Comparative proteomic analysis of early salt stress responsive proteins in roots and leaves of rice

Growth and productivity of rice (Oryza sativa L.) are severely affected by salinity. Understanding the mechanisms that protect rice and other important cereal crops from salt stress will help in the development of salt‐stress‐tolerant strains. In this study, rice seedlings of the same genetic species with various salt tolerances were studied. We first used 2DE to resolve the expressed proteome in rice roots and leaves and then used nanospray liquid chromatography/tandem mass spectrometry to identify the differentially expressed proteins in rice seedlings after salt treatment. The 2DE assays revealed that there were 104 differentially expressed protein spots in rice roots and 59 in leaves. Then, we identified 83 proteins in rice roots and 61 proteins in rice leaves by MS analysis. Functional classification analysis revealed that the differentially expressed proteins from roots could be classified into 18 functional categories while those from leaves could be classified into 11 functional categories. The proteins from rice seedlings that most significantly contributed to a protective effect against increased salinity were cysteine synthase, adenosine triphosphate synthase, quercetin 3‐O‐methyltransferase 1, and lipoxygenase 2. Further analysis demonstrated that the primary mechanisms underlying the ability of rice seedlings to tolerate salt stress were glycolysis, purine metabolism, and photosynthesis. Thus, we suggest that differentially expressed proteins may serve as marker group for the salt tolerance of rice.     

Comparative proteomic analysis of the Arabidopsis cbl1 mutant in response to salt stress

Many environmental stimuli, including light, biotic and abiotic stress factors, induce changes in cellular Ca(2+) concentrations in plants. Such Ca(2+) signatures are perceived by sensor molecules such as calcineurin B-like (CBL) proteins. AtCBL1, a member of the CBL family which is highly inducible by multiple stress signals, is known to function in the salt stress signal transduction pathway and to positively regulate the plant tolerance to salt. To shed light into the molecular mechanisms of the salt stress response mediated by AtCBL1, a two-dimensional DIGE proteomic approach was applied to identify the differentially expressed proteins in Arabidopsis wild-type and cbl1 null mutant plants in response to salt stress. Seventy-three spots were found altered in expression by least 1.2-fold and 50 proteins were identified by MALDI-TOF/TOF-MS, including some well-known and novel salt-responsive proteins. These proteins function in various processes, such as signal transduction, ROS scavenging, energy production, carbon fixation, metabolism, mRNA processing, protein processing and structural stability. Receptor for activated C kinase 1C (RACK1C, spot 715), a WD40 repeat protein, was up-regulated in the cbl1 null mutant, and two rack1c mutant lines showed decreased tolerance to salt stress, suggesting that RACK1C plays a role in salt stress resistance. In conclusion, our work demonstrated the advantages of the proteomic approach in studies of plant biology and identified candidate proteins in CBL1-mediated salt stress signaling network.     

Drought-avoidant soybean germplasm maintains nitrogen-fixation capacity under water stress

Inoculated soybeans (Glycine max L. (Merrill)) were grown in controlled environments to evaluate the relationship between genotype and plant water status on nodule function, nitrogen assimilation, growth rates, and seed yield. Plants were grown under well-watered (WW) and water-stressed (WS) conditions during the linear pod-filling growth stage in sand culture using N-free nutrient solution. Dry matter and N accumulation were greater for the drought-adapted Plant Introduction 416937 (PI) than for Forrest, a commercially adapted genotype of similar phenology. These differences are attributed to: (i) more favorable internal water balance throughout the pod-filling period (higher total leaf water potential), (ii) higher photosynthetic function (more total leaf area and higher net carbon exchange rates), and (iii) stronger nodule function (larger nodule mass, greater specific and total nodule activity, and thus more nitrogen assimilation) for the PI than for Forrest. While Forrest out yielded the PI under WW conditions, the percentage reduction in seed mass per plant was less for the PI than for Forrest when both genotypes were exposed to desiccating conditions. The inference is that soybean germplasm with the capacity to maintain tissue turgidity, and thus leaf and nodule function, during reproductively-imposed desiccation may reduce the extent to which yield is compromised during drought. These findings have implications for the role of symbiotic nitrogen fixation in conserving yield under dry weather conditions.Abbreviations DAE Days After Emergence - NCE Net CO₂ Exchange - PI PI 416937 - SNA Specific Nodule Activity - TNA Total Nodule Activity - WS Water Stressed - WW Well Watered     

