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...

Full description

Saved in:
Bibliographic Details
Published in:PLoS genetics 2013-04, Vol.9 (4), p.e1003485-e1003485
Main Authors: 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
Format: Article
Language:English
Subjects:
5' Untranslated Regions
Bacteria
Bacterial genetics
Binding sites
Bioinformatics
Biology
Comparative analysis
Gene Expression Profiling
Genetic aspects
Genetics
Genomes
Genomics
Hyperthermophiles
Life Style
Lifestyles
Molecular Sequence Data
Organisms
Physiological aspects
Scholarships & fellowships
Thermotoga maritima - genetics
Transcription Initiation Site
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1003485