Repression of CYSTATHIONINE γ-SYNTHASE in Seeds Recruits the S-Methylmethionine Cycle

Sulfate transport and metabolism: strategies to improve the seed protein quality

Sulfur-containing amino acids (SAA), namely methionine, and cysteine are crucial essential amino acids (EAA) considering the dietary requirements of humans and animals. However, a few crop plants, especially legumes, are characterized with suboptimal levels of these EAA thereby limiting their nutritive value. Hence, improved comprehension of the mechanistic perspective of sulfur transport and assimilation into storage reserve, seed storage protein (SSP), is imperative. Efforts to augment the level of SAA in seed storage protein form an integral component of strategies to balance nutritive quality and quantity. In this review, we highlight the emerging trends in the sulfur biofortification approaches namely transgenics, genetic and molecular breeding, and proteomic rebalancing with sulfur nutrition. The transgenic 'push and pull strategy' could enhance sulfur capture and storage by expressing genes that function as efficient transporters, sulfate assimilatory enzymes, sulfur-rich foreign protein sinks, or by suppressing catabolic enzymes. Modern molecular breeding approaches that adopt high throughput screening strategies and machine learning algorithms are invaluable in identifying candidate genes and alleles associated with SAA content and developing improved crop varieties. Sulfur is an essential plant nutrient and its optimal uptake is crucial for seed sulfur metabolism, thereby affecting seed quality and yields through proteomic rebalance between sulfur-rich and sulfur-poor seed storage proteins.

Overexpressing GmCGS2 Improves Total Amino Acid and Protein Content in Soybean Seed

Soybean (Glycine max (L.) Merr.) is an important source of plant protein, the nutritional quality of which is considerably affected by the content of the sulfur-containing amino acid, methionine (Met). To improve the quality of soybean protein and increase the Met content in seeds, soybean cystathionine γ-synthase 2 (GmCGS2), the first unique enzyme in Met biosynthesis, was overexpressed in the soybean cultivar "Jack", producing three transgenic lines (OE3, OE4, and OE10). We detected a considerable increase in the content of free Met and other free amino acids in the developing seeds of the three transgenic lines at the 15th and 75th days after flowering (15D and 75D). In addition, transcriptome analysis showed that the expression of genes related to Met biosynthesis from the aspartate-family pathway and S-methyl Met cycle was promoted in developing green seeds of OE10. Ultimately, the accumulation of total amino acids and soluble proteins in transgenic mature seeds was promoted. Altogether, these results indicated that GmCGS2 plays an important role in Met biosynthesis, by providing a basis for improving the nutritional quality of soybean seeds.

Cystathionine γ-synthase expression in seeds alters metabolic and DNA methylation profiles in Arabidopsis

Arabidopsis (Arabidopsis thaliana) seeds expressing the feedback-insensitive form of cystathionine γ-synthase (AtD-CGS), the key gene of methionine (Met) synthesis, under the control of a seed-specific phaseolin promoter (SSE plants) show a significant increase in Met content. This elevation is accompanied by increased levels of other amino acids (AAs), sugars, total protein, and starch, which are important from a nutritional aspect. Here, we investigated the mechanism behind this phenomenon. Gas chromatography-mass spectrometry (GC-MS) analysis of SSE leaves, siliques, and seeds collected at 3 different developmental stages showed high levels of Met, AAs, and sugars compared to the control plants. A feeding experiment with isotope-labeled AAs showed an increased flux of AAs from nonseed tissues toward the developing seeds of SSE. Transcriptome analysis of leaves and seeds displayed changes in the status of methylation-related genes in SSE plants that were further validated by methylation-sensitive enzymes and colorimetric assay. These results suggest that SSE leaves have higher DNA methylation rates than control plants. This occurrence apparently led to accelerated senescence, together with enhanced monomer synthesis, which further resulted in increased transport of monomers from the leaves toward the seeds. The developing seeds of SSE plants, however, show reduced Met levels and methylation rates. The results provide insights into the role of Met in DNA methylation and gene expression and how Met affects the metabolic profile of the plant.

