Patent Application
20230287398
This application claims priority to Chinese Patent Application NO: 202210248136.9, filed with China National Intellectual Property Administration on Mar. 14, 2022, the entire contents of which are incorporated herein by reference.
This disclosure relates to the biotechnology field. Specifically, this disclosure relates to a construction method of a tight regulation system for gene expression in Zymomonas mobilis and applications.
The statements herein provide background information relevant to the present disclosure only and do not necessarily constitute prior art.
Regulation of gene expression is a complicated process at multiple levels, which includes multiple levels of regulation, such as the gene level, the transcriptional level, the posttranscriptional level, the translational level, and so on, as well as the temporal and spatial regulations of gene expression in cells. Nevertheless, due to the complexity of the regulation of the gene expression, it may be toxic or lethal to the host cells in the process of gene expression, which restricts the study of gene function or the establishment of cell models.
Despite of the development of different prokaryotic or eukaryotic cell expression regulatory systems, current system for the expression regulation still has some limitations. For example, for prokaryotes, their system for the expression regulation has a slow and inefficient induction process and is lack of induction specificity and precise regulation of expression, which limits the application of the expression system. Therefore, a more tight gene regulation system is needed, so that the spatial and temporal expressions of genes can be strictly controlled efficiently and cell resources can be used effectively.
Zymomonas mobilis, a facultative anaerobic Gram-negative bacterium, is the only microorganisms known to undergo anaerobic fermentation through the Entner-Doudoroff (ED) pathway. Zymomonas mobilis has the characteristics with small genome, high. ethanol yield, high tolerances of sugar and ethanol, broad scopes of growth temperature (24-−45° C.) and pH (4.0˜8.0). Given these characteristics, Zymomonas mobilis is widely used in the industrial production of bioethanol and other products.
In recent years, a large number of researches have been carried out in the aspects of system biology and synthetic biology, genetic engineering and metabolic engineering for Zymomonas mobilis. By the development of high-throughput sequencing technology, genome sequences of multiple strains of Zymomonas mobilis have been reported, updated and accurately annotated, and the rational transformation and development of microbial cell factories have also been guided by the construction of genome-level metabolic models. In addition, the development of heterologous CRISPR-Cas12a and the endogenous type I-F CRISPR-Cas genome editing systems offer new genetic tools for efficient strain construction.
At the same time, combining the dual-reporter system with omics data, a batch of strong, medium and weak constitutive promoters as well as ethanol-inducible promoters and RBS of different strengths have been successfully predicted and characterized. The development of Zymomonas mobilis as a cell factory is supported by these technologies and methods. However. the lack of a tight regulation system for the gene expression and metabolic pathway construction in Zymomonas mobilis limits the applications of Zymomonas mobilis in gene function analysis, circuit construction, and spatial and temporal regulations of metabolic pathways.
Embodiments provide a construction method of a tight regulation system for the gene expression in Zymomonas mobilis. A recombinant plasmid is provided by a Gibson Reaction with pZM 39 (Genbank ID: CP023718) plasmid, T7 RNAP gene and araC gene. Among them, the inducible promoter PBAD is used as the promoter of the gene T7 RNAP, and the inducible promoter Ptet is used as the promoter of the gene araC. The reconbinant plasmid is transformed into Zymomonas mobilis (Zymomonas mobilis subsp. mobilis ZM4, ZM4), and colonies are obtained to establish the T7 expression system in Z. mobilis ZM4.
In some embodiments, the gene fragment to be expressed is transferred into the established T7 expression system for expression in Zymomonas mobilis (ZM4).
In some embodiments, the gene fragment to be expressed is transferred into a shuttle plasmid for expression. And the shuttle plasmid can shuttle in both Zymomonas mobilis (ZM4) and Escherichia coli (E, co/i).
In some embodiments, the shuttle plasmid is obtained by replacing the fl origin on E. coli pET22b or pET28a with a Zymo-replicon from Zymomonas mobilis (ZM4).
In some embodiments, the resistance gene of pET22b is replaced with the kanamycin resistance gene.
In some embodiments, the nucleotide sequence of the T7 RN AP gene is shown in SEQ ID NO.1, the nucleotide sequence of the PBAD is shown in SEQ ID NO.2, and the nucleotide sequence of the araC is shown in SEQ ID NO.3.
Embodiments also provide an application of a tight regulation system for the gene expression in Zymomonas mobilis, which is demonstrated by described above embodiments.
Embodiments also provide an expression plasmid that can be transformed in both Zymomonas mobilis (ZM4) and Escherichia coli (E. coli). The expression plasmid is pTZ22b, obtained by replacing the fl origin on 7. coli pET22b with a Zymo-replicon from Zymomonas mobilis (ZM4), and replacing the resistance gene with the kanamycin gene.
