Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise

Sangjin Kim, Christine Jacobs-Wagner

Research output: Contribution to journalArticle

Abstract

Genetically identical cells exhibit diverse phenotypes even when experiencing the same environment. This phenomenon in part originates from cell-to-cell variability (noise) in protein expression. Although various kinetic schemes of stochastic transcription initiation are known to affect gene expression noise, how posttranscription initiation events contribute to noise at the protein level remains incompletely understood. To address this question, we developed a stochastic simulation-based model of bacterial gene expression that integrates well-known dependencies between transcription initiation, transcription elongation dynamics, mRNA degradation, and translation. We identified realistic conditions under which mRNA lifetime and transcriptional pauses modulate the protein expression noise initially introduced by the promoter architecture. For instance, we found that the short lifetime of bacterial mRNAs facilitates the production of protein bursts. Conversely, RNA polymerase (RNAP) pausing at specific sites during transcription elongation can attenuate protein bursts by fluidizing the RNAP traffic to the point of erasing the effect of a bursty promoter. Pause-prone sites, if located close to the promoter, can also affect noise indirectly by reducing both transcription and translation initiation due to RNAP and ribosome congestion. Our findings highlight how the interplay between transcription initiation, transcription elongation, translation, and mRNA degradation shapes the distribution in protein numbers. They also have implications for our understanding of gene evolution and suggest combinatorial strategies for modulating phenotypic variability by genetic engineering.

Original languageEnglish (US)
Pages (from-to)1718-1729
Number of pages12
JournalBiophysical journal
Volume114
Issue number7
DOIs
StatePublished - Apr 10 2018
Externally publishedYes

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RNA Stability
Noise
DNA-Directed RNA Polymerases
Proteins
Gene Expression
Bacterial Genes
Messenger RNA
Genetic Engineering
Protein Biosynthesis
Ribosomes
Phenotype
Genes

ASJC Scopus subject areas

  • Biophysics

Cite this

Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise. / Kim, Sangjin; Jacobs-Wagner, Christine.

In: Biophysical journal, Vol. 114, No. 7, 10.04.2018, p. 1718-1729.

Research output: Contribution to journalArticle

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