472 results about "Gene cluster" patented technology

Methods for making synthetic gene clusters are described.

The invention provides a risk prediction method and system for cardiovascular and metabolic diseases. The method comprises the following steps: collecting continuous cardiovascular-metabolism time sequence data, and extracting phase delay parameters to construct a lipid transport rhythm out-of-synchronization characteristic spectrum; quantifying the topological connection strength of the gene cluster based on the three-dimensional genome interaction strength matrix, and generating a genetic prediction model; a vascular endothelial metabolism buffer attenuation trajectory is calculated through simulation, and a critical environment exposure parameter is determined by matching a genetic instability threshold value; and fusing multi-source data to construct a dynamic toughness model, calculating a phase space shrinkage rate of a vascular metabolism steady-state boundary, and triggering graded early warning. According to the technical scheme provided by the invention, ultra-early warning of cardiovascular metabolism risks is realized, and the individual intervention target spot recognition precision is improved.

The invention belongs to the technical field of biology, and particularly relates to a difunctional gene cluster biosynthesized by phenol amine and salicylic acid and application of the difunctional gene cluster. The gene cluster comprises five genes, the five genes are S1EPS1, S1PBS3, S1CoAOMT2, S1CoOOMT3 and S1CoAOMT4, the nucleotide sequence of the S1EPS1 gene is as shown in SEQ ID No.1, the nucleotide sequence of the S1PBS3 gene is as shown in SEQ ID No.3, the nucleotide sequence of the S1CoAOMT2 gene is as shown in SEQ ID No.5, the nucleotide sequence of the S1CoOOMT3 gene is as shown in SEQ ID No.7, and the nucleotide sequence of the S1CoAOMT4 gene is as shown in SEQ ID No.9. The invention further discloses a preparation method of the gene cluster. The overexpressed gene cluster component SlEPS1 gene can significantly enhance accumulation of spermidine derivatives and salicylic acid of tomato plants so as to enhance the resistance to Pst DC3000, lays a foundation for genetic improvement in the aspect of tomato disease resistance by using the gene cluster, and also provides technical reference for excavation of related metabolic gene clusters in other crops and in the aspect of resistance breeding.

The present invention relates to a method for finding global regulators in order to induce or increase production of target secondary metabolites. The method comprises providing a bacterium indicator strain producing two fluorescent reporter signals under the same control of two different biosynthetic gene clusters (BGC), preferably highly expressed BGC, performing random mutagenesis in said bacterium indicator strain, and selecting mutant bacteria not producing said reporter signals. The invention also relates to a method to activate the production of target secondary metabolites, and to a CRISPR / Cas based single plasmid to delete or inactivate a global regulator and / or activate a BGC. Finally, the inventive method can be performed in high-throughput format allowing to speed-up the procedure.

The invention relates to the technical field of biology, in particular to glycopeptide antibiotic and application thereof. According to the invention, a biosynthetic gene cluster for synthesizing a brand new glycopeptide antibiotic skeleton is excavated, and brand new glycopeptide antibiotics Varsomycin A, B and C with novel chemical structures are obtained through heterologous expression; the traditional Chinese medicine composition has a remarkable antibacterial effect on clinically drug-resistant strains. Important fermentation strains and precursor compound molecules are provided for research and development of new drugs of glycopeptide antibiotics, and important application prospects and economic values are achieved.

The invention discloses bacillus siamensis capable of antagonizing various phytopathogens and application of the bacillus siamensis. The preservation number of the bacillus siamensis A-2 is GDMCC (China General Microbiological Culture Collection Center) NO.64228. The bacillus siamensis A-2 has the advantages that the preservation number of the bacillus siamensis The strain has an obvious inhibition effect on Releasella syzygium jambos Indian niesia subspecies, pseudomonas solanacearum, fusarium solani, phomopsis, fusarium oxysporum, colletotrichum musae, colletotrichum laurosporum, fusarium fujikubin and fusarium sp. The gene clusters contain gene clusters for synthesizing plipastatin, abinogen, surfactin, siderophore, bacitracin, difixitin, butyrosidin A / B and some terpene compounds, and the gene clusters contain gene clusters for synthesizing plipastatin, abinogen, surfactin, siderophore, bacitracin, difixitin and butyrosidin A / B; the composition has a relatively good prevention and treatment effect (the relative prevention effect is 58.14%) on tomato bacterial wilt; and the strain has the capability of degrading tetracycline hydrochloride (the degradation rate in 3 days is 49.28%). Therefore, the bacillus siamensis A-2 has extremely high development and utilization value in agricultural production.

