UMP Kinase Regulates Chloroplast Development and Cold Response in Rice

Metabolic regulation of 5-oxoproline for enhanced heat tolerance in perennial ryegrass

Pyroglutamic acid [(5-oxoproline (5-oxp)], a non-protein amino acid, can be converted to glutamate to regulate amino acid metabolism in plants. Its roles in plant adaptation to abiotic stresses, including heat stress, are not well understood. The objectives of this study were to determine whether exogenous application of 5-oxp could promote heat tolerance in cool-season perennial grass species and identify the major metabolic pathways that could be activated or responsive to 5-oxp for enhancing heat tolerance. Perennial ryegrass (Lolium perenne L.) plants were foliar-sprayed with 5-oxp or water (untreated control) prior to and during the exposure to heat stress (35/33 ℃, day/night temperature) or ambient temperature (25/22 ℃, day/night temperature, non-stress control) in controlled-environment growth chambers. Application of 5-oxp improved the heat tolerance of perennial ryegrass, as manifested by the chlorophyll content, photochemical efficiency, cell membrane stability, and antioxidant enzyme activities increasing by 31.2%, 25.7%, 37.2%, and 57.1-258.3%, as well as the reduction in hydrogen peroxide production by 36.8%. Metabolic profiling identified metabolites up-regulated by 5-oxp that are involved in the metabolic pathways of carbon assimilation in photosynthesis, glycolysis and the tricarboxylic acid cycle of respiration, proteinogenic amino acid metabolism, glutathione metabolism, and nucleotide metabolism for DNA or RNA synthesis and ATP generation. The up-regulation or activation of those metabolic processes could contribute to 5-oxp-mediated enhancement in the heat tolerance of perennial ryegrass.

Allelopathic Interactions Between the Green-Tide-Forming Ulva prolifera and the Golden-Tide-Forming Sargassum horneri Under Controlled Laboratory Conditions

Harmful algal blooms (HABs) represent a significant global marine ecological disaster. In the Yellow Sea, green and golden tides often occur simultaneously or sequentially, suggesting that interspecific competition involves not only spatial and resource competition but also allelopathy. This study investigated the allelopathic interactions between Ulva prolifera and Sargassum horneri using physiological and biochemical parameters, including relative growth rate (RGR), cell ultrastructure, chlorophyll fluorescence, enzyme activity, and metabolomics analysis. The results showed that S. horneri filtrate significantly inhibited U. prolifera growth, while U. prolifera filtrate had no significant effect on S. horneri. Both algal filtrates caused cellular damage and affected photosynthesis, enzyme activities, and metabolism. However, their allelopathic responses differed: U. prolifera may rely on internal compensatory mechanisms, while S. horneri may depend on defense strategies. These findings provide insights into the dynamics of green and golden tides and support the scientific control of HABs through allelopathy.

Genome-wide association study and genotypic variation for the major tocopherol content in rice grain

Rice tocopherols, vitamin E compounds with antioxidant activity, play essential roles in human health. Even though the key genes involved in vitamin E biosynthetic pathways have been identified in plants, the genetic architecture of vitamin E content in rice grain remains unclear. A genome-wide association study (GWAS) on 179 genotypically diverse rice accessions with 34,323 SNP markers was conducted to detect QTLs that define total and α- tocopherol contents in rice grains. Total and α-tocopherol contents had a strong positive correlation and varied greatly across the accessions, ranging from 0.230-31.76 and 0.011-30.83 (μg/g), respectively. A total of 13 QTLs were identified, which were spread across five of the rice chromosomes. Among the 13 QTLs, 11 were considered major with phenotypic variation explained (PVE) greater than 10%. Twelve transcription factor (TF) genes, one microprotein (miP), and a transposon were found to be associated with the QTLs with putative roles in controlling tocopherol contents. Moreover, intracellular transport proteins, ABC transporters, nonaspanins, and SNARE, were identified as associated genes on chromosomes 1 and 8. In the vicinity of seven QTLs, protein kinases were identified as key signaling factors. Haplotype analysis revealed the QTLs qAlph1.1, qTot1.1, qAlph2.1, qAlph6.1, qTot6.1, and qTot8.3 to have significant haplogroups. Quantitative RT-PCR validated the expression direction and magnitude of WRKY39 (Os02g0265200), PIP5Ks (Os08g0450800), and MADS59 (Os06g0347700) in defining the major tocopherol contents. This study provides insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in rice and other cereals.

