The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

The generation of genome-scale data is becoming more routine,yet the subsequent analysis of omics data remains a significant challenge. here,an approach that integrates multiple omics datasets with bioinformatics tools was developed that produces a detailed annotation of several microbial genomic features. this methodology was used to characterize the genome of thermotoga maritima-a phylogenetically deep-branching,hyperthermophilic bacterium. experimental data were generated for whole-genome resequencing,transcription start site (tss) determination,transcriptome profiling,and proteome profiling. these datasets,analyzed in combination with bioinformatics tools,served as a basis for the improvement of gene annotation,the elucidation of transcription units (tus),the identification of putative non-coding rnas (ncrnas),and the determination of promoters and ribosome binding sites. this revealed many distinctive properties of the t. maritima genome organization relative to other bacteria. this genome has a high number of genes per tu (3.3),a paucity of putative ncrnas (12),and few tus with multiple tsss (3.7%). quantitative analysis of promoters and ribosome binding sites showed increased sequence conservation relative to other bacteria. the 5′utrs follow an atypical bimodal length distribution comprised of short 5′utrs (11-17 nt) and common 5′utrs (26-32 nt). transcriptional regulation is limited by a lack of intergenic space for the majority of tus. lastly,a high fraction of annotated genes are expressed independent of growth state and a linear correlation of mrna/protein is observed (pearson r = 0.63,p<2.2×10-16 t-test). these distinctive properties are hypothesized to be a reflection of this organism's hyperthermophilic lifestyle and could yield novel insights into the evolutionary trajectory of microbial life on earth. © 2013 latif et al.