Papers by Bijayalaxmi Mohanty
Metabolites, Apr 29, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Molecular Plant Pathology, Feb 18, 2020
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial ... more This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Rice, Aug 13, 2013
Background: Photorespiration, a highly wasteful process of energy dissipation, depresses the prod... more Background: Photorespiration, a highly wasteful process of energy dissipation, depresses the productivity of C3 plants such as rice (Oryza sativa) under dry and hot conditions. Thus, it is highly required to understand the cellular physiology and relevant metabolic states under photorespiration using systems approaches, thereby devising strategies for improving rice production. Findings: In silico model-driven gene deletion analysis was performed on photorespiring leaf cells under ambient and stressed environmental conditions using our central metabolic network of rice cells. As a result, we identified a number of essential genes for the cell growth across various functional pathways such as photorespiratory cycle, Calvin cycle, GS-GOGAT cycle and sucrose metabolism as well as certain inter-compartmental transporters, which are mostly in good agreement with previous experiments. Synthetic lethal (SL) screening was also performed to identify the pair of non-essential genes whose simultaneous deletion become lethal, revealing the existence of more than 220 pairs of SLs on rice central metabolism. Conclusions: The gene deletion and synthetic lethal analyses highlighted the rigid nature of rice photosynthetic pathways and characterized functional interactions between central metabolic genes, respectively. The biological roles of such reported essential genes should be further explored to better understand the rice photorespiration in future.
Plant Science, Sep 1, 2021
Lettuce is commonly consumed around the world, spurring the cultivation of green- and red-leaf va... more Lettuce is commonly consumed around the world, spurring the cultivation of green- and red-leaf varieties in indoor farms. One common consideration for indoor cultivation is the light wavelengths/spectrum, which is an important factor for regulating growth, development, and the accumulation of metabolites. Here, we show that Batavia lettuce (Lactuca sativa cv. "Batavia") grown under a combination of red (R) and blue (B) light (RB, R:B = 3:1) displayed better growth and accumulated more anthocyanin than lettuce grown under fluorescent light (FL). Anthocyanin concentration was also higher in mature stage than early stage lettuce. By performing a comparative transcriptome analysis of early and mature stage lettuce grown under RB or FL (RB or FL-lettuce), we found that RB induced the expression of genes related to oxidation-reduction reaction and secondary metabolite biosynthesis. Furthermore, plant age affected the transcriptome response to RB, as mature RB-lettuce had six times more differentially expressed genes than early RB-lettuce. Also, genes related to the accumulation of secondary metabolites such as flavonoids and anthocyanins were more induced in mature RB-lettuce. A detailed analysis of the anthocyanin biosynthesis pathway revealed key genes that were up-regulated in mature RB-lettuce. Concurrently, branching pathways for flavonol and lignin precursors were down-regulated.
Chemical Engineering Science, Nov 1, 2013
ABSTRACT H I G H L I G H T S c Developed in silico rational framework for synthetic terpenoid pro... more ABSTRACT H I G H L I G H T S c Developed in silico rational framework for synthetic terpenoid production. c Updated metabolic model of A. thaliana to describe terpenoid biosynthesis. c Analyzed heterologous expression of A. thaliana pathways in microbial systems. c Proposed novel in silico method of cofactor modification analysis. c Improve terpenoid yield by modifying enzyme cofactor specificity. a b s t r a c t Terpenoids are a large and diverse group of plant secondary metabolites with important applications in the pharmaceutical, cosmetic and food industries. However, low yields obtained from natural plant sources necessitate the search for alternative ways to increase the throughput of terpenoid production. Thus, fast-growing microbial systems, such as Escherichia coli and Saccharomyces cerevisiae, can be genetically engineered to achieve high productivity by systematically designing terpenoid synthetic routes and improving its precursor, isopentenyl diphosphate (IPP) production. To this end, we develop an in silico model-based rational framework where the cellular metabolism in natural terpenoid producer is analyzed to provide a basis for designing its synthetic pathways in microbial hosts. At the outset, we updated the genome-scale Arabidopsis thaliana metabolic model to characterize optimal metabolic utilization patterns that were subsequently incorporated into the in silico models of microbial hosts for improving terpenoid yield. We also developed a novel computational approach, cofactor modification analysis (CMA), to tackle potential limitations in terpenoid production caused by suboptimal balance of the different redox cofactors. The enzyme targets identified by CMA can potentially lead to better metabolic engineering strategies for enhancing terpenoid production in microbial systems.
