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Key message: Our results indicate that OsPGK2a-P gene is differentially regulated in contrasting rice cultivars under stress and its overexpression confers salt stress tolerance in transgenic tobacco. Abstract: Phosphoglycerate kinase (PGK; EC = 2.7.2.3) plays a major role for ATP production during glycolysis and 1, 3-bisphosphoglycerate production to participate in the Calvin cycle for carbon fixation in plants. Whole genome analysis of rice reveals the presence of four PGK genes (OsPgks) on different chromosomes. Comparative expression analysis of OsPgks in rice revealed highest level of transcripts for OsPgk2 at most of its developmental stages. Detailed characterization of OsPgk2 transcript and protein showed that it is strongly induced by salinity stress in two contrasting genotypes of rice, i.e., cv IR64 (salt sensitive) and landrace Pokkali (salt tolerant). Ectopic expression of OsPgk2a-P (isolated from Pokkali) in transgenic tobacco improved its salinity stress tolerance by higher chlorophyll retention and enhanced proline accumulation, besides maintaining better ion homeostasis. Ectopically expressing OsPgk2a-P transgenic tobacco plants showed tall phenotype with more number of pods than wild-type plants. Therefore, OsPgk2a-P appears to be a potential candidate for increasing salinity stress tolerance and enhanced yield in crop plants. [ABSTRACT FROM AUTHOR]

Microalgae accumulate substantial amount of cellular lipids. Nutritional stress studies in microalgae show diversion of the metabolic flux toward enhanced triglycerides (TAGs) production by blocking the carbohydrate synthesis pathway. This review focuses on current state of research on various nutritional approaches employed for enhancement of lipid and biomass accumulation for biofuel production. The review also discusses and summarizes the efforts made for biosequestration of CO2and genetic manipulation as a long-term solution to the fuel problem. An integrated method for complete utilization of microalgae for biodiesel, bio gasoline, and value-added products has also been put forward in this review. [ABSTRACT FROM AUTHOR]

Cyclophilins are a set of ubiquitous proteins present in all subcellular compartments, involved in a wide variety of cellular processes. Comparative bioinformatics analysis of the rice and Arabidopsis genomes led us to identify novel putative cyclophilin gene family members in both the genomes not reported previously. We grouped cyclophilin members with similar molecular weight and subtypes together in the phylogenetic tree which indicated their co-evolution in rice and Arabidopsis. We also characterized a rice cyclophilin gene, OsCyp2-P (Os02g0121300), isolated from a salinity-tolerant landrace, Pokkali. Publicly available massively parallel signature sequencing (MPSS) and microarray data, besides our quantitative real time PCR (qRT-PCR) data suggest that transcript abundance of OsCyp2-P is regulated under different stress conditions in a developmental and organ specific manner. Ectopic expression of OsCyp2-P imparted multiple abiotic stress tolerance to transgenic tobacco plants as evidenced by higher root length, shoot length, chlorophyll content, and K/Na ratio under stress conditions. Transgenic plants also showed reduced lipid peroxidase content, electrolyte leakage, and superoxide content under stress conditions suggesting better ion homeostasis than WT plants. Localization studies confirmed that OsCyp2-P is localized in both cytosol and nucleus, indicating its possible interaction with several other proteins. The overall results suggest the explicit role of OsCyp2-P in bestowing multiple abiotic stress tolerance at the whole plant level. OsCyp2-P operates via reactive oxygen species (ROS) scavenging and ion homeostasis and thus is a promising candidate gene for enhancing multiple abiotic stress tolerance in crop plants. [ABSTRACT FROM AUTHOR]

