1
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Carlson RP, Beck AE, Benitez MG, Harcombe WR, Mahadevan R, Gedeon T. Cell Geometry and Membrane Protein Crowding Constrain Growth Rate, Overflow Metabolism, Respiration, and Maintenance Energy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609071. [PMID: 39229203 PMCID: PMC11370460 DOI: 10.1101/2024.08.21.609071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
A metabolic theory is presented for predicting maximum growth rate, overflow metabolism, respiration efficiency, and maintenance energy flux based on the intersection of cell geometry, membrane protein crowding, and metabolism. The importance of cytosolic macromolecular crowding on phenotype has been established in the literature but the importance of surface area has been largely overlooked due to incomplete knowledge of membrane properties. We demonstrate that the capacity of the membrane to host proteins increases with growth rate offsetting decreases in surface area-to-volume ratios (SA:V). This increase in membrane protein is hypothesized to be essential to competitive Escherichia coli phenotypes. The presented membrane-centric theory uses biophysical properties and metabolic systems analysis to successfully predict the phenotypes of E. coli K-12 strains, MG1655 and NCM3722, which are genetically similar but have SA:V ratios that differ up to 30%, maximum growth rates on glucose media that differ by 40%, and overflow phenotypes that start at growth rates that differ by 80%. These analyses did not consider cytosolic macromolecular crowding, highlighting the distinct properties of the presented theory. Cell geometry and membrane protein crowding are significant biophysical constraints on phenotype and provide a theoretical framework for improved understanding and control of cell biology.
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Affiliation(s)
- Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT USA
| | - Ashley E Beck
- Department of Biological and Environmental Sciences, Carroll College, Helena, MT USA
| | | | - William R Harcombe
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN USA
| | | | - Tomáš Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, MT USA
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2
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Iyer A, Frallicciardi J, le Paige UBA, Narasimhan S, Luo Y, Sieiro PA, Syga L, van den Brekel F, Tran BM, Tjioe R, Schuurman-Wolters G, Stuart MCA, Baldus M, van Ingen H, Poolman B. The Structure and Function of the Bacterial Osmotically Inducible Protein Y. J Mol Biol 2024; 436:168668. [PMID: 38908784 DOI: 10.1016/j.jmb.2024.168668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024]
Abstract
The ability to adapt to osmotically diverse and fluctuating environments is critical to the survival and resilience of bacteria that colonize the human gut and urinary tract. Environmental stress often provides cross-protection against other challenges and increases antibiotic tolerance of bacteria. Thus, it is critical to understand how E. coli and other microbes survive and adapt to stress conditions. The osmotically inducible protein Y (OsmY) is significantly upregulated in response to hypertonicity. Yet its function remains unknown for decades. We determined the solution structure and dynamics of OsmY by nuclear magnetic resonance spectroscopy, which revealed that the two Bacterial OsmY and Nodulation (BON) domains of the protein are flexibly linked under low- and high-salinity conditions. In-cell solid-state NMR further indicates that there are no gross structural changes in OsmY as a function of osmotic stress. Using cryo-electron and super-resolution fluorescence microscopy, we show that OsmY attenuates plasmolysis-induced structural changes in E. coli and improves the time to growth resumption after osmotic upshift. Structure-guided mutational and functional studies demonstrate that exposed hydrophobic residues in the BON1 domain are critical for the function of OsmY. We find no evidence for membrane interaction of the BON domains of OsmY, contrary to current assumptions. Instead, at high ionic strength, we observe an interaction with the water channel, AqpZ. Thus, OsmY does not play a simple structural role in E. coli but may influence a cascade of osmoregulatory functions of the cell.