Methodological and physiological study of seed dormancy release in Tilia henryana

Tilia henryana is a rare tree of the Tilia family, found exclusively in China. Its seeds have severe dormancy features that limit its normal conditions of reproduction and renewal. Its seeds have severe dormant characteristics that limit its normal conditions of reproduction and renewal. The Dormancy in T. henryana seeds is a comprehensive dormancy (PY + PD) caused by mechanical and permeability barriers of seed coat and the presence of germination inhibitor in endosperm. L9 (34) orthogonal test was used to determine the best procedure for releasing the dormancy of T. henryana seeds, that is, first treating the seeds with H2SO4 for 15 min, followed by the application of 1 g L-1 GA3, stratification at 5 °C for 45 days, and finally germination at 20 °C, which can achieve a 98% seed germination rate. Large amounts of fat are consumed throughout the dormancy release process. As quantities of protein and starch marginally increase, soluble sugars are continuously decreased. Acid phosphatase and amylase activities increased rapidly, and the combined enzyme activities of G-6-PDH and 6-PGDH related to the PPP were also significantly increased. The levels of GA and ZR continued to increase, while the levels of ABA and IAA gradually decreased, among which GA and ABA changed most rapidly. The total amino acids content continued to decrease. Asp, Cys, Leu, Phe, His, Lys and Arg decreased with dormancy release, while Ser, Glu, Ala, Ile, Pro and Gaba showed an upward trend. The physical dormancy of T. henryana seeds is broken with H2SO4 in order to make the seed coat more permeable, which is a prerequisite for germination. As a result, the seeds can absorb water and engage in physiological metabolic activities, particularly the hydrolysis and metabolism of fat, which supply a significant amount of energy for dormancy release. In addition, rapid variations in the levels of different endogenous hormones and free amino acids, induced by cold stratification and GA3 application, are another important factor promoting the quick physiological activation of seeds and breaking the endosperm barrier.

Elucidating the importance of the catabolic enzyme, methionine-gamma-lyase, in stresses during Arabidopsis seed development and germination

The sulfur-containing essential amino acid, methionine, is a key metabolite in plant cells since it is used as a precursor for the synthesis of vital metabolites. The transcript level of methionine's catabolic enzyme, methionine γ-lyase (MGL), accumulates in the seeds to a high level compared to other organs. The aim of this study was to reveal the role of MGL during seed development and germination. Using [¹³C]S-methylmethionine (SMM), the mobile form of methionine that is used to feed flower stalks of wild-type (WT) plants, revealed that the contents of [¹³C]methionine in seeds were significantly reduced when the plants underwent heat and osmotic stresses. Moreover, the levels of [¹³C]isoleucine, a product of MGL, significantly increased. Also, using the MGL promoter and gene fused to the GUS reporter gene, it was demonstrated that the heat stress significantly increased the protein level in the seeds. Therefore, we can conclude that MGL became active under stresses apparently to produce isoleucine, which is used as an osmoprotectant and an energy source. Transgenic Arabidopsis thaliana RNAi seeds with targeted repression of AtMGL during the late developmental stages of seeds show that the seeds did not accumulate methionine when they were grown under standard growth conditions, unlike the mgl-2, a knockout mutant, which showed a three-fold higher level of methionine. Also, when the RNAi plants developed under mid-heat stress, the level of methionine significantly increased while the content of isoleucine decreased compared to the control seeds, which strengthened the assumption that MGL is active under stress. The germination efficiency of the RNAi lines and mgl seeds were similar to their controls. However, the seeds that developed during heat or salt stress showed significantly lower germination efficiency compared to the control seeds. This implies that MGL is important to maintain the ability of the seeds to germinate. The RNAi lines and mgl seeds that developed under regular conditions, but germinated during salt or osmotic stress, exhibited a lower germination rate, suggesting an essential role of MGL also during this process. The results of this study show the important role of AtMGL in seeds under stresses.

