Dataset Information

Central dogma rates and the trade-off between precision and economy in gene expression.

ABSTRACT: Steady-state protein abundance is set by four rates: transcription, translation, mRNA decay and protein decay. A given protein abundance can be obtained from infinitely many combinations of these rates. This raises the question of whether the natural rates for each gene result from historical accidents, or are there rules that give certain combinations a selective advantage? We address this question using high-throughput measurements in rapidly growing cells from diverse organisms to find that about half of the rate combinations do not exist: genes that combine high transcription with low translation are strongly depleted. This depletion is due to a trade-off between precision and economy: high transcription decreases stochastic fluctuations but increases transcription costs. Our theory quantitatively explains which rate combinations are missing, and predicts the curvature of the fitness function for each gene. It may guide the design of gene circuits with desired expression levels and noise.

SUBMITTER: Hausser J

PROVIDER: S-EPMC6325141 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Central dogma rates and the trade-off between precision and economy in gene expression.

Hausser Jean J Mayo Avi A Keren Leeat L Alon Uri U

Nature communications 20190108 1

Steady-state protein abundance is set by four rates: transcription, translation, mRNA decay and protein decay. A given protein abundance can be obtained from infinitely many combinations of these rates. This raises the question of whether the natural rates for each gene result from historical accidents, or are there rules that give certain combinations a selective advantage? We address this question using high-throughput measurements in rapidly growing cells from diverse organisms to find that a ...[more]

PMID: 30622246

Similar Datasets

Project description:BackgroundEnergy cost minimization has been widely accepted to regulate gait. Optimization principles have been frequently used to explain how individuals adapt their gait pattern. However, there have been rare attempts to account for the role of variability in this optimization process. Motor redundancy can enable individuals to perform tasks reliably while achieving energy optimization. However, we do not know how the non-goal-equivalent and goal-equivalent variability is regulated. In this study, we investigated how unilateral transfemoral amputees regulate step and stride variability based on the task to achieve energy economy.MethodsNine individuals with unilateral transfemoral amputation walked on a treadmill at speeds of 0.6, 0.8, 1.0, 1.2 and 1.4 m/s using their prescribed passive prostheses. We calculated the step-to-step and stride-to-stride variability and applied goal equivalent manifold (GEM) based control to decompose goal-equivalent and non-goal-equivalent manifold. To quantify the energy economy, the energy recovery rate (R) was calculated based on potential energy and kinetic energy. Comparisons were made between GEM variabilities and commonly used standard deviation measurements. A linear regression model was used to investigate the trade-off between R and GEM variabilities.ResultsOur analysis shows greater variability along the goal-equivalent manifold compared to the non-goal-equivalent manifold (p < 0.001). Moreover, our analysis shows lower energy recovery rate for amputee gait compared to nonamputee gait (at least 20% less at faster walking speed). We found a negative relationship between energy recovery rate and non-goal-equivalent variability. Compared to the standard deviation measurements, the variability decomposed using GEM reflected the preferred walking speed and the limitation of the passive prosthetic device.ConclusionIndividuals with amputation cleverly leverage task redundancy, regulating step and stride variability to the GEM. This result suggests that task redundancy enables unilateral amputees to benefit from motor variability in terms of energy economy. The differences observed between prosthetic step and intact step support the development of prosthetic limbs capable of enhancing positive work during the double support phase and of powered prosthesis controllers that allow for variability along the task space while minimizing variability that interferes with the task goal. This study provides a different perspective on amputee gait analysis and challenges the field to think differently about the role of variability.

Dataset Information

Central dogma rates and the trade-off between precision and economy in gene expression.

Publications

Central dogma rates and the trade-off between precision and economy in gene expression.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets