scholarly journals Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

2019 ◽  
Vol 116 (30) ◽  
pp. 15023-15032 ◽  
Author(s):  
Andrea Riba ◽  
Noemi Di Nanni ◽  
Nitish Mittal ◽  
Erik Arhné ◽  
Alexander Schmidt ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Theoretical Models ◽  
Open Reading Frames ◽  
Yeast Cells ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Translation Elongation ◽  
Lower Protein ◽  
Ribosome Footprinting ◽  
Protein Output

Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a 1,000 ORFs in exponentially growing wild-type yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and transfer RNA (tRNA) adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein (RP) genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared with other transcripts with equally high ribosome densities.

scholarly journals Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

2018 ◽  
Author(s):  
Andrea Riba ◽  
Noemi Di Nanni ◽  
Nitish Mittal ◽  
Erik Arhné ◽  
Alexander Schmidt ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Translation Initiation ◽  
Mrna Translation ◽  
Elongation Rate ◽  
Translation Elongation ◽  
Lower Protein ◽  
Protein Output

AbstractAlthough protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and tRNA adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output than other transcripts with equally high ribosome densities.Significance StatementAlthough sequencing of ribosome footprints has uncovered new aspects of mRNA translation, the determinants of ribosome flux remain incompletely understood. Combining ribosome footprint data with measurements of protein synthesis rates, we here inferred translation initiation and elongation rates for over a thousand ORFs in yeast strains with varying translation capacity. We found that the translation elongation rate varies up to ~20-fold among yeast transcripts, and is significantly correlated with the rate of translation initiation. Furthermore, the amino acid composition of synthesized proteins impacts the rate of translation elongation to the same extent as measures of codon and tRNA adaptation. Transcripts encoding ribosomal proteins are translated especially slow, having markedly lower protein output than other transcripts with equally high ribosome densities.

scholarly journals tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast

2020 ◽  
Author(s):  
Joana F Tavares ◽  
Nick K. Davis ◽  
Ana Poim ◽  
Andreia Reis ◽  
Stefanie Kellner ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Protein Aggregation ◽  
Gene Knockout ◽  
Mrna Translation ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Translation Elongation ◽  
Proteotoxic Stress ◽  
Knockout Mutants ◽  
Bona Fide

Abstract/SummaryProtein synthesis rate and accuracy are essential for bona fide protein synthesis and proteome homeostasis (proteostasis), however the mRNA translation elongation factors that prevent protein mistranslation, misfolding and aggregation are poorly understood. To address this question, we evaluated the role of 70 yeast tRNA modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated and mistranslated proteins. We show that the mitochondrial tRNA-modifying enzyme Slm3 thiolates the cytoplasmic tRNAs at position 34 and that decreased levels of mcm5s2U34 in SLM3 mutants are compensated by increasing mcm5U34, ncm5U34 and ncm5Um34 levels. In the tRNA gene knockout strains, stress response proteins are overrepresented in protein aggregates and their genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications. Increased rates of amino acid misincorporation were detected in the yeast ELP1, SLM3 and TRM9 gene knockout mutants at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, misfolding and cellular proteotoxic stress.

scholarly journals MECHANISMS IN ENDOCRINOLOGY: Exogenous insulin does not increase muscle protein synthesis rate when administered systemically: a systematic review

2015 ◽  
Vol 173 (1) ◽  
pp. R25-R34 ◽  
Author(s):  
Jorn Trommelen ◽  
Bart B L Groen ◽  
Henrike M Hamer ◽  
Lisette C P G M de Groot ◽  
Luc J C van Loon
Keyword(s):  
Systematic Review ◽  
Older Adults ◽  
Protein Synthesis ◽  
Muscle Protein ◽  
Muscle Protein Synthesis ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Exogenous Insulin ◽  
Insulin Administration ◽  
Muscle Protein Synthesis Rate

