Zhi-Qiang Xiong

Recent Advances in the Discovery and Development of Marine Microbial Natural Products

Marine microbial natural products (MMNPs) have attracted increasing attention from microbiologists, taxonomists, ecologists, agronomists, chemists and evolutionary biologists during the last few decades. Numerous studies have indicated that diverse marine microbes appear to have the capacity to produce an impressive array of MMNPs exhibiting a wide variety of biological activities such as antimicrobial, anti-tumor, anti-inflammatory and anti-cardiovascular agents. Marine microorganisms represent an underexplored reservoir for the discovery of MMNPs with unique scaffolds and for exploitation in the pharmaceutical and agricultural industries. This review focuses on MMNPs discovery and development over the past decades, including innovative isolation and culture methods, strategies for discovering novel MMNPs via routine screenings, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology. The potential problems and future directions for exploring MMNPs are also discussed.

Diversity of endophytic fungi and screening of fungal paclitaxel producer from Anglojap yew, Taxus x media

BackgroundEndophytic fungi represent underexplored resource of novel lead compounds and have a capacity to produce diverse class of plant secondary metabolites. Here we investigated endophytic fungi diversity and screening of paclitaxel-producing fungi from Taxus x media.ResultsEighty-one endophytic fungi isolated from T. media were grouped into 8 genera based on the morphological and molecular identification. Guignardia and Colletotrichum were the dominant genera, whereas the remaining genera were infrequent groups. The genera Glomerella and Gibberella were first reported in Taxus. Three representative species of the distinct genera gave positive hits by molecular marker screening and were capable of producing taxol which were validated by HPLC-MS. Among these 3 taxol-producing fungi, the highest yield of taxol was 720 ng/l by Guignardia mangiferae HAA11 compared with those of Fusarium proliferatum HBA29 (240 ng/l) and Colletotrichum gloeosporioides TA67 (120 ng/l). This is the first report of taxol producer from Guignardia. Moreover, the lower similarities of ts and bapt between microbial and plant origin suggested that fungal taxol biosynthetic cluster might be repeatedly invented during evolution, nor horizontal gene transfer from Taxus species.ConclusionsTaxol-producing endophytic fungi could be a fascinating reservoir to generate taxol-related drug lead and to elucidate the remained 5 unknown genes or the potential regulation mechanism in the taxol biosynthesis pathway.

Quantitative Design of Regulatory Elements Based on High-Precision Strength Prediction Using Artificial Neural Network

Accurate and controllable regulatory elements such as promoters and ribosome binding sites (RBSs) are indispensable tools to quantitatively regulate gene expression for rational pathway engineering. Therefore, de novo designing regulatory elements is brought back to the forefront of synthetic biology research. Here we developed a quantitative design method for regulatory elements based on strength prediction using artificial neural network (ANN). One hundred mutated Trc promoter & RBS sequences, which were finely characterized with a strength distribution from 0 to 3.559 (relative to the strength of the original sequence which was defined as 1), were used for model training and test. A precise strength prediction model, NET90_19_576, was finally constructed with high regression correlation coefficients of 0.98 for both model training and test. Sixteen artificial elements were in silico designed using this model. All of them were proved to have good consistency between the measured strength and our desired strength. The functional reliability of the designed elements was validated in two different genetic contexts. The designed parts were successfully utilized to improve the expression of BmK1 peptide toxin and fine-tune deoxy-xylulose phosphate pathway in Escherichia coli. Our results demonstrate that the methodology based on ANN model can de novo and quantitatively design regulatory elements with desired strengths, which are of great importance for synthetic biology applications.

Construction of polyketide overproducing Escherichia coli strains via synthetic antisense RNAs based on in silico fluxome analysis and comparative transcriptome analysis.

