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Publications (10 of 13) Show all publications
Sighel, D., Notarangelo, M., Aibara, S., Re, A., Ricci, G., Guida, M., . . . Quattrone, A. (2021). Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth. Cell Reports, 35(4), Article ID 109024.
Open this publication in new window or tab >>Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth
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2021 (English)In: Cell Reports, E-ISSN 2211-1247, Vol. 35, no 4, article id 109024Article in journal (Refereed) Published
Abstract [en]

Glioblastoma stem cells (GSCs) resist current glioblastoma (GBM) therapies. GSCs rely highly on oxidative phosphorylation (OXPHOS), whose function requires mitochondrial translation. Here we explore the therapeutic potential of targeting mitochondrial translation and report the results of high-content screening with putative blockers of mitochondrial ribosomes. We identify the bacterial antibiotic quinupristin/dalfopristin (Q/D) as an effective suppressor of GSC growth. Q/D also decreases the clonogenicity of GSCs in vitro, consequently dysregulating the cell cycle and inducing apoptosis. Cryoelectron microscopy (cryo-EM) reveals that Q/D binds to the large mitoribosomal subunit, inhibiting mitochondrial protein synthesis and functionally dysregulating OXPHOS complexes. These data suggest that targeting mitochondrial translation could be explored to therapeutically suppress GSC growth in GBM and that Q/D could potentially be repurposed for cancer treatment.

Keywords
glioblastoma, glioblastoma stem cells, OXPHOS, mitoribosome, mitochondrial translation, high-content screening, cryo-EM, quinupristin, dalfopristin, drug repurposing
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-193707 (URN)10.1016/j.celrep.2021.109024 (DOI)000644709600004 ()33910005 (PubMedID)
Available from: 2021-06-10 Created: 2021-06-10 Last updated: 2024-01-17Bibliographically approved
Tobiasson, V., Gahura, O., Aibara, S., Baradaran, R., Ziková, A. & Amunts, A. (2021). Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit. EMBO Journal, 40(6), Article ID e106292.
Open this publication in new window or tab >>Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit
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2021 (English)In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 40, no 6, article id e106292Article in journal (Refereed) Published
Abstract [en]

Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 angstrom, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.

Keywords
assembly, mitochondria, mitoribosome, translation, trypanosoma
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-192572 (URN)10.15252/embj.2020106292 (DOI)000617216000001 ()33576519 (PubMedID)2-s2.0-85100839371 (Scopus ID)
Funder
Swedish Foundation for Strategic Research, FFL15:0325Ragnar Söderbergs stiftelse, M44/16Swedish Cancer Society, 2017/1041Knut and Alice Wallenberg Foundation, 2018.0080
Available from: 2021-04-28 Created: 2021-04-28 Last updated: 2022-08-11Bibliographically approved
Forsberg, B. O., Aibara, S., Howard, R. J., Mortezaei, N. & Lindahl, E. (2020). Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex. Nature Communications, 11(1), Article ID 4667.
Open this publication in new window or tab >>Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex
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2020 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4667Article in journal (Refereed) Published
Abstract [en]

The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-187333 (URN)10.1038/s41467-020-18401-z (DOI)000573778500013 ()32938938 (PubMedID)2-s2.0-85091128355 (Scopus ID)
Available from: 2020-12-14 Created: 2020-12-14 Last updated: 2023-03-28Bibliographically approved
Aibara, S., Singh, V., Modelska, A. & Amunts, A. (2020). Structural basis of mitochondrial translation. eLIFE, 9, Article ID e58362.
Open this publication in new window or tab >>Structural basis of mitochondrial translation
2020 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 9, article id e58362Article in journal (Refereed) Published
Abstract [en]

Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report similar to 3.0 angstrom resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-185337 (URN)10.7554/eLife.58362 (DOI)000563031000001 ()32812867 (PubMedID)
Available from: 2020-12-03 Created: 2020-12-03 Last updated: 2023-03-16Bibliographically approved
Bigalke, J. M., Aibara, S., Roth, R., Dahl, G., Gordon, E., Dorbéus, S., . . . Sandmark, J. (2019). Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain. Science Advances, 5(7), Article ID eaau4202.
Open this publication in new window or tab >>Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain
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2019 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 7, article id eaau4202Article in journal (Refereed) Published
Abstract [en]

