Editorial: Functions, working mechanisms, and regulation of rotary ATPases and Ductin proteins
Tibor Páli
Boris Feniouk
Stephan Wilkens- 1Institute of Biophysics, HUN-REN Biological Research Centre, Szeged, Hungary
- 2A.N. Belozersky Institute, Lomonosov Moscow State University, Moscow, Russia
- 3Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
Editorial on the Research Topic
Functions, working mechanisms, and regulation of rotary ATPases and Ductin proteins
1 Remaining challenges on rotary enzymes
The rotary mechanism of the ion-transporting F-, V- and A-type ATPases is of great interest to the molecular bio-sciences. Connecting the regulation of their rotation-coupled catalysis-transport cycle with the various associated biological functions requires a detailed understanding of the enzymes’ rotary mechanism. Despite recent progress with developing new and alternative models [see, e.g., Frasch et al. (2022); Kishikawa et al. (2022); Nakano et al. (2023); Nath (2023)], a full understanding of the biological functions of these enzymes is limited by the fact that measuring the proton-transfer and rotation rates of rotary ATPases in the cellular context still represents a significant challenge. For instance, the native rotation rate of a chemically intact enzyme could be measured so far only using indirect methods (Ferencz et al., 2013; Ferencz et al., 2017; Petrovszki et al., 2021). Though recent cryo electron microscopy (cryo-EM) studies have provided near-atomic snapshots for some of the ion-transporting subcomplexes [e.g., Kishikawa et al. (2022); Pinke et al. (2020)], the challenge also remains that the “substrate”—protons—cannot be visualised directly. There is accumulating evidence that, as part of the Ductin family (Holzenburg et al., 1993; Lautemann and Bohrmann, 2016), some rotor or “c-ring” proteins are key players in certain membrane fusion and rearrangement processes even in the absence of the catalytic activity of the holoenzyme [see, e.g., Higashida et al. (2017); Rama et al. (2019); Amodeo et al. (2021); Lévêque et al. (2023)]. However, it is challenging to separate the physiological role of the isolated c-ring proteins from their role in the intact enzyme in those processes. This Research Topic gathered valuable articles presenting new data and views on the molecular mechanisms and physiological roles of these membrane-transporter rotary enzymes. The key findings of these articles are summarised in the next two sections.
2 On the catalytic and transport mechanisms of the rotary ATPases
Based on extensive time-resolved cryo-EM snapshot analyses, Yokoyama’s review provides a comprehensive overview of the structure and function of the rotary V/A-ATPase from the thermophilic bacterium Thermus thermophilus, one of the best characterised rotary ATPases. The authors of the study conclude that the rotary mechanism of the related F1-ATPase is more complex than that of the V/A-ATPase (regarding the events of ATP binding and hydrolysis coupled rotation), but also that the underlying principle is conserved. Suiter and Volkán-Kacsó analysed (at microsecond time-resolution) single-molecule rotational trajectories of F1-ATPase of a bacterial species, Paracoccus denitrificans, imaged by a nano-crystal probe attached to the rotor shaft of the motor (these data were generated by Noji and coworkers). They found a common mechanism for removing a nucleotide release bottleneck in the rotary mechanism in the P. denitrificans and Thermophilic bacillus F1-ATPase. The paper also discusses how the F-ATPase was perfected by evolution for efficient and robust energy conversion. In another single-molecule study Yanagisawa et al. present rotation-experiments carried out with high-resolution of time and rotational angle for the V1 subcomplex of the yeast, Saccharomyces cerevisiae V-ATPase. The results provide great detail on the molecular basis for the differences in rotor positions associated with substrate binding and product release between V- and F-type ATPases. A radically new theory that departs from the concept of the chemo-mechanical coupling (transduction of chemical free energy of ATP to mechanical work) for an ATP-driven protein complex is presented by Yasuda et al. According to the authors of the study, the entropy originating from the displacement of water molecules in the system plays a key role in driving rotation. The paper concludes that ATP hydrolysis (or synthesis) is tightly coupled to the rotation of the central shaft in the normal (or inverse) direction through a water-entropy effect.
