Abstract
Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato (Solanum lycopersicum) fruit. Quantitative data were collected for transcripts and proteins during fruit development. Clustering analysis showed smaller changes in protein abundance compared to mRNA abundance. Furthermore, protein and transcript abundance were poorly correlated, and the coefficient of correlation decreased during fruit development and ripening, with transcript levels decreasing more than protein levels. A mathematical model with one ordinary differential equation was used to estimate translation (kt) and degradation (kd) rate constants for almost 2,400 detected transcript-protein pairs and was satisfactorily fitted for >1,000 pairs. The model predicted median values of ∼2 min for the translation of a protein, and a protein lifetime of ∼11 d. The constants were validated and inspected for biological relevance. Proteins involved in protein synthesis had higher kt and kd values, indicating that the protein machinery is particularly flexible. Our model also predicts that protein concentration is more strongly affected by the rate of translation than that of degradation.
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Claims 9
Claim · model-written summary
Protein abundance changed less than mRNA abundance during tomato fruit development.
- Taxon
- tomato
Solanum lycopersicume0e1 - Outcome
- protein abundancee0
- Direction
- smaller changese0
- Comparator
- mRNA abundancee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Clustering analysis showed smaller changes in protein abundance compared to mRNA abundance.”
e1“developing tomato (Solanum lycopersicum) fruit”
Claim · model-written summary
Protein and transcript abundance were poorly correlated in tomato fruit.
- Taxon
- tomatoSolanum lycopersicume0e1
- Outcome
- protein and transcript abundancee0
- Direction
- poorly correlatede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“protein and transcript abundance were poorly correlated”
e1“developing tomato (Solanum lycopersicum) fruit”
Claim · model-written summary
The correlation between protein and transcript abundance declined during tomato fruit development and ripening.
- Taxon
- tomatoSolanum lycopersicume0e1
- Organ / stage
- fruit development and ripeninge0
- Outcome
- coefficient of correlatione0
- Direction
- decreasede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the coefficient of correlation decreased during fruit development and ripening, with transcript levels decreasing more than protein levels.”
e1“developing tomato (Solanum lycopersicum) fruit”
Claim · model-written summary
Transcript levels declined more than protein levels during tomato fruit development and ripening.
- Taxon
- tomatoSolanum lycopersicume0e1
- Outcome
- transcript levelse0
- Direction
- decreasinge0
- Comparator
- protein levelse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“transcript levels decreasing more than protein levels.”
e1“developing tomato (Solanum lycopersicum) fruit”
Claim · model-written summary
A one-equation model fitted over 1,000 tomato transcript-protein pairs satisfactorily.
Not reportedTaxon
Verbatim
e0“A mathematical model with one ordinary differential equation was used to estimate translation (kt) and degradation (kd) rate constants for almost 2,400 detected transcript-protein pairs and was satisfactorily fitted for >1,000 pairs.”
Claim · model-written summary
The model predicted a median translation time of about two minutes per protein.
Not reportedTaxon
Verbatim
e0“The model predicted median values of ∼2 min for the translation of a protein, and a protein lifetime of ∼11 d.”
Claim · model-written summary
The model predicted a median protein lifetime of about 11 days.
Not reportedTaxon
Verbatim
e0“The model predicted median values of ∼2 min for the translation of a protein, and a protein lifetime of ∼11 d.”
Claim · model-written summary
Proteins involved in protein synthesis had higher translation and degradation rate constants.
- Taxon
- tomatoSolanum lycopersicume0e1
- Outcome
- kt and kd valuese0
- Direction
- highere0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Proteins involved in protein synthesis had higher kt and kd values”
e1“developing tomato (Solanum lycopersicum) fruit”
Claim · model-written summary
The model predicted protein concentration to depend more strongly on translation than degradation rate.
- Outcome
- protein concentratione0
- Direction
- more strongly affectede0
- Comparator
- rate of translation than that of degradatione0
Not reportedTaxon
Verbatim
e0“protein concentration is more strongly affected by the rate of translation than that of degradation.”