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Affiliation(s)
- Aditya Iyer
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Jacopo Frallicciardi
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Ulric B A le Paige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Yanzhang Luo
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Patricia Alvarez Sieiro
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Lukasz Syga
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Floris van den Brekel
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Buu Minh Tran
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Rendy Tjioe
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Gea Schuurman-Wolters
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Marc C A Stuart
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
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3
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Raja Venkatesh A, Le KH, Weld DM, Brandman O. Diffusive lensing as a mechanism of intracellular transport and compartmentalization. eLife 2024; 12:RP89794. [PMID: 38896469 PMCID: PMC11186627 DOI: 10.7554/elife.89794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
While inhomogeneous diffusivity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales remain largely unexplored. In this work, we use agent-based simulations of diffusion to investigate how heterogeneous diffusivity affects the movement and concentration of diffusing particles. We propose that a nonequilibrium mode of membrane-less compartmentalization arising from the convergence of diffusive trajectories into low-diffusive sinks, which we call 'diffusive lensing,' is relevant for living systems. Our work highlights the phenomenon of diffusive lensing as a potentially key driver of mesoscale dynamics in the cytoplasm, with possible far-reaching implications for biochemical processes.
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Affiliation(s)
- Achuthan Raja Venkatesh
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) MohaliMohaliIndia
| | - Kathy H Le
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - David M Weld
- Department of Physics, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Onn Brandman
- Department of Biochemistry, Stanford UniversityStanfordUnited States
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4
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Chang MH, Lavrentovich MO, Männik J. Differentiating the roles of proteins and polysomes in nucleoid size homeostasis in Escherichia coli. Biophys J 2024; 123:1435-1448. [PMID: 37974398 PMCID: PMC11163298 DOI: 10.1016/j.bpj.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
A defining feature of the bacterial cytosolic interior is a distinct membrane-less organelle, the nucleoid, that contains the chromosomal DNA. Although increasing experimental evidence indicates that macromolecular crowding is the dominant mechanism for nucleoid formation, it has remained unclear which crowders control nucleoid volume. It is commonly assumed that polyribosomes play a dominant role, yet the volume fraction of soluble proteins in the cytosol is comparable with that of polyribosomes. Here, we develop a free energy-based model for the cytosolic interior of a bacterial cell to distinguish contributions arising from polyribosomes and cytosolic proteins in nucleoid volume control. The parameters of the model are determined from the existing experimental data. We show that, while the polysomes establish the existence of the nucleoid as a distinct phase, the proteins control the nucleoid volume in physiologically relevant conditions. Our model explains experimental findings in Escherichia coli that the nucleoid compaction curves in osmotic shock measurements do not depend on cell growth rate and that dissociation of polysomes in slow growth rates does not lead to significant nucleoid expansion, while the nucleoid phase disappears in fastest growth rates. Furthermore, the model predicts a cross-over in the exclusion of crowders by their linear dimensions from the nucleoid phase: below the cross-over of 30-50 nm, the concentration of crowders in the nucleoid phase decreases linearly as a function of the crowder diameter, while decreasing exponentially above the cross-over size. Our work points to the possibility that bacterial cells maintain nucleoid size and protein concentration homeostasis via feedback in which protein concentration controls nucleoid dimensions and the nucleoid dimensions control protein synthesis rate.
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Affiliation(s)
- Mu-Hung Chang
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee
| | - Maxim O Lavrentovich
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee; Department of Earth, Environment, and Physics, Worcester State University, Worcester, Massachusetts.
| | - Jaan Männik
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee.
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5
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Losa J, Heinemann M. Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli. Biophys J 2024; 123:1211-1221. [PMID: 38555507 PMCID: PMC11140462 DOI: 10.1016/j.bpj.2024.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Due to the high concentration of proteins, nucleic acids, and other macromolecules, the bacterial cytoplasm is typically described as a crowded environment. However, the extent to which each of these macromolecules individually affects the mobility of macromolecular complexes, and how this depends on growth conditions, is presently unclear. In this study, we sought to quantify the crowding experienced by an exogenous 40 nm fluorescent particle in the cytoplasm of E. coli under different growth conditions. By performing single-particle tracking measurements in cells selectively depleted of DNA and/or mRNA, we determined the contribution to crowding of mRNA, DNA, and remaining cellular components, i.e., mostly proteins and ribosomes. To estimate this contribution to crowding, we quantified the difference of the particle's diffusion coefficient in conditions with and without those macromolecules. We found that the contributions of the three classes of components were of comparable magnitude, being largest in the case of proteins and ribosomes. We further found that the contributions of mRNA and DNA to crowding were significantly larger than expected based on their volumetric fractions alone. Finally, we found that the crowding contributions change only slightly with the growth conditions. These results reveal how various cellular components partake in crowding of the cytoplasm and the consequences this has for the mobility of large macromolecular complexes.