Comparative analysis of proteome differential regulation during cell dedifferentiation in Arabidopsis

Cell dedifferentiation is a cell fate switching process in which differentiated cells undergo genome reprogramming to regain the competency of cell division and organ regeneration. The molecular mechanism underlying the cell dedifferentiation process remains obscure. In this report, we investigate the cell dedifferentiation process in Arabidopsis using a shotgun proteomics approach. A total of 758 proteins are identified by two or more matched peptides. Comparative analyses at four time points using two label-free methods reveal that 193 proteins display up-regulation and 183 proteins display down-regulation within 48 h. While the results of the two label-free quantification methods match well with each other, comparison with previously published 2-DE gel results reveal that label-free quantification results differ substantially from those of the 2-DE method for proteins with peptides common to multiple proteins, suggesting a limitation of the label-free methods in quantifying proteins with closely related family members in complex samples. Our results show that the shotgun approach and the traditional 2-DE gel approach complement each other in both protein identification and quantification. An interesting observation is that core histones and histone variants are subjected to extensive down-regulation, indicating that there is a dramatic change in the chromatin during cell differentiation.     

氯化钠胁迫下野生和栽培大豆幼苗体内的多胺水平变化

以通用的较耐盐的栽培大豆Lee68品种和对盐敏感的野生大豆N23232种群为参照,研究了盐胁迫下耐盐野生大豆BB52种群幼苗体内多胺(PAs)组分、含量及多胺氧化酶(PAO)活性的变化。结果表明,盐胁迫下BB52幼苗根PAs中Put和Spm含量下降较Lee68和N23232显著,但Spd含量下降较少．BB52叶片PAs中Put含量下降,Spd上升,(Spd+Spin)／Put值增加和Put／PAs值降低幅度与耐盐性呈正相关趋势．盐胁迫下,各材料根和叶中PAO活性上升,N23232上升最明显．探讨了多胺水平与BB52耐盐性的关系。     

Emergence and seedling growth of soybean cultivars and maturity groups under salinity

Soybean is an important agricultural crop and has, among its genotypes, a relatively wide variation in salt tolerance. As measured by vegetative growth and yield, however, the achievement or failure of a high emergence ratio and seedling establishment in saline soils can have significant economic implications in areas where soil salinity is a potential problem for soybean. This study was conducted to determine the effects of salinity, variety and maturation rate on soybean emergence and seedling growth. Included in the study were the variety ‘Manokin’; four near-isogenic sibling lines of the variety ‘Lee’ belonging to maturity groups IV, V, VI and VII; and the variety ‘Essex’ and two of its near-isogenic related lines representing maturity groups V, VI and VII, respectively. Field plots were salinized with sodium chloride and calcium chloride salts prior to planting. The soybeans were irrigated with furrow irrigation which redistributed the salts towards the tail ends of the field plots. Elevated soil salinity near the tail ends of the field significantly reduced soybean emergence rate, shoot height and root length. No significant reduction was found for emergence or seedling growth of variety ‘Manokin’ when the electrical conductivity of soil solution extract (ECe) was less than 3 dS m⁻¹. Soybean emergence and seedling growth was significantly reduced when soil ECe reached about 11 dS m⁻¹. Maturity groups V and VII of variety ‘Lee’ or V and VI of ‘Essex’ appeared to be more sensitive to salinity stress than other maturity groups. Salt tolerance of different genotypes and maturity groups should be considered, among other limiting factors, in minimizing salinity effects on soybean growth. This revised version was published online in June 2006 with corrections to the Cover Date.     

