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Polyansky AA, Gallego LD, Efremov RG, Köhler A, Zagrovic B. Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales. eLife 2023; 12:e80038. [PMID: 37470705 PMCID: PMC10406433 DOI: 10.7554/elife.80038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/18/2023] [Indexed: 07/21/2023] Open
Abstract
Non-membrane-bound biomolecular condensates have been proposed to represent an important mode of subcellular organization in diverse biological settings. However, the fundamental principles governing the spatial organization and dynamics of condensates at the atomistic level remain unclear. The Saccharomyces cerevisiae Lge1 protein is required for histone H2B ubiquitination and its N-terminal intrinsically disordered fragment (Lge11-80) undergoes robust phase separation. This study connects single- and multi-chain all-atom molecular dynamics simulations of Lge11-80 with the in vitro behavior of Lge11-80 condensates. Analysis of modeled protein-protein interactions elucidates the key determinants of Lge11-80 condensate formation and links configurational entropy, valency, and compactness of proteins inside the condensates. A newly derived analytical formalism, related to colloid fractal cluster formation, describes condensate architecture across length scales as a function of protein valency and compactness. In particular, the formalism provides an atomistically resolved model of Lge11-80 condensates on the scale of hundreds of nanometers starting from individual protein conformers captured in simulations. The simulation-derived fractal dimensions of condensates of Lge11-80 and its mutants agree with their in vitro morphologies. The presented framework enables a multiscale description of biomolecular condensates and embeds their study in a wider context of colloid self-organization.
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Affiliation(s)
- Anton A Polyansky
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational BiologyViennaAustria
| | - Laura D Gallego
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| | - Roman G Efremov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
| | - Alwin Köhler
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Biochemistry and Cell BiologyViennaAustria
| | - Bojan Zagrovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational BiologyViennaAustria
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Gallego LD, Schneider M, Mittal C, Romanauska A, Gudino Carrillo RM, Schubert T, Pugh BF, Köhler A. Phase separation directs ubiquitination of gene-body nucleosomes. Nature 2020; 579:592-597. [PMID: 32214243 DOI: 10.1038/s41586-020-2097-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 02/11/2020] [Indexed: 11/10/2022]
Abstract
The conserved yeast E3 ubiquitin ligase Bre1 and its partner, the E2 ubiquitin-conjugating enzyme Rad6, monoubiquitinate histone H2B across gene bodies during the transcription cycle1. Although processive ubiquitination might-in principle-arise from Bre1 and Rad6 travelling with RNA polymerase II2, the mechanism of H2B ubiquitination across genic nucleosomes remains unclear. Here we implicate liquid-liquid phase separation3 as the underlying mechanism. Biochemical reconstitution shows that Bre1 binds the scaffold protein Lge1, which possesses an intrinsically disordered region that phase-separates via multivalent interactions. The resulting condensates comprise a core of Lge1 encapsulated by an outer catalytic shell of Bre1. This layered liquid recruits Rad6 and the nucleosomal substrate, which accelerates the ubiquitination of H2B. In vivo, the condensate-forming region of Lge1 is required to ubiquitinate H2B in gene bodies beyond the +1 nucleosome. Our data suggest that layered condensates of histone-modifying enzymes generate chromatin-associated 'reaction chambers', with augmented catalytic activity along gene bodies. Equivalent processes may occur in human cells, and cause neurological disease when impaired.
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Affiliation(s)
- Laura D Gallego
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Maren Schneider
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Chitvan Mittal
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, USA
| | - Anete Romanauska
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | | | - Tobias Schubert
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, USA
| | - Alwin Köhler
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.
