The Next Generation of Molecular Tools for Natural Products

Varigen is developing revolutionary products for the sequence specific capture, amplification, sequencing, and over expression of long DNA (20-150 Kb) to dramatically simplify the production of natural products.

BigDNA™ Soil Metagenomic Libraries

Soil microorganisms encode a vast diversity of bioactive natural products; however, the majority of soil microbial taxa are recalcitrant to cultivation under laboratory conditions. Varigen’s BigDNA™ Soil Metagenomic Libraries contain 100 kb inserts, unlike most conventional soil library resources, ensuring more full length pathways are captured. Millions of new and variant genes and thousands of natural product pathways with complete operons from the most diverse microbial environment on earth are found in these unique products. Two large insert soil metagenomic libraries have been constructed and found to contain thousands of natural product pathways by sequencing as well as novel compounds and bioactivities by screening. The rediscovery rate for natural product pathways is less than 1%.

 

Library BAC
Clones
Average
Insert
Size
Giga bp Approximate
# Genes
Complete Insert
Sequenced
Anti-Microbial
Activity
Known
Structures
BigDNA™
Soil Diversity 1
19,200 110 Kb 2.1 1 Million Yes 33 Clones 9
BigDNA™
Soil
Diversity 2
103,680 100 Kb 10.3 5 Million In Development NA NA

 

The BigDNA™ Soil Metagenomic Libraries contain ~ 6 x 106 genes combined. The Soil Diversity 1 library has been fully sequenced and found to contain 1516 natural product pathways, 593 of which are classified as containing PKS or NRPS. These cloned pathways are very divergent from known pathways found by any other means, with the GC content varying from 41 to 76% and the amino acid identity of the KS domains ranging from 42 to 79% to the best matching BLAST hit. Screening the entire library in the original E. coli cloning host revealed 28 BACs with anti-MRSA activity and 14 compounds. 593 BACs identified by NGS to contain novel PKS and/or NRPS pathways are being shuttled into Streptomyces strains for functional expression of active compounds. Expression of PKS pathway-containing clones resulted in multiple cases of heterologous expression as determined by anti-infective and anti-cancer screening and structural analysis. These results indicate a high degree of unique sequence space has been recovered on large-insert metagenomic clones. A second library containing 103,000 large insert clones (10.3 Gbp) is being characterized by NGS to elucidate the contents of each BAC insert. These libraries are ideal for anti-microbial, anti-fungal, anti-viral, anti-cancer or enzyme discovery research.

 

BigDNA™ Soil Metagenomic Libraries are the only large insert libraries that contain full pathways and have been sequenced

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Varigen Biosciences
505 S. Rosa Road
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Madison, WI 53719

ABOUT VARIGEN

Varigen Biosciences Corporation is an NIH- and NSF-funded effort to harness naturally occurring variety of life in soil to develop the next generation of natural products through metagenomics. Varigen’s team is led by researchers with over 125 years of combined experience.