This article has been retracted by the Editor-in-Chief following concerns raised after publication. Specifically, duplication of two lanes within the same blot was identified in Figure 1b, where different samples were represented using the same data. The authors were unable to provide a satisfactory explanation or a suitable replacement figure. As a result, the editor has lost confidence in the data and conclusions presented in the study. One author (Swarup Roy Choudhury) disagreed with the retraction. The remaining authors did not respond to correspondence from the publisher regarding this issue.

14-3-3 isoforms were relatively less conserved at the C-terminal region across plant groups. Both Os 14-3-3f and Os 14-3-3g were inducible with differential gene expression levels under different abiotic stress and developmental stages in sensitive and tolerant indica rice cultivars as confirmed both at transcript and protein level.

The plants are constantly subjected to varying degree of environmental stress. These stresses results in severe damage to the DNA of the plants, which if not repaired can lead to the impairment of their genetic material, and can prove fatal for the plants. The present work studies the damage to the genomic DNA in response to salinity and drought stress on the indica rice cultivars. The comet assay results showed that maximum DNA damage was seen in the IR29 cultivar, whereas, the Nonabokra cultivar showed minimal DNA damage. The gene expression profiling of DNA polymerase λ (OsPolλ), the only X family DNA polymerase in rice which is involved in the repair of DNA damage, shows that the gene is up-regulated in all the rice cultivars irrespective of their degree of tolerance to the environmental stresses. Further the enzymatic activity of the OsPolλ protein was studied in the three rice cultivars and it was revealed that the OsPolλ activity increases in response to stresses in all the rice cultivars, however, the salinity-susceptible IR29 showed a more prominent increases in the activity of OsPolλ than Nonabokra (salinity tolerant) and N22 (drought tolerant) cultivars. The study on the upstream regions of the OsPolλ gene to identify the different cis acting upstream elements effecting the gene expression showed the presence of unique stress responsive regulatory elements was detected in the upstream region of OsPolλ gene. The present study suggest that the OsPolλ gene expression and enzymatic activity is enhanced in response to these abiotic stress, thus, playing an important role in the repair of salinity and drought induced DNA damages in indica rice cultivars.

Rice ( Oryza sativa L.), the staple food in South-East Asian countries, is a water-intensive crop so that its productivity is highly affected by drought, the most severe environmental stress factor. We report here the development of transgenic rice via overexpression of full length OsRab16A (driven by endogenous promoter) or AtDREB1A driven by rd29A promoter in the background of the aromatic indica rice cultivar, Pusa Sugandhi 2 (PS2) through biolistic transformation. Both the transgenes were stably introgretted in T 2 generations as indicated by the results of polymerase chain reaction (PCR). Reverse transcriptase (RT)-polymerase chain reaction (PCR) analyses showed that the expression of both the transgenes was induced by drought stress in all the T 2 transgenic plants examined, which were highly tolerant to water deficit stress during both the vegetative and reproductive stages without their morphological or agronomic traits being affected. Protein immunoblot analysis with Rab16A (= anti dehydrin) antiserum showed detectable accumulation of Rab16A protein in the transgenics in response to drought stress and exogenous abscisic acid (ABA) application. The physiological studies revealed that the expression of the transgene under drought stress in T 2 transgenics was associated with lesser shoot or root length inhibition, improved leaf relative water content, stable maintenance of chlorophyll, lesser hydrogen peroxide accumulation with higher catalase activity and an increased accumulation of the osmoprotectant proline, as compared with the wild type (WT) plants. The transgenic plants also showed significantly higher filled grain, spikelet fertility and grain yield under stressed conditions. All these findings highlighted the tremendous potentiality of both OsRab16A and AtDREB1A in conferring drought tolerance without affecting the normal phenotype and physiology of the plants. To our knowledge, this is the first report on the development of a drought-tolerant transgenic aromatic rice variety through overexpression of genes, one involved in ABA-dependent pathway ( OsRab16A ), while the other in ABA-independent pathway ( AtDREB1A ) of stress tolerance, thereby highlighting the significance of both the pathways in drought tolerance of the aromatic rice varieties.

Polyamines help to mitigate salt stress in plants. SAMdC or S-adenosyl methionine decarboxylase is a crucial enzyme in the polyamine biosynthetic pathway. Overexpressing the samdc gene of Pokkali (a salt-tolerant Indica rice landrace) in the model plant tobacco through Agrobacterium-mediated transformation resulted in tobacco plants capable of withstanding high salinity (200 mM) stress. The transgenic tobacco plants maintained a steady level of the higher polyamines and resisted ionic imbalance under salt stress. Since appropriate binding of the substrate with the enzyme is essential for an enzymatic reaction, we performed molecular docking experiment of SAMdC enzyme of Pokkali rice and tobacco to get an idea about its commonality in the two plants in the backdrop of Japonica rice and Arabidopsis. In silico characterization of SAMdC revealed that the enzyme used the same substrate in Pokkali rice and tobacco, from where the gene is introgressed and where it is overexpressed.

