386 results about "Gene cluster" patented technology

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 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 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 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 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 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.

The invention relates to the field of PQQ production, in particular to an engineering bacterium for producing pyrroloquinoline quinone and a preparation method of the engineering bacterium. According to the invention, different broad-host shuttle vectors are used, PQQ is expressed in denitrifying hyphomicrobe to synthesize related gene clusters, denitrifying hyphomicrobe engineering bacteria with high yield of PQQ are successfully constructed, and the engineering bacteria have the characteristics of rapid growth, high fermentation yield and the like, and lay a foundation for realizing green production of PQQ.

The invention discloses construction of an artificial multicellular system and application of the artificial multicellular system in nitrogen reduction, and belongs to the technical field of fermentative degradation. According to the artificial multi-cell system constructed by the method disclosed by the invention, a direct ammoxidation gene dnfABC is over-expressed by adopting Shinella zoogloeoides ATCC19623, and a urea degradation gene cluster ureDABCJEFG is over-expressed by adopting Paracoccus denrificans DYTN-1; the constructed recombinant bacteria are independently or jointly used for nitrogen reduction. According to the method, the synergistic effect of microorganisms in the nitrogen degradation process is utilized, the artificial multicellular system meeting the nitrogen pollution wastewater treatment requirement is developed, the degradation effect and the process stability are remarkably improved, and rapid degradation of nitrogen is achieved.

The invention discloses a biocontrol Chryseobacterium sp. With'contact sterilization 'activity. The PcE1 is a biocontrol bacterium which is separated from rhizosphere soil of Chinese cabbage by utilizing a germ enrichment method and can inhibit the growth of various pathogenic bacteria in a cell contact manner. The genome of the PcE1 encodes a type VI secretion system (T6SS) gene cluster and a plurality of T6SS effect proteins with antibacterial activity. The biocontrol effect determination on plants shows that the PcE1 can inhibit the infection of pectobacterium carotovorum on carrots and also can inhibit the infection of citrus canker pathogens on citrus.

The invention relates to the technical field of microbial metabolism engineering, and discloses a genetically engineered bacterium for producing L-ornithine as well as a construction method and application of the genetically engineered bacterium. According to the genetically engineered bacterium provided by the invention, putrescine synthesis pathway genes speC, speF and argF are knocked out in a genome of the genetically engineered bacterium, a dynamic regulation gene argI is achieved, an L-ornithine synthesis pathway gene cluster derived from corynebacterium glutamicum is over-expressed at a mazG site, a gene argG is knocked down, transcription of a proline pathway gene proB is controlled at a temperature on the genome, and the gene engineering bacterium is obtained. An efflux protein coding gene lysE which is started by a promoter PLtetO-1 and is derived from corynebacterium glutamicum is inserted into a trpR site, and an original promoter of an argO gene on a genome is replaced by the promoter PLtetO-1, so that synthesis and degradation pathways of L-ornithine are reasonably optimized, and expression of a competitive pathway and an efflux-related gene is controlled through temperature change, so that the yield of L-ornithine is increased, and the yield of L-ornithine is increased. In the fermentation process, normal growth of thalli can be maintained without adding arginine, and finally high yield of L-ornithine is achieved.

The invention provides an application of a bacillus subtilis strain A45 in preventing and treating plant diseases or an application of the bacillus subtilis strain A45 in preparing a microbial agent for preventing and treating the plant diseases and the prepared microbial agent. The bacillus subtilis A45 is preserved in the China General Microbiological Culture Collection Center (CGMCC), and the preservation number is CGMCC No.33289. According to the present invention, the mechanism of the liquid bacterial agent containing the bacillus subtilis A45 to efficiently inhibit the growth of the cucumber target leaf spot Corynespora cassicola is that the bacterial strain is encoded to synthesize the famogen, the purehydrazide acid, the subtilosin A and the surfactin synthesis gene cluster, the surfactin synthesis gene cluster is different from the synthesis gene of any known organism, and the highest sequence similarity is 82%. The invention further provides the application of the liquid bacterial agent containing the bacillus subtilis A45 to the preparation of the cucumber target leaf spot Corynespora cassicola, and the application of the liquid bacterial agent containing the bacillus subtilis A45 to the preparation of the cucumber target leaf spot Corynespora cassicola. Experiments show that the liquid fungicide containing the bacillus subtilis A45, provided by the invention, can be used for efficiently inhibiting the growth of the cucumber target leaf pathogen corynespora cassicola, and the prevention and treatment effect can be up to 80% when the liquid fungicide is used in a field.

The invention discloses a genetically engineered bacterium for high yield of L-alanine as well as a construction method and application of the genetically engineered bacterium, a dominant strain is obtained by knocking out an alanine racemase gene dadX and integrating coding sequences of alanine dehydrogenase from different sources, and the shake flask yield is 10.8 g / L; the activity of a corresponding mutant M18L / E75A / A78S / I266V is 4.3 times that of a wild type; 6 by-product related genes are knocked out, meanwhile, a multi-copy strain integrated with alanine dehydrogenase is constructed, and the yield of E.coli A-LB6 in a 5L fermentation tank is increased to 133.3 g / L. Through a dynamic regulation and control strategy, an oxygen-sensitive promoter Pomp * is adopted to replace a phosphoenolpyruvate carboxylase promoter, so that succinic acid byproducts are reduced by 85.8%, and the yield reaches 143.5 g / L after 48 hours of aerobic and anaerobic two-stage fermentation. And finally, by regulating and controlling the ATP synthetase gene cluster atp promoter, the yield of L-alanine in a 50 L fermentation tank reaches 151.3 g / L, and the saccharic acid conversion rate reaches 95.2%. The combination of polygene knockout and dynamic metabolism regulation effectively enhances the biosynthesis ability of alanine, and provides an efficient engineering strain for industrial production.

The invention discloses a phagocytosis-resistant indigo engineering strain, which can sensitively respond to enteritis-related thiosulfate inflammatory factors, timely release a drug indigo to treat gastrointestinal inflammation, and release sfGFP signal molecules to assist in diagnosis and monitoring of diseases, and is very helpful for slowing down disease progression. In addition, through knockout of fhuA and trxA genes related to bacteriophage infection and knockin of an sspB-sspC-sspD-sspE gene cluster, the survival rate of the strain in the intestinal tract can be improved, and the treatment and diagnosis effects of the strain are improved.

The invention provides a dynamic toughness evaluation and early warning 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 discloses preparation and application of a hand mycin derivative with gram-positive bacterium activity resistance, and belongs to the technical field of medicine preparation. According to the present invention, the ctd gene cluster is subjected to heterologous expression in the strain Streptomyces lividans TK64, such that the obtained hand mycin derivatives Carpatamide N and Carpatamide O show excellent biological activity on the gram-positive bacteria; the MIC (minimal inhibitory concentration) values of the Carpamide N and the Carpamide O on streptococcus faecium and enterococcus faecium are 4 mu g / mL and 1 mu g / mL respectively; the MIC (minimal inhibitory concentration) values for staphylococcus aureus and bacillus subtilis are respectively 0.25 mu g / mL and 0.125 mu g / mL, the MIC values for MRSA (Methicillin-Resistant Staphylococcus Aureus) are respectively 1 mu g / mL and 0.5 mu g / mL, and the Gram-positive bacterium resisting activity of the compound is equivalent to or better than that of vancomycin.