Embodiments also provide an expression plasmid that can shuttle in both Zymomonas mobilis (ZM4) and Escherichia coli (7. coli). The expression plasmid is pTZ28a, obtained by replacing the fi origin on E. coli pET28a with a Zymo-replicon from Zymomonas mobilis (ZM4).
Embodiments also provide an application of Zymomonas mobilis for the gene expression by the expression plasmid as said above, that can be transformed in both Zymomonas mobilis (ZM4) and Escherichia coli (E, coli).
Embodiments have constructed a T7 expression system, that is applied to construct the tight regulated lines, analyze the function of toxic genes, and execute the tight regulations of metabolic pathways in Zymomonas mobilis.
Embodiments have constructed shuttle plasmids that can be transformed in both Zymomonas mobilis (ZM4) and Escherichia coli (E. coli). The shuttle plasmid can be used to facilitate the construction of plasmids and improve the expression efficiency of foreign genes, laying a solid foundation for the optimal regulation of protein expression and metabolic pathways in Zymomonas mobilis (ZM4).
The establishment of the T7 expression system will improve the gene tight regulation system and the genetic operation tool system of Zymomonas nobilis, and solve the lack of gene tight regulation system for Zymomonas mobilis, and provide more possibilities for gene function analysis, circuitry construction, and temporal and spatial regulation of metabolic pathway of Zymomonas mobilis.
Meanwhile, Zymomonas mobilis is a GRAS (generally regarded as safe) strain, it has the advantages as a safe protein expression system.
Meanwhile, as Zymomonas mobilis is a GRAS strain with relatively small genome and simple metabolites, it has advantages as a safe protein expression system and a cell factory for safe protein expression replacing the Escherichia coli (E. coli).
In order to make the objectives, technical scheme, and advantages of this disclosure clearer, this disclosure is further explained in details in combination with the following embodiments, and the following examples. The specific embodiments described herein are intended to explain this disclosure and are not intended to define this disclosure.
According to the information contained in this present disclosure, it is easy for those skilled in the art to make various changes to the precise description of this disclosure without departing from the spirit and scope of the attached claims. It should be understood that the scope of this disclosure is not limited to the defined process, nature, or component, as these embodiments and other descriptions are merely schematic descriptions of specific aspects of this disclosure. In fact, the various changes made by the person of ordinary skill in the art to the embodiment of this disclosure are covered within the scope of the attached claims.
In order to better understand this disclosure rather than limit the scope of this disclosure. Therefore, unless otherwise specified, the numerical parameters listed in the specification and the attached claims are approximate values, which may be changed depending on the desirable nature of the attempted acquisition. Each numerical parameter should be seen at least as obtained based on valid figures reported and by conventional rounding methods. In this disclosure, about refers to within 10% of a given value or range, preferably within 5%.
When the temperature is not specifically defined in the following embodiment of this present disclosure, it is all normal temperature conditions. Normal temperature refers to indoor temperature in the four seasons, without additional cooling or heating treatment, and the normal temperature is generally controlled at 10˜30° C., preferably 15˜25C.
The genes, proteins, or fragments thereof involved in the present disclosure may be naturally purified products or chemically synthesized products, or generated from prokaryotic or eukaryotic hosts (e.g., bacteria, yeast, plants) using recombinant techniques.
Embodiments disclosed a construction method and application of a tight regulation system for the gene expression in. Zymomonas mobilis. A shuttle plasmid expressing T7 RNA polymerase co-induced by both tetracycline and arabinose was constructed to accomplish the T7 expression system with strong orthogonality in Zymomonas mobilis. Simultaneously, shuttled expression plasmids (pTZ series plasmids) that can be transformed into both Zymomonas mobilis (ZM4) and Escherichia coli (E. coli).
The shuttled expression plasmids were constructed by replacing the fl origin on pET plasmids from Escherichia coli with a Zymo-replicon from Zymomonas mobilis (ZM4). The shuttle expression plasmids were capable of expressing foreign genes driven by PT %.
In some embodiments, T7 expression was regulated due to its toxicity. T7 RNAP was controlled by promoter PSAD. while araC expression was regulated by Ptet, In the absence of arabinose inducer, the target protein GFP was not expressed or its expression level was very low.
The target protein expression level was high in the presence of both tetracycline and arabinose simultaneously.
In addition, the exogenous protein Superfold GFP (sfGFP) was selected to test its secretion ability in Zymomonas mobilis, which could achieve efficient expression and one-step secretion of the proteins to be expressed with the system established above.
The overall schematic diagram of the technical solution is shown in
Step 1
In some embodiments, using pZM39 plasmid as vector, Gibson assembly was used to construct a recombinant plasmid for regulating the expression in T7 RNAP. The underlined part of the primer is the connecting homologous arm. The amplification system and procedures are shown in Table 1 and Table 2.
