Name: rapid assembly of multi-gene constructs using modular golden gate cloning
Uploaded: 2021-02-05T13:30:00
Description: Watch this Scientific Journal Video about Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning at JoVE.com

This work was funded by the Research Foundation for the State University of New York (Award #: 71272) and the IMPACT Award of University at Buffalo (Award #: 000077).

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):
<ol>
	<li>Design the forward and reverse primers containing flanking nucleotides TTT at the 5&...

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...

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 sciences1,2. In synthetic biology, DNA fragments usually assemble hierarchically based on functionality: (i) Part level: &#34;parts&#34; refers to DNA fragments with a specific function, such as a promoter, a coding sequence, a terminator, an origin of replication; (ii) Transcription units (TU) level: a TU consists of a promoter, a coding sequence, and a terminator capable of transcribing a single gene; (iii) Multi-gene level: a multi-gene plasmid contains multiple TUs frequently comprised of an entire metabolic pathway. This hierarchical assembly pioneered by the BioBrick community is the foundational concept for the assembly of large sets of DNAs in synthetic biology3.
In the past decade4,5,6,7, the Golden Gate cloning technique has significantly facilitated hierarchical DNA assembly2. Many other multi-part cloning methods, such as Gibson cloning8, ligation-independent cloning (SLIC)9, uracil excision-based cloning (USER)10, the ligase cycling reaction (LCR)11, and in vivo recombination (DNA Assembler)12,13, have also been developed so far. But Golden Gate cloning is an ideal DNA assembly method because it is independent of gene-specific sequences, allowing scar-less, directional, and modular assembly in a one-pot reaction. Golden Gate cloning takes advantage of type IIS restriction enzymes that recognize a non-palindromic sequence to create staggered overhangs outside of the recognition site2. A ligase then joins the annealed DNA fragments to obtain a multi-part assembly. Applying this cloning strategy to the modular cloning (MoClo) system has enabled the assemble of up to 10 DNA fragments with over 90% transformants screened containing the correctly assembled construct4.
The MoClo system offers tremendous advantages that have accelerated the design-build-test cycle of synthetic biology. Firstly, the interchangeable parts enable combinatorial cloning to test a large space of parameters rapidly. For example, optimizing a metabolic pathway usually requires cycling through many promoters for each gene to balance the pathway flux. The MoClo system can easily handle such demanding cloning tasks. Secondly, one needs to sequence the part plasmid but typically not the TU or the multi-gene plasmids. In most cases, screening by colony PCR or restriction digestion is sufficient for verification at the TU and multi-gene plasmid level. This is because cloning the part plasmid is the only step requiring PCR, which frequently introduces mutations. Thirdly, the MoClo system is ideal for building multi-gene complex metabolic pathways. Lastly, because of the universal overhangs, the part plasmids can be reused and shared with the entire bioengineering community. Currently, MoClo kits are available for plants14,15,5,16,17, fungi6,18,19,20,21,22, bacteria7,23,24,25,26,27, and animals28,29. A multi-kingdom MoClo platform has also been introduced recently30.