Three Arabidopsis UMP kinases have different roles in pyrimidine nucleotide biosynthesis and (deoxy)CMP salvage

Pyrimidine nucleotide monophosphate biosynthesis ends in the cytosol with uridine monophosphate (UMP). UMP phosphorylation to uridine diphosphate (UDP) by UMP KINASEs (UMKs) is required for the generation of all pyrimidine (deoxy)nucleoside triphosphates as building blocks for nucleic acids and central metabolites like UDP-glucose. The Arabidopsis (Arabidopsis thaliana) genome encodes five UMKs and three belong to the AMP KINASE (AMK)-like UMKs, which were characterized to elucidate their contribution to pyrimidine metabolism. Mitochondrial UMK2 and cytosolic UMK3 are evolutionarily conserved, whereas cytosolic UMK1 is specific to the Brassicaceae. In vitro, all UMKs can phosphorylate UMP, cytidine monophosphate (CMP) and deoxycytidine monophosphate (dCMP), but with different efficiencies. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-induced null mutants were generated for UMK1 and UMK2, but not for UMK3, since frameshift alleles were lethal for germline cells. However, a mutant with diminished UMK3 activity showing reduced growth was obtained. Metabolome analyses of germinating seeds and adult plants of single- and higher-order mutants revealed that UMK3 plays an indispensable role in the biosynthesis of all pyrimidine (deoxy)nucleotides and UDP-sugars, while UMK2 is important for dCMP recycling that contributes to mitochondrial DNA stability. UMK1 is primarily involved in CMP recycling. We discuss the specific roles of these UMKs referring also to the regulation of pyrimidine nucleoside triphosphate synthesis.

Identification of novel genes associated with herbicide tolerance in Lentil (Lens culinaris ssp. culinaris Medik.)

Weeds pose a major constraint in lentil cultivation, leading to decrease farmers' revenues by reducing the yield and increasing the management costs. The development of herbicide tolerant cultivars is essential to increase lentil yield. Even though herbicide tolerant lines have been identified in lentils, breeding efforts are still limited and lack proper validation. Marker assisted selection (MAS) can increase selection accuracy at early generations. Total 292 lentil accessions were evaluated under different dosages of two herbicides, metribuzin and imazethapyr, during two seasons at Marchouch, Morocco and Terbol, Lebanon. Highly significant differences among accessions were observed for days to flowering (DF) and maturity (DM), plant height (PH), biological yield (BY), seed yield (SY), number of pods per plant (NP), as well as the reduction indices (RI) for PH, BY, SY and NP. A total of 10,271 SNPs markers uniformly distributed along the lentil genome were assayed using Multispecies Pulse SNP chip developed at Agriculture Victoria, Melbourne. Meta-GWAS analysis was used to detect marker-trait associations, which detected 125 SNPs markers associated with different traits and clustered in 85 unique quantitative trait loci. These findings provide valuable insights for initiating MAS programs aiming to enhance herbicide tolerance in lentil crop.

A splicing site change between exon 5 and 6 of the nuclear-encoded chloroplast-localized HvYGL8 gene results in reduced chlorophyll content and plant height in barley

The chloroplast is an important cellular organelle and metabolic hub, which is not only responsible for plant photosynthesis but is also involved in the de novo biosynthesis of pigments, fatty acids, and hormone metabolisms. Several genes that are responsible for rice leaf color variations have been reported to be directly or indirectly involved in chlorophyll biosynthesis and chloroplast development, whereas a few genes have been functionally confirmed to be responsible for leaf color changes in barley at the molecular level. In this study, we obtained a yellow leaf and dwarf ygl8 mutant from the progeny of Morex (a variety of barley) seeds treated with EMS. We performed bulked-segregant analysis (BSA) and RNA-seq analysis and targeted a UMP kinase encoding gene, YGL8, which generated a splicing site change between exon 5 and 6 of YGL8 due to a G to A single-nucleotide transition in the 5th exon/intron junction in the ygl8 mutant. The splicing site change between exon 5 and 6 of YGL8 had no effects on chloroplast subcellular localization but resulted in an additional loop in the UMP kinase domain, which might disturb the access of the substrates. On one hand, the splicing site change between exon 5 and 6 of YGL8 downregulated the transcriptional expression of chloroplast-encoded genes and chlorophyll-biosynthesis-related genes in a temperature-dependent manner in the ygl8 mutant. On the other hand, the downregulation of bioactive GA-biosynthesis-related GA20ox genes and cell-wall-cellulose-biosynthesis-related CesA genes was also observed in the ygl8 mutant, which led to a reduction in plant height. Our study will facilitate the understanding of the regulation of leaf color and plant height in barley.