The T7 RNAP gene sequence used in this disclosure (after codon optimization) is as follows:
Inducible promoter PBAD was used as the promoter of gene T7 RNAP, shown as follows:
Primers for amplifying the fragment of PBAD were synthesized, named PBAD-F and PBAD-R.
cggccgcttctagagaaaccaattgtccatattgcatcagacattg,
gatgttaatcgtgttcatgggagatcctttctcctctttag,
An inducable promoter Pti, was used as the promoter of gene araC, shown as follows:
cctcaacctactactttaagacccactttcacatttaagttgtttttcta
ttgcgcttcagccatgggagatcctttctcctctttagatc,
The recombinant plasmid vector was reversely amplified from pZM39, that the amplified reaction was implemented referred to Table 1 and Table 2. Primers for amplifying the fragment of pZM39 vector were synthesized, named 39p-F and 39p-R.
The above fragments were ligated to the pZM39 vector by Gibson assembly. The sequence of fragment connection was PBAD+T7 RNAP+TetR+Ptet+araC. The conjugated products were transformed into Escherichia coli. DH50: receptive cells were screened using plates containing antibiotics chloramphenicol (50 μg/mL). Colonies were selected the next day, and preliminarily verified by PCR using pEZ-dp-F (ctgaattcgcggccge, SEQ ID NO.17) and pEZ-15A-R (cacttcactgaeaccctcat, SEQ ID NO.18) as primers.
The recombinant plasmid was extracted from the colonies with expected band size (5012 bp) and overnight culture. The plasmid extraction process was referred to the standard steps of plasmid extraction kit. The recombinant plasmid obtained by preliminary verification and screening was further verified by sequencing.
The structure of the recombinant plasmid for regulating the expression in T7 RNAP is shown in
As shown in
Step 2
In some embodiments, the final strain was established by transforming the above recombinant plasmid into the receptive cells of Zymomonas mobilis (ZM4).
In some embodiments, ZM4 receptive cells were placed on ice. After the receptive cells melted, 50 μL was added into the pre-cooled electric cup, and 500 ng plasmid was added into the cup. The condition of transforming included 1.8 kV, 25 μF and 200 Ω.
After electroporation. the cells were resuscitated in RMG5 liquid medium in an incubator at 30° C.
Culture resuscitated for 6˜12 hours was centrifuged at 6000 rpm for 1 min to remove the 900 μL supernatant. The precipitate was suspended with the remaining 150 μL mediums, and coated with RC chloramphenicol resistant plate (120 μg/mL), and cultivated at 30° C. for 2 days.
After 2 days, monoclones were selected and verified by PCR.
The gel electrophoresis results of recombinant plasmid electro-transferred into strain ZM4 are shown in
Step 3
The strain obtained in the previous step was prepared into receptive cells. The process includes:
Step 4
Embodiments provided expression plasmid (pTZ series plasmids) that are able to be transformed into both Zymomonas mobilis (ZM4) and Escherichia coli. The expression plasmid (pTZ series plasmids) has been constructed by adding a Zymo-replicon from Zymomonas mobilis (ZM4) to pET vectors (e.g., pET22b, pET28a).
On account of different species have the different frequency of degenerate codon use, they are favorable to different degenerate codon. For example, the BamH1 recognition sequence for pET22b and pET28 is different, the BamH1 recognition sequence for pTZ28a is GGA triple codon, whereas pTZ22b is GAT.
In some embodiments, shuttle plasmids suitable for Zymomonas mobilis were constructed based on pET22b and pET28a, and the effect of expression in the target protein by Zymomonas mobilis that has been transformed the shuttle plasmids was compared.
The structural maps of the shuttle plasmids, including pTZ28a-GFP5-NSP7 and pTZ22b-GFP15-NSP7, are shown in
Examples use the following nucleotide sequence of a Zymo-replicon (pZymo_Ori) derived from Zymomonas mobilis.
pZymo_Ori
Examples use the following primer pairs (zymo-ori-F, zymo-ori-R) to amplify the Zymo-replicon from Zymomonas mobilis:
gaaaagtgccacctgttattctgattcgtcttgcttttggagcg,
In some embodiments, the fl origin of pET22b and the fl origin of pET28a were respectively replaced by the Zymo-replicon (pZImo Ori). The process included:
gcaggtcaccagctcaccgtcccattcgccaatccggatatag,
gcaggtcaccagctcaccgtcccattcgccaatccggatatag,
agctgtcaaacatgagaattctgtcagaccaagtttactcatatatact
gaaaagtgccacctgttattctgattcgtcttgcttttggagcg,
caggtggcacttttcggggaaatgtgttagaaaaactcatcgagc,
Step 5
Green fluorescent protein GFP was expressed by using pTZ series plasmids (e.g., pTZ22b, pTZ28a).
