Bacteria differently regulate mRNA abundance to specifically respond to various stresses
Abstract
Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up- and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs.
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7800 mRNAs were measured in E. coli.
“and 7800 mRNAs”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [95]
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“This poor correlation is often attributed to different time scales of transcript and protein turnover [27].”
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“Normalization by the median of the total number of reads aligned to all ORFs gives more stable normalization than normalization to reads per total mapped reads, rpM, or fragment per total mapped reads, FPM [20].”
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“Under normal conditions more than 90% of the ribosomes are involved in translation [52,53] thus leaving little capacity to reallocate ribosomes to new mRNAs [54].”
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Microbial single-cell RNA sequencing by split-pool barcoding
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Bringing the genetically minimal cell to life on a computer in 4D
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- Authors
- Bartholomäus, A., Fedyunin, I., Feist, P., Sin, C., Zhang, G., Valleriani, A., & Ignatova, Z.
- Affiliations
- Universität Hamburg (DE)
- University of Potsdam (DE)
- Max Planck Institute of Colloids and Interfaces (DE)
- Corresponding author
- Ignatova, Zoya
- Venue
- Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
- Publisher
- The Royal Society
- Published
- 2016-03-13
- Volume
- 374
- Issue
- 2063
- Pages
- 20150069
- ISSN
- 1364-503X (ISSN-L)
- 1471-2962
- OpenAlex
- W2258657513
- Cited by
- 81
- References
- 8
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 5 · 2023: 6 · 2022: 10 · 2021: 12 · 2020: 15 · 2019: 8 · 2018: 2 · 2017: 6 · 2016: 7
- FWCI
- 6.18
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences (publishedVersion)
- PubMed (publishedVersion)
- publish.UP (University of Potsdam) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Heat shock proteins research
- Keywords
- Escherichia coli, heat stress, osmotic stress, stress response, mRNA levels, ribosome-protected fragments, translational regulation, start codon, ribosome profiling, gene expression reprogramming
- MeSH terms
- Escherichia coli, RNA, Bacterial, RNA, Messenger, Stress, Physiological, Heat-Shock Response
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