A proline-, threonine-, and glycine-rich protein down-regulated by drought is localized in the cell wall of xylem elements

Responses of grapevine rootstocks to drought through altered root system architecture and root transcriptomic regulations

Roots are the major interface between the plant and various stress factors in the soil environment. Alteration of root system architecture (RSA) (root length, spread, number and length of lateral roots) in response to environmental changes is known to be an important strategy for plant adaptation and productivity. In light of ongoing climate changes and global warming predictions, the breeding of drought-tolerant grapevine cultivars is becoming a crucial factor for developing a sustainable viticulture. Root-trait modeling of grapevine rootstock for drought stress scenarios, together with high-throughput phenotyping and genotyping techniques, may provide a valuable background for breeding studies in viticulture. Here, tree grafted grapevine rootstocks (110R, 5BB and 41B) having differential RSA regulations and drought tolerance were investigated to define their drought dependent root characteristics. Root area, root length, ramification and number of root tips reduced less in 110R grafted grapevines compared to 5BB and 41B grafted ones during drought treatment. Root relative water content as well as total carbohydrate and nitrogen content were found to be much higher in the roots of 110R than it was in the roots of other rootstocks under drought. Microarray-based root transcriptome profiling was also conducted on the roots of these rootstocks to identify their gene regulation network behind drought-dependent RSA alterations. Transcriptome analysis revealed totally 2795, 1196 and 1612 differentially expressed transcripts at the severe drought for the roots of 110R, 5BB and 41B, respectively. According to this transcriptomic data, effective root elongation and enlargement performance of 110R were suggested to depend on three transcriptomic regulations. First one is the drought-dependent induction in sugar and protein transporters genes (SWEET and NRT1/PTR) in the roots of 110R to facilitate carbohydrate and nitrogen accumulation. In the roots of the same rootstock, expression increase in osmolyte producer genes revealed another transcriptomic regulation enabling effective root osmotic adjustment under drought stress. The third mechanism was linked to root suberization with upregulation of transcripts functional in wax producing enzymes (Caffeic acid 3-O-methyltransferase, Eceriferum3, 3-ketoacyl-CoAsynthase). These three transcriptomic regulations were suggested to provide essential energy and water preservation to the roots of 110R for its effective RSA regulation under drought. This phenotypic and genotypic knowledge could be used to develop root-dependent drought tolerant grapevines in breeding programs and could facilitate elucidation of genetic regulations behind RSA alteration in other plants.

Hydrolase treatments help unravel the function of intervessel pits in xylem hydraulics

Intervessel pits are structures that play a key role in the efficiency and safety functions of xylem hydraulics. However, little is known about the components of the pit membrane (PM) and their role in hydraulic functions, especially in resistance to cavitation. We tested the effect of commercial chemicals including a cellulase, a hemicellulase, a pectolyase, a proteinase and DTT on xylem hydraulic properties: vulnerability to cavitation (VC) and conductance. The effects were tested on branch segments from Fagus sylvatica (where the effects on pit structure were analyzed using TEM) and Populus tremula. Cellulose hydrolysis resulted in a sharp increase in VC and a significant increase in conductance, related to complete breakdown of the PM. Pectin hydrolysis also induced a sharp increase in VC but with no effect on conductance or pit structure observable by TEM. The other treatments with hemicellulase, proteinase or DTT showed no effect. This study brings evidence that cellulose and pectins are critical components underpinning VC, and that PM components may play distinct roles in the xylem hydraulic safety and efficiency.

Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora

The aim of this study was to investigate the molecular mechanisms underlying drought acclimation in coffee plants by the identification of candidate genes (CGs) using different approaches. The first approach used the data generated during the Brazilian Coffee expressed sequence tag (EST) project to select 13 CGs by an in silico analysis (electronic northern). The second approach was based on screening macroarrays spotted with plasmid DNA (coffee ESTs) with separate hybridizations using leaf cDNA probes from drought-tolerant and susceptible clones of Coffea canephora var. Conilon, grown under different water regimes. This allowed the isolation of seven additional CGs. The third approach used two-dimensional gel electrophoresis to identify proteins displaying differential accumulation in leaves of drought-tolerant and susceptible clones of C. canephora. Six of them were characterized by MALDI-TOF-MS/MS (matrix-assisted laser desorption-time of flight-tandem mass spectrometry) and the corresponding proteins were identified. Finally, additional CGs were selected from the literature, and quantitative real-time polymerase chain reaction (qPCR) was performed to analyse the expression of all identified CGs. Altogether, >40 genes presenting differential gene expression during drought acclimation were identified, some of them showing different expression profiles between drought-tolerant and susceptible clones. Based on the obtained results, it can be concluded that factors involved a complex network of responses probably involving the abscisic signalling pathway and nitric oxide are major molecular determinants that might explain the better efficiency in controlling stomata closure and transpiration displayed by drought-tolerant clones of C. canephora.

