What is it about?

Biology requires the seamless working together of genes and proteins, where genes encode information in their sequence, and proteins made from this information provide chemical activities that enable the fundamental processes of life to happen. Due to a property of the genetic code known as degeneracy, the same protein can be encoded in many different gene sequences. Such different sequences are not completely equivalent though, as they typically have different efficiencies for information storage. How sequences evolve to be most efficient so that they can produce the right kind of protein in the right amount is a hotly researched question. An emerging view is that sequences are shaped by many different forces, including for example requirements to avoid internal base pairing interactions, to enable strong interactions with the decoding machinery, to contain certain sequence motifs that enable binding to trans-acting factors, and many others. This study takes inspiration from an approach developed in the 1860s by Austrian Physicist Ludwig Boltzman, who was interested in the speed of atoms in gases, which is also shaped by a large number of forces too complicated to understand individually. However, Boltzman realised that statistical approaches can be used to characterise the overall effect of these forces even without understanding each force in detail. We succeeded in applying a similar approach to the many forces that shape the evolution of gene sequences. In doing so, we could distinguish two principal types of forces that either act on all genes equally, or that act only on specific subsets of genes. We showed that the balance between these two types of forces is unexpectedly varied in fungi and bacteria, two groups of microbes that are of strong industrial and medical interest.

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Why is it important?

Existing studies in this area often focus on individual forces and try to evaluate their importance for shaping sequences in isolation. Our study is one of the first to disregard the individual nature of evolutionary forces, and instead focuses on the overall outcome of these forces. It thereby extends our understanding of evolution and develops a novel approach for understanding the forces that shape our genes.

Perspectives

This was a very enjoyable collaboration between our group in Biosciences and the School of Computing, both at Kent. As with many interdisciplinary collaborations, we spent most of our time explaining the problem to each other from our specific points of view - but I think in the end we managed to bring our fields together in a way that enabled some real advance.

Dr Tobias von der Haar
University of Kent

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This page is a summary of: Hidden patterns of codon usage bias across kingdoms, Journal of The Royal Society Interface, February 2020, Royal Society Publishing, DOI: 10.1098/rsif.2019.0819.
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