The invention discloses Pseudomonas protegens for producing nitropyrrole, which is preserved in the China Center for Type Culture Collection, and the preservation number is CCTCC (China Center for Type Culture Collection) M20241968. The invention further discloses a preparation method of the Pseudomonas protegens for producing nitropyrrole. The invention also discloses an engineering bacterium for producing nitropyrrole and a construction method of the engineering bacterium. The engineering bacterium is a mutant strain for blocking a bypass metabolic pathway of the pseudomonas. For example, the pseudomonas is taken as a target, a core gene in a BGC1 biosynthetic gene cluster in the pseudomonas is knocked out through a gene knockout method, or a core gene in a BGC16 biosynthetic gene cluster is knocked out, or a mutant strain of the core genes in two biosynthetic gene clusters of BGC1 and BGC16 is knocked out at the same time. The invention also discloses a biocontrol microbial inoculum containing the pseudomonas or the engineering bacteria. The invention further discloses application of the pseudomonas or the engineering bacteria or the biocontrol microbial agent in prevention and treatment of rhizoctonia solani, and the pseudomonas or the engineering bacteria or the biocontrol microbial agent has a remarkable antibacterial effect.

The invention discloses recombinant streptomyces mobaraensis as well as a construction method and application thereof, and belongs to the technical field of bioengineering. According to the invention, smY2019 is used as an original strain, and a CRISPR / cas9 technology is utilized to construct five chassis cells of a GIs gene cluster; on the basis of smY2019-deltaG5, two kinds of chassis cells in which endogenous CRISPR / Cas system genes are knocked out are constructed. And on the basis of the smY2019-deltaG5-C2, further constructing a chassis cell smY2019-deltaG5-C3 of which a non-homologous end connection (NHEJ) repair pathway gene is knocked out. The TGase secretory enzyme activity of the chassis cell smY2019-deltaG5-C3 is improved by 37.3% compared with that of the original strain smY2019, and meanwhile, the transformation efficiency, the growth speed, the protein synthesis capability and the energy metabolism level of the chassis cell are obviously improved compared with that of the original strain smY2019.

The present disclosure relates to methods and systems for identifying genes associated with biosynthetic gene clusters (BGCs), including embedded target genes (ETaGs) that are homologs of potential therapeutic targets. The methods and systems described herein apply a comparative genomics and manual review or machine-learning model to analyze grid representations such as heat maps, which assess across a plurality of diverse genomes distribution of orthologs (e.g., bidirectional best hits) of a plurality of query genes that are co-localized with an anchor gene (e.g., a core synthase gene) of a BGC in a query genome.

The invention discloses a bisphenol F degradation gene cluster bpf and application thereof. The strain DN12 is separated and can degrade the BPF and grow by taking the BPF as the unique carbon source and energy. On the basis, a BPF degradation gene cluster bpf is obtained from the strain DN12 by adopting whole genome and comparative transcriptome sequencing analysis. Three different degrading enzymes (two-component oxidase BpfAB, monooxygenase BpfC and hydrolase BpfD) are found in the gene cluster and can catalyze gradual degradation of BPF, and a simple aromatic ring compound p-hydroxybenzoic acid is generated.

The invention discloses a gene cluster identification method and device of a bacterial genome, equipment and a storage medium. The method comprises the following steps: constructing a gene cluster recognition model by using a preprocessing unit, an ESM protein language unit, a cosine approximation calculation unit, a normalized pointwise mutual information unit, a term frequency-inverse document frequency unit, a graph convolution unit, a BERT unit and a softmax function unit; inputting a BGC sequence training sample of the bacterial genome into the gene cluster recognition model, training the gene cluster recognition model by using a cross entropy loss function, and performing iterative optimization on the training process by using an Adam optimizer; inputting the BGC sequence data set of the bacterial genome to be recognized into the target gene cluster recognition model for recognition; segments in the preliminary recognition result are corrected, and a final recognition result is obtained; by constructing an adjacent matrix and inputting the adjacent matrix into a graph convolution unit, global features contained in Pfam structural domain nodes in a BGC sequence are extracted, and the recognition and prediction performance of the model is improved.