Plant Science, 2016
In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of ... more In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of a drought-tolerant rice line, DK151, to identify the major transcriptional regulators involved in metabolic adjustments necessary for adaptation to drought. This was achieved by examining the differential expressions of transcription factors and metabolic genes in leaf, root and young panicle of rice plants subjected to drought stress during tillering, booting and panicle elongation stages. Critical transcription factors such as AP2/ERF, bZIP, MYB and NAC that control the important nodes in the gene regulatory pathway were identified through correlative analysis of the patterns of spatio-temporal expression and cis-element enrichment. We showed that many of the candidate transcription factors involved in metabolic adjustments were previously linked to phenotypic variation for drought tolerance. This approach represents the first attempt to integrate models of transcriptional regulation and metabolic pathways for the identification of candidate regulatory genes for targeted selection in rice breeding.
Aob Plants, 2014
The ability of rice to germinate under anoxia by extending the coleoptile is a highly unusual cha... more The ability of rice to germinate under anoxia by extending the coleoptile is a highly unusual characteristic and a key feature underpinning the ability of rice seeds to establish in such a stressful environment. The process has been a focal point for research for many years. However, the molecular mechanisms underlying the anoxic growth of the coleoptile still remain largely unknown. To unravel the key regulatory mechanisms of rice germination under anoxic stress, we combined in silico modelling with gene expression data analysis. Our initial modelling analysis via random flux sampling revealed numerous changes in rice primary metabolism in the absence of oxygen. In particular, several reactions associated with sucrose metabolism and fermentation showed a significant increase in flux levels, whereas reaction fluxes across oxidative phosphorylation, the tricarboxylic acid cycle and the pentose phosphate pathway were down-regulated. The subsequent comparative analysis of the differences in calculated fluxes with previously published gene expression data under air and anoxia identified at least 37 reactions from rice central metabolism that are transcriptionally regulated. Additionally, cis-regulatory content analyses of these transcriptionally controlled enzymes indicate a regulatory role for transcription factors such as MYB, bZIP, ERF and ZnF in transcriptional control of genes that are up-regulated during rice germination and coleoptile elongation under anoxia.
PLOS ONE, Jan 15, 2015
Phytohormones play a critical role in mediating plant stress response. They employ a variety of p... more Phytohormones play a critical role in mediating plant stress response. They employ a variety of proteins for coordinating such processes. In Arabidopsis thaliana, some members of a Cys-rich protein family known as C1-clan proteins were involved in stress response, but the actual function of the protein family is largely unknown. We studied At5g17960, a C1-clan protein member that possesses three unique C1 signature domains viz. C1_2, C1_3 and ZZ/PHD type. Additionally, we identified 72 other proteins in A. thaliana that contain all three unique signature domains. Subsequently, the 73 proteins were phylogenetically classified into IX subgroups. Promoter motif analysis of the 73 genes identified the presence of hormone-responsive and stress-responsive putative cis-regulatory elements. Furthermore, we observed that transcript levels of At5g17960 were induced in response to different hormones and stress treatments. At1g35610 and At3g13760, two other members of subgroup IV, also showed upregulation upon GA3, biotic and abiotic stress treatments. Moreover, seedlings of independent transgenic A. thaliana lines ectopically expressing or suppressing At5g17960 also showed differential regulation of several abiotic stress-responsive marker genes. Thus, our data suggest that C1-domain-containing proteins have a role to play in plant hormone-mediated stress responses, thereby assigning a putative function for the C1clan protein family.
