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New Target Gene Screening Using Shortened and Random sgRNA Libraries in Microbial CRISPR Interference
[Image: see text] CRISPR interference (CRISPRi) screening has been used for identification of target genes related to specific phenotypes using single-molecular guide RNA (sgRNA) libraries. In CRISPRi screening, the sizes of random sgRNA libraries contained with the original target recognition seque...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10028695/ https://www.ncbi.nlm.nih.gov/pubmed/36787424 http://dx.doi.org/10.1021/acssynbio.2c00595 |
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author | Jeong, Song Hee Kim, Hyun Ju Lee, Sang Jun |
author_facet | Jeong, Song Hee Kim, Hyun Ju Lee, Sang Jun |
author_sort | Jeong, Song Hee |
collection | PubMed |
description | [Image: see text] CRISPR interference (CRISPRi) screening has been used for identification of target genes related to specific phenotypes using single-molecular guide RNA (sgRNA) libraries. In CRISPRi screening, the sizes of random sgRNA libraries contained with the original target recognition sequences are large (∼10(12)). Here, we demonstrated that the length of the target recognition sequence (TRS) can be shortened in sgRNAs from the original 20 nucleotides (N(20)) to 9 nucleotides (N(9)) that is still sufficient for dCas9 to repress target genes in the xylose operon of Escherichia coli, regardless of binding to a promoter or open reading frame region. Based on the results, we constructed random sgRNA plasmid libraries with 5′-shortened TRS lengths, and identified xylose metabolic target genes by Sanger sequencing of sgRNA plasmids purified from Xyl(–) phenotypic cells. Next, the random sgRNA libraries were harnessed to screen for target genes to enhance violacein pigment production in synthetic E. coli cells. Seventeen target genes were selected by analyzing the redundancy of the TRS in sgRNA plasmids in dark purple colonies. Among them, seven genes (tyrR, pykF, cra, ptsG, pykA, sdaA, and tnaA) have been known to increase the intracellular l-tryptophan pool, the precursor of a violacein. Seventeen cells with a single deletion of each target gene exhibited a significant increase in violacein production. These results indicate that using shortened random TRS libraries for CRISPRi can be simple and cost-effective for phenotype-based target gene screening. |
format | Online Article Text |
id | pubmed-10028695 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-100286952023-03-22 New Target Gene Screening Using Shortened and Random sgRNA Libraries in Microbial CRISPR Interference Jeong, Song Hee Kim, Hyun Ju Lee, Sang Jun ACS Synth Biol [Image: see text] CRISPR interference (CRISPRi) screening has been used for identification of target genes related to specific phenotypes using single-molecular guide RNA (sgRNA) libraries. In CRISPRi screening, the sizes of random sgRNA libraries contained with the original target recognition sequences are large (∼10(12)). Here, we demonstrated that the length of the target recognition sequence (TRS) can be shortened in sgRNAs from the original 20 nucleotides (N(20)) to 9 nucleotides (N(9)) that is still sufficient for dCas9 to repress target genes in the xylose operon of Escherichia coli, regardless of binding to a promoter or open reading frame region. Based on the results, we constructed random sgRNA plasmid libraries with 5′-shortened TRS lengths, and identified xylose metabolic target genes by Sanger sequencing of sgRNA plasmids purified from Xyl(–) phenotypic cells. Next, the random sgRNA libraries were harnessed to screen for target genes to enhance violacein pigment production in synthetic E. coli cells. Seventeen target genes were selected by analyzing the redundancy of the TRS in sgRNA plasmids in dark purple colonies. Among them, seven genes (tyrR, pykF, cra, ptsG, pykA, sdaA, and tnaA) have been known to increase the intracellular l-tryptophan pool, the precursor of a violacein. Seventeen cells with a single deletion of each target gene exhibited a significant increase in violacein production. These results indicate that using shortened random TRS libraries for CRISPRi can be simple and cost-effective for phenotype-based target gene screening. American Chemical Society 2023-02-14 /pmc/articles/PMC10028695/ /pubmed/36787424 http://dx.doi.org/10.1021/acssynbio.2c00595 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Jeong, Song Hee Kim, Hyun Ju Lee, Sang Jun New Target Gene Screening Using Shortened and Random sgRNA Libraries in Microbial CRISPR Interference |
title | New Target Gene Screening Using Shortened and Random
sgRNA Libraries in Microbial CRISPR Interference |
title_full | New Target Gene Screening Using Shortened and Random
sgRNA Libraries in Microbial CRISPR Interference |
title_fullStr | New Target Gene Screening Using Shortened and Random
sgRNA Libraries in Microbial CRISPR Interference |
title_full_unstemmed | New Target Gene Screening Using Shortened and Random
sgRNA Libraries in Microbial CRISPR Interference |
title_short | New Target Gene Screening Using Shortened and Random
sgRNA Libraries in Microbial CRISPR Interference |
title_sort | new target gene screening using shortened and random
sgrna libraries in microbial crispr interference |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10028695/ https://www.ncbi.nlm.nih.gov/pubmed/36787424 http://dx.doi.org/10.1021/acssynbio.2c00595 |
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