Cloning the PvP5CS gene from common bean (Phaseolus vulgaris) and its expression patterns under abiotic stresses

Differential Gene Expression in Contrasting Common Bean Cultivars for Drought Tolerance during an Extended Dry Period

Common beans (Phaseolus vulgaris L.), besides being an important source of nutrients such as iron, magnesium, and protein, are crucial for food security, especially in developing countries. Common bean cultivation areas commonly face production challenges due to drought occurrences, mainly during the reproductive period. Dry spells last approximately 20 days, enough time to compromise production. Hence, it is crucial to understand the genetic and molecular mechanisms that confer drought tolerance to improve common bean cultivars' adaptation to drought. Sixty six RNASeq libraries, generated from tolerant and sensitive cultivars in drought time sourced from the R5 phenological stage at 0 to 20 days of water deficit were sequenced, generated over 1.5 billion reads, that aligned to 62,524 transcripts originating from a reference transcriptome, as well as 6673 transcripts obtained via de novo assembly. Differentially expressed transcripts were functionally annotated, revealing a variety of genes associated with molecular functions such as oxidoreductase and transferase activity, as well as biological processes related to stress response and signaling. The presence of regulatory genes involved in signaling cascades and transcriptional control was also highlighted, for example, LEA proteins and dehydrins associated with dehydration protection, and transcription factors such as WRKY, MYB, and NAC, which modulate plant response to water deficit. Additionally, genes related to membrane and protein protection, as well as water and ion uptake and transport, were identified, including aquaporins, RING-type E3 ubiquitin transferases, antioxidant enzymes such as GSTs and CYPs, and thioredoxins. This study highlights the complexity of plant response to water scarcity, focusing on the functional diversity of the genes involved and their participation in the biological processes essential for plant adaptation to water stress. The identification of regulatory and cell protection genes offers promising prospects for genetic improvement aiming at the production of common bean varieties more resistant to drought. These findings have the potential to drive sustainable agriculture, providing valuable insights to ensure food security in a context of climate change.

Introgression of Δ1-pyrroline-5-carboxylate synthetase (PgP5CS) confers enhanced resistance to abiotic stresses in transgenic tobacco

Δ1-pyrroline-5-carboxylate synthetase (P5CS) is one of the key regulatory enzymes involved in the proline biosynthetic pathway. Proline acts as an osmoprotectant, molecular chaperone, antioxidant, and regulator of redox homeostasis. The accumulation of proline during stress is believed to confer tolerance in plants. In this study, we cloned the complete CDS of the P5CS from pearl millet (Pennisetum glaucum (L.) R.Br. and transformed into tobacco. Three transgenic tobacco plants with single-copy insertion were analyzed for drought and heat stress tolerance. No difference was observed between transgenic and wild-type (WT) plants when both were grown in normal conditions. However, under heat and drought, transgenic plants have been found to have higher chlorophyll, relative water, and proline content, and lower malondialdehyde (MDA) levels than WT plants. The photosynthetic parameters (stomatal conductance, intracellular CO2 concentration, and transpiration rate) were also observed to be high in transgenic plants under abiotic stress conditions. qRT-PCR analysis revealed that the expression of the transgene in drought and heat conditions was 2-10 and 2-7.5 fold higher than in normal conditions, respectively. Surprisingly, only P5CS was increased under heat stress conditions, indicating the possibility of feedback inhibition. Our results demonstrate the positive role of PgP5CS in enhancing abiotic stress tolerance in tobacco, suggesting its possible use to increase abiotic stress-tolerance in crops for sustained yield under adverse climatic conditions.

The Δ1-pyrroline-5-carboxylate synthetase family performs diverse physiological functions in stress responses in pear (Pyrus betulifolia)

Δ1-Pyrroline-5-carboxylate synthetase (P5CS) acts as the rate-limiting enzyme in the biosynthesis of proline in plants. Although P5CS plays an essential role in plant responses to environmental stresses, its biological functions remain largely unclear in pear (Pyrus betulifolia). In the present study, 11 putative pear P5CSs (PbP5CSs) were identified by comprehensive bioinformatics analysis and classified into five subfamilies. Segmental and tandem duplications contributed to the expansion and evolution of the PbP5CS gene family. Various cis-acting elements associated with plant development, hormone responses, and/or stress responses were identified in the promoters of PbP5CS genes. To investigate the regulatory roles of PbP5CS genes in response to abiotic and biotic stresses, gene expression patterns in publicly available data were explored. The tissue-specific expressional dynamics of PbP5CS genes indicate potentially important roles in pear growth and development. Their spatiotemporal expression patterns suggest key functions in multiple environmental stress responses. Transcriptome and real-time quantitative PCR analyses revealed that most PbP5CS genes exhibited distinct expression patterns in response to drought, waterlogging, salinity-alkalinity, heat, cold, and infection by Alternaria alternate and Gymnosporangium haraeanum. The results provide insight into the versatile functions of the PbP5CS gene family in stress responses. The findings may assist further exploration of the physiological functions of PbP5CS genes for the development and enhancement of stress tolerance in pear and other fruits.

Gamma ray-induced tissue responses and improved secondary metabolites accumulation in Catharanthus roseus

The present study investigated the impact of gamma ray irradiation on callus biomass growth and the yield of vincristine and vinblastine of in vitro grown tissues of Catharanthus roseus. The biochemical alteration underlying the synthesis of secondary metabolites has also been studied and a comparison of yield was prepared. The embryogenic tissues were exposed to 20, 40, 60, 80, and 100 Gy gamma ray doses and the callus biomass fresh weight, the embryogenesis (the embryo numbers, germination, plant regeneration), the alteration of protein, proline, and sugar attributes at different morphogenetic stages were monitored. The callus biomass growth was maximum (1.65 g) in 20 Gy exposed tissues and was less in 100 Gy treatment (0.33 g). The gamma-irradiated embryogenic tissues differentiated into embryos but the embryogenesis % and somatic embryo number per culture reduced with increasing doses. It was least in 80 Gy where very low numbers of embryos were formed (3.45 and 3.30 mean torpedo and cotyledonary embryo numbers per callus mass, respectively) which later germinated into plantlets. Protein, proline, sugar, and different antioxidant enzymes, i.e., superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT) activities, were investigated as the tissues were exposed to gamma ray elicitation/signaling, evoking cellular stress. Increased 80 Gy gamma dose inhibited a 42.73% decrease in protein accumulation at initiation stages of embryogenic tissue. Soluble sugar level also declined gradually being least in 80 Gy treated tissues (14.51 mg gm^-1 FW) compared to control (20.2 mg gm^-1 FW). Proline content, however, increased with increasing gamma doses, maximum at 80 Gy (8.28 mg gm^-1 FW). The SOD, APX, and CAT activity increased linearly with enhanced level of gamma doses and maximum, i.e., 3.91 EU min^-1 mg^-1, 1.71 EU min^-1 mg^-1, and 4.89 EU min^-1 mg^-1, protein activity was noted for SOD, APX, and CAT, respectively, at 80 Gy gamma rays treated tissues. The quantification of vinblastine and vincristine in gamma ray elicitated tissues was made by using high-pressure thin layer chromatography (HPTLC). Somatic embryo-regenerated plant's leaves had the maximum yield of vinblastine (15.13 µgm gm^-1 DW) at 40 Gy irradiation dose compared to control (13.30 µgm gm^-1 DW)-the increased yield % is 13.75. The stem is also rich source producing 11.98 µgm gm^-1 DW of vinblastine. Among the various developmental stages of embryos, vinblastine content was highest in germinating stage of embryos (10.14 µgm gm^-1 DW) compared to other three, i.e., initiation, proliferation, and maturation embryo stages. Similarly, highest accumulation of vincristine (6.32 µg gm^-1 DW) was noted at low gamma irradiation dose (20 Gy) in leaf tissues. The present study indicates that the synthesis of vinblastine and vincristine was growth- and development-specific and the lower 20-40 Gy gamma levels were more effective in enriching alkaloids while higher doses declined yield. KEY POINTS: • Vinblastine and vincristine yield was quantified in in vitro grown tissues and leaves of embryo regenerated Catharanthus roseus after gamma ray treatment. • The accumulation of vinblastine and vincristine was maximum in regenerated leaves; low doses were more efficient in improving yield. • Gamma ray irradiation impacted biochemical profiles, caused cellular stress, and perhaps responsible for improved alkaloid yield.