Using transcriptomic and metabolomic data to investigate the molecular mechanisms that determine protein and oil contents during seed development in soybean

Soybean [Glycine max (L.) Merri.] is one of the most valuable global crops. And vegetable soybean, as a special type of soybean, provides rich nutrition in people's life. In order to investigate the gene expression networks and molecular regulatory mechanisms that regulate soybean seed oil and protein contents during seed development, we performed transcriptomic and metabolomic analyses of soybean seeds during development in two soybean varieties that differ in protein and oil contents. We identified a total of 41,036 genes and 392 metabolites, of which 12,712 DEGs and 315 DAMs were identified. Analysis of KEGG enrichment demonstrated that DEGs were primarily enriched in phenylpropanoid biosynthesis, glycerolipid metabolism, carbon metabolism, plant hormone signal transduction, linoleic acid metabolism, and the biosynthesis of amino acids and secondary metabolites. K-means analysis divided the DEGs into 12 distinct clusters. We identified candidate gene sets that regulate the biosynthesis of protein and oil in soybean seeds, and present potential regulatory patterns that high seed-protein varieties may be more sensitive to desiccation, show earlier photomorphogenesis and delayed leaf senescence, and thus accumulate higher protein contents than high-oil varieties.

Global Survey, Expressions and Association Analysis of CBLL Genes in Peanut

Cystathionine γ-synthase (CGS), methionine γ-lyase (MGL), cystathionine β-lyase (CBL) and cystathionine γ-lyase (CGL) share the Cys_Met_Meta_PP domain and play important roles in plant stress response and development. In this study, we defined the genes containing the Cys_Met_Meta_PP domain (PF01053.20) as CBL-like genes (CBLL). Twenty-nine CBLL genes were identified in the peanut genome, including 12 from cultivated peanut and 17 from wild species. These genes were distributed unevenly at the ends of different chromosomes. Evolution, gene structure, and motif analysis revealed that CBLL proteins were composed of five different evolutionary branches. Chromosome distribution pattern and synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CBLL genes. Comparative genomics analysis showed that there were three common collinear CBLL gene pairs among peanut, Arabidopsis, grape, and soybean, but no collinear CBLL gene pairs between peanut and rice. The prediction results of cis-acting elements showed that AhCBLLs, AdCBLLs, and AiCBLLs contained different proportions of plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCBLLs had significantly higher expression in pods and seeds. All AhCBLLs could respond to heat stress, and some of them could be rapidly induced by cold, salt, submergence, heat and drought stress. Furthermore, one polymorphic site in AiCBLL7 was identified by association analysis which was closely associated with pod length (PL), pod width (PW), hundred pod weight (HPW) and hundred seed weight (HSW). The results of this study provide a foundation for further research on the function of the CBLL gene family in peanut.

Discovery and characterization of small molecule inhibitors of cystathionine gamma-synthase with in planta activity

The synthesis of essential amino acids in plants is pivotal for their viability and growth, and these cellular pathways are therefore targeted for the discovery of new molecules for weed control. Herein, we describe the discovery and design of small molecule inhibitors of cystathionine gamma-synthase, a key enzyme in the biosynthesis of methionine. Based on in silico screening and filtering of a large molecular database followed by the in vitro selection of molecules, we identified small molecules capable of binding the target enzyme. Molecular modelling of the interaction and direct biophysical binding enabled us to explore a focussed chemical expansion set of molecules characterized by an active phenyl-benzamide chemical group. These molecules are bio-active and efficiently inhibit the viability of BY-2 tobacco cells and seedlings growth of Arabidopsis thaliana on agar plates.

