Recent progress in computational tools for designing editing sequences used in microbial genetic manipulations

doi:10.12211/2096-8280.2022-055

Abstract

Abstract:

Genetic manipulations such as homologous recombination and CRISPR are basic technologies of synthetic biology aiming to design and construct artificial life. One key factor affecting the efficiency and accuracy of microbial genetic manipulations is the editing sequences (ES), namely the assisting sequences used for precisely locating and editing a target sequence in a genome, such as a primer, a homologous arm or a sgRNA sequence. For different genetic manipulation technologies, diverse manipulation types and multiple ESs are required for different stages of manipulation processes, especially for the high-throughput design with recently developed biofoundries to enable automatic strain modifications. Therefore, it is becoming essential to use computational tools for precise, fast, high-throughput and whole workflow ES design. This article reviews tools for ES design at different stages using various microbial genetic manipulation technologies. The tools are classified into four categories based on the types of ESs and their application scenario: primer design, DNA assembly design, sgRNA design and whole workflow ES design. We first give a brief introduction to the tools used for basic primer design with an emphasis on the widely used open-source tool Primer3. Then we have an extensive discussion on the tools used in the design of ESs for DNA assembly using technologies like Gibson and Golden Gate assembly which are required for linking the editing sequences and/or the inserted sequences together as one big fragment to be transformed into target strains. Various tools for designing sgRNA used in the latest CRISPR technologies for genome and base editing are also evaluated and compared in detail. Moreover, we argue that one-stop ES design tools which integrate various design methods to cover the whole genetic manipulation workflow would be very important in addressing challenges for the high throughput design raised by automatic strain construction biofoundries to enable highly precise and efficient genome editing for different sequence manipulations at any location and in any organism. These ES design tools will seamlessly link the genotype "Design" step and the strain "Build" step in the "design-build-test-learn (DBTL)" working cycle of synthetic biology to facilitate the creation of artificial organisms. {L-End}

Key words: editing sequences, DNA assembly, genome editing, whole workflow design, biofoundry

摘要：

以同源重组、CRISPR等为代表的遗传操作技术是合成生物学的重要支撑技术。高效准确的遗传操作依赖于可准确定位编辑位点和实现序列改造的编辑序列（如引物序列、同源臂序列、sgRNA序列等）。由于遗传改造目标与遗传操作技术丰富多变，加之近年来基于生物铸造厂（BioFoundry）的自动化遗传改造模式对高通量设计的需求日益增加，使得通过计算机辅助设计工具实现精准快速的编辑序列设计愈发重要。本文针对不同阶段实现不同目标的微生物遗传操作技术和相应的编辑序列辅助设计工具的发展进行了综述。按照不同编辑序列类型和遗传操作应用场景，将编辑序列设计工具划分为四种类型：引物设计工具、DNA组装的设计工具、sgRNA设计工具、基因组编辑的全流程设计工具，对各类编辑序列设计工具的应用及存在的问题进行了分析总结并对未来的研究方向进行了展望。编辑序列设计工具的发展将有助于实现合成生物学“设计—构建—测试—学习”（design-build-test-learn，DBTL）工作循环中上游的基因型“设计”与下游“构建”两个关键环节之间的无缝衔接。

关键词: 编辑序列, DNA组装, 基因组编辑, 全流程设计, 生物工厂

CLC Number:

Q939.97

Yi YANG, Yufeng MAO, Chunhe YANG, Meng WANG, Xiaoping LIAO, Hongwu MA. Recent progress in computational tools for designing editing sequences used in microbial genetic manipulations[J]. Synthetic Biology Journal, 2023, 4(1): 30-46.

杨毅, 毛雨丰, 杨春贺, 王猛, 廖小平, 马红武. 面向微生物遗传操作的编辑序列设计工具的研究进展[J]. 合成生物学, 2023, 4(1): 30-46.

Figures/Tables 8

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工具	基于Primer3	特异性检验	批量设计	功能特色	可用性	URL
Primer3^{[15, 26-27]}	—	否	否	基础引物设计	在线/图形界面、离线/命令行	https://bioinfo.ut.ee/primer3/
BatchPrimer3^[28]	是	否	是	批量引物设计	在线/图形界面	http://probes.pw.usda.gov/cgi-bin/batchprimer3/batchprimer3.cgi
ConservedPrimer2.0^[35]	是	是	是	Sanger测序引物设计	在线/图形界面	https://probes.pw.usda.gov/ConservedPrimers/index.html
PrimerDesign-M^[40]	否	是	是	Sanger测序引物设计	在线/图形界面	www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html
Primer-BLAST^[41]	是	是	否	RT-PCR引物设计	在线/图形界面	https://www.ncbi.nlm.nih.gov/tools/primer-blast/
PCR designer^[42]	否	否	否	SNP分析引物设计	在线/图形界面	http://primer1.soton.ac.uk/primer.html
PRIMEGENS-v2^[37]	是	否	是	剪接变体引物设计	在线/图形界面、离线/命令行	http://primegens.org/
PrimerSeq^[43]	是	否	是	剪接变体引物设计	离线/图形界面	https://primerseq.sourceforge.net/
MSP-HTPrimer^[44]	是	否	是	DNA甲基化分析引物设计	离线/命令行	https://sourceforge.net/projects/msp-htprimer/
MPD^[45]	否	是	是	多重PCR引物设计	离线/命令行	https://wingolab-org.github.io/mpd-c/
Mutation Maker^[46]	是	是	是	多重PCR引物设计、氨基酸突变引物设计	离线/命令行	https://github.com/ra100/Mutation_Maker
PerlPrimer^[47]	否	否	是	Sanger测序引物设计、RT-PCR引物设计、开放阅读框（ORF）搜索及相关引物设计	离线/图形界面	https://perlprimer.sourceforge.net/