In this step, the vector of pTZ22b was obtained by a PCR amplification by using pTZ22b as templates, pTZ22b-F and pTZ22b-R as primers. The vector of pTZ28a was obtained by a PCR amplification by using pTZ28a as templates, pTZ28a-F and pTZ28a-R as primers. Recombinant plasmid pTZ22b-GFP15-NSP7 was obtained by Gibson assembly of the vector of pTZ22b with GFP15-NSP7 fragment. Recombinant plasmid pTZ28a-GFP15-NSP7 was obtained by Gibson assembly of the vector of pTZ28a with GFP15-NSP7 fragment. The fragment of GFP15-NSP7 was obtained by a PCR performed with sfGFP15-F and NSP7-R as primers, and the nucleotide sequence of SEQ ID NO.1 as template. And Recombinant plasmid pEZ15A-GFP15-NSP7 was obtained by Gibson assembly of the vector of pEZ15A with GFP15-NSP7 fragment. Sanger sequencing was used to determine the correct recombinant plasmids pTZ22b-GFP15-NSP7, pTZ28a-GFP 15-NSP7 and pEZ15A-GFP15-NSP7.
gcaaccttacaataactcgagcaccaccaccaccaccactg,
ctcgcccttgctcacatgatgatgatgatggtgcatatg,
gcaaccttacaataactcgagcaccaccaccaccaccactg,
gcccttgctcaccatgtgatgatgatgatgatggctgc,
Step 6
In this step, the pTZ22b-GFP15-NSP7, pTZ28a-GFP15-NSP7 and control plasmid (pEZ15A-GFP15-NSP7) were respectively electro-transformed into the competent cells of Zymomonas mobilis, and then RCK plates (Cm: 120 μg/mL; Kana: 200 μg/mL) were used for screening. Among them, the control plasmid had no T7 promoter and no T7 terminator compared to pTZ22b-GFP15-NSP7 and pTZ28a-GFP15-NSP7.
Step 7
In this step, the performance of the T7 expression system was tested by tetracycline and arabinose that were used as inducers.
In this step, the verified colonies cells were incubated with RCK plates (Cm: 120 μg/mL; Kin: 200 μg/mL), and cultured at 30° C. and 100 rpm in medium containing different concentrations of tetracycline (Tc) and arabinose (Ara) (e.g. 0.8 To/3Ara is 0.8 μg/mL tetracycline +3% arabinose). Among them, three parallels were set for each sample and each gradient.
After cultivating to logarithmic phase, each 200 μL bacterial solution sample was centrifuged at 12,000 rpm for 1 min, removed supernatant, washed cell precipitate and resuspended twice with 1×PBS. And the fluorescence intensity was measured by flow cytometry using a preset program, that the cell collection event was set to 20,000 in order to prevent small probabilities and accidental events.
The expression genes levels (fluorescence intensity) of pTZ22b-GFP15-NSP7, pTZ28a-GFP15-NSP7 and pEZ15A-GFP15-NSP7 were tested to examine the performance of the T7 expression system in Zymomonas mobilis.
Step 8
According to the data obtained by flow cytometry, the average fluorescence value of GFP15 for all events was taken for each sample and calculated to exclude the influence of errors from the outside.
The fluorescence intensity values of the control strain and the mutant strain, respectively in the exponential phase and the stationary phase, are shown in
The results have showed that the T7 expression system plays a crucial role in Zymomonas mobilis, and both pTZ22b and pTZ28a are expressed normally. In the presence of tetracycline or arabinose alone, the amount of protein expression is similar to that in the control expression plasmid pEZ15A-GFP-NSP7. Due to the leaky expression in Ptet, after the addition of arabinose, T7 RNAP is expressed, which induces the expression in the target gene for about 35-fold higher than the control-plasmid. When the expression in araC is further induced by adding of tetracycline, the expression in the target gene has been enhanced by 1 to 2 folds compared with arabinose alone. The highest expression in araC is realized with an inducer gradient of 0.8 Tc/3Ara, that is 55 to 85 folds higher than the control plasmid. These results are close to expectations.
The results have shown that when tetracycline and arabinose used as two inducers are present at the same time, the fluorescence intensity is higher than that of the control group, in other words, the target protein GFP expression is higher. In the absence of arabinose, the target protein GFP is not expressed or expressed at very low levels. The experimental results have shown that the T7 expression system is successfully established in Zymomonas mobilis, and the tight regulation for gene and circuit and high expression in protein is also achieved.
The above is only the preferred embodiments of this disclosure and is not intended to limit this disclosure. Any modification, equivalent replacement, improvement, etc., made within the spirit and principle of this disclosure shall be included in the scope of this disclosure.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2022102481369 | Mar 2022 | CN | national |