The Level of Methionine Residues in Storage Proteins Is the Main Limiting Factor of Protein-Bound-Methionine Accumulation in Arabidopsis Seeds

The low level of methionine, an essential sulfur-containing amino acid, limits the nutritional quality of seeds. Two main factors can control the level of protein-bound methionine: the level of free methionine that limits protein accumulation and the methionine residues inside the storage proteins. To reveal the main limiting factor, we generated transgenic Arabidopsis thaliana seed-specific plants expressing the methionine-rich sunflower seed storage (SSA) protein (A1/A2). The contents of protein-bound methionine in the water-soluble protein fraction that includes the SSA in A1/A2 were 5.3- and 10.5-fold, respectively, compared to control, an empty vector (EV). This suggests that free methionine can support this accumulation. To elucidate if the level of free methionine could be increased further in the protein-bound methionine, these lines were crossed with previously characterized plants having higher levels of free methionine in seeds (called SSE). The progenies of the crosses (A1S, A2S) exhibited the highest level of protein-bound methionine, but this level did not differ significantly from A2, suggesting that all the methionine residues of A2 were filled with methionine. It also suggests that the content of methionine residues in the storage proteins is the main limiting factor. The results also proposed that the storage proteins can change their content in response to high levels of free methionine or SSA. This was assumed since the water-soluble protein fraction was highest in A1S/A2S as well as in SSE compared to EV and A1/A2. By using these seeds, we also aimed at gaining more knowledge about the link between high free methionine and the levels of metabolites that usually accumulate during abiotic stresses. This putative connection was derived from a previous analysis of SSE. The results of metabolic profiling showed that the levels of 29 and 20 out of the 56 metabolites were significantly higher in SSE and A1, respectively, that had higher level of free methionine, compared A1S/A2S, which had lower free methionine levels. This suggests a strong link between high free methionine and the accumulation of stress-associated metabolites.

Suppressed Methionine γ-Lyase Expression Causes Hyperaccumulation of S-Methylmethionine in Soybean Seeds

Several soybean (Glycine max) germplasms, such as Nishiyamahitashi 98-5 (NH), have an intense seaweed-like flavor after cooking because of their high seed S-methylmethionine (SMM) content. In this study, we compared the amounts of amino acids in the phloem sap, leaves, pods, and seeds between NH and the common soybean cultivar Fukuyutaka. This revealed a comparably higher SMM content alongside a higher free Met content in NH seeds, suggesting that the SMM-hyperaccumulation phenotype of NH soybean was related to Met metabolism in seeds. To investigate the molecular mechanism behind SMM hyperaccumulation, we examined the phenotype-associated gene locus in NH plants. Analyses of the quantitative trait loci in segregated offspring of the cross between NH and the common soybean cultivar Williams 82 indicated that one locus on chromosome 10 explains 71.4% of SMM hyperaccumulation. Subsequent fine-mapping revealed that a transposon insertion into the intron of a gene, Glyma.10g172700, is associated with the SMM-hyperaccumulation phenotype. The Glyma.10g172700-encoded recombinant protein showed Met-γ-lyase (MGL) activity in vitro, and the transposon-insertion mutation in NH efficiently suppressed Glyma.10g172700 expression in developing seeds. Exogenous administration of Met to sections of developing soybean seeds resulted in transient increases in Met levels, followed by continuous increases in SMM concentrations, which was likely caused by Met methyltransferase activity in the seeds. Accordingly, we propose that the SMM-hyperaccumulation phenotype is caused by suppressed MGL expression in developing soybean seeds, resulting in transient accumulation of Met, which is converted into SMM to avoid the harmful effects caused by excess free Met.

Revisiting the attempts to fortify methionine content in plant seeds

The sulfur-containing amino acid methionine belongs to the group of essential amino acids, meaning that humans and animals must consume it in their diets. However, plant seeds have low levels of methionine, limiting their nutritional potential. For this reason, efforts have been made over the years to increase methionine levels in seeds. Here, we summarize these efforts and focus particularly on those utilizing diverse genetic and molecular tools. Four main approaches are described: (i) expression of methionine-rich storage proteins in a seed-specific manner to incorporate more soluble methionine into the protein fraction; (ii) reduction of methionine-poor storage proteins inside the seeds to reinforce the accumulation of methionine-rich proteins; (iii) silencing methionine catabolic enzymes; and (iv) up-regulation of key biosynthetic enzymes participating in methionine synthesis. We focus on the biosynthetic genes that operate de novo in seeds and that belong to the sulfur assimilation and aspartate family pathways, as well as genes from the methionine-specific pathway. We also include those enzymes that operate in non-seed tissues that contribute to the accumulation of methionine in seeds, such as S-methylmethionine enzymes. Finally, we discuss the biotechnological potential of these manipulations to increase methionine content in plant seeds and their effect on seed germination.

