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PreprintCited by 7Bacterial Genetics and BiotechnologyGenomics and Phylogenetic StudiesCRISPR and Genetic Engineering

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Comprehensive analysis of insertion sequences within rRNA genes of CPR bacteria and biochemical characterization of a homing endonuclease encoded by these sequences

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Tsurumaki, Megumi, Sato, Asako, Saito, Motofumi, Kanai, Akio·2024·Journal of Bacteriology
DOI 10.1101/2024.02.27.582315PMC PMC11270868

Preprint — published as 10.1128/jb.00074-24

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Abstract

The Candidate Phyla Radiation (CPR) represents an extensive bacterial clade comprising primarily uncultured lineages and is distinguished from other bacteria by a significant prevalence of insertion sequences (ISs) within their rRNA genes. However, our understanding of the taxonomic distribution and characteristics of these ISs remains limited. In this study, we used a comprehensive approach to systematically determine the nature of the rRNA ISs in CPR bacteria. The analysis of hundreds of rRNA gene sequences across 65 CPR phyla revealed that ISs are present in 48% of 16S rRNA genes and 82% of 23S rRNA genes, indicating a broad distribution across the CPR clade, with exceptions in the 16S and 23S rRNA genes of Saccharibacteria and the 16S rRNA genes of Peregrinibacteria. Over half the ISs display a group-I-intron-like structure, whereas specific 16S rRNA gene ISs display features reminiscent of group II introns. The ISs frequently encode proteins with homing endonuclease (HE) domains, centered around the LAGLIDADG motif. The LAGLIDADG HE (LHE) proteins encoded by the rRNA ISs of CPR bacteria predominantly have a single-domain structure, deviating from the usual single- or double-domain configuration observed in typical prokaryotic LHEs. Experimental analysis of one LHE protein, I-ShaI from Ca . Shapirobacteria, confirmed that its endonuclease activity targets the DNA sequence of its insertion site, and chemical cross-linking experiments demonstrated its capacity to form homodimers. These results provide robust evidence supporting the hypothesis that the explosive proliferation of rRNA ISs in CPR bacteria was facilitated by mechanisms involving LHEs. IMPORTANCE: Insertion sequences (ISs) in rRNA genes are relatively limited and infrequent in standard bacteria. With a comprehensive bioinformatic analysis, we show that in CPR bacteria, which are characterized by a high frequency of ISs, these ISs occur in 48% of 16S rRNA genes and 82% of 23S rRNA genes. We also report the systematic and biochemical characterization of the LAGLIDADG homing endonucleases (LHEs) encoded by these ISs in the first such analysis of the CPR bacteria. This study significantly extends our understanding of the phylogenetic positions of rRNA ISs within CPR bacteria and the biochemical features of their LHEs.

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Research works printed but not linked: 69

