Abstract
Gram-negative bacteria deliver effectors via the type VI secretion system (T6SS) to outcompete their rivals. Each bacterial strain carries a different arsenal of effectors; the identities of many remain unknown. Here, we present an approach to identify T6SS effectors encoded in bacterial genomes of interest, without prior knowledge of the effectors’ domain content or genetic neighborhood. Our pipeline comprises a comparative genomics analysis followed by screening using a surrogate T6SS+ strain. Using this approach, we identify an antibacterial effector belonging to the T6SS1 of Vibrio parahaemolyticus, representing a widespread family of T6SS effectors sharing a C-terminal domain that we name Tme (Type VI membrane-disrupting effector). Tme effectors function in the periplasm where they intoxicate bacteria by disrupting membrane integrity. We believe our approach can be scaled up to identify additional T6SS effectors in various bacterial genera.
Highlights
Gram-negative bacteria deliver effectors via the type VI secretion system (T6SS) to outcompete their rivals
To identify T6SS1 effectors in V. parahaemolyticus, we devise a methodology comprising two steps: a comparative genomics analysis to identify candidate effectors in a given bacterial genome, followed by a functional screen in a surrogate T6SS platform. Utilizing this pipeline to analyze the genome of the V. parahaemolyticus isolate BB22OP, we identify a family of T6SS effectors, which we name Tme (Type VI membrane-disrupting effector, as explained in the Results section); Tme members are widespread in many Proteobacterial genomes
To establish a comparative genomics pipeline for identifying T6SS1 effectors in V. parahaemolyticus, we first compiled a dataset of high-quality V. parahaemolyticus genomes
Summary
Gram-negative bacteria deliver effectors via the type VI secretion system (T6SS) to outcompete their rivals. Computational approaches, including analyses of genes found inside T6SS clusters and auxiliary modules[14,20,26,27,28,29], genes encoding proteins with T6SS marker domain (e.g., MIX and FIX)[17,23,26], or genes that neighbor T6SS adapters (e.g., DUF4123, DUF1795, and DUF2169)[13,15,19,30,31,32], have resulted in the discovery of many effector families that have proven useful in preliminary analyses of new bacterial genomes[33]. Much less is known about T6SS1 and its effector repertoire in other V. parahaemolyticus strains
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