Amino Acids Promote Mitochondrial-Derived Compartment Formation in Mammalian Cells

SUMMARYWe recently identified a new cellular structure in yeast, called the Mitochondrial-Derived Compartment (MDC), that forms on mitochondria in response to amino acid excess. While emerging evidence supports an important function for MDCs in protecting cells from metabolic stress, whether this system exists beyond yeast remains unclear. Here, we show that MDCs are conserved in mammals, and like their yeast counterparts, are responsive to the intracellular amino acid content. Specifically, we find that inhibition of protein translation stimulates formation of dynamic, micron-sized compartments that associate with the mitochondrial network. These compartments are enriched for the carrier receptor Tomm70A and other select mitochondrial outer and inner membrane cargo, associate with the ER membrane, and require the conserved GTPase Miro1 for formation. Mammalian MDCs are responsive to changes in amino acid levels during translation inhibition, and are not activated by other common cellular stressors. Thus, MDCs represent an evolutionarily conserved nutrient-responsive mitochondrial remodeling system.

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Ncl1-mediated metabolic rewiring critical during metabolic stress

Life Science Alliance ◽

10.26508/lsa.201900360 ◽

2019 ◽

Vol 2 (4) ◽

pp. e201900360 ◽

Cited By ~ 2

Author(s):

Ajay Bhat ◽

Rahul Chakraborty ◽

Khushboo Adlakha ◽

Ganesh Agam ◽

Kausik Chakraborty ◽

...

Keyword(s):

Amino Acid ◽

Translational Control ◽

Acid Metabolism ◽

Tricarboxylic Acid Cycle ◽

Metabolic Stress ◽

Protein Translation ◽

Leucine Supplementation ◽

Nutritional Limitation ◽

Amino Acid Levels

Nutritional limitation has been vastly studied; however, there is limited knowledge of how cells maintain homeostasis in excess nutrients. In this study, using yeast as a model system, we show that some amino acids are toxic at higher concentrations. With cysteine as a physiologically relevant example, we delineated the pathways/processes that are altered and those that are involved in survival in the presence of elevated levels of this amino acid. Using proteomics and metabolomics approach, we found that cysteine up-regulates proteins involved in amino acid metabolism, alters amino acid levels, and inhibits protein translation—events that are rescued by leucine supplementation. Through a comprehensive genetic screen, we show that leucine-mediated effect depends on a transfer RNA methyltransferase (NCL1), absence of which decouples transcription and translation in the cell, inhibits the conversion of leucine to ketoisocaproate, and leads to tricarboxylic acid cycle block. We therefore propose a role of NCL1 in regulating metabolic homeostasis through translational control.

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Ncl1 mediated metabolic rewiring critical during metabolic stress

10.1101/529578 ◽

2019 ◽

Author(s):

Ajay Bhat ◽

Rahul Chakraborty ◽

Khushboo Adlakha ◽

Ganesh Agam ◽

Kausik Chakraborty ◽

...

Keyword(s):

Amino Acid ◽

Translational Control ◽

Metabolic Stress ◽

Tca Cycle ◽

Protein Translation ◽

Leucine Supplementation ◽

Nutritional Limitation ◽

Trna Methyltransferase ◽

Amino Acid Levels

AbstractNutritional limitation has been vastly studied, however, there is limited knowledge of how cells maintain homeostasis in excess nutrients. In this study, using yeast as a model system, we show that some amino acids are toxic at higher concentrations. With cysteine as a physiologically relevant example, we delineated the pathways/processes that are altered and those that are involved in survival in presence of elevated levels of this amino acid. Using proteomics and metabolomics approach, we found that cysteine upregulates proteins involved in amino acid metabolism, alters amino acid levels, and inhibits protein translation, events that are rescued by leucine supplementation. Through a comprehensive genetic screen we show that leucine mediated effect depends on a tRNA methyltransferase (Ncl1), absence of which decouples cell’s transcription and translation, inhibits the conversation of leucine to ketoisocaproate and leads to TCA cycle block. We therefore, propose a role of Ncl1 in regulating metabolic homeostasis through translational control.

