Main Publications List

Origin of Life/RNA Polymerase

Original Papers

• An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins
  Yagi S, Tagami S
  Nature Communications 15, 5938 (2024)
  Experimental reconstruction showed that a simplified double-ψ β-barrel (DPBB), an ancient protein fold conserved in DNA and RNA polymerases, can be converted into several topologically distinct β-barrel folds related to proteins of the translation machinery. The results provide experimental evidence for evolutionary connections among DPBB, double-Z β-barrel (DZBB), RIFT, OB, and SH3 folds, suggesting how diverse protein folds associated with transcription and translation could have evolved from common ancestral peptides.


• Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail
  Chaban A, Minakhin L, Goldobina E, Bae B, Hao Y, Borukhov S, Putzeys L, Boon M, Kabinger F, Lavigne R, Makarova KS, Koonin EV, Nair SK, Tagami S, Severinov K, Sokolova ML
  Nature Communications 15, 317 (2024)
  The thermophilic bacteriophage P23-45 encodes two highly unusual DNA-dependent RNA polymerases: a virion-associated RNA polymerase fused to a giant tail tape-measure protein and a second non-virion RNA polymerase expressed after infection. Crystal structures revealed substantially different architectures despite their evolutionary relationship. Structural and sequence comparisons suggest that the two polymerases arose from an ancient gene duplication, illustrating the remarkable structural plasticity and evolution of multisubunit-like RNA polymerases.


• Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion
  Li P, Holliger P, Tagami S
  Nature Communications 13, 3050 (2022)
  Short hydrophobic-cationic peptides form amyloid-containing aggregates that reversibly concentrate RNA on their surfaces. Under high-Mg²⁺ conditions, these peptide aggregates enhance the activity of an RNA polymerase ribozyme, demonstrating a mechanism by which simple peptides could have concentrated and promoted functional RNAs in fluctuating prebiotic environments. The results provide an experimental model for RNA–peptide coevolution, in which primitive peptides can organize RNA and modulate RNA catalysis without requiring modern protein enzymes.


• Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase
  Yagi S, Padhi AK, Vucinic J, Barbe S, Schiex T, Nakagawa R, Simoncini D, Zhang KYJ, Tagami S
  Journal of the American Chemical Society 143, 15998–16006 (2021)
  A half-sized peptide derived from the ancient double-ψ β-barrel (DPBB) fold forms a homodimeric DPBB, providing a plausible evolutionary route from short peptides to a modern protein domain through peptide dimerization, gene duplication, and fusion. Further sequence simplification showed that the DPBB fold can be constructed using only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), demonstrating that an ancient protein fold could potentially have emerged from a reduced amino acid alphabet and an early genetic code.


• Simple peptides derived from the ribosomal core potentiate RNA polymerase ribozyme function
  Tagami S, Attwater J, Holliger P
  Nature Chemistry 9, 325–332 (2017)
  Simple positively charged peptides derived from putatively ancient regions of the ribosome strongly enhance RNA polymerase ribozyme activity. Homopolymeric peptides containing lysine or the non-proteinogenic, prebiotically plausible cationic amino acids ornithine and 2,4-diaminobutyric acid can also promote ribozyme function, even without defined stereochemical purity. These results demonstrate how simple non-coded peptides could have enhanced RNA function before the emergence of modern translation, providing a possible evolutionary bridge between an RNA world and the modern RNA–protein world.


• Structural basis for promoter specificity switching of RNA polymerase by a phage factor
  Tagami S, Sekine S, Minakhin L, Esyunina D, Akasaka R, Shirouzu M, Kulbachinskiy A, Severinov K, Yokoyama S
  Genes & Development 28, 521–531 (2014)
  The crystal structure of Thermus thermophilus RNA polymerase bound to the bacteriophage protein gp39 revealed how a viral transcription factor changes bacterial promoter specificity. Gp39 interacts with the RNA polymerase β-flap and σ factor and induces a large repositioning of σ region 4, selectively suppressing transcription from −10/−35 promoters while allowing transcription from extended −10 promoters. The study provides a structural mechanism for bacteriophage-mediated reprogramming of host RNA polymerase and transcription.


• Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
  Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S
  Nature 468, 978–982 (2010)
  The crystal structure of bacterial RNA polymerase bound to the transcription factor Gfh1 revealed the structural basis of transcription inhibition by Gfh1. Gfh1 binds through the secondary channel of RNA polymerase and stabilizes a distinct conformational state of the enzyme, providing insight into the structural dynamics that regulate transcription initiation and elongation.

Reviews

• Computational protein design
  Albanese KI, Barbe S, Tagami S, Woolfson DN, Schiex T
  Nature Reviews Methods Primers 5, Article 13 (2025)


• Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life
  Tagami S
  Biophysics and Physicobiology 20(2), e200026 (2023)


• The origin of life: RNA and protein co-evolution on the ancient Earth
  Tagami S, Li P
  Development, Growth & Differentiation 65(3), 167–174 (2023)

Peptides with Special Modifications

Original Papers

• RiPP recognition elements evolved to prevent pathway interference through leader peptide discrimination
  Popov A, Bikmetov D, Grigoreva A, Serebryakova M, Severinov K, Wolf YI, Lippens G, Wada A, Tagami S, Dubiley S
  Nature Communications 17, 6633 (2026)
  This study identifies a widespread family of ribosomally synthesized and post-translationally modified peptides in Bacillota, termed linear polyphosphorylated peptides (LPPs), whose biosynthetic gene clusters often co-localize with lasso peptide pathways. Although LPP and lasso peptide precursors share similar RiPP recognition element (RRE)-binding motifs, biochemical and structural analyses show that their RREs selectively recruit cognate precursor peptides and leader peptidases, preventing interference between the two pathways. The work also identifies a SipW-like signal peptidase as the RRE-dependent leader peptidase in LPP biosynthesis and provides a mechanistic view of how related RiPP pathways can diversify while coexisting in the same host.


• Lasso peptide microcin J25 variant containing RGD motif as a PET probe for integrin a v ß 3 in tumor imaging
  Mohri K, Huynh Nhat KP, Zouda M, Warashina S, Wada Y, Watanabe Y, Tagami S, Mukai H
  European Journal of Pharmaceutical Sciences 180, 106339 (2023)
  The mechanically interlocked lasso peptide microcin J25 (MccJ25) was reportedly engineered to display an RGD motif that recognizes integrin αvβ3. In this paper, a 64Cu-labeled MccJ25 variant enabled PET imaging of integrin-positive tumors in mice, demonstrating that the highly stable lasso peptide structure can serve as an engineerable scaffold for molecular imaging and peptide-based biotechnology.


• Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2
  Alfi A, Popov A, Kumar A, Zhang KYJ, Dubiley S, Severinov K, Tagami S
  ACS Synthetic Biology 11, 2022–2028 (2022)
  A cell-free protein synthesis system was combined with AlphaFold2 structure prediction to perform rapid mutational analysis of FusB2, a poorly soluble cysteine protease involved in lasso peptide biosynthesis. Analysis of 34 mutants supported the predicted structure and identified a surface hydrophobic region likely involved in interaction with the partner protein FusB1. The study demonstrates a strategy for combining cell-free mutagenesis and protein structure prediction to investigate difficult-to-purify biosynthetic enzymes.


• Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway
  Sumida T, Dubiley S, Wilcox B, Severinov K, Tagami S
  ACS Chemical Biology 14, 1619–1627 (2019)
  The crystal structure of the TfuB1 (FusB1)–leader peptide complex revealed how a RiPP recognition element (RRE) recognizes the leader region of a lasso peptide precursor. The structure and biochemical analyses define the molecular basis of precursor recognition during lasso peptide biosynthesis and provide insights into substrate specificity in RiPP maturation pathways.

Peptide Selection (Akira Wada)

• Development of Uniform Ribosome Display Technology Enabling Easy and Efficient Identification of Full-Length Proteins that Interact with Bioactive Small and Large Molecules
  Taguchi K, Sakai Y, Furuhashi T, Hara S, Wada A
  ChemBioChem 26(1), e202400352 (2025)


• Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides
  Furuhashi T, Sakamoto K, Wada A
  International Journal of Molecular Sciences 24(21), 15661 (2023)