Rapid assessment and optimization of the incompatible metabolic modules remain a challenge. Here, we developed a systematic approach to characterize the module interactions and improve the problematic modules during the 6-deoxyerythronolide B (6dEB) biosynthesis in E. coli. Tremendous differences in the overall trends of flux changes of various metabolic modules were firstly uncovered based on in silico fluxome analysis and comparative transcriptome analysis. Potential targets for improving 6dEB biosynthesis were identified through analyzing these discrepancies. All 25 predicted targets at modules of PP pathway and nucleotide metabolism were firstly tested for improving the 6dEB production in E. coli via synthetic antisense RNAs. Down-regulation of 18 targets genes leads to more than 20% increase in 6dEB yield. Combinatorial repression of targets with greater than 60% increase in 6dEB titer, e.g., anti-guaB/anti-zwf led to a 296.2% increase in 6dEB production (210.4 mg/L in flask) compared to the control (53.1 mg/L). This is the highest yield yet reported for polyketide heterologous biosynthesis in E. coli. This study demonstrates a strategy to enhance the yield of heterologous products in the chassis cell and indicates the effectiveness of antisense RNA for use in metabolic engineering.

Draft Genome Sequence of the Marine Streptomyces sp. Strain AA1529, Isolated from the Yellow Sea

Here we report the draft genome sequence of a Streptomyces strain, AA1529, isolated from marine sediment from the Yellow Sea. Its genome contains a subset of unique genes and gene clusters that encode diverse secondary metabolites, suggesting great potential as a source for the discovery of novel gene clusters and bioactive compounds.

Pathway mining-based integration of critical enzyme parts for de novo biosynthesis of steviolglycosides sweetener in Escherichia coli

Pathway mining-based integration of critical enzyme parts for de novo biosynthesis of steviolglycosides sweetener in Escherichia coli

Synthetic Biology Triggers New Era of Antibiotics Development

As a discipline to design and construct organisms with desired properties, synthetic biology has generated rapid progresses in the last decade. Combined synthetic biology with the traditional process, a new universal workflow for drug development has been becoming more and more attractive. The new methodology exhibits more efficient and inexpensive comparing to traditional methods in every aspect, such as new compounds discovery & screening, process design & drug manufacturing. This article reviews the application of synthetic biology in antibiotics development, including new drug discovery and screening, combinatorial biosynthesis to generate more analogues and heterologous expression of biosynthetic gene clusters with systematic engineering the recombinant microbial systems for large scale production.

Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated from the Yellow Sea, China

Here, we report the draft genome sequence of Streptomyces sp. strain AA0539, isolated from marine sediment of the Yellow Sea, China. Its small genome (∼5.8 Mb) contains large, unique genes and gene clusters for diverse secondary metabolites, suggesting great potential as a source for the discovery of novel natural products.

The Mechanism of Antifungal Action of a New Polyene Macrolide Antibiotic Antifungalmycin 702 from Streptomyces padanus JAU4234 on the Rice Sheath Blight Pathogen Rhizoctonia solani

Antifungalmycin 702, a new polyene macrolide antibiotic produced by Streptomyces padanus JAU4234, has a broad antifungal activity and may have potential future agricultural and/or clinical applications. However, the mechanism of antifungal action of antifungalmycin 702 remains unknown. Antifungalmycin 702 strongly inhibited mycelial growth and sclerotia formation/germination of Rhizoctonia solani. When treated with antifungalmycin 702, the hyphae morphology of R . solani became more irregular. The membrane and the cellular organelles were disrupted and there were many vacuoles in the cellular space. The lesion in the plasma membrane was detected through the increase of membrane permeability, lipid peroxidation and leakage of cell constituents. In summary, antifungalmycin 702 may exert its antifungal activity against R . solani by changing the structure of cell membranes and the cytoskeleton and interacting with the organelles.

Enhanced production of avermectin by deletion of type III PKSs biosynthetic cluster rpp in Streptomyces avermitilis

The rpp biosynthetic gene cluster (sav7130–7131) in Streptomyces avermitilis contains a type III polyketide synthases (PKSs) and a cytochrome P450 and was reportedly involved in producing a diffusible brown pigment. Since the same precursor malonyl‐CoA was used as substrate for the type I PKSs and type III PKSs, there might be a competition for precursor between rpp gene cluster and avermectin biosynthetic cluster. In this work, rpp biosynthetic gene cluster deletion mutants were constructed to improve avermectin production. In an industrial strain AV‐LP, rpp deletion improved avermectin production from 1024 to 1262 mg l−1 without any effect on the cell growth. In the same way, the production of an industrial overproducer increased from 3582 to 4450 mg l−1. Transcriptional analysis suggested that the deletion of rpp gene cluster stimulated transcription of aveR, leading to increased transcription of biosynthetic gene aveA1 and a consequent increase in avermectin production.