Protecting from Envelope Stress: Variations on the Phage-Shock-Protein Theme

Abstract

During envelope stress, critical inner-membrane functions are preserved by the phage-shock-protein (Psp) system, a stress response that emerged from work with Escherichia coli and other Gram-negative bacteria. Reciprocal regulatory interactions and multiple effector functions are well documented in these organisms. Searches for the Psp system across phyla reveal conservation of only one protein, PspA. However, examination of Firmicutes and Actinobacteria reveals that PspA orthologs associate with non-orthologous regulatory and effector proteins retaining functions similar to those in Gram-negative counterparts. Conservation across phyla emphasizes the long-standing importance of the Psp system in prokaryotes, while inter- and intra-phyla variations within the system indicate adaptation to different cell envelope structures, bacterial lifestyles, and/or bacterial morphogenetic strategies.

Keywords: Actinobacteria; ClgR; Firmicutes; Lia; PspA; envelope stress response; morphogenesis.

Figure 1. The Psp Systems of E. coli (A), B. subtilis (B), and M. tuberculosis (C)

This figure highlights interactions and functional parallels among orthologous and non-orthologous proteins in the three Psp systems rather than mechanistic/localization properties that are reviewed elsewhere [7]. Each factor in the system is indicated by a box. For regulators, the boxes are marked with broken borders when the protein is inactive and with solid borders when the protein becomes active. In all three panels, the system-specific regulator is shown in blue, the PspA ortholog is shown in orange, while the cognate membrane-targeting protein is shown in green. All other genes are in grey boxes. Lines connecting boxes are solid when indicating transcriptional effects and broken when indicating post-translational effects. Arrowhead = positive regulation; barhead = negative regulation. Stress is indicated by a lightening bolt.

Figure 2. Structure of psp Loci in Firmicutes and Actinobacteria

348 fully-sequenced, representative/reference genomes of the phyla Firmicutes and Actinobacteria in the PATRIC database [68] (one genome per species) were selected for analysis. The presence of genes encoding PspA orthologs (within ±50% of the query protein length) was determined using five iterations of PSI-BLAST and an E-value cutoff of 1E-5 based on primary amino acid sequence (which corresponds to ~27% sequence similarity). Multiple PspA query proteins were used (E. coli PspA, B. subtilis PspA and LiaH, and M. tuberculosis PspA) to reduce species-specific bias. Only genera having two or more genomes analysed are shown in the figure. (A, C) List of genomes analysed for the presence of genes coding PspA orthologs (loosely indicated as pspA) in Firmicutes (A) and Actinobacteria (C); genera containing at least one pspA gene are in bold. For each genus, the first column shows the number of pspA-containing genomes (pspA⁺) versus the total number of analysed genomes, the second column is a graphic depiction (expressed as %) of the data in the first column, while the third column shows the number of pspA genes per genome. (B, D) structure of psp loci in Firmicutes (B) and Actinobacteria (D). Arrow-shaped boxes indicate conserved genes, while the name inside the box indicates the protein encoded by the gene. An X below a gene box indicates absence of the corresponding gene in some genomes; a boxed R indicates that the corresponding gene is replaced with another gene in some genomes (R has a numbered subscript when more that one gene replacement was identified); numbered, small arrows at the base of a triangle indicate insertion of one or more genes in the corresponding position in some genomes. MP, membrane protein.