CN116768990B - Artificial intelligence auxiliary generated insecticidal protein - Google Patents
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Abstract
The application discloses an artificial intelligence-assisted insecticidal protein and application thereof, and belongs to the field of genetic engineering. The application is based on the structure prediction of an artificial intelligence algorithm, combines batch activity detection and screens to obtain a batch of novel insecticidal proteins. The insecticidal proteins have application value in the fields of preparing pesticides or cultivating genetically engineered plants.
Description
Technical Field
The application discloses an artificial intelligence-assisted insecticidal protein and application thereof, and belongs to the field of genetic engineering.
Background
Insecticidal proteins derived from bacillus thuringiensis are currently the proteins of interest commonly used in the development of transgenic crops and biopesticides. However, with the large-scale application of these commercial pesticides and insect-resistant crops, pests generally develop resistance to existing insecticidal proteins, and there is an urgent need to find or create new insecticidal proteins.
In recent years, spodoptera frugiperda is defined as a type of crop pest which affects crop planting in "a type of crop pest directory" formulated by agricultural rural areas according to the regulations for controlling crop pest. Spodoptera frugiperda (subject name: spodoptera frugiperda) belongs to the genus spodoptera of the family spodoptera, and larvae thereof can gnaw a large amount of gramineous crops such as rice, sugarcane and corn, and various crops such as asteraceae and cruciferae, so that serious economic loss is caused. The species is native to tropical areas of america and has strong migration ability, spodoptera frugiperda spreads to africa and asia countries from 2016, and appears in china in 2019, which causes huge agricultural losses. The major transgenic crop plants such as the united states were grown mainly using Cry1Fa, vip3Aa proteins to cultivate new varieties of corn and soybean for control of spodoptera frugiperda, however, due to the strong migration and rapid propagation characteristics of this insect, more and more resistant lines to Cry1Fa, vip3Aa have been found (motoreto J C, michel a P, silva Filho M C, silva n. Adaptive potential of fall armyworm (Lepidoptera: noctuidae) limits Bt trait durability in Brazil J, intelgr, pest manag, 2017, 8, 17). Thus, future spodoptera frugiperda resistant crop varieties are required to obtain novel insecticidal proteins that are completely different from Cry1Fa and Vip3 Aa.
The function of a protein in a cell is determined by its three-dimensional structure. However, it is time-consuming and laborious to determine the protein structure by experiment. With the development of artificial intelligence technology, protein structure prediction has made breakthrough progress. This provides new opportunities for massive research and creation of protein structures. The alpha field artificial intelligent network developed by google deep has given the three-dimensional structure of hundreds of thousands of proteins, including each protein which can be manufactured by human body, and the results are expected to bring more surprise to the fields of medicine and drug design. Although more accurate protein folding, ligand combination and other details have much space to be optimized, the method can realize the prediction of protein structure, experimental test, optimization improvement and finally generate new engineering functional protein by combining the mode of functional verification and screening of experimental layers through artificial intelligence algorithms of deep learning and neural networks.
Disclosure of Invention
In order to solve the problems, the application adopts the following technical scheme:
the application provides an artificial intelligence-assisted insecticidal protein, which is characterized in that the amino acid sequence of the protein is shown as any one of SEQ ID NO. 1 or SEQ ID NO. 7.
The application also provides a nucleic acid molecule which is characterized in that the nucleic acid molecule codes for the protein.
In some embodiments, the nucleotide sequence of the nucleic acid molecule encoding the SEQ ID NO. 1 protein is shown as SEQ ID NO. 11 and the nucleotide sequence of the nucleic acid molecule encoding the SEQ ID NO. 7 protein is shown as SEQ ID NO. 17.
The application also provides a vector, which is characterized by comprising the nucleic acid molecule.
The application also provides a recombinant cell, which is characterized in that the recombinant cell contains the nucleic acid molecule or the vector.
In some embodiments, the recombinant cell is a prokaryotic cell.
In some embodiments, the recombinant cell is an E.coli cell.
The application also provides application of the protein, the nucleic acid molecule, the vector and the recombinant cell in insect resistance or preparation of insect resistance preparations or cultivation of insect resistance plants.
