V. Mohan M. Achary

Enhancing C3 photosynthesis: an outlook on feasible interventions for crop improvement

Despite the declarations and collective measures taken to eradicate hunger at World Food Summits, food security remains one of the biggest issues that we are faced with. The current scenario could worsen due to the alarming increase in world population, further compounded by adverse climatic conditions, such as increase in atmospheric temperature, unforeseen droughts and decreasing soil moisture, which will decrease crop yield even further. Furthermore, the projected increase in yields of C3 crops as a result of increasing atmospheric CO2 concentrations is much less than anticipated. Thus, there is an urgent need to increase crop productivity beyond existing yield potentials to address the challenge of food security. One of the domains of plant biology that promises hope in overcoming this problem is study of C3 photosynthesis. In this review, we have examined the potential bottlenecks of C3 photosynthesis and the strategies undertaken to overcome them. The targets considered for possible intervention include RuBisCO, RuBisCO activase, Calvin-Benson-Bassham cycle enzymes, CO2 and carbohydrate transport, and light reactions among many others. In addition, other areas which promise scope for improvement of C3 photosynthesis, such as mining natural genetic variations, mathematical modelling for identifying new targets, installing efficient carbon fixation and carbon concentrating mechanisms have been touched upon. Briefly, this review intends to shed light on the recent advances in enhancing C3 photosynthesis for crop improvement.

Redox homeostasis via gene families of ascorbate-glutathione pathway

The imposition of environmental stresses on plants brings about disturbance in their metabolism thereby negatively affecting their growth and development and leading to reduction in the productivity. One of the manifestations of abiotic and biotic stress conditions is the enhanced production of reactive oxygen species (ROS) which can be hazardous to cells. Therefore, in order to protect themselves against toxic ROS, plant cells employ the anti-oxidant defense system. The ascorbate-glutathione pathway (Halliwell-Asada cycle) is an indispensible component of the ROS homeostasis mechanism of plants. This pathway entails the antioxidant metabolites: ascorbate, glutathione and NADPH along with the enzymes linking them. The ascorbate-glutathione pathway is functional in different subcellular compartments and all the enzymes of this pathway exist as multiple isoforms. The expression of different isoforms of the enzymes of ascorbate-glutathione pathway is developmentally as well as spatially regulated. Moreover, various abiotic and biotic stress conditions modulate the expression of the enzyme- isoforms differently. It is the intricate regulation of expression of different isoforms of the ascorbate-glutathione pathway enzymes that helps in the maintenance of redox balance in plants under various abiotic and biotic stress conditions. The present review provides an insight into the gene families of the ascorbate-glutathione pathway, shedding light on their role in different abiotic and biotic stress conditions as well as in the growth and development of plants.

The development of a phosphite-mediated fertilization and weed control system for rice

Fertilizers and herbicides are two vital components of modern agriculture. The imminent danger of phosphate reserve depletion and multiple herbicide tolerance casts doubt on agricultural sustainability in the future. Phosphite, a reduced form of phosphorus, has been proposed as an alternative fertilizer and herbicide that would address the above problems to a considerable extent. To assess the suitability of a phosphite-based fertilization and weed control system for rice, we engineered rice plants with a codon-optimized ptxD gene from Pseudomonas stutzeri. Ectopic expression of this gene led to improved root growth, physiology and overall phenotype in addition to normal yield in transgenic plants in the presence of phosphite. Phosphite functioned as a translocative, non-selective, pre- and post-emergent herbicide. Phosphite use as a dual fertilizer and herbicide may mitigate the overuse of phosphorus fertilizers and reduce eutrophication and the development of herbicide resistance, which in turn will improve the sustainability of agriculture.

Mitogen-activated protein kinase signal transduction and DNA repair network are involved in aluminum-induced DNA damage and adaptive response in root cells of Allium cepa L.

