CN114703189B - Fraxinus mandshurica U6 gene promoter proFMU6.3, cloning and application thereof - Google Patents
Fraxinus mandshurica U6 gene promoter proFMU6.3, cloning and application thereof Download PDFInfo
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Abstract
The invention relates to a fraxinus mandshurica U6 gene promoter proFMU6.3, and cloning and application thereof. The invention successfully clones the RNA polymerase III type promoter of the fraxinus mandshurica, namely the fraxinus mandshurica Liu Nayuan U6 gene promoter proFMU6.3 for the first time, successfully constructs the fraxinus mandshurica U6 gene promoter activity detection vector, and proves that the promoter has high-efficiency transcription activity through instant transformation fraxinus mandshurica Liu Youmiao and GUS dyeing verification, thereby providing high-efficiency promoter sequences for the transformation research of fraxinus mandshurica and related plants.
Description
Technical Field
The invention belongs to the technical field of biology, in particular to the technical field of plant transgenosis, and particularly relates to a fraxinus mandshurica RNA polymerase III type promoter, more particularly relates to a fraxinus mandshurica U6 gene promoter proFMU6.3, and further discloses a cloning method and application thereof.
Background
The fraxinus mandshurica is a deciduous big tree of fraxinus in Oleaceae, is classified as a national secondary protection progressive type, has high overall strength, good shock resistance and excellent wood, is commonly used for buildings, furniture and the like, and has important economic value. After the tobacco transgenic plant is obtained for the first time in 1983, genetic transformation of woody plants is also paid importance, and the genetic transformation is taken as an important component of forest genetic engineering and plays an important role in disease resistance, insect resistance, improvement of traits and genetic engineering breeding of woody plants. In the field of life sciences, mutants have a crucial role in the study of gene function. However, the forest generation period is long, the genetic heterozygosity is high, the genome ploidy is complex, the traditional random mutagenesis method often needs to construct a large population of mutant libraries and carry out large-scale screening to obtain mutants with lost functions of the target genes, and the process needs a great amount of manpower and material resources. In contrast, genome site-directed editing techniques have great advantages, enabling mutations to be introduced directly at specific locations in the genome.
The CRISPR/Cas9 system is the currently accepted gene editing technology with the most development potential, and Cas9 enzyme directionally cuts a target site under the guidance of sgRNA so as to accurately edit a target gene. Compared with zinc finger nuclease (zinc finger nucleases, ZFNs) and transcription activator-like effector nuclease (transcription activator-like effector nucleases, TALENs) technologies, the CRISPR/Cas9 system has the advantages of simple design flow, convenient operation and high gene editing efficiency, and is rapidly and widely applied to researches on animals, plants and microorganisms once developed. Since 2013 CRISPR/Cas9 was first used for model plants arabidopsis and tobacco, the gene editing system has been applied to 24 plants (Shan et al, applications in Plant sciences,2020,8 (1): e 11314.) of 45 plants in the family of 24 plants (Shan et al, applications in Plant sciences,2020,8 (1): e 11314.) in the family of 24 plants (nekraov et al, nat Biotechnol,2013,31 (8): 691-693), wheat (Wang et al, nature biotechnology,2014,32 (9): 947-951), corn (Zhen et al, journal of Genetics and Genomics,2014,41 (2): 63-68), sorghum (Jiang et al, nucleic acids research,2013,41 (20): e 188.), brachypodium distachyranum, tomato (Brooks et al, plant Physiology,2014,166 (3): 1292-1297) and the like). The CRISPR/Cas9 system also plays a great role in promoting the research and genetic improvement of the tree gene function. However, compared with herbaceous plants and food crops, the CRISPR/Cas9 system is more lag in related research and application of woody plants, and most of the CRISPR/Cas9 systems are still in the establishment stage of a gene editing system. Citrus plants were the first woody plants to attempt gene editing using CRISPR/Cas9, and this technique was also successfully applied to kiwi, vitis, malus, punica, caffeia, cocoa, tapioca, etc. Meanwhile, the successful application of the CRISPR/Cas9 system in economic woody plants such as poplars and the like shows great potential in aspects of regulating plant stress tolerance, shortening the tree breeding period and the like, realizes the cultivation of new varieties of drought-resistant and disease-resistant woods, provides a new path for basic research and molecular breeding of the woods, and provides a new idea for accurately improving plant characters and breeding new varieties.
