Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Summary

The goal of this protocol is to provide a detailed, step-by-step guide for assembling multi-gene constructs using the modular cloning system based on Golden Gate cloning. It also gives recommendations on critical steps to ensure optimal assembly based on our experiences.

Abstract

The Golden Gate cloning method enables the rapid assembly of multiple genes in any user-defined arrangement. It utilizes type IIS restriction enzymes that cut outside of their recognition sites and create a short overhang. This modular cloning (MoClo) system uses a hierarchical workflow in which different DNA parts, such as promoters, coding sequences (CDS), and terminators, are first cloned into an entry vector. Multiple entry vectors then assemble into transcription units. Several transcription units then connect into a multi-gene plasmid. The Golden Gate cloning strategy is of tremendous advantage because it allows scar-less, directional, and modular assembly in a one-pot reaction. The hierarchical workflow typically enables the facile cloning of a large variety of multi-gene constructs with no need for sequencing beyond entry vectors. The use of fluorescent protein dropouts enables easy visual screening. This work provides a detailed, step-by-step protocol for assembling multi-gene plasmids using the yeast modular cloning (MoClo) kit. We show optimal and suboptimal results of multi-gene plasmid assembly and provide a guide for screening for colonies. This cloning strategy is highly applicable for yeast metabolic engineering and other situations in which multi-gene plasmid cloning is required.

Introduction

Synthetic biology aims to engineer biological systems with new functionalities useful for pharmaceutical, agricultural, and chemical industries. Assembling large numbers of DNA fragments in a high-throughput manner is a foundational technology in synthetic biology. Such a complicated process can break down into multiple levels with decreasing complexity, a concept borrowed from basic engineering sciences^1,2. In synthetic biology, DNA fragments usually assemble hierarchically based on functionality: (i) Part level: "parts" refers to DNA fragments with a specific function, such as a promoter, a coding se....

Protocol

NOTE: The hierarchical cloning protocol offered in this toolkit can be divided into three major steps: 1. Cloning part plasmids; 2. Cloning transcription units (TUs); 3. Cloning multi-gene plasmids (Figure 1). This protocol starts from the primer design and ends with applications of the cloned multi-gene plasmid.

1. Primer design for cloning the part plasmid (pYTK001):

1. Design the forward and reverse primers containing flanking nucleotides TTT at the 5&.......

Discussion

The MoClo based cloning kit developed by Lee et al. provides an excellent resource for quick assembly of one to five transcription units into a multi-gene plasmid either for replication or integration into the yeast genome. The use of this kit eliminates the time-consuming cloning bottleneck that frequently exists for expressing multiple genes in yeast.

We tested five different conditions for the digestion/ligation cycles of Golden Gate cloning with T4 DNA ligase. We found that 30 cycles of di.......

Materials

Name	Company	Catalog Number	Comments
0.5 mm Glass beads	RPI research products	9831	For lysing yeast cells
Bacto Agar	BD & Company	214010	Component of the yeast complete synthetic medium (CSM)
Bacto Peptone	BD& Company	211677	Component of the yeast extract peptone dextrose medium (YPD)
BsaI-HFv2	New England Biolabs	R3733S	a highly efficient version of BsaI restriction enzyme
Carbenicillin	Fisher Bioreagents	4800-94-6	Antibiotic for screening at the transcription unit level
Chloramphenicol	Fisher Bioreagents	56-75-7	Antibiotic for screening at the entry vector level
CSM-His	Sunrise Sciences	1006-010	Amino acid supplement of the yeast complete synthetic medium (CSM)
Dextrose	Fisher Chemical	D16-500	Carbon source of the yeast complete synthetic medium (CSM)
Difco Yeast Nitrogen Base w/o Amino Acids	BD & Company	291940	Nitrogen source of the yeast complete synthetic medium (CSM)
dNTP mix	Promega	U1515	dNTPs for PCR
Esp3I	New England Biolabs	R0734S	a highly efficient isoschizomer of BsmBI
Frozen-EZ Yeast Trasformation II Kit	Zymo Research	T2001	For yeast transformation
Hexanes	Fisher Chemical	H302-1	For carotenoid extraction from yeast cells
Kanamycin	Fisher Bioreagents	25389-94-0	Antibiotic for screening at the multigene plasmid level
LB Agar, Miller	Fisher Bioreagents	BP1425-2	Lysogenic agar medium for E. coli culturing
LB Broth, Miller	Fisher Bioreagents	BP1426-2	Lysogenic liquid medium for E. coli culturing
Lycopene	Cayman chemicals	NC1142173	For lycopene quantification
MoClo YTK	Addgene	1000000061	Depositing Lab: John Deuber
Monarch Plasmid Miniprep Kit	New England Biolabs	T1010L	For plasmid purification from E.coli
Nanodrop Spectrophotometer	Thermo Scientific	ND2000c	For measuring accurate DNA concentrations
NotI-HF	New England Biolabs	R3189S	Restriction enzyme for integrative multigene plasmid linearization
Nourseothricin Sulphate	Goldbio	N-500-100	Antibiotic Selection marker for the pCAS plasmid used in this study
Phusion HF reaction Buffer (5X)	New England Biolabs	B0518S	Buffer for PCR using Phusion polymerase
Phusion High Fidelity DNA Polymerase	New England Biolabs	M0530S	High fidelity polymerase for all the PCR reactions
pLM494	Addgene	100539	Plasmid used to amplify crtI, crtYB and crtE used in this study
Quartz Cuvette	Thermo Electron	10050801	For quantifing carotenoids
T4 ligase	New England Biolabs	M0202S	Ligase for Golden Gate cloning
Thermocycler	BIO-RAD	1851148	For performing all the PCR and cloning reactions
Tissue Homogenizer	Bullet Blender	Model: BBX24	For homogenization of yeast cells
UV-Vis Spectrophotometer	Thermo Scientific	Genesys 150	For quantifing carotenoids
Yeast Extract	Fisher Bioreagents	BP1422-500	Component of the yeast extract peptone dextrose medium (YPD)
β-carotene	Alfa Aesar	AAH6010603	For β-carotene quantification