and proteomic responses of rice peduncles to drought stress

Panicle exsertion, an essential physiological process for obtaining high grain yield in rice is mainly driven by peduncle (uppermost internode) elongation. Drought at heading/panicle emergence prevented peduncle elongation from reaching its maximum length even after re-watering. This inhibitory effect of drought resulted in delayed heading and trapping spikelets lower down the panicle inside the flag-leaf sheath, thus increasing sterility in the lower un-exserted spikelets and also among the upper superior spikelets whose exsertion was delayed. Intermittent drought stress caused a significant reduction in relative water content (RWC) and an increase in the abscisic acid (ABA) level of the peduncles, while both returned to normal levels upon re-watering. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis revealed the down-regulation of GA biosynthetic genes during drought. 2D-PAGE analysis of proteins from peduncles collected under well-watered, drought-stressed, and re-watered plants revealed at least twofold differential changes in expression of 31 proteins in response to drought and most of these changes were largely reversed by re-watering. The results indicate that ABA-GA antagonism is a key focal point for understanding the failure of panicle exsertion under drought stress and the consequent increase in spikelet sterility.

Boron deficiency and transcript level changes

Boron (B) is an essential element for plant growth whose deficiency causes an alteration in the expression of a wide range of genes involved in several physiological processes. However, our understanding of the signal transduction pathways that trigger the B-deficiency responses in plants is still poor. The aims of this review are (i) to summarize the genes whose transcript levels are affected by B deficiency and (ii) to provide an update on recent findings that could help to understand how the signal(s) triggered by B deficiency is transferred to the nucleus to modulate gene expression. In this contribution we review the effects of B deficiency on the transcript level of genes related to B uptake and translocation, maintenance of cell wall and membrane function, nitrogen assimilation and stress response. In addition, we discuss the possible mediation of calcium, arabinogalactan-proteins and other cis-diol containing compounds in the signaling mechanisms that transfer the signal of B deficiency to nuclei. Finally, we conclude that the advance in the knowledge of the molecular basis of B deficiency response in plants will allow improving the tolerance of crops to B deficiency stress.