Details

Autor(en) / Beteiligte

• Latif, Haythem
• Lerman, Joshua A
• Portnoy, Vasiliy A
• Tarasova, Yekaterina
• Nagarajan, Harish
• Schrimpe-Rutledge, Alexandra C
• Smith, Richard D
• Adkins, Joshua N
• Lee, Dae-Hee
• Qiu, Yu
• Zengler, Karsten
• Hughes, Diarmaid

Titel

The genome organization of Thermotoga maritima reflects its lifestyle

Ist Teil von

• PLoS genetics, 2013-04, Vol.9 (4), p.e1003485-e1003485

Ort / Verlag

United States: Public Library of Science

Erscheinungsjahr

2013

Link zum Volltext

Quelle

Free E-Journal (出版社公開部分のみ）

Beschreibungen/Notizen

• 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.