Differential proteomic response of rice (Oryza sativa) leaves exposed to high- and low-temperature stress

Global mean surface temperature has been predicted to increase by 1.8-4°C within this century, accompanied by an increase in the magnitude and frequency of extreme temperature events. Developing rice cultivars better adapted to non-optimal temperatures is essential to increase rice yield in the future and, hence, understanding the molecular response of rice to temperature stress is necessary. In this study, we investigated the proteomic responses of leaves of 24-day-old rice seedlings to sudden temperature changes. Rice seedlings grown at 28/20°C (day/night) were subjected to 3-day exposure to 12/5°C or 20/12°C (day/night) for low-temperature stress, and 36/28°C or 44/36°C (day/night) for high-temperature stress, followed by quantitative label-free shotgun proteomic analysis on biological triplicates of each treatment. Out of over 1100 proteins identified in one or more temperature treatments, more than 400 were found to be responsive to temperature stress. Of these, 43, 126 and 47 proteins were exclusively found at 12/5, 20/12 and 44/36°C (day/night), respectively. Our results showed that a greater change occurs in the rice leaf proteome at 20/12°C (day/night) in comparison to other non-optimal temperature regimes. In addition, our study identified more than 20 novel stress-response proteins.     

T-DNA locus structure in a large population of soybean plants transformed using the Agrobacterium-mediated cotyledonary-node method

Designing transformation experiments for either functional genomics or crop improvement requires knowledge of the transgene locus structure, number, transmission and expression resulting from a specific transformation method. We recently reported an improvement to the soybean [Glycine max (L.) Merrill] cotyledonary-node transformation method that resulted in the efficient production of transgenic plants. To characterize the transgene loci resulting from this method, we analysed 270 independent T0 plants and 95 randomly selected T1 progenies for T-DNA locus complexity using Southern analysis. The lines were transformed with Agrobacterium tumefaciens strains LBA4404 or EHA105 carrying the binary plasmids pGPTV, pTOK233, pCAMBIA1303 or pCAMBIA1309, and regenerated in medium supplemented with or without silver nitrate (AgNO3). Analysis in the T0 generation showed that the number of hpt-hybridizing fragments per plant ranged from 1-15, with 31.5% of the lines having a single hpt-hybridizing fragment. Each primary soybean transformant had, on average, 2.0 unlinked transgene loci and that half of the segregating loci in the T1 progenies were single, simple T-DNA insertions. Of the loci containing multiple T-DNA fragments, a low frequency had tandem and inverted repeat T-DNA structures. Integration of binary plasmid backbone sequences occurred in 37% of primary transformants. A. tumefaciens strain, binary plasmid and thiol treatment had no significant effect on transgene locus structure, numbers or expression. Interestingly, exposure of soybean explants to AgNO3 throughout shoot induction and elongation increased T-DNA locus complexity in the primary transformants and decreased silencing of gusA expression in the T1 generation.     

Relative growth rates of leaves from soybean grown under drought-stressed and irrigated field conditions

Abstract. The relative growth rates and leaf area were graphed against leaf area, normalized with respect to final leaf area, to assess the applicability of the Lockhart cell wall expansion equation to soybean, Glycine max (L.) Merr., leaf development under field conditions. For leaves that had completed more than 20% of their growth, relative growth rates decreased linearly with an increase in the normalized leaf area, indicating that these leaves were undergoing strictly expansive growth. Drought stress significantly decreased the relative growth rate of these larger leaves. Small leaves which had completed less than 20% of their growth, were found to have highly variable relative growth rates. The large variability in relative growth rates indicated that the Lockhart cell wall expansion equation was inadequate to evaluate the growth of these young leaves. Drought stress had virtually no influence on the relative growth rates observed in the small leaves.     