BackgroundThough it is well appreciated that insulin plays an important role in the regulation of muscle protein metabolism, there is much discrepancy in the literature on the capacity of exogenous insulin administration to increase muscle protein synthesis ratesin vivoin humans.ObjectiveTo assess whether exogenous insulin administration increases muscle protein synthesis rates in young and older adults.DesignA systematic review of clinical trials was performed and the presence or absence of an increase in muscle protein synthesis rate was reported for each individual study arm. In a stepwise manner, multiple models were constructed that excluded study arms based on the following conditions: model 1, concurrent hyperaminoacidemia; model 2, insulin-induced hypoaminoacidemia; model 3, supraphysiological insulin concentrations; and model 4, older, more insulin resistant, subjects.ConclusionsFrom the presented data in the current systematic review, we conclude that: i) exogenous insulin and amino acid administration effectively increase muscle protein synthesis, but this effect is attributed to the hyperaminoacidemia; ii) exogenous insulin administered systemically induces hypoaminoacidemia which obviates any insulin-stimulatory effect on muscle protein synthesis; iii) exogenous insulin resulting in supraphysiological insulin levels exceeding 50 000 pmol/l may effectively augment muscle protein synthesis; iv) exogenous insulin may have a diminished effect on muscle protein synthesis in older adults due to age-related anabolic resistance; and v) exogenous insulin administered systemically does not increase muscle protein synthesis in healthy, young adults.

Relationship between glutamine concentration and protein synthesis in rat skeletal muscle

1988 ◽  
Vol 255 (2) ◽  
pp. E166-E172 ◽  
Author(s):  
M. M. Jepson ◽  
P. C. Bates ◽  
P. Broadbent ◽  
J. M. Pell ◽  
D. J. Millward
Keyword(s):  
Protein Synthesis ◽  
Protein Deficiency ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Glutamine Concentration ◽  
E Coli ◽  
Protein Group ◽  
Highly Correlated ◽  
Rna Concentration

Muscle glutamine concentration ([GLN]) and protein synthesis rate (Ks) have been examined in vivo in well-fed, protein-deficient, starved, and endotoxemic rats. With protein deficiency (8 or 5% casein diet), [GLN] fell from 7.70 to 5.58 and 3.56 mmol/kg in the 8 and 5% diet groups, with Ks falling from 15.42 to 9.1 and 6.84%/day. Three-day starvation reduced [GLN] and Ks to 2.38 mmol/kg and 5.6%/day, respectively. In all these groups food intakes and insulin were generally well maintained (except in the starved group), whereas free 3,5,3'-triiodothyronine (T3) was depressed in the starved and 5% protein group. The E. coli lipopolysaccharide endotoxin (3 mg/kg) reduced [GLN] to 5.85 and 4.72 mmol/kg and Ks to 10.5 and 9.10%/day in two well-fed groups. Insulin levels were increased, and free T3 levels fell. Combined protein deficiency and endotoxemia further reduced [GLN] and Ks to 1.88 mmol/kg and 4.01%/day, respectively, in the 5% protein rats. Changes in both ribosomal activity (KRNA) and concentration (RNA/protein) contributed to the fall in Ks in malnutrition and endotoxemia, although reductions in the RNA concentration were most marked with protein deficiency and reductions in the KRNA dominated the response to the endotoxin. The changes in [GLN] and Ks were highly correlated as were [GLN] and both KRNA and the RNA concentration, and these relationships were unique to glutamine. These relationships could reflect sensitivity of glutamine transport and protein synthesis to the same regulatory influences, and the particular roles of insulin and T3 are discussed, as well as any direct influence of glutamine on protein synthesis.

scholarly journals Dietary γ-Aminobutyric Acid Affects the Brain Protein Synthesis Rate in Ovariectomized Female Rats

2009 ◽  
Vol 55 (1) ◽  
pp. 75-80 ◽  
Author(s):  
Kazuyo TUJIOKA ◽  
Miho OHSUMI ◽  
Kenji HORIE ◽  
Mujo KIM ◽  
Kazutoshi HAYASE ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Female Rats ◽  
Aminobutyric Acid ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Brain Protein ◽  
Brain Protein Synthesis ◽  
The Brain

scholarly journals Dietary Ornithine Affects the Tissue Protein Synthesis Rate in Young Rats

