1
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Ghadirian N, Morgan RD, Horton NC. DNA Sequence Control of Enzyme Filamentation and Activation of the SgrAI Endonuclease. Biochemistry 2024; 63:326-338. [PMID: 38207281 DOI: 10.1021/acs.biochem.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Enzyme polymerization (also known as filamentation) has emerged as a new layer of enzyme regulation. SgrAI is a sequence-dependent DNA endonuclease that forms polymeric filaments with enhanced DNA cleavage activity as well as altered DNA sequence specificity. To better understand this unusual regulatory mechanism, full global kinetic modeling of the reaction pathway, including the enzyme filamentation steps, has been undertaken. Prior work with the primary DNA recognition sequence cleaved by SgrAI has shown how the kinetic rate constants of each reaction step are tuned to maximize activation and DNA cleavage while minimizing the extent of DNA cleavage to the host genome. In the current work, we expand on our prior study by now including DNA cleavage of a secondary recognition sequence, to understand how the sequence of the bound DNA modulates filamentation and activation of SgrAI. The work shows that an allosteric equilibrium between low and high activity states is modulated by the sequence of bound DNA, with primary sequences more prone to activation and filament formation, while SgrAI bound to secondary recognition sequences favor the low (and nonfilamenting) state by up to 40-fold. In addition, the degree of methylation of secondary sequences in the host organism, Streptomyces griseus, is now reported for the first time and shows that as predicted, these sequences are left unprotected from the SgrAI endonuclease making sequence specificity critical in this unusual filament-forming enzyme.
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Affiliation(s)
- Niloofar Ghadirian
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Richard D Morgan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
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2
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Nandana V, Rathnayaka-Mudiyanselage IW, Muthunayak NS, Hatami A, Mousseau CB, Ortiz-Rodríguez LA, Vaishnav J, Collins M, Gega A, Mallikaarachchi KS, Yassine H, Ghosh A, Biteen JS, Zhu Y, Champion MM, Childers WS, Schrader JM. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524314. [PMID: 36712072 PMCID: PMC9882336 DOI: 10.1101/2023.01.18.524314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bacterial RNP bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We found 111 BR-body enriched proteins, including several RNA binding proteins, many of which are also recruited directly to in vitro reconstituted RNase E droplets, showing BR-bodies are more complex than previously assumed. While most BR-body enriched proteins that were tested cannot phase separate, we identified five that undergo RNA-dependent phase separation in vitro, showing other RNP condensates interface with BR-bodies. RNA degradosome protein clients are recruited more strongly to RNase E droplets than droplets of other RNP condensates, implying that client specificity is largely achieved through direct protein-protein interactions. We observe that some RNP condensates assemble with preferred directionally, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body associated proteins have the capacity to dissolve the condensate. Finally, we find that RNA dramatically stimulates the rate of RNase E phase separation in vitro, explaining the dissolution of BR-bodies after cellular mRNA depletion observed previously. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing.
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Affiliation(s)
- V Nandana
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - I W Rathnayaka-Mudiyanselage
- Wayne State University, Department of Biological Sciences, Detroit, MI
- Wayne State University, Department of Chemistry, Detroit, MI
| | - N S Muthunayak
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - A Hatami
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - C B Mousseau
- University of Notre Dame, Department of Chemistry, Notre Dame, IN
| | | | - J Vaishnav
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - M Collins
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA
| | - A Gega
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | | | - H Yassine
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - A Ghosh
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - J S Biteen
- University of Michigan, Department of Chemistry, Ann Arbor, MI
| | - Y Zhu
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - M M Champion
- University of Notre Dame, Department of Chemistry, Notre Dame, IN
| | - W S Childers
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA
| | - J M Schrader
- Wayne State University, Department of Biological Sciences, Detroit, MI
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3
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Synchronized Swarmers and Sticky Stalks: Caulobacter crescentus as a Model for Bacterial Cell Biology. J Bacteriol 2023; 205:e0038422. [PMID: 36715542 PMCID: PMC9945503 DOI: 10.1128/jb.00384-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.
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4
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The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. Biochem Soc Trans 2022; 50:1703-1714. [PMID: 36398769 PMCID: PMC9788392 DOI: 10.1042/bst20220547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein-DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.
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5
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Quintero-Yanes A, Mayard A, Hallez R. The two-component system ChvGI maintains cell envelope homeostasis in Caulobacter crescentus. PLoS Genet 2022; 18:e1010465. [PMID: 36480504 PMCID: PMC9731502 DOI: 10.1371/journal.pgen.1010465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/09/2022] [Indexed: 12/13/2022] Open
Abstract
Two-component systems (TCS) are often used by bacteria to rapidly assess and respond to environmental changes. The ChvG/ChvI (ChvGI) TCS conserved in α-proteobacteria is known for regulating expression of genes related to exopolysaccharide production, virulence and growth. The sensor kinase ChvG autophosphorylates upon yet unknown signals and phosphorylates the response regulator ChvI to regulate transcription. Recent studies in Caulobacter crescentus showed that chv mutants are sensitive to vancomycin treatment and fail to grow in synthetic minimal media. In this work, we identified the osmotic imbalance as the main cause of growth impairment in synthetic minimal media. We also determined the ChvI regulon and found that ChvI regulates cell envelope architecture by controlling outer membrane, peptidoglycan assembly/recycling and inner membrane proteins. In addition, we found that ChvI phosphorylation is also activated upon antibiotic treatment with vancomycin. We also challenged chv mutants with other cell envelope related stress and found that treatment with antibiotics targeting transpeptidation of peptidoglycan during cell elongation impairs growth of the mutant. Finally, we observed that the sensor kinase ChvG relocates from a patchy-spotty distribution to distinctive foci after transition from complex to synthetic minimal media. Interestingly, this pattern of (re)location has been described for proteins involved in cell growth control and peptidoglycan synthesis upon osmotic shock. Overall, our data support that the ChvGI TCS is mainly used to monitor and respond to osmotic imbalances and damages in the peptidoglycan layer to maintain cell envelope homeostasis.
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Affiliation(s)
- Alex Quintero-Yanes
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
| | - Aurélie Mayard
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
| | - Régis Hallez
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
- WELBIO, University of Namur, Namur, Belgium
- * E-mail:
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6
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Tan W, Cheng S, Li Y, Li XY, Lu N, Sun J, Tang G, Yang Y, Cai K, Li X, Ou X, Gao X, Zhao GP, Childers WS, Zhao W. Phase separation modulates the assembly and dynamics of a polarity-related scaffold-signaling hub. Nat Commun 2022; 13:7181. [PMID: 36418326 PMCID: PMC9684454 DOI: 10.1038/s41467-022-35000-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Asymmetric cell division (ACD) produces morphologically and behaviorally distinct cells and is the primary way to generate cell diversity. In the model bacterium Caulobacter crescentus, the polarization of distinct scaffold-signaling hubs at the swarmer and stalked cell poles constitutes the basis of ACD. However, mechanisms involved in the formation of these hubs remain elusive. Here, we show that a swarmer-cell-pole scaffold, PodJ, forms biomolecular condensates both in vitro and in living cells via phase separation. The coiled-coil 4-6 and the intrinsically disordered regions are the primary domains that contribute to biomolecular condensate generation and signaling protein recruitment in PodJ. Moreover, a negative regulation of PodJ phase separation by the stalked-cell-pole scaffold protein SpmX is revealed. SpmX impedes PodJ cell-pole accumulation and affects its recruitment ability. Together, by modulating the assembly and dynamics of scaffold-signaling hubs, phase separation may serve as a general biophysical mechanism that underlies the regulation of ACD in bacteria and other organisms.