To improve the gene editing efficiency of the CRISPR/Cas9 system, vectors are continually optimized. The sgrnas that determine target specificity are small RNAs with specific secondary structures, usually driven by the U3/U6 series of promoters. The U3/U6 promoter is one of important elements of a CRISPR/Cas9 gene editing system, transcription initiation sites of the gene are A and G respectively, and the transcription activity is high. Wherein U3 is used for monocotyledonous plants and U6 is used for dicotyledonous plants. The selection of the U3 or U6 promoter with a defined start site allows accurate guidance of the transcription of sgRNA and thus reduces off-target effects from unrelated DNA transcription. Although U3/U6 has been successfully used in gene editing of multiple species, the same promoter is not necessarily suitable for species with far homology, and there are often multiple U3 or U6 promoters in the same species gene, and there are certain differences in activity and transcription efficiency. Therefore, more endogenous U3/U6 promoters of target plants are cloned, and the improvement of a CRISPR/Cas9 gene editing system is facilitated. Two PeU promoters were cloned from moso bamboo in Hui Jin et al and truncated to different lengths, and different promoters were found to have different transcriptional activities at different truncated lengths of the same promoter (Van Hui Jin et al, plant theory, 2020,55 (03): 299-307.). Pu Yan et al found that cloned U3 promoters were transcriptionally active within 250bp in length when the promoters were verified for transcriptional activity in tomato (Pu Yan, north China agricultural journal, 2019 (1): 33-39.). Based on the need to construct CRISPR/Cas9 gene editing vectors, the U3/U6 promoters used are required to be as short as possible on the basis of ensuring that they have a high transcriptional activity, so as to ensure that they contain as few cleavage sites as possible, and studies have shown that U6 promoters for CRISPR/Cas9 gene editing techniques are typically only 200-400bp long (Fauser et al The Plant Journal,2014,79 (2): 348-359), even shorter than 100bp (Vladimir et al Nature biotechnology,2013,31 (8): 691-693.). Long et al increased the expression level of sgRNA 6-7 fold with the cotton endogenous U6 promoter, and gene editing efficiency 4-5 fold (Longs et al, plant methods.2018,14 (1): 80.). Liu Chunxia et al utilized the tomato U6 promoter to drive expression of sgRNA, and increased tomato gene editing efficiency from 63% to 73% as compared to the Arabidopsis U6 promoter-driven sgRNA (Liu Chunxia et al, molecular plant breeding, 2020,18 (20): 6716-6724.).
The CRISPR/Cas9 gene editing system successfully established and applied to the fraxinus mandshurica can provide efficient and reliable technical support for the acquisition of the fraxinus mandshurica Liu Dingxiang mutant library, and provide precious material foundation for the deep research of fraxinus mandshurica gene functions and the development and utilization of gene resources thereof. However, the research on the U6 promoter on the fraxinus mandshurica is still lacking so far, and the lack of an applicable endogenous U6 promoter which is as short as possible and has higher transcriptional activity has become a limiting factor for the construction of the fraxinus mandshurica CRISPR/Cas9 gene editing system, and also limits the application of the CRISPR/Cas9 system in the aspects of fraxinus mandshurica genetic breeding, germplasm innovation and the like. Therefore, the cloned water yeast Liu Nayuan FmU promoter with high-efficiency transcriptional activity has important research significance and application value for construction of water yeast CRISPR/Cas9 vector, research of water yeast functional genes and genetic breeding.
Disclosure of Invention
Aiming at the current research situation, the invention aims to provide a fraxinus mandshurica U6 gene promoter FmU6.3, a cloning method and application of the promoter.
One of the technical schemes adopted for solving the technical problems is as follows: a promoter proFMU6.3 of a water yeast Liu Nayuan U6 gene is provided, and the nucleotide sequence of the promoter is shown as SEQ ID NO. 1.
Preferably, the fraxinus mandshurica U6 gene promoter proFMU6.3 belongs to the RNA polymerase III type promoter of fraxinus mandshurica U6 snRNA gene.
Preferably, the nucleotide sequence of the fraxinus mandshurica U6 gene promoter proFMU6.3 comprises 102bp U6 SnRNA.
The second technical scheme adopted by the invention for solving the technical problems is as follows: there is provided a method for cloning the fraxinus mandshurica FmU gene promoter proFmU6.3, comprising the steps of:
(1) Taking the DNA of the sterile seedlings of the fraxinus mandshurica as a template, and designing the following specific primers:
proFmU6.3-F:ACCACCGTCGTCTCCTCCA
proFmU6.3-R:CATCCAGAAGTTCACCTAAAGCA
(2) PCR cloning was performed in a 50. Mu.L system using LA Taq enzyme, and the PCR amplification reaction procedure was: pre-denaturation at 95℃for 2min, denaturation at 95℃for 30s, annealing at 58℃for 30s, extension at 72℃for 2min,35 cycles, and final extension at 70℃for 10min.
