ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements

Yongqun He,Guitian Liu,Zixin Deng,Hui Wang,Hong-Yu Ou,Jialin Liu,Xiaoli Wang,Meng Liu

doi:10.1038/s41597-021-01112-5

Abstract

Bacterial integrative and conjugative elements (ICEs) are highly modular mobile genetic elements critical to the horizontal transfer of antibiotic resistance and virulence factor genes. To better understand and analyze the ongoing increase of ICEs, we developed an Integrative and Conjugative Element Ontology (ICEO) to represent the gene components, functional modules, and other information of experimentally verified ICEs. ICEO is aligned with the upper-level Basic Formal Ontology and reuses existing reliable ontologies. There are 31,081 terms, including 26,814 classes from 14 ontologies and 4128 ICEO-specific classes, representing the information of 271 known experimentally verified ICEs from 235 bacterial strains in ICEO currently and 311 predicted ICEs of 272 completely sequenced Klebsiella pneumoniae strains. Three ICEO use cases were illustrated to investigate complex joins of ICEs and their harboring antibiotic resistance or virulence factor genes by using SPARQL or DL query. ICEO has been approved as an Open Biomedical Ontology library ontology. It may be dedicated to facilitating systematical ICE knowledge representation, integration, and computer-assisted queries.

Highlights

Integrative and conjugative elements (ICEs), previously named conjugative transposons, are important bacterial mobile genetic elements (MGEs) and active contributors in horizontal gene transfer[1,2,3,4]
We report the development of an Ontology of the Integrative and Conjugative Element (ICEO)
We developed the Integrative and Conjugative Element Ontology (ICEO) that ontologically represents the complex hierarchical structure of ICEs, ICE components, and the relations among ICEs and ICE components

Summary

Introduction

Integrative and conjugative elements (ICEs), previously named conjugative transposons, are important bacterial mobile genetic elements (MGEs) and active contributors in horizontal gene transfer[1,2,3,4]. ICEs are usually integrated into bacterial chromosomes; once induced or activated, they can transmit between bacterial cells through the self-encoded functional conjugation machinery, such as the type IV secretion system (T4SS)[2,3]. ICEs have highly mosaic modular structures, including the recombination, conjugation, regulation, and accessory modules[5,6]. ICEs are more widespread in prokaryote genomes than conjugative plasmids and are thought to be the most prevalent self-transmissible conjugative elements[3,5]. T4SS-type ICEs are widely distributed both in Gram-negative and -positive bacteria, while AICEs have only been found in Actinobacteria

Methods

Results

Conclusion