Plant Physiology, Jun 10, 2013
Rice (Oryza sativa) is one of the major food crops in world agriculture, especially in Asia. Howe... more Rice (Oryza sativa) is one of the major food crops in world agriculture, especially in Asia. However, the possibility of subsequent occurrence of flood and drought is a major constraint to its production. Thus, the unique behavior of rice toward flooding and drought stresses has required special attention to understand its metabolic adaptations. However, despite several decades of research investigations, the cellular metabolism of rice remains largely unclear. In this study, in order to elucidate the physiological characteristics in response to such abiotic stresses, we reconstructed what is to our knowledge the first metabolic/regulatory network model of rice, representing two tissue types: germinating seeds and photorespiring leaves. The phenotypic behavior and metabolic states simulated by the model are highly consistent with our suspension culture experiments as well as previous reports. The in silico simulation results of seed-derived rice cells indicated (1) the characteristic metabolic utilization of glycolysis and ethanolic fermentation based on oxygen availability and (2) the efficient sucrose breakdown through sucrose synthase instead of invertase. Similarly, flux analysis on photorespiring leaf cells elucidated the crucial role of plastid-cytosol and mitochondrion-cytosol malate transporters in recycling the ammonia liberated during photorespiration and in exporting the excess redox cofactors, respectively. The model simulations also unraveled the essential role of mitochondrial respiration during drought stress. In the future, the combination of experimental and in silico analyses can serve as a promising approach to understand the complex metabolism of rice and potentially help in identifying engineering targets for improving its productivity as well as enabling stress tolerance.
Phytochemistry, Aug 1, 1993
The aim of this work was to compare the carbohydrate metabolism of suspension cultures of soybean... more The aim of this work was to compare the carbohydrate metabolism of suspension cultures of soybean (Glycine max), intolerant of anoxia, with that of cultures of rice (Oryza sativa), tolerant of anoxia. Soybean cells in anoxia showed no increase in fresh weight, dry weight or extractable protein, and labelled few proteins when supplied with [35S]methionine. There were modest (50%) increases in the maximum catalytic activities of sucrose synthase, phosphofructokinase, pyruvate kinase and phosphoenolpyruvate carboxylase. There was a threefold increase in alcohol dehydrogenase and no detectable change in lactate dehydrogenase and pyrophosphate:fructose 6-phosphate 1-phosphotransferase [PFK(PP,)]. The rates of respiration (02 uptake and CO 2 production in air) and fermentation (CO2 production in nitrogen), all declined with time in anoxia and the cells died after six days in anoxia. Rice cells in anoxia showed small increases in weight and protein content, and labelled many proteins with [33 S]methionine. Increased maximum catalytic activities were found for sucrose synthase (x 2), PFK(PP .) (x 6), pyruvate kinase (x 2), alcohol dehydrogenase (x 5) and lactate dehydrogenase (x 2). When rice cells were grown in anoxia, respiration declined steadily. Fermentation increased after four days in anoxia and then declined steadily. However, both respiration and fermentation were still appreciable even after 52 days in anoxia .
Plant Cell Reports, Apr 10, 2020
Key message LRRop-1, induced by DOF6 transcription factor, negatively regulates abiotic stress re... more Key message LRRop-1, induced by DOF6 transcription factor, negatively regulates abiotic stress responses during Arabidopsis seed germination. The lrrop-1 mutant has reduced ABA signaling, which is part of the underlying stressremediation mechanism.