Establishment of reference (housekeeping) genes via quantitative real-time PCR for investigation of the genomic basis of abiotic stress resistance in Psammochloa villosa (Poaceae)

Psammochloa villosa is a desert plant growing in Northwest China with considerable resistance to abiotic stress, including drought, cold, and salt. To facilitate future studies of stress resistance in Psammochloa villosa, we sought to establish a suite of reference (or housekeeping) genes for utilization within future gene expression studies. Specifically, we selected nine candidate genes based on prior studies and new transcriptomic data for P. villosa, and we evaluated their expression stability in three different tissues of P. villosa under different treatments simulating abiotic stress conditions using four different bioinformatics assessments. Our results showed that TIP41 (TIP41-like family protein) was the most stable reference gene in drought- and salt-stressed leaves and salt-stressed stems, ELF-1α (elongation factor 1-α) was the most stable in cold-stressed leaves and drought- and salt-stressed roots, ACT (actin) was the most stable in drought-stressed stems, TUA (α-tubulin) was the most stable in cold-stressed stems, and 18S rRNA (18S ribosomal RNA) was the most stable in cold-stressed roots. Additionally, we tested the utility of these candidate reference genes to detect the expression pattern of P5CS (Δ¹-pyrroline-5-carboxylate synthetase), which is a drought-related gene. This study is the first report on selecting and validating reference genes of P. villosa under various stress conditions and will benefit future investigations of the genomic mechanisms of stress resistance in this ecologically important species.

Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)

Iron (Fe) and zinc (Zn) stress significantly affects fundamental metabolic and physiological processes in plants that results in reduction of plant growth and development. In the present study, common bean variety; Shalimar French Bean-1 (SFB-1) was used as an experimental material. Four different MGRL media i.e. normal MGRL medium (Control), media without Fe (0-Fe), media without Zn (0-Zn) and media with excess Zn (300-Zn) were used for growing seeds of SFB-1 under in vitro condition for three weeks under optimum conditions. Three week old shoot and root tissues were harvested from the plants grown in these four different in vitro conditions and were, subjected to Fe and Zn estimation. Further, extraction of total RNA for differential gene expression of ten candidate genes selected based on our in silico investigation and their classification, phylogeny and expression pattern was unraveled. Expression analysis of three candidate genes (OPT3, NRAMP2 and NRAMP3) in roots revealed possible cross talk among Fe/Zn stress that was further confirmed by observing less accumulation of Fe in roots under both these conditions. However, we observed, higher accumulation of Fe in shoots under 0-Fe condition compared to control that suggests precise sensing for priority based compartmentalization and partitioning leading to higher accumulation of Fe in shoots. Furthermore, the expression analysis of IRT1, FRO1 and Ferritin 1 genes under Fe/Zn stress suggested their role in uptake/transport and signaling of Fe and Zn, whereas the expression of ZIP2, NRAMP1, HA2 and GLP1 genes were highly responsive to Zn in Phaseolus vulgaris. The identified genes highly responsive to Fe and Zn stress condition can be potential candidates for overcoming mineral stress in dicot crop plants.

A methyl esterase 1 (PvMES1) promotes the salicylic acid pathway and enhances Fusarium wilt resistance in common beans

Methyl esterase (MES), PvMES1, contributes to the defense response toward Fusarium wilt in common beans by regulating the salicylic acid (SA) mediated signaling pathway from phenylpropanoid synthesis and sugar metabolism as well as others. Common bean (Phaseolus vulgaris L.) is an important food legume. Fusarium wilt caused by Fusarium oxysporum f. sp. phaseoli is one of the most serious soil-borne diseases of common bean found throughout the world and affects the yield and quality of the crop. Few sources of Fusarium wilt resistance exist in legumes and most are of quantitative inheritance. In this study, we have identified a methyl esterase (MES), PvMES1, that contributes to plant defense response by regulating the salicylic acid (SA) mediated signaling pathway in response to Fusarium wilt in common beans. The result showed the role of PvMES1 in regulating SA levels in common bean and thus the SA signaling pathway and defense response mechanism in the plant. Overexpression of the PvMES1 gene enhanced Fusarium wilt resistance; while silencing of the gene caused susceptibility to the diseases. RNA-seq analysis with these transiently modified plants showed that genes related to SA level changes included the following gene ontologies: (a) phenylpropanoid synthesis; (b) sugar metabolism; and (c) interaction between host and pathogen as well as others. These key signal elements activated the defense response pathway in common bean to Fusarium wilt. Collectively, our findings indicate that PvMES1 plays a pivotal role in regulating SA biosynthesis and signaling, and increasing Fusarium wilt resistance in common bean, thus providing novel insight into the practical applications of both SA and MES genes and pathways they contribute to for developing elite crop varieties with enhanced broad-spectrum resistance to this critical disease.

Root NRT, NiR, AMT, GS, GOGAT and GDH expression levels reveal NO and ABA mediated drought tolerance in Brassica juncea L

Little is known about the interactive effects of exogenous nitric oxide (NO) and abscisic acid (ABA) on nitrogen (N) metabolism and related changes at molecular and biochemical levels under drought stress. The present study highlights the independent and combined effect of NO and ABA (grouped as "nitrate agonists") on expression profiles of representative key genes known to be involved in N-uptake and assimilation, together with proline metabolism, N-NO metabolism enzyme's activity and nutrient content in polyethylene glycol (PEG) treated roots of Indian mustard (B. juncea cv. Varuna). Here we report that PEG mediated drought stress negatively inhibited growth performance, as manifested by reduced biomass (fresh and dry weight) production. Total N content and other nitrogenous compounds (NO3-, NO2-) were decreased; however, NH4+, NH4+/ NO3- ratio and total free amino acids content were increased. These results were positively correlated with the PEG induced changes in expression of genes and enzymes involved in N-uptake and assimilation. Also, PEG supply lowered the content of macro- and micro-nutrients but proline level and the activity of ∆1-pyrroline-5-carboxylate synthetase increased indicating increased oxidative stress. However, all these responses were reversed upon the exogenous application of nitrate agonists (PEG + NO, PEG + NO + ABA, and PEG + ABA) where NO containing nitrate agonist treatment i.e. PEG + NO was significantly more effective than PEG + ABA in alleviating drought stress. Further, increases in activities of L-arginine dependent NOS-like enzyme and S-nitrosoglutathione reductase were observed under nitrate agonist treatments. This indicates that the balanced endogenous change in NO and ABA levels together during synthesis and degradation of NO mitigated the oxidative stress in Indian mustard seedlings. Overall, our results reveal that NO independently or together with ABA may contribute to improved crop growth and productivity under drought stress.