Protein identification and quantification from riverbank grape,Vitis riparia: Comparing SDS‐PAGE and FASP‐GPF techniques for shotgun proteomic analysis

Protein sample preparation optimisation is critical for establishing reproducible high throughput proteomic analysis. In this study, two different fractionation sample preparation techniques (in‐gel digestion and in‐solution digestion) for shotgun proteomics were used to quantitatively compare proteins identified in Vitis riparia leaf samples. The total number of proteins and peptides identified were compared between filter aided sample preparation (FASP) coupled with gas phase fractionation (GPF) and SDS‐PAGE methods. There was a 24% increase in the total number of reproducibly identified proteins when FASP‐GPF was used. FASP‐GPF is more reproducible, less expensive and a better method than SDS‐PAGE for shotgun proteomics of grapevine samples as it significantly increases protein identification across biological replicates. Total peptide and protein information from the two fractionation techniques is available in PRIDE with the identifier PXD001399 ( http://proteomecentral.proteomexchange.org/dataset/PXD001399 ).     

Involvement of chalcone reductase in the soybean isoflavone metabolon: identification of GmCHR5, which interacts with 2‐hydroxyisoflavanone synthase

Soybean (Glycine max) 5‐deoxyisoflavonoids (daidzein and its conjugates) are precursors of glyceollin phytoalexins. They are also converted to equol by microbes in the human intestine, resulting in health benefits. 5‐Deoxyisoflavonoids accumulate in the roots (93% mol/mol of the total root isoflavonoids) and seeds of unstressed soybean plants. Chalcone reductase (CHR) is a key enzyme mediating 5‐deoxyisoflavonoid biosynthesis because it catalyzes the production of 6′‐deoxychalcone through its effects on the chalcone synthase (CHS)‐catalyzed reaction. The soybean genome encodes at least 11 CHR‐related homologs, but it is unclear which ones are functionally important for daidzein accumulation in unstressed plants. Among the CHR homologs, the temporal and spatial expression patterns of GmCHR5 were the most correlated with the distribution patterns of 5‐deoxyisoflavonoids. The CHR activity of GmCHR5 was confirmed in vitro and in planta. In the in vitro assays, the ratio of CHR products (6′‐deoxychalcone) to total CHS products (R value) was dependent on GmCHR5 and CHS concentrations, with higher concentrations resulting in higher R values (i.e. approaching 90%). Subcellular localization analyses revealed that GmCHR5 was present in the cytoplasm and nucleus. Protein–protein interaction assays indicated that GmCHR5, but not GmCHR1 and GmCHR6, interacted with 2‐hydroxyisoflavanone synthase (IFS) isozymes. The CHS isozymes also interacted with IFS isozymes but not with GmCHR5. The proposed micro‐compartmentalization of isoflavone biosynthesis through the formation of an IFS‐mediated metabolon is probably involved in positioning GmCHR5 close to CHS, resulting in an R value that is high enough for the accumulation of abundant 5‐deoxyisoflavonoids in soybean roots.     

RFLP mapping of QTLs conferring salt tolerance during germination in an interspecific cross of tomato

