Identifying Natural Product Biosynthetic Genes from a Soil Metagenome by Using T7 Phage Selection

Zhang, Keya; He, Jing; Yang, Min; Yen, Michelle; Yin, Jun

doi:10.1002/cbic.200900297

Cited by 16 publications

(12 citation statements)

References 62 publications

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“…Similar trends, in terms of relative differences, have been found for other soil samples (Castañeda & Barbosa, 2017). The higher differences in terms of relative abundance (1.1%) were found for the eggNOG category "Replication, recombination and repair", (which were also over-represented in Cq+Da) to fill gaps and complete the recombination process (Zhang et al, 2009). Insertion of a transposon in a certain genomic position may change underlying DNA sequences, subsequently activating or inactivating gene expression which ultimately may have an impact on their hosts' fitness (Aziz et al, 2010).…”

Section: Discussionsupporting

confidence: 75%

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants

Molina‐Montenegro

Ballesteros

Castro-Nallar

et al. 2018

Preprint

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Antarctica is one of the most stressful ecosystems worldwide with few vascular plants, which are limited by abiotic conditions. Here, plants such as Deschampsia antarctica (Da) could generate more suitable micro-environmental conditions for the establishment of other plants as Colobanthus quitensis (Cq). Although, plant-plant interaction is known to determine the plant performance, little is known about how microorganisms might modulate the ability of plants to cope with stressful environmental conditions. Several reports have focused on the possible ecological roles of microorganism with vascular plants, but if the rizospheric microorganisms can modulate the positive interactions among vascular Antarctic plants has been seldom assessed. In this study, we compared the rhizosphere microbiomes associated with Cq, either growing alone or associated with Da, using a shotgun metagenomic DNA sequencing approach and using eggNOG for comparative and functional metagenomics. Overall, results show higher diversity of taxonomic and functional groups in rhizospheric soil from Cq+Da than Cq. On the other hand, functional annotation shows that microorganisms from rhizospheric soil from Cq+Da have a significantly higher representation of genes associated to metabolic functions related with environmental stress tolerance than Cq soils. Additional research is needed to explore both the biological impact of these higher activities in terms of gene transfer on plant performance and in turn help to explain the still unsolved enigma about the strategy deployed by Cq to inhabit and cope with harsh conditions prevailing in Antarctica.

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Section: Discussionsupporting

confidence: 75%

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants

Molina‐Montenegro

Ballesteros

Castro-Nallar

et al. 2018

Preprint

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“…Microorganisms are considered to be the best indicators, due to their function, ubiquitous presence, and high sensitivity to pollutant stress (Andreoni et al, 2004;Abd Elsalam et al, 2006). However, as more than 99% of soil microorganisms cannot be cultivated by traditional laboratory techniques (Baker et al, 2001;Zhang et al, 2009a;Lee et al, 2010), culture-independent molecular techniques, such as denaturing gradient gel electrophoresis (DGGE), were developed to obtain both quantitative and qualitative microbial data in the respective environments (Ueno et al, 2001;Lee et al, 2010). The DGGE method has been widely applied to characterize microbial community shifts and to identify the affiliations of microbial populations affected by heavy metals, pesticides, polycyclic aromatic hydrocarbons (PAHs), and other pollutants in the soil (Andreoni et al, 2004;Wang et al, 2007;Wang et al, 2008;Zhang et al, 2009b).…”

Section: Introductionmentioning

confidence: 99%

Bacterial Communities of Polychlorinated Biphenyls Polluted Soil Around an E-waste Recycling Workshop

Tang

Qiao

Chen

et al. 2013

Soil and Sediment Contamination: An International Journal

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Polychlorinated biphenyls (PCBs) contamination that has resulted from the recycling of electronic power capacitors and transformers could lead to deterioration in soil quality and high ecological risk. As microorganisms are generally considered to be the best indicators of soil pollution, the diversity of bacterial communities in the soil around an e-waste recycling workshop in the Taizhou e-waste recycling area of China was studied using denaturing gradient gel electrophoresis (DGGE). The results indicated that the PCBs content in the soil decreased with increasing distance from the recycling workshop. Moreover, a gradual change in soil bacteria diversity along the PCBs pollution gradient was observed. Furthermore, the predominance of Proteobacteria and Bacteroidetes was found on the basis of sequence analysis and some highly similar subsequences of microorganisms were also found to be closely related to the catabolism of PCBs and other organic compounds. In a word, our results indicated that PCBs pollutants had an evident impact on the structure of the soil microbial community and the enriched microbes might serve to decompose PCBs in soil.

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“…Enzyme activities unique to secondary metabolism can be harnessed to greatly improve the efficiency of identifying eDNA clones with functional biosynthetic gene pathways for downstream phenotypic screens. Required for the posttranslational activation of NRPSs and PKSs, PPTases were harnessed in a phage display study to recover NRPS and PKS sequences from environmental samples [100]. By coupling pigment production or cellular growth to PPTase function, complementation of PPTase activity can be used to screen or select for eDNA clones that contain PKS and/or NRPS gene clusters [87, 101].…”

Section: Metagenomics-driven Drug Discoverymentioning

confidence: 99%

Using natural products for drug discovery: the impact of the genomics era

Zhang

Qiao

Ang

et al. 2017

Expert Opinion on Drug Discovery

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Introduction Evolutionarily selected over billions of years for their interactions with biomolecules, natural products have been and continue to be a major source of pharmaceuticals. In the 1990s, pharmaceutical companies scaled down their natural product discovery programs in favor of synthetic chemical libraries due to major challenges such as high rediscovery rates, challenging isolation, and low production titers. Propelled by advances in DNA sequencing and synthetic biology technologies, insights into microbial secondary metabolism provided have inspired a number of strategies to address these challenges. Areas covered This review highlights the importance of genomics and metagenomics in natural product discovery, and provides an overview of the technical and conceptual advances that offer unprecedented access to molecules encoded by biosynthetic gene clusters. Expert opinion Genomics and metagenomics revealed nature’s remarkable biosynthetic potential and her vast chemical inventory that we can now prioritize and systematically mine for novel chemical scaffolds with desirable bioactivities. Coupled with synthetic biology and genome engineering technologies, significant progress has been made in identifying and predicting the chemical output of biosynthetic gene clusters, as well as in optimizing cluster expression in native and heterologous host systems for the production of pharmaceutically relevant metabolites and their derivatives.

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Identifying Natural Product Biosynthetic Genes from a Soil Metagenome by Using T7 Phage Selection

Cited by 16 publications

References 62 publications

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants

Bacterial Communities of Polychlorinated Biphenyls Polluted Soil Around an E-waste Recycling Workshop

Using natural products for drug discovery: the impact of the genomics era

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