Corn seeds as bioreactors for the production of phytase in the feed industry

Synthetic biology and artificial intelligence in crop improvement

Synthetic biology plays a pivotal role in improving crop traits and increasing bioproduction through the use of engineering principles that purposefully modify plants through "design, build, test, and learn" cycles, ultimately resulting in improved bioproduction based on an input genetic circuit (DNA, RNA, and proteins). Crop synthetic biology is a new tool that uses circular principles to redesign and create innovative biological components, devices, and systems to enhance yields, nutrient absorption, resilience, and nutritional quality. In the digital age, artificial intelligence (AI) has demonstrated great strengths in design and learning. The application of AI has become an irreversible trend, with particularly remarkable potential for use in crop breeding. However, there has not yet been a systematic review of AI-driven synthetic biology pathways for plant engineering. In this review, we explore the fundamental engineering principles used in crop synthetic biology and their applications for crop improvement. We discuss approaches to genetic circuit design, including gene editing, synthetic nucleic acid and protein technologies, multi-omics analysis, genomic selection, directed protein engineering, and AI. We then outline strategies for the development of crops with higher photosynthetic efficiency, reshaped plant architecture, modified metabolic pathways, and improved environmental adaptability and nutrient absorption; the establishment of trait networks; and the construction of crop factories. We propose the development of SMART (self-monitoring, adapted, and responsive technology) crops through AI-empowered synthetic biotechnology. Finally, we address challenges associated with the development of synthetic biology and offer potential solutions for crop improvement.

Production of fungal phytases in solid state fermentation and potential biotechnological applications

Phytases are important enzymes used for eliminating the anti-nutritional properties of phytic acid in food and feed ingredients. Phytic acid is major form of organic phosphorus stored during seed setting. Monogastric animals cannot utilize this phytate-phosphorus due to lack of necessary enzymes. Therefore, phytic acid excretion is responsible for mineral deficiency and phosphorus pollution. Phytases have been reported from diverse microorganisms, however, fungal phytases are preferred due to their unique properties. Aspergillus species are the predominant producers of phytases and have been explored widely as compared to other fungi. Solid-state fermentation has been studied as an economical process for the production of phytases to utilize various agro-industrial residues. Mixed substrate fermentation has also been reported for the production of phytases. Physical and chemical parameters including pH, temperature, and concentrations of media components have significantly affected the production of phytases in solid state fermentation. Fungi produced high levels of phytases in solid state fermentation utilizing economical substrates. Optimization of culture conditions using different approaches has significantly improved the production of phytases. Fungal phytases are histidine acid phosphatases exhibiting broad substrate specificity, are relatively thermostable and protease-resistant. These phytases have been found effective in dephytinization of food and feed samples with concomitant liberation of minerals, sugars and soluble proteins. Additionally, they have improved the growth of plants by increasing the availability of phosphorus and other minerals. Furthermore, phytases from fungi have played an important roles in bread making, semi-synthesis of peroxidase, biofuel production, production of myo-inositol phosphates and management of environmental pollution. This review article describes the production of fungal phytases in solid state fermentation and their biotechnological applications.

Genetic engineering of complex feed enzymes into barley seed for direct utilization in animal feedstuff

Currently, feed enzymes are primarily obtained through fermentation of fungi, bacteria, and other microorganisms. Although the manufacturing technology for feed enzymes has evolved rapidly, the activities of these enzymes decline during the granulating process and the cost of application has increased over time. An alternative approach is the use of genetically modified plants containing complex feed enzymes for direct utilization in animal feedstuff. We co-expressed three commonly used feed enzymes (phytase, β-glucanase, and xylanase) in barley seeds using the Agrobacterium-mediated transformation method and generated a new barley germplasm. The results showed that these enzymes were stable and had no effect on the development of the seeds. Supplementation of the basal diet of laying hens with only 8% of enzyme-containing seeds decreased the quantities of indigestible carbohydrates, improved the availability of phosphorus, and reduced the impact of animal production on the environment to an extent similar to directly adding exogenous enzymes to the feed. Feeding enzyme-containing seeds to layers significantly increased the strength of the eggshell and the weight of the eggs by 10.0%-11.3% and 5.6%-7.7% respectively. The intestinal microbiota obtained from layers fed with enzyme-containing seeds was altered compared to controls and was dominated by Alispes and Rikenella. Therefore, the transgenic barley seeds produced in this study can be used as an ideal feedstuff for use in animal feed.

