Systematic Identification and Analysis of Acinetobacter baumannii Type VI Secretion System Effector and Immunity Components

Abstract

Many Gram-negative bacteria use a type VI secretion system (T6SS) for microbial warfare and/or host manipulation. Acinetobacter baumannii is an important nosocomial pathogen and many A. baumannii strains utilize a T6SS to deliver toxic effector proteins to surrounding bacterial cells. These toxic effectors are usually delivered together with VgrG proteins, which form part of the T6SS tip complex. All previously identified A. baumannii T6SS effectors are encoded within a three- or four-gene locus that also encodes a cognate VgrG and immunity protein, and sometimes a chaperone. In order to characterize the diversity and distribution of T6SS effectors and immunity proteins in this species, we first identified all vgrG genes in 97 A. baumannii strains via the presence of the highly conserved VgrG domain. Most strains encoded between two and four different VgrG proteins. We then analyzed the regions downstream of the identified vgrG genes and identified more than 240 putative effectors. The presence of conserved domains in these effectors suggested a range of functions, including peptidoglycan hydrolases, lipases, nucleases, and nucleic acid deaminases. However, 10 of the effector groups had no functionally characterized domains. Phylogenetic analysis of these putative effectors revealed that they clustered into 32 distinct groups that appear to have been acquired from a diverse set of ancestors. Corresponding immunity proteins were identified for all but two of the effector groups. Effectors from eight of the 32 groups contained N-terminal rearrangement hotspot (RHS) domains. The C-terminal regions of these RHS proteins, which are predicted to confer the toxic effector function, were very diverse, but the N-terminal RHS domains clustered into just two groups. While the majority of A. baumannii strains contained an RHS type effector, no strains encoded two RHS effectors with similar N-terminal sequences, suggesting that the presence of similar N-terminal RHS domains leads to competitive exclusion. Together, these analyses define the extreme diversity of T6SS effectors within A. baumannii and, as many have unknown functions, future detailed characterization of these effectors may lead to the identification of proteins with novel antibacterial properties.

Acinetobacter baumannii: An Ancient Commensal with Weapons of a Pathogen

“…Indeed, due to the high-demanding energy costs, T6SS is activated upon stressful stimuli, including nutrient limitation, cell damage and competing bacteria [ 146 ]. Accordingly, the T6SS enables A. baumannii to inject into other bacteria toxic proteins, including peptidoglycan hydrolases, nucleases, or those effectors targeting the cell membrane, to outcompete neighboring bacteria [ 147 ].…”

Peptidoglycan editing provides immunity to Acinetobacter baumannii during bacterial warfare

“…Strains from the most common lineages of clinical A. baumannii strains, such as international clone 1 (IC1), IC2, and IC3, do not carry the racK gene. This is reminiscent of the loss of the T6SS via genetic disruptions to the T6SS gene locus or the accumulation of inactivating point mutations in ~40% of A. baumannii clinical isolates (40,41). Both PG editing and a functional T6SS are crucial in the environment but appear to impose a fitness cost during infection.…”

Type VI secretion system killing by commensal Neisseria is influenced by the spatial dynamics of bacteria

“…hydrolases, metalloproteases and nucleases (Lewis et al, 2019). Effector activities can result in target cell lysis to varying degrees (Ringel et al, 2017;Smith et al, 2020).…”