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Affiliation(s)
- José Losa
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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6
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Basan M, Mukherjee A, Huang Y, Oh S, Sanchez C, Chang YF, Liu X, Bradshaw G, Benites N, Paulsson J, Kirschner M, Sung Y, Elgeti J. Homeostasis of cytoplasmic crowding by cell wall fluidization and ribosomal counterions. RESEARCH SQUARE 2024:rs.3.rs-4138690. [PMID: 38699329 PMCID: PMC11065075 DOI: 10.21203/rs.3.rs-4138690/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In bacteria, algae, fungi, and plant cells, the wall must expand in concert with cytoplasmic biomass production, otherwise cells would experience toxic molecular crowding1,2 or lyse. But how cells achieve expansion of this complex biomaterial in coordination with biosynthesis of macromolecules in the cytoplasm remains unexplained3, although recent works have revealed that these processes are indeed coupled4,5. Here, we report a striking increase of turgor pressure with growth rate in E. coli, suggesting that the speed of cell wall expansion is controlled via turgor. Remarkably, despite this increase in turgor pressure, cellular biomass density remains constant across a wide range of growth rates. By contrast, perturbations of turgor pressure that deviate from this scaling directly alter biomass density. A mathematical model based on cell wall fluidization by cell wall endopeptidases not only explains these apparently confounding observations but makes surprising quantitative predictions that we validated experimentally. The picture that emerges is that turgor pressure is directly controlled via counterions of ribosomal RNA. Elegantly, the coupling between rRNA and turgor pressure simultaneously coordinates cell wall expansion across a wide range of growth rates and exerts homeostatic feedback control on biomass density. This mechanism may regulate cell wall biosynthesis from microbes to plants and has important implications for the mechanism of action of antibiotics6.
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7
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Xu G, Cheng K, Liu M, Li C. Studying protein stability in crowded environments by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2024; 140-141:42-48. [PMID: 38705635 DOI: 10.1016/j.pnmrs.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/07/2024]
Abstract
Most proteins perform their functions in crowded and complex cellular environments where weak interactions are ubiquitous between biomolecules. These complex environments can modulate the protein folding energy landscape and hence affect protein stability. NMR is a nondestructive and effective method to quantify the kinetics and equilibrium thermodynamic stability of proteins at an atomic level within crowded environments and living cells. Here, we review NMR methods that can be used to measure protein stability, as well as findings of studies on protein stability in crowded environments mimicked by polymer and protein crowders and in living cells. The important effects of chemical interactions on protein stability are highlighted and compared to spatial excluded volume effects.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China.
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8
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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9
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Ong Q, Xufeng X, Stellacci F. Versatile Capillary Cells for Handling Concentrated Samples in Analytical Ultracentrifugation. Anal Chem 2024; 96:2567-2573. [PMID: 38301115 PMCID: PMC10867799 DOI: 10.1021/acs.analchem.3c05006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
In concentrated macromolecular dispersions, far-from-ideal intermolecular interactions determine the dispersion behaviors including phase transition, crystallization, and liquid-liquid phase separation. Here, we present a novel versatile capillary-cell design for analytical ultracentrifugation-sedimentation equilibrium (AUC-SE), ideal for studying samples at high concentrations. Current setups for such studies are difficult and unreliable to handle, leading to a low experimental success rate. The design presented here is easy to use, robust, and reusable for samples in both aqueous and organic solvents while requiring no special tools or chemical modification of AUC cells. The key and unique feature is the fabrication of liquid reservoirs directly on the bottom window of AUC cells, which can be easily realized by laser ablation or mechanical drilling. The channel length and optical path length are therefore tunable. The success rate for assembling this new cell is close to 100%. We demonstrate the practicality of this cell by studying: (1) the equation of state and second virial coefficients of concentrated gold nanoparticle dispersions in water and bovine serum albumin (BSA) as well as lysozyme solution in aqueous buffers, (2) the gelation phase transition of DNA and BSA solutions, and (3) liquid-liquid phase separation of concentrated BSA/polyethylene glycol (PEG) droplets.
