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PreprintCited by 7Bacterial Genetics and BiotechnologyMicrotubule and mitosis dynamicsGenomics and Chromatin Dynamics

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Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation

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Kaljević, Jovana, Sukhoverkov, Kirill V., Johnson, Katie, Hocher, Antoine, Le, Tung B. K.·2025·Proceedings of the National Academy of Sciences
DOI 10.1101/2025.10.10.680097PMC PMC12704722

Preprint — published as 10.1073/pnas.2527592122

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Abstract

Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states through nucleotide binding and hydrolysis. These mechanisms were long thought to rely exclusively on ATPase or GTPase proteins, until the discovery of CTPase activity in the bacterial chromosome segregation protein ParB. In the ParAB S system, CTP binding enables ParB accumulation around the centromere-like parS DNA sites to activate the ATPase ParA, thereby facilitating chromosome partitioning to daughter cells. CTP hydrolysis then releases ParB from DNA for recycling. This discovery uncovered a new regulatory principle, but the broader diversity of proteins employing a CTPase mechanism remains unclear. Here, we conduct a large-scale survey of proteins harboring the ParB-CTPase fold across bacteria, archaea, bacteriophages, and eukaryotes. While many ParB-like proteins follow the canonical ParAB S organization with ParA partners, we also identify numerous orphan homologs encoded outside of the parAB operon, frequently linked to mobile genetic elements that may have driven their rapid diversification. The ParB-CTPase folds in these divergent proteins are often fused to lineage-specific domains with diverse predicted biological activities. We further demonstrate that while many homologs retain CTP-binding, others instead bind ATP or GTP, revealing a broader spectrum of nucleotide specificities than previously appreciated. Our findings establish the ParB-CTPase fold as a widely distributed and evolutionarily versatile NTP-binding module, repeatedly co-opted through domain fusion and shifts in nucleotide specificity to enable functions far beyond the classical ParAB S -mediated DNA segregation.

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Metadata

Authors
Kaljević, J., Sukhoverkov, K. V., Johnson, K., Hocher, A., & Le, T. B. K.
Affiliations
  • John Innes Centre (GB)
  • University of Cambridge (GB)
Corresponding author
  • Kaljević, Jovana
  • Sukhoverkov, Kirill V.
  • Hocher, Antoine
  • Le, Tung B. K.
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
openRxiv
Published
2025-10-10
Volume
122
Issue
49
Pages
e2527592122-e2527592122
ISSN
0027-8424 (ISSN-L)
DOI
10.1101/2025.10.10.680097
PMC
PMC12704722
OpenAlex
W4417002201
Cited by
7
References
1
Citations by year
2026: 7
FWCI
4.09
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
Funders
Wellcome Trust (221776/Z/2/Z, 227755/Z/23/Z)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
chromosome segregation, domain fusion, nucleotide specificity, ATP binding, GTP binding, mobile genetic elements, protein evolution, bacterial chromosome partitioning, archaea, bacteriophages
MeSH terms
Protein Domains, Bacterial Proteins, Cytidine Triphosphate, Nucleotides, Chromosome Segregation

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