The genome organization of Thermotoga maritima reflects its lifestyle.

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Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K

The genome organization of Thermotoga maritima reflects its lifestyle.

PLoS Genet. 2013 Apr;9(4):e1003485. doi: 10.1371/journal.pgen.1003485. Epub 2013 Apr 25.

PubMed ID
23637642 [ View in PubMed
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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 x 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.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
Riboflavin biosynthesis proteinQ9WZW1Details
Mannoside ABC transport system, sugar-binding proteinQ9X0V0Details
Transcriptional regulator, IclR familyQ9WXS0Details
Putative L-rhamnose mutarotaseQ9X0F9Details
Putative deoxyribonuclease YcfHQ9WZD5Details
Purine nucleoside phosphorylaseQ9X1T2Details
LaminarinaseQ9WXN1Details
L-allo-threonine aldolaseQ9X266Details
tRNA-dihydrouridine synthaseQ9WXV1Details
Alcohol dehydrogenase, iron-containingQ9X022Details
NADH-dependent butanol dehydrogenase AQ9WZS7Details
Oxidoreductase, aldo/keto reductase familyQ9X0A2Details
Ribose 5-phosphate isomerase BQ9X0G9Details
Uncharacterized proteinQ9X0P2Details
Signal recognition particle receptor FtsYQ9WZ40Details
Glycerol uptake operon antiterminator regulatory proteinQ9X1F0Details
Rod shape-determining protein MreBQ9WZ57Details
5-methyltetrahydrofolate S-homocysteine methyltransferaseQ9WYA5Details
Sensor histidine kinaseQ9X180Details