Manipulating Natural Product Biosynthetic Pathways via DNA Assembler

Zengyi Shao1, Huimin Zhao2

1 Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 2 Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana‐Champaign, Urbana, Illinois
Publication Name:  Current Protocols in Chemical Biology
Unit Number:   
DOI:  10.1002/9780470559277.ch130191
Online Posting Date:  June, 2014
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DNA assembler is an efficient synthetic biology method for constructing and manipulating biochemical pathways. The rapidly increasing number of sequenced genomes provides a rich source for discovery of gene clusters involved in synthesizing new natural products. However, both discovery and economical production are hampered by our limited knowledge in manipulating most organisms and the corresponding pathways. By taking advantage of yeast in vivo homologous recombination, DNA assembler synthesizes an entire expression vector containing the target biosynthetic pathway and the genetic elements needed for DNA maintenance and replication. Here we use the spectinabilin clusters originated from two hosts as examples to illustrate the guidelines of using DNA assembler for cluster characterization and silent cluster activation. Such strategies offer unprecedented versatility in cluster manipulation, bypass the traditional laborious strategies to elicit pathway expression, and provide a new platform for de novo cluster assembly and genome mining for discovering new natural products. Curr. Protoc. Chem. Biol. 6:65‐100 © 2014 by John Wiley & Sons, Inc.

Keywords: natural product; gene cluster; regulation of natural product biosynthesis; pathway engineering; synthetic biology; cryptic pathway; DNA assembler

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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Characterization of the spn Gene Cluster via Direct Cloning
  • Basic Protocol 2: Reconstructing the Silent nor Gene Cluster from S. orinoci
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: Characterization of the spn Gene Cluster via Direct Cloning

  • S. spectabilis genomic DNA isolated using Wizard Genomic DNA Purification Kit (Promega)
  • FailSafe PCR 2×PreMix G (EPICENTRE Biotechnologies)
  • Primers (Table 13.1.9100)
  • Phusion DNA polymerase and GC Reaction buffer (New England Biolabs)
  • Dimethyl sulfoxide (DMSO)
  • dNTP premix containing 10 mM each nucleotide
  • Template plasmid pRS416 (New England Biolabs)
  • Template plasmid pAE4 (New England Biolabs)
  • QIAquick Gel Extraction Kit (Qiagen)
  • 3 M sodium acetate
  • 10 mg/ml glycogen
  • 100% ethanol
  • S. cerevisiae strain HZ848 or any auxotrophic S. cerevisiae strain (see annotation to step 5, below)
  • YPAD medium (see recipe)
  • 1 M sorbitol
  • SC‐Ura plates (see recipe)
  • SC‐Ura liquid medium (see recipe)
  • Zymoprep II kit (Zymo Research)
  • E. coli BW25141 cells or other E. coli strain (see annotation to step 10, below)
  • SOC medium (see recipe)
  • LB+Apr agar plates (see recipe)
  • 50 mg/ml apramycin (Apr)
  • LB liquid medium (see recipe)
  • QIAprep Miniprep Kit (Qiagen)
  • Restriction enzymes ApaLI, NotI, SacI, SspI, PacI, XhoI and corresponding 10× NEBuffers supplied with enzymes (New England Biolabs)
  • 100× BSA (New England Biolabs)
  • QIAquick Gel Extraction Kit (Qiagen)
  • E. coli WM6026 cells (details of strain construction can be obtained by request from the authors)
  • 38 mg/ml 2,6‐diaminopimelic acid (DAP; Sigma, cat. no. D1377)
  • Apramycin
  • LB+Apr+DAP plates (see recipe)
  • Streptomyces lividans spores (prepared as described in Tobias Kieser et al., )
  • R2‐sucrose agar plates (see recipe)
  • Nalidixic acid
  • ISP+Apr agar plates (see recipe)
  • MYG liquid medium (see recipe)
  • Ethyl acetate
  • Thermal cycler
  • Nanodrop microspectrophotometer (Thermo Fisher Scientific)
  • Incubator with shaker
  • Spectrophotometer for measurement of OD 600
  • Benchtop refrigerated centrifuge and microcentrifuge
  • 0.2 cm‐gap electroporation cuvette (Thermo Fisher Scientific), prechilled
  • Rotary evaporator
  • Agilent 1100 series LC/MSD XCT plus ion trap mass spectrometer
  • Agilent SB‐C18 reversed‐phase column
  • Additional reagents and equipment for agarose gel electrophoresis (Voytas, )
Table 3.1.1   MaterialsPrimers Used for Assembling the spn Cluster