Ornamental cabbage (Brassica oleracea var. acephala) responses to phytase enzyme purified from Lactobacillus coryniformis application

In order to increase the quality and yield of ornamental plants, especially potted ornamental plants, it is necessary to enrich the physical properties of the growing medium and to ensure the continuity of the growing medium. In order to achieve this, organic substances that create a serious cost in ornamental plant cultivation are added to the growing medium. This study was planned to assess the role of inoculation of different levels in the seeds and soaking times of purified phytase, on the plant growth and ornamental plant decorative values in ornamental cabbage plants under nutrient limiting condition in greenhouse. Different doses (E₀ : 0 EU, E₁ : 5 EU, E₂ : 10 EU), soaking times (W₁₅ : 15 min, W₃₀ : 30 min, W₆₀ : 60 min), and their combinations (W₁₅ + E₀ , W₁₅ + E₁ , W₁₅ + E₂ , W₃₀ + E₀ , W₃₀ + E₁ , W₃₀ + E₂ , W₆₀ + E₀ , W₆₀ + E₁ , W₆₀ + E₂ ) of phytase enzyme purified and isolated from the Lactobacillus coryniformis were applied to ornamental cabbage seeds, and they were sown in plug trays filled with appropriate growing medium. Seedlings were planted in plastic pots during their period when the seedlings had four to five true leaves. Treatments of phytase enzyme purified and isolated from the microorganism generally improved the observed parameters. The application of, especially, the highest level of phytase enzyme doses increased the plant height, main stem height, and stem diameter of ornamental cabbage as compared to control (E₀ treatment: distilled water). While the highest number of leaves per plant was obtained at E₁ and E₂ application doses and W₃₀ and W₆₀ soaking times; the highest stem diameter was obtained at E₂ application doses and W₃₀ and W₆₀ soaking times. The present study clarified that the purified phytase enzyme can increase ornamental cabbage quality at the appropriate concentration and soaking time and is a promising biotechnology material for agricultural applications, and especially in different ornamental plant species.

Safety assessment of phytase transgenic maize 11TPY001 by 90-day feeding study in rats

11TPY001 is a transgenic maize that expresses the Aspergillus niger phyA2 gene which could significantly improve phosphorus bioavailability in monogastric animals. The present study was conducted to investigate the potential health effects of phytase transgenic maize 11TPY001 through a 90-day subchronic rodent feeding study. Maize grains from 11TPY001 or its parental counterpart maize OSL963 were incorporated into rodent diets at 12.5%, 25% and 50% concentrations by mass and administered to Sprague-Dawley rats (n = 10/sex/group) for 90 days. An additional control group of rats (n = 10/sex/group) were fed with common maize Zhengdan958 diets at 50% by mass. All formulated diets were nutritionally balanced. Body weights, food intake, hematology, serum chemistry, absolute and relative organ weights were measured, and gross as well as microscopic pathology were examined. Compared with rats fed OSL963 maize and the common maize diet groups, no adverse diet-related differences were observed in rats fed 11TPY001 maize diets with respect to clinical signs of toxicity, body weight/gain, food consumption/efficiency, hematology, clinical chemistry, organ weights, and gross and microscopic pathology. Under the conditions of this study, the results indicated that 11TPY001 did not cause any treatment related adverse effects in rats compared with its non-transgenic parental maize OSL963.

