scholarly journals Author response: Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis

2020 ◽  
Author(s):  
Tatsuhisa Tsuboi ◽  
Matheus P Viana ◽  
Fan Xu ◽  
Jingwen Yu ◽  
Raghav Chanchani ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Volume Fraction ◽  
Mrna Localization ◽  
Author Response ◽  
Mitochondrial Volume

scholarly journals Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Tatsuhisa Tsuboi ◽  
Matheus P Viana ◽  
Fan Xu ◽  
Jingwen Yu ◽  
Raghav Chanchani ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Energy Demand ◽  
Volume Fraction ◽  
Protein Composition ◽  
Mrna Localization ◽  
Geometric Constraints ◽  
Specific Gene ◽  
Translation Elongation ◽  
Mitochondrial Volume ◽  
Necessary And Sufficient

Mitochondria are dynamic organelles that must precisely control their protein composition according to cellular energy demand. Although nuclear-encoded mRNAs can be localized to the mitochondrial surface, the importance of this localization is unclear. As yeast switch to respiratory metabolism, there is an increase in the fraction of the cytoplasm that is mitochondrial. Our data point to this change in mitochondrial volume fraction increasing the localization of certain nuclear-encoded mRNAs to the surface of the mitochondria. We show that mitochondrial mRNA localization is necessary and sufficient to increase protein production to levels required during respiratory growth. Furthermore, we find that ribosome stalling impacts mRNA sensitivity to mitochondrial volume fraction and counterintuitively leads to enhanced protein synthesis by increasing mRNA localization to mitochondria. This points to a mechanism by which cells are able to use translation elongation and the geometric constraints of the cell to fine-tune organelle-specific gene expression through mRNA localization.

scholarly journals Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins

2019 ◽  
Author(s):  
Tatsuhisa Tsuboi ◽  
Matheus P. Viana ◽  
Fan Xu ◽  
Jingwen Yu ◽  
Raghav Chanchani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Energy Demand ◽  
Protein Production ◽  
Volume Fraction ◽  
Nuclear Genome ◽  
Protein Composition ◽  
Mrna Localization ◽  
Specific Gene ◽  
Mitochondrial Volume ◽  
Size And Morphology

Mitochondria are dynamic in their size and morphology yet must also precisely control their protein composition according to cellular energy demand. This control is particularly complicated for mitochondria, as they must coordinate gene expression from both the nuclear and mitochondrial genome. We have found that cells are able to use this dynamic morphology to post-transcriptionally coordinate protein expression with the metabolic demands of the cell through enhanced mRNA localization to the mitochondria. As yeast switch to respiratory metabolism, they increase their mitochondrial volume fraction that is, the ratio of mitochondrial volume to intracellular volume which drives the localization of nuclear-encoded mitochondrial mRNAs to the surface of the mitochondria. Through artificial tethering experiments, we show that this mitochondrial localization is sufficient to increase protein production, whereas sequestering mRNAs away from the mitochondrial surface decreases protein production, and those cells are deficient in growth in respiratory conditions. Furthermore, we find that this mRNA sensitivity to mitochondrial volume fraction is driven by the speed of translation downstream of the mitochondrial targeting sequence (MTS), as local ribosome stalling through a stretch of polyprolines in the nascent peptide can drive constitutive localization of mRNAs to the mitochondria. This points to a mechanism by which organelle volume fraction provides feedback to regulate organelle-specific gene expression through mRNA localization while potentially circumventing the need to directly coordinate with the nuclear genome.

Author response for "A rational approach to improving titer in E. coli ‐based cell‐free protein synthesis reactions"

2020 ◽  
Author(s):  
Noelle Colant ◽  
Beatrice Melinek ◽  
Jaime Teneb ◽  
Stephen Goldrick ◽  
William Rosenberg ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Author Response ◽  
Rational Approach ◽  
Free Protein ◽  
E Coli ◽  
Synthesis Reactions ◽  
Cell Free Protein Synthesis

scholarly journals Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sarah L. Gillen ◽  
Chiara Giacomelli ◽  
Kelly Hodge ◽  
Sara Zanivan ◽  
Martin Bushell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Mrna Stability ◽  
Mrna Localization ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Translational Efficiency ◽  
Mrna Levels ◽  
Control Of Gene Expression ◽  
Mrna Fate

Abstract Background Regulation of protein output at the level of translation allows for a rapid adaptation to dynamic changes to the cell’s requirements. This precise control of gene expression is achieved by complex and interlinked biochemical processes that modulate both the protein synthesis rate and stability of each individual mRNA. A major factor coordinating this regulation is the Ccr4-Not complex. Despite playing a role in most stages of the mRNA life cycle, no attempt has been made to take a global integrated view of how the Ccr4-Not complex affects gene expression. Results This study has taken a comprehensive approach to investigate post-transcriptional regulation mediated by the Ccr4-Not complex assessing steady-state mRNA levels, ribosome position, mRNA stability, and protein production transcriptome-wide. Depletion of the scaffold protein CNOT1 results in a global upregulation of mRNA stability and the preferential stabilization of mRNAs enriched for G/C-ending codons. We also uncover that mRNAs targeted to the ER for their translation have reduced translational efficiency when CNOT1 is depleted, specifically downstream of the signal sequence cleavage site. In contrast, translationally upregulated mRNAs are normally localized in p-bodies, contain disorder-promoting amino acids, and encode nuclear localized proteins. Finally, we identify ribosome pause sites that are resolved or induced by the depletion of CNOT1. Conclusions We define the key mRNA features that determine how the human Ccr4-Not complex differentially regulates mRNA fate and protein synthesis through a mechanism linked to codon composition, amino acid usage, and mRNA localization.

Effect of auxin and phenobarbital on the ultrastructure and digitoxin content in Digitalis purpurea tissue culture

1996 ◽  
Vol 74 (3) ◽  
pp. 378-382 ◽  
Author(s):  
Mercedes Bonfill ◽  
Javier Palazón ◽  
Rosa M. Cusidó ◽  
M. Teresa Piñol ◽  
Carmen Morales
Keyword(s):  
Acetic Acid ◽  
Volume Fraction ◽  
Volume Ratio ◽  
Naphthaleneacetic Acid ◽  
Acetic Acid Medium ◽  
Digitalis Purpurea ◽  
Murashige Skoog ◽  
Mitochondrial Volume ◽  
Callus Tissues ◽  
Indole 3 Acetic Acid

Callus derived from Digitalis purpurea hypocotils were grown during a 6-week period on solid Murashige–Skoog medium supplemented with 1 mg/L 6-benzylaminopurine, 0.01 mg/L gibberellic acid and 0.1 mg/L indole-3-acetic acid or α-naphthaleneacetic acid, with or without phenobarbital (40 mg/L). The presence of phenobarbital in the culture medium caused a reduction of the vacuole/cytoplasm ratio. At the same time, the chloroplastic volume fraction decreased in callus tissue cells grown in media supplemented with phenobarbital, while the mitochondrial volume ratio increased. Digitoxin content was enhanced in callus tissues, especially in those grown on indole-3-acetic acid medium supplemented with phenobarbital. The relationship between ultrastructure of D. purpurea callus and digitoxin content is discussed. Keywords: Digitalis purpurea tissue cultures, digitoxin, phenobarbital, mitochondria, chloroplast.

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