In some embodiments, the insect-resistant agent is an agent that has insecticidal activity against Spodoptera frugiperda.
The application has the beneficial effects that: the application is based on the structure prediction of an artificial intelligent algorithm, combines batch activity detection and screening, obtains 2 novel spodoptera frugiperda insecticidal proteins with higher insecticidal activity, and can be used for developing biological pesticides or cultivating novel insect-resistant plants.
Drawings
FIG. 1 Structure-generated map of eCry1Gb.1Ig protein. D1, D2, D3 respectively identify three domains of the protein core insecticidal region; c identifies the C-terminal domain of the protein.
FIG. 2 shows the similarity analysis of the amino acid sequences of WBY-1 to WBY-10 and eCry1Gb.1Ig.
FIG. 3A structural generation of WBY-1 protein. D1, D2, D3 respectively identify three domains of the protein core insecticidal region; c identifies the C-terminal domain of the protein.
FIG. 4A structural generation of WBY-7 protein. D1, D2, D3 respectively identify three domains of the protein core insecticidal region; c identifies the C-terminal domain of the protein.
Detailed Description
The following definitions and methods are provided to better define the present application and to guide those of ordinary skill in the art in the practice of the present application. Unless otherwise indicated, terms are to be construed according to conventional usage by those of ordinary skill in the relevant art. All patent documents, academic papers, industry standards, and other publications cited herein are incorporated by reference in their entirety.
The following examples are illustrative of the application and are not intended to limit the scope of the application. Modifications and substitutions to methods, procedures, or conditions of the present application without departing from the spirit and nature of the application are intended to be within the scope of the present application. Examples follow conventional experimental conditions, such as the molecular cloning laboratory Manual of Sambrook et al (Sambrook J & Russell DW, molecular cloning: a laboratory manual, 2001), or conditions recommended by the manufacturer's instructions, unless otherwise indicated. Unless otherwise indicated, all chemical reagents used in the examples were conventional commercial reagents, and the technical means used in the examples were conventional means well known to those skilled in the art.
Example 1 Structure prediction and sequence Generation of novel proteins
eCry1Gb.1Ig is a chimeric Cry class Spodoptera frugiperda insecticidal protein obtained by taking Cry1Gb as a backbone and replacing the third domain with Cry1Ig, and has no cross-resistance to none of the commercialized Spodoptera frugiperda insecticidal proteins Cry1Fa, vip3Aa, cry1A.105/Cry2Ab (Chae H, wen Z, hootman T, et al eCry1Gb.1Ig, A Novel Chimeric Cry Protein with High Efficacy against Multiple Fall Armyworm (Spodoptera frugiperda) Strains Resistant to Different GM Traits [ J ]. Toxins (Basel), 2022, 14 (12)).
The present application uses ecry1gb.1ig protein as a template for structural analysis and fitting to form novel insecticidal proteins. Firstly, alpha Fold2 is used、RoseTTAFold on-line tool pre-domain assembly generates eCry1Gb.1Ig protein structure (see FIG. 1).
The protein sequences were then modeled, generated and designed using database and PROTEINGAN algorithm prediction tools (Repetka, D., jauniikis, V., karpus, L. Et al Expanding functional protein sequence spaces using generative adversarial networks Nat Mach Intel 3, 324-333 (2021)) based on deep learning, neural networks, and continued use of alpha Fold2、The rosettafid online tool generates protein structures. Since the third Domain of the core insecticidal region of ecry1gb.1ig (Domain 3, D3) plays an important role in the recognition of spodoptera frugiperda intestinal receptors, the D3 Domain sequence of the ecry1gb.1ig protein was kept unchanged when generating new protein sequences and structures, and only the D1 and D2 domains and the C-terminal Domain were generated by fitting.
The resulting sequence and the reference sequence were calculated and the high scoring sequence was selected (Chengxin Zhang, morgan Shine, anna Marie Pyle, yang Zhang. US-align: universal Structure Alignment of Proteins, nucleic Acids and Macromolecular Complexes. Nature Methods, 19: 1109-1115 (2022)). The protein structure was then generated using a Chimera 1.17 visual comparison.