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Affiliation(s)
- Quy Ong
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
| | - Xu Xufeng
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
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10
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Nishikawa S, Sato G, Takada S, Kohyama S, Honda G, Yanagisawa M, Hori Y, Doi N, Yoshinaga N, Fujiwara K. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308030. [PMID: 38054641 PMCID: PMC10853730 DOI: 10.1002/advs.202308030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.
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Affiliation(s)
- Saki Nishikawa
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Gaku Sato
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Sakura Takada
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Shunshi Kohyama
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
- Present address:
Department for Cellular and Molecular BiophysicsMax Planck Institute for BiochemistryAm Klopferspitz 18D‐82152MartinsriedGermany
| | - Gen Honda
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Miho Yanagisawa
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
- Graduate School of ScienceThe University of TokyoHongo 7‐3‐1BunkyoTokyo113‐0033Japan
- Center for Complex Systems BiologyUniversal Biology InstituteThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Yutaka Hori
- Department of Applied Physics and Physico‐informaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Nobuhide Doi
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Natsuhiko Yoshinaga
- WPI Advanced Institute for Materials Research (WPI‐AIMR)Tohoku UniversityKatahira 2‐1‐1, Aoba‐KuSendai980‐8577Japan
- MathAM‐OILAISTSendai980‐8577Japan
| | - Kei Fujiwara
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
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11
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Qiu X, Hu XM, Tang XX, Huang CH, Jian HH, Lin DH. Metabolic adaptations of Microbacterium sediminis YLB-01 in deep-sea high-pressure environments. Appl Microbiol Biotechnol 2024; 108:170. [PMID: 38265689 DOI: 10.1007/s00253-023-12906-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 01/25/2024]
Abstract
The deep-sea environment is an extremely difficult habitat for microorganisms to survive in due to its intense hydrostatic pressure. However, the mechanisms by which these organisms adapt to such extreme conditions remain poorly understood. In this study, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01, a cold and stress-tolerant microorganism isolated from deep-sea sediments, in response to high-pressure conditions. YLB-01 cells were cultured at normal atmospheric pressure and 28 ℃ until they reached the stationary growth phase. Subsequently, the cells were exposed to either normal pressure or high pressure (30 MPa) at 4 ℃ for 7 days. Using NMR-based metabolomic and proteomic analyses of YLB-01 cells exposed to high-pressure conditions, we observed significant metabolic changes in several metabolic pathways, including amino acid, carbohydrate, and lipid metabolism. In particular, the high-pressure treatment stimulates cell division and triggers the accumulation of UDP-glucose, a critical factor in cell wall formation. This finding highlights the adaptive strategies used by YLB-01 cells to survive in the challenging high-pressure environments of the deep sea. Specifically, we discovered that YLB-01 cells regulate amino acid metabolism, promote carbohydrate metabolism, enhance cell wall synthesis, and improve cell membrane fluidity in response to high pressure. These adaptive mechanisms play essential roles in supporting the survival and growth of YLB-01 in high-pressure conditions. Our study offers valuable insights into the molecular mechanisms underlying the metabolic adaptation of deep-sea microorganisms to high-pressure environments. KEY POINTS: • NMR-based metabolomic and proteomic analyses were conducted on Microbacterium sediminis YLB-01 to investigate the significant alterations in several metabolic pathways in response to high-pressure treatment. • YLB-01 cells used adaptive strategies (such as regulated amino acid metabolism, promoted carbohydrate metabolism, enhanced cell wall synthesis, and improved cell membrane fluidity) to survive in the challenging high-pressure environment of the deep sea. • High-pressure treatment stimulated cell division and triggered the accumulation of UDP-glucose, a critical factor in cell wall formation, in Microbacterium sediminis YLB-01 cells.