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Affiliation(s)
- Wei Tan
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Sihua Cheng
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Yingying Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Xiao-Yang Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.256922.80000 0000 9139 560XDepartment of Pharmacy, School of Life Sciences, Henan University, Kaifeng, 475004 China
| | - Ning Lu
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Jingxian Sun
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Guiyue Tang
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Yujiao Yang
- grid.9227.e0000000119573309CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kezhu Cai
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.263817.90000 0004 1773 1790Department of Materials Science and Engineering, School of Engineering, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xuefei Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Xijun Ou
- grid.263817.90000 0004 1773 1790Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xiang Gao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Guo-Ping Zhao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.9227.e0000000119573309CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443State Key Lab of Genetic Engineering & Institutes of Biomedical Sciences, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - W. Seth Childers
- grid.21925.3d0000 0004 1936 9000Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Wei Zhao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
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7
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Spatiotemporal localization of proteins in mycobacteria. Cell Rep 2021; 37:110154. [PMID: 34965429 PMCID: PMC8861988 DOI: 10.1016/j.celrep.2021.110154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 01/10/2023] Open
Abstract
Although prokaryotic organisms lack traditional organelles, they must still organize cellular structures in space and time, challenges that different species solve differently. To systematically define the subcellular architecture of mycobacteria, we perform high-throughput imaging of a library of fluorescently tagged proteins expressed in Mycobacterium smegmatis and develop a customized computational pipeline, MOMIA and GEMATRIA, to analyze these data. Our results establish a spatial organization network of over 700 conserved mycobacterial proteins and reveal a coherent localization pattern for many proteins of known function, including those in translation, energy metabolism, cell growth and division, as well as proteins of unknown function. Furthermore, our pipeline exploits morphologic proxies to enable a pseudo-temporal approximation of protein localization and identifies previously uncharacterized cell-cycle-dependent dynamics of essential mycobacterial proteins. Collectively, these data provide a systems perspective on the subcellular organization of mycobacteria and provide tools for the analysis of bacteria with non-standard growth characteristics. Zhu et al. develop a two-stage image analysis pipeline, MOMIA and GEMATRIA, that efficiently models the spatial and temporal dynamics of over 700 conserved proteins in M. smegmatis. Through the analysis they report spatial constraints of mycobacterial ribosomes and membrane complexes and reconstruct temporal dynamics from still image data.
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8
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Ishikawa F, Konno S, Takashima K, Kakeya H, Tanabe G. Inhibition of efflux pumps aids small-molecule probe-based fluorescence labeling and imaging in the Gram-negative bacterium Escherichia coli. Org Biomol Chem 2021; 19:8906-8911. [PMID: 34704577 DOI: 10.1039/d1ob01112j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A major challenge in fluorescence imaging experiments, which are essential to determine protein activity, expression, and localization, is the penetration of small-molecule probes through the outer membrane permeability barrier of bacteria. Here, we describe a novel strategy for small-molecule probe-based fluorescence protein labeling and imaging in the Gram-negative bacterium Escherichia coli. We targeted a siderophore enterobactin biosynthetic enzyme EntE in E. coli. When coupled with an efflux pump inhibitor carbonyl cyanide m-chlorophenylhydrazone, small-molecule probes were able to efficiently enter the cells, leading to the fluorescence labeling and imaging of overproduced EntE in E. coli. This study demonstrates that the combination of small-molecule probes with appropriate efflux pump inhibitors may substantially enhance their interaction with the target proteins in live bacteria.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
| | - Sho Konno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Katsuki Takashima
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
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9
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Gao Z, Zhang W, Chang R, Zhang S, Yang G, Zhao G. Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells. Front Microbiol 2021; 12:751880. [PMID: 34759902 PMCID: PMC8573418 DOI: 10.3389/fmicb.2021.751880] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS.
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Affiliation(s)
| | | | | | | | - Guiwen Yang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guoyan Zhao
- College of Life Science, Shandong Normal University, Jinan, China
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10
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Jeckel H, Drescher K. Advances and opportunities in image analysis of bacterial cells and communities. FEMS Microbiol Rev 2021; 45:fuaa062. [PMID: 33242074 PMCID: PMC8371272 DOI: 10.1093/femsre/fuaa062] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022] Open
Abstract
The cellular morphology and sub-cellular spatial structure critically influence the function of microbial cells. Similarly, the spatial arrangement of genotypes and phenotypes in microbial communities has important consequences for cooperation, competition, and community functions. Fluorescence microscopy techniques are widely used to measure spatial structure inside living cells and communities, which often results in large numbers of images that are difficult or impossible to analyze manually. The rapidly evolving progress in computational image analysis has recently enabled the quantification of a large number of properties of single cells and communities, based on traditional analysis techniques and convolutional neural networks. Here, we provide a brief introduction to core concepts of automated image processing, recent software tools and how to validate image analysis results. We also discuss recent advances in image analysis of microbial cells and communities, and how these advances open up opportunities for quantitative studies of spatiotemporal processes in microbiology, based on image cytometry and adaptive microscope control.
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Affiliation(s)
- Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
- Synmikro Center for Synthetic Microbiology, Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
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11
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Skinnider MA, Foster LJ. Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments. Nat Methods 2021; 18:806-815. [PMID: 34211188 DOI: 10.1038/s41592-021-01194-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
Co-fractionation mass spectrometry (CF-MS) has emerged as a powerful technique for interactome mapping. However, there is little consensus on optimal strategies for the design of CF-MS experiments or their computational analysis. Here, we reanalyzed a total of 206 CF-MS experiments to generate a uniformly processed resource containing over 11 million measurements of protein abundance. We used this resource to benchmark experimental designs for CF-MS studies and systematically optimize computational approaches to network inference. We then applied this optimized methodology to reconstruct a draft-quality human interactome by CF-MS and predict over 700,000 protein-protein interactions across 27 eukaryotic species or clades. Our work defines new resources to illuminate proteome organization over evolutionary timescales and establishes best practices for the design and analysis of CF-MS studies.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. .,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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12
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Zhu L, Rajendram M, Huang KC. Effects of fixation on bacterial cellular dimensions and integrity. iScience 2021; 24:102348. [PMID: 33912815 PMCID: PMC8066382 DOI: 10.1016/j.isci.2021.102348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/25/2021] [Accepted: 03/18/2021] [Indexed: 11/22/2022] Open
Abstract
Fixation facilitates imaging of subcellular localization and cell morphology, yet it remains unknown how fixation affects cellular dimensions and intracellular fluorescence patterns, particularly during long-term storage. Here, we characterized the effects of multiple fixatives on several bacterial species. Fixation generally reduced cell length by 5-15%; single-cell tracking in microfluidics revealed that the length decrease was an aggregate effect of many steps in the fixation protocol and that fluorescence of cytoplasmic GFP but not membrane-bound MreB-msfGFP was rapidly lost with formaldehyde-based fixatives. Cellular dimensions were preserved in formaldehyde-based fixatives for ≥4 days, but methanol caused length to decrease. Although methanol preserved cytoplasmic fluorescence better than formaldehyde-based fixatives, some Escherichia coli cells were able to grow directly after fixation. Moreover, methanol fixation caused lysis in a subpopulation of cells, with virtually all Bacillus subtilis cells lysing after one day. These findings highlight tradeoffs between maintenance of fluorescence and membrane integrity for future applications of fixation.
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Affiliation(s)
- Lillian Zhu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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13
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Judd JA, Canestrari J, Clark R, Joseph A, Lapierre P, Lasek-Nesselquist E, Mir M, Palumbo M, Smith C, Stone M, Upadhyay A, Wirth SE, Dedrick RM, Meier CG, Russell DA, Dills A, Dove E, Kester J, Wolf ID, Zhu J, Rubin ER, Fortune S, Hatfull GF, Gray TA, Wade JT, Derbyshire KM. A Mycobacterial Systems Resource for the Research Community. mBio 2021; 12:e02401-20. [PMID: 33653882 PMCID: PMC8092266 DOI: 10.1128/mbio.02401-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulceransIMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.
