Saori Yoshimura, Ryuki Shimada, Koji Kikuchi, Soichiro Kawagoe, Hironori Abe, Sakie Iisaka, Sayoko Fujimura, Kei-Ichiro Yasunaga, Shingo Usuki, Naoki Tani, Takashi Ohba, Eiji Kondoh, Tomohide Saio, Kimi Araki and Kei-Ichiro Ishiguro : Atypical heat shock transcription factor HSF5 is critical for male meiotic prophase under non-stress conditions., Nature Communications, 15, 1, 3330, 2024.
(Summary)
Meiotic prophase progression is differently regulated in males and females. In males, pachytene transition during meiotic prophase is accompanied by robust alteration in gene expression. However, how gene expression is regulated differently to ensure meiotic prophase completion in males remains elusive. Herein, we identify HSF5 as a male germ cell-specific heat shock transcription factor (HSF) for meiotic prophase progression. Genetic analyzes and single-cell RNA-sequencing demonstrate that HSF5 is essential for progression beyond the pachytene stage under non-stress conditions rather than heat stress. Chromatin binding analysis in vivo and DNA-binding assays in vitro suggest that HSF5 binds to promoters in a subset of genes associated with chromatin organization. HSF5 recognizes a DNA motif different from typical heat shock elements recognized by other canonical HSFs. This study suggests that HSF5 is an atypical HSF that is required for the gene expression program for pachytene transition during meiotic prophase in males.
A transcriptional regulatory system called heat shock response (HSR) has been developed in eukaryotic cells to maintain proteome homeostasis under various stresses. Heat shock factor-1 (Hsf1) plays a central role in HSR, mainly by upregulating molecular chaperones as a transcription factor. Hsf1 forms a complex with chaperones and exists as a monomer in the resting state under normal conditions. However, upon heat shock, Hsf1 is activated by oligomerization. Thus, oligomerization of Hsf1 is considered an important step in HSR. However, the lack of information about Hsf1 monomer structure in the resting state, as well as the structural change via oligomerization at heat response, impeded the understanding of the thermosensing mechanism through oligomerization. In this study, we applied solution biophysical methods, including fluorescence spectroscopy, nuclear magnetic resonance, and circular dichroism spectroscopy, to investigate the heat-induced conformational transition mechanism of Hsf1 leading to oligomerization. Our study showed that Hsf1 forms an inactive closed conformation mediated by intramolecular contact between leucine zippers (LZs), in which the intermolecular contact between the LZs for oligomerization is prevented. As the temperature increases, Hsf1 changes to an open conformation, where the intramolecular LZ interaction is dissolved so that the LZs can form intermolecular contacts to form oligomers in the active form. Furthermore, since the interaction sites with molecular chaperones and nuclear transporters are also expected to be exposed in the open conformation, the conformational change to the open state can lead to understanding the regulation of Hsf1-mediated stress response through interaction with multiple cellular components.
Shuhei Yoshida, Shota Uehara, Noriyasu Kondo, Yu Takahashi, Shiho Yamamoto, Atsushi Kameda, Soichiro Kawagoe, Naoko Inoue, Masami Yamada, Norito Yoshimura and Yuki Tachibana : Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides., Journal of Medicinal Chemistry, 65, 15, 10655-10673, 2022.
(Summary)
Recent technological innovations have led to the development of methods for the rapid identification of high-affinity macrocyclic peptides for a wide range of targets; however, it is still challenging to achieve the desired activity and membrane permeability at the same time. Here, we propose a novel small molecule lead discovery strategy, Peptide-to-Small Molecule, which is a combination of rapid identification of high-affinity macrocyclic peptides via peptide display screening followed by pharmacophore-guided de novo design of small molecules, and demonstrate the applicability using nicotinamide N-methyltransferase (NNMT) as a target. Affinity selection by peptide display technology identified macrocyclic peptide 1 that exhibited good enzymatic inhibitory activity but no cell-based activity. Thereafter, a peptide pharmacophore-guided de novo design and further structure-based optimization resulted in highly potent and cell-active small molecule 14 (cell-free IC50 = 0.0011 μM, cell-based IC50 = 0.40 μM), indicating that this strategy could be a new option for drug discovery.
(Keyword)
Cell Membrane Permeability / Drug Discovery / Peptides
Soichiro Kawagoe, Hiroshi Nakagawa, Hiroyuki Kumeta, Koichiro Ishimori and Tomohide Saio : Structural insight into proline cis/ trans isomerization of unfolded proteins catalyzed by the trigger factor chaperone, The Journal of Biological Chemistry, 293, 39, 15095-15106, 2018.
