Structural Insights into the Dimeric Form of Bacillus subtilis RNase Y Using NMR and AlphaFold
Open accessAbstract
RNase Y is a crucial component of genetic translation, acting as the key enzyme initiating mRNA decay in many Gram-positive bacteria. The N-terminal domain of Bacillus subtilis RNase Y (Nter-BsRNaseY) is thought to interact with various protein partners within a degradosome complex. Bioinformatics and biophysical analysis have previously shown that Nter-BsRNaseY, which is in equilibrium between a monomeric and a dimeric form, displays an elongated fold with a high content of α-helices. Using multidimensional heteronuclear NMR and AlphaFold models, here, we show that the Nter-BsRNaseY dimer is constituted of a long N-terminal parallel coiled-coil structure, linked by a turn to a C-terminal region composed of helices that display either a straight or bent conformation. The structural organization of the N-terminal domain is maintained within the AlphaFold model of the full-length RNase Y, with the turn allowing flexibility between the N- and C-terminal domains. The catalytic domain is globular, with two helices linking the KH and HD modules, followed by the C-terminal region. This latter region, with no function assigned up to now, is most likely involved in the dimerization of B. subtilis RNase Y together with the N-terminal coiled-coil structure.
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The degradosome is localized in the peripheral membrane region via its scaffold RNase Y, which anchors the complex through its N-terminal transmembrane helix embedded in the membrane.
“The degradosome is localized in the peripheral membrane region via its scaffold RNase Y, which anchors the complex through its N-terminal transmembrane helix embedded in the membrane.”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [93]
The Introduction states that a transmembrane region anchors B. subtilis RNase Y to the membrane. It describes RNase Y’s participation in a degradosome-like complex as proposed, and Discussion §4.3 suggests its N-terminal domain could tether other components. The paper does not establish that the assembled degradosome is localized at the membrane periphery, as the claim states. (LLM, conf=0.86)
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- Authors
- Morellet, N., Hardouin, P., Assrir, N., van Heijenoort, C., & Golinelli-Pimpaneau, B.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Institut de Chimie Des Substances Naturelles, Université Paris-Saclay, CNRS, UPR 2301, 91198 Gif-Sur-Yvette, France
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France Université, 75231 Paris, France
- Corresponding author
- Morellet, Nelly
- Venue
- Biomolecules
- Publisher
- MDPI AG
- Published
- 2022-12-01
- Volume
- 12
- Issue
- 12
- Pages
- 1798
- ISSN
- 2218-273X (ISSN-L)
- PMC
- PMC9775385
- OpenAlex
- W4311193936
- Cited by
- 7
- References
- 75
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 1 · 2023: 3
- FWCI
- 0.41
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Biomolecules (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- LillOA (Université de Lille (University Of Lille)) (submittedVersion, other-oa)
- Funders
- French State Program ‘Investissements d’Avenir’ (ANR-11-LABX-0011, ANR-11-BSV8-026, FR2054)
- IR INFRANALYTICS (ANR-11-LABX-0011, ANR-11-BSV8-026, FR2054)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- RNase Y, Bacillus subtilis, mRNA degradation, degradosome, N-terminal domain, protein dimerization, coiled coil, KH domain, catalytic domain, protein structure, AlphaFold models
- MeSH terms
- Protein Domains, Bacillus subtilis, Bacterial Proteins, Ribonucleases, Nuclear Magnetic Resonance, Biomolecular, Protein Multimerization
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