In the current study, we studied the role of signal transduction in aluminum (Al3+)-induced DNA damage and adaptive response in root cells of Allium cepa L. The root cells in planta were treated with Al3+ (800 μM) for 3 h without or with 2 h pre-treatment of inhibitors of mitogen-activated protein kinase (MAPK), and protein phosphatase. Also, root cells in planta were conditioned with Al3+ (10 μM) for 2 h and then subjected to genotoxic challenge of ethyl methane sulfonate (EMS; 5 mM) for 3 h without or with the pre-treatment of the aforementioned inhibitors as well as the inhibitors of translation, transcription, DNA replication and repair. At the end of treatments, roots cells were assayed for cell death and/or DNA damage. The results revealed that Al3+ (800 μM)-induced significant DNA damage and cell death. On the other hand, conditioning with low dose of Al3+ induced adaptive response conferring protection of root cells from genotoxic stress caused by EMS-challenge. Pre-treatment of roots cells with the chosen inhibitors prior to Al3+-conditioning prevented or reduced the adaptive response to EMS genotoxicity. The results of this study suggested the involvement of MAPK and DNA repair network underlying Al-induced DNA damage and adaptive response to genotoxic stress in root cells of A. cepa.

Phosphite: a novel P fertilizer for weed management and pathogen control

Summary The availability of orthophosphate (Pi) is a key determinant of crop productivity because its accessibility to plants is poor due to its conversion to unavailable forms. Weeds competition for this essential macronutrient further reduces its bio‐availability. To compensate for the low Pi use efficiency and address the weed hazard, excess Pi fertilizers and herbicides are routinely applied, resulting in increased production costs, soil degradation and eutrophication. These outcomes necessitate the identification of a suitable alternate technology that can address the problems associated with the overuse of Pi‐based fertilizers and herbicides in agriculture. The present review focuses on phosphite (Phi) as a novel molecule for its utility as a fertilizer, herbicide, biostimulant and biocide in modern agriculture. The use of Phi‐based fertilization will help to reduce the consumption of Pi fertilizers and facilitate weed and pathogen control using the same molecule, thereby providing significant advantages over current orthophosphate‐based fertilization.

Green Synthesized Zinc Oxide (ZnO) Nanoparticles Induce Oxidative Stress and DNA Damage in Lathyrus sativus L. Root Bioassay System

Zinc oxide nanoparticles (ZnONP-GS) were synthesised from the precursor zinc acetate (Zn(CH3COO)2) through the green route using the milky latex from milk weed (Calotropis gigantea L. R. Br) by alkaline precipitation. Formation of the ZnONP-GS was monitored by UV-visible spectroscopy followed by characterization and confirmation by energy-dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), and X-ray diffraction (XRD). Both the ZnONP-GS and the commercially available ZnONP-S (Sigma-Aldrich) and cationic Zn2+ from Zn(CH3COO)2 were tested in a dose range of 0–100 mg·L−1 for their potency (i) to induce oxidative stress as measured by the generation reactive oxygen species (ROS: O2•−, H2O2 and •OH), cell death, and lipid peroxidation; (ii) to modulate the activities of antioxidant enzymes: catalase (CAT), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and ascorbate peroxidase (APX); and (iii) to cause DNA damage as determined by Comet assay in Lathyrus sativus L. root bioassay system. Antioxidants such as Tiron and dimethylthiourea significantly attenuated the ZnONP-induced oxidative and DNA damage, suggesting the involvement of ROS therein. Our study demonstrated that both ZnONP-GS and ZnONP-S induced oxidative stress and DNA damage to a similar extent but were significantly less potent than Zn2+ alone.