(Summary)
Molecular chaperones often possess functional modules that are specialized in assisting the formation of specific structural elements, such as a disulfide bridges and peptidyl-prolyl bonds in cis form, in the client protein. A ribosome-associated molecular chaperone trigger factor (TF), which has a peptidyl-prolyl cis/trans isomerase (PPIase) domain, acts as a highly efficient catalyst in the folding process limited by peptidyl-prolyl isomerization. Herein we report a study on the mechanism through which TF recognizes the proline residue in the unfolded client protein during the cis/trans isomerization process. The solution structure of TF in complex with the client protein showed that TF recognizes the proline-aromatic motif located in the hydrophobic stretch of the unfolded client protein through its conserved hydrophobic cleft, which suggests that TF preferentially accelerates the isomerization of the peptidyl-prolyl bond that is eventually folded into the core of the protein in its native fold. Molecular dynamics simulation revealed that TF exploits the backbone amide group of Ile195 to form an intermolecular hydrogen bond with the carbonyl oxygen of the amino acid residue preceding the proline residue at the transition state, which presumably stabilizes the transition state and thus accelerates the isomerization. The importance of such intermolecular hydrogen-bond formation during the catalysis was further corroborated by the activity assay and NMR relaxation analysis.
Tomohide Saio, Soichiro Kawagoe, Koichiro Ishimori and G Charalampos Kalodimos : Oligomerization of a molecular chaperone modulates its activity., eLife, 7, e35731, 2018.
(Summary)
Molecular chaperones alter the folding properties of cellular proteins via mechanisms that are not well understood. Here, we show that Trigger Factor (TF), an ATP-independent chaperone, exerts strikingly contrasting effects on the folding of non-native proteins as it transitions between a monomeric and a dimeric state. We used NMR spectroscopy to determine the atomic resolution structure of the 100 kDa dimeric TF. The structural data show that some of the substrate-binding sites are buried in the dimeric interface, explaining the lower affinity for protein substrates of the dimeric compared to the monomeric TF. Surprisingly, the dimeric TF associates faster with proteins and it exhibits stronger anti-aggregation and holdase activity than the monomeric TF. The structural data show that the dimer assembles in a way that substrate-binding sites in the two subunits form a large contiguous surface inside a cavity, thus accounting for the observed accelerated association with unfolded proteins. Our results demonstrate how the activity of a chaperone can be modulated to provide distinct functional outcomes in the cell.
(Keyword)
Binding Sites / Escherichia coli / Escherichia coli Proteins / Molecular Chaperones / Peptidylprolyl Isomerase / Protein Binding / Protein Conformation / Protein Folding / Protein Multimerization
Soichiro Kawagoe, Koichiro Ishimori and Tomohide Saio : Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding., International Journal of Molecular Sciences, 23, 5, Feb. 2022.
(Summary)
Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics-activity relationships to explain the mechanism of functional diversity of molecular chaperones.
(Keyword)
Humans / Kinetics / Molecular Chaperones / Protein Folding
Soichiro Kawagoe, Mori Eiichiro and Tomohide Saio : Regulation of Liquid-Liquid Phase Separation by Molecular Chaperones, Thermal Medicine, 37, 2, 31-44, Aug. 2021.
Soichiro Kawagoe, Kumeta Hiroyuki and Tomohide Saio : Flipping of the tryptophan ring in the protein core probed by 19F NMR-based solvent accessibility profiling, 2025 Korea-Japan Joint Conference on Protein Science, Jun. 2025.
2.
Soichiro Kawagoe and Tomohide Saio : Structural dynamics regulating the molecular assembly of heat shock transcription factor 1, International Symposium on Multifaceted Protein Dynamics, Sep. 2024.
3.
Soichiro Kawagoe, Kumeta Hiroyuki and Tomohide Saio : Aromatic Ring Flipping in Structured Domain Modulates the Assembly of Intrinsically Disordered Region, The 30th International Conference on Magnetic Resonance in Biological Systems, Aug. 2024.
Structural insight into the interaction network driving the multi-state transition of heat shock transcription factor 1 (Project/Area Number: 24K18063 )
Kinetic analysis of multivalent interaction regulating the dynamic molecular assembly (Project/Area Number: 23K19353 )
Mechanism of chaperone activity modulation through promiscuous recognitions (Project/Area Number: 23K23824 )