High-lysine corn produced by the combination of enhanced lysine biosynthesis and reduced zein accumulation

Comparative transcriptome profiling reveals the mechanism of increasing lysine and tryptophan content through pyramiding opaque2, opaque16 and waxy1 genes in maize

To explore the molecular mechanism behind maize grain quality and use of different gene stacking to improve the nutritional quality of grain, marker-assisted selection (MAS) was used to select three recessive mutant lines containing o2o16wx, along with the double-recessive mutant lines containing o2o16, o2wx, and o16wx. The resulting seeds were taken for transcriptome sequencing analysis 18 days after pollination (DAP). Results: Compared with the recurrent parent genes, in the lysine synthesis pathway, the gene pyramiding lines (o2o16wx, o2wx, and o16wx) revealed that the gene encoding aspartate kinase (AK) was up-regulated and promoted lysine synthesis. In the lysine degradation pathway, 'QCL8010_1' (o2o16wx) revealed that the gene encoding saccharopine dehydrogenase (LKR/SDH) was down-regulated. In addition, the gene pyramiding lines (o2o16wx, o2o16, and o16wx) indicated that the gene encoding 2-oxoglutarate dehydrogenase E1 component (OGDH) was down-regulated, inhibiting the degradation of lysine. In the tryptophan synthesis pathway, the genes encoding anthranilate synthase (AS), anthranilate synthase (APT), and tryptophan synthase (TS) were up-regulated (in o2o16wx, o2o16, o2wx, and o16wx), and promote tryptophan synthesis. In the tryptophan degradation pathway, it was revealed that the genes encoding indole-3-producing oxidase (IAAO) and indole-3-pyruvate monooxygenase (YUCCA) were down-regulated. These results provide a reference for revealing the mechanism of the o2, o16, and wx with different gene pyramiding to improve grain quality in maize.

Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops

Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.

Regulation of seed storage protein synthesis in monocot and dicot plants: A comparative review

Seeds are a major source of nutrients for humans and animal livestock worldwide. With improved living standards, high nutritional quality has become one of the main targets for breeding. Storage protein content in seeds, which is highly variable depending on plant species, serves as a pivotal criterion of seed nutritional quality. In the last few decades, our understanding of the molecular genetics and regulatory mechanisms of storage protein synthesis has greatly advanced. Here, we systematically and comprehensively summarize breakthroughs on the conservation and divergence of storage protein synthesis in dicot and monocot plants. With regard to storage protein accumulation, we discuss evolutionary origins, developmental processes, characteristics of main storage protein fractions, regulatory networks, and genetic modifications. In addition, we discuss potential breeding strategies to improve storage protein accumulation and provide perspectives on some key unanswered problems that need to be addressed.

Engineering a feedback inhibition-insensitive plant dihydrodipicolinate synthase to increase lysine content in Camelina sativa seeds

Camelina sativa (camelina) is emerging as an alternative oilseed crop due to its short growing cycle, low input requirements, adaptability to less favorable growing environments and a seed oil profile suitable for biofuel and industrial applications. Camelina meal and oil are also registered for use in animal and fish feeds; however, like meals derived from most cereals and oilseeds, it is deficient in certain essential amino acids, such as lysine. In higher plants, the reaction catalyzed by dihydrodipicolinate synthase (DHDPS) is the first committed step in the biosynthesis of lysine and is subject to regulation by lysine through feedback inhibition. Here, we report enhancement of lysine content in C. sativa seed via expression of a feedback inhibition-insensitive form of DHDPS from Corynebacterium glutamicums (CgDHDPS). Two genes encoding C. sativa DHDPS were identified and the endogenous enzyme is partially insensitive to lysine inhibition. Site-directed mutagenesis was used to examine the impact of alterations, alone and in combination, present in lysine-desensitized DHDPS isoforms from Arabidopsis thaliana DHDPS (W53R), Nicotiana tabacum (N80I) and Zea mays (E84K) on C. sativa DHDPS lysine sensitivity. When introduced alone, each of the alterations decreased sensitivity to lysine; however, enzyme specific activity was also affected. There was evidence of molecular or structural interplay between residues within the C. sativa DHDPS allosteric site as coupling of the W53R mutation with the N80V mutation decreased lysine sensitivity of the latter, but not to the level with the W53R mutation alone. Furthermore, the activity and lysine sensitivity of the triple mutant (W53R/N80V/E84T) was similar to the W53R mutation alone or the C. glutamicum DHDPS. The most active and most lysine-insensitive C. sativa DHDPS variant (W53R) was not inhibited by free lysine up to 1 mM, comparable to the C. glutamicums enzyme. Seed lysine content increased 13.6 -22.6% in CgDHDPS transgenic lines and 7.6–13.2% in the mCsDHDPS lines. The high lysine-accumulating lines from this work may be used to produce superior quality animal feed with improved essential amino acid profile.

Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency

In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.

Genetic engineering to improve essential and conditionally essential amino acids in maize: transporter engineering as a reference

Ruminants and humans are unable to synthesize essential amino acids (EAAs) and conditionally essential amino acids (CEAAs) under normal conditions and need to acquire them from plant sources. Maize plays, as a major crop, a central role in global food security. However, maize is deficient in several EAAs and CEAAs. Genetic engineering has been successfully used to enrich the EAA content of maize to some extent, including the content of Lys, Trp, and Met. However, research on other EAAs is lacking. Genetic engineering provides several viable approaches for increasing the EAA content in maize, including transformation of a single gene, transformation of multiple genes in a single cassette, overexpression of putative amino acid transporters, engineering the amino acid biosynthesis pathway including silencing of feedback inhibition enzymes, and overexpression of major enzymes in this pathway. These challenging processes require a deep understanding of the biosynthetic and metabolic pathways of individual amino acids, and the interaction of individual amino acids with other metabolic pathways.