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3
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Fischböck-Halwachs J, Singh S, Potocnjak M, Hagemann G, Solis-Mezarino V, Woike S, Ghodgaonkar-Steger M, Weissmann F, Gallego LD, Rojas J, Andreani J, Köhler A, Herzog F. The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore. eLife 2019; 8:42879. [PMID: 31112132 PMCID: PMC6546395 DOI: 10.7554/elife.42879] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/20/2019] [Indexed: 01/14/2023] Open
Abstract
Kinetochores are macromolecular protein complexes at centromeres that ensure accurate chromosome segregation by attaching chromosomes to spindle microtubules and integrating safeguard mechanisms. The inner kinetochore is assembled on CENP-A nucleosomes and has been implicated in establishing a kinetochore-associated pool of Aurora B kinase, a chromosomal passenger complex (CPC) subunit, which is essential for chromosome biorientation. By performing crosslink-guided in vitro reconstitution of budding yeast kinetochore complexes we showed that the Ame1/Okp1CENP-U/Q heterodimer, which forms the COMA complex with Ctf19/Mcm21CENP-P/O, selectively bound Cse4CENP-A nucleosomes through the Cse4 N-terminus. The Sli15/Ipl1INCENP/Aurora-B core-CPC interacted with COMA in vitro through the Ctf19 C-terminus whose deletion affected chromosome segregation fidelity in Sli15 wild-type cells. Tethering Sli15 to Ame1/Okp1 rescued synthetic lethality upon Ctf19 depletion in a Sli15 centromere-targeting deficient mutant. This study shows molecular characteristics of the point-centromere kinetochore architecture and suggests a role for the Ctf19 C-terminus in mediating CPC-binding and accurate chromosome segregation.
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Affiliation(s)
- Josef Fischböck-Halwachs
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sylvia Singh
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mia Potocnjak
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Götz Hagemann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victor Solis-Mezarino
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan Woike
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Medini Ghodgaonkar-Steger
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Laura D Gallego
- Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Julie Rojas
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alwin Köhler
- Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Franz Herzog
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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Turco E, Gallego LD, Schneider M, Köhler A. Monoubiquitination of histone H2B is intrinsic to the Bre1 RING domain-Rad6 interaction and augmented by a second Rad6-binding site on Bre1. J Biol Chem 2014; 290:5298-310. [PMID: 25548288 DOI: 10.1074/jbc.m114.626788] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin signaling on chromatin is linked to diverse aspects of genome regulation, including gene expression and DNA repair. The yeast RING E3 ligase Bre1 combines with the E2 Rad6 to monoubiquitinate histone H2B during transcription. Little is known about how Bre1 directs Rad6 toward transferring only a single ubiquitin to a specific lysine residue. Using a defined in vitro system, we show that the Bre1 RING domain interaction with Rad6 is minimally sufficient to monoubiquitinate nucleosomes at histone H2B Lys-123. In addition, we reveal a cluster of charged residues on the Bre1 RING domain that is critical for recognizing the nucleosome surface. Notably, a second Rad6 binding domain of Bre1 interacts with the E2 backside and potentiates ubiquitin transfer to the substrate. Taken together, our study establishes a molecular framework for how distinct RING and non-RING E3 elements cooperate to regulate E2 reactivity and substrate selection during gene expression.
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Affiliation(s)
- Eleonora Turco
- From the Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Laura D Gallego
- From the Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Maren Schneider
- From the Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Alwin Köhler
- From the Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
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López-Sánchez A, Jiménez-Fernández A, Calero P, Gallego LD, Govantes F. New methods for the isolation and characterization of biofilm-persistent mutants in Pseudomonas putida. Environ Microbiol Rep 2013; 5:679-685. [PMID: 24115618 DOI: 10.1111/1758-2229.12067] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/15/2013] [Indexed: 06/02/2023]
Abstract
Here we describe two new methods for the genetic characterization of bacterial biofilm development. First, we have designed a microtitre dish-based approach for high-throughput screening of Pseudomonas putida mutants showing increased biofilm under dispersal conditions. Using this method, nine such biofilm-persistent mutants, bearing transposon insertions in four loci: lapG, bifA, mvaB and dksA, were isolated. Second, we have developed a serial dilution-based scheme to monitor biofilm development and dispersal in microtitre dish wells in a simple, time-efficient and reproducible manner. Using this method, we showed that (i) mutants in bifA and dksA do not undergo starvation-induced biofilm dispersal in LB or minimal medium, (ii) a mvaB mutant does not disperse the biofilm in LB, but shows a normal dispersal response in minimal medium, and (iii) unlike the lapG mutant, the bifA, mvaB and dksA mutants do not show an increase in biofilm production. The procedures shown here are useful tools for the identification of previously uncharacterized biofilm-related genes and considerably simplify the characterization of biofilm growth phenotypes.
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Affiliation(s)
- Aroa López-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
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