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Peer-reviewedCC BY 4.0Proteins

An (αβ)2 Architecture of the Arabidopsis thaliana tRNA Splicing Endonuclease Complex: Structural Modeling and Evolutionary Analyses

  • Mohammad Moniruzzaman1
  • Markus Englert2
  • Kazuhito Akama1,3
  1. 1Graduate School of Natural Science & Technology Shimane University Matsue Shimane Japan
  2. 2Independent Researcher Whittlesford UK
  3. 3Department of Life Sciences Shimane University Matsue Shimane Japan
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Abstract

The tRNA splicing endonuclease (TSEN) removes introns from precursor tRNAs (pre‐tRNAs) in eukaryotes and archaea, but the architecture and subunit organization of plant TSEN remain poorly defined. Here, we integrated in planta bimolecular fluorescence complementation (BiFC) assays with AlphaFold3 (AF3)‐based structural modeling, molecular dynamics simulations, molecular mechanics generalized Born surface area (MMGBSA) decomposition, and ConSurf analysis to characterize the Arabidopsis thaliana TSEN complex (AtTSEN), focusing on AtTSEN1, AtTSEN2, and AtTSEN54. Sequence‐ and structure‐based homology searches did not detect a canonical TSEN15 homolog, a structural subunit conserved in yeast and human TSEN. BiFC supported pairwise interactions between AtTSEN54 and the catalytic subunits AtTSEN1 and AtTSEN2, but not between AtTSEN1 and AtTSEN2, suggesting AtTSEN54‐mediated heterodimeric pairing. AF3 multimer modeling predicted a pseudo‐symmetric archaeal‐like (αβ)2 architecture for AtTSEN rather than a canonical eukaryotic αβγδ arrangement. In the AF3 pre‐tRNA‐bound model, AtTSEN54 was positioned near the pre‐tRNA elbow, whereas the intron‐containing anticodon arm was oriented asymmetrically toward the AtTSEN1 catalytic sites. Per‐residue MMGBSA decomposition identified basic protein residues, particularly Arg and Lys, as putative pre‐tRNA‐binding hotspots, many of which corresponded to evolutionarily constrained interface positions across plant, fungal, and metazoan TSEN complexes. Together, these findings support an archaeal‐like (αβ)2 structural model for AtTSEN and suggest that shared RNA‐binding features are preserved alongside plant‐specific remodeling of TSEN architecture.

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Cite

BibTeXRIS
BibTeX
@article{moniruzzaman2026αβ2,
  title = {{An (αβ)2 Architecture of the Arabidopsis thaliana tRNA Splicing Endonuclease Complex: Structural Modeling and Evolutionary Analyses}},
  author = {Mohammad Moniruzzaman and Markus Englert and Kazuhito Akama},
  journal = {Proteins},
  year = {2026},
  month = jul,
  doi = {10.1002/prot.70155},
  url = {https://doi.org/10.1002/prot.70155},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - An (αβ)2 Architecture of the Arabidopsis thaliana tRNA Splicing Endonuclease Complex: Structural Modeling and Evolutionary Analyses
AU  - Mohammad Moniruzzaman
AU  - Markus Englert
AU  - Kazuhito Akama
PY  - 2026
DA  - 2026/07/09
JO  - Proteins
DO  - 10.1002/prot.70155
UR  - https://doi.org/10.1002/prot.70155
AB  - The tRNA splicing endonuclease (TSEN) removes introns from precursor tRNAs (pre‐tRNAs) in eukaryotes and archaea, but the architecture and subunit organization of plant TSEN remain poorly defined. Here, we integrated in planta bimolecular fluorescence complementation (BiFC) assays with AlphaFold3 (AF3)‐based structural modeling, molecular dynamics simulations, molecular mechanics generalized Born surface area (MMGBSA) decomposition, and ConSurf analysis to characterize the Arabidopsis thaliana TSEN complex (AtTSEN), focusing on AtTSEN1, AtTSEN2, and AtTSEN54. Sequence‐ and structure‐based homology searches did not detect a canonical TSEN15 homolog, a structural subunit conserved in yeast and human TSEN. BiFC supported pairwise interactions between AtTSEN54 and the catalytic subunits AtTSEN1 and AtTSEN2, but not between AtTSEN1 and AtTSEN2, suggesting AtTSEN54‐mediated heterodimeric pairing. AF3 multimer modeling predicted a pseudo‐symmetric archaeal‐like (αβ)2 architecture for AtTSEN rather than a canonical eukaryotic αβγδ arrangement. In the AF3 pre‐tRNA‐bound model, AtTSEN54 was positioned near the pre‐tRNA elbow, whereas the intron‐containing anticodon arm was oriented asymmetrically toward the AtTSEN1 catalytic sites. Per‐residue MMGBSA decomposition identified basic protein residues, particularly Arg and Lys, as putative pre‐tRNA‐binding hotspots, many of which corresponded to evolutionarily constrained interface positions across plant, fungal, and metazoan TSEN complexes. Together, these findings support an archaeal‐like (αβ)2 structural model for AtTSEN and suggest that shared RNA‐binding features are preserved alongside plant‐specific remodeling of TSEN architecture.
SN  - 0887-3585
SN  - 1097-0134
ER  -