Safety evaluation of BPL9K-4 rice in a subchronic rodent feeding study

In the present study, a new genetically modified rice producing phytase-lactoferricin fusion protein, BPL9K-4, was evaluated for safety in a 90-day rat feeding study. Rats were fed rodent diets formulated with BPL9K-4 rice, and were compared with rats fed diets formulated with its corresponding non-transgenic parental rice 9 K, commercially available non-transgenic rice Weiyou64, and a basal diet. BPL9K-4 and 9 K rice were formulated into diets at concentrations of 15%, 30% and 60%, and Weiyou64 common rice was added to diets at concentration of 60%. AIN93G diet was set as a basal-diet control. Diets of all groups were fed to rats (10/sex/group) for 90 days. Compared with rats in the 9 K, Weiyou64 and the basal-diet group, rats fed the BPL9K-4 diet did not show any treatment-related adverse effects on mortality, body weights, feed consumption, clinical chemistry, hematology, organ weights and gross and microscopic pathology. Under the conditions of this study, the genetically modified BPL9K-4 diets did not cause any toxicologically significant effects in rats following 90 days of dietary administration as compared with rats fed diets with the corresponding non-transgenic control diet and the basal-diet group. The results indicated that BPL9K-4 rice is as safe as its conventional comparators.

Purification of the phytase enzyme from Lactobacillus plantarum: The effect on pansy growth and macro-micro element content

In the present study, the phytase enzyme was purified from Lactobacillus plantarum with a 3.08% recovery, 9.57-purification fold, and with a specific activity of 278.82 EU/mg protein. Then, the effects of the 5 EU and 10 EU purified phytase was determined on the plant growth, quality, the macro-micro nutrient content of pansy (Viola × wittrockiana), which is of great importance in ornamental plants industry. The research was established under greenhouse conditions with natural light in 2017. The pansy seeds were coated with phytase enzyme solution, sown in a peat environment, and transferred to pots at the seedling period. In general, the 5 EU and 10 EU applications increase plant height, the number of leaves per plant, the number of side branches per plant, and flower height parameters compared to control. Also, micro- and macronutrient values in soil and plant samples were examined. According to the results, the phytase application on pansy cultivation positively affected the properties and yielded high quality of plants.

Synthesis of Seed-Specific Bidirectional Promoters for Metabolic Engineering of Anthocyanin-Rich Maize

Tissue-specific promoters play an important role in plant molecular farming. Here, we describe a strategy to modify the tissue specificity of a maize embryo-specific bidirectional promoter PZmBD1. Six types of cis-elements, i.e. RY repeats (R), GCN4 (G), the prolamin box (P), Skn-1 (S), and the ACGT and AACA (A) motifs, were collected and fused to PZmBD1 to generate eight chimeric putative bidirectional promoters. Qualitative and quantitative analysis of reporter genes driven by the promoters showed that two promoters exhibited high seed-specific bidirectional activity in maize transient and stable transformed systems. The stronger one was chosen and fused to the intergenic region of two gene clusters consisting of four anthocyanin biosynthesis-related genes (ZmBz1, ZmBz2, ZmC1 and ZmR2) and seven reporter genes, resulting in the first embryo and endosperm anthocyanin-rich purple maize. Anthocyanin analysis showed that the total anthocyanin content reaches 2,910 mg kg-1 DW in transgenic maize and cyanidin is the major anthocyanin in transgenic maize, as in natural varieties. The expression profile analysis of endogenous genes showed that the anthocyanin biosynthesis pathway was activated by two transgenic transcription factor genes ZmC1 and ZmR2. Our results indicate that both the modification strategy and these functionally characterized tissue-specific bidirectional promoters generated could be used for genetic research and development of plant biotechnology products. The anthocyanin-rich purple maize could provide economic natural colorants for the food and beverage industry, and valuable germplasm for developing anthocyanin-rich fresh corn.

Proteomic analysis of phytase transgenic and non-transgenic maize seeds

Proteomics has become a powerful technique for investigating unintended effects in genetically modified crops. In this study, we performed a comparative proteomics of the seeds of phytase-transgenic (PT) and non-transgenic (NT) maize using 2-DE and iTRAQ techniques. A total of 148 differentially expressed proteins (DEPs), including 106 down-regulated and 42 up-regulated proteins in PT, were identified. Of these proteins, 32 were identified through 2-DE and 116 were generated by iTRAQ. It is noteworthy that only three proteins could be detected via both iTRAQ and 2-DE, and most of the identified DEPs were not newly produced proteins but proteins with altered abundance. These results indicated that many DEPs could be detected in the proteome of PT maize seeds and the corresponding wild type after overexpression of the target gene, but the changes in these proteins were not substantial. Functional classification revealed many DEPs involved in posttranscriptional modifications and some ribosomal proteins and heat-shock proteins that may generate adaptive effects in response to the insertion of exogenous genes. Protein-protein interaction analysis demonstrated that the detected interacting proteins were mainly ribosomal proteins and heat-shock proteins. Our data provided new information on such unintended effects through a proteomic analysis of maize seeds.