Metabolic regulation of α-Ketoglutarate associated with heat tolerance in perennial ryegrass

α-Ketoglutarate (AKG) is a key intermediate metabolite in the tricarboxylic acid cycle of respiration and a precursor for glutamate, playing important roles in regulating plant growth and stress tolerance. The objectives of this study were to examine effects of AKG on heat tolerance characterized by leaf senescence in a cool-season grass species by foliar application and to determine major metabolites and associated metabolic pathways regulated by AKG for its effects on heat tolerance. Perennial ryegrass (Lolium perenne L.) plants were exposed to heat stress (35/30 °C, day/night) or optimal temperature (25/20 °C, day/night, non-stress control) in controlled-environment growth chambers. The solution containing AKG (5 mM) was applied to leaves by spraying 7 d prior to the initiation of heat stress and every 7 d during the heat stress period. Exogenous application of AKG enhanced heat tolerance in perennial ryegrass, as manifested by significant increases in leaf chlorophyll content, photochemical efficiency, and membrane stability, as well as activities of antioxidant enzymes for H₂O₂ scavenging in AKG-treated plants relative to untreated control plants exposed to heat stress. Metabolic profiling and pathway analysis demonstrated that exogenous AKG application enhanced metabolite accumulation in four major metabolic pathways, including antioxidant metabolism, amino acid metabolism, glycolysis and tricarboxylic acid cycle of respiration, and pyrimidine metabolism, contributing to AKG-improved heat tolerance in perennial ryegrass.

Multiple Facets of Nitrogen: From Atmospheric Gas to Indispensable Agricultural Input

Nitrogen (N) is a gas and the fifth most abundant element naturally found in the atmosphere. N's role in agriculture and plant metabolism has been widely investigated for decades, and extensive information regarding this subject is available. However, the advent of sequencing technology and the advances in plant biotechnology, coupled with the growing interest in functional genomics-related studies and the various environmental challenges, have paved novel paths to rediscovering the fundamentals of N and its dynamics in physiological and biological processes, as well as biochemical reactions under both normal and stress conditions. This work provides a comprehensive review on multiple facets of N and N-containing compounds in plants disseminated in the literature to better appreciate N in its multiple dimensions. Here, some of the ancient but fundamental aspects of N are revived and the advances in our understanding of N in the metabolism of plants is portrayed. It is established that N is indispensable for achieving high plant productivity and fitness. However, the use of N-rich fertilizers in relatively higher amounts negatively affects the environment. Therefore, a paradigm shift is important to shape to the future use of N-rich fertilizers in crop production and their contribution to the current global greenhouse gases (GHGs) budget would help tackle current global environmental challenges toward a sustainable agriculture.

Regulation of Chloroplast Development and Function at Adverse Temperatures in Plants

The chloroplast is essential for photosynthesis, plant growth and development. As semiautonomous organelles, the biogenesis and development of chloroplasts need to be well-regulated during plant growth and stress responses. Low or high ambient temperatures are adverse environmental stresses that affect crop growth and productivity. As sessile organisms, plants regulate the development and function of chloroplasts in a fluctuating temperature environment to maintain normal photosynthesis. This review focuses on the molecular mechanisms and regulatory factors required for chloroplast biogenesis and development under cold or heat stress conditions and highlights the importance of chloroplast gene transcription, RNA metabolism, ribosome function and protein homeostasis essential for chloroplast development under adverse temperature conditions.

Metabolic and Physiological Regulation of Aspartic Acid-Mediated Enhancement of Heat Stress Tolerance in Perennial Ryegrass

Aspartate is the most critical amino acid in the aspartate metabolic pathway, which is associated with multiple metabolic pathways, such as protein synthesis, nucleotide metabolism, TCA cycle, glycolysis, and hormone biosynthesis. Aspartate also plays an important role in plant resistance to abiotic stress, such as cold stress, drought stress, salt stress or heavy metal stress. This study found that the chlorophyll content and antioxidant active enzyme content (SOD, CAT, POD and APX) of perennial ryegrass treated with 2 mM aspartate were significantly higher than those treated with water under heat stress. The electrolyte leakage rate, MDA content and peroxide levels (O^2- and H₂O₂) of perennial ryegrass treated with aspartate were significantly lower than those of perennial ryegrass treated with water, indicating that exogenous aspartate increases the content of chlorophyll, maintain the integrity of cell membrane system, and enhances SOD-CAT antioxidant pathway to eliminate the oxidative damage caused by ROS in perennial ryegrass under heat stress. Furthermore, exogenous aspartate could enhance the TCA cycle, the metabolism of the amino acids related to the TCA cycle, and pyrimidine metabolism to enhance the heat tolerance of perennial ryegrass.