(3) Cloning the amplified product onto pCloneEZ-TOPO vector, converting colibacillus DH5 alpha, and picking up recombinant monoclonal sequencing to obtain the promoter proFMU6.3 of U6 gene of fraxinus mandshurica with length of 1442 bp.
The fourth technical scheme adopted for solving the technical problems is as follows: provides the application of the fraxinus mandshurica U6 gene promoter proFMU6.3 in the technical field of fraxinus mandshurica molecular breeding.
The invention has the following beneficial effects: the RNA polymerase III type promoter of the fraxinus mandshurica U6 snRNA gene, namely the fraxinus mandshurica Liu Nayuan U6 gene promoter proFMU6.3, is cloned in fraxinus mandshurica for the first time, and the fraxinus mandshurica U6 gene promoter proFMU6.3 and GUS gene are fused for expression to transform fraxinus mandshurica tissue culture Miao Youmiao, so that the fraxinus mandshurica U6 gene promoter proFMU6.3 can be efficiently expressed on fraxinus mandshurica through transient expression, and a high-efficiency promoter sequence is provided for transformation research of fraxinus mandshurica and related plants.
Drawings
FIG. 1 shows the alignment of the promoter proFMU6.3 of the U6 gene of fraxinus mandshurica with the sequences of the U6 promoters of Arabidopsis thaliana and soybean, wherein the positions of the frame lines are respectively the key element USE (Upstream Sequence Element), the TATA-like Box and the transcription initiation site of the transcription of the U6 snRNA, and the horizontal line mark positions are the U6 snRNA;
FIG. 2 is a cloning electrophoresis diagram of the fraxinus mandshurica U6 gene promoter proFmU6.3, and a 1442bp fraxinus mandshurica U6 gene promoter proFmU6.3 fragment can be obtained through PCR amplification;
FIG. 3 shows the GUS staining of the sterile seedlings of Salix mandshurica, control being a Control group transiently infected with Agrobacterium GV 3101.
Detailed Description
For a better understanding of the present invention, reference will now be made in detail to the following examples and accompanying drawings, which are included to provide a further understanding of the invention, but it should be understood by those skilled in the art that the following examples are not intended to limit the scope of the invention and that any changes and modifications that would be made to the present invention are within the scope of the invention.
In the following examples, the experimental methods used are conventional methods unless otherwise specified.
The promoter activity detection vector pNC-121-pro in the following examples was a pNC series vector from NC Biotech, which was used only for repeated experiments related to the present invention, and was not used for other purposes.
Materials, reagents and the like used in the examples described below are commercially available unless otherwise specified.
Example 1:
the acquisition of the fraxinus mandshurica U6 gene promoter proFMU6.3 is specifically performed as follows:
(1) According to the conservation of the U6 snRNA sequence among different species, the alignment (BLAST) of the Arabidopsis AtU snRNA sequence (GTCCCTTCGGGGACATCCGATAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCATAAATCGAGAAATGGTCCAAATTTT) and the soybean GmU6 snRNA sequence (GTCCCTTCGGGGACATCCGATAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCACAAATCGAGAAATGGTCCAAATTTT) with the fraxinus mandshurica genome sequence was performed. Checking the comparison result, selecting the position with the sequence homology higher than or equal to 99%, and analyzing the upstream 1800bp sequence by using Plant CARE on-line analysis software. As a result of the analysis, USE (Upstream Sequence Element) and basic transcription related TATA-like Box were found to be located 60bp and 30bp upstream of the transcription initiation sites of these U6 genes, respectively. One of the promoter sequences was selected and designated proFMU6.3.
(2) The genome DNA of the sterile seedlings of the fraxinus mandshurica is used as a template, and a specific primer is designed on the upstream and downstream of a fraxinus mandshurica U6 gene promoter proFMU 6.3:
proFmU6.3-F:ACCACCGTCGTCTCCTCCA
proFmU6.3-R:CATCCAGAAGTTCACCTAAAGCA
wherein the downstream primer is positioned 300bp downstream of the fraxinus mandshurica snRNA in the genome sequence to ensure that the clone sequence contains the complete 102bp snRNA.
(3) PCR cloning was performed in a 50. Mu.L system using LA Taq enzyme, and the PCR amplification reaction procedure was: pre-denaturation at 95℃for 2min, denaturation at 95℃for 30s, annealing at 58℃for 30s, extension at 72℃for 2min,35 cycles, and final extension at 70℃for 10min.