The invention discloses enterobacter mori capable of resisting fish aeromonas and application of the enterobacter mori, the bacterial strain is classified and named as enterobacter mori SCH0241, the enterobacter mori SCH0241 is preserved in the China Center for Type Culture Collection on October 17, 2024, and the preservation number is CCTCC NO: M 20242236. The enterobacter mori SCH0241 disclosed by the invention is derived from the intestinal tract of high-stress-resistance healthy hybrid crucian carassius auratus No. 2, has good contact dependence antibacterial activity on aeromonas veronii, and can improve the capability of resisting aeromonas veronii infection of zebra fish. Through construction of an insertion mutation library and phenotype screening, it is found that a gene cluster of SCH0241, which exerts contact inhibition toxicity, is T6SS-2. The enterobacter mori SCH0241 disclosed by the invention provides a new powerful tool for biological prevention and treatment of fish diseases caused by aeromonas veronii.

The invention discloses escherichia coli recombinant engineering bacteria for producing citicoline as well as a construction method and application of the escherichia coli recombinant engineering bacteria, and belongs to the technical field of biology. A genome cytidine deaminase coding gene cdd is knocked out on the basis of Escherichia coli K-12 MG1655, a temperature control expression vector PBV220 is used for expressing a SpnCCT-SpnCKI-pRpLpyrG mutant gene cluster, the expression of choline transporter protein BetT is enhanced, the gene locus of Escherichia coli ptsH-ptsI-crr is destroyed, meanwhile, a glucose permease gene glf and a glucokinase gene glk from Zymomonas mobilis are introduced, and the mutant gene cluster of the Escherichia coli K-12 MG1655 is obtained. The escherichia coli recombinant engineering bacterium ZMCB02NCL capable of efficiently biosynthesizing citicoline is obtained, and the preservation number of the escherichia coli recombinant engineering bacterium ZMCB02NCL is CCTCC NO: M 2025483.

The invention belongs to the technical field of synthetic biology genome editing, and relates to a chassis strain for gene cluster in-vivo traceless editing, a construction method and a gene cluster traceless editing method.The chassis strain is based on escherichia coli BL21 (DE3) and integrates a CRISPR-Cas9 system and a homologous recombination system (lambda Red) of a lambda bacteriophage source; and then knocking in an inducible sgRNA expression cassette (sgT) of a targeted editing vector to construct the vector. The strain has an efficient editing capability aiming at exogenous DNA, traceless editing of a target biosynthetic gene cluster is realized, and editing plasmids can be quickly eliminated, so that iterative editing is facilitated. The method is simple, convenient and rapid to operate and high in practicability, and provides powerful technical support for metabolic engineering and synthetic biology breeding transformation of streptomyces industrial strains, activation of synthetic gene clusters of recessive natural products and excavation of novel natural products.

The invention discloses an ectoine gene cluster, mutant and application derived from halophilic bacillus, belonging to the field of synthetic biotechnology. The ectoine gene cluster nucleic acid sequence is shown in SEQ ID NO.7, including the following three genes: ectA gene, the nucleic acid sequence is shown in SEQ ID NO.1, ectB gene, the nucleic acid sequence is shown in SEQ ID NO.2, ectC gene, the nucleic acid sequence is shown in SEQ ID NO.3, and the gene cluster is designed and mutated to obtain a mutant, the nucleic acid sequence is shown in SEQ ID NO.8. The invention can improve the synthesis efficiency of ectoine, improve the fermentation content of ectoine, reduce the production cost of ectoine, and is conducive to the popularization and application of ectoine by constructing a recombinant strain using the ectoine gene cluster and its mutant.

The invention relates to the technical field of microorganisms, and discloses a pseudomonas putida strain and a preparation method and application thereof.The strain is pseudomonas putida which is separated from soil and has the capacity of dissimilatory reduction of nitrate into ammonium and is classified into a new pseudomonas putida strain based on GTDB-TK. A dissimilatory NOreductive gene cluster, namely an nirBD gene cluster, exists on a genome of the gene, nirK / nirS genes are deleted, and NOs can be reduced into NH under the anaerobic culture condition. According to the application of the pseudomonas putida strain in improvement of soil nitrogen management, the pseudomonas putida strain can be mixed with organic fertilizer for use so as to enhance the effective utilization and conversion capacity of nitrogen in soil. By means of the pseudomonas putida strain, NON can be reduced into NHH under the anaerobic condition, the culture method is simple, the growth speed is high, variation is not prone to occurring, and a brand new microbial resource is provided for soil nitrogen cycle research.

Methods for making synthetic gene clusters are described.

The disclosure provides methods for increasing saturated, monounsaturated, and poly unsaturated fatty acid production using the PUFA gene cluster plasmid and the gene regulator pfaR.