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Affiliation(s)
- Xu Qiu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xiao-Min Hu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xi-Xiang Tang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
| | - Cai-Hua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen, China
| | - Hua-Hua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Hai Lin
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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12
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Kompella VPS, Romano MC, Stansfield I, Mancera RL. What determines sub-diffusive behavior in crowded protein solutions? Biophys J 2024; 123:134-146. [PMID: 38073154 PMCID: PMC10808025 DOI: 10.1016/j.bpj.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/07/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
The aqueous environment inside cells is densely packed. A typical cell has a macromolecular concentration in the range 90-450 g/L, with 5%-40% of its volume being occupied by macromolecules, resulting in what is known as macromolecular crowding. The space available for the free diffusion of metabolites and other macromolecules is thus greatly reduced, leading to so-called excluded volume effects. The slow diffusion of macromolecules under crowded conditions has been explained using transient complex formation. However, sub-diffusion noted in earlier works is not well characterized, particularly the role played by transient complex formation and excluded volume effects. We have used Brownian dynamics simulations to characterize the diffusion of chymotrypsin inhibitor 2 in protein solutions of bovine serum albumin and lysozyme at concentrations ranging from 50 to 300 g/L. The predicted changes in diffusion coefficient as a function of crowder concentration are consistent with NMR experiments. The sub-diffusive behavior observed in the sub-microsecond timescale can be explained in terms of a so-called cage effect, arising from rattling motion in a local molecular cage as a consequence of excluded volume effects. By selectively manipulating the nature of interactions between protein molecules, we determined that excluded volume effects induce sub-diffusive dynamics at sub-microsecond timescales. These findings may help to explain the diffusion-mediated effects of protein crowding on cellular processes.
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Affiliation(s)
- Vijay Phanindra Srikanth Kompella
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia; Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Maria Carmen Romano
- Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom; Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia.
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13
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Cai Y, Hu H, Wu Z, Yu C. A dual-lock-controlled mitochondria-targeted ratiometric fluorescence probe for simultaneous detection of atherosclerosis-related HClO and viscosity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123225. [PMID: 37586279 DOI: 10.1016/j.saa.2023.123225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/22/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023]
Abstract
Precise detection of inflammatory microenvironment-related viscosity and hypochlorous acid (HClO) contributes to illuminating the pathogenesis and further diagnosing of atherosclerosis (AS). Herein, a dual-lock-controlled mitochondria-targeted fluorescence probe (NS) for simultaneous imaging of HClO and viscosity in AS-related foam cells is presented. NS performs linear increase in green-fluorescence along with increased viscosity (excited at 425 nm), permitting "off-on" fluorescence imaging of viscosity. Meanwhile, upon HClO activation, NS exhibits red-shifted and enhanced fluorescence in orange, thus leading to ratiometric fluorescence quantification of HClO (excited at 465 nm). Such dual-lock-controlled effect makes NS realize simultaneous imaging of viscosity and HClO with high sensitivity and selectivity via "off-on" and ratiometric fluorescence readouts, respectively. Besides, endowed with mitochondria-targeting capacity, NS achieves in situ imaging of mitochondria viscosity and HClO in living RAW264.7 cells. Importantly, for the first time, NS realizes simultaneous imaging of mitochondria viscosity and HClO in macrophage-derived foam cells, revealing the close association between HClO level and viscosity change in mitochondria during foaming translation of macrophages in atherogenesis. This work not only provides a novel strategy and tool to image organelle-located viscosity and HClO in living systems, but also holds great potential in early diagnosis of AS.
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Affiliation(s)
- Yang Cai
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Hui Hu
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhen Wu
- University of Science and Technology Beijing, School of Materials Science and Engineering, Beijing 100083, PR China
| | - Chao Yu
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
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14
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Holt LJ, Delarue M. Macromolecular crowding: Sensing without a sensor. Curr Opin Cell Biol 2023; 85:102269. [PMID: 37897928 DOI: 10.1016/j.ceb.2023.102269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/28/2023] [Accepted: 10/01/2023] [Indexed: 10/30/2023]
Abstract
All living cells are crowded with macromolecules. Crowding can directly modulate biochemical reactions to various degrees depending on the sizes, shapes, and binding affinities of the reactants. Here, we explore the possibility that cells can sense and adapt to changes in crowding through the widespread modulation of biochemical reactions without the need for a dedicated sensor. Additionally, we explore phase separation as a general physicochemical response to changes in crowding, and a mechanism to both transduce information and physically restore crowding homeostasis.