2012 ◽  
Vol 58 (4) ◽  
pp. 297-302 ◽  
Author(s):  
Kazuyo TUJIOKA ◽  
Takashi YAMADA ◽  
Mami AOKI ◽  
Koji MORISHITA ◽  
Kazutoshi HAYASE ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Tissue Protein ◽  
Young Rats ◽  
Tissue 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 Dietary Restriction on Protein Synthesis and Wound Healing after Surgery in the Rat

1995 ◽  
Vol 89 (4) ◽  
pp. 383-388 ◽  
Author(s):  
Peter W. Emery ◽  
Peter Sanderson
Keyword(s):  
Wound Healing ◽  
Protein Synthesis ◽  
Dietary Restriction ◽  
Muscle Protein ◽  
Muscle Protein Synthesis ◽  
Chronically Ill ◽  
Abdominal Muscle ◽  
Collagen Content ◽  
Synthesis Rate ◽  
Protein Synthesis Rate

1. The healing of an abdominal muscle wound after surgery is associated with a considerable increase in the rate of protein synthesis. We have investigated whether this increase in protein synthesis is affected by chronic undernutrition, and whether this causes a delay in wound healing. 2. A group of rats was fed 58% of the voluntary food intake of a matched control group. After 7 days half the rats in each group underwent abdominal surgery. Forty-eight hours later all the rats were killed and muscle protein synthesis rate was measured by the flooding dose technique. 3. In a second experiment using the same dietary regimen rats were placed in metabolic cages after surgery and killed 7 days later. In addition to measurements of muscle protein synthesis, wound breaking strength was measured with a tensiometer and collagen content was also measured at the wound site. 4. Dietary restriction caused a loss of body weight, a decrease in nitrogen balance and a deficit in muscle protein mass. It also caused a decrease in protein synthesis rate in gastrocnemius muscle and in parts of the abdominal muscle distant from the site of the wound. However, it had no effect on the rate of muscle protein synthesis at the site of the wound either 2 or 7 days after surgery. The tensile strength and the collagen content of the wound were also unaffected by food restriction. 5. It is concluded that the wound healing process is uniquely protected from the effects of moderate undernutrition such as might be experienced by a chronically ill patient.

scholarly journals Phosphorylation of the α subunit of initiation factor 2 correlates with the inhibition of translation following transient cerebral ischaemia in the rat

1994 ◽  
Vol 302 (2) ◽  
pp. 335-338 ◽  
Author(s):  
J Burda ◽  
M E Martín ◽  
A García ◽  
A Alcázar ◽  
J L Fando ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Cerebral Ischaemia ◽  
Ternary Complex ◽  
Initiation Factor ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Vessel Occlusion ◽  
Α Subunit ◽  
Free System ◽  
Initiation Factor 2

Rats were subjected to the standard four-vessel occlusion model of cerebral transient ischaemia (vertebral and carotid arteries) for 15 and 30 min. After a 30 min recirculation period, protein synthesis rate, initiation factor 2 (eIF-2) and guanine nucleotide exchange factor (GEF) activities, and the level of phosphorylation of the alpha subunit of eIF-2 (eIF-2 alpha) were determined in the neocortex region of the brain from sham-operated controls and ischaemic animals. Following reversible cerebral ischaemia, the protein synthesis rate, as measured in a cell-free system, was significantly inhibited (70%) in the ischaemic animals. eIF-2 activity, as measured by its ability to form a ternary complex, also decrease parallel to the decrease in protein synthesis. As eIF-2 activity was assayed in the presence of Mg2+ and GTP-regenerating capacity, the decrease in ternary-complex formation indicated the possible impairment of GEF activity. Since phosphorylated eIF-2 [eIF-2(alpha P)] is a powerful inhibitor of GEF, the levels of phosphorylated eIF-2 alpha were determined, and an increase from 7% phosphorylation in sham control rats to 20% phosphorylation in 15 min and 29% phosphorylation in 30 min in ischaemic rats was observed, providing evidence for a tight correlation of phosphorylation of eIF-2 alpha and inhibition of protein synthesis. Moreover, GEF activity measured in the GDP-exchange assay was in fact inhibited in the ischaemic animals, proving that protein synthesis is impaired by the presence of eIF-2(alpha P), which blocks eIF-2 recycling.

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