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Affiliation(s)
- J A Judd
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - J Canestrari
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - R Clark
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - A Joseph
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - P Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - E Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Mir
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Palumbo
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - C Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Stone
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - A Upadhyay
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - S E Wirth
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - R M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - C G Meier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - D A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - A Dills
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - E Dove
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - J Kester
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - I D Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - J Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - E R Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - S Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - G F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - T A Gray
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - J T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - K M Derbyshire
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
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14
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Abstract
Bacteria possess a sophisticated arsenal of defense mechanisms that allow them to survive in adverse conditions. Adaptation to acid stress and hypoxia is crucial for the enterobacterial transmission in the gastrointestinal tract of their human host. When subjected to low pH, Escherichia coli and many other enterobacteria activate a proton-consuming resistance system based on the acid stress-inducible lysine decarboxylase LdcI. Here we develop generally applicable tools to uncover the spatial localization of LdcI inside the cell by superresolution fluorescence microscopy and investigate the in vitro supramolecular organization of this enzyme by cryo-EM. We build on these results to propose a mechanistic model for LdcI function and offer tools for further in vivo investigations. Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid stress-response regulation of Escherichia coli LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localization of nanobody-labeled endogenous wild-type LdcI in acid-stressed E. coli cells and show that it organizes into distinct patches at the cell periphery. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerization as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-EM and reveal the molecular determinants of LdcI polymerization, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organization in the acid stress response.
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15
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Nordyke CT, Ahmed YM, Puterbaugh RZ, Bowman GR, Varga K. Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature. J Mol Biol 2020; 432:6092-6107. [PMID: 33058876 DOI: 10.1016/j.jmb.2020.09.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 11/15/2022]
Abstract
The polar organizing protein Z (PopZ) is necessary for the formation of three-dimensional microdomains at the cell poles in Caulobacter crescentus, where it functions as a hub protein that recruits multiple regulatory proteins from the cytoplasm. Although a large portion of the protein is predicted to be natively unstructured, in reconstituted systems PopZ can self-assemble into a macromolecular scaffold that directly binds to at least ten different proteins. Here we report the solution NMR structure of PopZΔ134-177, a truncated form of PopZ that does not self-assemble but retains the ability to interact with heterologous proteins. We show that the unbound form of PopZΔ134-177 is unstructured in solution, with the exception of a small amphipathic α-helix in residues M10-I17, which is included within a highly conserved region near the N-terminal. In applying NMR techniques to map the interactions between PopZΔ134-177 and one of its binding partners, RcdA, we find evidence that the α-helix and adjoining amino acids extending to position E23 serve as the core of the binding motif. Consistent with this, a point mutation at position I17 severely compromises binding. Our results show that a partially structured Molecular Recognition Feature (MoRF) within an intrinsically disordered domain of PopZ contributes to the assembly of polar microdomains, revealing a structural basis for complex network assembly in Alphaproteobacteria that is analogous to those formed by intrinsically disordered hub proteins in other kingdoms.
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Affiliation(s)
- Christopher T Nordyke
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Yasin M Ahmed
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, United States
| | - Ryan Z Puterbaugh
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Grant R Bowman
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, United States.
| | - Krisztina Varga
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States.
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16
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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17
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Herrero E, Stinus S, Bellows E, Berry LK, Wood H, Thorpe PH. Asymmetric Transcription Factor Partitioning During Yeast Cell Division Requires the FACT Chromatin Remodeler and Cell Cycle Progression. Genetics 2020; 216:701-716. [PMID: 32878900 PMCID: PMC7648576 DOI: 10.1534/genetics.120.303439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022] Open
Abstract
The polarized partitioning of proteins in cells underlies asymmetric cell division, which is an important driver of development and cellular diversity. The budding yeast Saccharomyces cerevisiae divides asymmetrically, like many other cells, to generate two distinct progeny cells. A well-known example of an asymmetric protein is the transcription factor Ace2, which localizes specifically to the daughter nucleus, where it drives a daughter-specific transcriptional network. We screened a collection of essential genes to analyze the effects of core cellular processes in asymmetric cell division based on Ace2 localization. This screen identified mutations that affect progression through the cell cycle, suggesting that cell cycle delay is sufficient to disrupt Ace2 asymmetry. To test this model, we blocked cells from progressing through mitosis and found that prolonged metaphase delay is sufficient to disrupt Ace2 asymmetry after release, and that Ace2 asymmetry is restored after cytokinesis. We also demonstrate that members of the evolutionarily conserved facilitates chromatin transcription (FACT) chromatin-reorganizing complex are required for both asymmetric and cell cycle-regulated localization of Ace2, and for localization of the RAM network components.
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Affiliation(s)
- Eva Herrero
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Sonia Stinus
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UT3, 31062, France
| | - Eleanor Bellows
- School of Biosciences, The University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
| | - Lisa K Berry
- School of Biological and Chemical Sciences, Queen Mary, University of London, E1 4NS, United Kingdom
| | - Henry Wood
- School of Biological and Chemical Sciences, Queen Mary, University of London, E1 4NS, United Kingdom
| | - Peter H Thorpe
- School of Biological and Chemical Sciences, Queen Mary, University of London, E1 4NS, United Kingdom
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18
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AimB Is a Small Protein Regulator of Cell Size and MreB Assembly. Biophys J 2020; 119:593-604. [PMID: 32416080 DOI: 10.1016/j.bpj.2020.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022] Open
Abstract
The MreB actin-like cytoskeleton assembles into dynamic polymers that coordinate cell shape in many bacteria. In contrast to most other cytoskeleton systems, few MreB-interacting proteins have been well characterized. Here, we identify a small protein from Caulobacter crescentus, an assembly inhibitor of MreB (AimB). AimB overexpression mimics inhibition of MreB polymerization, leading to increased cell width and MreB delocalization. Furthermore, aimB appears to be essential, and its depletion results in decreased cell width and increased resistance to A22, a small-molecule inhibitor of MreB assembly. Molecular dynamics simulations suggest that AimB binds MreB at its monomer-monomer protofilament interaction cleft and that this interaction is favored for C. crescentus MreB over Escherichia coli MreB because of a closer match in the degree of opening with AimB size, suggesting coevolution of AimB with MreB conformational dynamics in C. crescentus. We support this model through functional analysis of point mutants in both AimB and MreB, photo-cross-linking studies with site-specific unnatural amino acids, and species-specific activity of AimB. Together, our findings are consistent with AimB promoting MreB dynamics by inhibiting monomer-monomer assembly interactions, representing a new mechanism for regulating actin-like polymers and the first identification of a non-toxin MreB assembly inhibitor. Because AimB has only 104 amino acids and small proteins are often poorly characterized, our work suggests the possibility of more bacterial cytoskeletal regulators to be found in this class. Thus, like FtsZ and eukaryotic actin, MreB may have a rich repertoire of regulators to tune its precise assembly and dynamics.
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19
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Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation. Proc Natl Acad Sci U S A 2020; 117:18540-18549. [PMID: 32675239 PMCID: PMC7414142 DOI: 10.1073/pnas.2005019117] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid–liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid–liquid phase separation is a common mechanism for intracellular organization in both eukaryotic and prokaryotic cells. Once described as mere “bags of enzymes,” bacterial cells are in fact highly organized, with many macromolecules exhibiting nonuniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid–liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in Escherichia coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and demonstrates that this process can serve as a mechanism for intracellular organization in prokaryotes and eukaryotes alike.
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20
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Blocher McTigue WC, Perry SL. Protein Encapsulation Using Complex Coacervates: What Nature Has to Teach Us. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1907671. [PMID: 32363758 DOI: 10.1002/smll.201907671] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 06/11/2023]
Abstract
Protein encapsulation is a growing area of interest, particularly in the fields of food science and medicine. The sequestration of protein cargoes is achieved using a variety of methods, each with benefits and drawbacks. One of the most significant challenges associated with protein encapsulation is achieving high loading while maintaining protein viability. This difficulty is exacerbated because many encapsulant systems require the use of organic solvents. By contrast, nature has optimized strategies to compartmentalize and protect proteins inside the cell-a purely aqueous environment. Although the mechanisms whereby aspects of the cytosol is able to stabilize proteins are unknown, the crowded nature of many newly discovered, liquid phase separated "membraneless organelles" that achieve protein compartmentalization suggests that the material environment surrounding the protein may be critical in determining stability. Here, encapsulation strategies based on liquid-liquid phase separation, and complex coacervation in particular, which has many of the key features of the cytoplasm as a material, are reviewed. The literature on protein encapsulation via coacervation is also reviewed and the parameters relevant to creating protein-containing coacervate formulations are discussed. Additionally, potential opportunities associated with the creation of tailored materials to better facilitate protein encapsulation and stabilization are highlighted.
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Affiliation(s)
| | - Sarah L Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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21
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Kerr CH, Skinnider MA, Andrews DDT, Madero AM, Chan QWT, Stacey RG, Stoynov N, Jan E, Foster LJ. Dynamic rewiring of the human interactome by interferon signaling. Genome Biol 2020; 21:140. [PMID: 32539747 PMCID: PMC7294662 DOI: 10.1186/s13059-020-02050-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulated genes have been established across species and cell types by transcriptomic and biochemical approaches, but their antiviral mechanisms remain incompletely characterized. Here, we apply a combination of quantitative proteomic approaches to describe the effects of IFN signaling on the human proteome, and apply protein correlation profiling to map IFN-induced rearrangements in the human protein-protein interaction network. RESULTS We identify > 26,000 protein interactions in IFN-stimulated and unstimulated cells, many of which involve proteins associated with human disease and are observed exclusively within the IFN-stimulated network. Differential network analysis reveals interaction rewiring across a surprisingly broad spectrum of cellular pathways in the antiviral response. We identify IFN-dependent protein-protein interactions mediating novel regulatory mechanisms at the transcriptional and translational levels, with one such interaction modulating the transcriptional activity of STAT1. Moreover, we reveal IFN-dependent changes in ribosomal composition that act to buffer IFN-stimulated gene protein synthesis. CONCLUSIONS Our map of the IFN interactome provides a global view of the complex cellular networks activated during the antiviral response, placing IFN-stimulated genes in a functional context, and serves as a framework to understand how these networks are dysregulated in autoimmune or inflammatory disease.
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Affiliation(s)
- Craig H Kerr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Current Address: Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Daniel D T Andrews
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Angel M Madero
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Queenie W T Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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22
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Tn FLX: a Third-Generation mariner-Based Transposon System for Bacillus subtilis. Appl Environ Microbiol 2020; 86:AEM.02893-19. [PMID: 32169936 DOI: 10.1128/aem.02893-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/26/2020] [Indexed: 01/05/2023] Open
Abstract
Random transposon mutagenesis is a powerful and unbiased genetic approach to answer fundamental biological questions. Here, we introduce an improved mariner-based transposon system with enhanced stability during propagation and versatile applications in mutagenesis. We used a low-copy-number plasmid as a transposon delivery vehicle, which affords a lower frequency of unintended recombination during vector construction and propagation in Escherichia coli We generated a variety of transposons allowing for gene disruption or artificial overexpression, each in combination with one of four different antibiotic resistance markers. In addition, we provide transposons that will report gene/protein expression due to transcriptional or translational coupling. We believe that the TnFLX system will help enhance the flexibility of future transposon modification and application in Bacillus and other organisms.IMPORTANCE The stability of transposase-encoding vectors during cloning and propagation is crucial for the reliable application of transposons. Here, we increased the stability of the mariner delivery vehicle in E. coli Moreover, the TnFLX transposon system will improve the application of forward genetic methods with an increased number of antibiotic resistance markers and the ability to generate unbiased green fluorescent protein (GFP) fusions to report on protein translation and subcellular localization.
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23
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ImageJ for Partially and Fully Automated Analysis of Trypanosome Micrographs. Methods Mol Biol 2020. [PMID: 32221933 DOI: 10.1007/978-1-0716-0294-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Trypanosomes and related parasites such as Leishmania are unicellular parasites with a precise internal structure. This makes light microscopy a powerful tool for interrogating their biology-whether considering advance techniques for visualizing the precise localization of proteins within the cell or simply measuring parasite cell shape. Methods to partially or fully automate analysis and interpretation are extremely powerful and provide easier access to microscope images as a source of quantitative data. This chapter provides an introduction to these methods using ImageJ/FIJI, free and open source software for scientific image analysis. It provides an overview of how ImageJ handles images and introduces the ImageJ macro/scripting language for automated images, starting at a basic level and assuming no previous programming/scripting experience. It then outlines three methods using ImageJ for automated analysis of trypanosome micrographs: Semiautomated cropping and setting image contrast for presentation, automated analysis of cell properties from a light micrograph field of view, and example semiautomated tools for quantitative analysis of protein localization. These are not presented as strict methods, but are instead described in detail with the intention of furnishing the reader with the ability to "hack" the scripts for their own needs or write their own scripts for partially and fully automated quantitation of trypanosomes from light micrographs. Most of the methods described here are transferrable to other types of microscope image and other cell types.
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24
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Sing CE, Perry SL. Recent progress in the science of complex coacervation. SOFT MATTER 2020; 16:2885-2914. [PMID: 32134099 DOI: 10.1039/d0sm00001a] [Citation(s) in RCA: 296] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Complex coacervation is an associative, liquid-liquid phase separation that can occur in solutions of oppositely-charged macromolecular species, such as proteins, polymers, and colloids. This process results in a coacervate phase, which is a dense mix of the oppositely-charged components, and a supernatant phase, which is primarily devoid of these same species. First observed almost a century ago, coacervates have since found relevance in a wide range of applications; they are used in personal care and food products, cutting edge biotechnology, and as a motif for materials design and self-assembly. There has recently been a renaissance in our understanding of this important class of material phenomena, bringing the science of coacervation to the forefront of polymer and colloid science, biophysics, and industrial materials design. In this review, we describe the emergence of a number of these new research directions, specifically in the context of polymer-polymer complex coacervates, which are inspired by a number of key physical and chemical insights and driven by a diverse range of experimental, theoretical, and computational approaches.
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Affiliation(s)
- Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews, Urbana, IL, USA.
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25
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Johnson MC, Kollman JM. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. eLife 2020; 9:e53243. [PMID: 31999252 PMCID: PMC7018514 DOI: 10.7554/elife.53243] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.
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Affiliation(s)
- Matthew C Johnson
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
| | - Justin M Kollman
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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Polley S, Lyumkis D, Horton NC. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. Structure 2019; 27:1497-1507.e3. [PMID: 31447289 DOI: 10.1016/j.str.2019.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/10/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
Filament formation by enzymes is increasingly recognized as an important phenomenon with potentially unique regulatory properties and biological roles. SgrAI is an allosterically regulated type II restriction endonuclease that forms filaments with enhanced DNA cleavage activity and altered sequence specificity. Here, we present the cryoelectron microscopy (cryo-EM) structure of the filament of SgrAI in its activated configuration. The structural data illuminate the mechanistic origin of hyperaccelerated DNA cleavage activity and suggests how indirect DNA sequence readout within filamentous SgrAI may enable recognition of substantially more nucleotide sequences than its low-activity form, thereby altering and partially relaxing its DNA sequence specificity. Together, substrate DNA binding, indirect readout, and filamentation simultaneously enhance SgrAI's catalytic activity and modulate substrate preference. This unusual enzyme mechanism may have evolved to perform the specialized functions of bacterial innate immunity in rapid defense against invading phage DNA without causing damage to the host DNA.