DNA polymerase λ (Pol λ) is the only member of DNA polymerase family X present in plants. The enzyme is ddNTP sensitive as it contains the conserved C-terminal Pol β domain. The 1.1 kb partial coding sequence isolated spanned the whole 3' regions of the gene containing functionally important domains of the Pol λ gene. Comparative in silico studies from both indica and japonica cultivars involving homology modelling showed that the model for the partial Pol λ gene was stable and acceptable. The alignment of both the protein models showed a RMS value of 0.783. Apart from this, expression of Pol λ and its relative activity is studied during different development stages of three different indica rice cultivars (IR29, Nonabokra and N22). Enhanced accumulation and higher activity of Pol λ during the early seedling stage was detected. Higher expression and activity were observed in the anthers, which was probably necessary for DNA repair during microspore formation. However, during the maturation stage of seed development and plant growth, expression and the activity of Pol λ decreased due to slow metabolic activity and a reduced rate of cell division respectively. Furthermore, the expression and activity of Pol λ were found to be higher in IR29 in comparison to Nonabokra and N22. IR29 is a rice cultivar susceptible to environmental stresses and hence it encounters higher DNA damages. The enhanced presence and activity of the Pol λ enzyme in IR29 with respect to the other two cultivars, which are more tolerant to the environmental stresses during various developmental stages, is therefore explainable.

Involvement of DNA polymerase (pol) enzymes in meiotic DNA repair has not been clearly understood in plants. DNA polymerase λ is involved in short patch DNA synthesis and base excision repair in both plants and animals. The presence and activity of the pol λ enzyme was studied in a protein isolated from spikelets during flower development stages of rice (Oryza sativa L.) and maize (Zea mays L.). Western blot analysis showed a 2- to 2.5-fold higher accumulation of pol λ in spikelets than in shoots. Assays of pol and in-gel activity showed the dideoxynucleotide triphosphate sensitive pol λ enzyme in spikelets of both the plants. An enhanced presence of the enzyme and its high activity suggests an active role of pol λ in meiotic recombination during microspore development.

X family DNA polymerases are single polypeptide enzymes essential for short patch DNA synthesis and repair. DNA polymerase λ is the only member of the family reported in plants. It is involved in base excision repair and translesion DNA synthesis. Objective of this study was to search for and analysis of DNA polymerase λ (pol λ) in Zea mays. The protein sequence of DNA polymerase λ from Japonica rice (Oryza sativa) was used for BLAST algorithm with maize reference protein sequences to find out orthologous protein. It indicated presence of one uncharacterised protein of maize (LOC100383279) which was found to have high homology with rice pol λ. Conserved domain search showed presence of BRCT (Breast cancer susceptibility protein A-1 C-terminal domain), dRP (5′-deoxyribosephosphate) lyase domain in addition to polymerase domain in the uncharacterised enzyme of maize. Homology of DNA sequence between rice and maize DNA polymerase was found in Southern blot. Variable expression of the protein was detected during seed development by Western blot. Result suggested presence of 61 kDa DNA polymerase λ protein in maize plant.

DNA polymerase λ (DNA pol λ) is the only reported X-family DNA polymerases in plants and has been shown to play a significant role in dry quiescent seeds, growth, development and nuclear DNA repair. cDNA for DNA pol λ has been reported in Arabidopsis and japonica rice cultivar and has been characterized from E. coli expressed protein, but very little is known about its activity at protein level in plants. The enzymatic activity of DNA pol λ was studied in dry, imbibed and during different germination stages of indica rice IR-8 (salt sensitive) by in-gel activity assay to determine its physiological role in important stages of growth and development. The upstream sequence was also analyzed using plantCARE database and was found to contain several cis-acting elements, including light responsive elements, dehydration responsive elements, Myb binding sites, etc. Hence, 4-day-old germinating seedlings of IR29, a salt-sensitive, but high yielding indica rice cultivar and Nonabokra, a salt-tolerant, but low yielding cultivar were treated with water (control) or 250 mM NaCl or 20% polyethyleneglycol-6000 for 4 and 8 h. The protein was analyzed by in vitro DNA pol λ activity assay, in-gel activity assay and Western blot analysis. DNA pol λ was not detected in dry seeds, but enhanced after imbibition and detectable from low level to high level during subsequent germination steps. Both salinity and dehydration stress led to the enhancement of the activity and protein level of DNA pol λ, as compared to control tissues. This is the first evidence of the salinity or dehydration stress induced enhancement of DNA pol λ activity in the plumules of rice (Oryza sativa L.) cultivars.