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REGRESSION ESTIMATES OF LYSINE AND OTHER AMINO ACIDS IN MANITOBA BARLEY

Canadian Journal of Animal Science ◽

10.4141/cjas90-042 ◽

1990 ◽

Vol 70 (1) ◽

pp. 333-336 ◽

Cited By ~ 2

Author(s):

K. M. DUPCHAK ◽

D. HICKLING

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Acid Content ◽

Good Predictor ◽

Crude Protein ◽

Amino Acid Content ◽

Prediction Equation ◽

Regression Equations ◽

Key Words Barley ◽

Amino Acid Levels

Manitoba barley samples from the 1986 and 1987 crop years were analyzed for lysine and crude protein. The 1987 samples were also analyzed for other amino acids and for proximate components. Regression equations were developed to predict amino acid content. Crude protein was found to be a good predictor of amino acid levels. There was no effect of crop year on the prediction equation for lysine. Key words: Barley, lysine, prediction

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Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation

Nucleic Acids Research ◽

10.1093/nar/gkaa469 ◽

2020 ◽

Vol 48 (12) ◽

pp. 6445-6457 ◽

Cited By ~ 4

Author(s):

Meirong Chen ◽

Bernhard Kuhle ◽

Jolene Diedrich ◽

Ze Liu ◽

James J Moresco ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Mammalian Cells ◽

Trna Synthetase ◽

Intrinsic Activity ◽

Trna Synthetases ◽

Evolutionarily Conserved ◽

Trna Species ◽

In Trans ◽

Editing Activity

Abstract The accuracy in pairing tRNAs with correct amino acids by aminoacyl-tRNA synthetases (aaRSs) dictates the fidelity of translation. To ensure fidelity, multiple aaRSs developed editing functions that remove a wrong amino acid from tRNA before it reaches the ribosome. However, no specific mechanism within an aaRS is known to handle the scenario where a cognate amino acid is mischarged onto a wrong tRNA, as exemplified by AlaRS mischarging alanine to G4:U69-containing tRNAThr. Here, we report that the mischargeable G4:U69-containing tRNAThr are strictly conserved in vertebrates and are ubiquitously and abundantly expressed in mammalian cells and tissues. Although these tRNAs are efficiently mischarged, no corresponding Thr-to-Ala mistranslation is detectable. Mistranslation is prevented by a robust proofreading activity of ThrRS towards Ala-tRNAThr. Therefore, while wrong amino acids are corrected within an aaRS, a wrong tRNA is handled in trans by an aaRS cognate to the mischarged tRNA species. Interestingly, although Ala-tRNAThr mischarging is not known to occur in bacteria, Escherichia coli ThrRS also possesses robust cross-editing ability. We propose that the cross-editing activity of ThrRS is evolutionarily conserved and that this intrinsic activity allows G4:U69-containing tRNAThr to emerge and be preserved in vertebrates to have alternative functions without compromising translational fidelity.

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Translational control through differential ribosome pausing during amino acid limitation in mammalian cells

10.1101/321448 ◽

2018 ◽

Author(s):

Alicia M. Darnell ◽

Arvind R. Subramaniam ◽

Erin K. O’Shea

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Translational Control ◽

Mammalian Cells ◽

Mrna Levels ◽

Evolutionarily Conserved ◽

Insufficient Response ◽

Ribosome Pausing ◽

Robust Response ◽

Abundant Amino Acid

SummaryLimitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that limitation for the amino acid arginine causes a selective loss of tRNA charging, which regulates translation through ribosome pausing at two of six arginine codons. Surprisingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevents ribosome pausing, while an insufficient response to arginine limitation led to loss of arginine tRNA charging and ribosome pausing. Codon-specific ribosome pausing decreased protein production and triggered premature ribosome termination without significantly reducing mRNA levels. Together, our results suggest that amino acids which are not optimally sensed by the mTORC1 and GCN2 pathways still regulate translation through an evolutionarily conserved mechanism based on codon-specific ribosome pausing.

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REPLACEMENT OF SOYBEAN MEAL IN CHICKEN BROILER DIETS BY RAPESEED MEAL AND FISH MEAL COMPLEMENTARY SOURCES OF DIETARY PROTEIN

Canadian Journal of Animal Science ◽

10.4141/cjas81-123 ◽

1981 ◽

Vol 61 (4) ◽

pp. 999-1004 ◽

Cited By ~ 10

Author(s):

H. W. HULAN ◽

F. G. PROUDFOOT

Keyword(s):

