Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies

Abstract

Background: Genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. This process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria represent the most extreme cases of genome reduction consequence of a massive process of gene inactivation and loss during their evolution from free-living ancestors. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, contains one of the few complete genomes of bacteria at the very beginning of the symbiotic association, allowing to evaluate the relative impact of mobile genetic element proliferation and gene inactivation over the structure and functional capabilities of this bacterial endosymbiont during the transition to a host dependent lifestyle.

Results: A detailed characterization of mobile genetic elements and pseudogenes reveals a massive presence of different types of prophage elements together with five different families of IS elements that have proliferated across the genome of Sodalis glossinidius at different levels. In addition, a detailed survey of intergenic regions allowed the characterization of 1501 pseudogenes, a much higher number than the 972 pseudogenes described in the original annotation. Pseudogene structure reveals a minor impact of mobile genetic element proliferation in the process of gene inactivation, with most of pseudogenes originated by multiple frameshift mutations and premature stop codons. The comparison of metabolic profiles of Sodalis glossinidius and tsetse fly primary endosymbiont Wiglesworthia glossinidia based on their whole gene and pseudogene repertoires revealed a novel case of pathway inactivation, the arginine biosynthesis, in Sodalis glossinidius together with a possible case of metabolic complementation with Wigglesworthia glossinidia for thiamine biosynthesis.

Conclusions: The complete re-analysis of the genome sequence of Sodalis glossinidius reveals novel insights in the evolutionary transition from a free-living ancestor to a host-dependent lifestyle, with a massive proliferation of mobile genetic elements mainly of phage origin although with minor impact in the process of gene inactivation that is taking place in this bacterial genome. The metabolic analysis of the whole endosymbiotic consortia of tsetse flies have revealed a possible phenomenon of metabolic complementation between primary and secondary endosymbionts that can contribute to explain the co-existence of both bacterial endosymbionts in the context of the tsetse host.

Figure 1

Results of the re-annotation process. The functional categories correspond to the "colour" qualifier in Additional File 1. Red bars show the number of CDSs (genes and pseudogenes) in each functional category. Green bars show the number of genes in each functional category. Blue bars show the number of pseudogenes in each functional category.

Figure 2

Functional re-assignments of genes originally annotated as "hypothetical proteins". Functional categories correspond to the "colour" qualifier in the final re-annotation file. There is a single gene re-assigned to "energy metabolism" category.

Figure 3

Complete prophages characterized during the re-annotation process. Comparisons were generated with ACT based on TBLASTX comparisons of whole genome sequences: (a) S. glossinidius complete prophage region SGLp1 (top) vs. enterobacteria phage Mu (NC_000929.1) (bottom) (b) S. glossinidius complete prophage region SGLp2 (top) vs. Burkholderia phage BcepMu (NC_005882) (bottom).

Figure 4

Metabolic profile of L-arginine biosynthesis from L-glutamate in S. glossinidius and its implication in spermidine, L-lysine and peptidoglycan biosynthesis. Red coloured enzymatic reactions represent gene inactivation events, whereas blue coloured ones are those encoded by functional genes.

Figure 5

Metabolic profile of thiamine biosynthesis pathway in S. glossinidius and W. glossinidia. (A) Schematic diagram of thiamine biosynthesis pathway. Reactions coloured in blue represents the functional profile of thiamine biosynthesis in W. glossinidia, whereas reactions coloured in green represents the functional profile of thiamine biosynthesis in S. glossinidius; Pseudogenized activities are represented by dashed lines. Functional thiamine ABC transport system, thiamine kinase (thiK) and thiamine phosphate kinase (thiL) allow thiamine diphosphate biosynthesis from exogenous thiamine. (B) Structure of the thiamine biosynthesis operon in S. glossinidius, E. coli K12, and W. glossinidia. Functional genes (blue), pseudogenes (red), and the thiS gene of W. glossinidia characterized in this study (green). The thiH gene in S. glossinidius corresponds to an originally annotated gene (SG0136) with a premature stop codon detected during the reannotation process (*1)

Figure 6

Pontetial metabolic complementation between W. glossinidia and S. glossinidius at thiamine biosynthesis level. Thiazole phosphate carboxylate (THZ-P) is synthesized by S. glossinidius from exogenous thiamin through salvage pathway (tenA2, thiM), whereas hydroxymethyl pyrimidine pyrophosphate (HMP-PP) is synthesized by W. glossinidia from 5-aminoimidazole ribonucleotide (AIR) (thiC, thiD). THZ-P and HMP-PP are shared between both bacteria to produce the functional thiamine diphosphate that is provided to the tsetse host.