Fig. 4

An overview of metabolic pathways of the P. echinospica endosymbiont. Different metabolic pathways are presented in squares of different colors. Nitrogen metabolism is in a light blue square, including dissimilatory nitrate reduction, denitrification, and ammonia assimilation. Carbon metabolism is in a green square, including CBB and rTCA cycles for carbon fixation, TCA and glycolysis cycles for organic carbon utilization and bidirectional reactions of carbon monoxide and formate. Sulfur metabolism is in a yellow square. The sulfur oxidation depends on the Dsr, Apr and Sox systems. The sulfur globule protein is highly expressed and acts as an energy storage compound. The hydrogen oxidation is in a blue violet square. The above energy-conversion pathways provide substrates and energy for the production of nutrients such as amino acids and vitamins (Table 2). Enzymes found in both the symbiont genome and transcriptome are shown in red, whereas those found in the symbiont genome only are shown in yellow, and the missing enzymes are shown in gray. The histogram at the bottom shows the relative gene expression levels (log₁₀TPM) of enzymes in different metabolic pathways and key proteins involved in intracellular survival mechanisms. The membrane transport proteins, bacterial chemotaxis proteins and some of the characterized proteins for bacterial infection, which were encoded in the symbiont genome but not expressed, are marked with dashed circles. The flagellum, fimbriae and pilus of the symbiont, which were encoded in the symbiont genome but not expressed, are indicated in dashed line. The full names of enzymes are given in the list of abbreviations in Supplementary Information, and the involved genes are listed in Supplementary Table S9