Abstract
To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.
Highlights
Chlamydiae are different from typical eubacteria for their obligate intracellular nature, which manifests itself in a biphasic developmental cycle comprising extracellular and intracellular stages
The data of this study show that the absence of a tryptophan (Trp) operon is a common feature of the avian species C. psittaci, C. gallinacea, C. avium, and the closely related C. abortus
We have identified a tendency towards reduction in inclusion membrane (Inc) family size among some avian Chlamydia spp., in C. gallinacea and C. avium
Summary
Chlamydiae are different from typical eubacteria for their obligate intracellular nature, which manifests itself in a biphasic developmental cycle comprising extracellular and intracellular stages. Along this cycle, infectious, but metabolically largely inactive elementary bodies (EBs) enter host cells to transform into non-infectious, metabolically active reticulate bodies (RBs) within a vacuole-like inclusion. Chlamydiae rely on host cells for nutrients, such as amino acids, nucleotides and lipids [2,3] since they are incapable of synthesizing these substrates Instead, they seem to compensate for this by co-opting suitable cellular pathways that provide the necessary nutrients [4,5]. Recent genome analysis helped to qualify the long-held hypothesis of chlamydiae being ‘energy parasites’ [6] by revealing the presence of a metabolic chain leading to ATP production [7,8,9]
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