A vital role of chitosan nanoparticles in improvisation the drought stress tolerance in Catharanthus roseus (L.) through biochemical and gene expression modulation

Drought is a main abiotic stress that restricts plant growth and development. The increased global demand of anti-cancer alkaloids extracted from periwinkle (Catharanthus roseus) is mainly related to plant growth and development, which are severely affected by drought. Chitosan nanoparticles (CSNPs) have been used to boost plant growth and defense mechanism, however their impact to alleviate drought stress of C. roseus has not been investigated yet. In this study, control and stressed plants (100 and 50% of field capacity [FC], respectively) were subjected to CSNPs application at 1%. Drought stress considerably reduced plant growth, relative water content (RWC), stomatal conductance and total chlorophyll; however, CSNPs mitigated these effects. They enhanced proline accumulation and the activity of catalase (CAT) and ascorbate peroxidase (APX) with possible mitigation of drought-induced oxidative stress. Therefore, they reduced H₂O₂ and malondialdehyde (MDA) accumulation, and eventually preserved membrane integrity. Drought stress increased alkaloid accumulation, and further increase was observed with the application of CSNPs. High alkaloid content was associated with induced gene expression of strictosidine synthase (STR), deacetylvindoline-4-O-acetyltransferase (DAT), peroxidase 1 (PRX1) and geissoschizine synthase (GS) up to 5.6 folds under drought stress, but more accumulation was noticed with the application of CSNPs. Overall, this study is the first on using CSNPs to mitigate drought stress of C. roseus by inducing the antioxidant potential and gene expression of alkaloid biosynthesis.

Insights into role of STP13 in sugar driven signaling that leads to decrease in photosynthesis in dicot legume crop model (Phaseolus vulgaris L.) under Fe and Zn stress

Mineral (Fe/Zn) stress significantly affects fundamental metabolic and physiological responses in plants that results in reduction of plant growth and development. Deficiency of these micronutrients leads to inhibition of photosynthesis by having impact on various crucial biological processes like protein synthesis, primary and secondary metabolism and carbohydrate partitioning between source and sink tissues. In the present study, common bean variety Shalimar French Bean-1 (SFB-1) plants were used as an experimental material and were grown under in vitro condition on four different MGRL media i.e. normal MGRL medium (Control), MGRL without Fe (0-Fe), MGRL without Zinc (0-Zn) and MGRL with excess Zn (300-Zn) for 21 days under optimum conditions. Shoot and root tissues from all the treatments were harvested and further subjected to estimation of total chlorophyll, total sugar and extraction of total RNA for differential gene expression of sugar transporter 13 (STP13). We observed significant decrease in total chlorophyll content in samples harvested from mineral stress plants. However, the concentration of total sugar and fold expression of STP13 gene was significantly higher in shoots of Fe/Zn stressed and in roots of 300-Zn plants. We observed higher accumulation of sugar under stress condition that correlated with high expression of sugar transporter 13 (STP 13). Further, we observed decrease in the chlorophyll content under stress conditions. Based on these findings, we propose the role of sugar driven signaling in decreasing photosynthesis in case of common bean. The decrease in photosynthesis is confirmed by observing significant decrease in chlorophyll content in stressed plants.

Shotgun label-free proteomic and biochemical study of somatic embryos (cotyledonary and maturation stage) in Catharanthus roseus (L.) G. Don

Somatic embryogenesis is an important and wonderful biotechnological tool used to develop whole plant from a single or a group of somatic cells. The differentiated somatic cells become totipotent stem cells by drastic reprogramming of a wide range of cellular activities, leading to the acquisition of embryogenic competence. After acquiring competence, the cells pass through globular, heart, torpedo and cotyledonary stages of embryo; however, all advanced embryos do not convert into full plant, produce adventive embryos or callus instead, thus reverses the programming. This is a big limitation in propagation of many plants. Understanding and unraveling the proteins at this 'embryo to plantlet' transition stage will help to get more numbers of plants. Thus, our study was aimed at an identification of differentially abundant proteins between two important advanced stages, i.e. cotyledonary-(T1) and maturation stage (T2) of somatic embryos in Catharanthus roseus. A total of 2949 and 3030 proteins were identified in cotyledonary and maturation stage, respectively. Of these, 1129 proteins were common to both. Several proteins were found to be differentially accumulated in two different embryo stages in which over 60 proteins were most accumulated during somatic embryo maturation time. More chlorophyll accumulation was noted at this time under the influence of gibberellic acid (GA3). Proteins like Mg-protoporphyrin IX chelatase, chlorophyll a-b-binding protein, photosystem I iron-sulfur center, photosystem II Psb, photosystem II subunit P-1, P-II domain-containing protein, RuBisCO large chain, RuBisCO small chain, RuBisCO activase, RuBisCO large subunit-binding proteins were synthesized. Some of the identified proteins are linked to chlorophyll synthesis, carbohydrate metabolism and stress. The identified proteins are categorized into different groups on the basis of their cellular location, role and other metabolic processes. Biochemical attributes like protein, sugar, proline, antioxidant enzyme (APX, SOD and CAT) activities were high in T2 as compared to T1. The proteins like peroxidases, pathogenesis-related proteins, the late-embryogenesis abundant proteins, argonaute, germin and others have been discussed in C. roseus somatic embryo maturation process.

Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.

Proline metabolism and molecular cloning of AmP5CS in the mangrove Avicennia marina under heat stress

Proline is one of the most important compatible osmolyte in cells, which accumulates in response to various stresses, including salt, water deficit, heavy metal, pathogen infection and extreme temperature. In this study, a growth chamber was employed to simulate heat environment for Avicennia marina seedlings. We detected some physiological indices in the leaves of A. marina at 40 °C, including the activity of delta-1-pyrroline-5-carboxylate synthase (P5CS), the content of free proline and soluble protein, transpiration rate and membrane permeability, and discussed the relationship between these five indices and heat resistant ability. And then a P5CS gene was cloned from A. marina using homologous cloning and rapid amplification of cDNA ends methods. It was designated as AmP5CS, encoding a protein that contained a feedback inhibition site of proline, proA, proB, conserved Leu zipper, GSA-DH domain and other functional domains of P5CS protein in high plants. Expression analysis of AmP5CS gene indicated it was involved in heat stress response. It is the first time that P5CS from A. marina has been cloned and the findings laid the foundation of figuring out heat resistant mechanisms and relieving heat damage, which is significant during global warming.

Metabolomics reveals the "Invisible" detoxification mechanisms of Amaranthus hypochondriacus at three ages upon exposure to different levels of cadmium

To decipher the Cd hyperaccumulation and tolerance mechanisms of plants and increase phytoremediation efficiency, in this study, the physiological effects induced by environmentally relevant concentrations (0, 25 and 200 mg/kg) of Cd were characterized in Amaranthus hypochondriacus (K472) at three growth stages using LC/MS-based metabolomics. Metabolomic analysis identified 31, 29 and 30 significantly differential metabolites (SDMs) in K472 exposed to Cd at the early, intermediate and late stages of vegetative growth, respectively. These SDMs are involved in nine metabolic pathways responsible for antioxidation, osmotic balance regulation, energy supplementation and the promotion of metabolites that participate in phytochelatin (PC) synthesis. K472 at the intermediate stage of vegetative growth had the strongest tolerance to Cd with the combined action of Ala, Asp and Glu metabolism, purine metabolism, Gly, Ser and Thr metabolism and Pro and Arg metabolism. Among these crucial metabolic biomarkers, purine metabolism could be the primary regulatory target for increasing the Cd absorption of K472 for the restoration of Cd-contaminated soil.

