Informational and Regulatory Systems
Comparison with an obligatory gene set characteristic for free-living alpha-proteobacteria (Table 2) shows that both Wolbachia spp. and Rickettsia have retained an almost intact gene set for translational processes (greater than 84%). Several RNA metabolism genes are among the few shared losses, including tRNA and rRNA modification enzymes (LasT, RsmC, Sun, TrmA, CspR) and even pseudouridine synthase, TruB (pseudogenes in both lineages). TruB is present in all gamma-proteobacterial endosymbionts but absent in other parasites and endosymbionts, including Mycoplasma, Chlamydia, and spirochetes. It is likely that the lack of these modifications affects reading frame maintenance and translation efficiency in both Wolbachia spp. and in Rickettsia. Further reduction of genes involved in RNA modification occurs specifically in wBm and in wMel, which have lost several genes involved in queuosine biosynthesis (COG0809, COG603, COG702, COG0602, COG0780) [118] and 16S rRNA uridine-516 pseudouridylate synthase. The absence of RNA methylase (COG1189) highlights the loss of RNA modification systems, which is a general trend in evolution of endosymbionts among various lineages [119].
Although wBm retains most of the genes for DNA replication and repair, the loss of several genes present in other alpha-proteobacteria (except wMel) is notable. These include the chi subunit of DNA polymerase III (HolC), chromosome partitioning proteins ParB and ParA, repair ATPase (RecN), exonuclease VII (XseAB), and the RNA processing enzyme RNase PH (Rph).
Both Wolbachia spp. and Rickettsia have a complete repertoire of UV-excision (UVR-ABCD-mediated), recombinational synaptic (RecA/RecFOR-mediated), and postsynaptic (RuvABC-mediated) DNA repair pathways. In contrast, Buchnera and Blochmannia are devoid of conventional homologous recombination and uvr pathways, although they encode a putative phrB familyphotolyase [107,109,110,112,120,121]. Wolbachia, Rickettsia, Buchnera, and Wigglesworthia all encode enzymatic machinery to counter the deleterious effects of various types of base oxidative damage, which could be important for defense against mutagenic metabolic by-products in the intracellular environment [103,108,109,119,122].
Many proteins categorized as being involved in protein fate in the two Wolbachia spp. and Rickettsia spp. (CcmF, CcmB, CcmH, CcmE, CcmC, Cox11, CtaA), but which are absent in the genomes of gamma-proteobacterial endosymbionts, are involved in biogenesis of cytochrome c oxidase and c-type cytochromes typical of alpha-proteobacterial aerobic respiratory chains. Respiratory chains of gamma-proteobacterial endosymbionts employ quinol oxidase rather than cytochrome c oxidase.
A major loss of transcriptional regulators likely occurred in the common ancestor of Wolbachia and Rickettsia spp. (Table 2). Only a few of these genes have been additionally lost in the wBm lineage, including those from COG1396, COG1959, COG1329, COG1678, and COG1475. This is a general trend in evolution of endosymbionts and parasites [118,122,123], suggesting that most of their genes are likely constitutively expressed. Those few regulators found in wBm that are not present in other alpha-proteobacteria, including two Xre-like regulators (COG5606), may be of interest for future experimental characterization. Similarly, most genes implicated in signal transduction systems are absent in both Wolbachia and Rickettsia spp. Several regulatory proteins that remain in the genome are involved in various stress responses (Wbm0660, MerR/SoxR family; Wbm0707, cold shock protein; Wbm0494, stress response morphogen; Wbm0061, TypA-like GTPase) or in cell cycle regulation (Wbm0184, PleD-like regulator; Wbm0596, cell cycle transcriptional regulator CtrA).