Imbibition of water by dry seeds initiates active metabolic processes that lead to seed germination. Intact and damage free DNA is required in embryonic cells before the DNA replication in every cycle of cell division that occurs during seed germination. DNA polymerase-λ (pol-λ) is a dideoxynucleotidetriphosphate (ddNTP) sensitive single polypeptide enzyme involved in DNA repair and present in imbibed seeds of rice. Activity of pol-λ was studied in dry, imbibed and germinating seeds of Zea mays. DNA polymerase enzyme assay showed enhanced activity of the ddNTP sensitive enzyme after imbibition. Western blot analysis showed presence of the enzyme during seed germination. Prominent presence of the ddNTP sensitive DNA pol-λ was found after imbibition in Zea mays in activity gel analysis. Results indicate crucial role of the enzyme during seed germination and early seedling stage in maize plant.

S-adenosylmethionine decarboxylase (SAMdC, EC 4.1.1.50) and Spermidine synthase (SPDS, EC 2.5.1.1), two enzymes of plant polyamine biosynthetic pathway were cloned to gain further insight on the polyamine metabolism through a molecular approach. cDNAs for SAMdC and SPDS were isolated from Oryza sativa cv. Pokkali and Nicotiana tabacum cv. Jayasri respectively. Rice SAMdC (rSAMdC) and Tobacco SPDS (tSPDS) proteins were overexpressed in E. coli using expression vectors pEZZ18 and pGEX-3X respectively. N-terminally protein-A-tagged 43.8 kDa pre-protein of rSAMdC and Nterminally GST-tagged 34.7 kDa of tSPDS were purified by affinity chromatography. The activities of the recombinant proteins were confirmed by the appearance of spermidine, product of the coupled reaction involving rSAMdC and tSPDS. As a direct evidence of the function of these plant enzymes, the complementation assay using extract of E. coli mutant strain, HT252 (F-∆(speAspeB) ∆(speCglc) ∆(speED) thr-1 proA2 thi-1 lacY1 galK2 m-), deficient in polyamine biosynthetic enzymes was performed. Reconstitution of the E. coli polyamine biosynthetic pathway by two different plant enzymes rSAMdC and tSPDS, simultaneously supplemented with exogenous S-adenosylmethionine and putrescine, was the novel observation of the

Abiotic stress affects the growth and productivity of crop plants; to cope with the adverse environmental conditions, plants have developed efficient defense machinery comprising of antioxidants like phenolics and flavonoids, and osmolytes like polyamines. SamDC is a key enzyme in the polyamine biosynthesis pathway in plants. In our present communication we have done in silico analysis of the promoter region of SamDC to look for the presence of different cis-regulatory elements contributing to its expression. Based on the presence of different cis-regulatory elements we completed comparative analysis of SamDC gene expression in rice lamina of IR-29 and Nonabokra by qPCR in response to the abiotic stress treatments of salinity, drought, cold and the biotic stress treatments of ABA and light. Additionally, to explore the role of the cis-regulatory elements in regulating the expression of SamDC gene in plants we comparatively analyzed the binding of rice nuclear proteins prepared from IR-29 and Nonabokra undergoing various stress treatments. The intensity of the complex formed was low and inducible in IR-29 in contrast to Nonabokra. Southwestern blot analysis helped in predicting the size of the trans-acting factors binding to these cis-elements. To our knowledge this is the first report on the comprehensive analysis of SamDC gene expression in rice and identification of the trans-acting factors regulating its expression.

Lately we have published on the characterization of the upstream of SamDC gene from rice and investigated the involvement of various cis-elements present in the promoter region in its transcriptional regulation. Analysis of SamDC expression showed that it was inducible by abiotic stresses like salinity, drought, and cold as well as by light and ABA treatment. Furthermore, DNA protein interaction studies have identified transacting actors responsible for its expression after abiotic stresses or light inducibility. Here we have further discussed on the possible role of these cis-elements in modulating the transcriptional network and comment on their function in relation to polyamine biosynthesis during periods of abiotic stress in rice.

