Myxo Portal - A comprehensive genomic database for Myxobacteria

Overview

Myxobacteria are ubiquitous microbial predators with a fascinating lifestyle exhibiting interesting features like fruiting body formation, gliding motility, social interactions, predation, and secondary metabolite production. They are gram negative slender vegetative rods which, under nutritionally limiting circumstances, aggregate to form fruiting bodies. Myxobacteria belong to the Phylum Myxococcota, currently comprising of two classes, (Myxococcia and Polyangia), four orders (Myxococcales, Nannocystales, Polyangiales and Haliangiales), seven families (Myxococcaceae, Vulgatibacteraceae, Anaeromyxobacteraceae, Polyangiaceae, Sandaracinaceae, Nannocystaceae and Haliangiaceae), 19 genera and over 30 species. They possess unusually large genomes ranging between 9.0 and 16.0 Mbp with a G+C content ~70.0 mol%, harbouring biosynthetic gene clusters and genes encoding antimicrobial peptides and hydrolytic enzymes, all contributing to their predatory behaviour. There are over 260 publicly available genomes (complete and draft) on the NCBI database, which have already facilitated taxonomical reappraisal, genome mining for secondary metabolites, and elucidation of the molecular mechanisms myxobacteria use to regulate their social behaviour and predation.

Myxo Portal is a comprehensive genomic database for myxobacteria. Genome annotations for the biosynthetic gene clusters, antimicrobial peptides, CRISPR genes, phage sequences and two-component systems of 260 genomes are manually curated in the database. Genome annotations for all myxobacteria were generated using the prokaryotic genome annotation service, Rapid Annotation using Subsystem Technology (RAST) (1, 2) . Biosynthetic gene clusters of all myxobacteria were generated using the antiSMASH tool (3) . Antimicrobial peptides of all myxobacteria were generated using dbAMP tool (4). CRISPR-Cas genes of all myxobacteria were generated using CRISPRminer (5) . Phages of all myxobacteria were generated using the PHASTER tool (6) . Regulatory proteins such as transcription factors, two-component systems and other DNA-binding proteins were generated using the Predicted Prokaryotic Regulatory Proteins (P2RP) database (7) . Genome assembly links provides genome assemblies of all myxobacteria from National Centre for Biotechnology Information (NCBI) (8).

References
  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
  2. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42(Database issue):D206-14.
  3. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, et al. AntiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 2021;49(W1):W29-W35.
  4. Jhong JH, Yao L, Pang Y, Li Z, Chung CR, Wang R, et al. dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. Nucleic Acids Res. 2022;50(D1):D460-D70.
  5. Zhang F, Zhao S, Ren C, Zhu Y, Zhou H, Lai Y, et al. CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions. Commun Biol. 2018;1:180.
  6. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44(W1):W16-21.
  7. Barakat M, Ortet P, Whitworth DE. P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes. BMC Genomics. 2013;14:269.
  8. Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2022;50(D1):D20-D6.