Identification of gene modules associated with drought response in rice by network-based analysis

Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice.

GC-MS metabolomic differentiation of selected citrus varieties with different sensitivity to citrus huanglongbing

Huanglongbing (HLB) is the most destructive disease of citrus worldwide. The rapid identification of tolerant varieties is considered a critical step towards controlling HLB. GC-MS metabolite profiles were used to differentiate HLB-tolerant citrus varieties 'Poncirus trifoliata' (TR) and 'Carrizo citrange' (CAR) from HLB-sensitive varieties 'Madam Vinous sweet orange' (MV) and 'Duncan' grapefruit (DG). PCR analyses revealed that MV was the most sensitive variety followed by DG and the tolerant varieties CAR and TR. Metabolomic multivariate analysis allowed classification of the cultivars in apparent agreement with PCR results. Higher levels of the amino acids l-proline, l-serine, and l-aspartic acid, as well as the organic acids butanedioic and tetradecanoic acid, and accumulation of galactose in healthy plants were characteristic of the most sensitive variety MV when compared to all other varieties. Only galactose was significantly higher in DG when compared to the tolerant varieties TR and CAR. The tolerant varieties showed higher levels of l-glycine and mannose when compared to sensitive varieties MV and DG. Profiling of the sensitive varieties MV and DG over a 20-week period after inoculation of those with the HLB-containing material revealed strong responses of metabolites to HLB infection that differed from the response of the tolerant varieties. Significant changes of l-threonine level in the leaves from old mature flushes and l-serine, l-threonine, scyllo-inositol, hexadecanoic acid, and mannose in the leaves from young developing flushes were observed in MV. Significant changes in myo-inositol in old flushes and l-proline, indole, and xylose in new flushes were observed in DG.

Heterogeneous distribution of pectin epitopes and calcium in different pit types of four angiosperm species

Intervessel pits act as safety valves that prevent the spread of xylem embolism. Pectin-calcium crosslinks within the pit membrane have been proposed to affect xylem vulnerability to cavitation. However, as the chemical composition of pit membranes is poorly understood, this hypothesis has not been verified. Using electron microscopy, immunolabeling, an antimonate precipitation technique, and ruthenium red staining, we studied the distribution of selected polysaccharides and calcium in the pit membranes of four angiosperm tree species. We tested whether shifts in xylem vulnerability resulting from perfusion of stems with a calcium chelating agent corresponded with the distribution of pectic homogalacturonans (HG) and/or calcium within interconduit pit membranes. No HG were detected in the main part of intervessel pit membranes, but were consistently found in the marginal membrane region known as the annulus. Calcium colocalized with HG in the annulus. In contrast to intervessel pits, the membrane of vessel-ray pits showed a high pectin content. The presence of two distinct chemical domains, the annulus and the actual pit membrane, can have substantial implications for pit membrane functioning. We propose that the annulus could affect the observed shift in xylem vulnerability after calcium removal by allowing increased pit membrane deflection.

Mind the bubbles: achieving stable measurements of maximum hydraulic conductivity through woody plant samples

The maximum specific hydraulic conductivity (k(max)) of a plant sample is a measure of the ability of a plants' vascular system to transport water and dissolved nutrients under optimum conditions. Precise measurements of k(max) are needed in comparative studies of hydraulic conductivity, as well as for measuring the formation and repair of xylem embolisms. Unstable measurements of k(max) are a common problem when measuring woody plant samples and it is commonly observed that k(max) declines from initially high values, especially when positive water pressure is used to flush out embolisms. This study was designed to test five hypotheses that could potentially explain declines in k(max) under positive pressure: (i) non-steady-state flow; (ii) swelling of pectin hydrogels in inter-vessel pit membranes; (iii) nucleation and coalescence of bubbles at constrictions in the xylem; (iv) physiological wounding responses; and (v) passive wounding responses, such as clogging of the xylem by debris. Prehydrated woody stems from Laurus nobilis (Lauraceae) and Encelia farinosa (Asteraceae) collected from plants grown in the Fullerton Arboretum in Southern California, were used to test these hypotheses using a xylem embolism meter (XYL'EM). Treatments included simultaneous measurements of stem inflow and outflow, enzyme inhibitors, stem-debarking, low water temperatures, different water degassing techniques, and varied concentrations of calcium, potassium, magnesium, and copper salts in aqueous measurement solutions. Stable measurements of k(max) were observed at concentrations of calcium, potassium, and magnesium salts high enough to suppress bubble coalescence, as well as with deionized water that was degassed using a membrane contactor under strong vacuum. Bubble formation and coalescence under positive pressure in the xylem therefore appear to be the main cause for declining k(max) values. Our findings suggest that degassing of water is essential for achieving stable and precise measurements of k(max) through woody plant samples. For complete rehydration of woody samples, incubation in water under vacuum for 24 h is suggested as a reliable technique that avoids bubble problems associated with flushing under high positive pressure.