Signaling through the receptor tyrosine kinase RET is essential during normal development. Both gain- and loss-of-function mutations are involved in a variety of diseases, yet the molecular details of receptor activation have remained elusive. We have reconstituted the complete extracellular region of the RET signaling complex together with Neurturin (NRTN) and GFR alpha 2 and determined its structure at 5.7-angstrom resolution by cryo-EM. The proteins form an assembly through RET-GFR alpha 2 and RET-NRTN interfaces. Two key interaction points required for RET extracellular domain binding were observed: (i) the calcium-binding site in RET that contacts GFR alpha 2 domain 3 and (ii) the RET cysteine-rich domain interaction with NRTN. The structure highlights the importance of the RET cysteine-rich domain and allows proposition of a model to explain how complex formation leads to RET receptor dimerization and its activation. This provides a framework for targeting RET activity and for further exploration of mechanisms underlying neurological diseases.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-171772 (URN)10.1126/sciadv.aau4202 (DOI)000478770400007 ()31392261 (PubMedID)
Available from: 2019-08-28 Created: 2019-08-28 Last updated: 2022-03-23Bibliographically approved
Aibara, S., Andréll, J., Singh, V. & Amunts, A. (2018). Rapid Isolation of the Mitoribosome from HEK Cells. Journal of Visualized Experiments (140), Article ID e57877.
Open this publication in new window or tab >>Rapid Isolation of the Mitoribosome from HEK Cells
2018 (English)In: Journal of Visualized Experiments, E-ISSN 1940-087X, no 140, article id e57877Article in journal (Refereed) Published
Abstract [en]

The human mitochondria possess a dedicated set of ribosomes (mitoribosomes) that translate 13 essential protein components of the oxidative phosphorylation complexes encoded by the mitochondria! genome. Since all proteins synthesized by human mitoribosomes are integral membrane proteins, human mitoribosomes are tethered to the mitochondrial inner membrane during translation. Compared to the cytosolic ribosome the mitoribosome has a sedimentation coefficient of 55S, half the rRNA content, no 5S rRNA and 36 additional proteins. Therefore, a higher protein-to-RNA ratio and an atypical structure make the human mitoribosome substantially distinct from its cytosolic counterpart. Despite the central importance of the mitoribosome to life, no protocols were available to purify the intact complex from human cell lines. Traditionally, mitoribosomes were isolated from mitochondria-rich animal tissues that required kilograms of starting material. We reasoned that mitochondria in dividing HEK293-derived human cells grown in nutrient-rich expression medium would have an active mitochondrial translation, and, therefore, could be a suitable source of material for the structural and biochemical studies of the mitoribosome. To investigate its structure, we developed a protocol for large-scale purification of intact mitoribosomes from HEK cells. Herein, we introduce nitrogen cavitation method as a faster, less labor-intensive and more efficient alternative to traditional mechanical shear-based methods for cell lysis. This resulted in preparations of the mitoribosome that allowed for its structural determination to high resolution, revealing the composition of the intact human mitoribosome and its assembly intermediates. Here, we follow up on this work and present an optimized and more cost-effective method requiring only similar to 10(10) cultured HEK cells. The method can be employed to purify human mitoribosomal translating complexes, mutants, quality control assemblies and mitoribosomal subunits intermediates. The purification can be linearly scaled up tenfold if needed, and also applied to other types of cells.

Keywords
Biochemistry, Issue 140, Mitochondria, translation, ribosome, cryo-EM, protein synthesis, biochemistry
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-166868 (URN)10.3791/57877 (DOI)000456452800018 ()30346389 (PubMedID)
Available from: 2019-03-06 Created: 2019-03-06 Last updated: 2024-01-17Bibliographically approved
Perez Boerema, A., Aibara, S., Paul, B., Tobiasson, V., Kimanius, D., Forsberg, B. O., . . . Amunts, A. (2018). Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor. Nature Plants, 4, 212-217
Open this publication in new window or tab >>Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
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2018 (English)In: Nature Plants, ISSN 2055-026X, Vol. 4, p. 212-217Article in journal (Refereed) Published
Abstract [en]

Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome1,2. Despite recent structural information3,4,5,6, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9–3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.