Construct Primer name Primer sequence (5′‐3′)
pZS‐SpnDEFJAGKH spn‐1‐for gtagaaacagacgaagaagctagctttgcactggattgcgcccctgctcacggacgcgga
spn‐1‐rev gaagtcgaagtcgacctcac
spn‐2‐for cgcccgggacgactcgatcc
spn‐2‐rev gggtgtggccgatgttggac
spn‐3‐for ctgcgcaagggcgagtgccg
spn‐3‐rev agggcgtcgaccgtcacgac
spn‐4‐for gacgtcaccctctactcccg
spn‐4‐rer tcacaggggttcgccgggca
spn‐5‐for ccggaggtgaagcacaccgg
spn‐5‐rev cacgtgatgaaaaggacccaggtggcacttttcgaatatttcacgcggcgccgaagcgca
SspI‐yeast‐for aatattcgaaaagtgccacctgggtc
PacI‐yeast‐rev ttaattaagtgagtttagtatacatgca
PacI‐E. coli‐for attataagtaaatgcatgtatactaaactcacttaattaatgtcatcacgatactgtgat
E. coli‐rev ggcccatgagttcggccacgtccgcgtccgtgagcaggggcgatctgctcacggtaactg
pZS‐Spn(H)A’(B) spn‐6‐for caaatacggcatcagttaccgtgagcagatcgttaattaaactcgcgccccaggcggtcg
spn‐6‐rev tacggcgagggactccacgg
spn‐7‐for ttggaggcgtggccgccacc
spn‐7‐rev catccggtcgtagaactccg
spn‐8‐for ggctcgccggagaccctcct
spn‐8‐rev cacgtgatgaaaaggacccaggtggcacttttcgaatattcccaggcggtctccaggagc
SspI‐yeast‐for aatattcgaaaagtgccacctgggtc
yeast‐rev gtgagtttagtatacatgca
E. coli‐for aaaactgtattataagtaaatgcatgtatactaaactcactgtcatcacgatactgtgat
PacI‐E. coli‐rev gcagcacctcctcgaccgcctggggcgcgagtttaattaacgatctgctcacggtaactg
pZS‐SpnBCILM spn‐9‐for caaatacggcatcagttaccgtgagcagatcgttaattaaatgcccgctggtgacgagag
spn‐9‐rev atgacgtggtccgcgagcca
spn‐10‐for ccgcccaccctcccgatcgt
spn‐10‐rev ctcgtggcggtccgcgacct
spn‐11‐for ttcgccgaggccgcgtccgt
spn‐11‐rev gggtcgccgagcgcggtgcc
spn‐12‐for gctggtggccctgcacctgg
spn‐12‐rev gcagcggctcctgccaggtg
spn‐13‐for ggccctcgtcttccagcacc
spn‐13‐rev ttatagcacgtgatgaaaaggacccaggtggcacttttcggcgctgcccgaggcggccgg
yeast‐for cgaaaagtgccacctgggtc
SspI‐yeast‐rev aatattgtgagtttagtatacatgca
SspI‐E. coli‐for gtattataagtaaatgcatgtatactaaactcacaatatttgtcatcacgatactgtgat
PacI‐E. coli‐rev gcctcgacgaacctctcgtcaccagcgggcatttaattaacgatctgctcacggtaactg
pZS‐SpnMutK spnK‐stop199‐rev cggtcgcggtgtccgggtccgtgccgaagagcgtgcgtcagtcgtcggcgaggcgccgca
spnK‐stop199‐for ggccgcgtccgcgggctcggcctgcatctgcggcgcctcgccgacgactgacgcacgctcttcggcac
pZS‐SpnBCIM spnM‐rev ttatagcacgtgatgaaaaggacccaggtggcacttttcgacgcgcgacctgccatccct
pZS‐SpnBCI spnI‐rev ttatagcacgtgatgaaaaggacccaggtggcacttttcgggcgactccggagcgtgtac
Master helper plasmid yeast‐for cgaaaagtgccacctgggtc
SspI‐yeast‐rev aatattgtgagtttagtatacatgca
SspI–Strep‐for gtattataagtaaatgcatgtatactaaactcacaatattatggcgcgccgacgtgctca
PacI‐Strep‐rev attagccatggcatcacagtatcgtgatgacattaattaacgcaatccagtgcaaagcta
PacI‐E.coli‐for gacgaagaagctagctttgcactggattgcgttaattaatgtcatcacgatactgtgatg
E. coli‐rev ttatagcacgtgatgaaaaggacccaggtggcacttttcgaccggtcgatctgctcacgg

Basic Protocol 2: Reconstructing the Silent nor Gene Cluster from S. orinoci

  • Streptomyces griseus
  • RNeasy Mini Kit (Qiagen) containing buffers RLT, RW1, RPE, columns, and collection tubes
  • RNase‐free H 2O (available from most molecular biology suppliers)
  • TE buffer (see recipe)
  • Lysozyme
  • 2‐mercaptoethanol
  • 100% ethanol
  • Ambion 10× TURBO DNase Buffer, TURBO DNase, and inactivation reagent (Life Technology)
  • First‐strand cDNA Synthesis Kit (Roche Applied Science)
  • Dithiothreitol (DTT)
  • Transcriptor reverse transcriptase (Roche Applied Science)
  • Primers for real‐time PCR (designed and synthesized by Integrated DNA Technologies)
  • S. griseus and S. orinoci genomic DNA isolated using Wizard Genomic DNA Purification Kit (Promega)
  • SYBR Green PCR Master Mix (Life Technologies, cat. no. 4368577)
  • Restriction enzymes: AflII, NdeI, and AvrII and corresponding 10× buffers (New England Biolabs)
  • T4 DNA ligase and T4 DNA ligation buffer (New England Biolabs)
  • LB+Apr liquid medium (see recipe)
  • ϵ‐Caprolactam (Sigma, cat. no. C2204)
  • 3‐ to 4‐mm glass beads (Fisher Scientific, cat. no. 580024)
  • MicroAmp optical 384‐well reaction plate (Applied Biosystems)
  • 7900HT Fast Real‐Time PCR System (Applied Biosystems)
  • SDS2.4 software (Applied Biosystems)
  • Thermal cycler
  • Additional reagents and equipment for characterization of the spn gene cluster via direct cloning ( protocol 1) and XylE activity assay (Tobias Kieser et al., )
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