 Most cultivars of tomato (Lycopersicon esculentum) are sensitive to salinity during seed germination and at later stages. Genetic resources for salt tolerance have been identified within the related wild species of tomato. The purpose of the present study was to identify quantitative trait loci (QTLs) for salt tolerance during germination in an inbred backcross (BC₁S₁) population of an interspecific cross between a salt-sensitive tomato breeding line (NC84173, maternal and recurrent parent) and a salt-tolerant Lycopersicon pimpinellifolium accession (LA722). Onehundred and nineteen BC₁ individuals were genotyped for 151 restriction fragment length polymorphism (RFLP) markers and a genetic linkage map was constructed. The parental lines and 119 BC₁S₁ families (self-pollinated progeny of 119 BC₁ individuals) were evaluated for germination at an intermediate salt-stress level (150 mM NaCl+15 mM CaCl₂, water potential approximately −850 kPa). Germination was scored visually as radicle protrusion at 8-h intervals for 28 consecutive days. Germination response was analyzed by survival analysis and the time to 25, 50, and 75% germination was determined. In addition, a germination index (GI) was calculated as the weighted mean of the time from imbibition to germination for each family/line. Interval mapping, single-marker analysis and distributional extreme analysis, were used to identify QTLs and the results of all three mapping methods were generally similar. Seven chromosomal locations with significant effects on salt tolerance were identified. The L. pimpinellifolium accession had favorable QTL alleles at six locations. The percentage of phenotypic variation explained (PVE) by individual QTLs ranged from 6.5 to 15.6%. Multilocus analysis indicated that the cumulative action of all significant QTLs accounted for 44.5% of the total phenotypic variance. A total of 12 pairwise epistatic interactions were identified, including four between QTL-linked and QTL-unlinked regions and eight between QTL-unlinked regions. Transgressive phenotypes were observed in the direction of salt sensitivity. The graphical genotyping indicated a high correspondence between the phenotypes of the extreme families and their QTL genotypes. The results indicate that tomato salt tolerance during germination can be improved by marker-assisted selection using interspecific variation. Received: 29 January 1998 / Accepted: 4 June 1998     

NaCl胁迫下海滨锦葵种子萌发和幼苗生长过程的生理特性变化

以1／4 Hoagland溶液为基础培养液,研究了0．5％、1．0%、1．5％、2．0％和2．5％NaCl处理对海滨锦葵[Kostelezkya rirginica（L．）Presl．]种子萌发和幼苗生长的影响,发现随着培养液中NaCl浓度的增加,海滨锦葵种子萌发率逐渐降低;当NaCl浓度达2．5％时种子不萌发,但NaCl胁迫解除后,种子的萌发率水平与对照相当。幼苗在含0．5％～1．0%NaCl的培养液中生长状况良好,叶绿素含量和根系活力明显增高;但当NaCl浓度达1．5％-2．0％时,叶绿素含量和根系活力逐渐下降;与对照相比,NaCl胁迫下幼苗的MDA水平降低。结果表明,NaCl胁迫对海滨锦葵种子萌发和幼苗牛长有一定的影响,但海滨锦葵可通过种子休眠、增加根系活力、降低体内MDA水平来缓解一定的盐害效应．以适应盐胁迫的生长环境．     

Genome‐wide association and epistasis studies unravel the genetic architecture of sudden death syndrome resistance in soybean

Soybean [Glycine max (L.) Merr.] is an economically important crop that is grown worldwide. Sudden death syndrome (SDS), caused by Fusarium virguliforme, is one of the top yield‐limiting diseases in soybean. However, the genetic basis of SDS resistance, especially with respect to epistatic interactions, is still unclear. To better understand the genetic architecture of soybean SDS resistance, genome‐wide association and epistasis studies were performed using a population of 214 germplasm accessions and 31 914 SNPs from the SoySNP50K Illumina Infinium BeadChip. Twelve loci and 12 SNP–SNP interactions associated with SDS resistance were identified at various time points after inoculation. These additive and epistatic loci together explained 24–52% of the phenotypic variance. Disease‐resistant, pathogenesis‐related and chitin‐ and wound‐responsive genes were identified in the proximity of peak SNPs, including stress‐induced receptor‐like kinase gene 1 (SIK1), which is pinpointed by a trait‐associated SNP and encodes a leucine‐rich repeat‐containing protein. We report that the proportion of phenotypic variance explained by identified loci may be considerably improved by taking epistatic effects into account. This study shows the necessity of considering epistatic effects in soybean SDS resistance breeding using marker‐assisted and genomic selection approaches. Based on our findings, we propose a model for soybean root defense against the SDS pathogen. Our results facilitate identification of the molecular mechanism underlying SDS resistance in soybean, and provide a genetic basis for improvement of soybean SDS resistance through breeding strategies based on additive and epistatic effects.