(4) Cloning the amplified product onto pCloneEZ-TOPO vector, converting colibacillus DH5 alpha, picking up recombinant monoclonal sequencing, and finally obtaining the fraxinus mandshurica U6 gene promoter proFMU6.3 with 1442bp length as shown in figure 2.
(5) The promoter sequence was analyzed by DNAMAN alignment with the Arabidopsis AtU-1, atU-26, atU6-29 and soybean GmU-16 g-1, gmU6-16g-2, gmU-19 g-2 base sequences, and found that the fraxinus mandshurica U6 gene promoter proFMU6.3 sequence contained the USE element and the U6 snRNA transcription key site TATA-like Box, as shown in FIG. 1, and that the positions of these two elements in the fraxinus mandshurica U6 gene promoter proFMU6.3 sequence relative to the transcription start site were consistent with the Arabidopsis AtU6-1, atU6-26, atU6-29 and soybean GmU-16 g-1, gmU6-16g-2, gmU6-19g-2 promoter sequences, which are important for the functioning thereof.
Example 2:
the activity detection of the fraxinus mandshurica U6 gene promoter proFMU6.3 comprises the following specific operations:
(1) Construction of a fraxinus mandshurica U6 gene promoter proFMU6.3 activity detection vector:
specific primers containing homology arms for homologous recombination cloning with pNC-121-pro (pBI 121 framework, GUS reporter gene, NC cloning cassette substituted for 35S promoter of pBI 121) were designed as follows:
pNC-proFmU6.3-F:CAGTGGTCTCTGTCCAGTCCTACCACCGTCGTCTCCTCCA
pNC-proFmU6.3-R:CGGTCTCAGCAGACCACAAGTCATCCAGAAGTTCACCTAAAGCA
(homologous sequences to the pNC-121-pro vector are underlined)
The positive recombinant monoclonal plasmid of the fraxinus mandshurica U6 gene promoter proFMU6.3 is used as a template, a proFMU6.3 DNA fragment with homology arms at two ends is obtained through PCR amplification, the fragment is mixed with the pNC-121-pro plasmid by using a Nimble Mix (A), the mixture is sucked and beaten for 10 to 20 times, the mixture is treated for 45 minutes at 50 ℃ by a PCR instrument, and the temperature is kept at 4 ℃ to finally obtain the pNC-121-pro FMU6.3 promoter activity detection vector.
(2) Agrobacterium transformation verification of the fraxinus mandshurica U6 gene promoter proFMU 6.3:
FmU6.3 of the constructed promoter activity detection vector pNC-121-pro is transformed into an agrobacterium GV3101 strain, 15d of water yeast Liu Youmiao is inoculated as a transient transformation explant material, transient infection of the agrobacterium is carried out, the water yeast Liu Youmiao is taken out after co-culture for 3 days, GUS staining observation is carried out, and the promoter capability and the expression activity of the water yeast U6 gene promoter proFmU6.3 are evaluated.
And (3) adding the fraxinus mandshurica tissue culture seedlings for detection into GUS dye liquor, carrying out vacuum filtration for half an hour, dyeing overnight in a shaking table at 37 ℃ in a dark place, pouring out the dye liquor, decoloring with 95% alcohol for 3d, and observing GUS dyeing condition. The staining was performed as shown in FIG. 3, with reference to the empty GV3101 Agrobacterium-infected water curve Liu Youmiao.
Therefore, the RNA polymerase III type promoter of the fraxinus mandshurica U6 snRNA gene, namely the fraxinus mandshurica U6 gene promoter proFMU6.3, is obtained in fraxinus mandshurica, and is verified to have the starting activity. Therefore, the invention provides a high-efficiency promoter sequence for transformation research of the fraxinus mandshurica and the related plants.
While the foregoing describes specific embodiments of the present invention, it will be appreciated by those skilled in the art that the specific embodiments described are illustrative only and not limiting of the scope of the invention, as modifications and variations may be made by those skilled in the art without departing from the principles of the invention, and such modifications and variations are to be regarded as being within the scope of the invention as claimed.
