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1.
Article in Chinese | WPRIM | ID: wpr-879008

ABSTRACT

In order to enrich the transcriptome data of Fagopyrum dibotrys plants, analyze the genes encoding key enzyme involved in flavonoid biosynthesis pathway, and mine their functional genes, in this study, we performed RNA sequencing analysis for the rhizomes, roots, flowers, leaves and stems of F. dibotrys on the BGISEQ-500 sequencing platform. After de novo assembly of transcripts, a total of 205 619 unigenes were generated and 132 372 unigenes were obtained and annotated into seven public databases, of which, 81 327 unigenes were mapped to the GO database and most of the unigenes were annotated in cellular process, biological regulation, binding and catalytic activity. Besides, 86 922 unigenes were enriched in 136 pathways using KEGG database' and we identified 82 unigenes that encodes key enzymes involved in flavonoid biosynthesis. Comparing rhizome with root, flower, leaf or stem in F. dibotrys, 27 962 co-expressed differentially expressed genes(DEGs) were obtained. Among them, 23 515 DEGs of rhizome tissue-specific were enriched into 132 pathways and 13 unigenes were significantly enriched in biosynthesis of flavone and flavonol. In addition, we also identified 3 427 unigenes encoding 60 transcription factor(TFs) families as well as four unigenes encoding bHLH TFs were enriched in flavonoid biosynthesis. Our results greatly enriched the transcriptome database of plants, provided a reference for the analysis of key enzymes involved in flavonoid biosynthesis in plants, and will facilitate the study of the functions and regulatory mechanisms of key enzymes involved in flavonoid biosynthesis in F. dibotrys at the genetic level.


Subject(s)
Biosynthetic Pathways/genetics , Fagopyrum , Flavonoids , Flowers , Gene Expression Profiling , Gene Expression Regulation, Plant , Humans , Transcriptome/genetics
2.
Chinese Journal of Biotechnology ; (12): 1821-1826, 2021.
Article in Chinese | WPRIM | ID: wpr-887765

ABSTRACT

Natural products, important sources of innovative drugs, food, spices and daily chemicals, are closely related to people's healthy life. With the development and integration of modern biological and chemical technologies of natural products, the researches on biosynthesis of natural products have made great progresses in recent years. The biosynthetic pathways of a number of natural products have been analyzed. Many pathway enzymes and modifying enzymes involved in the biosynthesis of natural products have been mined and functionally characterized. Furthermore, genes encoding pathway enzymes have been introduced into chassis to construct cell factories producing natural products through synthetic biology technologies. Also, other biotechnologies including genome editing and genome mining, have been used in the biosynthesis of natural products. In order to further promote the development of researches on biosynthesis of natural products, we edited a Special Issue on the topic of "biosynthesis of natural products", focusing on the researches progress in three aspects: the analysis of biosynthetic pathways of natural products, genome-wide mining and functional characterization of genes encoding tool enzymes, and the scale preparation of natural products by biosynthetic technology. Also included in this Special Issue was the prospect of the biosynthesis of natural products. This Special Issue can provide reference and guidance for the further development of natural product biosynthesis.


Subject(s)
Biological Products , Biosynthetic Pathways/genetics , Biotechnology , Genome , Synthetic Biology
3.
Chinese Journal of Biotechnology ; (12): 1178-1188, 2021.
Article in Chinese | WPRIM | ID: wpr-878623

ABSTRACT

As a naturally occurring steroid sapogenin, diosgenin acts as the precursor of hundreds of steroid medicines, and thereby has important medicinal value. Currently, industrial production of diosgenin relies primarily on chemical extraction from plant materials. Clearly, this strategy shows drawbacks of excessive reliance on plant materials and farmland as well as environment pollution. Due to development of metabolic engineering and synthetic biology, bio-production of diosgenin has garnered plenty of attention. Although the biosynthetic pathways of diosgenin have not been completely identified, in this review, we outline the identified biosynthetic pathways and key enzymes. In particular, we suggest heterologous biosynthesis of diosgenin in Saccharomyces cerevisiae. Overall, this review aims to provide valuable insights for future complete biosynthesis of diosgenin.