Finally, 10 generated novel proteins are obtained, which are named WBY-1-WBY-10, and the sequences are shown as SEQ ID NO. 1-SEQ ID NO. 10. From the sequence similarity, the 10 proteins were very low in similarity to ecry1gb.1ig, and at the highest did not exceed 42% (fig. 2). This provides the basis for fundamentally creating new proteins.
Example 2 testing of the insecticidal Effect of the newly produced proteins
These protein entities were synthesized using a protein expression experimental system and tested for their insecticidal effect on spodoptera frugiperda.
The nucleic acid sequence encoding the sequence was first designed on the basis of the amino acid sequence (http:// www.friendbio.com/codon. Html. In the following in-line tool), with codons set to E.coli (K12 strain) preference and avoiding XhoI and HindIII cleavage sites. Obtaining the nucleic acid sequences (shown as SEQ ID NO. 11-SEQ ID NO. 20) for encoding WBY-1-WBY-10.
The nucleic acid molecules of the sequences are synthesized artificially, and are cloned together with the nucleic acid molecules of the encoding eCry1Gb.1Ig protein between sites of restriction enzymes XhoI and HindIII in a vector pET28a expression vector respectively to obtain a protein expression vector. The vector is transferred into an escherichia coli BL21 cell line and protein expression is carried out. The method comprises the following specific steps:
inoculating a single colony to 0.5 mL of LB liquid medium, culturing at 37 ℃ until the culture medium is turbid, adding IPTG (isopopyl-beta-D-thiohinging) into 100 uL bacterial liquid to a final concentration of 0.8 mM, simultaneously taking 100 uL bacterial liquid as negative control, continuously culturing 4 h, adding 25 uL loading buffer into 100 uL bacterial liquid for sample preparation electrophoresis, and comparing according to the negative control and the result induced by adding IPTG, and judging whether the expression exists. The remaining 20. 20 uL with expression was inoculated into 2 mL of LB liquid medium and cultured at 37 ℃ for 12 to 16 h as seed liquid, the seed liquid was inoculated into 250 mL of LB liquid medium again to an OD 600=0.5 to 0.6, IPTG (isopopyl- β -D-thiogaside) was then added to a concentration of 0.8 mM, and the culture was continued under the same conditions for 4 hours. The culture medium was centrifuged at 5000 g for 10 minutes to pellet E.coli cells, and the supernatant was discarded to collect the pellet. The precipitate was sonicated with 30mL of 20mM Tris-50mM NaCl buffer. After centrifugation, the supernatant was checked for the presence of recombinant proteins.
And further testing the insecticidal activity of the recombinant protein obtained by the experiment. The method comprises the following steps:
the biological assay is carried out by adopting a surface smearing method, firstly, about 1 mL of non-solidified artificial feed (about 0.5 g) is added into a 24-hole plate, the feed is paved on the bottom of the hole plate by slight shaking, after the feed is solidified, protein solutions (10 mu L/hole) with different concentrations are added, after the addition, the liquid medicine is evenly paved on the surface of the feed by slight shaking, and then the feed is naturally dried in a fume hood for 1 h. Experiment was performed with 6 gradient concentrations (0.01, 0.1, 0.5, 1, 2, 5. Mu.g/g) and a blank (buffer) with 24 joints per treatmentSpodoptera frugiperda) The initially hatched larvae (hatching time is 2-12 h), are repeatedly placed at the temperature of 25+/-2 ℃ for 14:10 (L: D) h of photoperiod, are cultured in an insect-raising room with the relative humidity of 50-70%, and are investigated for mortality after 7 days. To use writing brushLight touch of the larvae tail, the larvae were regarded as dead, and the larvae that did not develop 2 years old were also regarded as dead.
Mortality and corrected mortality were calculated according to the following formulas, and LC50 values were calculated using graphpad.