Overexpression of the GmDREB6 gene enhances proline accumulation and salt tolerance in genetically modified soybean plants

Soybean plants are sensitive to the effects of abiotic stress and belong to the group of crops that are less drought and salt tolerant. The identification of genes involved in mechanisms targeted to cope with water shortage is an essential and indispensable task for improving the drought and salt tolerance of soybean. One of the approaches for obtaining lines with increased tolerance is genetic modification. The dehydration-responsive element binding proteins (DREBs), belonging to the AP2 family, are trans-active transcription factors that bind to the cis-sequences of the promoter for activating the expression of the target genes that mediate drought and salt tolerant responses. In this study, the GmDREB6 transgene was introduced into DT84 cultivar soybean plants, using Agrobacterium-mediated transformation. The efficacy of GmDREB6 overexpression in enhancing the transcriptional level of GmP5CS and proline accumulation in genetically modified (GM) soybean plants was also assayed. The results demonstrated that ten GM soybean plants (T0 generation) were successfully generated from the transformed explants after selecting with kanamycin. Among these plantlets, the presence of the GmDREB6 transgene was confirmed in nine plants by Polymerase Chain Reaction (PCR), and eight plants showed positive results in Southern blot. In the T1 generation, four GM lines, labelled T1-2, T1-4, T1-7, and T1-10, expressed the recombinant GmDREB6 protein. In the T2 generation, the transcriptional levels of the GmP5CS gene were higher in the GM lines than in the non-transgenic plants, under normal conditions and also under conditions of salt stress and drought, ranging from 1.36 to 2.01 folds and 1.58 to 3.16 folds that of the non-transgenic plants, respectively. The proline content was higher in the four GM soybean lines, T2-2, T2-4, T2-7, and T2-10 than in the non-transgenic plants, ranging from 0.82 μmol/g to 4.03 μmol/g. The proline content was the highest in the GM T2-7 line (7.77 μmol/g). In GM soybean lines, T2-2, T2-4, T2-7, and T2-10 proline content increased after plants were subjected to salt stress for seven days, in comparison to that under normal conditions, and ranged from 247.83% to 300%, while that of the non-GM plants was 238.22%. These results suggested that GmDREB6 could act as a potential candidate for genetic engineering for improving tolerance to salt stresses.

Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection

Molecular changes elicited by common bean (Phaseolus vulgaris L.) in response to Fusarium oxysproum f. sp. Phaseoli (FOP) remain elusive. We studied the changes in root metabolism during common bean–FOP interactions using a combined de novo transcriptome and metabolome approach. Our results demonstrated alterations of transcript levels and metabolite concentrations in common bean roots 24 h post infection as compared to control. The transcriptome and metabolome responses in common bean roots revealed significant changes in structural defense i.e., cell-wall loosening and weakening characterized by hyper accumulation of cell-wall loosening and degradation related transcripts. The levels of pathogenesis related genes were significantly higher upon FOP inoculation. Interestingly, we found the involvement of glycosylphosphatidylinositol- anchored proteins (GPI-APs) in signal transduction in response to FOP infection. Our results confirmed that hormones have strong role in signaling pathways i.e., salicylic acid, jasmonate, and ethylene pathways. FOP induced energy metabolism and nitrogen mobilization in infected common bean roots as compared to control. Importantly, the flavonoid biosynthesis pathway was the most significantly enriched pathway in response to FOP infection as revealed by the combined transcriptome and metabolome analysis. Overall, the observed modulations in the transcriptome and metabolome flux as outcome of several orchestrated molecular events are determinant of host’s role in common bean–FOP interactions.

Characterization and expression analysis of P5CS (Δ1-pyrroline-5-carboxylate synthase) gene in two distinct populations of the Atlantic Forest native species Eugenia uniflora L

Eugenia uniflora is an Atlantic Forest native species, occurring in contrasting edaphoclimatic environments. The identification of genes involved in response to abiotic factors is very relevant to help in understanding the processes of local adaptation. 1-Pyrroline-5-carboxylate synthetase (P5CS) is one interesting gene to study in this species since it encodes a key enzyme of proline biosynthesis, which is an osmoprotectant during abiotic stress. Applying in silico analysis, we identified one P5CS gene sequence of E. uniflora (EuniP5CS). Phylogenetic analysis, as well as, gene and protein structure investigation, revealed that EuniP5CS is a member of P5CS gene family. Plants of E. uniflora from two distinct environments (restinga and riparian forest) presented differences in the proline accumulation and P5CS expression levels under growth-controlled conditions. Both proline accumulation and gene expression level of EuniP5CS were higher in the genotypes from riparian forest than those from restinga. When these plants were submitted to drought stress, EuniP5CS gene was up-regulated in the plants from restinga, but not in those from riparian forest. These results demonstrated that EuniP5CS is involved in proline biosynthesis in this species and suggest that P5CS gene may be an interesting candidate gene in future studies to understand the processes of local adaptation in E. uniflora.

Towards Sustainable Agriculture—Agronomic and Economic Effects of Biostimulant Use in Common Bean Cultivation

Today, one of the greatest challenges faced by the agriculture industry is the development of sustainable and environmentally-friendly systems to meet nutritional demands of the continuously growing global population. A number of research studies have recently been undertaken with the aim to indicate types of parameters used in plant production that would be able to improve plant growth as well as the effectiveness and quality of yield, and to help plants cope with environmental stress. The aim of this study was to verify a hypothesis that the implementation of a sustainable agricultural technology, based on the use of synthetic biostimulants, will allow not only increasing crop yield and quality but also improving the cost-effectiveness of common bean cultivation. The field experiment was conducted in three growing seasons (2016–2018). In the growing season, the plants were treated with Atonik and Tytanit biostimulants in the form of single or double spraying. We determinated biometric traits, seed yield, seed number, and 1000-seed weight. Further analyses included contents of nutraceutical potential. The economic effect of using biostimulants was also calculated. The results of our experiment allowed verifying a hypothesis that the implementation of a sustainable agricultural technology based on the use of synthetic preparations was an effective method to increase plant productivity and, consequently, economic profits to farmers.

Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes

Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.

Toward Unravelling the Genetic Determinism of the Acquisition of Salt and Osmotic Stress Tolerance Through In Vitro Selection in Medicago truncatula

Changes in global climate and the nonstop increase in demographic pressure have provoked a stronger demand for agronomic resources at a time where land suitable for agriculture is becoming a rare commodity. They have also generated a number of abiotic stresses which exacerbate effects of diseases and pests and result in physiological and metabolic disorders that ultimately impact on yield when and where it is most needed. Therefore, a major scientific and agronomic challenge today is that of understanding and countering the impact of stress on yield. In this respect, in vitro biotechnology would be an efficient and feasible breeding alternative, particularly now that the genetic and genomic tools needed to unravel the mechanisms underlying the acquisition of tolerance to stress have become available. Legumes in general play a central role in a sustainable agriculture due to their capacity to symbiotically fix the atmospheric nitrogen, thereby reducing the need for fertilizers. They also produce grains that are rich in protein and thus are important as food and feed. However, they also suffer from abiotic stresses in general and osmotic stress and salinity in particular. This chapter provides a detailed overview of the methods employed for in vitro selection in the model legume Medicago truncatula for the generation of novel germplasm capable of resisting NaCl- and PEG-induced osmotic stress. We also address the understanding of the genetic determinism in the acquisition of stress resistance, which differs between NaCl and PEG. Thus, the expression of genes linked to growth (WEE1), in vitro embryogenesis (SERK), salt tolerance (SOS1) proline synthesis (P5CS), and ploidy level and cell cycle (CCS52 and WEE1) was upregulated under NaCl stress, while under PEG treatment the expression of MtWEE1 and MtCCS52 was significantly increased, but no significant differences were observed in the expression of genes MtSERK1 and MtP5CS, and MtSOS1 was downregulated. A number of morphological and physiological traits relevant to the acquisition of stress resistance were also assessed, and methods used to do so are also detailed.