Analysis of cell wall proteins regulated in stem of susceptible and resistant tomato species after inoculation with Ralstonia solanacearum: a proteomic approach

Proteomics approach was used to elucidate the molecular interactions taking place at the stem cell wall level when tomato species were inoculated with Ralstonia solanacearum, a causative agent of bacterial wilt. Cell wall proteins from both resistant and susceptible plants before and after the bacterial inoculation were extracted from purified cell wall with salt buffers and separated with 2-D IEF/SDS-PAGE and with 3-D IEF/SDS/SDS-PAGE for basic proteins. The gels stained with colloidal Coomassie revealed varied abundance of protein spots between two species (eight proteins in higher abundance in resistant and six other in susceptible). Moreover, proteins were regulated differentially in response to bacterial inoculation in resistant (seven proteins increased and eight other decreased) as well as in susceptible plants (five proteins elevated and eight other suppressed). Combination of MALDI-TOF/TOF MS and LC-ESI-IonTrap MS/MS lead to the identification of those proteins. Plants responded to pathogen inoculation by elevating the expression of pathogenesis related, other defense related and glycolytic proteins in both species. However, cell wall metabolic proteins in susceptible, and antioxidant, stress related as well as energy metabolism proteins in resistant lines were suppressed. Most of the proteins of the comparative analysis and other randomly picked spots were predicted to have secretion signals except some classical cytosolic proteins.

Identification of genes induced upon water-deficit stress in a drought-tolerant rice cultivar

Among the abiotic stresses, the availability of water is the most important factor that limits the productive potential of higher plants. The identification of novel genes, determination of their expression patterns, and the understanding of their functions in stress adaptation is essential to improve stress tolerance. Amplified fragment length polymorphism analysis of cDNA was used to identify rice genes differentially expressed in a tolerant rice variety upon water-deficit stress. In total, 103 transcript-derived fragments corresponding to differentially induced genes were identified. The results of the sequence comparison in BLAST database revealed that several differentially expressed TDFs were significantly homologous to stress regulated genes/proteins isolated from rice or other plant species. Most of the transcripts identified here were genes related to metabolism, energy, protein biosynthesis, cell defence, signal transduction, and transport. New genes involved in the response to water-deficit stress in a tolerant rice variety are reported here.

A root-specific bZIP transcription factor is responsive to water deficit stress in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris)

Root cDNA libraries were differentially screened to isolate water deficit-responsive transcripts in the relatively drought-resistant plant tepary bean (Phaseolus acutifolius). A novel root-specific, water deficit-responsive transcript was identified and predicted to encode a bZIP transcription factor. The orthologous form of this gene was isolated from the drought-sensitive P. vulgaris and the patterns of expression of these genes compared. These genes have predicted amino acid sequences in the bZIP domain that are 64% similar to a soybean bZIP protein. There were three amino acid differences between the P. acutifolius bZIP and the P. vulgaris gene product. Both species transcribed this gene in a root-specific and water deficit-responsive manner. The cell-specific pattern of expression for the gene was determined using in situ hybridization and immunolocalization. Two tissues in the root accumulated the protein: epidermis and phloem. The nuclear localization of this protein was determined by electron microscopy. The bZIP protein accumulated in the nuclei of both the epidermal cell and the vascular cell in response to water deficit stress in both species in a similar manner.

Glycine-rich proteins encoded by a nodule-specific gene family are implicated in different stages of symbiotic nodule development in Medicago spp

Four genes encoding small proteins with significantly high glycine content have been identified from root nodules of Medicago sativa. All of these proteins as well as their Medicago truncatula homologues carried an amino terminal signal peptide and a glycine-rich carboxy terminal domain. All except nodGRP3 lacked the characteristic repeat structure described for cell wall and stress response-related glycine-rich proteins (GRP). Expression of these GRP genes was undetectable in flower, leaf, stem, and hypocotyl cells, whereas expression was highly induced during root nodule development, suggesting that GRP genes act as nodulins. Moreover, none of these nodule-expressed GRP genes were activated by hormones or stress treatments, which are inducers of many other GRPs. In Rhizobium-free spontaneous nodules and in nodules induced by a noninfective mutant strain of Sinorhizobium meliloti, all these genes were repressed, while they were induced in Fix- nodules, unaffected in bacterial infection, but halted in bacteroid differentiation. These results demonstrated that bacterial infection but not bacteroid differentiation is required for the induction of the nodule-specific GRP genes. Differences in kinetics and localization of gene activation as well as in the primary structure of proteins suggest nonredundant roles for these GRPs in nodule organogenesis.