(equation 1)
(equation 2)
Test results show that the insecticidal activity of WBY-1 and WBY-7 in the 10 newly generated proteins exceeds that of eCry1Gb.1Ig, and the novel insecticidal protein with higher activity can be used for development of biological pesticides and insect-resistant transgenic plants. The insecticidal activity data of the proteins are shown in table 1. The protein structure of WBY-1 and WBY-7 are shown in FIGS. 3 and 4.
Table 1 insecticidal Activity of proteins
| Protein name | Amino acid sequence | Nucleic acid sequences | Insecticidal Activity (LC 50) 1 ） |
| eCry1Gb.1Ig | SEQ ID NO. 21 | SEQ ID NO. 22 | 0.09 |
| WBY-1 | SEQ ID NO. 1 | SEQ ID NO. 11 | 0.06* |
| WBY-2 | SEQ ID NO. 2 | SEQ ID NO. 12 | 0.69 |
| WBY-3 | SEQ ID NO. 3 | SEQ ID NO. 13 | 1.67 |
| WBY-4 | SEQ ID NO. 4 | SEQ ID NO. 14 | 1.07 |
| WBY-5 | SEQ ID NO. 5 | SEQ ID NO. 15 | 3.35 |
| WBY-6 | SEQ ID NO. 6 | SEQ ID NO. 16 | 1.13 |
| WBY-7 | SEQ ID NO. 7 | SEQ ID NO. 17 | 0.07* |
| WBY-8 | SEQ ID NO. 8 | SEQ ID NO. 18 | 0.35 |
| WBY-9 | SEQ ID NO. 9 | SEQ ID NO. 19 | 0.76 |
| WBY-10 | SEQ ID NO. 10 | SEQ ID NO. 20 | 0.89 |
". Times" indicate significant differences (α=0.05) relative to ecry1gb.1ig protein. 1: in μg/g.
While the application has been described in detail in the foregoing general description and with reference to specific embodiments thereof, it will be apparent to one skilled in the art that modifications and improvements can be made thereto. Accordingly, such modifications or improvements may be made without departing from the spirit of the application and are intended to be within the scope of the application as claimed.
Claims (8)
1. A protein is characterized in that the amino acid sequence of the protein is shown as SEQ ID NO. 1 or SEQ ID NO. 7.
2. A nucleic acid molecule encoding the protein of claim 1.
3. The nucleic acid molecule of claim 2, wherein the nucleotide sequence of the nucleic acid molecule is set forth in SEQ ID No. 11 or SEQ ID No. 17.
4. A vector comprising the nucleic acid molecule of any one of claims 2-3.
5. A recombinant cell comprising the nucleic acid molecule of any one of claims 2 to 3 or the vector of claim 4.
6. The recombinant cell of claim 5, wherein the recombinant cell is a prokaryotic cell.
7. The recombinant cell of claim 6, wherein the recombinant cell is an e.
8. Use of a protein according to claim 1, or a nucleic acid molecule according to any one of claims 2 to 3, or a vector according to claim 4, or a recombinant cell according to any one of claims 5 to 7, for combating spodoptera frugiperda, or for preparing an anti-spodoptera frugiperda preparation, or for growing an anti-spodoptera frugiperda plant.
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| CN116948046B (en) * | 2023-09-21 | 2023-11-24 | 莱肯生物科技(海南)有限公司 | Artificial intelligence assisted insecticidal protein and application thereof |
| CN116948045B (en) * | 2023-09-21 | 2023-11-24 | 莱肯生物科技(海南)有限公司 | Artificial intelligence assisted insecticidal protein and application thereof |
| CN117003841B (en) * | 2023-09-28 | 2023-12-12 | 莱肯生物科技(海南)有限公司 | Method for controlling soybean leaf roller pests |
| CN117003842B (en) * | 2023-10-07 | 2023-12-12 | 莱肯生物科技(海南)有限公司 | Method for controlling prodenia litura pests |
| CN117024536B (en) * | 2023-10-08 | 2024-07-23 | 莱肯生物科技(海南)有限公司 | Method for controlling Asian corn borer pests |
| CN117777255B (en) * | 2023-12-28 | 2024-08-06 | 武汉艾迪晶生物科技有限公司 | Novel insecticidal protein |
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