Barley HvPAPhy_a as transgene provides high and stable phytase activities in mature barley straw and in grains

The phytase purple acid phosphatase (HvPAPhy_a) expressed during barley seed development was evaluated as transgene for overexpression in barley. The phytase was expressed constitutively driven by the cauliflower mosaic virus 35S-promoter, and the phytase activity was measured in the mature grains, the green leaves and in the dry mature vegetative plant parts left after harvest of the grains. The T2 -generation of HvPAPhy_a transformed barley showed phytase activity increases up to 19-fold (29 000 phytase units (FTU) per kg in mature grains). Moreover, also in green leaves and mature dry straw, phytase activities were increased significantly by 110-fold (52 000 FTU/kg) and 57-fold (51 000 FTU/kg), respectively. The HvPAPhy_a-transformed barley plants with high phytase activities possess triple potential utilities for the improvement of phosphate bioavailability. First of all, the utilization of the mature grains as feed to increase the release of bio-available phosphate and minerals bound to the phytate of the grains; secondly, the utilization of the powdered straw either directly or phytase extracted hereof as a supplement to high phytate feed or food; and finally, the use of the stubble to be ploughed into the soil for mobilizing phytate-bound phosphate for plant growth.

Development of a Rapid Immunochromatographic Lateral Flow Device Capable of Differentiating Phytase Expressed from Recombinant Aspergillus niger phyA2 and Genetically Modified Corn

Phytase is a phosphohydrolase considered highly specific for the degradation of phytate to release bound phosphorus for animal consumption and aid in the reduction of environmental nutrient loading. New sources of phytase have been sought that are economically and efficiently productive including the construction of genetically modified (GM) phytase products designed to bypass the costs associated with feed processing. Four monoclonal antibodies (EH10a, FA7, AF9a, and CC1) raised against recombinant Aspergillus niger phyA2 were used to develop a highly specific and sensitive immunochromatographic lateral flow device for rapid detection of transgenic phytase, such as in GM corn. Antibodies sequentially paired and tested along lateral flow strips showed that the EH10a-FA7 antibody pair was able to detect the recombinant yeast-phytase at 5 ng/mL, whereas the AF9a-CC1 antibody pair to GM phytase corn was able to detect at 2 ng/mL. Concurrent to this development, evidence was revealed which suggests that antibody binding sites may be glycosylated.

Identification and characterization of promoters specifically and strongly expressed in maize embryos

The use of maize seeds as bioreactors has several advantages for the production of recombinant proteins in plant biotechnology, but available embryo-specific and strong promoters are limited. Here, we describe a genome-scale microarray-based approach to identify embryo-specifically and strongly expressed genes and their promoters in maize. We identified 28 embryo-preferred and abundantly expressed genes based on our microarray data. These embryo-preferred genes were further analysed using the UniGene database and by quantitative reverse transcriptase-PCR leading to the identification of seven genes (Zm.2098, Zm.13387, Zm.66589, Zm.85502, Zm.68129, Zm.3896 and Zm.2941) as embryo-specific genes with higher expression levels relative to maize globulin-1. The putative promoters of five embryo-specific genes (Zm.13387, Zm.66589, Zm.85502, Zm.3896 and Zm.2941) were isolated and all exhibited strong promoter activities when transiently expressed in maize embryos of 20 DAP. The embryo specificity and expression levels of the promoters of four genes (Zm.13387, Zm.85502, Zm.3896 and Zm.2941) were further examined in transgenic maize plants, revealing that they are strong promoters in embryos of all four developmental stages tested compared with reference globulin-1 promoter. Moreover, Zm.2941 and Zm.3896 promoters are stringently embryo-specific promoters, while Zm.85502 promoter is basically embryo specific yet wounding inducible in non-seed tissues, and Zm.13387 promoter is developmentally expressed in both embryo and aleurone with wounding-induced activity in non-seed tissues. Our study provides novel embryo-specific and strong promoters that are suitable for production of high-level recombinant proteins in maize embryos.