Comparative transcriptome and translatome analysis in contrasting rice genotypes reveals differential mRNA translation in salt-tolerant Pokkali under salt stress.

BACKGROUND: Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace, whereas IR29 is a salt-sensitive but widely cultivated genotype. Comparative analysis of these genotypes may offer a better understanding of the salinity tolerance mechanisms in rice. Although most stress-responsive genes are regulated at the transcriptional level, in many cases, changes at the transcriptional level are not always accompanied with the changes in protein abundance, which suggests that the transcriptome needs to be studied in conjunction with the proteome to link the phenotype of stress tolerance or sensitivity. Published reports have largely underscored the importance of transcriptional regulation during salt stress in these genotypes, but the regulation at the translational level has been rarely studied. Using RNA-Seq, we simultaneously analyzed the transcriptome and translatome from control and salt-exposed Pok and IR29 seedlings to unravel molecular insights into gene regulatory mechanisms that differ between these genotypes. RESULTS: Clear differences were evident at both transcriptional and translational levels between the two genotypes even under the control condition. In response to salt stress, 57 differentially expressed genes (DEGs) were commonly upregulated at both transcriptional and translational levels in both genotypes; the overall number of up/downregulated DEGs in IR29 was comparable at both transcriptional and translational levels, whereas in Pok, the number of upregulated DEGs was considerably higher at the translational level (544 DEGs) than at the transcriptional level (219 DEGs); in contrast, the number of downregulated DEGs (58) was significantly less at the translational level than at the transcriptional level (397 DEGs). These results imply that Pok stabilizes mRNAs and also efficiently loads mRNAs onto polysomes for translation during salt stress. CONCLUSION: Under salt stress, Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis. The present study confirmed the known salt stress-associated genes and also identified a number of putative new salt-responsive genes. Most importantly, the study revealed that the translational regulation under salinity plays an important role in salt-tolerant Pok, but such regulation was less evident in the salt-sensitive IR29.

Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants.

Tonoplast intrinsic proteins (TIPs) play a vital role in water transport across membranes. In the present study, we performed a comparative analysis of TIP genes in ten plant species including both monocots and dicots. A total of 100 TIP aquaporin genes were identified, and their relationships among the plant species were analyzed. Phylogenetic analysis was performed to evaluate the relationship of these genes within the plant species. Based on the phylogenetic analysis results, TIPs were classified into five distinct arbitrary groups (group I to group V), which represented TIP2, TIP5, TIP4, TIP1, and TIP3, respectively. Group I represented the largest arbitrary group, followed by group IV, in the phylogenetic tree. The result clearly indicates that TIP2 and TIP1 are abundant aquaporins and highly related among the species. In the present review, a comparative study of gene structure analysis between dicots and monocots has been performed to analyze their structural variation. Most of the predicted motifs are conserved among the species, signifying an evolutionary relationship. The gene expression analysis indicated that the expression of TIP genes varies during different developmental stages and also during stressed conditions. The results indicated a great degree of evolutionary relationship and variation in the expression levels of TIPs in plants.

Arsenic stress in rice: redox consequences and regulation by iron.

Arsenic (As) contamination is a serious hazard to human health and agriculture. It has emerged as an important threat for rice cultivation mainly in South Asian countries. In this study, we investigated the effect of iron (Fe) supplementation on arsenic (As(V)) induced oxidative stress responses in rice (Oryza sativa L.). Rice seedlings treated with As(V) for 24 and 48 h in presence or absence of 2.5 mM Fe after which the root and shoot tissues were harvested for analysis. The results indicate significant (p ≤ 0.05) reduction in root and shoot length/dry biomass. Supplementation of Fe showed improved growth responses under stress as compared to As(V) alone. The scanning electron microscopy (SEM) analysis of roots under As(V) treatment for 48 h showed major alterations in root structure and integrity, although no noticeable changes were observed in Fe - supplemented seedlings. Significantly high (p ≤ 0.05) accumulation of As(V) was observed in root and shoot after 24 and 48 h of stress. However, under Fe - supplementation As accumulation in root and shoot were considerably low after 24 and 48 h of As(V) treatment. The hydrogen peroxide (H2O2) and malondialdehyde (MDA) content in both root and shoot increased significantly (p ≤ 0.05) after 24 and 48 h of As(V) treatment. In Fe - supplemented seedlings, the levels of H2O2 and MDA were considerably low as compared to As(V) alone. Ascorbate (AsA) and glutathione (GSH) levels also increased significantly (p ≤ 0.05) under As(V) stress as compared to control and Fe-supplemented seedlings. Activities of catalase (CAT) and superoxide dismutase (SOD) were significantly (p ≤ 0.05) high after 24 and 48 h of As(V) treatment as compared to Fe-supplemented seedlings. The gene expression analysis revealed up-regulation of metallothionein (MT1, MT2) and nodulin 26-like intrinsic protein (NIP2;1) genes after 5d of As treatment, while their expressions were repressed under Fe-supplementation. Our results indicate that Fe regulates oxidative stress and promotes growth under As stress.

