Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota
- 1Indian Institute of Technology Hyderabad
Abstract
Phylum Actinomycetota (syn. Actinobacteriota or Actinobacteria), one of the largest well-studied bacterial phyla, is renowned for complex morphology, non-motility, ecological versatility, and secondary metabolite production. Chemosensory systems (CSS) are among the most sophisticated prokaryotic signal transduction architectures, yet their evolutionary distribution in this phylum remains poorly understood. Here, a comparative genomic analysis of 693 high-quality genomes spanning the phylum resolves the diversity, distribution, and evolutionary trajectories of CSS. Despite extensive genomic complexity and ecological versatility, only 6.9% of genomes encode complete CSS clusters, confined to a subset of lineages within a few classes, indicating lineage-specific retention or loss. In contrast, two-component systems (TCS) are ubiquitously abundant, with hybrid kinases enriched in CSS-deficient classes, suggesting functional compensation for the absence of dedicated chemosensory pathways. Basal lineages retain simplified CSS (F1 or F5), whereas Actinomycetes show lineage-specific expansion into multiple classes (F5, F8, F9, and ACF), often co-occurring, indicative of enhanced sensory complexity. The phylogeny of CheA homologs shows a polyphyletic distribution, supporting a mosaic evolutionary history shaped by multiple independent acquisitions, diversification, and gene loss. Collectively, our findings show that, unlike motile bacteria, members of Actinomycetota rely predominantly on TCS-driven regulatory networks, with CSS retained only in select lineages where ecological demands require enhanced environmental sensing. This work provides a phylum-wide evolutionary framework for the emergence, diversification, and functional specialization of CSS in non-motile bacteria.
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BibTeX
@misc{n2026polyphyletic,
title = {{Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota}},
author = {S. N. S and S. Brighty and G. Sharma},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.03.764138},
url = {https://www.biorxiv.org/content/10.64898/2026.11.03.764138v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota
AU - S. N. S
AU - S. Brighty
AU - G. Sharma
PY - 2026
DA - 2026/11/03
PB - bioRxiv
DO - 10.64898/2026.11.03.764138
UR - https://www.biorxiv.org/content/10.64898/2026.11.03.764138v1
AB - Phylum Actinomycetota (syn. Actinobacteriota or Actinobacteria), one of the largest well-studied bacterial phyla, is renowned for complex morphology, non-motility, ecological versatility, and secondary metabolite production. Chemosensory systems (CSS) are among the most sophisticated prokaryotic signal transduction architectures, yet their evolutionary distribution in this phylum remains poorly understood. Here, a comparative genomic analysis of 693 high-quality genomes spanning the phylum resolves the diversity, distribution, and evolutionary trajectories of CSS. Despite extensive genomic complexity and ecological versatility, only 6.9% of genomes encode complete CSS clusters, confined to a subset of lineages within a few classes, indicating lineage-specific retention or loss. In contrast, two-component systems (TCS) are ubiquitously abundant, with hybrid kinases enriched in CSS-deficient classes, suggesting functional compensation for the absence of dedicated chemosensory pathways. Basal lineages retain simplified CSS (F1 or F5), whereas Actinomycetes show lineage-specific expansion into multiple classes (F5, F8, F9, and ACF), often co-occurring, indicative of enhanced sensory complexity. The phylogeny of CheA homologs shows a polyphyletic distribution, supporting a mosaic evolutionary history shaped by multiple independent acquisitions, diversification, and gene loss. Collectively, our findings show that, unlike motile bacteria, members of Actinomycetota rely predominantly on TCS-driven regulatory networks, with CSS retained only in select lineages where ecological demands require enhanced environmental sensing. This work provides a phylum-wide evolutionary framework for the emergence, diversification, and functional specialization of CSS in non-motile bacteria.
ER -