Tomato is a crop plant with high fruit nutritive value and other useful properties. The cultivation of this species is dependent on many environmental factors, e.g. temperature, salinity, nutrients etc, affecting the yield and reproductive potential of the plant. Salinity in soil or water is of increasing importance to agriculture because it causes stress to crop plants. Plants exposed to an excess amount of salts such as NaCl undergo osmotic stress, water deficit and ionic imbalances and can increase production of reactive oxygen species(ROS). Higher plants possess very efficient enzymatic and non-enzymatic antioxidative defense mechanisms that allow the scavenging of ROS and protection of cellular components from oxidative damage. Studies were conducted to investigate the effect of short term salinity stress on some physiological alterations in three tomato cultivars Pusa Ruby(PR), Punjab Keshari (PK) and Ailsa Craig(AC). Some biochemical parameters (anthocyanin and carotenoeid content, polyamines, proline, cysteine, peroxidase and malondialdehyde) were set and applied at two month old stage of tomato plants. Three tomato cultivars were grown in 0.5xMS for 2 months and at this stage, they were treated with 0 and 200mM NaCl for a short period of six hours in hydroponic conditions. The genotypes exhibited different responses in terms of different osmoprotectant, antioxidant, and pigment level. The relationships among the salinity and accumulation of these compounds in leaf were then determined. It was concluded that, tomato cultivars under study responded differently showing their sensitivity or tolerance to salinity stress. Among three cultivars PK appeared to be more tolerant genotype than the other two cultivars PR and AC. PK could rapidly evolve physiological and antioxidant mechanisms to adapt to salt and manage the oxidative stress. The research was conducted in a completely randomized design with three replications.

The genetic and molecular biological studies mainly in Arabidopsis and in some other plants have begun to uncover the various components of ripening signaling pathway in plants. Although transcriptional regulation of major ripening genes have been studied in detail, information on role of phosphorylation in regulating the activity and stability of core ripening pathway associated proteins in relation to ethylene biosynthesis during fruit ripening is still limited. Recently we have demonstrated the evidence for post-translational regulation of MA-ACS1 (Musa acuminata ACC synthase 1), the rate limiting step enzyme regulating ripening ethylene production in banana, through phosphorylation at the C-terminal Ser 476 and 479 residues by a 41-kDa Ser/Thr protein kinase.1 Here we have further discussed role of protein phosphorylation in regulation of stability and activity of ACS enzymes and the mechanistic and evolutionary perspective of phosphorylation pattern of Type I ACC synthase enzymes.

Since 1995, whole-genome sequencing projects have been revealing DNA sequence information from simple bacteria to plants and animals. Free and easy access to DNA sequence data to the scientific community is crucial for the maximal utilization of this data for biological research. Several DNA databases are now available online that allow downloading of sequence data or interactive analysis of the data using online software tools such as BLAST (Basic Local Alignment Search Tool).

DNA polymerase λ (Pol λ) is the sole member of family X DNA polymerase in plants and plays a crucial role in nuclear DNA damage repair. Here, we report the transcriptional up-regulation of Arabidopsis (Arabidopsis thaliana) AtPolλ in response to abiotic and genotoxic stress, including salinity and the DNA cross-linking agent mitomycin C (MMC). The increased sensitivity of atpolλ knockout mutants toward high salinity and MMC treatments, with higher levels of accumulation of double strand breaks (DSBs) than wild-type plants and delayed repair of DSBs, has suggested the requirement of Pol λ in DSB repair in plants. AtPolλ overexpression moderately complemented the deficiency of DSB repair capacity in atpolλ mutants. Transcriptional up-regulation of major nonhomologous end joining (NHEJ) pathway genes KU80, X-RAY CROSS COMPLEMENTATION PROTEIN4 (XRCC4), and DNA Ligase4 (Lig4) along with AtPolλ in Arabidopsis seedlings, and the increased sensitivity of atpolλ-2/atxrcc4 and atpolλ-2/atlig4 double mutants toward high salinity and MMC treatments, indicated the involvement of NHEJ-mediated repair of salinity- and MMC-induced DSBs. The suppressed expression of NHEJ genes in atpolλ mutants suggested complex transcriptional regulation of NHEJ genes. Pol λ interacted directly with XRCC4 and Lig4 via its N-terminal breast cancer-associated C terminus (BRCT) domain in a yeast two-hybrid system, while increased sensitivity of BRCT-deficient Pol λ-expressing transgenic atpolλ-2 mutants toward genotoxins indicated the importance of the BRCT domain of AtPolλ in mediating the interactions for processing DSBs. Our findings provide evidence for the direct involvement of DNA Pol λ in the repair of DSBs in a plant genome.