For Saccharomyces cerevisiae, Lee et al.6 have developed a versatile MoClo toolkit, an excellent resource for the yeast synthetic biology community. This kit comes in a convenient 96-well format and defines eight types of interchangeable DNA parts with a diverse collection of well-characterized promoters, fluorescent proteins, terminators, peptide tags, selection markers, origin of replication, and genome editing tools. This toolkit allows the assembly of up to five transcription units into a multi-gene plasmid. These features are valuable for yeast metabolic engineering, in which partial or entire pathways are over-expressed to produce targeted chemicals. Using this kit, researchers have optimized the production of geraniol, linalool31, penicillin32, muconic acid33, indigo34, and betalain35 in yeast.
Here we provide a detailed, step-by-step protocol to guide the use of the MoClo toolkit to generate multi-gene pathways for either episomal or genomic expression. Through extensive use of this kit, we have found that the accurate measurement of DNA concentrations is key to ensuring the equimolar distribution of each part in the Golden Gate reaction. We also recommend the T4 DNA ligase over the T7 DNA ligase because the former works better with larger numbers of overhangs36. Lastly, any internal recognition sites of BsmBI and BsaI must be removed or domesticated prior to assembly. Alternatively, one may consider synthesizing parts to remove multiple internal sites and to achieve simultaneous codon optimization. We demonstrate how to use this toolkit by expressing a five-gene pathway for &#946;-carotene and lycopene production in S. cerevisiae. We further show how to knock out the ADE2 locus using the genome-editing tools from this kit. These color-based experiments were selected for easy visualization. We also demonstrate how to generate fusion proteins and to create amino acid mutations using Golden Gate cloning.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.5 mm Glass beads</td>
			<td>RPI research products</td>
			<td>9831</td>
			<td>For lysing yeast cells</td>
		</tr>
		<tr>
			<td>Bacto Agar</td>
			<td>BD &#38; Company</td>
			<td>214010</td>
			<td>Component of the yeast complete synthetic medium (CSM)</td>
		</tr>
		<tr>
			<td>Bacto Peptone</td>
			<td>BD&#38; Company</td>
			<td>211677</td>
			<td>Component of the yeast extract peptone dextrose medium (YPD)</td>
		</tr>
		<tr>
			<td>BsaI-HFv2</td>
			<td>New England Biolabs</td>
			<td>R3733S</td>
			<td>a highly efficient version of BsaI restriction enzyme</td>
		</tr>
		<tr>
			<td>Carbenicillin</td>
			<td>Fisher Bioreagents</td>
			<td>4800-94-6</td>
			<td>Antibiotic for screening at the transcription unit level</td>
		</tr>
		<tr>
			<td>Chloramphenicol</td>
			<td>Fisher Bioreagents</td>
			<td>56-75-7</td>
			<td>Antibiotic for screening at the entry vector level</td>
		</tr>
		<tr>
			<td>CSM-His</td>
			<td>Sunrise Sciences</td>
			<td>1006-010</td>
			<td>Amino acid supplement of the yeast complete synthetic medium (CSM)</td>
		</tr>
		<tr>
			<td>Dextrose</td>
			<td>Fisher Chemical</td>
			<td>D16-500</td>
			<td>Carbon source of the yeast complete synthetic medium (CSM)</td>
		</tr>
		<tr>
			<td>Difco Yeast Nitrogen Base w/o Amino Acids</td>
			<td>BD &#38; Company</td>
			<td>291940</td>