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Affiliation(s)
- Smarajit Polley
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Dmitry Lyumkis
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA.
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Inducible asymmetric cell division and cell differentiation in a bacterium. Nat Chem Biol 2019; 15:925-931. [PMID: 31406376 PMCID: PMC7439754 DOI: 10.1038/s41589-019-0340-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 07/08/2019] [Indexed: 12/14/2022]
Abstract
Multicellular organisms achieve greater complexity through cell divisions that generate different cell types. We engineered a simple genetic circuit that induces asymmetric cell division and subsequent cell differentiation in Escherichia coli. The circuit involves a scaffolding protein, PopZ, that is stably maintained at a single cell pole over multiple asymmetric cell divisions. PopZ was functionalized to degrade the signaling molecule, c-di-GMP. By regulating synthesis of functionalized PopZ via small molecules or light, we can chemically or optogenetically control the relative abundance of two distinct cell types, characterized by either low or high c-di-GMP levels. Differences in c-di-GMP levels can be transformed into genetically programmable differences in protein complex assembly or gene expression, which in turn produce differential behavior or biosynthetic activities. This study shows emergence of complex biological phenomena from a simple genetic circuit and adds programmable bacterial cell differentiation to the genetic toolbox of synthetic biology and biotechnology.
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Yildirim A, Feig M. High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization. Nucleic Acids Res 2019. [PMID: 29529244 PMCID: PMC5934669 DOI: 10.1093/nar/gky141] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-resolution three-dimensional models of Caulobacter crescentus nucleoid structures were generated via a multi-scale modeling protocol. Models were built as a plectonemically supercoiled circular DNA and by incorporating chromosome conformation capture based data to generate an ensemble of base pair resolution models consistent with the experimental data. Significant structural variability was found with different degrees of bending and twisting but with overall similar topologies and shapes that are consistent with C. crescentus cell dimensions. The models allowed a direct mapping of the genomic sequence onto the three-dimensional nucleoid structures. Distinct spatial distributions were found for several genomic elements such as AT-rich sequence elements where nucleoid associated proteins (NAPs) are likely to bind, promoter sites, and some genes with common cellular functions. These findings shed light on the correlation between the spatial organization of the genome and biological functions.
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Affiliation(s)
- Asli Yildirim
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, Michigan State University, MI 48824, USA
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Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B 12 Scavenging. mSystems 2019; 4:4/4/e00170-19. [PMID: 31138672 PMCID: PMC6538847 DOI: 10.1128/msystems.00170-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Caulobacter crescentus is a model system of the bacterial cell cycle culminating in asymmetric cell division, with each daughter cell inheriting a distinct set of proteins. While a genetic network of master transcription factors coordinates the cell cycle timing of transcription for nearly 20% of Caulobacter genes, we lack knowledge of how many of each protein “part” encoded in the genome are synthesized. Therefore, to determine the absolute production rates across the genome, we performed ribosome profiling, providing, for the first time, a quantitative resource with measurements of each protein “part” needed to generate daughter cells. This resource furthers the goal of a systems-level understanding of the genetic network controlling asymmetric cell division. To highlight the utility of this data set, we probe the protein synthesis cost of a B12 utilization pathway and provide new insights into Caulobacter’s adaptation to its natural environments. Caulobacter crescentus is a model for the bacterial cell cycle which culminates in asymmetric cell division, yet little is known about the absolute levels of protein synthesis of the cellular parts needed to complete the cell cycle. Here we utilize ribosome profiling to provide absolute measurements of mRNA translation in C. crescentus, providing an important resource with quantitative genome-wide measurements of protein output across individual genes. Analysis of protein synthesis rates revealed ∼4.5% of cellular protein synthesis is for genes related to vitamin B12 import (btuB) and B12-independent methionine biosynthesis (metE) when grown in common growth media lacking B12. While its facultative B12 lifestyle provides a fitness advantage in the absence of B12, we find that it provides a fitness disadvantage of the cells in the presence of B12, potentially explaining why many Caulobacter species have lost the metE gene and become obligates for B12. IMPORTANCECaulobacter crescentus is a model system of the bacterial cell cycle culminating in asymmetric cell division, with each daughter cell inheriting a distinct set of proteins. While a genetic network of master transcription factors coordinates the cell cycle timing of transcription for nearly 20% of Caulobacter genes, we lack knowledge of how many of each protein “part” encoded in the genome are synthesized. Therefore, to determine the absolute production rates across the genome, we performed ribosome profiling, providing, for the first time, a quantitative resource with measurements of each protein “part” needed to generate daughter cells. This resource furthers the goal of a systems-level understanding of the genetic network controlling asymmetric cell division. To highlight the utility of this data set, we probe the protein synthesis cost of a B12 utilization pathway and provide new insights into Caulobacter’s adaptation to its natural environments. Author Video: An author video summary of this article is available.
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Passaris I, Tadesse WM, Gayán E, Aertsen A. Construction and validation of the Tn5-P LtetO-1-msfGFP transposon as a tool to probe protein expression and localization. J Microbiol Methods 2019; 161:56-62. [PMID: 31004623 DOI: 10.1016/j.mimet.2019.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 11/28/2022]
Abstract
In this study we report the design, construction and validation of a novel transposon aimed to systematically screen for protein localization and expression patterns in prokaryotes using fluorescence microscopy. Upon random insertion in an open reading frame in the proper frame and orientation, the transposon creates an N-terminal fluorescent protein fusion to the msfGFP reporter. Moreover, in order to examine the localization of fusion proteins whose native expression might be too low or absent, the transposon was fitted with a PLtetO-1 promoter that makes the expression of the generated fluorescent protein fusions controllable by anhydrotetracycline. Importantly, upon flipping out the PLtetO-1 promoter and neighboring antibiotic resistance marker, an in-frame "sandwich" msfGFP fusion is created in which the N- and C-terminal portions of the targeted protein are again controlled by its native promoter.
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Affiliation(s)
- Ioannis Passaris
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 22, 3000 Leuven, Belgium
| | - Wubishet M Tadesse
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 22, 3000 Leuven, Belgium
| | - Elisa Gayán
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 22, 3000 Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 22, 3000 Leuven, Belgium.
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Blocher McTigue WC, Perry SL. Design rules for encapsulating proteins into complex coacervates. SOFT MATTER 2019; 15:3089-3103. [PMID: 30916112 DOI: 10.1039/c9sm00372j] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We investigated the encapsulation of the model proteins bovine serum albumin (BSA), human hemoglobin (Hb), and hen egg white lysozyme (HEWL) into two-polymer complex coacervates as a function of polymer and solution conditions. Electrostatic parameters such as pH, protein net charge, salt concentration, and polymer charge density can be used to modulate protein uptake. While the use of a two-polymer coacervation system enables the encapsulation of weakly charged proteins that would otherwise require chemical modification to facilitate electrostatic complexation, we observed significantly higher uptake for proteins whose structure includes a cluster of like-charged residues on the protein surface. In addition to enhancing uptake, the presence of a charge patch also increased the sensitivity of the system to modulation by other parameters, including the length of the complexing polymers. Lastly, our results suggest that the distribution of charge on a protein surface may lead to different scaling behaviour for both the encapsulation efficiency and partition coefficient as a function of the absolute difference between the protein isoelectric point and the solution pH. These results provide insight into possible biophysical mechanisms whereby cells can control the uptake of proteins into coacervate-like granules, and suggest future utility in applications ranging from medicine and sensing to remediation and biocatalysis.
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Affiliation(s)
- Whitney C Blocher McTigue
- Department of Chemical Engineering and the Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA 01003 USA.
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Barahona CJ, Basantes LE, Tompkins KJ, Heitman DM, Chukwu BI, Sanchez J, Sanchez JL, Ghadirian N, Park CK, Horton NC. The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity. J Virol 2019; 93:e01647-18. [PMID: 30518649 PMCID: PMC6384071 DOI: 10.1128/jvi.01647-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/26/2018] [Indexed: 01/29/2023] Open
Abstract
Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.
