Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing

Abstract

The mode of action of the bacterial ter cluster and TelA genes, implicated in natural resistance to tellurite and other xenobiotic toxic compounds, pore-forming colicins and several bacteriophages, has remained enigmatic for almost two decades. Using comparative genomics, sequence-profile searches and structural analysis we present evidence that the ter gene products and their functional partners constitute previously underappreciated, chemical stress response and anti-viral defense systems of bacteria. Based on contextual information from conserved gene neighborhoods and domain architectures, we show that the ter gene products and TelA lie at the center of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing. Our analysis suggests that the multiple metal-binding and non-binding TerD paralogs and TerC are likely to constitute a membrane-associated complex, which might also include TerB and TerY, and feature several, distinct metal-binding sites. Versions of the TerB domain might also bind small molecule ligands and link the TerD paralog-TerC complex to biosynthetic modules comprising phosphoribosyltransferases (PRTases), ATP grasp amidoligases, TIM-barrel carbon-carbon lyases, and HAD phosphoesterases, which are predicted to synthesize novel nucleoside-like molecules. One of the PRTases is also likely to interact with RNA by means of its Pelota/Ribosomal protein L7AE-like domain. The von Willebrand factor A domain protein, TerY, is predicted to be part of a distinct phosphorylation switch, coupling a protein kinase and a PP2C phosphatase. We show, based on the evidence from numerous conserved gene neighborhoods and domain architectures, that both the TerB and TelA domains have been linked to diverse lipid-interaction domains, such as two novel PH-like and the Coq4 domains, in different bacteria, and are likely to comprise membrane-associated sensory complexes that might additionally contain periplasmic binding-protein-II and OmpA domains. We also show that the TerD and TerB domains and the TerY-associated phosphorylation system are functionally linked to many distinct DNA-processing complexes, which feature proteins with SWI2/SNF2 and RecQ-like helicases, multiple AAA+ ATPases, McrC-N-terminal domain proteins, several restriction endonuclease fold DNases, DNA-binding domains and a type-VII/Esx-like system, which is at the center of a predicted DNA transfer apparatus. These DNA-processing modules and associated genes are predicted to be involved in restriction or suicidal action in response to phages and possibly repairing xenobiotic-induced DNA damage. In some eukaryotes, certain components of the ter system appear to be recruited to function in conjunction with the ubiquitin system and calcium-signaling pathways.

Figure 1

Principal Component Analysis of the phyletic patterns of ter and associated genes in 1348 genomes. Plotting of PC1 vs PC2 resolved the organisms into four major groups, which reflect the presence of the biosynthetic module in combination with the TerBCD and TerY-P triad gene modules, the presence of primarily TerBC without associated biosynthetic operons, the presence of the SWI2/SNF2 four-gene module, and the combined presence of all these modules. The underlying phyletic pattern for the PCA is available in the Supplementary material.

Figure 2

Operons of the ter system and associated systems. The gene neighborhood data for some of the genes encoding Ter system proteins is depicted using arrows. The direction of the arrow is the direction of transcription of the gene. The gene name, Genbank identifier (gi), and the species name of the starred gene is shown next to the operon. The multi-gene modules that always occur together have been boxed. The genes are cartoon representation and not to scale. The depicted operons are representative of many operons spanning a range of diverse organisms. The complete list is provided in the Supplementary material. (A) Ter system genes found with the novel biosynthetic operons. (B) Other operons of Ter and TelA genes. (C) DNA-processing related operons. In the T7SS containing operon of Bordetella the gene with two stars (**) has not been translated in Genbank. The protein and the gene can be found in the Supplementary materials. (D) Standalone versions of DNA processing and Type 7 Secretion System. Abbreviations of domain names are as in Table 1. Other abbreviations: SF-1 – SF-I Helicase; SF-II – SF-II Helicase; SNF2 – SNF2 Helicase;CC – coiled coil; Z -uncharacterized globular region.

Figure 3

Domain architectures of proteins found in the ter system and associated operons. The domains are not to scale. (A) Domain Architectures of the TerD domain. (B) Domain architectures of TerB, TerY and TerC domain. (C) Domain Architectures of proteins found in the ter system operons. Domain architectures are labeled with a representative gene name, the Genbank identifier (GI) number, and the species name separated by semicolons. The eukaryotes are shown in green. The functional categories are shown in red letters. Domain abbreviations are in the Table 1. Coiled coil regions are shown with a grey rectangle. Other abbreviations: TM – Transmembrane Helix; SIG –Signal peptide; H – Hydrophobic Helix.

Figure 4

Domain network graph of the Ter system proteins and the proteins encoded in their gene neighborhood. The graphs were rendered using the Cytoscape program. The network is an ordered graph with the blue edges representing the connection between adjacent domains combined in the same polypeptides and the grey edges representing the context in the gene neighborhood. (A) The nodes of the network arranged by function. (B) The “force-directed” network was derived using spring-embedded layout utilizing the Kamada-Kawai algorithm, which works well for graphs with 50–100 nodes. The natural clustering of the functional categories has been pointed out. (C) Condensed network, where the domain belonging to a given functional category have been collapsed in to that category name.

Figure 5

Cartoon structures illustrating (A) TerD with its calcium-binding residues and conserved shallow cavity, and (B) TerB and its metal-binding residues and ligand binding region. Helices in the two individual repeat units of TerB are colored red and blue to highlight the repeat structure. In TerD, the conserved surface residues that comprise the shallow cavity are colored in magenta.

Figure 6

A schematic showing a virtual bacterial cell that summarizes the connections between proteins and systems described in this study along with their predicted sub-cellular localization. Predicted complexes comprised of multiple proteins are enclosed in shaded boxes. Domains that are, on occasion, fused to proteins of the core modules of the predicted complexes are shown in shaded boxes outlined by dashed lines. Bidirectional grey arrows denote connections between: individual modules of complexes or different complexes, proteins and particular complexes or between different proteins, as deciphered by conserved gene neighborhood/domain architecture analysis. These connections are only present in species where these modules are clustered in the same gene neighborhood and can be retrieved from Figures 1, 2 and the Supplementary material. Red arrows illustrate the biological consequence of the action of various complexes. Standard names are used for domain abbreviations.