Exploring the Genetic Basis for the Sit-and-wait Hypothesis Abiotic Stress Resistance and Energy Storage Mechanisms

[Truncated abstract] According to Walther and Ewald, the sit-and-wait hypothesis predicts that bacterial 'virulence should be positively correlated with durability in the external environment because high durability reduces the dependence of transmission on host mobility'. However, currently only epidemiological, empirical, and theoretical evidence exists to support this hypothesis. This thesis aims to study bacterial durability both theoretically and experimentally in order to provide genetic basis so as that experimentally testing the sit-and-wait hypothesis is possible. Currently, two major factors determine bacterial durability: resistance to environmental stresses and energy storage mechanisms. Thus, we constructed two sets of hidden Markov models (HMMs) for abiotic stress resistance and energy storage mechanisms, respectively. For HMMs corresponding to abiotic stress resistance, we screened 14 pairs of virulent/avirulent bacterial strains in order to identify proteins uniquely existing in the virulent bacteria, which were considered as theoretically genetic basis for the sit-and-wait hypothesis. For HMMs corresponding to energy storage mechanisms, 1202 annotated bacterial proteomes from HAMAP database were scanned for the distribution of five major energy storage compounds: wax ester (WE), triacylglycerol (TAG), polyhydroxybutyrate (PHB), polyphosphate (PolyP), and glycogen. Then, we analyzed the distribution of enzymes for the synthesis of WE, PHB, and glycogen in 131 selected human pathogens in terms of transmission modes, host-pathogen interactions, and virulence, etc. The second part of this study is about a novel mechanism called durable energy storage mechanism (DESM). Several studies have noted that glycogen with short average chain length (ACL) in some bacteria is degraded very slowly, and slow utilization of glycogen is correlated with bacterial viability, hence virulence. In this study, we manipulated glycogen average chain length by progressively truncating the N-terminus of glycogen branching enzyme in situ and examined its effects on bacterial durability under environmental stresses in order to test the validity of DESM hypothesis experimentally. In sum, we tried to provide genetic background for the sit-and-wait hypothesis by studying the core factor of the hypothesis, bacterial durability. The linkage between durability and virulence was explored primarily by using HMMs. A set of durability-related proteins was successfully identified in virulent bacteria. Besides, theoretical distribution of glycogen in 1202 bacterial proteomes showed a significant correlation between large proteome size and glycogen metabolism. Since large proteome size is generally considered as a necessity for complex living styles, glycogen metabolism should be statistically considered as a supporter for bacterial durability. In addition, distribution of synthesis pathways in 131 human pathogens for PHB, glycogen, and WE indicated that energy reserves have a potential linkage with virulence. Finally, the novel DESM hypothesis, also considered as a factor for bacterial durability, was explored through physical experimentation...