Polyvinyl polypyrrolidone attenuates genotoxicity of silver nanoparticles synthesized via green route, tested in Lathyrus sativus L. root bioassay

The silver nanoparticles (AgNPs) were synthesized extracellularly from silver nitrate (AgNO3) using kernel extract from ripe mango Mengifera indica L. under four different reaction conditions of the synthesis media such as the (i) absence of the reducing agent, trisodium citrate (AgNPI), (ii) presence of the reducing agent (AgNPII), (iii) presence of the cleansing agent, polyvinyl polypyrrolidone, PVPP (AgNPIII), and (iv) presence of the capping agent, polyvinyl pyrrolidone, PVP (AgNPIV). The synthesis of the AgNPs was monitored by UV-vis spectrophotometry. The AgNPs were characterised by the energy-dispersive X-ray spectroscopy, transmission electron microscopy, X-ray diffraction, and small-angle X-ray scattering. Functional groups on the AgNPs were established by the Fourier transform infrared spectroscopy. The AgNPs (AgNPI, AgNPII, AgNPIII and AgNPIV) were spherical in shape with the diameters and size distribution-widths of 14.0±5.4, 19.2±6.6, 18.8±6.6 and 44.6±13.2nm, respectively. Genotoxicity of the AgNPs at concentrations ranging from 1 to 100mgL(-1) was determined by the Lathyrus sativus L. root bioassay and several endpoint assays including the generation of reactive oxygen species and cell death, lipid peroxidation, mitotic index, chromosome aberrations (CA), micronucleus formation (MN), and DNA damage as determined by the Comet assay. The dose-dependent induction of genotoxicity of the silver ion (Ag(+)) and AgNPs was in the order Ag(+)>AgNPII>AgNPI>AgNPIV>AgNPIII that corresponded with their relative potencies of induction of DNA damage and oxidative stress. Furthermore, the findings underscored the CA and MN endpoint-based genotoxicity assay which demonstrated the genotoxicity of AgNPs at concentrations (≤10mgL(-1)) lower than that (≥10mgL(-1)) tested in the Comet assay. This study demonstrated the protective action of PVPP against the genotoxicity of AgNPIII which was independent of the size of the AgNPs in the L. sativus L. root bioassay system.

Cell cycle stage-specific differential expression of topoisomerase I in tobacco BY-2 cells and its ectopic overexpression and knockdown unravels its crucial role in plant morphogenesis and development

DNA topoisomerases catalyze the inter-conversion of different topological forms of DNA. Cell cycle coupled differential accumulation of topoisomerase I (Topo I) revealed biphasic expression maximum at S-phase and M/G1-phase of cultured synchronized tobacco BY-2 cells. This suggested its active role in resolving topological constrains during DNA replication (S-phase) and chromosome decondensation (M/G1 phase). Immuno-localization revealed high concentrations of Topo I in nucleolus. Propidium iodide staining and Br-UTP incorporation patterns revealed direct correlation between immunofluorescence intensity and rRNA transcription activity within nucleolus. Immuno-stained chromosomes during metaphase and anaphase suggested possible role of Topo I in resolving topological constrains during mitotic chromosome condensation. Inhibitor studies showed that in comparison to Topo I, Topo II was essential in resolving topological constrains during chromosome condensation. Probably, Topo II substituted Topo I functioning to certain extent during chromosome condensation, but not vice-versa. Transgenic Topo I tobacco lines revealed morphological abnormalities and highlighted its crucial role in plant morphogenesis and development.

Dynamics of tobacco DNA topoisomerases II in cell cycle regulation: to manage topological constrains during replication, transcription and mitotic chromosome condensation and segregation

