Understanding the Retention of Genes Following Duplication

Lead Research Organisation: University of Manchester
Department Name: Life Sciences

Abstract

The genome is in a state of constant flux, with genes being added and lost continually over evolutionary time. Recent genome sequencing projects of populations suggest that the numbers of copies of many genes vary between individuals. When we study organisms such as yeast, we also see large differences in the numbers of copies of genes within a species. This suggests that duplication of genes is the major source of new genetic material, innovation of biological function, and the complexity of organisms. Moreover, duplication appears to be a key mechanism by which organisms can adapt to their environments. Gain and loss of genes are the two ways in which the genetic content can differ within one species and between species. By looking at the genomes of existing species we can attempt to reconstruct the evolutionary history. However, these studies can miss some of the immediate events, such as a gene being duplicated and then lost. In this project we will make artificial copies of genes in yeast, and determine how this affects how they grow under different conditions. We predict that many gene duplications will be advantageous, whereas others will be deleterious, but this may differ according to the conditions under which the yeast are grown. We will also grow the yeast strains that contain the duplicates for long periods of time in the lab, and determine whether they have lost the genes we previously duplicated. We will also study closely-related species to see whether there is functional innovation in duplicated genes. We will be able to study the immediate functional effects of gene duplication, and also the immediate evolutionary events. We will therefore be able to study the 'cutting edge' of evolutionary change. This work will provide a new understanding of how an organisms set of genes can adapt to new environments, and how complex biological systems evolve.

Technical Summary

We propose a multidisciplinary study to investigate the phenotypic consequences of gene duplication, and the subsequent evolution of duplicate genes. For this research we will use the yeast Saccharomyces cerevisiae. The key aspect of this proposal is the combination of hypothesis generation using bioinformatic analysis of biological systems in yeast, coupled with experimental testing of these hypotheses. We will computationally model various systems, and predict the likely effects of gene duplication on protein interaction networks, metabolic networks, protein complexes and a range of other systems. Based on these predictions we will make 'artificial duplicates' by knocking-in extra copies of genes. We will measure the fitness of these strains carrying extra copies of genes, thereby determining the accuracy of our predictions and adding to our knowledge of the various systems involved. We will also determine the relationship between fitness of the duplicate-bearing strains and the probability that the new duplicates will be lost from the genome. In addition, this work will be supplemented by the computational analysis of changes in protein-coding regions that have recently been duplicated. Such changes can be an indication of functional innovation. Finally, we will attempt to alter the probability of gene loss by changing the complement of genes knocked in, by adding genes to a cassette that will provide positive balancing fitness, and by altering the growth conditions to promote gene retention. In this way we will, for the first time, be able to study the immediate functional effects of gene duplication, and evolutionary dynamics of duplicated genes.

Planned Impact

The impact of this research will be felt by: 1. Biotechnology companies, and in particular, developing synthetic biology companies. As outlined in the 'academic beneficiaries' section, this project has clear applications to synthetic biology. Specifically, knowledge of the rates of gene loss, and interventions that may be made to prevent gene loss are important precursors to manipulating organisms for technological ends. Synthetic biology is a new approach that has not yet been widely explored by biotechnology companies. However, this situation is likely to change in the near future. Our research will therefore have broad impact to this developing commercial area. 2. The broader public. There is a widespread public interest in evolution, but also a general wariness with regard to engineering of organisms. It is therefore important that we continue with, and expand, our ongoing efforts for public engagement.

Publications

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Ames RM (2015) DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML. in Bioinformatics (Oxford, England)

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Naseeb S (2017) Rapid functional and evolutionary changes follow gene duplication in yeast. in Proceedings. Biological sciences

 
Description Gene duplication can significantly speed up evolution by providing new redundant genetic material that has no constraints and can freely evolve new functions. However, since genetic redundancy is not a selective trait per se, the fate of the majority of duplicate gene copies is to be lost from the genome.
Numerous mechanisms have been proposed to explain the retention and loss of duplicate genes. However, the comparative genomics approaches that are used to study gene duplication are inevitably retrospective. In particular, rapid changes are difficult to detect and identification would require high-density sampling of strains at a time relevant to the duplication.

We investigated the most rapid mechanisms that govern the retention or loss of duplicate genes by introducing an artificial duplicate into the genome of Saccharomyces cerevisiae. The study of an artificial duplicate in yeast allowed us to test whether there is an immediate fitness benefit after duplication, and the molecular mechanism by which a benefit may arise. Allowing the duplicate strains to evolve in different environments will allow us to test whether environmental selection plays a role in duplicate retention.

We find that introduction of an extra copy of the gene IFA38 triggers a global transcriptional response and can confer a fitness benefit, although the magnitude of this benefit depends on both the genomic location of the duplicated gene and the environment. We find that changes in expression that arise from duplication are rapidly accommodated, although this also depends on growth conditions and genomic context. Expression changes are additionally observed in a large number of other genes, immediately after duplication and over the course of experimental evolution. We found that approximately 50% of genes show significant differential expression in both tandem and non-tandem duplication strains, suggesting that even single gene duplications may perturb the system as much as environmental changes.

We find that gene loss can happen much more rapidly than previously appreciated, with the deletion of four out of five non-tandem artificial duplicates within 500 generations, with the first loss detected after 25 generations.
Our results reconcile the apparent difference between the immediate and longer-term effects of duplication as we see both effects in our experiment. Since the effects of the duplication are contingent both on genomic position and growth environment, our results also offer an explanation of why evolutionary trends of retention ascribed to dosage and stoichiometric balance are significant, but not universal. The extremely rapid loss of the duplicated gene we observe here happens so quickly that neither the duplication nor the loss can be observed by previous computational studies.

Given the importance of environmental conditions for determining duplicate loss or retention, the set of genes lost or retained in one growth condition may limit an organism in its ability to colonize other environments. Condition-specific gene loss may therefore be an early contributor to speciation.
Exploitation Route A common aspect of many biotechnology and synthetic biology projects is to knock new genes into organisms of interest. We have shown how this may lead to large-scale changes in transcription, which should be monitored for adverse or unexpected effects. We have also shown how relatively small fitness differences lead to gene loss in a small number of generations. Again, should this happen in a biotechnological context, the genetically modified organisms may behave in expected ways. Our work shows how such as situation can be monitored and suggest methods by which these problems can be mitigated.
Sectors Environment

Manufacturing

including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology