Diversification and functional expansion of archaeal T4F machineries
- 1Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- 2CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
Abstract
Archaea have several cell surface structures belonging to the type 4 filament (T4F) superfamily. All share a minimal core assembly system consisting of an ATPase, a platform protein, a filament-forming protein, and a class III signal peptidase. Here, we generated novel MacSyFinder2 models to identify and classify archaeal T4F systems. Our analysis revealed a vast diversity of archaeal T4F, with many organisms harboring one or more assembly machineries. Structure-based phylogenetic analysis showed that the variable N-terminal domain of T4F-related ATPases mirrors the subsystem clustering, indicating that the core machinery has diversified within the archaeal secretion ATPase family through structural innovation. Genome-wide screening for signal peptidase III cleavage site (SPIII) containing proteins revealed the widespread presence of substrate-binding proteins carrying a class III signal peptide. We propose that these binding proteins, with canonical SPIII cleavage sites, functionalize T4F machineries for efficient substrate scavenging, expanding the functional repertoire of archaeal T4F systems beyond their currently characterized roles. Author summary: The type IV filament superfamily T4F comprises a broad group of surface structures that are widespread across both archaea and bacteria. While most well-characterized members are bacterial, only a limited number of archaeal T4F systems have been experimentally studied. Here, we expand the known diversity of archaeal T4F loci through bioinformatic and comparative genomic analyses. Our results show that these systems are far more diverse and versatile than previously appreciated, often exhibiting specialized functions. Structural diversification of the ATPase machinery likely played a key role in driving the functional diversification of T4F systems. Together, these findings deepen our understanding of how archaea adapt and persist in diverse environments, highlighting their surface structures as essential tools for communication, adhesion, and nutrient acquisition.
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BibTeX
@article{sivabalasarma2026diversification,
title = {{Diversification and functional expansion of archaeal T4F machineries}},
author = {Shamphavi Sivabalasarma and Sonja-Verena Albers},
journal = {PLOS Genetics},
year = {2026},
month = oct,
doi = {10.1371/journal.pgen.1012139},
url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012139},
note = {CC BY},
}
RIS
TY - JOUR
TI - Diversification and functional expansion of archaeal T4F machineries
AU - Shamphavi Sivabalasarma
AU - Sonja-Verena Albers
PY - 2026
DA - 2026/10/14
JO - PLOS Genetics
DO - 10.1371/journal.pgen.1012139
UR - https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012139
AB - Archaea have several cell surface structures belonging to the type 4 filament (T4F) superfamily. All share a minimal core assembly system consisting of an ATPase, a platform protein, a filament-forming protein, and a class III signal peptidase. Here, we generated novel MacSyFinder2 models to identify and classify archaeal T4F systems. Our analysis revealed a vast diversity of archaeal T4F, with many organisms harboring one or more assembly machineries. Structure-based phylogenetic analysis showed that the variable N-terminal domain of T4F-related ATPases mirrors the subsystem clustering, indicating that the core machinery has diversified within the archaeal secretion ATPase family through structural innovation. Genome-wide screening for signal peptidase III cleavage site (SPIII) containing proteins revealed the widespread presence of substrate-binding proteins carrying a class III signal peptide. We propose that these binding proteins, with canonical SPIII cleavage sites, functionalize T4F machineries for efficient substrate scavenging, expanding the functional repertoire of archaeal T4F systems beyond their currently characterized roles. Author summary: The type IV filament superfamily T4F comprises a broad group of surface structures that are widespread across both archaea and bacteria. While most well-characterized members are bacterial, only a limited number of archaeal T4F systems have been experimentally studied. Here, we expand the known diversity of archaeal T4F loci through bioinformatic and comparative genomic analyses. Our results show that these systems are far more diverse and versatile than previously appreciated, often exhibiting specialized functions. Structural diversification of the ATPase machinery likely played a key role in driving the functional diversification of T4F systems. Together, these findings deepen our understanding of how archaea adapt and persist in diverse environments, highlighting their surface structures as essential tools for communication, adhesion, and nutrient acquisition.
SN - 1553-7404
SN - 1553-7390
ER -