Relief Role of Lysine Chelated Zinc (Zn) on 6-Week-Old Maize Plants under Tannery Wastewater Irrigation Stress

Tannery wastewater mainly comes from leather industries. It has high organic load, high salinity, and many other pollutants, including chromium (Cr). Tannery wastewater is generally used for crop irrigation in some areas of Pakistan and worldwide, due to the low availability of good quality of irrigation water. As tannery wastewater has many nutrients in it, its lower concentration benefits the plant growth, but at a higher concentration, it damages the plants. Chromium in tannery wastewater accumulates in plants, and causes stress at physiological and biochemical levels. In recent times, the role of micronutrient-amino acid chelated compounds has been found to be helpful in reducing abiotic stress in plants. In our present study, we used lysine chelated zinc (Zn-lys) as foliar application on maize (Zea mays L.), growing in different concentrations of tannery wastewater. Zinc (Zn) is required by plants for growth, and lysine is an essential amino acid. Maize plants were grown in tannery wastewater in four concentrations (0, 25%, 50%, and 100%) and Zn-lys was applied as a foliar spray in three concentrations (0 mM, 12.5 mM, and 25 mM) during plant growth. Plants were cautiously harvested right after 6 weeks of treatment. Foliar spray of Zn-lys on maize increased the biomass and improved the plant growth. Photosynthetic pigments such as total chlorophyll, chlorophyll a, chlorophyll b and contents of carotenoids also increased with Zn-lys application. In contrast to control plants, the hydrogen peroxide (H2O2) contents were increased up to 12%, 50%, and 68% in leaves, as well as 16%, 51% and 89% in roots at 25%, 50%, and 100% tannery water application, respectively, without Zn-lys treatments. Zn-lys significantly reduced the damages caused by oxidative stress in maize plant by decreasing the overproduction of H2O2 and malondialdehyde (MDA) in maize that were produced, due to the application of high amount of tannery wastewater alone. The total free amino acids and soluble protein decreased by 10%, 31% and 64% and 18%, 61% and 122% at 25%, 50% and 100% tannery water treatment. Zn-lys application increased the amino acids production and antioxidant activities in maize plants. Zn contents increased, and Cr contents decreased, in different parts of plants with Zn-lys application. Overall, a high concentration of tannery wastewater adversely affected the plant growth, but the supplementation of Zn-lys assertively affected the plant growth and enhanced the nutritional quality, by enhancing Zn and decreasing Cr levels in plants simultaneously irrigated with tannery wastewater.

Connections Between Amino Acid Metabolisms in Plants: Lysine as an Example

Extensive efforts have been made to fortify essential amino acids and boost nutrition in plants, but unintended effects on growth and physiology are also observed. Understanding how different amino acid metabolisms are connected with other biological pathways is therefore important. In addition to protein synthesis, amino acid metabolism is also tightly linked to energy and carbohydrate metabolism, the carbon-nitrogen budget, hormone and secondary metabolism, stress responses, and so on. Here, we update the currently available information on the connections between amino acid metabolisms, which tend to be overlooked in higher plants. Particular emphasis was placed on the connections between lysine metabolism and other pathways, such as tryptophan metabolism, the tricarboxylic acid cycle, abiotic and biotic stress responses, starch metabolism, and the unfolded protein response. Interestingly, regulation of lysine metabolism was found to differ between plant species, as is the case between dicots and monocots. Determining the metabolic connection between amino acid metabolisms will help improve our understanding of the metabolic flux, supporting studies on crop nutrition.

Characterization of recombinant dihydrodipicolinate synthase from the bread wheat Triticum aestivum

Recombinant wheat DHDPS was produced for the first time in milligram quantities and shown to be an enzymatically active tetramer in solution using analytical ultracentrifugation and small angle X-ray scattering. Wheat is an important cereal crop with an extensive role in global food supply. Given our rapidly growing population, strategies to increase the nutritional value and production of bread wheat are of major significance in agricultural science to satisfy our dietary requirements. Lysine is one of the most limiting essential amino acids in wheat, thus, a thorough understanding of lysine biosynthesis is of upmost importance to improve its nutritional value. Dihydrodipicolinate synthase (DHDPS; EC 4.3.3.7) catalyzes the first committed step in the lysine biosynthesis pathway of plants. Here, we report for the first time the expression and purification of recombinant DHDPS from the bread wheat Triticum aestivum (Ta-DHDPS). The optimized protocol yielded 36 mg of > 98% pure recombinant Ta-DHDPS per liter of culture. Enzyme kinetic studies demonstrate that the recombinant Ta-DHDPS has a K_M (pyruvate) of 0.45 mM, K_M (l-aspartate-4-semialdehyde) of 0.07 mM, k_cat of 56 s^-1, and is inhibited by lysine (IC ₅₀ ^LYS of 0.033 mM), which agree well with previous studies using labor-intensive purification from wheat suspension cultures. We subsequently employed circular dichroism spectroscopy, analytical ultracentrifugation and small angle X-ray scattering to show that the recombinant enzyme is folded with 60% α/β structure and exists as a 7.5 S tetrameric species with a R_g of 33 Å and D_max of 118 Å. This study is the first to report the biophysical properties of the recombinant Ta-DHDPS in aqueous solution and offers an excellent platform for future studies aimed at improving nutritional value and primary production of bread wheat.