The paper presents the ultra-performance liquid chromatography (UPLC) and high-resolution mass spectrometric analysis and comparison of total lipid profiles of two green algal species, Chlamydomonas reinhardtii and Scenedesmus ( Acutodesmus) obliquus. The targeted UPLC-mass spectroscopy (MS) analysis revealed that both the green algae showed the presence of almost similar types of lipids. However, there were differences in the presence of three triacylglycerol (TAG) species (TAG 54:4, TAG 54:5 and TAG 54:8) and two diacylglycerol (DAG) species (DAG 36:3 and DAG 36:4) in C. reinhardtii that were found to be completely absent in Scenedesmus obliquus. The triacylglycerol content in S. obliquus was five times more than that in C. reinhardtii. In addition, amount of diacylglycerol-O-(N,N,N-trimethyl) homoserine, a characteristic algal lipid, in S. obliquus was only half of that in C. reinhardtii. The paper also discusses the metabolic roles of the lipids produced by these algal species with reference to the lipids identified by UPLC-MS analysis. [ABSTRACT FROM AUTHOR]

The independent origin and evolution of leaves as small, simple microphylls or larger, more complex megaphylls in plants has shaped and influenced the natural composition of the environment. Significant contributions have come from megaphyllous leaves, characterized usually as flat, thin lamina entrenched with photosynthetic organelles and stomata, which serve as the basis of primary productivity. During the course of evolution, the megaphylls have attained complexity not only in size or venation patterns but also in shape. This has fascinated scientists worldwide, and research has progressed tremendously in understanding the concept of leaf shape determination. Here, we review these studies and discuss the various factors that contributed towards shaping the leaf; initiated as a small bulge on the periphery of the shoot apical meristem (SAM) followed by asymmetric outgrowth, expansion and maturation until final shape is achieved. We found that the underlying factors governing these processes are inherently genetic: PIN1 and KNOX1 are indicators of leaf initiation, HDZIPIII, KANADI, and YABBY specify leaf outgrowth while ANGUSTIFOLIA3 and GROWTHREGULATING FACTOR5 control leaf expansion and maturation; besides, recent research has identified new players such as APUM23, known to specify leaf polarity. In addition to genetic control, environmental factors also play an important role during the final adjustment of leaf shape. This immense amount of information available will serve as the basis for studying and understanding innovative leaf morphologies viz. the pitchers of the carnivorous plant Nepenthes which have evolved to provide additional support to the plant survival in its nutrient-deficient habitat. In hindsight, formation of the pitcher tube in Nepenthes might involve the recruitment of similar genetic mechanisms that occur during sympetaly in Petunia. [ABSTRACT FROM AUTHOR]

Glyoxalase II ( GLY II), the second enzyme of glyoxalase pathway that detoxifies cytotoxic metabolite methylglyoxal ( MG), belongs to the superfamily of metallo-β-lactamases. Here, detailed analysis of one of the uncharacterized rice glyoxalase II family members, Os GLYII-2 was conducted in terms of its metal content, enzyme kinetics and stress tolerance potential. Functional complementation of yeast GLY II mutant (∆ GLO2) and enzyme kinetics data suggested that Os GLYII-2 possesses characteristic GLY II activity using S-lactoylglutathione ( SLG) as the substrate. Further, Inductively Coupled Plasma Atomic Emission spectroscopy and modelled structure revealed that Os GLYII-2 contains a binuclear Zn/Fe centre in its active site and chelation studies indicated that these are essential for its activity. Interestingly, reconstitution of chelated enzyme with Zn2+, and/or Fe2+ could not reactivate the enzyme, while addition of Co2+ was able to do so. End product inhibition study provides insight into the kinetics of GLY II enzyme and assigns hitherto unknown function to reduced glutathione ( GSH). Ectopic expression of Os GLYII-2 in Escherichia coli and tobacco provides improved tolerance against salinity and dicarbonyl stress indicating towards its role in abiotic stress tolerance. Maintained levels of MG and GSH as well as better photosynthesis rate and reduced oxidative damage in transgenic plants under stress conditions seems to be the possible mechanism facilitating enhanced stress tolerance. [ABSTRACT FROM AUTHOR]

