Characterisation of an Escherichia coli line that completely lacks ribonucleotide reduction yields insights into the evolution of parasitism and endosymbiosis

Abstract

All life requires ribonucleotide reduction for de novo synthesis of deoxyribonucleotides. A handful of obligate intracellular species are known to lack ribonucleotide reduction and are instead dependent on their host for deoxyribonucleotide synthesis. As ribonucleotide reduction has on occasion been lost in obligate intracellular parasites and endosymbionts, we reasoned that it should in principle be possible to knock this process out entirely under conditions where deoxyribonucleosides are present in the growth media. We report here the creation of a strain of E. coli where all three ribonucleotide reductase operons have been fully deleted following introduction of a broad spectrum deoxyribonucleoside kinase from Mycoplasma mycoides. Our strain is able to grow in the presence of deoxyribonucleosides and shows slowed but substantial growth. Under limiting deoxyribonucleoside levels, we observe a distinctive filamentous cell morphology, where cells grow but do not appear to divide regularly. Finally, we examined whether our lines are able to adapt to limited supplies of deoxyribonucleosides, as might occur in the evolutionary switch from de novo synthesis to dependence on host production during the evolution of parasitism or endosymbiosis. Over the course of an evolution experiment, we observe a 25-fold reduction in the minimum concentration of exogenous deoxyribonucleosides necessary for growth. Genome analysis of replicate lines reveals that several lines carry mutations in deoB and cdd. deoB codes for phosphopentomutase, a key part of the deoxyriboaldolase pathway, which has been hypothesised as an alternative to ribonucleotide reduction for deoxyribonucleotide synthesis. Rather than synthesis via this pathway complementing the loss of ribonucleotide reduction, our experiments reveal that mutations appear that reduce or eliminate the capacity for this pathway to catabolise deoxyribonucleotides, thus preventing their loss via central metabolism. Mutational inactivation of both deoB and cdd is also observed in a number of obligate intracellular bacteria that have lost ribonucleotide reduction. We conclude that our experiments recapitulate key evolutionary steps in the adaptation to intracellular life without ribonucleotide reduction.

Data availability

All genome data have been deposited to the Single Read Archive (https://www.ncbi.nlm.nih.gov/sra) under accessions SRX17677859-SRX17677886. The following biosamples are associated with this project: SAMN30957267-SAMN30957273. The data have been deposited with links to BioProject accession number PRJNA882995 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/).

The following data sets were generated

Article and author information

Author details

  1. Samantha D Arras

    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Competing interests
    The authors declare that no competing interests exist.
  2. Nellie Sibaeva

    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Competing interests
    The authors declare that no competing interests exist.
  3. Ryan J Catchpole

    School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6641-647X
  4. Nobuyuki Horinouchi

    Division of Applied Life Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  5. Dayong Si

    Division of Applied Life Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  6. Alannah M Rickerby

    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Competing interests
    The authors declare that no competing interests exist.
  7. Kengo Deguchi

    Division of Applied Life Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  8. Makoto Hibi

    Division of Applied Life Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  9. Koichi Tanaka

    Division of Applied Life Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  10. Michiki Takeuchi

    Division of Applied Life Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  11. Jun Ogawa

    Division of Applied Life Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2741-621X
  12. Anthony M Poole

    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    For correspondence
    a.poole@auckland.ac.nz
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9940-2824

Funding

Royal Society Te Apārangi (17-UOA-257)

  • Jun Ogawa
  • Anthony M Poole

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Amie K Boal, Pennsylvania State University, United States

Version history

  1. Preprint posted: September 30, 2022 (view preprint)
  2. Received: September 30, 2022
  3. Accepted: April 5, 2023
  4. Accepted Manuscript published: April 6, 2023 (version 1)
  5. Version of Record published: April 21, 2023 (version 2)

Copyright

© 2023, Arras et al.

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

Metrics

  • 741
    Page views
  • 112
    Downloads
  • 0
    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. Samantha D Arras
  2. Nellie Sibaeva
  3. Ryan J Catchpole
  4. Nobuyuki Horinouchi
  5. Dayong Si
  6. Alannah M Rickerby
  7. Kengo Deguchi
  8. Makoto Hibi
  9. Koichi Tanaka
  10. Michiki Takeuchi
  11. Jun Ogawa
  12. Anthony M Poole
(2023)
Characterisation of an Escherichia coli line that completely lacks ribonucleotide reduction yields insights into the evolution of parasitism and endosymbiosis
eLife 12:e83845.
https://doi.org/10.7554/eLife.83845

Further reading

    1. Evolutionary Biology
    2. Neuroscience
    Katja Heuer, Nicolas Traut ... Roberto Toro
    Research Article

    The process of brain folding is thought to play an important role in the development and organisation of the cerebrum and the cerebellum. The study of cerebellar folding is challenging due to the small size and abundance of its folia. In consequence, little is known about its anatomical diversity and evolution. We constituted an open collection of histological data from 56 mammalian species and manually segmented the cerebrum and the cerebellum. We developed methods to measure the geometry of cerebellar folia and to estimate the thickness of the molecular layer. We used phylogenetic comparative methods to study the diversity and evolution of cerebellar folding and its relationship with the anatomy of the cerebrum. Our results show that the evolution of cerebellar and cerebral anatomy follows a stabilising selection process. We observed 2 groups of phenotypes changing concertedly through evolution: a group of 'diverse' phenotypes - varying over several orders of magnitude together with body size, and a group of 'stable' phenotypes varying over less than 1 order of magnitude across species. Our analyses confirmed the strong correlation between cerebral and cerebellar volumes across species, and showed in addition that large cerebella are disproportionately more folded than smaller ones. Compared with the extreme variations in cerebellar surface area, folial anatomy and molecular layer thickness varied only slightly, showing a much smaller increase in the larger cerebella. We discuss how these findings could provide new insights into the diversity and evolution of cerebellar folding, the mechanisms of cerebellar and cerebral folding, and their potential influence on the organisation of the brain across species.

    1. Developmental Biology
    2. Evolutionary Biology
    Salvatore D'Aniello, Stephanie Bertrand, Hector Escriva
    Feature Article

    Cephalochordates and tunicates represent the only two groups of invertebrate chordates, and extant cephalochordates – commonly known as amphioxus or lancelets – are considered the best proxy for the chordate ancestor, from which they split around 520 million years ago. Amphioxus has been an important organism in the fields of zoology and embryology since the 18th century, and the morphological and genomic simplicity of cephalochordates (compared to vertebrates) makes amphioxus an attractive model for studying chordate biology at the cellular and molecular levels. Here we describe the life cycle of amphioxus, and discuss the natural histories and habitats of the different species of amphioxus. We also describe their use as laboratory animal models, and discuss the techniques that have been developed to study different aspects of amphioxus.