Analysis of the Gli-D2 locus identifies a genetic target for simultaneously improving the breadmaking and health-related traits of common wheat

Gliadins are a major component of wheat seed proteins. However, the complex homoeologous Gli-2 loci (Gli-A2, -B2 and -D2) that encode the α-gliadins in commercial wheat are still poorly understood. Here we analyzed the Gli-D2 locus of Xiaoyan 81 (Xy81), a winter wheat cultivar. A total of 421.091 kb of the Gli-D2 sequence was assembled from sequencing multiple bacterial artificial clones, and 10 α-gliadin genes were annotated. Comparative genomic analysis showed that Xy81 carried only eight of the α-gliadin genes of the D genome donor Aegilops tauschii, with two of them each experiencing a tandem duplication. A mutant line lacking Gli-D2 (DLGliD2) consistently exhibited better breadmaking quality and dough functionalities than its progenitor Xy81, but without penalties in other agronomic traits. It also had an elevated lysine content in the grains. Transcriptome analysis verified the lack of Gli-D2 α-gliadin gene expression in DLGliD2. Furthermore, the transcript and protein levels of protein disulfide isomerase were both upregulated in DLGliD2 grains. Consistent with this finding, DLGliD2 had increased disulfide content in the flour. Our work sheds light on the structure and function of Gli-D2 in commercial wheat, and suggests that the removal of Gli-D2 and the gliadins specified by it is likely to be useful for simultaneously enhancing the end-use and health-related traits of common wheat. Because gliadins and homologous proteins are widely present in grass species, the strategy and information reported here may be broadly useful for improving the quality traits of diverse cereal crops.

Breeding Major Cereal Grains through the Lens of Nutrition Sensitivity

Cereal grains are the common food staples that collectively provide over 50% of dietary calories and proteins for the world's population. Although the Green Revolution has greatly increased the yield of commercial cereal crops, they often lack nutrients essential for human health in the edible tissues. In developing nutrition-sensitive agriculture, the nutritional quality of cereal grains has been a major target for improvement using breeding and biotechnology approaches. This review examines recent progress on biofortification of micronutrients (provitamin A and folates) and an essential amino acid (lysine) in three major cereal grains, wheat, rice, and maize, through plant breeding. In addition, how natural variations, induced mutations, and the advanced genome-editing technologies can be applied to improving the nutrient content and stability in these cereal grains are discussed. High-yield cereal crops pyramided with improved (micro)nutrient contents hold great promise to meet the increasing demand of nutritionally limited populations and to contribute to achieving sustainable nutrition security.

Improving protein content and quality by over-expressing artificially synthetic fusion proteins with high lysine and threonine constituent in rice plants

Rice grains are rich in starch but low in protein with very low level of both lysine and threonine. Thus, it is important to further improve protein quality and quantity, especially to increase lysine and threonine content in rice grains. We artificially synthesized two new genes by fusing endogenous rice genes with lysine (K)/threonine (T) motif (TKTKK) coding sequences. They were designated as TKTKK1 and TKTKK2 and their encoded proteins consist of 73.1% and 83.5% of lysine/threonine, respectively. These two genes were under the control of 35S promoter and were independently introduced into the rice genome to generate transgenic plants. Our data showed that overexpression of TKTKK1 generated stable proteins with expected molecular weight and the transgenic rice seeds significantly increased lysine, threonine, total amino acids and crude protein content by 33.87%, 21.21%, 19.43% and 20.45%, respectively when compared with wild type control; significant improvement was also observed in transgenic rice seeds overexpressing TKTKK2. However, limited improvement in protein quality and quantity was observed in transgenic seeds carrying tandom array of these two new genes. Our data provide the basis and alternative strategy on further improving protein quality and quantity in other crops or vegetable plants by synthetic biology.

Improving Nutritional Quality of Plant Proteins Through Genetic Engineering

Humans and animals are unable to synthesize essential amino acids such as branch chain amino acids methionine (Met), lysine (Lys) and tryptophan (Trp). Therefore, these amino acids need to be supplied through the diets. Several essential amino acids are deficient or completely lacking among crops used for human food and animal feed. For example, soybean is deficient in Met; Lys and Trp are lacking in maize. In this mini review, we will first summarize the roles of essential amino acids in animal nutrition. Next, we will address the question: “What are the amino acids deficient in various plants and their biosynthesis pathways?” And: “What approaches are being used to improve the availability of essential amino acids in plants?” The potential targets for metabolic engineering will also be discussed, including what has already been done and what remains to be tested.

Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development

Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysine biosynthesis. We identified lysine biosynthesis pathway genes (LBPGs) and investigated whether a diaminopimelate pathway variant exists in maize. We analyzed two genes encoding the key enzyme dihydrodipicolinate synthase, and determined that they contribute differently to lysine synthesis during maize seed development. A coexpression network of LBPGs was constructed using RNA-sequencing data from 21 developmental stages of B73 maize seed. We found a large set of genes encoding ribosomal proteins, elongation factors and zein proteins that were coexpressed with LBPGs. The coexpressed genes were enriched in cellular metabolism terms and protein related terms. A phylogenetic analysis of the LBPGs from different plant species revealed different relationships. Additionally, six transcription factor (TF) families containing 13 TFs were identified as the Hub TFs of the LBPGs modules. Several expression quantitative trait loci of LBPGs were also identified. Our results should help to elucidate the lysine biosynthesis pathway network in maize seed.

The contribution of wheat to human diet and health

Wheat is the most important staple crop in temperate zones and is in increasing demand in countries undergoing urbanization and industrialization. In addition to being a major source of starch and energy, wheat also provides substantial amounts of a number of components which are essential or beneficial for health, notably protein, vitamins (notably B vitamins), dietary fiber, and phytochemicals. Of these, wheat is a particularly important source of dietary fiber, with bread alone providing 20% of the daily intake in the UK, and well-established relationships between the consumption of cereal dietary fiber and reduced risk of cardio-vascular disease, type 2 diabetes, and forms of cancer (notably colo-rectal cancer). Wheat shows high variability in the contents and compositions of beneficial components, with some (including dietary fiber) showing high heritability. Hence, plant breeders should be able to select for enhanced health benefits in addition to increased crop yield.