The glyoxalase system constitutes the major pathway for the detoxification of metabolically produced cytotoxin methylglyoxal ( MG) into a non-toxic metabolite d-lactate. Glyoxalase I (GLY I) is an evolutionarily conserved metalloenzyme requiring divalent metal ions for its activity: Zn2+ in the case of eukaryotes or Ni2+ for enzymes of prokaryotic origin. Plant GLY I proteins are part of a multimember family; however, not much is known about their physiological function, structure and metal dependency. In this study, we report a unique GLY I (Os GLYI-11.2) from Oryza sativa (rice) that requires Ni2+ for its activity. Its biochemical, structural and functional characterization revealed it to be a monomeric enzyme, possessing a single Ni2+ coordination site despite containing two GLY I domains. The requirement of Ni2+ as a cofactor by an enzyme involved in cellular detoxification suggests an essential role for this otherwise toxic heavy metal in the stress response. Intriguingly, the expression of Os GLYI-11.2 was found to be highly substrate inducible, suggesting an important mode of regulation for its cellular levels. Heterologous expression of Os GLYI-11.2 in Escherichia coli and model plant Nicotiana tabacum (tobacco) resulted in improved adaptation to various abiotic stresses caused by increased scavenging of MG, lower Na+/ K+ ratio and maintenance of reduced glutathione levels. Together, our results suggest interesting links between MG cellular levels, its detoxification by GLY I, and Ni2+ - the heavy metal cofactor of Os GLYI-11.2, in relation to stress response and adaptation in plants. [ABSTRACT FROM AUTHOR]

The two-component system (TCS), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. Employing the tools of bioinformatics, we have characterized TCS signaling candidate genes in the genome of Oryza sativa L. subsp. japonica. We present a complete overview of TCS gene families in O. sativa, including gene structures, conserved motifs, chromosome locations, and phylogeny. Our analysis indicates a total of 51 genes encoding 73 putative TCS proteins. Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. The variations seen between gene and protein numbers are assumed to result from alternative splicing. These putative proteins have high homology with TCS members that have been shown experimentally to participate in several important physiological phenomena in plants, such as ethylene and cytokinin signaling and phytochrome-mediated responses to light. We conclude that the overall architecture of the TCS machinery in O. sativa and Arabidopsis thaliana is similar, and our analysis provides insights into the conservation and divergence of this important signaling machinery in higher plants. [ABSTRACT FROM AUTHOR]

The two-component system (TCS), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. Employing the tools of bioinformatics, we have characterized TCS signaling candidate genes in the genome of Oryza sativa L. subsp. japonica. We present a complete overview of TCS gene families in O. sativa, including gene structures, conserved motifs, chromosome locations, and phylogeny. Our analysis indicates a total of 51 genes encoding 73 putative TCS proteins. Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. The variations seen between gene and protein numbers are assumed to result from alternative splicing. These putative proteins have high homology with TCS members that have been shown experimentally to participate in several important physiological phenomena in plants, such as ethylene and cytokinin signaling and phytochrome-mediated responses to light. We conclude that the overall architecture of the TCS machinery in O. sativa and Arabidopsis thaliana is similar, and our analysis provides insights into the conservation and divergence of this important signaling machinery in higher plants. [ABSTRACT FROM AUTHOR]

Salinity stress affects plant growth, development, biomass, yield, as well as their survival. A series of signaling cascade is activated to cope the deleterious effect of salinity stress. Cytokinins are known for their regulatory roles from cell growth and expansion to abiotic stress signaling. Two component system (TCS) are important multistep phosphorelay signal transduction machinery converging cytokinin, ethylene and light signal transduction pathways together. Plant TCS comprises of histidine kinases, phosho-transfer proteins and response regulators. Histidine kinases perceive the signal and relay it to response regulator via histidine containing phosphor-transfer proteins. Response regulators are one of the major and diverse component of TCS system which have been extensively studied for their role in plant growth, development and circadian rhythm. However, knowledge of their regulatory role in abiotic stress signaling is limited. This mini-review specifically focus on role of response regulators in salinity stress signaling. Response regulators is the divergent node of TCS machinery, where cross-talks with other stress-mediated, phytohormone-mediated, as well as, light-mediated signaling pathways ensues. Studies from past few years have established central role of response regulators in salinity stress, however, the detailed mechanism of their actions need to be studied further. Response regulators act as both negative as well as positive regulator of salinity and cytokinin signaling, making it an excellent target to increase crop yield as well as stress tolerance capabilities. • Cytokinin plays a key role in plant growth, development and abiotic stress signaling. • Response regulators are one of the three component of Two Component System involved in cytokinin signaling. • Response regulators are comprehensively studied for their role in plant growth, development and circadian rhythm. • However, studies focusing on their role in abiotic stress signaling have been gaining momentum in the past decade. • This review mainly focuses on their role in salinity stress signaling. [ABSTRACT FROM AUTHOR]