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Affiliation(s)
- Claudia J Barahona
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - L Emilia Basantes
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kassidy J Tompkins
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Desirae M Heitman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Barbara I Chukwu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Juan Sanchez
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Jonathan L Sanchez
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Chad K Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - N C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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35
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Subramanian A, Sarkar RR. Perspectives on Leishmania Species and Stage-specific Adaptive Mechanisms. Trends Parasitol 2018; 34:1068-1081. [DOI: 10.1016/j.pt.2018.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/10/2018] [Accepted: 09/21/2018] [Indexed: 12/23/2022]
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Skinnider MA, Stacey RG, Foster LJ. Genomic data integration systematically biases interactome mapping. PLoS Comput Biol 2018; 14:e1006474. [PMID: 30332399 PMCID: PMC6192561 DOI: 10.1371/journal.pcbi.1006474] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
Elucidating the complete network of protein-protein interactions, or interactome, is a fundamental goal of the post-genomic era, yet existing interactome maps are far from complete. To increase the throughput and resolution of interactome mapping, methods for protein-protein interaction discovery by co-migration have been introduced. However, accurate identification of interacting protein pairs within the resulting large-scale proteomic datasets is challenging. Consequently, most computational pipelines for co-migration data analysis incorporate external genomic datasets to distinguish interacting from non-interacting protein pairs. The effect of this procedure on interactome mapping is poorly understood. Here, we conduct a rigorous analysis of genomic data integration for interactome recovery across a large number of co-migration datasets, spanning diverse experimental and computational methods. We find that genomic data integration leads to an increase in the functional coherence of the resulting interactome maps, but this comes at the expense of a decrease in power to discover novel interactions. Importantly, putative novel interactions predicted by genomic data integration are no more likely to later be experimentally discovered than those predicted from co-migration data alone. Our results reveal a widespread and unappreciated limitation in a methodology that has been widely used to map the interactome of humans and model organisms.
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Affiliation(s)
| | - R. Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Leonard J. Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Biochemistry, University of British Columbia, Vancouver, Canada
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37
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Al-Husini N, Tomares DT, Bitar O, Childers WS, Schrader JM. α-Proteobacterial RNA Degradosomes Assemble Liquid-Liquid Phase-Separated RNP Bodies. Mol Cell 2018; 71:1027-1039.e14. [PMID: 30197298 DOI: 10.1016/j.molcel.2018.08.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/11/2018] [Accepted: 07/31/2018] [Indexed: 12/30/2022]
Abstract
Ribonucleoprotein (RNP) granules play an important role in organizing eukaryotic mRNA metabolism via liquid-liquid phase separation (LLPS) of mRNA decay factors into membrane-less organelles in the cytoplasm. Here we show that the bacterium Caulobacter crescentus Ribonuclease (RNase) E assembles RNP LLPS condensates that we term bacterial RNP-bodies (BR-bodies), similar to eukaryotic P-bodies and stress granules. RNase E requires RNA to assemble a BR-body, and disassembly requires RNA cleavage, suggesting BR-bodies provide localized sites of RNA degradation. The unstructured C-terminal domain of RNase E is both necessary and sufficient to assemble the core of the BR-body, is functionally conserved in related α-proteobacteria, and influences mRNA degradation. BR-bodies are rapidly induced under cellular stresses and provide enhanced cell growth under stress. To our knowledge, Caulobacter RNase E is the first bacterial protein identified that forms LLPS condensates, providing an effective strategy for subcellular organization in cells lacking membrane-bound compartments.
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Affiliation(s)
- Nadra Al-Husini
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Dylan T Tomares
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Obaidah Bitar
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
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Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. The run-on oligomer filament enzyme mechanism of SgrAI: Part 1. Assembly kinetics of the run-on oligomer filament. J Biol Chem 2018; 293:14585-14598. [PMID: 30068553 DOI: 10.1074/jbc.ra118.003680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/30/2018] [Indexed: 01/06/2023] Open
Abstract
Filament or run-on oligomer formation by metabolic enzymes is now recognized as a widespread phenomenon having potentially unique enzyme regulatory properties and biological roles, and its dysfunction is implicated in human diseases such as cancer, diabetes, and developmental disorders. SgrAI is a bacterial allosteric type II restriction endonuclease that binds to invading phage DNA, may protect the host DNA from off-target cleavage activity, and forms run-on oligomeric filaments with enhanced DNA-cleavage activity and altered DNA sequence specificity. However, the mechanisms of SgrAI filament growth, cooperativity in filament formation, sequestration of enzyme activity, and advantages over other filament mechanisms remain unknown. In this first of a two-part series, we developed methods and models to derive association and dissociation rate constants of DNA-bound SgrAI in run-on oligomers and addressed the specific questions of cooperativity and filament growth mechanisms. We show that the derived rate constants are consistent with the run-on oligomer sizes determined by EM analysis and are most consistent with a noncooperative growth mode of the run-on oligomer. These models and methods are extended in the accompanying article to include the full DNA-cleavage pathway and address specific questions related to the run-on oligomer mechanism including the sequestration of DNA-cleavage activity and trapping of products.
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Affiliation(s)
- Chad K Park
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Jonathan L Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Claudia Barahona
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - L Emilia Basantes
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Juan Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Christian Hernandez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - N C Horton
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. The run-on oligomer filament enzyme mechanism of SgrAI: Part 2. Kinetic modeling of the full DNA cleavage pathway. J Biol Chem 2018; 293:14599-14615. [PMID: 30054273 DOI: 10.1074/jbc.ra118.003682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/17/2018] [Indexed: 11/06/2022] Open
Abstract
Filament or run-on oligomer formation by enzymes is now recognized as a widespread phenomenon with potentially unique enzyme regulatory properties and biological roles. SgrAI is an allosteric type II restriction endonuclease that forms run-on oligomeric filaments with activated DNA cleavage activity and altered DNA sequence specificity. In this two-part work, we measure individual steps in the run-on oligomer filament mechanism to address specific questions of cooperativity, trapping, filament growth mechanisms, and sequestration of activity using fluorophore-labeled DNA, kinetic FRET measurements, and reaction modeling with global data fitting. The final models and rate constants show that the assembly step involving association of SgrAI-DNA complexes into the run-on oligomer filament is relatively slow (3-4 orders of magnitude slower than diffusion limited) and rate-limiting at low to moderate concentrations of SgrAI-DNA. The disassembly step involving dissociation of complexes of SgrAI-DNA from each other in the run-on oligomer filament is the next slowest step but is fast enough to limit the residence time of any one copy of SgrAI or DNA within the dynamic filament. Further, the rate constant for DNA cleavage is found to be 4 orders of magnitude faster in the run-on oligomer filament than in isolated SgrAI-DNA complexes and faster than dissociation of SgrAI-DNA complexes from the run-on oligomer filament, making the reaction efficient in that each association into the filament likely leads to DNA cleavage before filament dissociation.