3 On the biological functions and regulation of rotary ATPases and Ductin proteins
Tuli and Kane’s review provides strong arguments for why the cytosolic N-terminal domain of the a-subunit of V-ATPases functions as a regulatory hub for enzyme targeting via multiple signals. One such regulatory mechanism, binding to phosphoinositides, targets mammalian a-subunit isoforms to specific membranes, and regulates the enzymes’ ATP hydrolysis and proton pumping activities. The study of Mendoza-Hoffmann et al. presents a sizeable amount of (bioinformatic, biochemical, molecular biology, functional and structural) data about the evolution and regulatory role of the ζ-subunit of the F-ATPase of P. denitrificans and α-proteobacteria. It is convincingly argued that the ζ-subunit evolved by preserving its inhibitory function in free-living α-proteobacteria, however, this function was lost in some symbiotic α-proteobacteria where it became non-essential given the possible exchange of nutrients and ATP with the host. The report of Wang et al. relates to the role of V-ATPase in synaptic vesicle neurotransmitter loading and in vesicle fusion, and it is considered as an ideal candidate to regulate the fusogenic status of secretory vesicles according to their loading state. Their experimental results argue that, via Vo-V1 dissociation, V-ATPase modulates exocytosis in neuroendocrine cells through the activation of the synthesis of phosphatidic acid. And finally, Sebők-Nagy et al. hypothesise that binding of divalent cations to the c-ring, or more generally Ductin protein assemblies, acts as a new regulatory mechanism of certain membrane trafficking processes. The authors of the study propose that such non-covalent binding of certain divalent cations could structurally modulate the various functions of Ductin assemblies by affecting their stability.
4 Perspectives
Structural biology of membrane proteins is rapidly catching up thanks to improved experimental approaches (for example, cryo-EM) (e.g., Pinke et al., 2020; Gerle et al., 2022; Yamamori and Tomii, 2022) and structure predictions enhanced with artificial intelligence (Versini et al., 2023; Wuyun et al., 2024). Structure models with atomic detail are already available, also for the Fo, Vo and Ao domains. The improved structure models combined with kinetic single-molecule spectroscopic and other novel biophysical studies (e.g., Otomo et al., 2022; Kobayashi et al., 2023; Pérez et al., 2023) and molecular simulations (e.g., Blanc and Hummer, 2024) will lead to more detailed theoretical description of the catalysis-transport mechanism of F-, V- and A-type rotary enzymes. Regarding biological function, research is strong on the assembly and the activity of the rotary enzymes (and some of their subunits, e.g., c-ring proteins) in general, but also in certain membrane fusion and pore formation processes (Novitskaia et al., 2019; Banerjee and Kane, 2020; Mnatsakanyan and Jonas, 2020; Abuammar et al., 2021; Lapashina et al., 2022; Nesci, 2022; Wilkens et al., 2023; Yamamoto et al., 2023). Therefore, new insights will likely emerge on the biological regulation of the reversible assembly and activity of rotary enzymes in the near future.
Author contributions
TP: Conceptualization, Writing–original draft, Writing–review and editing. BF: Writing–review and editing. SW: Writing–review and editing.