Subject(s)
Biosynthetic Pathways/genetics , Diosgenin , Metabolic Engineering
4.
Chinese Journal of Biotechnology ; (12): 404-417, 2021.
Article in Chinese | WPRIM | ID: wpr-878571

ABSTRACT

Curcuminoids are rare diketone compounds in plants and can be found in the rhizome of Curcuma longa as well as other Zingiberaceae and Araceae. Curcuminoids have been widely used in food and medical area owing to the yellow colors, as well as the antioxidant and many other pharmacological activities. Curcuminoids are a mixture of compounds containing curcumin, demethoxycurcumin and bisdemethoxycurcumin, which have distinct benzene ring substituents. Currently, curcuminoids are exclusively produced through plant extraction, which do not satisfy the meeting of the market demand. Empowered with new synthetic biology tools and metabolic engineering strategies, there is renewed interest in production of curcuminoids using microorganisms. Heterologous production of curcuminoids has been achieved using Escherichia coli, Yarrowia lipolytica, Pseudomonas putida and Aspergillus oryzae via engineering of curcuminoids biosynthesis pathway. In this review, we first describe the biological activities and various applications of curcuminoids. Next, we summarize the biosynthetic pathway of curcuminoids in Curcuma longa and discuss the catalytic mechanisms of curcumin synthases. Then, we thoroughly explore recent advances in the use of distinct microorganisms for the production of curcuminoids with a special focus on metabolic engineering strategies. Finally, we prospect the microbial production of curcuminoids by highlighting some promising techniques and approaches.


Subject(s)
Antioxidants , Biosynthetic Pathways/genetics , Curcumin , Diarylheptanoids , Metabolic Engineering , Plant Extracts
5.
Mem. Inst. Oswaldo Cruz ; 115: e200371, 2020. tab, graf
Article in English | SES-SP, LILACS, SES-SP | ID: biblio-1135238

ABSTRACT

BACKGROUND Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.


Subject(s)
Humans , Acinetobacter Infections/microbiology , Acinetobacter baumannii/drug effects , Acinetobacter baumannii/genetics , Biosynthetic Pathways/genetics , Melanins , beta-Lactamases , Microbial Sensitivity Tests , Electrophoresis, Gel, Pulsed-Field , Acinetobacter baumannii/isolation & purification , Multilocus Sequence Typing , Pandemics , Anti-Bacterial Agents/pharmacology
6.
Braz. j. microbiol ; 46(2): 613-617, Apr-Jun/2015. tab, graf
Article in English | LILACS | ID: lil-749716

ABSTRACT

In this study, we revealed that OA and UA significantly inhibited the expression of most genes related to peptidoglycan biosynthesis in S. mutans UA159. To the best of our knowledge, this is the first report to introduce the antimicrobial mechanism of OA and UA against S. mutans.


Subject(s)
Anti-Bacterial Agents/pharmacology , Biosynthetic Pathways/drug effects , Biosynthetic Pathways/genetics , Oleanolic Acid/pharmacology , Peptidoglycan/biosynthesis , Streptococcus mutans/drug effects , Triterpenes/pharmacology , Gene Expression Regulation, Bacterial/drug effects
7.
Braz. j. microbiol ; 45(2): 439-445, Apr.-June 2014. graf, tab
Article in English | LILACS | ID: lil-723099

ABSTRACT

The time courses for production of fungal biomass, lipid, phenolic and arachidonic acid (ARA) as well as expression of the genes involved in biosynthesis of ARA and lipid were examined in Mortierella alpina CBS 754.68. A significant increase in the arachidonic acid content in lipids that coincided with reduced levels of lipid was obtained. Reduced gene expression occurred presumably due to the steady reduction of carbon and nitrogen resources. However, these energy resources were inefficiently compensated by the breakdown of the accumulated lipids that in turn, induced up-regulated expression of the candidate genes. The results further indicated that the expression of the GLELO encoding gene is a rate-limiting step in the biosynthesis of ARA in the early growth phase.