Integrated global analysis reveals a vitamin E-vitamin K1 sub-network, downstream of COLD1, underlying rice chilling tolerance divergence

Rice, a staple food with tropical/subtropical origination, is susceptible to cold stress, one of the major constraints on its yield and distribution. Asian cultivated rice consists of two subspecies with diverged chilling tolerance to adapt to different environments. The mechanism underlying this divergence remains obscure with a few known factors, including membrane protein CHILLING-TOLERANCE DIVERGENCE 1 (COLD1). Here, we reveal a vitamin E-vitamin K1 sub-network responsible for chilling tolerance divergence through global analyses. Rice genome regions responsible for tolerance divergence are identified with chromosome segment substitution lines (CSSLs). Comparative transcriptomic and metabolomic analysis of chilling-tolerant CSSL4-1 and parent lines uncovered a vitamin E-vitamin K1 sub-network in chloroplast with tocopherol (vitamin E) mediating chloroplast-to-nucleus signaling. COLD1, located in the substitution segment in CSSL4-1, is confirmed as its upstream regulator by transgenic material analysis. Our work uncovers a pathway downstream of COLD1, through which rice modulates chilling tolerance for thermal adaptation, with potential utility in crop improvement.

β-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study

Non-proteinogenic neurotoxic amino acid β-N-methylamino-L-alanine (BMAA) is synthesized by cyanobacteria, diatoms, and dinoflagellates, and is known to be a causative agent of human neurodegenerative diseases. Different phytoplankton organisms' ability to synthesize BMAA could indicate the importance of this molecule in the interactions between microalgae in nature. We were interested in the following: what kinds of mechanisms underline BMAA's action on cyanobacterial cells in different nitrogen supply conditions. Herein, we present a proteomic analysis of filamentous cyanobacteria Nostoc sp. PCC 7120 cells that underwent BMAA treatment in diazotrophic conditions. In diazotrophic growth conditions, to survive, cyanobacteria can use only biological nitrogen fixation to obtain nitrogen for life. Note that nitrogen fixation is an energy-consuming process. In total, 1567 different proteins of Nostoc sp. PCC 7120 were identified by using LC-MS/MS spectrometry. Among them, 123 proteins belonging to different functional categories were selected-due to their notable expression differences-for further functional analysis and discussion. The presented proteomic data evidences that BMAA treatment leads to very strong (up to 80%) downregulation of α (NifD) and β (NifK) subunits of molybdenum-iron protein, which is known to be a part of nitrogenase. This enzyme is responsible for catalyzing nitrogen fixation. The genes nifD and nifK are under transcriptional control of a global nitrogen regulator NtcA. In this study, we have found that BMAA impacts in a total of 22 proteins that are under the control of NtcA. Moreover, BMAA downregulates 18 proteins that belong to photosystems I or II and light-harvesting complexes; BMAA treatment under diazotrophic conditions also downregulates five subunits of ATP synthase and enzyme NAD(P)H-quinone oxidoreductase. Therefore, we can conclude that the disbalance in energy and metabolite amounts leads to severe intracellular stress that induces the upregulation of stress-activated proteins, such as starvation-inducible DNA-binding protein, four SOS-response enzymes, and DNA repair enzymes, nine stress-response enzymes, and four proteases. The presented data provide new leads into the ecological impact of BMAA on microalgal communities that can be used in future investigations.

The First Proteomics Study of Nostoc sp. PCC 7120 Exposed to Cyanotoxin BMAA under Nitrogen Starvation

The oldest prokaryotic photoautotrophic organisms, cyanobacteria, produce many different metabolites. Among them is the water-soluble neurotoxic non-protein amino acid beta-N-methylamino-L-alanine (BMAA), whose biological functions in cyanobacterial metabolism are of fundamental scientific and practical interest. An early BMAA inhibitory effect on nitrogen fixation and heterocyst differentiation was shown in strains of diazotrophic cyanobacteria Nostoc sp. PCC 7120, Nostocpunctiforme PCC 73102 (ATCC 29133), and Nostoc sp. strain 8963 under conditions of nitrogen starvation. Herein, we present a comprehensive proteomic study of Nostoc (also called Anabaena) sp. PCC 7120 in the heterocyst formation stage affecting by BMAA treatment under nitrogen starvation conditions. BMAA disturbs proteins involved in nitrogen and carbon metabolic pathways, which are tightly co-regulated in cyanobacteria cells. The presented evidence shows that exogenous BMAA affects a key nitrogen regulatory protein, PII (GlnB), and some of its protein partners, as well as glutamyl-tRNA synthetase gltX and other proteins that are involved in protein synthesis, heterocyst differentiation, and nitrogen metabolism. By taking into account the important regulatory role of PII, it becomes clear that BMAA has a severe negative impact on the carbon and nitrogen metabolism of starving Nostoc sp. PCC 7120 cells. BMAA disturbs carbon fixation and the carbon dioxide concentrating mechanism, photosynthesis, and amino acid metabolism. Stress response proteins and DNA repair enzymes are upregulated in the presence of BMAA, clearly indicating severe intracellular stress. This is the first proteomic study of the effects of BMAA on diazotrophic starving cyanobacteria cells, allowing a deeper insight into the regulation of the intracellular metabolism of cyanobacteria by this non-protein amino acid.

Nucleotide Metabolism in Plants

Nucleotide metabolism is an essential function in plants.