Metabolism: Evolution retraces its steps to advance

  1. Daniel J Kliebenstein  Is a corresponding author
  1. University of California,Davis, United States

Selection can increase the fitness of a species in a stable environment by acting on random mutations. The same process can also create new traits if there is a change in the environment. Metabolism may evolve largely via the creation of new traits that either allow the organism to make use of new energy sources or provide new defense mechanisms in a complex environment (Blount et al. 2012; Prasad et al. 2012). However, we do not fully understand how new metabolic traits evolve or how they are integrated into existing metabolic networks.

Studying the creation of new traits is greatly complicated because evolution usually occurs over relatively long timescales. However, the Lenski long-term evolution experiment was designed to alleviate this problem and has been running at Michigan State University since 1988 (Fox and Lenski, 2015). Now, in eLife, Jeffrey Barrick and colleagues – including Erik Quandt as first author – make use of this resource to describe the molecular evolution of a new metabolic trait in E. coli (Quandt et al. 2015).

The long-term evolution experiment started with twelve identical populations of E. coli. These bacteria were forced to grow on culture medium that contained an excess of citrate, but very little glucose. Thus, for tens of thousands of generations of E. coli, the bacteria have been selected to evolve to use citrate as their main carbon source. This is something that E. coli would not normally do if they had access to oxygen. However, one of the populations did indeed evolve this exact ability (Blount et al. 2008; 2012). Sequencing the genome of this unique population throughout the long-term experiment identified the molecular changes that had generated this new trait. The new trait required two separate mutations within the gene that encodes an enzyme called citrate synthase (Quandt et al. 2015).

Barrick and colleagues – who are based at the University of Texas at Austin and Michigan State – now show that these two mutations have opposing effects (Quandt et al. 2015). The first mutation, called gltA1, abolished feedback inhibition in the enzyme and allowed the bacteria to use citrate, albeit weakly. This initial mutation was then followed by evolutionary shifts in genes that transcriptionally regulate primary metabolism (Leiby and Marx, 2014). Critically, this new transcriptional environment made the initial gltA1 mutation detrimental to fitness which, in turn, led to the rapid selection of variants of the citrate synthase gene that made the enzyme less active. Thus, while two opposing mutations within a single gene were required, they had to occur in a specific order and this order caused the mutations to be positive in both instances.

These new results show that the apparently unwavering march of evolution towards a new trait hides a meandering process underneath. In particular, they show that mutations that were at one time beneficial can consequently become a drag on fitness, and that mutations within existing genes can allow the creation of a new metabolic trait. This is in contrast to the standard view that the creation of new genes, often by gene duplication, is essential to the evolution of new metabolic traits (Chae et al. 2014; Wisecaver et al. 2014).

The use of the long-term evolution experiment has illuminated the complex mechanisms that allow adaptation to a consistent selective pressure in a single direction. However, it is possible that fluctuating and unpredictable stresses in the environment are more important drivers of evolution in nature (Kerwin et al. 2015), so there is a need for long-term experiments that include such stresses. The work of Quandt et al. represents, I hope, only the beginning of our ability to empirically study evolution in action.


Article and author information

Author details

  1. Daniel J Kliebenstein, Reviewing editor

    Department of Plant Sciences, University of California,Davis, Davis, United States
    For correspondence
    Competing interests
    The author declares that no competing interests exist.

Publication history

  1. Version of Record published: December 15, 2015 (version 1)


© 2015, Kliebenstein

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.


  • 1,625
    Page views
  • 159
  • 0

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. Daniel J Kliebenstein
Metabolism: Evolution retraces its steps to advance
eLife 4:e12386.

Further reading

    1. Evolutionary Biology
    2. Genetics and Genomics
    Henrike Indrischek et al.
    Research Article

    Despite decades of research, knowledge about the genes that are important for development and function of the mammalian eye and are involved in human eye disorders remains incomplete. During mammalian evolution, mammals that naturally exhibit poor vision or regressive eye phenotypes have independently lost many eye-related genes. This provides an opportunity to predict novel eye-related genes based on specific evolutionary gene loss signatures. Building on these observations, we performed a genome-wide screen across 49 mammals for functionally uncharacterized genes that are preferentially lost in species exhibiting lower visual acuity values. The screen uncovered several genes, including SERPINE3, a putative serine proteinase inhibitor. A detailed investigation of 381 additional mammals revealed that SERPINE3 is independently lost in 18 lineages that typically do not primarily rely on vision, predicting a vision-related function for this gene. To test this, we show that SERPINE3 has the highest expression in eyes of zebrafish and mouse. In the zebrafish retina, serpine3 is expressed in Müller glia cells, a cell type essential for survival and maintenance of the retina. A CRISPR-mediated knockout of serpine3 in zebrafish resulted in alterations in eye shape and defects in retinal layering. Furthermore, two human polymorphisms that are in linkage with SERPINE3 are associated with eye-related traits. Together, these results suggest that SERPINE3 has a role in vertebrate eyes. More generally, by integrating comparative genomics with experiments in model organisms, we show that screens for specific phenotype-associated gene signatures can predict functions of uncharacterized genes.

    1. Evolutionary Biology
    2. Microbiology and Infectious Disease
    Isabel Nocedal, Michael T Laub
    Research Article Updated

    Gene duplication is crucial to generating novel signaling pathways during evolution. However, it remains unclear how the redundant proteins produced by gene duplication ultimately acquire new interaction specificities to establish insulated paralogous signaling pathways. Here, we used ancestral sequence reconstruction to resurrect and characterize a bacterial two-component signaling system that duplicated in α-proteobacteria. We determined the interaction specificities of the signaling proteins that existed before and immediately after this duplication event and then identified key mutations responsible for establishing specificity in the two systems. Just three mutations, in only two of the four interacting proteins, were sufficient to establish specificity of the extant systems. Some of these mutations weakened interactions between paralogous systems to limit crosstalk. However, others strengthened interactions within a system, indicating that the ancestral interaction, although functional, had the potential to be strengthened. Our work suggests that protein-protein interactions with such latent potential may be highly amenable to duplication and divergence.