title: Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli.
abstract: The Neutral Theory of Molecular Evolution is considered the most powerful theory to understand the evolutionary behavior of proteins. One of the main predictions of this theory is that essential proteins should evolve slower than dispensable ones owing to increased selective constraints. Comparison of genomes of different species, however, has revealed only small differences between the rates of evolution of essential and nonessential proteins. In some analyses, these differences vanish once confounding factors are controlled for, whereas in other cases essentiality seems to have an independent, albeit small, effect. It has been argued that comparing relatively distant genomes may entail a number of limitations. For instance, many of the genes that are dispensable in controlled lab conditions may be essential in some of the conditions faced in nature. Moreover, essentiality can change during evolution, and rates of protein evolution are simultaneously shaped by a variety of factors, whose individual effects are difficult to isolate. Here, we conducted two parallel mutation accumulation experiments in Escherichia coli, during 5,500-5,750 generations, and compared the genomes at different points of the experiments. Our approach (a short-term experiment, under highly controlled conditions) enabled us to overcome many of the limitations of previous studies. We observed that essential proteins evolved substantially slower than nonessential ones during our experiments. Strikingly, rates of protein evolution were only moderately affected by expression level and protein length.
authors: Department of Biology, University of Nevada, Reno, USA dap@unr.edu mfares@ibmcp.upv.es.
authors: David
authors: D
authors: Alvarez-Ponce
authors: Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin, Ireland.
authors: Beatriz
authors: B
authors: Sabater-Muñoz
authors: Department of Genetics, University of Valencia, Valencia, Spain Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Valencia, Spain.
authors: Christina
authors: C
authors: Toft
authors: Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain Current Address: Secretaría de Educación Superior, Ciencia, Tecnología e Innovación, Proyecto Prometeo; Departamento de Ciencias Biológicas, Universidad Tócnica Particular de Loja, Loja, Ecuador.
authors: Mario X
authors: MX
authors: Ruiz-González
authors: Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin, Ireland dap@unr.edu mfares@ibmcp.upv.es.
authors: Mario A
authors: MA
authors: Fares
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D020043:Genes, Essential; D016680:Genome, Bacterial; D008957:Models, Genetic; D009154:Mutation
chemical_list: D029968:Escherichia coli Proteins
keywords: dN/dS; essentiality; experimental evolution; neutral theory; rates of evolution