Biofortification of rice with lysine using endogenous histones

Rice is the most consumed cereal grain in the world, but deficient in the essential amino acid lysine. Therefore, people in developing countries with limited food diversity who rely on rice as their major food source may suffer from malnutrition. Biofortification of stable crops by genetic engineering provides a fast and sustainable method to solve this problem. In this study, two endogenous rice lysine-rich histone proteins, RLRH1 and RLRH2, were over-expressed in rice seeds to achieve lysine biofortification. Their protein sequences passed an allergic sequence-based homology test. Their accumulations in rice seeds were raised to a moderate level by the use of a modified rice glutelin 1 promoter with lowered expression strength to avoid the occurrence of physiological abnormalities like unfolded protein response. The expressed proteins were further targeted to protein storage vacuoles for stable storage using a glutelin 1 signal peptide. The lysine content in the transgenic rice seeds was enhanced by up to 35 %, while other essential amino acids remained balanced, meeting the nutritional standards of the World Health Organization. No obvious unfolded protein response was detected. Different degrees of chalkiness, however, were detected in the transgenic seeds, and were positively correlated with both the levels of accumulated protein and lysine enhancement. This study offered a solution to the lysine deficiency in rice, while at the same time addressing concerns about food safety and physiological abnormalities in biofortified crops.

Lysine metabolism in antisense C-hordein barley grains

The grain proteins of barley are deficient in lysine and threonine due to their low concentrations in the major storage protein class, the hordeins, especially in the C-hordein subgroup. Previously produced antisense C-hordein transgenic barley lines have an improved amino acid composition, with increased lysine, methionine and threonine contents. The objective of the study was to investigate the possible changes in the regulation of key enzymes of the aspartate metabolic pathway and the contents of aspartate-derived amino acids in the nontransgenic line (Hordeum vulgare L. cv. Golden Promise) and five antisense C-hordein transgenic barley lines. Considering the amounts of soluble and protein-bound aspartate-derived amino acids together with the analysis of key enzymes of aspartate metabolic pathway, we suggest that the C-hordein suppression did not only alter the metabolism of at least one aspartate-derived amino acid (threonine), but major changes were also detected in the metabolism of lysine and methionine. Modifications in the activities and regulation of aspartate kinase, dihydrodipicolinate synthase and homoserine dehydrogenase were observed in most transgenic lines. Furthermore the activities of lysine α-ketoglutarate reductase and saccharopine dehydrogenase were also altered, although the extent varied among the transgenic lines.

The catabolic enzyme methionine gamma-lyase limits methionine accumulation in potato tubers

Increasing methionine in potato tubers is desirable, both to increase the availability of this limiting essential amino acid and to enhance the aroma of baked and fried potatoes. Previous attempts to elevate potato methionine content using transgenic approaches have focused on increasing methionine biosynthesis. Higher isoleucine accumulation in these transgenic tubers suggested that the potatoes compensate for increased methionine biosynthesis with enhanced catabolism via methionine gamma-lyase (MGL), thereby producing 2-ketybutyrate for isoleucine biosynthesis. In the current study, we show that potato StMGL1 encodes a functional MGL in potato tubers. In planta silencing of StMGL1 results in an increased methionine to isoleucine ratio in the free amino acid profile of potato tubers and, in some transgenic lines, elevated accumulation of free methionine. In both wild-type and transgenic tubers, the ratio of methionine to isoleucine is negatively correlated with the level of StMGL1 transcript. A three-dimensional distribution of free amino acids in potato tubers is also described.

Safety assessment of genetically modified plants with deliberately altered composition

The development and marketing of 'novel' genetically modified (GM) crops in which composition has been deliberately altered poses a challenge to the European Union (EU)'s risk assessment processes, which are based on the concept of substantial equivalence with a non-GM comparator. This article gives some examples of these novel GM crops and summarizes the conclusions of a report that was commissioned by the European Food Safety Authority on how the EU's risk assessment processes could be adapted to enable their safety to be assessed.

Mutational breeding and genetic engineering in the development of high grain protein content

Cereals are the most important crops in the world for both human consumption and animal feed. Improving their nutritional values, such as high protein content, will have significant implications, from establishing healthy lifestyles to helping remediate malnutrition problems worldwide. Besides providing a source of carbohydrate, grain is also a natural source of dietary fiber, vitamins, minerals, specific oils, and other disease-fighting phytocompounds. Even though cereal grains contain relatively little protein compared to legume seeds, they provide protein for the nutrition of humans and livestock that is about 3 times that of legumes. Most cereal seeds lack a few essential amino acids; therefore, they have imbalanced amino acid profiles. Lysine (Lys), threonine (Thr), methionine (Met), and tryptophan (Trp) are among the most critical and are a limiting factor in many grain crops for human nutrition. Tremendous research has been put into the efforts to improve these essential amino acids. Development of high protein content can be outlined in four different approaches through manipulating seed protein bodies, modulating certain biosynthetic pathways to overproduce essential and limiting amino acids, increasing nitrogen relocation to the grain through the introduction of transgenes, and exploiting new genetic variance. Various technologies have been employed to improve protein content including conventional and mutational breeding, genetic engineering, marker-assisted selection, and genomic analysis. Each approach involves a combination of these technologies. Advancements in nutrigenomics and nutrigenetics continue to improve public knowledge at a rapid pace on the importance of specific aspects of food nutrition for optimum fitness and health. An understanding of the molecular basis for human health and genetic predisposition to certain diseases through human genomes enables individuals to personalize their nutritional requirements. It is critically important, therefore, to improve grain protein quality. Highly nutritious grain can be tailored to functional foods to meet the needs for both specific individuals and human populations as a whole.

Characterization of a cruciferin deficient mutant of Arabidopsis and its utility for overexpression of foreign proteins in plants

Plant seeds naturally accumulate storage reserves (proteins, carbohydrates, lipids) that are mobilized during germination to provide energy and raw materials to support early seedling growth. Seeds have been exploited as bioreactors for the production to foreign materials, but stable, high level expression has been elusive, in part due to the intrinsic bias for producing the natural reserves in their typical proportions. To identify mutants governing seed filling, we screened a population of mutagenized Arabidopsis plants for a mutant that failed to fill its seeds. Here we report the identification of ssp1, a recessive, viable mutant that accumulates approximately 15% less protein than wildtype seeds. Molecular analyses revealed that ssp1 is due to the introduction of a premature stop codon in CRU3, one of the major cruciferin genes. Unlike many other reserve mutants or transgenic lines in which seed storage protein levels are reduced by antisense/RNAi technologies, ssp1 exhibits low level compensation by other reserves, and represents a mutant background that might prove useful for high level expression of foreign proteins. To test this hypothesis, we used a bean phytohemagglutinin (PHA) gene as a reporter and compared PHA expression levels in single copy insertion lines in ssp1 vs. wildtype. These near isogenic lines allow reporter protein levels to be compared without the confounding and sometimes unknown influences of transgene copy number and position effects on gene expression. The ssp1 lines consistently accumulated more PHA than the backcrossed counterparts, with increases ranging from 12% to 126%. This proof of principle study suggests that similar strategies in crop plants may improve the yield of foreign proteins of agronomic and economic interest.

