Amino acid metabolism conflicts with protein diversity
The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporati...
Guardado en:
| Autores principales: | , , , , , , |
|---|---|
| Formato: | JOUR |
| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_07374038_v31_n11_p2905_Krick |
| Aporte de: |
| id |
todo:paper_07374038_v31_n11_p2905_Krick |
|---|---|
| record_format |
dspace |
| spelling |
todo:paper_07374038_v31_n11_p2905_Krick2023-10-03T15:37:59Z Amino acid metabolism conflicts with protein diversity Krick, T. Verstraete, N. Alonso, L.G. Shub, D.A. Ferreiro, D.U. Shub, M. Sánchez, I.E. amino acid decay amino acid metabolism information theory maximum entropy proteomics adenosine triphosphate nonessential amino acid proteome amino acid proteome amino acid composition amino acid metabolism amino acid sequence Article biodiversity biosynthesis codon correlation analysis DNA base composition DNA sequence energy cost entropy genetic code metabolic flux analysis nucleophilicity protein synthesis proteomics theoretical model biological model chemistry genetic variability genetics genome metabolism molecular genetics regression analysis Adenosine Triphosphate Amino Acid Sequence Amino Acids Entropy Genome Genomic Structural Variation Least-Squares Analysis Models, Biological Molecular Sequence Data Protein Biosynthesis Proteome The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data are remarkably well explained when the cost function accounts for amino acid chemical decay. More than 100 organisms reach comparable solutions to the trade-off by different combinations of proteome cost and sequence diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse. © 2014 The Author. Fil:Krick, T. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Ferreiro, D.U. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Shub, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_07374038_v31_n11_p2905_Krick |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
amino acid decay amino acid metabolism information theory maximum entropy proteomics adenosine triphosphate nonessential amino acid proteome amino acid proteome amino acid composition amino acid metabolism amino acid sequence Article biodiversity biosynthesis codon correlation analysis DNA base composition DNA sequence energy cost entropy genetic code metabolic flux analysis nucleophilicity protein synthesis proteomics theoretical model biological model chemistry genetic variability genetics genome metabolism molecular genetics regression analysis Adenosine Triphosphate Amino Acid Sequence Amino Acids Entropy Genome Genomic Structural Variation Least-Squares Analysis Models, Biological Molecular Sequence Data Protein Biosynthesis Proteome |
| spellingShingle |
amino acid decay amino acid metabolism information theory maximum entropy proteomics adenosine triphosphate nonessential amino acid proteome amino acid proteome amino acid composition amino acid metabolism amino acid sequence Article biodiversity biosynthesis codon correlation analysis DNA base composition DNA sequence energy cost entropy genetic code metabolic flux analysis nucleophilicity protein synthesis proteomics theoretical model biological model chemistry genetic variability genetics genome metabolism molecular genetics regression analysis Adenosine Triphosphate Amino Acid Sequence Amino Acids Entropy Genome Genomic Structural Variation Least-Squares Analysis Models, Biological Molecular Sequence Data Protein Biosynthesis Proteome Krick, T. Verstraete, N. Alonso, L.G. Shub, D.A. Ferreiro, D.U. Shub, M. Sánchez, I.E. Amino acid metabolism conflicts with protein diversity |
| topic_facet |
amino acid decay amino acid metabolism information theory maximum entropy proteomics adenosine triphosphate nonessential amino acid proteome amino acid proteome amino acid composition amino acid metabolism amino acid sequence Article biodiversity biosynthesis codon correlation analysis DNA base composition DNA sequence energy cost entropy genetic code metabolic flux analysis nucleophilicity protein synthesis proteomics theoretical model biological model chemistry genetic variability genetics genome metabolism molecular genetics regression analysis Adenosine Triphosphate Amino Acid Sequence Amino Acids Entropy Genome Genomic Structural Variation Least-Squares Analysis Models, Biological Molecular Sequence Data Protein Biosynthesis Proteome |
| description |
The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data are remarkably well explained when the cost function accounts for amino acid chemical decay. More than 100 organisms reach comparable solutions to the trade-off by different combinations of proteome cost and sequence diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse. © 2014 The Author. |
| format |
JOUR |
| author |
Krick, T. Verstraete, N. Alonso, L.G. Shub, D.A. Ferreiro, D.U. Shub, M. Sánchez, I.E. |
| author_facet |
Krick, T. Verstraete, N. Alonso, L.G. Shub, D.A. Ferreiro, D.U. Shub, M. Sánchez, I.E. |
| author_sort |
Krick, T. |
| title |
Amino acid metabolism conflicts with protein diversity |
| title_short |
Amino acid metabolism conflicts with protein diversity |
| title_full |
Amino acid metabolism conflicts with protein diversity |
| title_fullStr |
Amino acid metabolism conflicts with protein diversity |
| title_full_unstemmed |
Amino acid metabolism conflicts with protein diversity |
| title_sort |
amino acid metabolism conflicts with protein diversity |
| url |
http://hdl.handle.net/20.500.12110/paper_07374038_v31_n11_p2905_Krick |
| work_keys_str_mv |
AT krickt aminoacidmetabolismconflictswithproteindiversity AT verstraeten aminoacidmetabolismconflictswithproteindiversity AT alonsolg aminoacidmetabolismconflictswithproteindiversity AT shubda aminoacidmetabolismconflictswithproteindiversity AT ferreirodu aminoacidmetabolismconflictswithproteindiversity AT shubm aminoacidmetabolismconflictswithproteindiversity AT sanchezie aminoacidmetabolismconflictswithproteindiversity |
| _version_ |
1807322707284459520 |