Length-dependent translation of messenger RNA by ribosomes

Valleriani, Angelo; Zhang, Gong; Nagar, Apoorva; Ignatova, Zoya; Lipowsky, Reinhard

doi:10.1103/physreve.83.042903

Cited by 23 publications

(39 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…If we define to be the degradation rate of proteins in a cell population under balanced conditions, the long time limit of (11) gives the steady state amount of proteins. This amount is given by , as derived for instance in [7], and this limit leads toNote that in principle the steady state protein level is different for the two lifetime densities since they give rise to different stationary age distributions as was pointed out in the previous section. However, this difference is small if the average lifetime is large compared to .…”

Section: Resultsmentioning

confidence: 94%

Transient Phenomena in Gene Expression after Induction of Transcription

Deneke¹,

Rudorf²,

Valleriani

2012

PLoS ONE

Self Cite

View full text Add to dashboard Cite

When transcription of a gene is induced by a stimulus, the number of its mRNA molecules changes with time. Here we discuss how this time evolution depends on the shape of the mRNA lifetime distribution. Analysis of the statistical properties of this change reveals transient effects on polysomes, ribosomal profiles, and rate of protein synthesis. Our studies reveal that transient phenomena in gene expression strongly depend on the specific form of the mRNA lifetime distribution.

show abstract

Section: Resultsmentioning

confidence: 94%

Transient Phenomena in Gene Expression after Induction of Transcription

Deneke¹,

Rudorf²,

Valleriani

2012

PLoS ONE

Self Cite

View full text Add to dashboard Cite

show abstract

“…It was shown that the aging of mRNA affects both the polysomal size distributions [33], [34] and the rate of protein synthesis [35]. From the point of view of mRNA degradation, aging becomes manifest in the residual lifetime R of the molecule.…”

Section: Resultsmentioning

confidence: 99%

Complex Degradation Processes Lead to Non-Exponential Decay Patterns and Age-Dependent Decay Rates of Messenger RNA

2013

Self Cite

View full text Add to dashboard Cite

Experimental studies on mRNA stability have established several, qualitatively distinct decay patterns for the amount of mRNA within the living cell. Furthermore, a variety of different and complex biochemical pathways for mRNA degradation have been identified. The central aim of this paper is to bring together both the experimental evidence about the decay patterns and the biochemical knowledge about the multi-step nature of mRNA degradation in a coherent mathematical theory. We first introduce a mathematical relationship between the mRNA decay pattern and the lifetime distribution of individual mRNA molecules. This relationship reveals that the mRNA decay patterns at steady state expression level must obey a general convexity condition, which applies to any degradation mechanism. Next, we develop a theory, formulated as a Markov chain model, that recapitulates some aspects of the multi-step nature of mRNA degradation. We apply our theory to experimental data for yeast and explicitly derive the lifetime distribution of the corresponding mRNAs. Thereby, we show how to extract single-molecule properties of an mRNA, such as the age-dependent decay rate and the residual lifetime. Finally, we analyze the decay patterns of the whole translatome of yeast cells and show that yeast mRNAs can be grouped into three broad classes that exhibit three distinct decay patterns. This paper provides both a method to accurately analyze non-exponential mRNA decay patterns and a tool to validate different models of degradation using decay data.

show abstract

“…We found that degradation can have a significant effect on experimentally measurable quantities such as the polysome size distribution and the density of ribosomes as a function of codon position. We also showed that degradation induces a length dependence in the translation rate leading to a decrease in the steady state amount of proteins per mRNA, the so-called translational ratio, with increasing protein length [17].…”

Section: Introductionmentioning

confidence: 99%

“…1. We have tried to capture this effect in our recent work [16,17] where we have studied a simple model with very low entry rates, neglecting the hard core exclusion interaction between the ribosomes. We found that degradation can have a significant effect on experimentally measurable quantities such as the polysome size distribution and the density of ribosomes as a function of codon position.…”

Section: Introductionmentioning

confidence: 99%

Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks

2011

Self Cite

View full text Add to dashboard Cite

We investigate the role of degradation of mRNA on protein synthesis using the totally asymmetric simple exclusion process (TASEP) as the underlying model for ribosome dynamics. mRNA degradation has a strong effect on the lifetime distribution of the mRNA, which in turn affects polysome statistics such as the number of ribosomes present on an mRNA strand of a given size. An average over mRNA of all ages is equivalent to an average over possible configurations of the corresponding TASEP-both before steady state and in steady state. To evaluate the relevant quantities for the translation problem, we first study the approach towards steady state of the TASEP, starting with an empty lattice representing an unloaded mRNA. When approaching the high density phase, the system shows two distinct phases with the entry and exit boundaries taking control of the density at their respective ends in the second phase. The approach towards the maximal current phase exhibits the surprising property that the ribosome entry flux can exceed the maximum possible steady state value. In all phases, the averaging over the mRNA age distribution shows a decrease in the average ribosome density profile as a function of distance from the entry boundary. For entry/exit parameters corresponding to the high density phase of TASEP, the average ribosome density profile also has a maximum near the exit end.

show abstract

Length-dependent translation of messenger RNA by ribosomes

Cited by 23 publications

References 28 publications

Transient Phenomena in Gene Expression after Induction of Transcription

Transient Phenomena in Gene Expression after Induction of Transcription

Complex Degradation Processes Lead to Non-Exponential Decay Patterns and Age-Dependent Decay Rates of Messenger RNA

Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks

Contact Info

Product

Resources

About