Targeting clusters of transferred genes in Thermotoga maritima.
We screened a Thermotoga sp. strain RQ2 lambda library for genes present in that strain but absent from the closely related completely sequenced relative Thermotoga maritima strain MSB8, by using probes generated in an earlier genomic subtraction study. Five lambda insert fragments were sequenced, containing, respectively, an archaeal type ATPase operon, rhamnose biosynthetic genes, ORFs with similarity to an arabinosidase, a Thermotoga sp. strain RQ2-specific alcohol dehydrogenase and a novel archaeal Mut-S homologue. All but one of these fragments contained additional Thermotoga sp. strain RQ2-specific sequences not screened for, suggesting that many such strain-specific genes will be found clustered in the genome. Moreover, phylogenetic analyses, phylogenetic distribution and/or G + C content suggests that all the Thermotoga sp. strain RQ2 specific sequences in the sequenced lambda clones have been acquired by lateral gene transfer. We suggest that the use of strain-specific small insert clones obtained by subtractive hybridization to target larger inserts for sequencing is an efficient, economical way to identify environmentally (or clinically) relevant interstrain differences and novel gene clusters, and will be invaluable in comparative genomics.
Nesbø
Camilla L
CL
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada. cnesbo@dal.ca
Doolittle
W Ford
WF
D000251:Adenosine Triphosphatases / Q000235:genetics; D000426:Alcohol Dehydrogenase / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004268:DNA-Binding Proteins / Q000235:genetics; D015723:Gene Library; D023061:Gene Order; D022761:Gene Transfer, Horizontal / Q000235:genetics; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D015698:Genomic Library; D006026:Glycoside Hydrolases / Q000235:genetics; D008969:Molecular Sequence Data; D051719:MutS DNA Mismatch-Binding Protein; D010802:Phylogeny; D012210:Rhamnose / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D020124:Thermotoga maritima / Q000235:genetics*
D001426:Bacterial Proteins; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D000426:Alcohol Dehydrogenase; D006026:Glycoside Hydrolases; C019713:alpha-N-arabinofuranosidase; D000251:Adenosine Triphosphatases; D051719:MutS DNA Mismatch-Binding Protein; D012210:Rhamnose