Metabolic engineering and profiling of rice with increased lysine

Lysine (Lys) is the first limiting essential amino acid in rice, a stable food for half of the world population. Efforts, including genetic engineering, have not achieved a desirable level of Lys in rice. Here, we genetically engineered rice to increase Lys levels by expressing bacterial lysine feedback-insensitive aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS) to enhance Lys biosynthesis; through RNA interference of rice lysine ketoglutaric acid reductase/saccharopine dehydropine dehydrogenase (LKR/SDH) to down-regulate its catabolism; and by combined expression of AK and DHPS and interference of LKR/SDH to achieve both metabolic effects. In these transgenic plants, free Lys levels increased up to ~12-fold in leaves and ~60-fold in seeds, substantially greater than the 2.5-fold increase in transgenic rice seeds reported by the only previous related study. To better understand the metabolic regulation of Lys accumulation in rice, metabolomic methods were employed to analyse the changes in metabolites of the Lys biosynthesis and catabolism pathways in leaves and seeds at different stages. Free Lys accumulation was mainly regulated by its biosynthesis in leaves and to a greater extent by catabolism in seeds. The transgenic plants did not show observable changes in plant growth and seed germination nor large changes in levels of asparagine (Asn) and glutamine (Gln) in leaves, which are the major amino acids transported into seeds. Although Lys was highly accumulated in leaves of certain transgenic lines, a corresponding higher Lys accumulation was not observed in seeds, suggesting that free Lys transport from leaves into seeds did not occur.

Improved nutritive quality and salt resistance in transgenic maize by simultaneously overexpression of a natural lysine-rich protein gene, SBgLR, and an ERF transcription factor gene, TSRF1

Maize (Zea mays L.), as one of the most important crops in the world, is deficient in lysine and tryptophan. Environmental conditions greatly impact plant growth, development and productivity. In this study, we used particle bombardment mediated co-transformation to obtain marker-free transgenic maize inbred X178 lines harboring a lysine-rich protein gene SBgLR from potato and an ethylene responsive factor (ERF) transcription factor gene, TSRF1, from tomato. Both of the target genes were successfully expressed and showed various expression levels in different transgenic lines. Analysis showed that the protein and lysine content in T1 transgenic maize seeds increased significantly. Compared to non-transformed maize, the protein and lysine content increased by 7.7% to 24.38% and 8.70% to 30.43%, respectively. Moreover, transgenic maize exhibited more tolerance to salt stress. When treated with 200 mM NaCl for 48 h, both non-transformed and transgenic plant leaves displayed wilting and losing green symptoms and dramatic increase of the free proline contents. However, the degree of control seedlings was much more serious than that of transgenic lines and much more increases of the free proline contents in the transgenic lines than that in the control seedlings were observed. Meanwhile, lower extent decreases of the chlorophyll contents were detected in the transgenic seedlings. Quantitative RT-PCR was performed to analyze the expression of ten stress-related genes, including stress responsive transcription factor genes, ZmMYB59 and ZmMYC1, proline synthesis related genes, ZmP5CS1 and ZmP5CS2, photosynthesis-related genes, ZmELIP, ZmPSI-N, ZmOEE, Zmrbcs and ZmPLAS, and one ABA biosynthesis related gene, ZmSDR. The results showed that with the exception of ZmP5CS1 and ZmP5CS2 in line 9-10 and 19-11, ZmMYC1 in line 19-11 and ZmSDR in line 19-11, the expression of other stress-related genes were inhibited in transgenic lines under normal conditions. After salt treatment, the expressions of the ten stress-related genes were significantly induced in both wild-type (WT) and transgenic lines. However, compared to WT, the increases of ZmP5CS1 in all these three transgenic lines and ZmP5CS2 in line 9-10 were less than WT plants. This study provides an effective approach of maize genetic engineering for improved nutritive quality and salt tolerance.

Identification and characterization of lysine-rich proteins and starch biosynthesis genes in the opaque2 mutant by transcriptional and proteomic analysis

BACKGROUND

The opaque2 mutant is valuable for producing maize varieties with enhanced nutritional value. However, the exact mechanisms by which it improves protein quality and creates a soft endosperm texture are unclear. Given the importance of improving nutritional quality in grain crops, a better understanding of the physiological basis for these traits is necessary.

RESULTS

In this study, we combined transcript profiling and proteomic analysis to better understand which genes and proteins are altered by opaque2 in the W64A inbred line. These analyses showed that the accumulation of some lysine-rich proteins, such as sorbitol dehydrogenase and glyceraldehyde3-phosphate dehydrogenase, was increased in mature kernels and may contribute substantially to the lysine content of opaque2 endosperm. Some defense proteins such as beta-glucosidase aggregating factor were strongly down regulated and may be regulated directly by opaque2. The mutant also had altered expression of a number of starch biosynthesis genes and this was associated with a more highly crystalline starch.

CONCLUSIONS

The results of these studies revealed specific target genes that can be investigated to further improve nutritional quality and agronomic performance of high lysine maize lines, particularly those based on the presence of the opaque2 mutation. Alteration of amylopectin branching patterns in opaque2 starch could contribute to generation of the soft, starchy endosperm.