Zinc ameliorates copper-induced oxidative stress in developing rice (Oryza sativa L.) seedlings.

Rice (Oryza sativa L.) seedlings were treated with different concentrations of copper (Cu) either in presence or absence of zinc (Zn), and different events were investigated to evaluate the ameliorative effect of Zn on Cu stress. In presence of high Cu concentration, growth of both root and shoots were considerably reduced. Decline in elongation and fresh mass was observed in root and shoot. Zn alone did not show any considerable difference as compared to control, but when supplemented along with high concentration Cu, it prompted the growth of both root and shoot. After 7 days, root growth was 9.36 and 9.59 cm, respectively, at 200 and 500 µM of Cu alone as compared to 10.59 and 12.26 cm at similar Cu concentrations, respectively, in presence of Zn. Cu accumulation was considerably high after 7 days of treatment. In absence of Zn, significant accumulation of Cu was observed. Zn supplementation ameliorated the toxic impact of Cu and minimized its accumulation. Cu treatment for 1 and 7 days resulted in a dose-dependent increase in hydrogen peroxide (H2O2). When Cu was added in presence of Zn, the H2O2 production in root and shoot was reduced significantly. The increase in H2O2 production under Cu stress was accompanied by augmentation of lipid peroxidation. In absence of Zn, Cu alone enhanced the malondialdehyde (MDA) production in both root and shoot after 1 and 7 days of treatment. The MDA content drastically reduced in root and shoot as when Zn was added during Cu treatment. The activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), and guaiacol peroxidase (GPX) were elevated under Cu stress both in root and shoot. Addition of Zn further stimulated the activities of these enzymes. Both ascorbate (AsA) and glutathione (GSH) contents were high under Cu stress either in presence or absence of Zn. The results suggests that Zn supplementation improves plant survival capacity under high Cu stress by modulating oxidative stress through stimulation of antioxidant mechanisms and restricts the accumulation of toxic concentrations of Cu.

Reactive oxygen species signaling in plants under abiotic stress.

Abiotic stresses like heavy metals, drought, salt, low temperature, etc. are the major factors that limit crop productivity and yield. These stresses are associated with production of certain deleterious chemical entities called reactive oxygen species (ROS), which include hydrogen peroxide (H2O2), superoxide radical (O2(-)), hydroxyl radical (OH(-)), etc. ROS are capable of inducing cellular damage by degradation of proteins, inactivation of enzymes, alterations in the gene and interfere in various pathways of metabolic importance. Our understanding on ROS in response to abiotic stress is revolutionized with the advancements in plant molecular biology, where the basic understanding on chemical behavior of ROS is better understood. Understanding the molecular mechanisms involved in ROS generation and its potential role during abiotic stress is important to identify means by which plant growth and metabolism can be regulated under acute stress conditions. ROS mediated oxidative stress, which is the key to understand stress related toxicity have been widely studied in many plants and the results in those studies clearly revealed that oxidative stress is the main symptom of toxicity. Plants have their own antioxidant defense mechanisms to encounter ROS that is of enzymic and non-enzymic nature . Coordinated activities of these antioxidants regulate ROS detoxification and reduces oxidative load in plants. Though ROS are always regarded to impart negative impact on plants, some reports consider them to be important in regulating key cellular functions; however, such reports in plant are limited. Molecular approaches to understand ROS metabolism and signaling have opened new avenues to comprehend its critical role in abiotic stress. ROS also acts as secondary messenger that signals key cellular functions like cell proliferation, apoptosis and necrosis. In higher eukaryotes, ROS signaling is not fully understood. In this review we summarize our understanding on ROS and its signaling behavior in plants under abiotic stress.

Excess copper induced oxidative stress and response of antioxidants in rice.

To investigate the effects of copper (Cu), rice plant (Oryza sativa. L. var. MSE-9) was treated with different Cu concentrations (0, 10, 50 and 100 µM) for 5 days in hydroponic condition. Gradual decrease in shoot and root growth was observed with the increase of Cu concentration and duration of treatment where maximum inhibition was recorded in root growth. Cu was readily absorbed by the plant though the maximum accumulation was found in root than shoot. Hydrogen peroxide (H(2)O(2)) production and lipid peroxidation were found increased with the elevated Cu concentration indicating excess Cu induced oxidative stress. Antioxidant enzymes superoxide dismutase (SOD), guaiacol peroxidase (GPX) and ascorbate peroxidase (APX) and glutathione reductase (GR) were effectively generated at the elevated concentrations of Cu though catalase (CAT) did not show significant variation with respect to control. Ascorbate (ASH), glutathione (GSH) and proline contents were also increased in all the Cu treated plants compared with the control. SOD isoenzyme was greatly affected by higher concentration of Cu and it was consistent with the changes of the activity assayed in solution. The present study confirmed that excess Cu inhibits growth, induced oxidative stress by inducing ROS formation while the stimulated antioxidative system appears adaptive response of rice plant against Cu induced oxidative stress. Moreover proline accumulation in Cu stress plant seems to provide additional defense against the oxidative stress.