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Affiliation(s)
- Chad K Park
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Jonathan L Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Claudia Barahona
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - L Emilia Basantes
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Juan Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Christian Hernandez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - N C Horton
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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40
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The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems. Int J Biol Macromol 2018; 117:1224-1251. [PMID: 29890250 DOI: 10.1016/j.ijbiomac.2018.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
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41
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Connelly KE, Hedrick V, Paschoal Sobreira TJ, Dykhuizen EC, Aryal UK. Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry Profiling. Proteomics 2018; 18:e1700427. [PMID: 29655301 DOI: 10.1002/pmic.201700427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Analysis of protein complexes provides insights into how the ensemble of expressed proteome is organized into functional units. While there have been advances in techniques for proteome-wide profiling of cytoplasmic protein complexes, information about human nuclear protein complexes are very limited. To close this gap, we combined native size exclusion chromatography (SEC) with label-free quantitative MS profiling to characterize hundreds of nuclear protein complexes isolated from human glioblastoma multiforme T98G cells. We identified 1794 proteins that overlapped between two biological replicates of which 1244 proteins were characterized as existing within stably associated putative complexes. co-IP experiments confirmed the interaction of PARP1 with Ku70/Ku80 proteins and HDAC1 (histone deacetylase complex 1) and CHD4. HDAC1/2 also co-migrated with various SIN3A and nucleosome remodeling and deacetylase components in SEC fractionation including SIN3A, SAP30, RBBP4, RBBP7, and NCOR1. Co-elution of HDAC1/2/3 with both the KDM1A and RCOR1 further confirmed that these proteins are integral components of human deacetylase complexes. Our approach also demonstrated the ability to identify potential moonlighting complexes and novel complexes containing uncharacterized proteins. Overall, the results demonstrated the utility of SEC fractionation and LC-MS analysis for system-wide profiling of proteins to predict the existence of distinct forms of nuclear protein complexes.
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Affiliation(s)
- Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University Street, 47907, West Lafayette, IN, USA
| | - Victoria Hedrick
- Purdue Proteomics Facility, Bindley Biosciences Center, Discovery Park, Purdue University, 1203 W. State Street, 47907, West Lafayette, IN, USA
| | - Tiago Jose Paschoal Sobreira
- Purdue Proteomics Facility, Bindley Biosciences Center, Discovery Park, Purdue University, 1203 W. State Street, 47907, West Lafayette, IN, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University Street, 47907, West Lafayette, IN, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Biosciences Center, Discovery Park, Purdue University, 1203 W. State Street, 47907, West Lafayette, IN, USA
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42
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Using transposition to introduce eGFP fusions in Sinorhizobium meliloti: A tool to analyze protein localization patterns in bacteria. J Biotechnol 2017; 257:139-149. [PMID: 28007516 DOI: 10.1016/j.jbiotec.2016.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/14/2016] [Accepted: 12/18/2016] [Indexed: 11/23/2022]
Abstract
Conventional methods used for the in vivo analysis of subcellular protein localizations and their spatio-temporal dynamics in prokaryotes are based on either the engineering of N(amino)- or C(carboxy)-terminal fusions of fluorescent proteins with the protein of interest, or involved probing internal sites for tag integration. In addition, the use of inducible or constitutive promoters for the expression of fluorescent fusion proteins can lead to overexpression and result in localization artifacts. Here, we describe a method for the synthesis of fluorescent fusion proteins using transposable elements, which can randomly integrate in the internal sections of the protein coding sequence to produce full-length fluorescent fusion proteins expressed at endogenous levels. The established method was used for investigating subcellular localization of proteins in the soil bacterium and plant symbiont Sinorhizobium meliloti. Two constructs for transposition-based insertion of the enhanced green fluorescent protein (eGFP), as well as for in vivo excision of the selection marker for the production of full-length proteins were engineered. Conjugation with pHB14 plasmid and induction of the transposition in S. meliloti produced approx. 3.22×104 transconjugant colonies harboring the fluorescent marker with the transposition efficiency of 0.8%. Sixteen randomly targeted proteins of diverse functions, fused to the eGFP were identified and analyzed in living cells by epifluorescence microscopy, demonstrating the suitability of the novel tool for massive, random production of fluorescent proteins and for following of these proteins with different localizations inside the prokaryotic cell.
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43
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Curtis PD. Stalk formation of Brevundimonas and how it compares to Caulobacter crescentus. PLoS One 2017; 12:e0184063. [PMID: 28886080 PMCID: PMC5590869 DOI: 10.1371/journal.pone.0184063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
The Caulobacter crescentus cell extension known as a stalk represents an unusual bacterial morphology. C. crescentus produces stalks under multiple nutrient conditions, but the length of the stalk is increased in response to phosphate starvation. However, the exact function of the stalk is not known, nor is it known how much stalk biogenesis or function is conserved with other stalked bacteria. Work presented here shows that many organisms in the Caulobacter genus and the next closest genus (Brevundimonas) generally do not synthesize stalks in the relatively-rich PYE growth medium, suggesting that the synthesis of a stalk under nutrient-rich conditions by C. crescentus may be the exception instead of the norm among its phylogenetic group. Brevundimonas subvibrioides can be induced to synthesize stalks by genetically mimicking phosphate starvation conditions, indicating stalk synthesis in this organism may be performed on an as-need basis. This mutation, however, does not appear to increase the incidence of holdfast synthesis. While B. subvibrioides stalks appear to be synthesized with the same polarity with respect to holdfast as C. crescentus stalks, evidence is presented that suggests B. subvibrioides may disassemble stalks when they are no longer needed. Many homologs of C. crescentus genes encoding stalk-associated proteins are absent in the B. subvibrioides genome, and B. subvibrioides PstA-GFP as well as C. crescentus StpX-GFP are able to enter the B. subvibrioides stalk compartment, calling into question the level of compartmentalization of the B. subvibrioides stalk. In summary, this work begins to address how much the C. crescentus model for this unusual morphological adaptation can be extended to related organisms.
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Affiliation(s)
- Patrick D. Curtis
- Department of Biology, University of Mississippi, University, MS, United States of America
- * E-mail:
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44
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Goudsmits JMH, van Oijen AM, Robinson A. A Tool for Alignment and Averaging of Sparse Fluorescence Signals in Rod-Shaped Bacteria. Biophys J 2017; 110:1708-1715. [PMID: 27119631 DOI: 10.1016/j.bpj.2016.02.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 02/08/2016] [Accepted: 02/16/2016] [Indexed: 11/15/2022] Open
Abstract
Fluorescence microscopy studies have shown that many proteins localize to highly specific subregions within bacterial cells. Analyzing the spatial distribution of low-abundance proteins within cells is highly challenging because information obtained from multiple cells needs to be combined to provide well-defined maps of protein locations. We present (to our knowledge) a novel tool for fast, automated, and user-impartial analysis of fluorescent protein distribution across the short axis of rod-shaped bacteria. To demonstrate the strength of our approach in extracting spatial distributions and visualizing dynamic intracellular processes, we analyzed sparse fluorescence signals from single-molecule time-lapse images of individual Escherichia coli cells. In principle, our tool can be used to provide information on the distribution of signal intensity across the short axis of any rod-shaped object.
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Affiliation(s)
- Joris M H Goudsmits
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; School of Chemistry, University of Wollongong, Wollongong, New South Wales, Australia
| | - Andrew Robinson
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; School of Chemistry, University of Wollongong, Wollongong, New South Wales, Australia.
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45
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Reinke AW, Mak R, Troemel ER, Bennett EJ. In vivo mapping of tissue- and subcellular-specific proteomes in Caenorhabditis elegans. SCIENCE ADVANCES 2017; 3:e1602426. [PMID: 28508060 PMCID: PMC5425238 DOI: 10.1126/sciadv.1602426] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
Multicellular organisms are composed of tissues that have distinct functions requiring specialized proteomes. To define the proteome of a live animal with tissue and subcellular resolution, we adapted a localized proteomics technology for use in the multicellular model organism Caenorhabditis elegans. This approach couples tissue- and location-specific expression of the enzyme ascorbate peroxidase (APX), which enables proximity-based protein labeling in vivo, and quantitative proteomics to identify tissue- and subcellular-restricted proteomes. We identified and localized more than 3000 proteins from strains of C. elegans expressing APX in either the nucleus or cytoplasm of the intestine, epidermis, body wall muscle, or pharyngeal muscle. We also identified several hundred proteins that were specifically localized to one of the four tissues analyzed or specifically localized to the cytoplasm or the nucleus. This approach resulted in the identification both of proteins with previously characterized localizations and of those not known to localize to the nucleus or cytoplasm. Further, we confirmed the tissue- and subcellular-specific localization of a subset of identified proteins using green fluorescent protein tagging and fluorescence microscopy, validating our in vivo proximity-based proteomics technique. Together, these results demonstrate a new approach that enables the tissue- and subcellular-specific identification and quantification of proteins within a live animal.