AbstractKey messageThe topoisomerase II expression varies as a function of cell proliferation. Maximal topoisomerase II expression was tightly coupled to S phase and G2/M phase via both transcriptional and post-transcriptional regulation. Investigation in meiosis using pollen mother cells also revealed that it is not the major component of meiotic chromosomes, it seems to diffuse out once meiotic chromosomal condensation is completed.AbstractSynchronized tobacco BY-2 cell cultures were used to study the role of topoisomerase II in various stages of the cell cycle. Topoisomerase II transcript accumulation was observed during the S- and G2/M- phase of cell cycle. This biphasic expression pattern indicates the active requirement of topoisomerase II during these stages of the cell cycle. Through immuno-localization of topoisomerase II was observed diffusely throughout the nucleoplasm in interphase nuclei, whereas, the nucleolus region exhibited a more prominent immuno-positive staining that correlated with rRNA transcription, as shown by propidium iodide staining and BrUTP incorporation. The immuno-staining analysis also showed that topoisomerase II is the major component of mitotic chromosomes and remain attached to the chromosomes during cell division. The inhibition of topoisomerase II activity using specific inhibitors revealed quite dramatic effect on condensation of chromatin and chromosome individualization from prophase to metaphase transition. Partially condensed chromosomes were not arranged on metaphase plate and chromosomal perturbations were observed when advance to anaphase, suggesting the importance of topoisomerase II activity for proper chromosome condensation and segregation during mitosis. Contrary, topoisomerase II is not the major component of meiotic chromosomes, even though mitosis and meiosis share many processes, including the DNA replication, chromosome condensation and precisely regulated partitioning of chromosomes into daughter cells. Even if topoisomerase II is required for individualization and condensation of meiotic chromosomes, it seems to diffuse out once meiotic chromosomal condensation is completed.

Editorial: Maintenance of Genome Integrity: DNA Damage Sensing, Signaling, Repair, and Replication in Plants