Sequence listing
<110> university of northeast forestry
<120> a fraxinus mandshurica U6 gene promoter proFmU6.3, cloning and application thereof
<130> proFmU6.3
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<170> SIPOSequenceListing 1.0
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<213> fraxinus mandshurica (Fraxinus mandshurica)
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accaccgtcg tctcctccac caacaccaac accaacacta cagaaacgca ctacaatggt 60
ttgatgtcac atgttaataa tgagtctcaa tgaaccaaaa tgtcggttac atccatcaaa 120
cacctcacac ccatcccgat tctccaccaa aatttggtca caaatcaacc ctcgagaccc 180
ctaccaccac cattattatc gccgcagcca gacccaccgc cactgcagct agaaaaccca 240
aaacccccca acagcaccaa aaccaccact accaccaaca taagcaccac catctccacc 300
acaaatccac catatccaac acattcaaaa ccaaaacgcg aaacacatct tagatctaaa 360
cacccaaatc acaccgcatc accgctacaa caacgaccac cacccaaaca ccaccactac 420
gagcactgca ccatagcagt gattgcccat gaacaataga tcttctcaat aagagagact 480
tcgttgcgga tcctgtggtg ccgctgcacc aacacaacga catctctctt ggtgaagctt 540
gaaatggttc cgtttcaaac acccacggcc tcgggcgggg caaaaagtga agccccgatt 600
ttgaaaccaa ggaccgttgg gtcgaccacg aagattatca aatggaagtc tcatgggaaa 660
ggtgcaacaa cgacgagaga gagaacggaa atagaaatga attagggttt aatttataat 720
atttaaatat ggattattaa ttaaaacctg acttgattct tgatttatga aaatggaaaa 780
ttaaaatcca ttatagctgt aatttcctca gtaaacggtt ctaaacaagt ttaaggtaga 840
caaaatgaat aaaatgcaaa tcaaatactt tgtaggctca ccaacaaggc ctggcccgta 900
attgaaacta gaagtgaagc ctaagaaccc gagcccaaaa acttaccagt cctattggaa 960
ctgaatctca tatattctag tcccacatcg acaaaaggca gaattccttt gcaatttata 1020
ttgcgattgc tggcaataga gtttgtccct tcggggacat ccgataaaat tggaacgata 1080
cagagaagat tagcatggcc cctgcgcaag gatgacacgc acaaatcgag aaatggtcca 1140
aatttttttt gttcttgaat tcatgtagtt ttccgtagaa aaatcatcct ttggtttttt 1200
tatttttttt gtcgatttgc agtttgtcta tatttttgag gactttggtg agtggttctt 1260
atggacctta atttgatgag gtttttgtca aaaaaccatc tatattgtta gggtttcagg 1320
caagctttat ttattattaa ggtttctatc gcgaaatgac gatttttttc ttttttttcg 1380
gtatgcagtt tcatcgaaat tgttgaggta tttgtcgaat gctttaggtg aacttctgga 1440
tg 1442
Claims (6)
1. The promoter proFMU6.3 of the fraxinus mandshurica U6 gene is characterized in that the DNA nucleotide sequence of the promoter proFMU6.3 is shown as SEQ ID NO. 1.
2. A method for cloning a gene promoter, characterized in that a method for cloning the fraxinus mandshurica U6 gene promoter profmu6.3 according to claim 1 comprises the steps of:
(1) Designing a specific primer proFMU6.3-F: ACCACCGTCGTCTCCTCCA, proFmU6.3-R: CATCCAGAAGTTCACCTAAAGCA by taking the fraxinus mandshurica DNA as a template;
(2) PCR amplification was performed in a 50. Mu.L system using LA Taq enzyme;
(3) Cloning the amplified product onto pCloneEZ-TOPO vector, converting colibacillus DH5 alpha, picking up recombinant monoclonal sequencing to obtain the promoter proFMU6.3 of fraxinus mandshurica U6 gene with length of 1442 bp.
3. The method of cloning the fraxinus mandshurica U6 gene promoter profmu6.3 according to claim 2, wherein in the step (2), the PCR amplification reaction procedure is as follows: pre-denaturation at 95℃for 2min, denaturation at 95℃for 30s, annealing at 58℃for 30s, extension at 72℃for 2min,35 cycles, and final extension at 70℃for 10min.
4. The method of cloning the fraxinus mandshurica U6 gene promoter fmu6.3 as claimed in claim 2, wherein the downstream primer is located 300bp downstream of fraxinus mandshurica snRNA in the genomic sequence to ensure that the cloned sequence contains the complete 102bp U6 snRNA.
5. A method for detecting the promoter activity of fraxinus mandshurica is characterized in that the method is a method for detecting the promoter activity of the U6 gene promoter proFMU6.3 in claim 1, and the promoter activity detection vectors pNC-121-pro: FMU6.3 are respectively and instantly introduced into fraxinus mandshurica seedlings.
6. The application of the mangrove Liu Qi promoter is characterized in that the application of the mangrove U6 gene promoter proFMU6.3 in the technical field of molecular breeding of the mangrove is disclosed in claim 1.
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