Rice, Sep 29, 2016
Background: Rice is the only crop that germinates and elongates the coleoptile under complete sub... more Background: Rice is the only crop that germinates and elongates the coleoptile under complete submergence. It has been shown that alcohol dehydrogenase 1 (ADH1)-deficient mutant of rice with reduced alcohol dehydrogenase activity (rad) and reduced ATP level, is viable with much reduced coleoptile elongation under such condition. To understand the altered transcriptional regulatory mechanism of this mutant, we aimed to establish possible relationships between gene expression and cis-regulatory information content. Findings: We performed promoter analysis of the publicly available differentially expressed genes in ADH1 mutant. Our results revealed that a crosstalk between a number of key transcription factors (TFs) and different phytohormones altered transcriptional regulation leading to the survival of the mutant. Amongst the key TFs identified, we suggest potential involvement of MYB, bZIP, ARF and ERF as transcriptional activators and WRKY, ABI4 and MYC as transcriptional repressors of coleoptile elongation to maintain metabolite levels for the cell viability. Out of the repressors, WRKY TF is most likely playing a major role in the alteration of the physiological implications associated with the cell survival. Conclusions: Overall, our analysis provides a possible transcriptional regulatory mechanism underlying the survival of the rad mutant under complete submergence in an energy crisis condition and develops hypotheses for further experimental validation.
Frontiers in Plant Science, Nov 29, 2016
Crop productivity is severely limited by various biotic and abiotic stresses. Thus, it is highly ... more Crop productivity is severely limited by various biotic and abiotic stresses. Thus, it is highly needed to understand the underlying mechanisms of environmental stress response and tolerance in plants, which could be addressed by systems biology approach. To this end, high-throughput omics profiling and in silico modeling can be considered to explore the environmental effects on phenotypic states and metabolic behaviors of rice crops at the systems level. Especially, the advent of constraint-based metabolic reconstruction and analysis paves a way to characterize the plant cellular physiology under various stresses by combining the mathematical network models with multi-omics data. Rice metabolic networks have been reconstructed since 2013 and currently six such networks are available, where five are at genome-scale. Since their publication, these models have been utilized to systematically elucidate the rice abiotic stress responses and identify agronomic traits for crop improvement. In this review, we summarize the current status of the existing rice metabolic networks and models with their applications. Furthermore, we also highlight future directions of rice modeling studies, particularly stressing how these models can be used to contextualize the affluent multi-omics data that are readily available in the public domain. Overall, we envisage a number of studies in the future, exploiting the available metabolic models to enhance the yield and quality of rice and other food crops.
Potato Research, Jun 1, 1992
Summary Tissue from developing tubers, mature tubers, and mature tubers that had been stored at ... more Summary Tissue from developing tubers, mature tubers, and mature tubers that had been stored at 4C, was killed and extracted with trichloroacetic acid in diethylether. Inorganic pyrophosphate was detected in the aqueous phase of the extracts with pyrophosphate fructose-6-phosphate-1-phosphotransferase. No pyrophosphate could be detected in extracts that had been pretreated with pyrophosphatase. Pyrophosphate contents of about 3–12 nmol/g fresh weight were
Rice, Feb 28, 2015
Dissecting the upstream regulatory architecture of rice genes and their cognate regulator protein... more Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and transacting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and transacting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.