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Affiliation(s)
- Liam J Holt
- New York University Grossman School of Medicine, Institute for Systems Genetics, New York, NY, USA
| | - Morgan Delarue
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.
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15
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Yao Y, Shi X, Zhao Z, Zhang A, Li W. Dendronization of chitosan to afford unprecedent thermoresponsiveness and tunable microconfinement. J Mater Chem B 2023; 11:11024-11034. [PMID: 37975703 DOI: 10.1039/d3tb01803b] [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: 11/19/2023]
Abstract
Convenient chemical modification of biomacromolecules to create novel biocompatible functional materials satisfies the current requirements of sustainable chemistry. Dendronization of chitosan with dendritic oligoethylene glycols (OEGs) paves a strategy for the preparation of functional dendronized chitosans (DCSs) with unprecedent thermoresponsive behavior, which inherit biological features from polysaccharides and the topological features from dendritic OEGs. In addition, densely packed dendritic OEG chains around the backbone provide efficient cooperative interactions and form an intriguing confined microenvironment based on the degradable biopolymers. In this perspective, we describe the principle for the preparation of the thermoresponsive DCSs, and focus on the molecular envelop effect from the hydrophobic microconfinement to the encapsulated guest molecules or moieties. Particular attention is put on their capacity to regulate behavior and the functions of the encapsulated guests through thermally-mediated dehydration and collapse of the densely packed dendritic OEGs. We believe that the methodology described here may provide prospects for the fabrication of functional materials from biomacromolecules, especially when used as environmentally friendly nanomaterials or in accurate diagnosis and therapy.
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Affiliation(s)
- Yi Yao
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Nanchen Street 333, Shanghai 200444, China.
| | - Xiaoxin Shi
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Nanchen Street 333, Shanghai 200444, China.
| | - Zihong Zhao
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Nanchen Street 333, Shanghai 200444, China.
| | - Afang Zhang
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Nanchen Street 333, Shanghai 200444, China.
| | - Wen Li
- International Joint Laboratory of Biomimetic and Smart Polymers, School of Materials Science and Engineering, Shanghai University, Nanchen Street 333, Shanghai 200444, China.
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16
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Mouton SN, Boersma AJ, Veenhoff LM. A physicochemical perspective on cellular ageing. Trends Biochem Sci 2023; 48:949-962. [PMID: 37716870 DOI: 10.1016/j.tibs.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Cellular ageing described at the molecular level is a multifactorial process that leads to a spectrum of ageing trajectories. There has been recent discussion about whether a decline in physicochemical homeostasis causes aberrant phase transitions, which are a driver of ageing. Indeed, the function of all biological macromolecules, regardless of their participation in biomolecular condensates, depends on parameters such as pH, crowding, and redox state. We expand on the physicochemical homeostasis hypothesis and summarise recent evidence that the intracellular milieu influences molecular processes involved in ageing.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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17
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Junier I, Ghobadpour E, Espeli O, Everaers R. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling. Front Microbiol 2023; 14:1192831. [PMID: 37965550 PMCID: PMC10642903 DOI: 10.3389/fmicb.2023.1192831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023] Open
Abstract
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to a minimum and we provide some explanatory background material for the two communities.
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Affiliation(s)
- Ivan Junier
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
| | - Elham Ghobadpour
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Ralf Everaers
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
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18
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Prass T, Garidel P, Blech M, Schäfer LV. Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations. J Chem Inf Model 2023; 63:6129-6140. [PMID: 37757589 PMCID: PMC10565822 DOI: 10.1021/acs.jcim.3c00947] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 09/29/2023]
Abstract
The computational prediction of the viscosity of dense protein solutions is highly desirable, for example, in the early development phase of high-concentration biopharmaceutical formulations where the material needed for experimental determination is typically limited. Here, we use large-scale atomistic molecular dynamics (MD) simulations with explicit solvation to de novo predict the dynamic viscosities of solutions of a monoclonal IgG1 antibody (mAb) from the pressure fluctuations using a Green-Kubo approach. The viscosities at simulated mAb concentrations of 200 and 250 mg/mL are compared to the experimental values, which we measured with rotational rheometry. The computational viscosity of 24 mPa·s at the mAb concentration of 250 mg/mL matches the experimental value of 23 mPa·s obtained at a concentration of 213 mg/mL, indicating slightly different effective concentrations (or activities) in the MD simulations and in the experiments. This difference is assigned to a slight underestimation of the effective mAb-mAb interactions in the simulations, leading to a too loose dynamic mAb network that governs the viscosity. Taken together, this study demonstrates the feasibility of all-atom MD simulations for predicting the properties of dense mAb solutions and provides detailed microscopic insights into the underlying molecular interactions. At the same time, it also shows that there is room for further improvements and highlights challenges, such as the massive sampling required for computing collective properties of dense biomolecular solutions in the high-viscosity regime with reasonable statistical precision.