Amino Acid ◽

Soybean Meal ◽

Dietary Protein ◽

Fish Meal ◽

Amino Acid Content ◽

Rapeseed Meal ◽

Complete Replacement ◽

Amino Acid Levels ◽

Biological Performance ◽

Finisher Diets

Two experiments were conducted to evaluate the nutritional value of Brassica napus 'Tower' rapeseed meal (Tower RSM) and B. campestris 'Candle' RSM or combinations of Tower RSM and fish meal (FM) or Candle RSM and FM as partial or complete replacement for soybean meal (SM) in chicken broiler starter and finisher diets. Amino acid levels were maintained in diets where SM was replaced by RSM by increasing the level of FM. The results of these experiments indicate that RSM can replace up to 80% of the SM in chicken broiler starter and finisher diets on a straight replacement basis without adversely affecting body weight or feed efficiency. Moreover, RSM can replace all of the SM in such diets without adverse effects on biological performance provided energy, protein and amino acid differences are compensated. The calculated amino acid content of the diets indicate that FM is a complementary source of dietary protein in diets containing high levels of RSM.

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Quantitative modelling of amino acid transport and homeostasis in mammalian cells

Nature Communications ◽

10.1038/s41467-021-25563-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Gregory Gauthier-Coles ◽

Jade Vennitti ◽

Zhiduo Zhang ◽

William C. Comb ◽

Shuran Xing ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Transport ◽

Mammalian Cells ◽

Stable Equilibrium ◽

Amino Acid Transporters ◽

Acid Transport ◽

Amino Acid Levels ◽

Amino Acid Concentrations ◽

Remarkable Progress

AbstractHomeostasis is one of the fundamental concepts in physiology. Despite remarkable progress in our molecular understanding of amino acid transport, metabolism and signaling, it remains unclear by what mechanisms cytosolic amino acid concentrations are maintained. We propose that amino acid transporters are the primary determinants of intracellular amino acid levels. We show that a cell’s endowment with amino acid transporters can be deconvoluted experimentally and used this data to computationally simulate amino acid translocation across the plasma membrane. Transport simulation generates cytosolic amino acid concentrations that are close to those observed in vitro. Perturbations of the system are replicated in silico and can be applied to systems where only transcriptomic data are available. This work explains amino acid homeostasis at the systems-level, through a combination of secondary active transporters, functionally acting as loaders, harmonizers and controller transporters to generate a stable equilibrium of all amino acid concentrations.

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Comparisons of amino acid and protein levels in oil-extracted seeds of Brassica and Sinapis species, with observations on environmental effects

Canadian Journal of Animal Science ◽

10.4141/a97-117 ◽

2000 ◽

Vol 80 (1) ◽

pp. 169-174 ◽

Cited By ~ 15

Author(s):

J. M. Bell ◽

G. Rakow ◽

R. K. Downey

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Acid Content ◽

Crude Protein ◽

Amino Acid Content ◽

Protein Levels ◽

Protein Amino Acids ◽

Amino Acid Levels ◽

Lower Magnitude ◽

Dispensable Amino Acids

Seeds from 21 selections of Brassica and Sinapis were analyzed for crude protein (CP; N × 6.25) and amino acid content following oil extraction and grinding. In exp. 1 three cultivars of B. napus, B. rapa and B. juncea were grown in four locations in 4 successive years, with duplicate samples taken from each plot. Brassica juncea contained more CP (P < 0.001) than B. napus or B. rapa (44.6 > 40.1 > 38.8%, respectively). Location affected CP level but not the ranking among cultivars. Year-to-year effects on CP levels (P < 0.001) were of lower magnitude than location effects. Treatments (cultivar, location, year) affected CP and amino acid levels differently. Amino acid levels expressed as percent of CP differed among many cultivars (P < 0.01). Threonine, valine, histidine, lysine and arginine were strongly influenced by location (P < 0.001), as were the dispensable amino acids serine, glutamine and tyrosine. In exp. 2, 10 cultivars and strains grown in one location and in three replicates resulted in greater CP levels in two B. juncea cultivars than in B. napus and B. rapa (42.9 and 43.2 vs. 39.7 and 38.8%), respectively, but lower levels of lysine and threonine in the CP (lysine: 5.4 vs. 6.3; threonine: 3.5 and 3.7 vs. 3.8 and 4.0%). Brassica napus and B. rapa ranked among the lowest in percent CP. In exp. 3, comparisons of eight samples from B. napus, B. rapa and Sinapis alba plots revealed a CP range of 38.1 to 45.0% but differences in amino acid content of the CP were relatively small. Key words: Brassica, Sinapis, protein, amino acids

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