SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing

Abstract

Background Microbial strain information databases provide valuable data for microbial basic research and applications. However, they rarely contain information on the genetic operating system of microbial strains. Results We established a comprehensive microbial strain database, SynBioStrainFinder, by integrating CRISPR/Cas gene-editing system information with cultivation methods, genome sequence data, and compound-related information. It is presented through three modules, Strain2Gms/PredStrain2Gms, Strain2BasicInfo, and Strain2Compd, which combine to form a rapid strain information query system conveniently curated, integrated, and accessible on a single platform. To date, 1426 CRISPR/Cas gene-editing records of 157 microbial strains have been manually extracted from the literature in the Strain2Gms module. For strains without established CRISPR/Cas systems, the PredStrain2Gms module recommends the system of the most closely related strain as a reference to facilitate the construction of a new CRISPR/Cas gene-editing system. The database contains 139,499 records of strain cultivation and genome sequences, and 773,298 records of strain-related compounds. To facilitate simple and intuitive data application, all microbial strains are also labeled with stars based on the order and availability of strain information. SynBioStrainFinder provides a user-friendly interface for querying, browsing, and visualizing detailed information on microbial strains, and it is publicly available at http://design.rxnfinder.org/biosynstrain/. Conclusion SynBioStrainFinder is the first microbial strain database with manually curated information on the strain CRISPR/Cas system as well as other microbial strain information. It also provides reference information for the construction of new CRISPR/Cas systems. SynBioStrainFinder will serve as a useful resource to extend microbial strain research and application for biomanufacturing.

MCF2Chem: A manually curated knowledge base of biosynthetic compound production

“…For microbial chassis recommendation, Ding et al constructed novoPathFinder based on metabolic pathway design [ 33 ] and Cai et al have recommended this from the perspective of gene editing tools, genome sequencing, and culture conditions [ 11 ]. In the current study, data from MCF2Chem were further combined with data from SynBioStrainFinder and genomic metabolic network models to make microbial chassis recommendations.…”

“…All natural products in LOTUS [ 38 ] were downloaded and merged with compounds in MCF2Chem for further use as a candidate chemical compound library of recommendation system. The collected strain-related data included information regarding culture media, genome sequencing, genetic operating system from SynBioStrainFinder [ 11 ], and genomic metabolic network models from the Biochemical Genetic and Genomic (BiGG) model database [ 39 ]. All data were cleaned and used to construct recommendation system.…”

“…With the rapid development of synthetic biological techniques, such as DNA sequencing and CRISPR/Cas technology, more microbes are being engineered for the biosynthesis of various compounds [11]. As of June 2020, the genomes of 11.4% of fungi, 62.8% of bacteria, 69.0% of archaea, and 9.6% of algae have been sequenced, and the CRISPR/Cas gene-editing system has been developed for 157 strains [11]. Technological advances and bottleneck breakthroughs have facilitated the development of microbial cell factories used for biosynthesis [12][13][14].…”

Recent Advances on Key Enzymes of Microbial Origin in the Lycopene Biosynthesis Pathway

“…35 A comprehensive microbial strain database, integrating information on CRISPR/Cas gene editing systems with culture methods, genome sequence data, and compound-related information was established by Cai et al, aiming to be an important resource for mining new functional genes and products for application in biomanufacturing. 105 Compared to traditional marker-based genome editing tools, CRISPR/Cas9 technology enables rapid engineered genome editing of prototrophic wild and industrial strains, allowing simultaneous multiplex genome editing and integration independently of the marker cassette. It is able to achieve metabolic balancing and network regulating in a modular and high-throughput manner, which is a viable alternative strategy to increase the lycopene titer in engineered microorganisms.…”

“…A new phytoene desaturase gene was identified rapidly among 2470 recombinant mutants of Methylorubrum extorquens using the developed CRISPR/Cas9 system combined with a pool of 26 sgRNAs . A comprehensive microbial strain database, integrating information on CRISPR/Cas gene editing systems with culture methods, genome sequence data, and compound-related information was established by Cai et al, aiming to be an important resource for mining new functional genes and products for application in biomanufacturing …”