ABSTRACT Plant two‐component system (TCS) is crucial for phytohormone signalling, stress response, and circadian rhythms, yet the precise role of most of the family members in rice remain poorly understood. In this study, we investigated the function of OsPHP1, a pseudo‐histidine phosphotransfer protein in rice, using a functional genomics approach. OsPHP1 is localised in the nucleus and cytosol, and it exhibits strong interactions with all sensory histidine kinase proteins (OsHK1‐6) and cytokinin catabolism genes. Our results demonstrate that OsPHP1 functions as a negative regulator of cytokinin signalling. Knockdown of OsPHP1 enhanced the expression of positive cytokinin signalling regulators, such as OsHKs and OsAHPs (authentic phosphotransfer proteins), while downregulating negative regulators, such as type‐A response regulators (OsRRs) and cytokinin catabolism genes (CKXs). Furthermore, OsPHP1 negatively influences abiotic stress tolerance, as evidenced by the increased sensitivity of OsPHP1‐OE (overexpression) lines to salinity and drought. In contrast, OsPHP1‐KD (knockdown) lines showed enhanced stress resilience, with better photosynthesis, increased tiller and panicle production, higher spikelet fertility, and grain filling. The study demonstrates that OsPHP1 suppresses antioxidant and stress‐responsive genes, exacerbating ion toxicity and reducing osmolyte accumulation, thereby impairing plant growth and yield under stress conditions. These findings highlight OsPHP1 as a critical modulator of plant responses to abiotic stress and suggest potential genetic targets for enhancing crop stress tolerance. [ABSTRACT FROM AUTHOR]

Salinity and high temperature stresses adversely affect growth and development of rice plants. To investigate the response of rice cells to these stresses, we have analysed short-term stress-induced subcellular alterations in undifferentiated leaf cells of rice seedlings by transmission electron microscopy. Perturbations noted particularly with respect to plasma membrane, mitochondrial membranes, endoplasmic reticulum, polyribosomes and dictyosomes are highlighted. The subcellular changes evoked by both stresses after 4 h were lysis of the cytoplasm, accumulation of electron-dense granules in the cytoplasm, distension in the ER membranes, enhanced association of ribosomes with the endoplasmic reticulum, reduction in the number of mitochondrial cristae, as well as disorganization of cell wall fibrillar material. Certain changes were found to be unique to either the salinity or high temperature stress. Plasmolysis and increased cytoplasmic vesiculation were seen only in response to salinity stress, while discontinuity in the plasma membrane with close association of the osmiophilic granules were observed only in response to high temperature.Copyright 1997 Annals of Botany Company [ABSTRACT FROM AUTHOR]

The flavin monooxygenase (FMO) enzyme was discovered in mammalian liver cells that convert a carcinogenic compound, N-N′-dimethylaniline, into a non-carcinogenic compound, N-oxide. Since then, many FMOs have been reported in animal systems for their primary role in the detoxification of xenobiotic compounds. In plants, this family has diverged to perform varied functions like pathogen defense, auxin biosynthesis, and S-oxygenation of compounds. Only a few members of this family, primarily those involved in auxin biosynthesis, have been functionally characterized in plant species. Thus, the present study aims to identify all the members of the FMO family in 10 different wild and cultivated Oryza species. Genome-wide analysis of the FMO family in different Oryza species reveals that each species has multiple FMO members in its genome and that this family is conserved throughout evolution. Taking clues from its role in pathogen defense and its possible function in ROS scavenging, we have also assessed the involvement of this family in abiotic stresses. A detailed in silico expression analysis of the FMO family in Oryza sativa subsp. japonica revealed that only a subset of genes responds to different abiotic stresses. This is supported by the experimental validation of a few selected genes using qRT-PCR in stress-sensitive Oryza sativa subsp. indica and stress-sensitive wild rice Oryza nivara. The identification and comprehensive in silico analysis of FMO genes from different Oryza species carried out in this study will serve as the foundation for further structural and functional studies of FMO genes in rice as well as other crop types. [ABSTRACT FROM AUTHOR]