  1. 10.1016/j.cell.2018.02.016 · DOI · Paper page
  2. 10.1038/nature14486 · DOI · Paper page
  3. 2016, A new view of the tree of life, Nat Microbiol, 1, 16048, 10.1038/nmicrobiol.2016.48 · DOI · Paper page
  4. 10.1038/nature12352 · DOI · Paper page
  5. 10.1126/science.1224041 · DOI
  6. 10.1128/mBio.00708-13 · DOI
  7. 10.1038/ncomms7372 · DOI
  8. 10.1038/ncomms13219 · DOI
  9. 2018, Differential depth distribution of microbial function and putative symbionts through sediment- hosted aquifers in the deep terrestrial subsurface, Nat Microbiol, 3, 328, 10.1038/s41564-017-0098-y · DOI
  10. 10.1038/s41467-018-07418-0 · DOI
  11. 2021, Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities, mSystems, 6, e0120520, 10.1128/mSystems.01205-20 · DOI
  12. 2023, Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment, Front Microbiol, 14, 1114548, 10.3389/fmicb.2023.1114548 · DOI
  13. 10.1186/s40168-023-01494-1 · DOI
  14. 2021, Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing, Nat Commun, 12, 2009, 10.1038/s41467-021-22203-2 · DOI
  15. 10.1073/pnas.0704662104 · DOI
  16. 10.1073/pnas.1419038112 · DOI
  17. 10.1038/s41467-019-12171-z · DOI
  18. Coleman GA , Davin AA , Mahendrarajah TA , Szantho LL , Spang A , Hugenholtz P , Szollosi GJ , Williams TA . 2021. A rooted phylogeny resolves early bacterial evolution. Science 372. · DOI · Paper page
  19. 10.3389/fmicb.2015.00713 · DOI
  20. 10.1038/s41579-018-0076-2 · DOI · Paper page
  21. 10.1261/rna.079103.122 · DOI
  22. 10.1038/s41467-021-22762-4 · DOI
  23. 2019, Targeted isolation and cultivation of uncultivated bacteria by reverse genomics, Nat Biotechnol, 37, 1314, 10.1038/s41587-019-0260-6 · DOI
  24. 2014, "Candidatus Sonnebornia yantaiensis", a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea). Syst Appl Microbiol, 37, 35, 10.1016/j.syapm.2013.08.007 · DOI
  25. 10.1111/1462-2920.15823 · DOI
  26. 2021, Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams, Nat Microbiol, 6, 703, 10.1038/s41564-021-00892-1 · DOI
  27. 10.1016/S0022-2836(02)00895-1 · DOI
  28. 10.1073/pnas.1434268100 · DOI
  29. 10.1128/JB.181.16.4734-4740.1999 · DOI
  30. 10.1128/JB.00812-07 · DOI
  31. 10.1186/1471-2148-7-159 · DOI
  32. 10.1073/pnas.1120192109 · DOI
  33. 10.1128/JB.183.19.5782-5787.2001 · DOI
  34. 10.1128/JB.182.7.1923-1929.2000 · DOI
  35. 2016, The Intervening Sequence of Coxiella burnetii: Characterization and Evolution, Front Cell Infect Microbiol, 6, 83
  36. 10.1128/AEM.69.9.5512-5518.2003 · DOI
  37. 10.1093/nar/29.18.3757 · DOI
  38. 10.1093/nar/gks226 · DOI
  39. 10.1186/1759-8753-5-7 · DOI
  40. 10.1101/gad.1162503 · DOI
  41. 10.1021/bi048970c · DOI
  42. 10.1093/nar/gkp004 · DOI
  43. 10.1073/pnas.1100862108 · DOI
  44. 10.1016/j.gde.2004.09.010 · DOI
  45. 10.1093/NAR/GKAA1047 · DOI
  46. 10.1093/NAR/GKAA913 · DOI · Paper page
  47. 10.1128/JB.182.4.1109-1117.2000 · DOI
  48. 10.1186/s12915-020-00804-5 · DOI
  49. 10.1093/nar/gkg274 · DOI · Paper page
  50. 10.1128/mbio.01711-22 · DOI
  51. 10.1093/nar/gky989 · DOI
  52. Schoch CL , Ciufo S , Domrachev M , Hotton CL , Kannan S , Khovanskaya R , Leipe D , McVeigh R , O’Neill K , Robbertse B , Sharma S , Soussov V , Sullivan JP , Sun L , Turner S , Karsch-Mizrachi I . 2020. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford) 2020. · DOI · Paper page
  53. 10.1093/nar/gkv1189 · DOI · Paper page
  54. 10.1093/bioinformatics/btt509 · DOI
  55. 10.1093/nar/gkx1038 · DOI
  56. 10.1016/S0168-9525(00)02024-2 · DOI · Paper page
  57. 10.1073/pnas.1303090110 · DOI
  58. 10.1093/nar/gks365 · DOI
  59. 10.1371/journal.pcbi.1002195 · DOI · Paper page
  60. 10.1093/molbev/mst010 · DOI · Paper page
  61. 10.1093/bioinformatics/btp033 · DOI
  62. 10.1093/bioinformatics/9.6.745 · DOI
  63. 10.1093/bioinformatics/btp348 · DOI
  64. 10.1093/bioinformatics/btu033 · DOI · Paper page
  65. 10.1093/NAR/GKAB301 · DOI
  66. 10.1093/bioinformatics/bts565 · DOI · Paper page
  67. 10.1038/S41592-022-01488-1 · DOI · Paper page
  68. 10.1093/nar/28.1.235 · DOI · Paper page
  69. 10.1002/jcc.20084 · DOI

Metadata

Authors
Tsurumaki, M., Sato, A., Saito, M., & Kanai, A.
Affiliations
Keio University (JP)
Corresponding author
Kanai, Akio
ORCID
Venue
Journal of Bacteriology
Publisher
openRxiv
Published
2024-02-29
Volume
206
Issue
7
Pages
e0007424-e0007424
ISSN
0021-9193 (ISSN-L)
DOI
10.1101/2024.02.27.582315
PMC
PMC11270868
OpenAlex
W4399495856
Cited by
7
References
1
Citations by year
2026: 3 · 2025: 2 · 2024: 2
FWCI
1.85
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Journal of Bacteriology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Keio University
  • Ministry of Education, Culture, Sports, Science and Technology (22K19340, 21J12231)
  • Japan Society for the Promotion of Science (22K19340, 21J12231)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
Keywords
insertion sequences, ribosomal DNA, Candidate Phyla Radiation, homing endonucleases, group I introns, group II introns, 16S rRNA, 23S rRNA, endonuclease activity, homodimerization, uncultured bacteria, bacterial genome evolution, transposable elements
MeSH terms
Bacteria, Bacterial Proteins, DNA Transposable Elements, Endonucleases, Phylogeny, RNA, Ribosomal, 16S

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