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Adiguzel Y. Information-theoretic approach in allometric scaling relations of DNA and proteins. Chem Biol Drug Des 2021; 99:331-343. [PMID: 34855304 DOI: 10.1111/cbdd.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/06/2021] [Accepted: 11/14/2021] [Indexed: 11/28/2022]
Abstract
Allometric scaling relations can be observed in between molecular parameters. Hence, we looked for presence of such relation among sizes (i.e., lengths) of proteins and genes. Protein lengths exist in the literature as the number of amino acids. They can also be derived from the mRNA lengths. Here, we looked for allometric scaling relation by using such data and simultaneously, the data was compared with the sizes of genes and proteins that were obtained from our modified information-theoretic approach. Results implied presence of scaling relation in the calculated results. This was expected due to the implemented modification in the information-theoretic calculation. Relation in the literature-based data was lacking high goodness of fit value. It could be due to physical factors and selective pressures, which ended up in deviations of the literature-sourced values from those in the model. Genome size is correlated with cell size. Intracellular volume, which is related to the DNA size, would require certain number of proteins, the sizes of which can therefore be correlated with the protein sizes. Cell sizes, genome sizes, and average protein and gene sizes, along with the number of proteins, namely the expression levels of the genes, are the physical factors, and the molecular factors influence those physical factors. The selective pressures on those can act through the connection between those physical factors and limit the dynamic ranges. Biological measures could be prone to such forces and are likely to deviate from expected models, regardless of the validity of assumptions, unless those are also implemented in the models. Yet, present discrepancies could be pointing at the need for model improvement, data imperfection, invalid assumptions, etc. Still, current work highlights possible use of information-theoretic approach in allometric scaling relations' studies.
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Affiliation(s)
- Yekbun Adiguzel
- Department of Medical Biology, School of Medicine, Atilim University, Ankara, Turkey
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Ballal A, Laurendon C, Salmon M, Vardakou M, Cheema J, Defernez M, O'Maille PE, Morozov AV. Sparse Epistatic Patterns in the Evolution of Terpene Synthases. Mol Biol Evol 2020; 37:1907-1924. [PMID: 32119077 DOI: 10.1093/molbev/msaa052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We explore sequence determinants of enzyme activity and specificity in a major enzyme family of terpene synthases. Most enzymes in this family catalyze reactions that produce cyclic terpenes-complex hydrocarbons widely used by plants and insects in diverse biological processes such as defense, communication, and symbiosis. To analyze the molecular mechanisms of emergence of terpene cyclization, we have carried out in-depth examination of mutational space around (E)-β-farnesene synthase, an Artemisia annua enzyme which catalyzes production of a linear hydrocarbon chain. Each mutant enzyme in our synthetic libraries was characterized biochemically, and the resulting reaction rate data were used as input to the Michaelis-Menten model of enzyme kinetics, in which free energies were represented as sums of one-amino-acid contributions and two-amino-acid couplings. Our model predicts measured reaction rates with high accuracy and yields free energy landscapes characterized by relatively few coupling terms. As a result, the Michaelis-Menten free energy landscapes have simple, interpretable structure and exhibit little epistasis. We have also developed biophysical fitness models based on the assumption that highly fit enzymes have evolved to maximize the output of correct products, such as cyclic products or a specific product of interest, while minimizing the output of byproducts. This approach results in nonlinear fitness landscapes that are considerably more epistatic. Overall, our experimental and computational framework provides focused characterization of evolutionary emergence of novel enzymatic functions in the context of microevolutionary exploration of sequence space around naturally occurring enzymes.
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Affiliation(s)
- Aditya Ballal
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
| | - Caroline Laurendon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Melissa Salmon
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Vardakou
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Department of Computational and Systems Biology, Norwich Research Park, Norwich, United Kingdom
| | - Marianne Defernez
- Core Science Resources, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich, United Kingdom.,Food & Health Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom.,SRI International, Menlo Park, CA
| | - Alexandre V Morozov
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ
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