Acknowledgments
We deeply thank all the authors and reviewers who have contributed to this Research Topic. We gratefully acknowledge and thank for the support of Frontiers in Molecular Biosciences staff for the continuous and passionate technical support.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
References
Abuammar, H., Bhattacharjee, A., Simon-Vecsei, Z., Blastyák, A., Csordás, G., Páli, T., et al. (2021). Ion channels and pumps in autophagy: A reciprocal relationship. Cells 10. doi:10.3390/cells10123537
Amodeo, G., Lee, B., Krilyuk, N., Filice, C., Valyuk, D., Otzen, D., et al. (2021). C subunit of the ATP synthase is an amyloidogenic calcium dependent channel-forming peptide with possible implications in mitochondrial permeability transition. Sci. Rep. 11, 8744. doi:10.1038/s41598-021-88157-z
Banerjee, S., and Kane, P. (2020). Regulation of V-ATPase activity and organelle pH by phosphatidylinositol phosphate lipids. Front. Cell Dev. Biol. 8, 510. doi:10.3389/fcell.2020.00510
Blanc, F., and Hummer, G. (2024). Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. Proc. Natl. Acad. Sci. U. S. A. 121, e2314199121. doi:10.1073/pnas.2314199121
Ferencz, C., Petrovszki, P., Dér, A., Sebők-Nagy, K., Kóta, Z., and Páli, T. (2017). Oscillating electric field measures the rotation rate in a native rotary enzyme. Sci. Rep. 7, 45309. doi:10.1038/srep45309
Ferencz, C., Petrovszki, P., Kota, Z., Fodor-Ayaydin, E., Haracska, L., Bota, A., et al. (2013). Estimating the rotation rate in the vacuolar proton-atpase in native yeast vacuolar membranes. Eur. Biophysics J. 42, 147–158. doi:10.1007/s00249-012-0871-z
Frasch, W., Bukhari, Z., and Yanagisawa, S. (2022). F1Fo-ATP synthase molecular motor mechanisms. Front. Microbiol. 13, 965620. doi:10.3389/fmicb.2022.965620
Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, O., Makino, F., et al. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. Microsc. (Oxf) 71, 249–261. doi:10.1093/jmicro/dfac037
Higashida, H., Yokoyama, S., Tsuji, C., and Muramatsu, S. (2017). Neurotransmitter release: vacuolar ATPase V0 sector c-subunits in possible gene or cell therapies for Parkinson’s, Alzheimer’s, and psychiatric diseases. J. Physiol. Sci. 67, 11–17. doi:10.1007/s12576-016-0462-3
Holzenburg, A., Jones, P. C., Franklin, T., Pali, T., Heimburg, T., Marsh, D., et al. (1993). Evidence for a common structure for a class of membrane channels. Eur. J. Biochem. 213, 21–30. doi:10.1111/j.1432-1033.1993.tb17730.x
Kishikawa, J., Nakanishi, A., Nakano, A., Saeki, S., Furuta, A., Kato, T., et al. (2022). Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases. Nat. Commun. 13, 1213. doi:10.1038/s41467-022-28832-5
Kobayashi, R., Ueno, H., Okazaki, K., and Noji, H. (2023). Molecular mechanism on forcible ejection of ATPase inhibitory factor 1 from mitochondrial ATP synthase. Nat. Commun. 14, 1682. doi:10.1038/s41467-023-37182-9
Lapashina, A., Kashko, N., Zubareva, V., Galkina, K., Markova, O., Knorre, D., et al. (2022). Attenuated ADP-inhibition of F0F1 ATPase mitigates manifestations of mitochondrial dysfunction in yeast. Biochim. Biophys. Acta Bioenerg. 1863, 148544. doi:10.1016/j.bbabio.2022.148544
Lautemann, J., and Bohrmann, J. (2016). Relating proton pumps with gap junctions: colocalization of ductin, the channel-forming subunit c of V-ATPase, with subunit a and with innexins 2 and 3 during Drosophila oogenesis. BMC Dev. Biol. 16, 24. doi:10.1186/s12861-016-0124-y
Lévêque, C., Maulet, Y., Wang, Q., Rame, M., Rodriguez, L., Mochida, S., et al. (2023). A role for the V0 sector of the V-ATPase in neuroexocytosis: exogenous V0d blocks complexin and SNARE interactions with V0c. Cells 12, 750. doi:10.3390/cells12050750