Subject(s)
Arachidonic Acid/biosynthesis , Biosynthetic Pathways/genetics , Gene Expression Profiling , Mortierella/genetics , Mortierella/metabolism , Carbon/metabolism , Genes, Fungal , Nitrogen/metabolism , Real-Time Polymerase Chain Reaction
8.
Braz. j. microbiol ; 44(4): 1007-1034, Oct.-Dec. 2013. ilus, graf, tab
Article in English | LILACS | ID: lil-705250

ABSTRACT

The discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. In fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply adjust the focus from "micro" to "nano", that means changing the look from microorganisms to nanograms of DNA. Then, the search for new drugs, driven by genetic engineering combined with metagenomic strategies, shows us a way to bypass the barriers imposed by methodologies limited to isolation and culturing. However, we are far from solving the problem of supplying new molecules that are effective against the plasticity of multi- or pan-drug-resistant pathogens. Although the first advances in genetic engineering date back to 1990, there is still a lack of high-throughput methods to speed up the screening of new genes and design new molecules by recombination of pathways. In addition, it is necessary an increase in the variety of heterologous hosts and improvements throughout the full drug discovery pipeline. Among numerous studies focused on this subject, those on polyketide antibiotics stand out for the large technical-scientific efforts that established novel solutions for the transfer/engineering of major metabolic pathways using transposons and other episomes, overcoming one of the main methodological constraints for the heterologous expression of major pathways. In silico prediction analysis of three-dimensional enzymatic structures and advances in sequencing technologies have expanded access to the metabolic potential of microorganisms.


Subject(s)
Animals , Humans , Anti-Bacterial Agents/metabolism , Biosynthetic Pathways/genetics , Biotechnology/methods , Drug Discovery/methods , Metagenomics/methods , Polyketides/metabolism , Anti-Bacterial Agents/isolation & purification , Biotechnology/trends , Drug Discovery/trends , Metabolic Engineering/methods , Metabolic Engineering/trends , Metagenomics/trends , Polyketides/isolation & purification , Secondary Metabolism
9.
Braz. j. microbiol ; 44(2): 649-655, 2013. ilus, tab
Article in English | LILACS | ID: lil-688596

ABSTRACT

This study aims at evaluating the effects of Zataria multiflora (Z. multiflora) essential oil (EO) on growth, aflatoxin production and transcription of aflatoxin biosynthesis pathway genes. Total RNAs of Aspergillus parasiticus (A.parasiticus) ATCC56775 grown in yeast extract sucrose (YES) broth medium treated with Z. multiflora EO were subjected to reverse transcription-polymerase chain reaction (RT-PCR). Specific primers of nor-1, ver-1, omt-A and aflR genes were used. In parallel mycelial dry weight of samples were measured and all the media were assayed by high-pressure liquid chromatography (HPLC) for aflatoxinB1 (AFB1), aflatoxinB2 (AFB2), aflatoxinG1 (AFG1), aflatoxinG2 (AFG2) and aflatoxin total (AFTotal) production. The results showed that mycelial dry weight and aflatoxin production reduce in the presence of Z. multiflora EO (100 ppm) on day 5 of growth. It was found that the expression of nor-1, ver-1, omt-A and aflR genes was correlated with the ability of fungus to produce aflatoxins on day 5 in YES medium. RT-PCR showed that in the presence of Z.multiflora EO (100 ppm) nor-1, ver-1 and omtA genes expression was reduced. It seems that toxin production inhibitory effects of Z. multiflora EO on day 5 may be at the transcription level and this herb may cause reduction in aflatoxin biosynthesis pathway genes activity.


Subject(s)
Aflatoxins/biosynthesis , Antifungal Agents/metabolism , Aspergillus/drug effects , Biosynthetic Pathways/drug effects , Lamiaceae/chemistry , Oils, Volatile/metabolism , Transcription, Genetic/drug effects , Antifungal Agents/isolation & purification , Aspergillus/genetics , Aspergillus/growth & development , Aspergillus/metabolism , Biosynthetic Pathways/genetics , Chromatography, High Pressure Liquid , Gene Expression Profiling , Oils, Volatile/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction
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