			<td>Nitrogen source of the yeast complete synthetic medium (CSM)</td>
		</tr>
		<tr>
			<td>dNTP mix</td>
			<td>Promega</td>
			<td>U1515</td>
			<td>dNTPs for PCR</td>
		</tr>
		<tr>
			<td>Esp3I</td>
			<td>New England Biolabs</td>
			<td>R0734S</td>
			<td>a highly efficient isoschizomer of BsmBI</td>
		</tr>
		<tr>
			<td>Frozen-EZ Yeast Trasformation II Kit</td>
			<td>Zymo Research</td>
			<td>T2001</td>
			<td>For yeast transformation</td>
		</tr>
		<tr>
			<td>Hexanes</td>
			<td>Fisher Chemical</td>
			<td>H302-1</td>
			<td>For carotenoid extraction from yeast cells</td>
		</tr>
		<tr>
			<td>Kanamycin</td>
			<td>Fisher Bioreagents</td>
			<td>25389-94-0</td>
			<td>Antibiotic for screening at the multigene plasmid level</td>
		</tr>
		<tr>
			<td>LB Agar, Miller</td>
			<td>Fisher Bioreagents</td>
			<td>BP1425-2</td>
			<td>Lysogenic agar medium for E. coli culturing</td>
		</tr>
		<tr>
			<td>LB Broth, Miller</td>
			<td>Fisher Bioreagents</td>
			<td>BP1426-2</td>
			<td>Lysogenic liquid medium for E. coli culturing</td>
		</tr>
		<tr>
			<td>Lycopene</td>
			<td>Cayman chemicals</td>
			<td>NC1142173</td>
			<td>For lycopene quantification</td>
		</tr>
		<tr>
			<td>MoClo YTK</td>
			<td>Addgene</td>
			<td>1000000061</td>
			<td>Depositing Lab: John Deuber</td>
		</tr>
		<tr>
			<td>Monarch Plasmid Miniprep Kit</td>
			<td>New England Biolabs</td>
			<td>T1010L</td>
			<td>For plasmid purification from E.coli</td>
		</tr>
		<tr>
			<td>Nanodrop Spectrophotometer</td>
			<td>Thermo Scientific</td>
			<td>ND2000c</td>
			<td>For measuring accurate DNA concentrations</td>
		</tr>
		<tr>
			<td>NotI-HF</td>
			<td>New England Biolabs</td>
			<td>R3189S</td>
			<td>Restriction enzyme for integrative multigene plasmid linearization</td>
		</tr>
		<tr>
			<td>Nourseothricin Sulphate</td>
			<td>Goldbio</td>
			<td>N-500-100</td>
			<td>Antibiotic Selection marker for the pCAS plasmid used in this study</td>
		</tr>
		<tr>
			<td>Phusion HF reaction Buffer (5X)</td>
			<td>New England Biolabs</td>
			<td>B0518S</td>
			<td>Buffer for PCR using Phusion polymerase</td>
		</tr>
		<tr>
			<td>Phusion High Fidelity DNA Polymerase</td>
			<td>New England Biolabs</td>
			<td>M0530S</td>
			<td>High fidelity polymerase for all the PCR reactions</td>
		</tr>
		<tr>
			<td>pLM494</td>
			<td>Addgene</td>
			<td>100539</td>
			<td>Plasmid used to amplify crtI, crtYB and crtE used in this study</td>
		</tr>
		<tr>
			<td>Quartz Cuvette</td>
			<td>Thermo Electron</td>
			<td>10050801</td>
			<td>For quantifing carotenoids</td>
		</tr>
		<tr>
			<td>T4 ligase</td>
			<td>New England Biolabs</td>
			<td>M0202S</td>
			<td>Ligase for Golden Gate cloning</td>
		</tr>
		<tr>
			<td>Thermocycler</td>
			<td>BIO-RAD</td>
			<td>1851148</td>
			<td>For performing all the PCR and cloning reactions</td>
		</tr>
		<tr>
			<td>Tissue Homogenizer</td>
			<td>Bullet Blender</td>
			<td>Model: BBX24</td>
			<td>For homogenization of yeast cells</td>
		</tr>
		<tr>
			<td>UV-Vis Spectrophotometer</td>
			<td>Thermo Scientific</td>
			<td>Genesys 150</td>
			<td>For quantifing carotenoids</td>
		</tr>
		<tr>
			<td>Yeast Extract</td>
			<td>Fisher Bioreagents</td>
			<td>BP1422-500</td>
			<td>Component of the yeast extract peptone dextrose medium (YPD)</td>
		</tr>
		<tr>
			<td>&#946;-carotene</td>
			<td>Alfa Aesar</td>
			<td>AAH6010603</td>
			<td>For &#946;-carotene quantification</td>
		</tr>
	</tbody>
</table>

