Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain and loss of polyP pathway. Literature mining and phylogenetic analysis were recruited to support the study. Our analyzes revealed that the presence of polyP metabolism is positively correlated with bacterial proteome size and the number of virulence genes. A potential relationship of polyP in bacterial lifestyle and environmental durability is suggested. Evolutionary analysis shows that polyP genes are randomly lost along the phylogenetic tree. In sum, based on our theoretical analysis, we confirmed that bacteria with polyP metabolism are associated with high environmental durability and more VFs.
Conclusion and Future Perspectives
The sit-and-wait hypothesis predicts that pathogenic bacteria with longer external survival time tend to evolve toward higher virulence (Walther and Ewald, 2004; Wang et al., 2017). Thus, the correlation of durability and virulence phenotypes should be reflected at the genomic level. polyP has long been considered as a widespread energy storage mechanism in bacteria, contributing to bacterial persistence in hash conditions (Brown and Kornberg, 2008; Rao et al., 2009; Chuang et al., 2013; Moreno and Docampo, 2013; Nikel et al., 2013; Albi and Serrano, 2016). In this study, we thoroughly searched the distribution of polyP metabolism related enzymes in 944 bacterial genera. According to our study, gain of key polyP metabolism enzymes, PPK1 and PPK2, is significantly linked to higher numbers of VFs. This conclusion connects bacterial durability with virulence and provides a preliminary support for the sit-and-wait hypothesis. In addition, bacteria with polyP metabolism pathway are associated with comparatively larger proteome size, which reflects their complex life cycle while those without polyP metabolism are exclusively host-associated organisms. The result matches well with a previous study, which examined the distribution of glycogen metabolism enzymes in bacteria (Henrissat et al., 2002) and indicates that gain or loss of energy storage mechanism might be a potential indicator of host–bacteria relationship. Literature mining of bacterial lifestyles for 214 Full_Path and 14 No_Path bacteria validated the observation that bacteria with polyP pathway may have a more durable lifestyle, while phylogenetic study showed that polyP metabolism is widespread across bacterial genera (Figure 4). However, no evolutionary relatedness is identified in terms of enzyme loss of polyP enzymes.
Although multiple studies have already shown that polyP deficiency reduces bacterial biofilm formation (Rashid et al., 2000b), survival rate (Rao et al., 2009), and stress resistance (Kim et al., 2002), there is no study on how inactivation of polyP enzymes has an impact on the evolution of bacterial virulence. Serial passaging of pathogens through host–environment–host cycles, such as P. aeruginosa with PPK1 and/or PPK2 deletion, will reveal how virulence evolves by comparing with wild-type strains that go through the same cycles. Genome sequencing of the passaged wild-type and mutated pathogens will also reveal the types of genes lost during the serial passages. Such experiments, if matched with the theoretical analysis in this study, will be reliable evidence at molecular level for investigating the role of durability in the evolution of virulence.