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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-04-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3636130?pdf=render |
| _version_ | 1811326765203718144 |
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| author | Haythem Latif Joshua A Lerman Vasiliy A Portnoy Yekaterina Tarasova Harish Nagarajan Alexandra C Schrimpe-Rutledge Richard D Smith Joshua N Adkins Dae-Hee Lee Yu Qiu Karsten Zengler |
| author_facet | Haythem Latif Joshua A Lerman Vasiliy A Portnoy Yekaterina Tarasova Harish Nagarajan Alexandra C Schrimpe-Rutledge Richard D Smith Joshua N Adkins Dae-Hee Lee Yu Qiu Karsten Zengler |
| author_sort | Haythem Latif |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T14:54:47Z |
| format | Article |
| id | doaj.art-e24e7e0d1dda454ea4079c80962aad27 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-13T14:54:47Z |
| publishDate | 2013-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-e24e7e0d1dda454ea4079c80962aad272022-12-22T02:42:28ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042013-04-0194e100348510.1371/journal.pgen.1003485The genome organization of Thermotoga maritima reflects its lifestyle.Haythem LatifJoshua A LermanVasiliy A PortnoyYekaterina TarasovaHarish NagarajanAlexandra C Schrimpe-RutledgeRichard D SmithJoshua N AdkinsDae-Hee LeeYu QiuKarsten ZenglerThe 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.http://europepmc.org/articles/PMC3636130?pdf=render |
| spellingShingle | Haythem Latif Joshua A Lerman Vasiliy A Portnoy Yekaterina Tarasova Harish Nagarajan Alexandra C Schrimpe-Rutledge Richard D Smith Joshua N Adkins Dae-Hee Lee Yu Qiu Karsten Zengler The genome organization of Thermotoga maritima reflects its lifestyle. PLoS Genetics |
| title | The genome organization of Thermotoga maritima reflects its lifestyle. |
| title_full | The genome organization of Thermotoga maritima reflects its lifestyle. |
| title_fullStr | The genome organization of Thermotoga maritima reflects its lifestyle. |
| title_full_unstemmed | The genome organization of Thermotoga maritima reflects its lifestyle. |
| title_short | The genome organization of Thermotoga maritima reflects its lifestyle. |
| title_sort | genome organization of thermotoga maritima reflects its lifestyle |
| url | http://europepmc.org/articles/PMC3636130?pdf=render |
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