Characterization of LhSorP5CS, a gene catalyzing proline synthesis in Oriental hybrid lily Sorbonne: molecular modelling and expression analysis

BACKGROUND

Abiotic stresses negatively affect plant growth and flower production. In plants, P5CS proteins are key enzymes that catalyzed the rate-limiting steps of proline synthesis, and proline is a well-known osmoprotectant that is closely related to abiotic stress tolerance. However, information about the P5CS genes, their effects on proline accumulation, and their role in abiotic stress tolerance in Lilium is still lacking.

RESULTS

We isolated and characterized a novel gene (LhSorP5CS) from Oriental hybrid lily cultivar Sorbonne. Phylogenetic analysis indicated that LhSorP5CS is a member of the P5CS family. The three-dimensional structure of LhSorP5CS predicted by homology modeling showed high similarity to its correspondant human P5CS template. Further gene expression analysis revealed that LhSorP5CS expression was up-regulated by NaCl, mannitol, and ABA, and that stress-exposed plants accumulated proline at a significantly higher level than in the control.

CONCLUSIONS

LhSorP5CS characterized in this study is involved in proline synthesis in lily, and that it might play an important role in abiotic stress tolerance. However, there should be other P5CS homologues in the lily genome, and some of them could be highly stress-induced and more important for proline accumulation. Future studies on P5CS family genes would be of great importance to proline-related stress tolerance in lily.

PEG Induces High Expression of the Cell Cycle Checkpoint Gene WEE1 in Embryogenic Callus of Medicago truncatula: Potential Link between Cell Cycle Checkpoint Regulation and Osmotic Stress

Polyethylene glycol (PEG) can be used to mimic osmotic stress in plant tissue cultures to study mechanisms of tolerance. The aim of this experiment was to investigate the effects of PEG (M.W. 6000) on embryogenic callus of Medicago truncatula. Leaf explants were cultured on MS medium with 2 mg L-1 NAA and 0.5 mg L-1 BAP for 5 months. Then, calli were transferred to the same medium further supplemented with 10% (w/v) 6000 PEG for 6 months in order to study physiological and putative molecular markers of water stress. There were no significant differences in growth rate of callus or mitotic index ± PEG although embryogenic potential of PEG treated callus was morphologically enhanced. Cells were rounder on PEG medium and cell size, nuclear size and endoreduplication increased in response to the PEG treatment. Significant increases in soluble sugar and proline accumulation occurred under PEG treatment compared with the control. Significantly, high MtWEE1 and MtCCS52 expression resulted from 6 months of PEG treatment with no significant differences in MtSERK1 or MtP5CS expression but down regulation of MtSOS expression. The results are consistent in showing elevated expression of a cell cycle checkpoint gene, WEE1. It is likely that the cell cycle checkpoint surveillance machinery, that would include WEE1 expression, is ameliorating the effects of the stress imposed by PEG.

Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana

The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.

Phaseolus vulgaris L. Seedlings Exposed to Prometryn Herbicide Contaminated Soil Trigger an Oxidative Stress Response

Herbicides from the family of S-triazines, such as prometryn, have been widely used in crop production and can constitute an environmental pollution in both water and soil. As a valuable crop, the common bean (Phaseolus vulgaris L.) is grown all over the world and could be exposed to such herbicides. We wanted to investigate the possible stress sustained by the common bean growing in prometryn-polluted soil. Two situations were observed: when soil was treated with ≥100 μM prometryn, some, but not all, measured growth parameters were affected in a dose-dependent manner. Growth was reduced, and photosynthetic pigments and photosynthetic products were less accumulated when soil was treated with ≥100 μM prometryn. Reactive oxygen species (ROS) produced had a deleterious effect, as seen by the accumulation of oxidized lipid in the form of malondialdehyde (MDA). Higher prometryn (500 μM) concentrations had a disastrous effect, reducing antioxidant activities. At a low (10 μM) concentration, prometryn increased antioxidant enzymatic activities without affecting plant growth or MDA production. Gene expression of proline metabolism genes and proline accumulation confirm that bean plants respond to a stress according to the prometryn concentration. Physiological responses such as antioxidative enzymes APX, CAT, and the enzyme implicated in the metabolization of xenobiotics, GST, were increased at 10 and 100 μM, which indicated a prevention of deleterious effects of prometryn, suggesting that bean is a suitable material both for herbicide pollution sensing and as a crop on a low level of herbicide pollution.

Physiological and Molecular Aspects of Tolerance to Environmental Constraints in Grain and Forage Legumes

Despite the agronomical and environmental advantages of the cultivation of legumes, their production is limited by various environmental constraints such as water or nutrient limitation, frost or heat stress and soil salinity, which may be the result of pedoclimatic conditions, intensive use of agricultural lands, decline in soil fertility and environmental degradation. The development of more sustainable agroecosystems that are resilient to environmental constraints will therefore require better understanding of the key mechanisms underlying plant tolerance to abiotic constraints. This review provides highlights of legume tolerance to abiotic constraints with a focus on soil nutrient deficiencies, drought, and salinity. More specifically, recent advances in the physiological and molecular levels of the adaptation of grain and forage legumes to abiotic constraints are discussed. Such adaptation involves complex multigene controlled-traits which also involve multiple sub-traits that are likely regulated under the control of a number of candidate genes. This multi-genetic control of tolerance traits might also be multifunctional, with extended action in response to a number of abiotic constraints. Thus, concrete efforts are required to breed for multifunctional candidate genes in order to boost plant stability under various abiotic constraints.

Differentially Expressed Genes in Resistant and Susceptible Common Bean (Phaseolus vulgaris L.) Genotypes in Response to Fusarium oxysporum f. sp. phaseoli

Fusarium wilt of common bean (Phaseolus vulgaris L.), caused by Fusarium oxysporum Schlechtend.:Fr. f.sp. phaseoli (Fop), is one of the most important diseases of common beans worldwide. Few natural sources of resistance to Fop exist and provide only moderate or partial levels of protection. Despite the economic importance of the disease across multiple crops, only a few of Fop induced genes have been analyzed in legumes. Therefore, our goal was to identify transcriptionally regulated genes during an incompatible interaction between common bean and the Fop pathogen using the cDNA amplified fragment length polymorphism (cDNA-AFLP) technique. We generated a total of 8,730 transcript-derived fragments (TDFs) with 768 primer pairs based on the comparison of a moderately resistant and a susceptible genotype. In total, 423 TDFs (4.9%) displayed altered expression patterns after inoculation with Fop inoculum. We obtained full amplicon sequences for 122 selected TDFs, of which 98 were identified as annotated known genes in different functional categories based on their putative functions, 10 were predicted but non-annotated genes and 14 were not homologous to any known genes. The 98 TDFs encoding genes of known putative function were classified as related to metabolism (22), signal transduction (21), protein synthesis and processing (20), development and cytoskeletal organization (12), transport of proteins (7), gene expression and RNA metabolism (4), redox reactions (4), defense and stress responses (3), energy metabolism (3), and hormone responses (2). Based on the analyses of homology, 19 TDFs from different functional categories were chosen for expression analysis using quantitative RT-PCR. The genes found to be important here were implicated at various steps of pathogen infection and will allow a better understanding of the mechanisms of defense and resistance to Fop and similar pathogens. The differential response genes discovered here could also be used as molecular markers in association mapping or QTL analysis.

