مورد إلكتروني
Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing
| العنوان: | Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing |
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| المصدر: | Gummesson , B , Shah , S A , Borum , A S , Fessler , M , Mitarai , N , Sørensen , M A & Svenningsen , S L 2020 , ' Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing ' , Frontiers in Genetics , vol. 11 , 144 . |
| بيانات النشر: | 2020 |
| تفاصيل مُضافة: | Gummesson, Bertil Shah, Shiraz Ali Borum, Alexander Skov Fessler, Mathias Mitarai, Namiko Sørensen, Michael Askvad Svenningsen, Sine Lo |
| نوع الوثيقة: | Electronic Resource |
| مستخلص: | Escherichia coli cells respond to a period of famine by globally reorganizing their gene expression. The changes are known as the stringent response, which is orchestrated by the alarmone ppGpp that binds directly to RNA polymerase. The resulting changes in gene expression are particularly well studied in the case of amino acid starvation. We used deep RNA sequencing in combination with spike-in cells to measure global changes in the transcriptome after valine-induced isoleucine starvation of a standard E. coli K12 strain. Owing to the whole-cell spike-in method that eliminates variations in RNA extraction efficiency between samples, we show that ribosomal RNA levels are reduced during isoleucine starvation and we quantify how the change in cellular RNA content affects estimates of gene regulation. Specifically, we show that standard data normalization relying on sample sequencing depth underestimates the number of down-regulated genes in the stringent response and overestimates the number of up-regulated genes by approximately 40%. The whole-cell spike-in method also made it possible to quantify how rapidly the pool of total messenger RNA (mRNA) decreases upon amino acid starvation. A principal component analysis showed that the first two components together described 69% of the variability of the data, underlining that large and highly coordinated regulons are at play in the stringent response. The induction of starvation by sudden addition of high valine concentrations provoked prominent regulatory responses outside of the expected ppGpp, RpoS, and Lrp regulons. This underlines the notion that with the high resolution possible in deep RNA sequencing analysis, any different starvation method (e.g., nitrogen-deprivation, removal of an amino acid from an auxotroph strain, or valine addition to E. coli K12 strains) will produce measurable variations in the stress response produced by the cells to cope with the specific treatment. |
| مصطلحات الفهرس: | dk/atira/pure/core/keywords/TheFacultyOfScience, Faculty of Science, stringent response, Deep RNA sequencing, ribosomal RNA degradataion, Transcriptome, ppGpp, Gene expression, whole-cell spike-in normalization, article |
| الإتاحة: | Open access content. Open access content info:eu-repo/semantics/openAccess |
| ملاحظة: | application/pdf English |
| أرقام أخرى: | DAV oai:pure.atira.dk:publications/934c402b-edf5-4a9b-9c97-5b0805eda629 https://curis.ku.dk/portal/da/publications/valineinduced-isoleucine-starvation-in-escherichia-coli-k12-studied-by-spikein-normalized-rna-sequencing(934c402b-edf5-4a9b-9c97-5b0805eda629).html https://doi.org/10.3389/fgene.2020.00144 https://curis.ku.dk/ws/files/239621138/Valine_Induced_Isoleucine_Starvation_in_Escherichia_coli_K_12_Studied_by_Spike_In_Normalized_RNA_Sequencing.pdf 1322741181 |
| المصدر المساهم: | UNIV OF COPENHAGEN From OAIster®, provided by the OCLC Cooperative. |
| رقم الأكسشن: | edsoai.on1322741181 |
| قاعدة البيانات: | OAIster |
| الوصف غير متاح. |