Fortifying plants with the essential amino acids lysine and methionine to improve nutritional quality

Humans, as well as farm animals, cannot synthesize a number of essential amino acids, which are critical for their survival. Hence, these organisms must obtain these essential amino acids from their diets. Cereal and legume crops, which represent the major food and feed sources for humans and livestock worldwide, possess limiting levels of some of these essential amino acids, particularly Lys and Met. Extensive efforts were made to fortify crop plants with these essential amino acids using traditional breeding and mutagenesis. However, aside from some results obtained with maize, none of these approaches was successful. Therefore, additional efforts using genetic engineering approaches concentrated on increasing the synthesis and reducing the catabolism of these essential amino acids and also on the expression of recombinant proteins enriched in them. In the present review, we discuss the basic biological aspects associated with the synthesis and accumulation of these amino acids in plants and also describe recent developments associated with the fortification of crop plants with essential amino acids by genetic engineering approaches.

Control limits for accumulation of plant metabolites: brute force is no substitute for understanding

Which factors limit metabolite accumulation in plant cells? Are theories on flux control effective at explaining the results? Many biotechnologists cling to the idea that every pathway has a rate limiting enzyme and target such enzymes first in order to modulate fluxes. This often translates into large effects on metabolite concentration, but disappointing small increases in flux. Rate limiting enzymes do exist, but are rare and quite opposite to what predicted by biochemistry. In many cases however, flux control is shared among many enzymes. Flux control and concentration control can (and must) be distinguished and quantified for effective manipulation. Flux control for several 'building blocks' of metabolism is placed on the demand side, and therefore increasing demand can be very successful. Tampering with supply, particularly desensitizing supply enzymes, is usually not very effective, if not dangerous, because supply regulatory mechanisms function to control metabolite homeostasis. Some important, but usually unnoticed, metabolic constraints shape the responses of metabolic systems to manipulation: mass conservation, cellular resource allocation and, most prominently, energy supply, particularly in heterotrophic tissues. The theoretical basis for this view shall be explored with recent examples gathered from the manipulation of several metabolites (vitamins, carotenoids, amino acids, sugars, fatty acids, polyhydroxyalkanoates, fructans and sugar alcohols). Some guiding principles are suggested for an even more successful engineering of plant metabolism.

Overproduction of recombinant proteins in plants

Recombinant protein production in microbial hosts and animal cell cultures has revolutionized the pharmaceutical and industrial enzyme industries. Plants as alternative hosts for the production of recombinant proteins are being actively pursued, taking advantage of their unique characteristics. The key to cost-efficient production in any system is the level of protein accumulation, which is inversely proportional to the cost. Levels of up to 5 g/kg biomass have been obtained in plants, making this production system competitive with microbial hosts. Increasing protein accumulation at the cellular level by varying host, germplasm, location of protein accumulation, and transformation procedure is reviewed. At the molecular level increased expression by improving transcription, translation and accumulation of the protein is critically evaluated. The greatest increases in protein accumulation will occur when various optimized parameters are more fully integrated with each other. Because of the complex nature of plants, this will take more time and effort to accomplish than has been the case for the simpler unicellular systems. However the potential for plants to become one of the major avenues for protein production appears very promising.

High-value products from transgenic maize

Maize (also known as corn) is a domesticated cereal grain that has been grown as food and animal feed for tens of thousands of years. It is currently the most widely grown crop in the world, and is used not only for food/feed but also to produce ethanol, industrial starches and oils. Maize is now at the beginning of a new agricultural revolution, where the grains are used as factories to synthesize high-value molecules. In this article we look at the diversity of high-value products from maize, recent technological advances in the field and the emerging regulatory framework that governs how transgenic maize plants and their products are grown, used and traded.

Compositional and transcriptional analyses of reduced zein kernels derived from the opaque2 mutation and RNAi suppression

Corn protein is largely made up of a group of nutritionally limited storage proteins known as zein. The reduction of zein can be achieved by a transcriptional mutation, opaque2 (o2), or a transgene targeting zein through RNA interference (RNAi). Zein reduction results in an increase of more nutritionally balanced non-zein proteins, and therefore enhance the overall quality of corn protein. In this study, the composition of mature kernels and the transcriptional profile of developing kernels of these two types of zein reduced kernels were compared. Both zein reduced kernels contained higher levels of lysine and tryptophan and free amino acids were 10-20-folds more abundant than the wild-type counterpart. We also found that free lysine contributed partially to the increased lysine in o2 kernels while protein-bound lysine was mainly responsible for the increased lysine in transgenic zein reduction (TZR) kernels. Although they had relatively similar gene expression patterns in developing endosperm, o2 kernels had greater transcriptional changes than TZR kernels in general. A number of transcripts that were specifically down-regulated in o2 were identified. Many promoter sequences of these transcripts contain putative O2 binding motifs, suggesting that their expression is directly regulated by O2.

High-lysine maize: the key discoveries that have made it possible

Forty-five years ago, a paper published by Mertz et al. (Science 145:279-280, 1964) initiated a revolution in the history of plant protein quality and affected dramatically the study of cereal crop storage proteins. The observation of the high lysine content of the endosperm of the opaque-2 (o2) maize mutant was a key factor in bringing about a new concept in the production of cereal seeds with a high nutritional value. It has been a long and very interesting road with astonishing results over these 45 years. We are now probably about to see the release of commercially engineered high-lysine maize lines. We have decided to pinpoint some key contributions to the science behind high-lysine plants and concentrated on the research done on maize, which is possibly the most complete and simple example to illustrate the advances achieved. However, studies on other plant species such as barley and model species such as tobacco are totally relevant and will be briefly addressed.

Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte

All crop species have been domesticated from their wild relatives, and geneticists are just now beginning to understand the consequences of artificial (human) selection on agronomic traits that are relevant today. The primary consequence is a basal loss of diversity across the genome, and an additional reduction in diversity for genes underlying traits targeted by selection. An understanding of attributes of the wild relatives may provide insight into target traits and valuable allelic variants for modern agriculture. This is especially true for maize (Zea mays ssp. mays), where its wild ancestor, teosinte (Z. mays ssp. parviglumis), is so strikingly different than modern maize. One obvious target of selection is the size and composition of the kernel. We evaluated kernel characteristics, kernel composition, and zein profiles for a diverse set of modern inbred lines, teosinte accessions, and landraces, the intermediate between inbreds and teosinte. We found that teosinte has very small seeds, but twice the protein content of landraces and inbred lines. Teosinte has a higher average alpha zein content (nearly 89% of total zeins as compared to 72% for inbred lines and 76% for landraces), and there are many novel alcohol-soluble proteins in teosinte relative to the other two germplasm groups. Nearly every zein protein varied in abundance among the germplasm groups, especially the methionine-rich delta zein protein, and the gamma zeins. Teosinte and landraces harbor phenotypic variation that will facilitate genetic dissection of kernel traits and grain quality, ultimately leading to improvement via traditional plant breeding and/or genetic engineering.

Tissue-print immunodetection of transgene products in endosperm for high-throughput screening of seeds

This method allows high-throughput qualitative screening to identify seeds containing a transgene product in endosperm tissue. It is particularly useful for determining genetic segregation ratios or identifying seeds to be advanced in a breeding program. Tissue printing is used to avoid time-consuming extraction steps. Antibody-based detection of the transgene product makes this method suitable to any transgene product for which a specific antibody is available. It is possible to screen thousands of seeds per week using this method.

Genetic manipulation of lysine catabolism in maize kernels

In plants, lysine catabolism is thought to be controlled by a bifunctional enzyme, lysine ketoglutarate reductase/saccharopine dehydrogenase (LKR/SDH). Lysine is converted to saccharopine, through condensation with alpha-ketoglutarate, by LKR, and subsequently to glutamate and alpha-aminoadipate-delta-semialdehyde by SDH. To investigate lysine catabolism in maize kernels, we generated transgenic plants with suppressed LKR/SDH activity in either endosperm or embryo. We found that the suppression of LKR/SDH in endosperm induced an increase in free lysine in developing endosperm, which peaked at 32 days after pollination. At later stages of kernel development, most of the free lysine was found in the embryo along with an elevated level of saccharopine. By combining endosperm LKR/SDH suppression with embryo LKR/SDH suppression through crosses, the saccharopine level in embryo was reduced and resulted in higher lysine accumulation in mature kernels. These results reveal new insights into how free lysine level is regulated and distributed in developing maize kernels and demonstrate the possibility of engineering high lysine corn via the suppression of lysine catabolism.

Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein

The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS, we expressed, purified, kinetically characterized the protein, and solved its X-ray crystal structure. The cDHDPS enzyme has a fold and overall structure that is highly similar to other DHDPS proteins. A noteworthy feature of the active site is the evidence that the catalytic lysine residue forms a Schiff base adduct with pyruvate. Analyses of the cDHDPS structure in the vicinity of the putative binding site for S-lysine revealed that the allosteric binding site in the Escherichia coli DHDPS protein does not exist in cDHDPS due to three non-conservative amino acids substitutions, and this is likely why cDHDPS is not feedback inhibited by lysine.

Modifying lysine biosynthesis and catabolism in corn with a single bifunctional expression/silencing transgene cassette

Although it is one of the major crops in the world, corn has poor nutritional quality for human and animal consumption due to its low lysine content. Here, we report a method of simultaneous expression of a deregulated lysine biosynthetic enzyme, CordapA, and reduction of a bifunctional lysine degradation enzyme, lysine-ketoglutarate reductase/saccharophine dehydrogenase (LKR/SDH), in transgenic corn plants by a single transgene cassette. This is accomplished by inserting an inverted-repeat sequence targeting the maize LKR/SDH gene into an intron of a transgene cassette that expresses CordapA. This combination of LKR/SDH silencing and CordapA expression led to the accumulation of free lysine to over 4000 p.p.m. in transgenic corn grain, compared to less than 100 p.p.m. in wild-type controls. This intron-embedded silencing cassette design reduces the number of transgene cassettes needed in transgenic approaches for manipulating metabolic pathways that sometimes require expression of one gene and silencing of another.

High-lysine corn generated by endosperm-specific suppression of lysine catabolism using RNAi

Because of the limited lysine content in corn grain, synthetic lysine supplements are added to corn meal-based rations for animal feed. The development of biotechnology, combined with the understanding of plant lysine metabolism, provides an alternative solution for increasing corn lysine content through genetic engineering. Here, we report that by suppressing lysine catabolism, transgenic maize kernels accumulated a significant amount of lysine. This was achieved by RNA interference (RNAi) through the endosperm-specific expression of an inverted-repeat (IR) sequence targeting the maize bifunctional lysine degradation enzyme, lysine-ketoglutarate reductase/saccharopine dehydrogenase (ZLKR/SDH). Although plant-short interfering RNA (siRNA) were reported to lack tissue specificity due to systemic spreading, we confirmed that the suppression of ZLKR/SDH in developing transgenic kernels was restricted to endosperm tissue. Furthermore, results from our cloning and sequencing of siRNA suggested the absence of transitive RNAi. These results support the practical use of RNAi for plant genetic engineering to specifically target gene suppression in desired tissues without eliciting systemic spreading and the transitive nature of plant RNAi silencing.