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Affiliation(s)
- Aaron W. Reinke
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Raymond Mak
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Emily R. Troemel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Eric J. Bennett
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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46
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Mathis R, Ackermann M. Asymmetric cellular memory in bacteria exposed to antibiotics. BMC Evol Biol 2017; 17:73. [PMID: 28274196 PMCID: PMC5343395 DOI: 10.1186/s12862-017-0884-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 01/15/2017] [Indexed: 11/30/2022] Open
Abstract
Background The ability to form a cellular memory and use it for cellular decision-making could help bacteria to cope with recurrent stress conditions. We analyzed whether bacteria would form a cellular memory specifically if past events are predictive of future conditions. We worked with the asymmetrically dividing bacterium Caulobacter crescentus where past events are expected to only be informative for one of the two cells emerging from division, the sessile cell that remains in the same microenvironment and does not migrate. Results Time-resolved analysis of individual cells revealed that past exposure to low levels of antibiotics increases tolerance to future exposure for the sessile but not for the motile cell. Using computer simulations, we found that such an asymmetry in cellular memory could be an evolutionary response to situations where the two cells emerging from division will experience different future conditions. Conclusions Our results raise the question whether bacteria can evolve the ability to form and use cellular memory conditionally in situations where it is beneficial. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0884-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roland Mathis
- Department of Environmental Systems Science, ETH Zurich (Swiss Federal Institute of Technology in Zurich), Universitaetsstrasse 16, 8092, Zurich, Switzerland. .,Eawag (Swiss Federal Institute of Aquatic Science and Technology), Ueberlandstrasse 133, 8600, Duebendorf, Switzerland.
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zurich (Swiss Federal Institute of Technology in Zurich), Universitaetsstrasse 16, 8092, Zurich, Switzerland.,Eawag (Swiss Federal Institute of Aquatic Science and Technology), Ueberlandstrasse 133, 8600, Duebendorf, Switzerland
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47
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Ursell T, Lee TK, Shiomi D, Shi H, Tropini C, Monds RD, Colavin A, Billings G, Bhaya-Grossman I, Broxton M, Huang BE, Niki H, Huang KC. Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library. BMC Biol 2017; 15:17. [PMID: 28222723 PMCID: PMC5320674 DOI: 10.1186/s12915-017-0348-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/06/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The determination and regulation of cell morphology are critical components of cell-cycle control, fitness, and development in both single-cell and multicellular organisms. Understanding how environmental factors, chemical perturbations, and genetic differences affect cell morphology requires precise, unbiased, and validated measurements of cell-shape features. RESULTS Here we introduce two software packages, Morphometrics and BlurLab, that together enable automated, computationally efficient, unbiased identification of cells and morphological features. We applied these tools to bacterial cells because the small size of these cells and the subtlety of certain morphological changes have thus far obscured correlations between bacterial morphology and genotype. We used an online resource of images of the Keio knockout library of nonessential genes in the Gram-negative bacterium Escherichia coli to demonstrate that cell width, width variability, and length significantly correlate with each other and with drug treatments, nutrient changes, and environmental conditions. Further, we combined morphological classification of genetic variants with genetic meta-analysis to reveal novel connections among gene function, fitness, and cell morphology, thus suggesting potential functions for unknown genes and differences in modes of action of antibiotics. CONCLUSIONS Morphometrics and BlurLab set the stage for future quantitative studies of bacterial cell shape and intracellular localization. The previously unappreciated connections between morphological parameters measured with these software packages and the cellular environment point toward novel mechanistic connections among physiological perturbations, cell fitness, and growth.
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Affiliation(s)
- Tristan Ursell
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Department of Physics, University of Oregon, Eugene, OR, 97403, USA
| | - Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Daisuke Shiomi
- National Institute of Genetics, Shizuoka, Japan.,Current address: Department of Life Science, Rikkyo University, Tokyo, Japan
| | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Carolina Tropini
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Russell D Monds
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Current address: Synthetic Genomics Inc., La Jolla, CA, 92037, USA
| | - Alexandre Colavin
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gabriel Billings
- Department of Physics, Stanford University, Stanford, CA, 94305, USA
| | | | - Michael Broxton
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | | | | | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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48
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Subramanian K, Tyson JJ. Spatiotemporal Models of the Asymmetric Division Cycle of Caulobacter crescentus. Results Probl Cell Differ 2017; 61:23-48. [PMID: 28409299 DOI: 10.1007/978-3-319-53150-2_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The spatial localization of proteins within the cytoplasm of bacteria is an underappreciated but critical aspect of cell cycle regulation for many prokaryotes. In Caulobacter crescentus-a model organism for the study of asymmetric cell reproduction in prokaryotes-heterogeneous localization of proteins has been identified as the underlying cause of asymmetry in cell morphology, DNA replication, and cell division. However, significant questions remain. Firstly, the mechanisms by which proteins localize in the organelle-free prokaryotic cytoplasm remain obscure. Furthermore, how variations in the spatial and temporal dynamics of cell fate determinants regulate signaling pathways and orchestrate the complex programs of asymmetric cell division and differentiation are subjects of ongoing research. In this chapter, we review current efforts in investigating these two questions. We describe how mathematical models of spatiotemporal protein dynamics are being used to generate and test competing hypotheses and provide complementary insight about the control mechanisms that regulate asymmetry in protein localization and cell division.
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Affiliation(s)
- Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
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49
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Ho SH, Tirrell DA. Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells. J Am Chem Soc 2016; 138:15098-15101. [PMID: 27933886 DOI: 10.1021/jacs.6b07067] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Reliable methods to determine the subcellular localization of bacterial proteins are needed for the study of prokaryotic cell biology. We describe here a simple and general technique for imaging of bacterial proteins in situ by fluorescence microscopy. The method uses the eukaryotic enzyme N-myristoyltransferase to modify the N-terminus of the protein of interest with an azido fatty acid. Subsequent strain-promoted azide-alkyne cycloaddition allows conjugation of dyes and imaging of tagged proteins by confocal fluorescence microscopy. We demonstrate the method by labeling the chemotaxis proteins Tar and CheA and the cell division proteins FtsZ and FtsA in Escherichia coli. We observe distinct spatial patterns for each of these proteins in both fixed and live cells. The method should prove broadly useful for protein imaging in bacteria.
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Affiliation(s)
- Samuel H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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50
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Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles. Proc Natl Acad Sci U S A 2016; 113:12490-12495. [PMID: 27791060 DOI: 10.1073/pnas.1602380113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their relative simplicity, bacteria have complex anatomy at the subcellular level. At the cell poles of Caulobacter crescentus, a 177-amino acid (aa) protein called PopZ self-assembles into 3D polymeric superstructures. Remarkably, we find that this assemblage interacts directly with at least eight different proteins, which are involved in cell cycle regulation and chromosome segregation. The binding determinants within PopZ include 24 aa at the N terminus, a 32-aa region near the C-terminal homo-oligomeric assembly domain, and portions of an intervening linker region. Together, the N-terminal 133 aa of PopZ are sufficient for interacting with all binding partners, even in the absence of homo-oligomeric assembly. Structural analysis of this region revealed that it is intrinsically disordered, similar to p53 and other hub proteins that organize complex signaling networks in eukaryotic cells. Through live-cell photobleaching, we find rapid binding kinetics between PopZ and its partners, suggesting many pole-localized proteins become concentrated at cell poles through rapid cycles of binding and unbinding within the PopZ scaffold. We conclude that some bacteria, similar to their eukaryotic counterparts, use intrinsically disordered hub proteins for network assembly and subcellular organization.
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