Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

Abstract

The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.

Trends in Codon and Amino Acid Usage in Thermotoga maritima

“…Indeed, the orders of the absolute r values were T3s (+0.79), C3s (−0.74), G3s (−0.45), and A3s (+0.40). When the sequences were sorted according to their GC3s we could not detect any common biological trait among those genes displaying similar values except, as noted by Nelson et al (1999), among a group of sequences encoding lipopolysaccharide biosynthesis proteins, spanning approximately from position 635,000 to position 666,000. Another group of genes with low GC3s, composed mainly of hypothetical proteins conserved among thermophilic prokaryotes and ABC transporters, is clustered around position 1,340,000.…”

“…The complete genome and coding sequences of T. maritima (Nelson et al 1999) were obtained from ftp://ftp.tigr.org/pub/data/ t_maritima/.…”

“…Another group of genes with low GC3s, composed mainly of hypothetical proteins conserved among thermophilic prokaryotes and ABC transporters, is clustered around position 1,340,000. Since the majority of the predicted genes in these two regions are most similar to proteins in thermophilic prokaryotes, it seems reasonable to suppose that they were relatively recently acquired by horizontal transfer from thermophilic genomes more biased toward A + T. This phenomenon has been postulated to be very common in Thermotoga (Nelson et al 1999;Logsdon and Faguy 1999).…”

“…Recently the complete genome sequence of Thermotoga maritima (Nelson et al 1999), a hyperthermophilic bacterium which is probably one of the deepest lineages in the Eubacteria (Tiboni et al 1991), has been reported. This genome is characterized by an average genomic G + C content of 46% and consists of 1860 kbp with 1846 predicted coding regions, but perhaps the most striking result that emerged from its sequencing was the finding that 24% of its genes seem to be derived from Archaea (Nelson et al 1999;Logsdon and Faguy 1999).…”

“…This genome is characterized by an average genomic G + C content of 46% and consists of 1860 kbp with 1846 predicted coding regions, but perhaps the most striking result that emerged from its sequencing was the finding that 24% of its genes seem to be derived from Archaea (Nelson et al 1999;Logsdon and Faguy 1999).…”