The level of threonine in tobacco seeds is limited by substrate availability, while the level of methionine is limited also by the activity of cystathionine γ-synthase

Methionine and threonine are two essential amino acids whose low levels limit the nutritional quality of seeds. The current objective was to define factors that regulate and might increase their levels in seeds. Feeding experiments carried out on receptacles of developing tobacco (Nicotiana tabacum) capsules showed that 1 mM of S-methylmethionine increased the level of methionine to contents similar to 2.5 mM of homoserine, an intermediate metabolite of the aspartate family of amino acids. The latter also increased the level of threonine. Based on these findings, we generated tobacco seeds that expressed a combination of bacterial feedback-insensitive aspartate kinase (bAK), which was previously reported to have a high level of threonine/methionine, and feedback-insensitive cystathionine γ-synthase (CGS), the regulatory enzyme of the methionine biosynthesis pathway. Plants expressing this latter gene previously showed having higher levels of methionine. The results of total amino acids analysis showed that the level of threonine was highest in the bAK line, which has moderate levels of methionine and lysine, while the highest level of methionine was found in seeds expressing both heterologous genes. The results suggest that the level of threonine in tobacco seeds is limited by the substrate, while that of methionine is limited also by the activity of CGS.

Molecular evolution and expression divergence of three key Met biosynthetic genes in plants: CGS, HMT and MMT

Methionine (Met) is an essential sulfur-containing amino acid in animals. Cereal and legume crops with limiting levels of Met represent the major food and feed sources for animals. In plants, cystathionine gamma-synthase (CGS), methionine methyltransferase (MMT) and homocysteine methyltransferase (HMT) are committing enzymes synergistically synthesizing Met through the aspartate (Asp) family pathway and the S-methylmethionine (SMM) cycle. The biological functions of CGS, MMT and HMT genes have been respectively studied, whereas their evolution patterns and their contribution to the evolution of Met biosynthetic pathway in plants are unknown. In the present study, to reveal their evolution patterns and contribution, the evolutionary relationship of CGS, MMT and HMT gene families were reconstructed. The results showed that MMTs began in the ancestor of the land plants and kept conserved during evolution, while the CGSs and HMTs had diverged. The CGS genes were divided into two branches in the angiosperms, Class 1 and Class 2, of which Class 2 only contained the grasses. However, the HMT genes diverged into Class 1 and Class 2 in all of the seed plants. Further, the gene structure analysis revealed that the CGSs, MMTs and HMTs were relatively conserved except for the CGSs in Class 2. According to the expression of CGS, HMT and MMT genes in soybeans, as well as in the database of soybean, rice and Arabidopsis, the expression patterns of the MMTs were shown to be consistently higher in leaves than in seeds. However, the expression of CGSs and HMTs had diverged, either expressed higher in leaves or seeds, or showing fluctuated expression. Additionally, the functions of HMT genes had diverged into the repair of S-adenosylmethionine and SMM catabolism during the evolution. The results indicated that the CGS and HMT genes have experienced partial subfunctionalization. Finally, given the evolution and expression of the CGS, HMT and MMT gene families, we built the evolutionary model of the Met biosynthetic pathways in plants. The model proposed that the Asp family pathway existed in all the plant lineages, while the SMM cycle began in the ancestor of land plants and then began to diverge in the ancestor of seed plants. The model suggested that the evolution of Met biosynthetic pathway is basically consistent with that of plants, which might be vital to the growth and development of different botanical lineages during evolution.