Evolution of proline biosynthesis: enzymology, bioinformatics, genetics, and transcriptional regulation

Proline is not only an essential component of proteins but it also has important roles in adaptation to osmotic and dehydration stresses, redox control, and apoptosis. Here, we review pathways of proline biosynthesis in the three domains of life. Pathway reconstruction from genome data for hundreds of eubacterial and dozens of archaeal and eukaryotic organisms revealed evolutionary conservation and variations of this pathway across different taxa. In the most prevalent pathway of proline synthesis, glutamate is phosphorylated to γ-glutamyl phosphate by γ-glutamyl kinase, reduced to γ-glutamyl semialdehyde by γ-glutamyl phosphate reductase, cyclized spontaneously to Δ(1)-pyrroline-5-carboxylate and reduced to proline by Δ(1)-pyrroline-5-carboxylate reductase. In higher plants and animals the first two steps are catalysed by a bi-functional Δ(1) -pyrroline-5-carboxylate synthase. Alternative pathways of proline formation use the initial steps of the arginine biosynthetic pathway to ornithine, which can be converted to Δ(1)-pyrroline-5-carboxylate by ornithine aminotransferase and then reduced to proline or converted directly to proline by ornithine cyclodeaminase. In some organisms, the latter pathways contribute to or could be fully responsible for the synthesis of proline. The conservation of proline biosynthetic enzymes and significance of specific residues for catalytic activity and allosteric regulation are analysed on the basis of protein structural data, multiple sequence alignments, and mutant studies, providing novel insights into proline biosynthesis in organisms. We also discuss the transcriptional control of the proline biosynthetic genes in bacteria and plants.

Isolation and characterization of a Δ1-pyrroline-5-carboxylate synthetase (NtP5CS) from Nitraria tangutorum Bobr. and functional comparison with its Arabidopsis homologue

Several functional and regulatory proteins play important roles in controlling plant stress tolerance. Proline (Pro) is one of the most accumulated osmolytes correlated with tolerance to stresses. Δ(1)-Pyrroline-5-carboxylate synthetase (P5CS) is a rate-limiting enzyme in Pro biosynthesis. In the present study, we isolated the cDNA for a P5CS gene (NtP5CS) from the halophyte Nitraria tangutorum. Phylogenetic analysis and subcellular localization analysis of NtP5CS-GFP protein in onion cells showed that NtP5CS was a new P5CS gene and was involved in Pro synthesis in N. tangutorum. Expression of the NtP5CS gene was induced by salt stress, dehydration, and high and low temperatures. Escherichia coli overexpressing AtP5CS or NtP5CS exhibited better growth in all treatments, including high salinity, high alkalinity, dehydration, osmotic, heat and cold stresses. Additionally, NtP5CS recombinant E. coli cells grew better than did AtP5CS recombinant cells in response to abiotic stresses. Our data demonstrate that the P5CS from a halophytic species functions more efficiently than its homologue from a glycophytic species in improving the stress tolerance of E. coli.

LcSAIN1, a novel salt-induced gene from sheepgrass, confers salt stress tolerance in transgenic Arabidopsis and rice

Previously, we identified >1,500 genes that were induced by high salt stress in sheepgrass (Leymus chinensis, Gramineae: Triticeae) when comparing the changes in their transcription levels in response to high salt stress by next-generation sequencing. Among the identified genes, a gene of unknown function (designated as Leymus chinensis salt-induced 1, LcSAIN1) showed a high sequence identity to its homologs from wheat, Hordeum vulgare and Oryza sativa, but LcSAIN1 and its homologs produce hypothetical proteins with no conserved functional domains. Transcription of the LcSAIN1 gene was up-regulated by various stresses. The overexpression of LcSAIN1 in Arabidopsis and rice increased the greening rate of cotyledons, the fresh weight, root elongation, plant height and the plant survival rate when compared with control plants and conferred a tolerance against salt stress. Subcellular localization analysis indicated that LcSAIN1 is localized predominantly in the nucleus. Our results show that the LcSAIN1 gene might play an important positive modulation role in increasing the expression of transcription factors (MYB2 and DREB2A) and functional genes (P5CS and RAB18) in transgenic plants under salt stress and that it augments stress tolerance through the accumulation of compatible solutes (proline and soluble sugar) and the alleviation of changes in reactive oxygen species. The LcSAIN1 gene could be a potential resource for engineering salinity tolerance in important crop species.

A novel salt-induced gene from sheepgrass, LcSAIN2, enhances salt tolerance in transgenic Arabidopsis

Salt stress affects plant growth and development, and limits the productivity of crops. Sheepgrass can grow well under various environmental and soil conditions and is a good wild resource in Triticeae. Using 454 high throughout sequencing technique, a large number of salt stress responsive genes have been picked out from sheepgrass. In this study, a novel salt-induced gene and its promoter were cloned and the gene was designated as LcSAIN2 (Leymus chinensissalt-induced 2). Bioinformatics analysis predicted that LcSAIN2 has one transmembrane helix and is localized in nucleus. Experiments of subcellular localization in tobacco leaf cells also indicated that it was mainly localized in nucleus. Several stress responsive elements were found in the promoter region of the LcSAIN2 gene. The expression analysis confirmed that LcSAIN2 was induced by salinity, PEG, ABA, and cold stresses, especially by high salinity. Overexpression of LcSAIN2 in Arabidopsis enhanced salt tolerance of transgenic plants by accumulating osmolytes, such as soluble sugars and free proline, and improving the expression levels of some stress-responsive transcription factors and key genes. Our results suggest that LcSAIN2 might play an important positive modulation role in salt stress tolerance and be a candidate gene utilized for enhancing stress tolerance in wheat and other crops.

Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress

BACKGROUND

Despite the importance of osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources.

METHODS

A curated set of osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome.

RESULTS

The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo-inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs.

CONCLUSIONS

Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.

Genetic transformation and analysis of rice OsAPx2 gene in Medicago sativa

The OsAPx2 gene from rice was cloned to produce PBI121::OsAPx2 dual-expression plants, of which expression level would be increasing under stressful conditions. The enzyme ascorbate peroxidase (APX) in the leaves and roots of the plants increased with increasing exposure time to different sodium chloride (NaCl) and hydrogen peroxide (H(2)O(2))concentrations, as indicated by protein gel blot analysis. The increased enzyme yield improved the ability of the plants to resist the stress treatments. The OsAPx2 gene was localized in the cytoplasm of epidermal onion cells as indicated by the instantaneous expression of green fluorescence. An 80% regeneration rate was observed in Medicago sativa L. plants transformed with the OsAPx2 gene using Agrobacterium tumefaciens, as indicated by specific primer PCR. The OsAPx2 gene was expressed at the mRNA level and the individual M. sativa (T#1,T#2,T#5) were obtained through assaying the generation of positive T2 using RNA gel blot analysis. When the seeds of the wild type (WT) and the T2 (T#1,T#5) were incubated in culture containing MS with NaCl for 7 days, the results as shown of following: the root length of transgenic plant was longer than WT plants, the H(2)O(2) content in roots of WT was more than of transgenic plants, the APX activity under stresses increased by 2.89 times compared with the WT, the malondialdehyde (MDA) content of the WT was higher than the transgenic plants, the leaves of the WT turned yellow, but those of the transgenic plants remained green and remained healthy. The chlorophyll content in the WT leaves was less than in the transgenic plants, after soaking in solutions of H(2)O(2), sodium sulfite (Na(2)SO(3)), and sodium bicarbonate (NaHCO(3)). Therefore, the OsAPx2 gene overexpression in transgenic M. sativa improves the removal of H(2)O(2) and the salt-resistance compared with WT plants. A novel strain of M. sativa carrying a salt-resistance gene was obtained.

