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Sequence-dependent ...
Sequence-dependent model of genes with dual s factor preference
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- Baptista, Ines S. C. (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.
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- Kandavalli, Vinodh (author)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi,Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.
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- Chauhan, Vatsala (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.
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- Bahrudeen, Mohamed N. M. (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.
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- Almeida, Bilena L. B. (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.
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- Palma, Cristina S. D. (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.
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- Dash, Suchintak (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.
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- Ribeiro, Andre S. (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland.;NOVA Univ Lisbon, Ctr Technol & Syst CTS Uninova, P-2829516 Monte De Caparica, Portugal.;Arvo Ylpon katu 34, Tampere 33520, Finland.
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Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere 33520, Finland Institutionen för cell- och molekylärbiologi (creator_code:org_t)
- Elsevier, 2022
- 2022
- English.
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In: Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. - : Elsevier. - 1874-9399 .- 1876-4320. ; 1865:3
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Abstract
Subject headings
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- Escherichia coli uses sigma factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single sigma factor, approximately 5% of them have dual sigma factor preference. The most common are those responsive to both sigma(70), which controls housekeeping genes, and sigma(38), which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that 'sigma(70+38) genes' are nearly as upregulated in stationary growth as 'sigma(38) genes'. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in sigma(38) levels. We then propose and validate a sequence dependent model of sigma(70+38) genes, with dual sensitivity to sigma(38) and sigma(70), that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and sigma factor combinations. Given this, promoters controlling sigma 70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Keyword
- Dual s factor preference
- Sequence-dependent gene expression model
- RNA-seq
- Flow cytometry
- E. coli
Publication and Content Type
- ref (subject category)
- art (subject category)
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