The invention relates to the discovery of a biosynthetic gene cluster of an alkaloid, namely, exopoid C, and the biosynthetic gene cluster of the exopoid. A biosynthetic gene cluster exo of an exopoid compound is obtained from a fungus Penicillium sp.HDN14-431 through genome mining, the gene cluster comprises a heme-dependent oxidase gene exoA which is composed of indole dioxygenase and a cytochrome b5 structural domain, a cytochrome P450 enzyme gene exoB and an isopentenyl transferase gene exoC which is composed of indole dioxygenase and a cytochrome b5 structural domain, and the cytochrome P450 enzyme gene exoB and the isopentenyl transferase gene exoC are used as biosynthetic genes of the exopoid compound. All genes in a gene cluster are expressed through an aspergillus nidulans heterologous expression system, two isopentenyl indole alkaloids are obtained in total, and a compound I is a new compound exopoid C. And the compound II, namely the exopoid, is a known compound. The biosynthesis pathway of the compound is reported for the first time.

The invention discloses gene-simplified bacillus subtilis for producing surfactin and application of the gene-simplified bacillus subtilis, and belongs to the technical field of gene engineering. According to the method disclosed by the invention, the variety of non-essential genes is determined by analyzing and identifying the bad performance influencing the fermentation production of the surfactin by the bacillus subtilis. Therefore, on the basis of the bacillus subtilis 168, a phosphopantetheinyl transferase (sfp) gene is firstly integrated, so that the surfactin production capacity of host bacteria is recovered; then, genes (clusters) in five aspects of a biological membrane synthesis pathway, a metabolic by-product pathway, spore generation, a protease system and flagellum generation are simplified. After the strain EX10 is simplified, the fermentation performance is optimized, and the fermentation yield reaches up to 11.2 g / L, which is 2.1 times higher than that of the original strain. Therefore, the genome-simplified strain has a good application prospect as a chassis cell for industrially and efficiently producing surfactin.

The present disclosure relates to computer-implemented methods and systems for identifying biosynthetic gene clusters (BGCs) that encode pathways for the production of secondary metabolites. Secondary metabolites that target genes or gene products that are homologous to, e.g., human genes or gene products may have utility as potential drug compounds.

The invention provides an oxazomycin high-yield engineering strain as well as a construction method and application thereof. The method for constructing the oxazomycin high-yield engineering strain comprises the following steps: driving high expression of a gene cluster by using a strong promoter in streptomyces longsheng, enhancing transcription of a key resistance gene module (ozmS-oxaA), and optimizing ribosome engineering of strain chassis cells and a culture medium. According to the invention, the rational synthetic biology and metabolic engineering technology is combined with the irrational ribosome engineering technology to gradually increase the yield of the streptomyces longsheng oxazomycin, and the established efficient biosynthesis system lays a foundation for further development of the oxazomycin.

The invention relates to an engineering bacterium for synthesizing mannitol by using fructose and nicotinamide ribose and application thereof. The invention provides genetic recombination escherichia coli for synthesizing D-mannitol by using D-fructose and nicotinamide ribose, which comprises the following modifications: insertion or enhanced expression of a gene cluster 1, the gene cluster 1 comprises a D-mannitol dehydrogenase coding gene MDH and a formate dehydrogenase coding gene FDH; deletion or inhibitory expression of a gene cluster 2, wherein the gene cluster 2 comprises a 6-phosphofructokinase 1 coding gene pfkA; and insertion or enhanced expression of a gene cluster 3, wherein the gene cluster 3 comprises a nicotinamide ribokinase coding gene NRK, a nicotinamide mononucleotide adenosine transferase coding gene NMNAT, a polyphosphate kinase coding gene PPK2 and a pyrophosphohydrolase coding gene IPPa. The strain disclosed by the invention can effectively synthesize high-purity D-mannitol by using D-fructose as a production raw material and nicotinamide ribose as a co-substrate through an enzyme catalytic reaction under the condition of not additionally adding NAD < + > or NADP < + >, so that the production cost is greatly reduced.

