A First-Principles Model of Early Evolution

July 11, 2007

In a study publishing in PLoS Computational Biology, Shakhnovich et al present a new model of early biological evolution – the first that directly relates the fitness of a population of evolving model organisms to the properties of their proteins.

Key to understanding biological evolution is an important, but elusive, connection, known as the genotype-phenotype relationship, which translates the survival of entire organisms into microscopic selection for particular advantageous genes, or protein sequences. The study of Shakhnovich et al establishes such connections by postulating that the death rate of an organism is determined by the stability of the least stable of their proteins.

The simulation of the model proceeds via random mutations, gene duplication, organism births via replication, and organism deaths.

The authors find that survival of the population is possible only after a ‘’Big Bang’’ when a very small number of advantageous protein structures is suddenly discovered and exponential growth of the population ensues. The subsequent evolution of the Protein Universe occurs as an expansion of this small set of proteins through a duplication and divergence process that accompanies discovery of new proteins.

The model resolves one of the key mysteries of molecular evolution – the origin of highly uneven distribution of fold family and gene family sizes in the Protein Universe. It quantitatively reproduces these distributions pointing out their origin in biased post “Big Bang’’ evolutionary dynamics of discovery of new proteins. The number of genes in the evolving organisms depends on the mutation rate, demonstrating the intricate relationship between macroscopic properties of organisms – their genome sizes – and microscopic properties – stabilities – of their proteins.

The results of the study suggest a plausible comprehensive scenario of emergence and growth of the Protein Universe in early biological evolution.

Citation: Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI (2007) A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds. PLoS Comput Biol 3(7): e139. doi:10.1371/journal.pcbi.0030139
compbiol.plosjournals.org/perl … journal.pcbi.0030139

Source: PLOS

Explore further: Carnivores know that eating other carnivore carcasses transmits diseases

Related Stories

Want to save the world? Start by eating less beef

December 5, 2017

Cows are like the Humvees of the animal world; they're not very efficient, at least when it comes to producing food for humans. A hectare of land that would be able to grow 1,500 or 2,000 pounds of protein from peanuts or ...

Structure of primary optogenetic tool revealed

November 28, 2017

An international team of researchers has determined the 3-D structure of channelrhodopsin 2, a membrane protein widely used in optogenetics to control nerve cells with light. Optogenetics is a relatively new technique that ...

A new molecule to inhibit lymphoma growth

November 28, 2017

The prestigious scientific journal Clinical Cancer Research has published a study conducted by the research group led by Dr. Francesco Bertoni of the Institute of Oncology Research (IOR, affiliated to USI Università della ...

Recommended for you

The oldest plesiosaur was a strong swimmer

December 14, 2017

Plesiosaurs were especially effective swimmers. These long extinct "paddle saurians" propelled themselves through the oceans by employing "underwater flight"—similar to sea turtles and penguins. Paleontologist from the ...

US faces moment of truth on 'net neutrality'

December 14, 2017

The acrimonious battle over "net neutrality" in America comes to a head Thursday with a US agency set to vote to roll back rules enacted two years earlier aimed at preventing a "two-speed" internet.

Scientists develop new, rapid pipeline for antimicrobials

December 14, 2017

With hospitals more often reaching for antibiotics of last resort to fight infections and recent Ebola and Zika outbreaks crossing borders like never before, the worldwide scientific community has been challenged with developing ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.