Long-term microclimatic stress causes rapid adaptive radiation of kaiABC clock gene family in a cyanobacterium, Nostoc linckia, from "Evolution Canyons" I and II, Israel

Cyanobacteria are the only prokaryotes known thus far possessing regulation of physiological functions with approximate daily periodicity, or circadian rhythms, that are controlled by a cluster of three genes, kaiA, kaiB, and kaiC. Here we demonstrate considerably higher genetic polymorphism and extremely rapid evolution of the kaiABC gene family in a filamentous cyanobacterium, Nostoc linckia, permanently exposed to the acute natural environmental stress in the two microsite evolutionary models known as "Evolution Canyons," I (Mount Carmel) and II (Upper Galilee) in Israel. The family consists of five distinct subfamilies (kaiI-kaiV) comprising at least 20 functional genes and pseudogenes. The obtained data suggest that the duplications of kai genes have adaptive significance, and some of them are evolutionarily quite recent (approximately 80,000 years ago). The observed patterns of within- and between-subfamily polymorphisms indicate that positive diversifying, balancing, and purifying selections are the principal driving forces of the kai gene family's evolution.

Yellow lupine cyclophilin transcripts are highly accumulated in the nodule meristem zone

Cyclophilin (CyP) is one of the enzymes that act as peptidylprolyl cis-trans isomerases (EC 5.2.1.8). The cDNA and an intronless gene coding for cytosolic CyP have been isolated from yellow lupine. The deduced amino acid sequence of the characterized open reading frame shows approximately 80% homology with cytosolic CyP from other organisms. Southern blots of genomic DNA indicate that there is a small family of genes for CyP-related genes in the yellow lupine genome. RNA blot analyses demonstrate that CyP genes are expressed in all plant organs. The amount of CyP transcripts is dramatically increased in root nodules. In situ hybridization experiments indicate that CyP transcripts are localized mainly in meristematic tissues, with the highest level observed in the nodule meristem zone. The promoter of the sequenced gene contains 5' AAAGAT 3' and AT-rich motifs that are characteristic for some nodulin promoters.

MIP genes are down-regulated under drought stress in Nicotiana glauca

Water flux across cell membranes has been shown to occur not only through the lipid bilayer, but also through aquaporins, which are members of the major intrinsic protein (MIP) super-family of channel proteins. Aquaporins greatly increase the membrane permeability for water, but may also be regulated, allowing cellular control over the rate of water influx/efflux. Water flux is crucial for stomatal opening and closing, but little is known about the role that aquaporins play in stomatal physiology. Our initial goal was to isolate and characterize the MIP genes expressed in guard cells of the model plant, Nicotiana glauca. Degenerate oligonucleotides corresponding to amino acid sequences conserved in tonoplast intrinsic proteins (TIPs) or plasma membrane intrinsic proteins (PIPs) were used to amplify portions of MIP genes by RT-PCR. These PCR products were used as probes in screening a N. glauca guard cell cDNA library. We isolated three clones (NgMIP1, NgMIP2 and NgMIP3) homologous to TIPs and two clones (NgMIP4 and NgMIP5) homologous to PIPs. All of the MIP genes we characterized displayed highest levels of mRNA accumulation in roots or stems, with lower levels of expression in mesophyll cells and whole leaves, and lowest transcript accumulation in guard cell RNA. Interestingly, the accumulation of transcripts arising from NgMIP2, NgMIP3 and NgMIP4 diminished dramatically in drought-stressed plants. This down-regulation of MIP gene expression may result in reduced membrane water permeability and may encourage cellular water conservation during periods of dehydration stress.

Isolation and characterization of a gene encoding a drought-induced cysteine protease in tomato (Lycopersicon esculentum)

In a previous study, a 65 kDa protein, TDI-65, was found to be accumulated in the leaves of drought-stressed tomato (Lycopersicon esculentum cv. Starfire) plants. The protein level returns to control level when the drought-stressed plants are rewatered. Antibodies raised against the purified protein were used to elucidate the subcellular localization of the protein. The protein was found to be mainly localized in the nuclei and chloroplasts of drought-stressed leaf cells. To identify the nature of the protein, a cDNA library was constructed and screened by the purified anti-TDI-65 antibody. A cDNA clone designated tdi-65 was isolated and characterized. The deduced amino acid sequences of tdi-65 protein has extensive homology with known cysteine proteases such as actinidin and papain. Northern blot analysis revealed that tdi-65 mRNA is 10-fold higher in drought-stressed plants as compared to control and rewatered plants. Similar results were observed in the tomato cultivar Ailsa and its near isogenic abscisic acid (ABA)-deficient mutant line, flacca, suggesting that the gene does not require ABA for its expression under drought conditions. Based on the previous immunolocalization findings we suggest that tdi-65 encoded cysteine protease functions in relation to drought-induced senescence and programmed cell death.