Towards a synthetic view of potato cold and salt stress response by transcriptomic and proteomic analyses

Potato can suffer from several abiotic stresses such as cold temperature, high soil salinity, lack of water or heavy metal exposure, to name a few. They are known to affect plant growth as well as productivity, with differential regulations at several levels. Potato response to cold and salt exposure was investigated at both transcriptomic and proteomic levels in a growth chamber experiment. Cold exposure in potato resulted in a higher number of significantly differentially regulated genes compared to salt exposure, whereas there were nearly three times more differentially regulated proteins after salt exposure when compared to cold exposure. The allocation of up and down-regulated genes at the functional category level also differed between salt and cold exposure although common trends, previously described in various abiotic stresses, were observed. In both stresses, the majority of photosynthesis-related genes were down-regulated whereas cell rescue and transcription factor-related genes were mostly up-regulated. In the other functional categories no common trend was observed; salt exposure results displayed a strong down-regulation of genes implicated in primary metabolism, detoxication apparatus and signal transduction, whereas upon cold exposure, up and down-regulated genes were similar in number. At the proteomic level, the abundance of the majority of identified proteins was increased except for the photosynthesis-related proteins, which were mostly less abundant after both salt and cold exposure. Common responses between salt and cold stress and specific responses inherent to these abiotic stresses are described.

Cloning two P5CS genes from bioenergy sorghum and their expression profiles under abiotic stresses and MeJA treatment

Sweet sorghum (Sorghum bicolor (Linn.) Moench) has promise as a bioenergy feedstock in China and other countries for its use in the production of ethanol as the result of its high fermentable sugar accumulation in stems. To boost biofuel production and extend its range, we seek to improve its stress tolerance. Proline acts as an osmolyte that accumulates when plants are subjected to abiotic stress. P5CS (Δ1-pyrroline-5-carboxylate synthetase) is a key regulatory enzyme that plays a crucial role in proline biosynthesis. We isolated two closely related P5CS genes from sweet sorghum, designated SbP5CS1 (GenBank accession number: GQ377719) and SbP5CS2 (GenBank accession number: GQ377720), which are located on chromosome 3 and 9 and encode 729 and 716 amino acid polypeptides, respectively. The homology between the two sweet sorghum P5CS genes was 76%. Promoter analysis of the two P5CS genes revealed that both sequences not only contained the expected cis regulatory regions such as TATA and CAAT boxes, but also had many stress response elements. Expression analysis revealed that SbP5CS1 and SbP5CS2 transcripts were up-regulated after treatment of 10-day-old seedlings of sweet sorghum with drought, salt (250mM NaCl) and MeJA (10μM). The expression levels of the both SbP5CS genes were significantly increased after 3-day drought stress. Under high salt treatment, peak SbP5CS1 expression was detected at 4h and 8h for SbP5CS2 in roots, while the trends of expression were nearly identical in leaves. In contrast, under drought and high salt stress, the up-regulated expression of SbP5CS1 was higher than that of SbP5CS2. When the seedlings were exposed to MeJA, rapid transcript induction of SbP5CS1 was detected at 2h in leaves, and the SbP5CS2 expression level increase was detected at 4h post-treatment. SbP5CS1 and SbP5CS2 also show different temporal and spatial expression patterns. SbP5CS2 gene was ubiquitously expressed whereas SbP5CS1 was mainly expressed in mature vegetative and reproductive organs. Proline concentration increased after stress application and was correlated with SbP5CS expression. Our results suggest that the SbP5CS1 and SbP5CS2 are stress inducible genes but might play non-redundant roles in plant development. The two genes could have the potential to be used in improving stress tolerance of sweet sorghum and other bioenergy feedstocks.

Transcriptional activation of OsDERF1 in OsERF3 and OsAP2-39 negatively modulates ethylene synthesis and drought tolerance in rice

The phytohormone ethylene is a key signaling molecule that regulates a variety of developmental processes and stress responses in plants. Transcriptional modulation is a pivotal process controlling ethylene synthesis, which further triggers the expression of stress-related genes and plant adaptation to stresses; however, it is unclear how this process is transcriptionally modulated in rice. In the present research, we report the transcriptional regulation of a novel rice ethylene response factor (ERF) in ethylene synthesis and drought tolerance. Through analysis of transcriptional data, one of the drought-responsive ERF genes, OsDERF1, was identified for its activation in response to drought, ethylene and abscisic acid. Transgenic plants overexpressing OsDERF1 (OE) led to reduced tolerance to drought stress in rice at seedling stage, while knockdown of OsDERF1 (RI) expression conferred enhanced tolerance at seedling and tillering stages. This regulation was supported by negative modulation in osmotic adjustment response. To elucidate the molecular basis of drought tolerance, we identified the target genes of OsDERF1 using the Affymetrix GeneChip, including the activation of cluster stress-related negative regulators such as ERF repressors. Biochemical and molecular approaches showed that OsDERF1 at least directly interacted with the GCC box in the promoters of ERF repressors OsERF3 and OsAP2-39. Further investigations showed that OE seedlings had reduced expression (while RI lines showed enhanced expression) of ethylene synthesis genes, thereby resulting in changes in ethylene production. Moreover, overexpression of OsERF3/OsAP2-39 suppressed ethylene synthesis. In addition, application of ACC recovered the drought-sensitive phenotype in the lines overexpressing OsERF3, showing that ethylene production contributed to drought response in rice. Thus our data reveal that a novel ERF transcriptional cascade modulates drought response through controlling the ethylene synthesis, deepening our understanding of the regulation of ERF proteins in ethylene related drought response.

Role of transgenic plants in agriculture and biopharming

At present, environmental degradation and the consistently growing population are two main problems on the planet earth. Fulfilling the needs of this growing population is quite difficult from the limited arable land available on the globe. Although there are legal, social and political barriers to the utilization of biotechnology, advances in this field have substantially improved agriculture and human life to a great extent. One of the vital tools of biotechnology is genetic engineering (GE) which is used to modify plants, animals and microorganisms according to desired needs. In fact, genetic engineering facilitates the transfer of desired characteristics into other plants which is not possible through conventional plant breeding. A variety of crops have been engineered for enhanced resistance to a multitude of stresses such as herbicides, insecticides, viruses and a combination of biotic and abiotic stresses in different crops including rice, mustard, maize, potato, tomato, etc. Apart from the use of GE in agriculture, it is being extensively employed to modify the plants for enhanced production of vaccines, hormones, etc. Vaccines against certain diseases are certainly available in the market, but most of them are very costly. Developing countries cannot afford the disease control through such cost-intensive vaccines. Alternatively, efforts are being made to produce edible vaccines which are cheap and have many advantages over the commercialized vaccines. Transgenic plants generated for this purpose are capable of expressing recombinant proteins including viral and bacterial antigens and antibodies. Common food plants like banana, tomato, rice, carrot, etc. have been used to produce vaccines against certain diseases like hepatitis B, cholera, HIV, etc. Thus, the up- and down-regulation of desired genes which are used for the modification of plants have a marked role in the improvement of genetic crops. In this review, we have comprehensively discussed the role of genetic engineering in generating transgenic lines/cultivars of different crops with improved nutrient quality, biofuel production, enhanced production of vaccines and antibodies, increased resistance against insects, herbicides, diseases and abiotic stresses as well as the safety measures for their commercialization.

