title: The genome organization of Thermotoga maritima reflects its lifestyle.
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<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.
authors: Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
authors: Haythem
authors: H
authors: Latif
authors: Joshua A
authors: JA
authors: Lerman
authors: Vasiliy A
authors: VA
authors: Portnoy
authors: Yekaterina
authors: Y
authors: Tarasova
authors: Harish
authors: H
authors: Nagarajan
authors: Alexandra C
authors: AC
authors: Schrimpe-Rutledge
authors: Richard D
authors: RD
authors: Smith
authors: Joshua N
authors: JN
authors: Adkins
authors: Dae-Hee
authors: DH
authors: Lee
authors: Yu
authors: Y
authors: Qiu
authors: Karsten
authors: K
authors: Zengler
mesh_terms: D020121:5' Untranslated Regions; D020869:Gene Expression Profiling; D008019:Life Style; D008969:Molecular Sequence Data; D020124:Thermotoga maritima / Q000235:genetics; D024363:Transcription Initiation Site
chemical_list: D020121:5' Untranslated Regions
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