Frontiers in Genetics, Mar 16, 2021
Rice has the natural morphological adaptation to germinate and elongate its coleoptile under subm... more Rice has the natural morphological adaptation to germinate and elongate its coleoptile under submerged flooding conditions. The phenotypic deviation associated with the tolerance to submergence at the germination stage could be due to natural variation. However, the molecular basis of this variation is still largely unknown. A comprehensive understanding of gene regulation of different genotypes that have diverse rates of coleoptile elongation can provide significant insights into improved rice varieties. To do so, publicly available transcriptome data of five rice genotypes, which have different lengths of coleoptile elongation under submergence tolerance, were analyzed. The aim was to identify the correlation between promoter architecture, associated with transcriptional and hormonal regulation, in diverse genotype groups of rice that have different rates of coleoptile elongation. This was achieved by identifying the putative cis-elements present in the promoter sequences of genes upregulated in each group of genotypes (tolerant, highly tolerant, and extremely tolerant genotypes). Promoter analysis identified transcription factors (TFs) that are common and unique to each group of genotypes. The candidate TFs that are common in all genotypes are MYB, bZIP, AP2/ERF, ARF, WRKY, ZnF, MADS-box, NAC, AS2, DOF, E2F, ARR-B, and HSF. However, the highly tolerant genotypes interestingly possess binding sites associated with HY5 (bZIP), GBF3, GBF4 and GBF5 (bZIP), DPBF-3 (bZIP), ABF2, ABI5, bHLH, and BES/BZR, in addition to the common TFs. Besides, the extremely tolerant genotypes possess binding sites associated with bHLH TFs such as BEE2, BIM1, BIM3, BM8 and BAM8, and ABF1, in addition to the TFs identified in the tolerant and highly tolerant genotypes. The transcriptional regulation of these TFs could be linked to phenotypic variation in coleoptile elongation in response to submergence tolerance. Moreover, the results indicate a cross-talk between the key TFs and phytohormones such as gibberellic acid, abscisic acid, ethylene, auxin, jasmonic acid, and brassinosteroids, for an altered transcriptional regulation leading to differences in germination and coleoptile elongation under submergence. The information derived from the current in silico analysis can potentially assist in developing new rice breeding targets for direct seeding.
Primer list for qRT-PCR. (DOCX 13 kb)
Phytohormones play a critical role in mediating plant stress response. They employ a varie-ty of ... more Phytohormones play a critical role in mediating plant stress response. They employ a varie-ty of proteins for coordinating such processes. In Arabidopsis thaliana, some members of a Cys-rich protein family known as C1-clan proteins were involved in stress response, but the actual function of the protein family is largely unknown. We studied At5g17960, a C1-clan protein member that possesses three unique C1 signature domains viz. C1_2, C1_3 and ZZ/PHD type. Additionally, we identified 72 other proteins in A. thaliana that contain all three unique signature domains. Subsequently, the 73 proteins were phylogenetically classified into IX subgroups. Promoter motif analysis of the 73 genes identified the presence of hormone-responsive and stress-responsive putative cis-regulatory elements. Furthermore, we observed that transcript levels of At5g17960 were induced in response to different hor-mones and stress treatments. At1g35610 and At3g13760, two other members of subgroup IV, also showed...
Plant physiology, Jan 9, 2015
Light quality is an important signaling component upon which plants orchestrate various morpholog... more Light quality is an important signaling component upon which plants orchestrate various morphological processes including the seed germination and seedling photomorphogenesis. However, it is still unclear how plants, especially food crops, sense various light qualities, and modulates their cellular growth and other developmental processes. Therefore, in this work, we initially profiled the transcripts of model crop, rice, under four different light treatments, blue (B), green (G), red (R) and white (W), as well as in dark (D). Concurrently, we reconstructed a fully compartmentalized genome-scale metabolic model (GEM) of rice cells, iOS2164, containing 2164 unique genes, 2284 reactions and 1999 metabolites. We then combined the model with transcriptome profiles to elucidate the light-specific transcriptional signatures of rice metabolism. Clearly, light signals mediated rice gene expressions, differentially regulating numerous metabolic pathways: photosynthesis and secondary metaboli...
The responses of rice to cold and water deficit are multidimensional. A holistic approach to maxi... more The responses of rice to cold and water deficit are multidimensional. A holistic approach to maximize tolerance potential requires the optimization of ideal combinations of multiple interacting entities in a genetic network. This chapter presents a modern view for engineering stress-resilient rice cultivars. The first section summarizes the physiological and biochemical aspects of cold and water deficit at the whole-plant and cellular levels. The second part summarizes the major hubs of signaling and transcriptional regulation that lead to biochemical and physiological changes as validated by functional genomics. The rapidly emerging area of investigation on epigenetic regulatory mechanisms as critical layer of control for fine-tuning is presented in brief in the third section. And finally, the last section summarizes the large-effect QTL for cold tolerance and yield stability under drought. By integrating these four layers of information, this chapter should inspire a holistic appr...
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Papers by Bijayalaxmi Mohanty