[2S05m] 12. Environmental Microbiology and Technology - Part 1

11:20 AM - 11:40 AM JST(2:20 AM - 2:40 AM UTC)

[2EMT-05] A Comprehensive Plasmid Database: Tools for Genetic Engineering and Behavioral Insight

○Masaki Shintani^1,2 (1. Shizuoka University (Japan), 2. RIKEN BioResource Research Center (Japan))

Keywords:

plasmid,horizontal gene transfer,database,replication,winged-helix domain

Plasmids are among the most influential mobile genetic elements in the microbial world. They drive bacterial evolution by mediating horizontal gene transfer and enabling the rapid dissemination of adaptive traits including antimicrobial resistance, metabolic versatility, and virulence. At the same time, plasmids are indispensable tools in molecular microbiology, biotechnology, and synthetic biology. Despite their dual importance in both nature and engineering, our global understanding of plasmid diversity, compatibility, and host range remains fragmented. A major reason for this limitation is the incomplete annotation and conceptual organization of replication initiation proteins (RIPs), which determine plasmid host range and incompatibility. Although replication systems fundamentally shape plasmid behavior, public databases have lacked a unified framework centered on replication machinery. To address this, we have established a comprehensive plasmid database structured around RIPs¹⁾. Through experimental identification of RIPs in Pseudomonas plasmids and large-scale phylogenetic reconstruction of RIPs containing winged-helix (WH) domain, we constructed the largest evolutionary framework for this major class of replication proteins. Our analysis resolves WH-type RIPs into eight clades, comprising four single WH-domain groups and four tandem double WH-domain groups. This phylogenetic backbone enables systematic mapping of fully sequenced plasmids onto defined replication clades. By integrating genetic organization, host lineage, and environmental metadata, we establish a replication-centered classification system that extends beyond traditional plasmid typing schemes and allows the consistent categorization of many previously unclassified plasmids.Importantly, this organization provides practical and predictive value. Mapping plasmids to defined replication clades reveals which plasmid groups are preferentially associated with particular bacterial taxa. Such information offers a rational guideline for vector design: replication clade affiliation becomes an indicator for anticipating host compatibility. The framework also yields epidemiologically meaningful insights. By overlaying functional annotations—particularly antimicrobial resistance genes—onto the phylogenetic structure, we can identify plasmid lineages that disproportionately carry resistance determinants. Furthermore, linking replication clades to environmental distribution reveals ecological patterns. Certain plasmid groups are recurrently detected in specific habitats, suggesting distinct adaptive strategies and ecological niches. These associations provide insight into how plasmids persist, circulate, and diversify across environmental boundaries. ¹⁾Nishimura et al., 2025, bioRxiv, doi:10.1101/2024.09.03.610885.