Mnatsakanyan, N., and Jonas, E. (2020). ATP synthase c-subunit ring as the channel of mitochondrial permeability transition: regulator of metabolism in development and degeneration. J. Mol. Cell Cardiol. 144, 109–118. doi:10.1016/j.yjmcc.2020.05.013
Nakano, A., Kishikawa, J., Mitsuoka, K., and Yokoyama, K. (2023). Mechanism of ATP hydrolysis dependent rotation of bacterial ATP synthase. Nat. Commun. 14, 4090. doi:10.1038/s41467-023-39742-5
Nath, S. (2023). Phosphorus chemistry at the roots of bioenergetics: ligand permutation as the molecular basis of the mechanism of ATP synthesis/hydrolysis by FoF1-ATP synthase. Molecules 28, 7486. doi:10.3390/molecules28227486
Nesci, S. (2022). Protein folding and unfolding: proline cis-trans isomerization at the c subunits of F1Fo-ATPase might open a high conductance ion channel. Proteins 90, 2001–2005. doi:10.1002/prot.26383
Novitskaia, O., Buslaev, P., and Gushchin, I. (2019). Assembly of spinach chloroplast ATP synthase rotor ring protein-lipid complex. Front. Mol. Biosci. 6, 135. doi:10.3389/fmolb.2019.00135
Otomo, A., Iida, T., Okuni, Y., Ueno, H., Murata, T., and Iino, R. (2022). Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between Vo and V1 motors. Proc. Natl. Acad. Sci. U. S. A. 119, e2210204119. doi:10.1073/pnas.2210204119
Pérez, I., Heitkamp, T., and Börsch, M. (2023). Mechanism of ADP-inhibited ATP hydrolysis in single proton-pumping FoF1-ATP synthase trapped in solution. Int. J. Mol. Sci. 24, 8442. doi:10.3390/ijms24098442
Petrovszki, P., Sebők-Nagy, K., and Páli, T. (2021). The activity of native vacuolar proton-ATPase in an oscillating electric field - demystifying an apparent effect of music on a biomolecule. Front. Mol. Biosci. 8, 772167. doi:10.3389/fmolb.2021.772167
Pinke, G., Zhou, L., and Sazanov, L. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. Nat. Struct. Mol. Biol. 27, 1077–1085. doi:10.1038/s41594-020-0503-8
Rama, S., Boumedine-Guignon, N., Sangiardi, M., Youssouf, F., Maulet, Y., Lévêque, C., et al. (2019). Chromophore-assisted light inactivation of the V-ATPase V0c subunit inhibits neurotransmitter release downstream of synaptic vesicle acidification. Mol. Neurobiol. 56, 3591–3602. doi:10.1007/s12035-018-1324-1
Versini, R., Sritharan, S., Aykac Fas, B., Tubiana, T., Aimeur, S. Z., Henri, J., et al. (2023). A perspective on the prospective use of AI in protein structure prediction. J. Chem. Inf. Model. 64, 26–41. doi:10.1021/acs.jcim.3c01361
Wilkens, S., Khan, M., Knight, K., and Oot, R. (2023). Tender love and disassembly: how a TLDc domain protein breaks the V-ATPase. Bioessays 45, e2200251. doi:10.1002/bies.202200251
Wuyun, Q., Chen, Y., Shen, Y., Cao, Y., Hu, G., Cui, W., et al. (2024). Recent progress of protein tertiary structure prediction. Molecules 29, 832. doi:10.3390/molecules29040832
Yamamori, Y., and Tomii, K. (2022). Application of homology modeling by enhanced profile-profile alignment and flexible-fitting simulation to cryo-EM based structure determination. Int. J. Mol. Sci. 23, 1977. doi:10.3390/ijms23041977
Keywords: rotary enzyme, membrane, ATP hydrolysis, ATP synthesis, ATPase, c-ring, reversible disassembly, Ductin protein
Citation: Páli T, Feniouk B and Wilkens S (2024) Editorial: Functions, working mechanisms, and regulation of rotary ATPases and Ductin proteins. Front. Mol. Biosci. 11:1399421. doi: 10.3389/fmolb.2024.1399421
Received: 11 March 2024; Accepted: 13 March 2024;
Published: 28 March 2024.
Edited and reviewed by:
Annalisa Pastore, King’s College London, United KingdomCopyright © 2024 Páli, Feniouk and Wilkens. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Tibor Páli, tpali@brc.hu