scholarly journals Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli

2017 ◽  
Author(s):  
Eric Girard ◽  
Pouria Dasmeh ◽  
Adrian W.R. Serohijos
Keyword(s):  
Protein Evolution ◽  
Protein Unfolding ◽  
Long Term Evolution ◽  
Fitness Cost ◽  
Sequence Evolution ◽  
E Coli ◽  
Term Evolution ◽  
Highly Expressed Genes

ABSTRACTEpistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes in E. coli using several hundreds of orthologs for each gene within the class Gammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation. Our results highlight the coupling between selection and epistasis in the long-term evolution of a proteome.

scholarly journals Universal constraints on protein evolution in the long-term evolution experiment with Escherichia coli

2020 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Protein Evolution ◽  
Long Term Evolution ◽  
Protein Abundance ◽  
Interacting Proteins ◽  
Protein Thermostability ◽  
Protein Protein Interaction ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Positive Correlations

AbstractAlthough it is well known that highly expressed and highly interacting proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that highly abundant and highly interacting proteins evolve slowly in the hypermutator populations of Lenski’s long-term evolution experiment with E. coli (LTEE). Specifically, the density of observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, strongly anti-correlates with mRNA abundance, protein abundance, and degree of protein-protein interaction. Weaker positive correlations between protein thermostability and mutation density are observed in the hypermutator populations, counterbalanced by negative correlations between protein thermostability and mRNA and protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why highly expressed and highly interacting proteins evolve slowly.

scholarly journals Evolution and coexistence in response to a key innovation in a long-term evolution experiment withEscherichia coli

2015 ◽  
Author(s):  
Caroline B. Turner ◽  
Zachary D. Blount ◽  
Daniel H. Mitchell ◽  
Richard E. Lenski
Keyword(s):  
Environmental Changes ◽  
Carbon Sources ◽  
Dicarboxylic Acids ◽  
Long Term Evolution ◽  
E Coli ◽  
Term Evolution ◽  
Key Innovation ◽  
Evolution Experiment ◽  
Evolutionary Trajectories

Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following evolution of a novel function in the long-term evolution experiment (LTEE) withEscherichia coli. A characteristic feature ofE. coliis its inability to consume citrate aerobically. However, that ability evolved in one of the LTEE populations. In this population, citrate-utilizing bacteria (Cit+) coexisted stably with another clade of bacteria that lacked the capacity to utilize citrate (Cit−). This coexistence was shaped by the evolution of a cross-feeding relationship in which Cit+cells released the dicarboxylic acids succinate, fumarate, and malate into the medium, and Cit−cells evolved improved growth on these carbon sources, as did the Cit+cells. Thus, the evolution of citrate consumption led to a flask-based ecosystem that went from a single limiting resource, glucose, to one with five resources either shared or partitioned between two coexisting clades. Our findings show how evolutionary novelties can change environmental conditions, thereby facilitating diversity and altering both the structure of an ecosystem and the evolutionary trajectories of coexisting organisms.

Avoidance of protein unfolding constrains protein stability in long-term evolution

2021 ◽  
Author(s):  
Rostam M. Razban ◽  
Pouria Dasmeh ◽  
Adrian W.R. Serohijos ◽  
Eugene I. Shakhnovich
Keyword(s):  
Protein Stability ◽  
Protein Unfolding ◽  
Long Term Evolution ◽  
Term Evolution

scholarly journals Universal constraints on protein evolution in the long-term evolution experiment with Escherichia coli

2021 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Escherichia Coli ◽  
Protein Evolution ◽  
Long Term Evolution ◽  
Protein Abundance ◽  
Nonsynonymous Mutation ◽  
Protein Protein Interaction ◽  
Term Evolution ◽  
Mutation Density ◽  
Evolution Experiment

Abstract Although it is well known that abundant proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that abundant proteins evolve slowly in the hypermutator populations of Lenski’s long-term evolution experiment with Escherichia coli (LTEE). Specifically, the density of all observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, significantly anti-correlates with mRNA abundance, protein abundance, and degree of protein-protein interaction. The same pattern holds for nonsynonymous mutation density. However, synonymous mutation density, measured across the LTEE hypermutator populations, positively correlates with protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why abundant proteins evolve slowly.

scholarly journals Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

2016 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Philip J. Hatcher ◽  
Anna G. Green ◽  
Barry L. Williams ◽  
Debora S. Marks ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Positive Selection ◽  
Long Term Evolution ◽  
Fine Tuning ◽  
Adaptive Mutations ◽  
E Coli ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Core Genes

AbstractBacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that are fast evolving in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. We identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to fine-tune protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to the long sweep of its evolution in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.Competing Interests StatementWe, the authors, declare that we have no conflicts of interest.

Link-Level Simulator for Wireless local Area Network

2018 ◽  
Vol 6 (7) ◽  
pp. 314
Author(s):  
Chaithra. H. U ◽  
Vani H.R
Keyword(s):  
Wireless Local Area Network ◽  
Local Area Network ◽  
Local Area Networks ◽  
Local Area ◽  
Long Term Evolution ◽  
Wireless Local Area Networks ◽  
Area Network ◽  
Network Simulator ◽  
Term Evolution

Now a days in Wireless Local Area Networks (WLANs) used in different fields because its well-suited simulator and higher flexibility. The concept of WLAN  with  advanced 5th Generation technologies, related to a Internet-of-Thing (IOT). In this project, representing the Network Simulator (NS-2) used linked-level simulators for Wireless Local Area Networks and still utilized IEEE 802.11g/n/ac with advanced IEEE 802.11ah/af technology. Realization of the whole Wireless Local Area Networking linked-level simulators inspired by the recognized Vienna Long Term Evolution- simulators. As a outcome, this is achieved to link together that simulator to detailed performances of Wireless Local Area Networking with Long Term Evolution, operated in the similar RF bands. From the advanced 5th Generation support cellular networking, such explore is main because different coexistences scenario can arise linking wireless communicating system to the ISM and UHF bands.

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