Phylogenetic analyses of two "Archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria

The genome sequence of Thermotoga maritima revealed that 24% of its open re ading frames (ORFs) showed the highest similarity scores to archaeal genes in BLAST analyses. Here we screened 16 strains from the genus Thermotoga an d other related Thermotogales for the occurrence of two of these "archaeal" genes: the gene encoding the large subunit of glutamate synthase (gltB) an d the mpo-inositol 1P synthase gene (ino1). Both genes were restricted to t he Thermotoga species within the Thermotogales. The distribution of the two genes, along with results from phylogenetic analyses, showed that they wer e acquired from Archaea during the divergence of the Thermotogales. Databas e searches revealed that three other bacteria-Dehalococcoides ethenogenes, Sinorhizobium meliloti, and Clostridium difficile-possess archaeal-type glt Bs, and the phylogenetic analyses confirmed at least two lateral gene trans fer (LGT) events between Bacteria and Archaea. These LGT events were also s trongly supported by gene structure data, as the three domains in bacterial -type gltB are homologous to three independent ORFs in Archaea and Bacteria with archaeal-type gltBs. The ino1 gene has a scattered distribution among Bacteria, and apart from the Thermotoga strains it is found only in Aquife x aeolicus, D. ethenogenes, and some high-G + C Gram-positive bacteria. Phy logenetic analysis of the ino1 sequences revealed three highly supported pr okaryotic clades, all containing a mixture of archaeal and bacterial sequen ces, and suggested that all bacterial ino1 genes had been recruited from ar chaeal donors. The Thermotoga strains and A. aeolicus acquired this gene in dependently from different archaeal species. Although transfer of genes fro m hyperthermophilic Archaea may have facilitated the evolution of bacterial hyperthermophily, between-domain transfers also affect mesophilic species. For hyperthermophiles, we hypothesize that LGT may be as much a consequenc e as the cause of adaptation to hyperthermophily.