Title The genome organization of Thermotoga maritima reflects its lifestyle.
Year of Publication 2013
Authors H. Latif; J.A. Lerman; V.A. Portnoy; Y. Tarasova; H. Nagarajan; A.C. Schrimpe-Rutledge; R.D. Smith; J.N. Adkins; D.H. Lee; Y. Qiu; K. Zengler
Journal PLoS Comput Biol
Abstract 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
URL http://www.ncbi.nlm.nih.gov/pubmed/23637642?dopt=Abstract
PubMed ID 23637642