Because of their sessile lifestyles, plants are continuously exposed to DNA-damaging agents present in the environment. Although the basic mechanisms of genome maintenance are conserved between animal and plant kingdom, plants also have evolved specific mechanisms to cope with DNA damage. Indeed, studies in past decades have demonstrated the presence of elastic mechanisms in plants. For example, when exposed to DNA damaging agents, plants respond immediately to start repairing the damage, regulating cell proliferation, changing metabolic pathways. Here we are proud to have twelve outstanding articles focus on the maintenance of genome integrity: DNA damage sensing, signaling, repair and replication in plants. The present e-book is opened by several comprehensive reviews dealing with genomic and extra-genomic DNA maintenance, as well as the role of double strand break (DSB) signaling in plants. In his minireview, Roy provides an upgraded view on the link connecting chromatin structure stability and DNA damage response at the genetic and epigenetic levels, while Amiard et al. present an overview on DSB repair pathways in Arabidopsis thaliana, with focus on the signaling of DNA breaks and deprotected telomeres. Stability of genomic DNA, not only in nuclei, but also in organelles is crucial for plant development. In contrast to nuclear genomes, the amount and structural integrity of organellar genomes changes during plant development. It is very interesting to consider why organellar genomes are less stable as the replication and repair machineries are encoded by the nuclear genome, yet the cause of the instability is poorly understood. Oldenburg and Bendich first explain the history of the studies into the size and structure of organellar DNA (orgDNA). They then address the copy number and integrity of orgDNA during plant development. The review continues with an overview of the proteins which are involved in the processes of orgDNA replication, repair, and recombination, and changes in the amount of these proteins during leaf development. It has been observed that plastid DNA (ptDNA) maintenance in grasses differs from that in dicots as it rapidly declines upon light exposure. From these observations, the authors propose the idea that instead of repairing damaged DNA, grasses use a cost-saving involving a loss of ptDNA. DNA polymerases are crucial for maintenance of genome integrity in organisms. The family X DNA polymerases work in DNA repairs such as base excision repair (BER) and/or DSB repair. Plants are unique in having only one member of this family, polymerase lambda (Polλ). Furukawa et al. showed that the Polλ knockout Arabidopsis (atpolλ-1) is only mildly sensitive to DSB-inducing treatments, whereas the double-knockouts of AtPolλ and AtLig4 made the plants hypersensitive to DSB compared to each single knockout. These results suggest that the AtPolλ has a role in DSB repair, probably in an AtLig4-independent non-homologous end-joining (NHEJ) pathway. Proliferating cell nuclear antigen (PCNA) is a key component of eukaryotic DNA replication machinery. PCNA usually accompanies the DNA polymerase to gather a specific set of proteins onto the replication fork when replication is disturbed. Cyclin Ds are expressed in G2 and degraded during G2/M transition. When the checkpoint is activated, the degradation of cyclin D is inhibited to arrest cells at G2. Strzalka et al. demonstrated that Arabidopsis PCNAs directly interact with some members of the cyclin Ds in yeast and plant cells, suggesting that PCNAs link the signal of disturbed replication with cell cycle control. Ultraviolet (UV) light has been used to analyze cellular DNA-damage responses. UV induces cyclobutanate pyrimidine dimmers (CPDs) and other damage to DNA, which triggers various cellular responses: DNA repair, cell cycle delay or arrest, and cell death. Thus, UVB in sunlight can confer severe stress to plants, but plants have photorepair enzymes to correct the damage. Takahashi et al. investigated the responses of plant cells irradiated with low or high dose of UVB. UVB irradiated cells showed different reactions, depending on the dose, suggesting that accumulation of CPDs caused by high dose UVB induces formation of single or DSBs, which leads to cell death. In their research article, Questa et al. discuss on the roles of the DDM1 and ROS1 genes in UVB-induced DNA repair by using Arabidopsis mutants and a set of analytical measurements. Disruption of these genes had an opposite impact of these two genes, with the ddm1 mutants accumulating more DNA damage, while the ros1 mutants showed less amount of DNA damage. Based on experimental work, they hypothesize that the DNA demethylation in the ddm1 mutant can affect the accessibility of DNA repair systems in this region, while the better performance of ros1 mutants can arise as a result of increased levels of photolyases. In their research on the MAPK signal transduction in response to aluminum (Al) treatments, Panda and Achary underline the biphasic mode of action of Al-induced DNA damage in Allium cepa. They observed that at high concentrations Al induces DNA damage, while at low concentration an adaptive response is present, and hypothesize that the MAPK-DNA repair network is responsible for both actions. The role played by DNA/RNA helicases against the genotoxic effects of abiotic stress is documented. XPB (xeroderma pigmentosum type B) helicases promote nucleotide excision repair (NER) by unwinding double strand DNA at the damaged sites. In the attempt to assess the potential of plant XPB helicases as tools in counteracting adverse environmental conditions, Raikwar et al. carried out an in silico and functional characterization of the rice OsXPB2 gene promoter in response to abiotic stress and hormone-based treatments. Based on its multi-stress responsiveness, the OsXPB2 promoter represents a promising tool for improving the response of crops to genotoxic stress. Huefner et al. investigated the short- and long-term impact of high-LET (Linear Energy Transfer) HZE (high atomic weight, high energy) particles vs. low-LET gamma rays on genome stability, using Arabidopsis mutants defective in DNA repair and cell-cycle checkpoint. This study highlights the increased sensitivity of Arabidopsis plants to HZE radiation, revealing the predominant role played by ATR (ATM and Rad3-related) protein kinase compared to ATM (ataxia-telangiectasia mutated) in the response to high-LET radiation. In the accompanying article, Missirian et al. compared the transcriptional response in Arabidopsis seedlings exposed to HZE radiation vs. DSB-inducing agents as gamma rays, bleomycin and mitomycin C. These treatments triggered an intense, short-term DSB-specific repair response which was not detected in plants challenged with conventional stresses. A distinctive feature of the HZE transcriptional response was the early activation of key genes involved in the catabolism of cellular components. With genome editing being the cutting-edge topic of present days, the article by Cantos et al. deals with the implementation of such tool (zinc finger nucleases, ZFNs) for the identification of appropriate regions for safe gene insertion. By harnessing their ability to induce DSBs at the cutting site, ZFNs trigger the NHEJ or homologous recombination (HR) DNA repair pathways at the targeted site. This study used ZFNs with short DNA recognition domains, able to target multiple sites within the rice genome, and subsequently study the integration patterns of the GUS marker gene, allowing the identification of “safe harbors,” intergenic regions with potential high expression. The present e-book provides an up-date overview of the ongoing research dealing with different aspects of the DNA damage response in plants, highlighting the complexity of molecular networks involved in genome maintenance. A better understanding of DNA damage accumulation/perception/signaling/repair mechanisms in planta is expected to speed up crop improvement through conventional breeding and gene-transfer based techniques.