Differential effects of cold acclimation and abscisic acid on free amino acid composition in wheat

The effect of cold acclimation and abscisic acid (ABA) treatment on the free amino acid composition was compared in Chinese Spring chromosome 5A substitution lines with different levels of freezing tolerance. The total amino acid content gradually increased during the 3-week cold acclimation period, while the effect of ABA became visible only after 7 d. The ratio of members of the glutamate family increased during cold acclimation and the ratio of amino acids belonging to the aspartate family decreased. Opposite changes were observed after treatment with ABA. Consistently with these results, ABA only induced a major increase in the Asn content, while the Asp, Glu, Gln and Pro levels were greatly induced by cold. A corresponding alteration at the gene expression level was only found for Pro and Glu. With the exception of Pro, cold- or ABA-induced changes in the amino acid levelsor Pro, did not correlate with the freezing tolerance of the three genotypes examined and were not affected by chromosome 5A. Since cold acclimation induced the accumulation of most of the amino acids, while ABA had a significant effect only on Asn, the cold-induced changes in free amino acid levels were probably not mediated by ABA.

Identification of drought-responsive compounds in potato through a combined transcriptomic and targeted metabolite approach

Two potato clones (Solanum tuberosum L.) of the Andean cultivar group, called Sullu and SS2613, with different drought-tolerance phenotypes were exposed to a continuously increasing drought stress in a field trial. At the physiological level, while relative leaf water contents were similar in both clones, osmotic potential was lower in Sullu and declined more strongly during drought compared with SS2613. In the drought-stressed plants, tuber yield was reduced by about 70% compared with control plants in both clones. Potato cDNA microarrays and target metabolite analysis were performed on leaves sampled at several time-points after the onset of drought. At the transcriptomic level, photosynthesis-related genes were already strongly repressed in Sullu after 28 d of withholding irrigation and even more strongly after a longer stress duration, whereas, in SS2613, repression occurred only after 49 d of soil drying; similarly, a strong perturbation of carbohydrate-related genes was observed in Sullu. At the metabolite level, differential accumulation of osmotically active solutes was observed between the two cultivars; indeed, in Sullu, contents of galactose, inositol, galactinol, proline, and proline analogues were higher upon drought stress compared with SS2613. These results point to different drought responses in the cultivars at the leaf level, with, however, similar tuber yield reductions. The previously shown tolerant clone Sullu lost part of its tolerance under the experimental conditions used here; it was, however, able to maintain an absolute yield three times higher than SS2613.

Cloning and genetic diversity analysis of a new P5CS gene from common bean (Phaseolus vulgaris L.)

Delta(1)-pyrroline-5-carboxylate synthetase (P5CS) is the rate-limiting enzyme involved in the biosynthesis of proline in plants. By the 3' rapid amplification of cDNA ends (3'-RACE) approach, a 2,246-bp cDNA sequence was obtained from common bean (Phaseolus vulgaris L.), denominated PvP5CS2 differing from another P5CS gene that we cloned previously from common bean (PvP5CS). The predicted amino acid sequence of PvP5CS2 has an overall 93.2% identity GmP5CS (Glycine max L. P5CS). However, PvP5CS2 shows only 83.7% identity in amino acid sequence to PvP5CS, suggesting PvP5CS2 represents a homolog of the soybean P5CS gene. Abundant indel (insertion and deletion events) and SNP (single nucleotide polymorphisms) were found in the cloned PvP5CS2 genome sequence when comparing 24 cultivated and 3 wild common bean accessions and these in turn reflected aspects of common bean evolution. Sequence alignment showed that genotypes from the same gene pool had similar nucleotide variation, while genotypes from different gene pools had distinctly different nucleotide variation for PvP5CS2. Furthermore, diversity along the gene sequence was not evenly distributed, being low in the glutamic-g-semialdehyde dehydrogenase catalyzing region, moderate in the Glu-5-kinase catalyzing region and high in the intervening region. Neutrality tests showed that PvP5CS2 was a conserved gene undergoing negative selection. A new marker (Pv97) was developed for genetic mapping of PvP5CS2 based on an indel between DOR364 and G19833 sequences and the gene was located between markers Bng126 and BMd045 on chromosome b01. The relationship of PvP5CS2 and a previously cloned pyrroline-5-carboxylate synthetase gene as well as the implications of this work on selecting for drought tolerance in common bean are discussed.

Transcriptional differences in gene families of the ascorbate-glutathione cycle in wheat during mild water deficit

When comparing the responses of two wheat (Triticum aestivum L.) genotypes, the drought-tolerant Plainsman V and the drought-sensitive Cappelle Desprez, to reduced amounts of irrigation water, we found differences in ascorbate metabolism: both ascorbate oxidation and transcription levels of enzymes processing ascorbate were changed. Relative transcript levels of ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR), dehydroascorbate reductase (DHAR) and glutathione reductase (GR) isoenzymes, predicted to localize in distinct subcellular organelles, showed different transcriptional changes in the two genotypes. Among APX coding mRNAs, expression levels of two cytosolic (cAPX I, II) and a thylakoid-bound (tAPX) variants increased significantly in Plainsman V while a cytosolic (cAPX I) and a stromal (sAPX II) APX coding transcripts were found to be higher in Cappelle Desprez after a 4-week-long water-deficit stress. Examining the MDARs, two cytosolic isoforms (cMDAR I, II) displayed significant up-regulation of mRNA levels in the sensitive genotype, whereas only one of them (cMDAR II) did in the tolerant cultivar. We found an up-regulated chloroplastic DHAR (chlDHAR) mRNA only in the sensitive Cappelle Desprez. However, increased expression levels of a cytosolic GR (cGR) and a chloroplastic GR (chlGR) were detected only in the tolerant Plainsman V. After 4 weeks of reduced irrigation, a significantly lower ascorbate/dehydroascorbate ratio was detected in leaves of the sensitive Cappelle Desprez than in the tolerant Plainsman V. Our results indicate that more robust transcription of ascorbate-based detoxification machinery may prevent an adverse shift of the cellular redox balance.

Hydrogen peroxide-induced proline and metabolic pathway of its accumulation in maize seedlings

Exogenous H(2)O(2) treatment led to a significant accumulation of proline in coleoptiles and radicles of maize seedlings. It also induced an almost immediate and rapid increase of activity of the key enzymes Delta(1)-pyrroline-5-carboxylate synthetase and glutamate dehydrogenase of the glutamate pathway of proline biosynthesis and an up-regulation of Delta(1)-pyrroline-5-carboxylate synthetase gene expression. Activities of the key enzymes arginase and ornithine aminotransferase of the ornithine pathway of proline biosynthesis increased only after 12h of H(2)O(2) treatment. Furthermore, the H(2)O(2) treatment caused an early decrease of the activity of proline dehydrogenase, a key enzyme of proline degradation. These results indicate that H(2)O(2) might be involved in signal transduction events, leading to proline accumulation in maize seedlings, and that the H(2)O(2)-induced proline accumulation is a combined result of the sequential activation of the glutamate and ornithine pathways of proline biosynthesis and the simultaneous inhibition of proline degradation by H(2)O(2).