Background: A structural phenomenon seen in certain lineages of angiosperms that has captivated many scholars including Charles Darwin is the evolution of plant carnivory. Evidently, these structural features collectively termed carnivorous syndrome, evolved to aid nutritional acquisition from attracted, captured and digested prey. We now understand why plant carnivory evolved but how carnivorous plants acquired these attributes remains a mystery. In an attempt to understand the evolution of Nepenthes pitcher and to shed more light on its role in prey digestion, we analyzed the transcriptome data of the highly specialized Nepenthes khasiana leaf comprising the leaf base lamina, tendril and the different parts/zones of the pitcher tube viz. digestive zone, waxy zone and lid. Results: In total, we generated around 262 million high-quality Illumina reads. Reads were pooled, normalized and de novo assembled to generate a reference transcriptome of about 412,224 transcripts. We then estimated transcript abundance along the N. khasiana leaf by mapping individual reads from each part/zone to the reference transcriptome. Correlation-based hierarchical clustering analysis of 27,208 commonly expressed genes indicated functional relationship and similar cellular processes underlying the development of the leaf base and the pitcher, thereby implying that the Nepenthes pitcher is indeed a modified leaf. From a list of 2386 differentially expressed genes (DEGs), we identified transcripts encoding key enzymes involved in prey digestion and protection against pathogen attack, some of which are expressed at high levels in the digestive zone. Interestingly, many of these enzyme-encoding genes are also expressed in the unopened N. khasiana pitcher. Transcripts showing homology to both bacteria and fungi were also detected; and in the digestive zone, fungi are more predominant as compared to bacteria. Taking cues from histology and scanning electron microscopy (SEM) photomicrographs, we found altered expressions of key regulatory genes involved in leaf development. Of particular interest, the expression of class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) and ARGONAUTE (AGO) genes were upregulated in the tendril. Conclusions: Our findings suggest that N. khasiana pitchers employ a wide range of enzymes for prey digestion and plant defense, harbor microbes and probably evolved through altered expression of leaf polarity genes. [ABSTRACT FROM AUTHOR]

ABSTRACT Nitric oxide (NO) is one of the byproducts of nitrogen metabolism. Excess amount of NO is scavenged by phytoglobins. The role of phytoglobin mediated NO homoeostasis in modulation of nitrate transporters was investigated using NO scavenger cPTIO, phytoglobin overexpressing rice and Arabidopsis. Growing plants under low nitrate leads to generation of reduced levels of NO accompanied by elevated expression of high affinity transporters (HATs) such as NRT2.1, NRT2.3 and NRT2.4. Scavenging of NO by cPTIO under optimal nitrate caused enhanced HATs expression. Phytoglobin overexpressing Arabidopsis showed improved growth and enhanced expression of HATs under low nitrogen in comparison to WT. Pretreatment of optimal nitrate grown plants with NO scavenger cPTIO enhanced HATs expression and shifting of these primed plants from optimal to low nitrate leads to further elevation of HATs expression accompanied by enhanced nitrogen uptake and its accumulation with positive effect on growth. Phytoglobin overexpression in rice leads to enhanced HATs expression, improved growth, nitrogen accumulation under low nitrate. Pgb OE lines showed enhanced accumulation of amino acids. Taken together our results suggest an important role of phytoglobins in nitrogen uptake and assimilation. [ABSTRACT FROM AUTHOR]