rapid assembly of multi-gene constructs using modular golden gate cloning

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.

Here the results of four replicative multi-gene plasmids for &#946;-carotene (yellow) and lycopene (red) production. One integrative multi-gene plasmid for disrupting the ADE2 locus was constructed, the colonies of which are red.
Cloning CDSs into the entry vector (pYTK001) 
ERG20 was amplified from the yeast genome and the three carotenoid genes crtE, crtYB, crtI</em...

Watch this Scientific Journal Video about Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning at JoVE.com

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

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.

The Golden Gate cloning method enables the rapid assembly of multiple genes in any user-defined arrangement. It utilizes type IIS restriction enzymes that ...

This is a detailed protocol for assembling multi-gene plasmids using the Yeast MoClo kit. This method enables the convenient cloning of a variety of multi-gene classmates. It is ideal for generating a big library of related parts.Begin by setting up the Golden Gate reaction mix. Add 20 femtomoles of each PCR product and the entry vector, one microliter of 10X T4 Ligase buffer, 0.5 microliters of Esp3I, and 0.5 microliters of T4 ligase. Add double-distilled water to bring the total volume to 10 microliters.Then, run the cloning reaction. Transform the entire reaction mix into the DH5 alpha strain or equivalent Escherichia coli chemically competent cells by heat shock. Spread the cells on an lb plate with 35 micrograms per milliliter chloramphenicol.Then incubate the plate at 37 degrees Celsius overnight. After 16 to 18 hours, take the plate out of the incubator and leave it at four degrees Celsius for about five hours to let the superfolder green fluorescent protein or sfGFP develop for a more intense green color. To screen the plate, place it on an ultra-violet or blue light transilluminator.The sfGFP containing colonies will fluoresce under the UV light. The green colonies are negative because they contain the uncut part plasmid. The white colonies are likely positive.The cloning is successful if there are 30 to 100%white colonies. Assemble an intermediate vector with the left connector, the sfGFP dropout, the right connector, a yeast selection marker, a yeast origin of replication, and the part plasmid with an mRFP1, an E.coli origin, and the ampicillin resistant gene. Perform the cloning reaction as described in the text manuscript.Transform the entire reaction mix into the DH5 alpha strain then spread the cells on an lb plate with 50 micrograms per milliliter carbenicillin or ampicillin. Incubate at 37 degrees Celsius overnight. After 16 to 18 hours, take the plate out of the incubator.The plate will contain both pale red and pale green colonies. Keep it at four degrees Celsius for about five hours to let the mRFP1 and sfGFP mature. Use a UV or blue light transilluminator to identify the green colonies which contain the potentially correct intermediate vector.Streak out the green colonies on an lb carbenicillin plate and incubate at 37 degrees Celsius overnight. On the next day, streak them out again on a chloramphenicol plate and incubate at 37 degrees Celsius overnight. The colonies growing on chloramphenicol plates contain misassembled plasmids.Once the intermediate vector has been successfully assembled, proceed with assembling the transcription units. This four-piece assembly contains the intermediate vector, a promoter, a CDS, and determinator. Purify the plasmids, record their concentrations, and dilute each plasmid to 20 femtomoles of DNA per microliter.After performing the cloning reaction, transform the entire cloning reaction mix into the DH5 alpha or equivalent E.coli competent cells and plate them on LBN carbenicillin. Then incubate the plate at 37 degrees Celsius overnight. After 16 to 18 hours, take the plate out of the incubator and keep it at four degrees Celsius for about five hours to let the sfGFP mature.Use a UV or a blue light transilluminator to identify the non-fluorescent white colonies which contain the potentially correct transcription units. Assemble an intermediate vector for the multi-gene plasmids as described in the text manuscript. Then transform the entire cloning reaction mix into DH5 alpha cells and plate them on lb with 50 micrograms per milliliter kanamycin.Incubate the plate at 37 degrees Celsius overnight. Perform red and green color-based screening, then streak and grow the green colonies on an lb kanamycin plate to screen for misassemblies as previously demonstrated. Next, assemble the multi-gene plasmid by setting up a cloning reaction as described in the text manuscript.Transform the entire cloning reaction mix into DH5 alpha cells and plate them on lb kanamycin. Incubate the plate at 37 degrees Celsius overnight. Then perform the green and white screening as previously described.This protocol was used to construct one integrative multi-gene plasmid for disrupting the ADE2 locus. Four replicative and one integrative multi-gene plasmids were assembled. The ratio of potentially correct colonies for the intermediate vector cloning was 1.83%Once the intermediate plasmid was cloned, the success rate of assembling multi-gene plasmids from the intermediate was 93.77%The negligible numbers of positive white colonies demonstrate a suboptimal assembly of multi-gene plasmids.After transforming into yeast, colonies producing beta-carotene and lycopene grew on day three. Four colonies from each plate were streaked out onto fresh plates and grown for two more days. The carotenoids were extracted and quantified by UV-Vis spectrophotometry.BTS1/ERG20 leads to 35 fold higher production of beta-carotene compared to the strain with ERG20 alone. Likewise, the production of lycopene is approximately 16.5 fold higher in the strain with BTS1/ERG20 compared to ERG20 alone. The multi-gene integrative plasmid was used for the disruption of the ADE2 locus, either with a gRNA and no helper DNA or with gRNA and a multi-gene integrative plasmid as helper DNA.After three to four days, red colonies were observed on the YPD plate with Nourseothricin, indicating that ADE2 had been successfully disrupted. While attempting this method, the most important thing to remember is to measure the DNA concentrations accurately and pipette carefully while setting up this reaction mix. This technique allows researchers in the field of Yeast Metabolic Engineering to survey a large number of genes and promoters for maximized product yield.

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