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Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea

Nature Microbiology volume 2, Article number: 17045 (2017) Cite this article

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Abstract

Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life1–5. The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability6–8, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.

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Figure 1: Prevalence of DGRs identified in groundwater metagenomes.
Figure 2: Phylogeny of DGRs and radiation of novel lineages.
Figure 3: Putative functional classes of DGR variable proteins.

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Acknowledgements

This research was funded by National Science Foundation grant no. OCE-1046144 to D.L.V., National Institutes of Health grant no. R01 AI096838 to J.F.M. and P.G., and by the US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research under award no. DE-AC02-05CH11231 (Sustainable Systems Scientific Focus Area; Lawrence Berkley National Laboratory operated by the University of California) and award no. DE-SC0004918 (Systems Biology Knowledge Base Focus Area). Sequencing was performed at the US DOE Joint Genome Institute, a DOE Office of Science User Facility, supported under contract no. DE-AC02-05CH11231. Metatranscriptomes were sequenced at the DOE-supported Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory. B.G.P. was supported by a postdoctoral fellowship from the Center for Dark Energy Biosphere Investigations (C-DEBI). D.B. was supported by a long-term EMBO fellowship. The authors thank K. Anantharaman for assistance with genome binning, A. Singh and C.T. Brown, who aided in examining CPR and DPANN genomes and C. Magnabosco for offering insights on phylogenetic reconstruction. This is C-DEBI contribution no. 361.

Author information

Authors and Affiliations

  1. Marine Science Institute, University of California, Santa Barbara, 93106, California, USA

    Blair G. Paul & David L. Valentine

  2. Department of Earth and Planetary Science, University of California, Berkeley, 94720, California, USA

    David Burstein, Cindy J. Castelle, Brian C. Thomas & Jillian F. Banfield

  3. Department of Chemistry and Biochemistry, UC San Diego, La Jolla, 92093, California, USA

    Sumit Handa & Partho Ghosh

  4. Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, 90095, California, USA

    Diego Arambula, Elizabeth Czornyj & Jeff F. Miller

  5. Molecular Biology Institute, University of California, Los Angeles, 90095, California, USA

    Jeff F. Miller

  6. California NanoSystems Institute, University of California, Los Angeles, 90095, California, USA

    Jeff F. Miller

  7. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    Jillian F. Banfield

  8. Department of Environmental Science, Policy, and Management, University of California, Berkeley, 94720, California, USA

    Jillian F. Banfield

  9. Department of Earth Science, UC Santa Barbara, Santa Barbara, 93106, California, USA

    David L. Valentine

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Contributions

B.G.P. and D.L.V. developed the project. B.G.P., D.B., C.J.C., B.C.T. and J.F.B. performed reassembly, read mapping and annotation of the metagenomic and metatranscriptomics data sets. B.G.P., D.B., C.J.C., E.C., D.A., S.H., P.G., J.F.M., J.F.B. and D.L.V. conducted bioinformatic analyses on DGR sequences. B.G.P., D.B., C.J.C., J.F.B. and D.L.V. wrote the manuscript.

Corresponding author

Correspondence to David L. Valentine.

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Competing interests

J.F.M. is a cofounder, equity holder and chair of the scientific advisory board of AvidBiotics Inc., a biotherapeutics company in San Francisco. No other authors declare competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–9 (PDF 1731 kb)

Supplementary Tables 1–10

Supplementary Table 1: DGRs that appear to be active based on readmapping and a stemloop-like sequence. Ns substitutions linked to TR adenines were inferred from VR-read-mapping and putative DGR stemloops were predicted using the Mfold DNA folding server (see Methods). The number of stemloops is shown incrementally for the same DGR. (3'-) distance from VR to the beginning of the stemloop is given in nucleotides. (XLSX 211 kb)

Supplementary Table 2: Metatranscriptomic readmapping analysis for DGRs that recruited at least ten perfect-matching transcripts. Relative proportions are given for transcripts mapping to DGRs versus the whole contig, and separately for transcripts mapping to TR versus the sum for all other DGR features. 

Supplementary Table 3: Annotation details for DUF1566 (PF07603) containing DGR variable proteins. Variable protein length is given in amino acids. Transmembrane (TM) predictions are shown as “yes”, “no”, or “signal peptide”. The best hit from HMMER is listed with its corresponding e-value. Phyre2 values are given as per cent confidence (conf) and per cent coverage of the variable protein (covg). 

Supplementary Table 4: Taxonomic affiliations of AAA_5 ATPase (PF07728) domain-containing DGR variable proteins. Rows are coloured by domain. Best hits were retrieved using pHMMER searches against the Uniprot database. 

Supplementary Table 5: DGR-containing scaffolds and feature coordinates, including RT, VP (up to three), VR (up to three), and TR. Genome bin affiliations are given for each scaffold. 

Supplementary Table 6: DGR-containing scaffolds and feature coordinates for scaffolds with more than one DGR cassette (up to three distinct DGRs for a single scaffold). 

Supplementary Table 7: DGR-containing scaffolds and feature annotations for DGRs with split/interrupted RT open reading frames. 

Supplementary Table 8: Variable proteins with homology to known pfams or database UniProtKB representatives. NA, or not applicable, indicates that no significant hit was returned from the database. 

Supplementary Table 9: Index of reverse transcriptase (RT) tree labels. Representatives listed under Database as “Genbank”, have tree labels that are NCBI accession numbers. 

Supplementary Table 10: DGR-containing scaffolds and corresponding Genbank accession codes. 

Supplementary Data 1

All DGR-containing sequences that are described in this study, which were derived from draft genomes. (TXT 44046 kb)

Supplementary Data 2

Reverse transcriptase protein sequences for all DGRs from draft genomes. (TXT 259 kb)

Supplementary Data 3

All DGR targeted variable protein sequences. (TXT 255 kb)

Supplementary Data 4

Reverse transcriptase tree that corresponds to Fig. 2. (TXT 20 kb)

Supplementary Data 5

The reverse transcriptase multiple sequence alignment used to construct the phylogenetic tree in Fig. 2. (TXT 157 kb)

Supplementary Data 6

DGR-containing sequences as assembled metagenomic fragments, which are not contained in a draft genome. (TXT 36182 kb)

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Paul, B., Burstein, D., Castelle, C. et al. Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nat Microbiol 2, 17045 (2017). https://doi.org/10.1038/nmicrobiol.2017.45

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