Developing rice types with shorter life cycle without compromising yield is vital for sustainable agriculture, as it can significantly reduce water and fertilizer consumption while enabling early harvest. Despite recent advancements in identifying the genes associated with heading date, the intricate regulatory network governing this process remains largely unexplored. In rice, one such gene, GHD7 (QTL for grain‐heading‐date on chromosome 7), encodes a CCT (CONSTANS, CONSTANS‐LIKE and TIMING OF CAB1) domain protein and plays a pivotal role in regulating flowering time and associated developmental processes. To gain insight into the role of OsGHD7 in improving yield, we have overexpressed OsGHD7 in the widely cultivated and photoperiod‐insensitive rice variety IR64. This led to notable phenotypic changes in rice, including tiller number and grain number (66% increase), along with the promotion of early flowering (8–9 days preponement). Interestingly, these plants also exhibited enhanced tolerance to drought and salinity stress and showed better post‐stress recovery. This study emphasizes the potential of manipulating the multifaceted genetic determinants of key traits to optimize rice productivity under changing climate conditions. [ABSTRACT FROM AUTHOR]

Saffron stigma, derived from Crocus sativus L., has long been revered in global traditional medicine and continues to hold significant market value. However, despite the extensive focus on saffron stigma, the therapeutic potential of other floral components remains underexplored, primarily due to limited insights into their complex molecular architectures and chemical diversity. To address this gap, we performed a comprehensive metabolomic analysis of various floral organs utilizing advanced analytical platforms, including GC–MS and UPLC‐MS/MS. This in‐depth profiling revealed a diverse array of 248 metabolites, encompassing amino acids, sugar derivatives, fatty acids, flavonoids, vitamins, polyamines, organic acids, and a broad spectrum of secondary metabolites. Distinct correlation patterns among these metabolites were identified through PCA and PLS‐DA, highlighting unique metabolomic signatures inherent to each floral organ. We further integrated these metabolomic findings with our transcriptomic data, enabling a detailed understanding of the molecular and metabolic variations across different floral organs. The pronounced abundance of differentially expressed genes and metabolites in the stamen (424), leaf (345), tepal (196), stigma (177), and corm (133) underscores the intricate regulatory networks governing source‐to‐sink partitioning and dynamic metabolic processes. Notably, our study identified several bioactive compounds, including crocin, picrocrocin, crocetin, safranal, cannabielsoin, quercetin, prenylnaringenin, isorhamnetin, pelargonidin, kaempferol, and gallic acid, all of which exhibit potential therapeutic properties. In conclusion, this comprehensive analysis significantly enhances our understanding of the molecular mechanisms driving the biosynthesis of apocarotenoids, cannabinoids, anthocyanins, and flavonoids in saffron, thereby providing valuable insights and paving the way for future research in this area. [ABSTRACT FROM AUTHOR]

Methylglyoxal (MG) is a metabolically generated highly cytotoxic compound that accumulates in all living organisms, from Escherichia coli to humans, under stress conditions. To detoxify MG, nature has evolved reduced glutathione (GSH)‐dependent glyoxalase and NADPH‐dependent aldo‐keto reductase systems. But both GSH and NADPH have been reported to be limiting in plants under stress conditions, and thus detoxification might not be performed efficiently. Recently, glyoxalase III (GLY III)‐like enzyme activity has been reported from various species, which can detoxify MG without any cofactor. In the present study, we have tested whether an E. coli gene, hchA, encoding a functional GLY III, could provide abiotic stress tolerance to living systems. Overexpression of this gene showed improved tolerance in E. coli and Saccharomyces cerevisiae cells against salinity, dicarbonyl, and oxidative stresses. Ectopic expression of the E. coli GLY III gene (EcGLY‐III) in transgenic tobacco plants confers tolerance against salinity at both seedling and reproductive stages as indicated by their height, weight, membrane stability index, and total yield potential. Transgenic plants showed significantly increased glyoxalase and antioxidant enzyme activity that resisted the accumulation of excess MG and reactive oxygen species (ROS) during stress. Moreover, transgenic plants showed more anti‐glycation activity to inhibit the formation of advanced glycation end product (AGE) that might prevent transgenic plants from stress‐induced senescence. Taken together, all these observations indicate that overexpression of EcGLYIII confers salinity stress tolerance in plants and should be explored further for the generation of stress‐tolerant plants. [ABSTRACT FROM AUTHOR]