The invention discloses a method for constructing an engineered bacterium of Clostridium aeruginosa, comprising the following steps: preparing a desired gene in a biosynthetic pathway of a target product, namely a pathway gene, to form a pathway gene cluster; embedding the pathway gene cluster into a transposase recognition site of a mariner transposon to form a pathway gene expression cassette; selecting a constitutive strong promoter commonly used in Clostridium jundal for driving transposase expression, loading the pathway gene expression cassette into a multiple cloning site of a plasmid, and inserting an inducible repressor element upstream of the replicon to obtain a transposition plasmid; transforming the transposition plasmid into Clostridium aeruginosa to obtain an engineered bacterium of Clostridium aeruginosa. The yield of 3-hydroxybutyric acid expressed by the engineered bacterium constructed by the above method is as high as 3g / L.

The present disclosure discloses a Functional Genomic Imaging method. Genes are filtered based on the expression levels and other information first to improve the ratio of effective genes, and then a correlation matrix of gene co-expression is generated based on the filtered gene data to obtain a co-expression network; data conversion is performed based on the correlation matrix of gene co-expression to obtain a distance matrix; and finally, the co-expression network is subjected to dimensionality reduction and cluster analysis, thus obtaining the visualized gene expression according to the analysis result. The Functional Genomic Imaging method provided by the present disclosure achieves a better visualization effect of the genetic co-expression network and can obtain a co-expressed gene cluster more effectively.

The invention belongs to the technical field of molecular biology, and particularly relates to a DNA binding site of a fungus transcription factor AniJ and application. According to the invention, an echinocandin B gene cluster regulatory factor AniJ is taken as a research object, a ptH-SpRY-ACBE base editor and an sgRNA library covering an aniA promoter are utilized, 5-FOA screening is combined, and a binding motif RNGCTGAS of the AniJ in a core promoter region is excavated. The construction of an engineering strain containing a modified promoter (increasing the number of motifs) proves that the motifs can significantly enhance the expression of aniA and the yield of echinocandin B. And a novel molecular tool is provided for metabolic engineering of natural products of fungi.

The invention discloses a method for simultaneously producing ergothioneine and an enzyme preparation by utilizing trichoderma reesei, and belongs to the technical field of biological engineering. By optimizing the culture medium, a culture medium formula capable of enabling the trichoderma reesei which has almost no ergothioneine production capacity originally to synthesize the ergothioneine is screened out, and the trichoderma reesei can simultaneously produce the ergothioneine and an enzyme preparation. By further increasing the number of ergothioneine gene clusters of the trichoderma reesei, under the condition of not introducing any exogenous gene, an industrial production optimized strain of the ergothioneine and the enzyme preparation conforming to food safety is constructed, the yield of the ergothioneine and the enzyme preparation can be remarkably improved, and the production cost of the ergothioneine and the enzyme preparation is reduced. Meanwhile, the problems of biological safety, transgenosis safety and the like are solved, and technical support is provided for industrial production of ergothioneine and enzyme preparations.

The invention relates to a preparation method for producing a polyketone compound by using a recombinant strain Streptomyces coelicola A3 (2) / p15A-KOspiH3 (the preservation number is CCTCC NO: M 20241470), and also relates to an application of the polyketone compound in tumor resistance, and the structural formula of the polyketone compound is # imgabs0 #, the structural formula of the polyketone compound is as shown in the specification, the structural formula of the polyketone compound is as shown in the specification, and the structural formula of the polyketone compound is as shown in the specification. A fermentation product containing the compound can be obtained through fermentation culture of Streptomyces coelicola A3 (2) / p15A-KOspiH3, and then the compound is obtained through separation and purification of methods such as VLC normal-phase column chromatography separation, C-18 ODS reversed-phase column chromatography separation and semi-preparative HPLC. The invention aims to obtain a novel compound with an anti-tumor effect in a gene cluster of a heterologous expression actinomycete source, and the novel compound has a good application prospect.

The invention discloses a genetically engineered bacterium for producing iturin A as well as a construction method and application of the genetically engineered bacterium. The construction method of the genetically engineered bacterium comprises the following steps: (1) knocking out bacillus amyloliquefaciens HM618 and a gamma-polyglutamic acid synthesis gene capBCA with the preservation number of CGMCC (China General Microbiological Culture Collection Center) No.7097; (2) integrating a Ph03 promoter in front of the ituDABC gene cluster; (3) knocking out spores to form regulatory genes sigE and sigF; (4) replacing an original promoter of the cell division regulation gene ezrA in situ by using a Ph03 promoter; the genetically engineered bacterium for producing the iturin A, constructed by the invention, is high in yield of the iturin A, good in strain stability and high in production intensity. And the production yield of the fermentation tank reaches 6 g / L or above. The construction method is simple and easy to operate. The method has important industrial application value.