Impact of genetics and environment on nutritional and metabolite components of maize grain

The Organization for Economic Co-operation and Development (OECD) recommends the measurement of specific plant components for compositional assessments of new biotechnology-derived crops. These components include proximates, nutrients, antinutrients, and certain crop-specific secondary metabolites. A considerable literature on the natural variability of these components in conventional and biotechnology-derived crops now exists. Yet the OECD consensus also suggests measurements of any metabolites that may be directly associated with a newly introduced trait. Therefore, steps have been initiated to assess natural variation in metabolites not typically included in the OECD consensus but which might reasonably be expected to be affected by new traits addressing, for example, nutritional enhancement or improved stress tolerance. The compositional study reported here extended across a diverse genetic range of maize hybrids derived from 48 inbreds crossed against two different testers. These were grown at three different, but geographically similar, locations in the United States. In addition to OECD analytes such as proximates, total amino acids and free fatty acids, the levels of free amino acids, sugars, organic acids, and selected stress metabolites in harvested grain were assessed. The major free amino acids identified were asparagine, aspartate, glutamate, and proline. The major sugars were sucrose, glucose, and fructose. The most predominant organic acid was citric acid, with only minor amounts of other organic acids detected. The impact of genetic background and location was assessed for all components. Overall, natural variation in free amino acids, sugars, and organic acids appeared to be markedly higher than that observed for the OECD analytes.

Impact of genetics and environment on nutritional and metabolite components of maize grain

The Organization for Economic Co-operation and Development (OECD) recommends the measurement of specific plant components for compositional assessments of new biotechnology-derived crops. These components include proximates, nutrients, antinutrients, and certain crop-specific secondary metabolites. A considerable literature on the natural variability of these components in conventional and biotechnology-derived crops now exists. Yet the OECD consensus also suggests measurements of any metabolites that may be directly associated with a newly introduced trait. Therefore, steps have been initiated to assess natural variation in metabolites not typically included in the OECD consensus but which might reasonably be expected to be affected by new traits addressing, for example, nutritional enhancement or improved stress tolerance. The compositional study reported here extended across a diverse genetic range of maize hybrids derived from 48 inbreds crossed against two different testers. These were grown at three different, but geographically similar, locations in the United States. In addition to OECD analytes such as proximates, total amino acids and free fatty acids, the levels of free amino acids, sugars, organic acids, and selected stress metabolites in harvested grain were assessed. The major free amino acids identified were asparagine, aspartate, glutamate, and proline. The major sugars were sucrose, glucose, and fructose. The most predominant organic acid was citric acid, with only minor amounts of other organic acids detected. The impact of genetic background and location was assessed for all components. Overall, natural variation in free amino acids, sugars, and organic acids appeared to be markedly higher than that observed for the OECD analytes.

Fractionation of zein by size exclusion chromatography

Zein is a group of alcohol-soluble corn proteins, which consists of several individual proteins. A single-step gel filtration chromatography method was developed to fractionate individual zeins from ethanol extracts of whole corn. A Superdex prep 75 column was used with different mobile phases to fractionate the zeins, which were analyzed by SDS-PAGE and UV spectrophotometry. With 70% aqueous ethanol as the mobile phase, fractions containing a mixture of alpha-zein/beta-zein and alpha-zein/delta-zein were obtained. With ammonium bicarbonate added to the 70% ethanol mobile phase, it was possible to obtain beta-zein and delta-zein fractions devoid of other proteins. However, all fractions containing alpha-zein also contained minor amounts of delta-zein and/or beta-zein. Almost all fractions also contained non-protein impurities.

Altered expression of plant lysyl tRNA synthetase promotes tRNA misacylation and translational recoding of lysine

The Arabidopsis thaliana lysyl tRNA synthetase (AtKRS) structurally and functionally resembles the well-characterized prokaryotic class IIb KRS, including the propensity to aminoacylate tRNA(Lys) with suboptimal identity elements, as well as non-cognate tRNAs. Transient expression of AtKRS in carrot cells promotes aminoacylation of such tRNAs in vivo and translational recoding of lysine at nonsense codons. Stable expression of AtKRS in Zea mays causes translational recoding of lysine into zeins, significantly enriching the lysine content of grain.

Genetically modified organisms in the United States: implementation, concerns, and public perception

We examine the state of biotechnology with respect to genetically modified (GM) organisms in agriculture. Our focus is on the USA, where there has been significant progress and implementation but where, to date, the matter has drawn little attention. GM organisms are the result of lateral gene transfers, the transfer of genes from one species to another, or sometimes, from one kingdom to another. The introduction of foreign genes makes some people very uncomfortable, and a small group of activists have grave concerns about the technology. Attempts by activists to build concern in the general public have garnered little attention; however, the producers of GM organisms have responded to their concerns and established extensive testing programs to be applied to each candidate organism that is produced. In the meantime, GM varieties of corn, cotton, soybean and rapeseed have been put into agricultural production and are now extensively planted. These crops, and the other, newer GM crops, have produced no problems and have pioneered a silent agricultural revolution in the USA.

Enhancement of essential amino acid contents in crops by genetic engineering and protein design

The importance and urgency of providing humans and animals with quality proteins are reflected in the growing scientific and industrial interest in augmenting the nutritive value of the world's protein sources. Such nutritive value is determined by the protein content in 'essential amino acids', those that cannot be synthesized de novo and that must be supplied from the diet. It is the object of this review to discuss recent advances in the genetic modification of crops that aim to provide enhanced quantities of essential amino acids.

High lysine and high tryptophan transgenic maize resulting from the reduction of both 19- and 22-kD alpha-zeins

The major maize seed storage proteins, zeins, are deficient in lysine and tryptophan content, which contribute to the poor nutritional quality of corn. Whether through the identification of mutations or genetic engineering, kernels with reduced levels of zein proteins have been shown to have increased levels of lysine and tryptophan. It has been hypothesized that these increases are due to the reduction of lysine-poor zeins and a pleiotropic increase in the lysine-rich non-zein proteins. By transforming maize with constructs expressing chimeric double-stranded RNA, kernels derived from stable transgenic plants displayed significant declines in the accumulation of both 19- and 22-kD alpha-zeins, which resulted in higher lysine and tryptophan content than previously reported for kernels with reduced zein levels. The observation that lysine and tryptophan content is correlated with the protein levels measured in transgenic maize kernels is consistent with the hypothesis that a pleiotropic increase in non-zein proteins is contributing to an improved amino acid balance. In addition, a large increase in accumulation of free amino acids, consisting predominantly of asparagine, aspartate and glutamate, was observed in the zein reduction kernels.