National Category
Biological Sciences Chemical Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-156633 (URN)10.1038/s41477-018-0129-6 (DOI)000430648300011 ()
Available from: 2018-05-28 Created: 2018-05-28 Last updated: 2022-02-26Bibliographically approved
Forsberg, B. O., Aibara, S., Kimanius, D., Paul, B., Lindahl, E. & Amunts, A. (2017). Cryo-EM reconstruction of the chlororibosome to 3.2 angstrom resolution within 24 h. IUCrJ, 4, 723-727
Open this publication in new window or tab >>Cryo-EM reconstruction of the chlororibosome to 3.2 angstrom resolution within 24 h
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2017 (English)In: IUCrJ, E-ISSN 2052-2525, Vol. 4, p. 723-727Article in journal (Refereed) Published
Abstract [en]

The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 angstrom resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 angstrom resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.

Keywords
cryo-EM, image processing, chlororibosome
National Category
Biological Sciences Chemical Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-149831 (URN)10.1107/S205225251701226X (DOI)000414266200004 ()29123673 (PubMedID)
Available from: 2017-12-13 Created: 2017-12-13 Last updated: 2022-09-28Bibliographically approved
Wiedmann, M. M., Tan, Y. S., Wu, Y., Aibara, S., Xu, W., Sore, H. F., . . . Spring, D. R. (2017). Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer. Angewandte Chemie International Edition, 56(2), 524-529
Open this publication in new window or tab >>Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer
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2017 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, no 2, p. 524-529Article in journal (Refereed) Published
Abstract [en]

There is a lack of current treatment options for ovarian clear cell carcinoma (CCC) and the cancer is often resistant to platinum-based chemotherapy. Hence there is an urgent need for novel therapeutics. The transcription factor hepatocyte nuclear factor 1 beta (HNF1 beta) is ubiquitously overexpressed in CCC and is seen as an attractive therapeutic target. This was validated through shRNA-mediated knockdown of the target protein, HNF1 beta, in five high-and low-HNF1 beta-expressing CCC lines. To inhibit the protein function, cellpermeable, non-helical constrained proteomimetics to target the HNF1 beta-importin a protein-protein interaction were designed, guided by X-ray crystallographic data and molecular dynamics simulations. In this way, we developed the first reported series of constrained peptide nuclear import inhibitors. Importantly, this general approach may be extended to other transcription factors.

Keywords
constrained peptides, drug discovery, nuclear import, peptide therapeutics, peptidomimetics
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-141397 (URN)10.1002/anie.201609427 (DOI)000394996100012 ()27918136 (PubMedID)
Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2022-03-23Bibliographically approved
Lehmann, L. C., Hewitt, G., Aibara, S., Leitner, A., Marklund, E., Maslen, S. L., . . . Deindl, S. (2017). Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1. Molecular Cell, 68(5), 847-859 (e7)
Open this publication in new window or tab >>Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1
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2017 (English)In: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 68, no 5, p. 847-859 (e7)Article in journal (Refereed) Published
Abstract [en]

Human ALC1 is an oncogene-encoded chromatin-remodeling enzyme required for DNA repair that possesses a poly(ADP-ribose) (PAR)-binding macro domain. Its engagement with PARylated PARP1 activates ALC1 at sites of DNA damage, but the underlying-mechanism remains unclear. Here, we establish a dual role for the macro domain in autoinhibition of ALC1 ATPase activity and coupling to nucleosome mobilization. In the absence of DNA damage, an inactive conformation of the ATPase is maintained by juxtaposition of the macro domain against predominantly the C-terminal ATPase lobe through conserved electrostatic interactions. Mutations within this interface displace the macro domain, constitutively activate the ALC1 ATPase independent of PARylated PARP1, and alter the dynamics of ALC1 recruitment at DNA damage sites. Upon DNA damage, binding of PARylated PARP1 by the macro domain induces a conformational change that relieves autoinhibitory interactions with the ATPase motor, which selectively activates ALC1 remodeling upon recruitment to sites of DNA damage.

Keywords
ATP-dependent chromatin remodeler, chromatin remodeling, allosteric regulation, allostery, ATPase, structure, macro domain, PARP, ADP-ribosylation, DNA repair
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-150983 (URN)10.1016/j.molcel.2017.10.017 (DOI)000417646500006 ()29220652 (PubMedID)
Available from: 2018-01-12 Created: 2018-01-12 Last updated: 2022-03-23Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-2221-482x

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