Alteration of S-adenosylhomocysteine levels affects lignin biosynthesis in switchgrass

Methionine (Met) synthesized from aspartate is a fundamental amino acid needed to produce S-adenosylmethionine (SAM) that is an important cofactor for the methylation of monolignols. As a competitive inhibitor of SAM-dependent methylation, the effect of S-adenosylhomocysteine (SAH) on lignin biosynthesis, however, is still largely unknown in plants. Expression levels of Cystathionine γ-synthase (PvCGS) and S-adenosylhomocysteine hydrolase 1 (PvSAHH1) were down-regulated by RNAi technology, respectively, in switchgrass, a dual-purpose forage and biofuel crop. The transgenic switchgrass lines were subjected to studying the impact of SAH on lignin biosynthesis. Our results showed that down-regulation of PvCGS in switchgrass altered the accumulation of aspartate-derived and aromatic amino acids, reduced the content of SAH, enhanced lignin biosynthesis and stunted plant growth. In contrast, down-regulation of PvSAHH1 raised SAH levels in switchgrass, impaired the biosynthesis of both guaiacyl and syringyl lignins and therefore significantly increased saccharification efficiency of cell walls. This work indicates that SAH plays a crucial role in monolignol methylation in switchgrass. Genetic regulation of either PvCGS or PvSAHH1 expression in switchgrass can change intracellular SAH contents and SAM to SAH ratios and therefore affect lignin biosynthesis. Thus, our study suggests that genes involved in Met metabolism are of interest as new valuable targets for cell wall bioengineering in future.

The metabolic roles of free amino acids during seed development

Amino acids play vital roles in the central metabolism of seeds. They are primarily utilized for the synthesis of seed-storage proteins, but also serve as precursors for the biosynthesis of secondary metabolites and as a source of energy. Here, we aimed at describing the knowledge accumulated in recent years describing the changes occurring in the contents of free amino acids (FAAs) during seed development. Since several essential amino acids are found in low levels in seeds (e.g., Lys, Met, Thr, Val, Leu, Ile and His), or play unique functional roles in seed development (e.g., Pro and the non-proteinogenic γ-aminobutyrate [GABA]), we also briefly describe studies carried out in order to alter their levels in seeds and determine the effects of the manipulation on seed biology. The lion share of these studies highlights strong positive correlations between the biosynthetic pathways of FAAs, meaning that when the levels of a certain amino acid change in seeds, the contents of other FAAs tend to elevate as well. These observations infer a tight regulatory network operating in the biosynthesis of FAAs during seed development.

CYSTATHIONINE GAMMA-SYNTHASE activity in rice is developmentally regulated and strongly correlated with sulfate

An important goal of rice cultivar development is improvement of protein quality, especially with respect to essential amino acids such as methionine. With the goal of increasing seed methionine content, we generated Oryza sativa ssp. japonica cv. Taipei 309 transgenic lines expressing a feedback-desensitized CYSTATHIONINE GAMMA-SYNTHASE from Arabidopsis thaliana (AtD-CGS) under the control of the maize ubiquitin promoter. Despite persistently elevated cystathionine gamma-synthase (CGS) activity in the AtD-CGS transgenic lines relative to untransformed Taipei, sulfate was the only sulfur-containing compound found to be elevated throughout vegetative development. Accumulation of methionine and other sulfur-containing metabolites was limited to the leaves of young plants. Sulfate concentration was found to strongly and positively correlate with CGS activity across vegetative development, irrespective of whether the activity was provided by the endogenous rice CGS or by a combination of endogenous and AtD-CGS. Conversely, the concentrations of glutathione, valine, and leucine were clearly negatively correlated with CGS activity in the same tissues. We also observed a strong decrease in CGS activity in both untransformed Taipei and the AtD-CGS transgenic lines as the plants approached heading stage. The mechanism for this downregulation is currently unknown and of potential importance for efforts to increase methionine content in rice.