Genetic Novelty: How new genes are born

Analysis of yeast, fly and human genomes suggests that sequence divergence is not the main source of orphan genes.
  1. Urminder Singh
  2. Eve Syrkin Wurtele  Is a corresponding author
  1. Department of Genetics, Developmental and Cell Biology, Iowa State University, United States

For half a century, most scientists believed that new protein-coding genes arise as a result of mutations in existing protein-coding genes. It was considered impossible for anything as complex as a functional new protein to arise from scratch. However, every species has certain genes, known as 'orphan genes', which code for proteins that are not homologous to proteins found in any other species. What do these orphan genes do, and how are they formed?

To date the roles of hundreds of orphan genes have been characterized. Although this is just a tiny fraction of the total, it is known that most of them code for proteins that bind to conserved proteins such as transcription factors or receptors. Some of these proteins are toxins, some are involved in reproduction, some integrate into existing metabolic and regulatory networks, and some confer resistance to stress (Carvunis et al., 2012; Li et al., 2009; Xiao et al., 2009; Arendsee et al., 2014; Belcaid et al., 2019). However, none of them are enzymes (Arendsee et al., 2014). Orphan genes arise quickly, so they may provide a disruptive mechanism that allows a given species to survive changes to its environment. Thus, the study of how orphan genes arise (and fall) is central to understanding the forces that drive evolution (Figure 1).

Life cycle of orphan genes.

Every species has orphan genes that have no homologs in other species. This schematic shows the genome of the fruit fly (bottom) and the genome of an ancestor of the fruit fly (top). Each panel also shows (from left to right): genes that are highly conserved and can be traced back to prokaryotic organisms (yellow background); genes that are found in just a few related species (taxonomically restricted genes), orphan genes and potential orphan genes that are not currently expressed and are thus free from selection pressure (proto-orphan genes); and regions of the genome that do not code for proteins (blue background) (Van Oss and Carvunis, 2019; Palmieri et al., 2014). An orphan gene can form through the rapid divergence of the coding sequence (CDS) of an existing gene (1), or arise de novo from regions of the genome that do not code for proteins (including the non-coding parts of genes that evolve to code for proteins; 2). Some orphan genes will be important for survival, and will thus be selected for and gradually optimized (3). This means that the genes in a single organism will have a gradient of ages (Tautz and Domazet-Lošo, 2011). Many proto-orphan genes will undergo pseudogenation (that is, they will not be retained; 4). Coding sequences (shown as thick colored bars) with detectable homology are shown in similar colors. Vakirlis et al. estimate that a minority of orphan genes have arisen by divergence of the coding sequence of existing genes.

One possible mechanism is the 'de novo' appearance of a gene from an intergenic region or a completely new reading frame within an existing gene (Tautz and Domazet-Lošo, 2011). An alternative mechanism is that the coding sequence of the orphan gene arises by rapid divergence from the coding sequence of a preexisting gene: this would mean that an entire set of regulatory and structural elements would be available to the gene as it evolves. Now, in eLife, Nikolaos Vakirlis and Aoife McLysaght (both from Trinity College Dublin) and Anne-Ruxandra Carvunis (University of Pittsburgh) report how they have studied yeast, fly and human genes to compare the contributions of these two mechanisms to the emergence of orphan genes (Vakirlis et al., 2020).

Previous studies have used simulations to estimate the number of orphan genes that appear by divergence; until now, no one had relied on actual genomics data to study this phenomenon. Vakirlis et al. use a new approach to analyze orphan genes that have originated through divergence. They examine regions of the genome that correspond to each other (so-called syntenic regions) in related species to determine whether a gene exists in both regions and, if so, whether the proteins are non-homologous. If the genes have no homology, they may have originated by rapid divergence from the coding sequence of a preexisting gene.

Using this method, Vakirlis et al. infer that at most 45% of S. cerevisiae (yeast) orphan genes, 25% of D. melanogaster (fruit fly) orphan genes, and 18% of human orphan genes arose by rapid divergence, but this is an upper estimate. For example, it is possible that a new coding sequence might have arisen de novo within an existing gene, rather than the existing coding sequence having been modified beyond recognition.

But how can a protein sequence continue to be selected for as it rapidly diverges? Vakirlis et al. suggest that divergence might occur by a process of partial pseudogenation: the existing gene becomes non-functional, and then, with no selection pressure to retain the old protein, it diverges to form an orphan gene.

Many orphan genes may not have been identified yet, because they do not have homologs in other species, and have few recognizable sequence features. This means that up to 80% of orphan genes can be missed when a new genome is annotated (Seetharam et al., 2019). The approach detailed by Vakirlis, Carvunis and McLysaght evaluates specifically those annotated orphan genes for which a similar gene exists in a related species (which is ~50% of them; Arendsee et al., 2019). As high-quality genomes from more species become available, and as more orphan genes are annotated, the approach will provide yet deeper insights into the origin of these genes.

One of the many open questions in this field deals with genes of ‘mixed age’. Some such genes have incorporated ‘chunks’ of orphans into their coding sequences. A gene that has done this is (somewhat arbitrarily) considered to be the age of its most ancient segment, but we know little about the mechanism of this process or its significance. Another question involves the unique strategies and rates of evolution of each gene (Revell et al., 2018). How might the abundance and mechanisms of orphan gene origin vary among species? And how do different environments affect the emergence of orphan genes?

References

Article and author information

Author details

  1. Urminder Singh

    Urminder Singh is in the Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, United States

    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3703-0820
  2. Eve Syrkin Wurtele

    Eve Syrkin Wurtele is in the Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, United States

    For correspondence
    mash@iastate.edu
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1552-9495

Publication history

  1. Version of Record published: February 19, 2020 (version 1)

Copyright

© 2020, Singh and Syrkin Wurtele

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,018
    Page views
  • 363
    Downloads
  • 15
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Urminder Singh
  2. Eve Syrkin Wurtele
(2020)
Genetic Novelty: How new genes are born
eLife 9:e55136.
https://doi.org/10.7554/eLife.55136
  1. Further reading

Further reading

    1. Computational and Systems Biology
    2. Evolutionary Biology
    Roee Ben Nissan, Eliya Milshtein ... Ron Milo
    Research Article

    Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzyme’s activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle’s electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.

    1. Computational and Systems Biology
    James D Brunner, Nicholas Chia
    Research Article

    The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter 'probiotic' treatments intended to alter the composition of the microbiome. Despite so much promise and commercial interest, the factors that contribute to the success or failure of microbiome-targeted treatments remain unclear. We investigate the biotic interactions that lead to successful engraftment of a novel bacterial strain introduced to the microbiome as in probiotic treatments. We use pairwise genome-scale metabolic modeling with a generalized resource allocation constraint to build a network of interactions between taxa that appear in an experimental engraftment study. We create induced sub-graphs using the taxa present in individual samples and assess the likelihood of invader engraftment based on network structure. To do so, we use a generalized Lotka-Volterra model, which we show has strong ability to predict if a particular invader or probiotic will successfully engraft into an individual's microbiome. Furthermore, we show that the mechanistic nature of the model is useful for revealing which microbe-microbe interactions potentially drive engraftment.