工具	基于Primer3	特异性检验	批量设计	功能特色	可用性	URL
Primer3^{[15, 26-27]}	—	否	否	基础引物设计	在线/图形界面、离线/命令行	https://bioinfo.ut.ee/primer3/
BatchPrimer3^[28]	是	否	是	批量引物设计	在线/图形界面	http://probes.pw.usda.gov/cgi-bin/batchprimer3/batchprimer3.cgi
ConservedPrimer2.0^[35]	是	是	是	Sanger测序引物设计	在线/图形界面	https://probes.pw.usda.gov/ConservedPrimers/index.html
PrimerDesign-M^[40]	否	是	是	Sanger测序引物设计	在线/图形界面	www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html
Primer-BLAST^[41]	是	是	否	RT-PCR引物设计	在线/图形界面	https://www.ncbi.nlm.nih.gov/tools/primer-blast/
PCR designer^[42]	否	否	否	SNP分析引物设计	在线/图形界面	http://primer1.soton.ac.uk/primer.html
PRIMEGENS-v2^[37]	是	否	是	剪接变体引物设计	在线/图形界面、离线/命令行	http://primegens.org/
PrimerSeq^[43]	是	否	是	剪接变体引物设计	离线/图形界面	https://primerseq.sourceforge.net/
MSP-HTPrimer^[44]	是	否	是	DNA甲基化分析引物设计	离线/命令行	https://sourceforge.net/projects/msp-htprimer/
MPD^[45]	否	是	是	多重PCR引物设计	离线/命令行	https://wingolab-org.github.io/mpd-c/
Mutation Maker^[46]	是	是	是	多重PCR引物设计、氨基酸突变引物设计	离线/命令行	https://github.com/ra100/Mutation_Maker
PerlPrimer^[47]	否	否	是	Sanger测序引物设计、RT-PCR引物设计、开放阅读框（ORF）搜索及相关引物设计	离线/图形界面	https://perlprimer.sourceforge.net/

工具	基于Primer3	支持的DNA片段组装技术	批量设计	可用性	URL
J5^[16]	是	Golden Gate/Gibson/ CPEC/SLIC	是	在线/图形界面	https://j5.jbei.org/
Geneious	否	Gibson	是	在线/图形界面	https://www.geneious.com/
Raven^[59]	否	Gibson	是	在线/图形界面	http://ravencad.org/
MCDS^[60]	否	GoldenGate/Gibson/ SLIC/Gateway	否	离线/命令行	https://github.com/errisy/MCDS
NEBbridge Golden Gate^[61]	未知	Golden Gate	是	在线/图形界面	https://goldengate.neb.com/
iBioCAD GGA^[62]	未知	Golden Gate	是	在线/图形界面	https://ibiocad.igb.illinois.edu/
PlasmidMaker^[13]	是	Golden Gate/Gibson	是	在线/图形界面	https://biofoundry.web.illinois.edu/

工具	基于Primer3	支持的DNA片段组装技术	批量设计	可用性	URL
J5^[16]	是	Golden Gate/Gibson/ CPEC/SLIC	是	在线/图形界面	https://j5.jbei.org/
Geneious	否	Gibson	是	在线/图形界面	https://www.geneious.com/
Raven^[59]	否	Gibson	是	在线/图形界面	http://ravencad.org/
MCDS^[60]	否	GoldenGate/Gibson/ SLIC/Gateway	否	离线/命令行	https://github.com/errisy/MCDS
NEBbridge Golden Gate^[61]	未知	Golden Gate	是	在线/图形界面	https://goldengate.neb.com/
iBioCAD GGA^[62]	未知	Golden Gate	是	在线/图形界面	https://ibiocad.igb.illinois.edu/
PlasmidMaker^[13]	是	Golden Gate/Gibson	是	在线/图形界面	https://biofoundry.web.illinois.edu/

工具	编辑效率预测方法	特异性预测方法	PAM	支持的改造类型	URL
E-CRISP^[98]	假设先验	假设先验	NGG	敲除、激活、抑制	http://www.e-crisp.org/E-CRISP/index.html
CRISPR-ERA^[99]	假设先验	假设先验	NGG	敲除、激活、抑制	http://CRISPR-ERA.stanford.edu
EuPaGDT^[100]	假设先验	假设先验	NGG、TTTN、NGA等	敲除	http://grna.ctegd.uga.edu/
CRISPOR^{[94, 101]}	假设先验/机器学习	假设先验	NGG、TTTN、NGA等	敲除	http://crispor.tefor.net/
CHOPCHOP^{[17, 102-103]}	假设先验/机器学习	假设先验	NGG、TTTN、NGA等	敲除、敲入、激活、抑制	http://chopchop.cbu.uib.no/
CRISPETa^[104]	假设先验	数据库搜索	NGG	敲除	http://crispeta.crg.eu
CRISPR-P^[105]	假设先验	假设先验	NGG、NRG、TTN等	敲除	http://crispr.hzau.edu.cn/CRISPR2/
CRISPRscan^[106]	机器学习	假设先验	NGG、TTTN、NGN等	敲除	https://www.crisprscan.org
WU-CRISPR^[107]	机器学习	假设先验	NGG	敲除	http://crisprdb.org/wu-crispr/
CRISTA^[108]	机器学习	机器学习	NGG	敲除	https://crista.tau.ac.il/
Elevation^[109]	机器学习	机器学习	NGG	敲除	https://crispr.ml/