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Affiliation(s)
- Tobias
M. Prass
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Patrick Garidel
- Boehringer
Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, D-88397 Biberach
an der Riss, Germany
| | - Michaela Blech
- Boehringer
Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, D-88397 Biberach
an der Riss, Germany
| | - Lars V. Schäfer
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
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19
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Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ. Mesoscale molecular assembly is favored by the active, crowded cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558334. [PMID: 37781612 PMCID: PMC10541124 DOI: 10.1101/2023.09.19.558334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The mesoscale organization of molecules into membraneless biomolecular condensates is emerging as a key mechanism of rapid spatiotemporal control in cells1. Principles of biomolecular condensation have been revealed through in vitro reconstitution2. However, intracellular environments are much more complex than test-tube environments: They are viscoelastic, highly crowded at the mesoscale, and are far from thermodynamic equilibrium due to the constant action of energy-consuming processes3. We developed synDrops, a synthetic phase separation system, to study how the cellular environment affects condensate formation. Three key features enable physical analysis: synDrops are inducible, bioorthogonal, and have well-defined geometry. This design allows kinetic analysis of synDrop assembly and facilitates computational simulation of the process. We compared experiments and simulations to determine that macromolecular crowding promotes condensate nucleation but inhibits droplet growth through coalescence. ATP-dependent cellular activities help overcome the frustration of growth. In particular, actomyosin dynamics potentiate droplet growth by reducing confinement and elasticity in the mammalian cytoplasm, thereby enabling synDrop coarsening. Our results demonstrate that mesoscale molecular assembly is favored by the combined effects of crowding and active matter in the cytoplasm. These results move toward a better predictive understanding of condensate formation in vivo.
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Affiliation(s)
- Tong Shu
- Institute for Systems Genetics, NYU Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Gaurav Mitra
- Department of Chemistry, New York University, New York, New York, USA
| | | | | | - Emmanuel D. Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Glen M. Hocky
- Department of Chemistry, New York University, New York, New York, USA
- Simons Center for Computational Physical Chemistry, New York University, New York, New York, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
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20
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Abelenda-Núñez I, Ortega F, Rubio RG, Guzmán E. Anomalous Colloidal Motion under Strong Confinement. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302115. [PMID: 37116105 DOI: 10.1002/smll.202302115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/13/2023] [Indexed: 06/19/2023]
Abstract
Diffusion of biological macromolecules in the cytoplasm is a paradigm of colloidal diffusion in an environment characterized by a strong restriction of the accessible volume. This makes of the understanding of the physical rules governing colloidal diffusion under conditions mimicking the reduction in accessible volume occurring in the cell cytoplasm, a problem of a paramount importance. This work aims to study how the thermal motion of spherical colloidal beads in the inner cavity of giant unilamellar vesicles (GUVs) is modified by strong confinement conditions, and the viscoelastic character of the medium. Using single particle tracking, it is found that both the confinement and the environmental viscoelasticity lead to the emergence of anomalous motion pathways for colloidal microbeads encapsulated in the aqueous inner cavity of GUVs. This anomalous diffusion is strongly dependent on the ratio between the volume of the colloidal particle and that of the GUV under consideration as well as on the viscosity of the particle's liquid environment. Therefore, the results evidence that the reduction of the free volume accessible to colloidal motion pushes the diffusion far from a standard Brownian pathway as a result of the change in the hydrodynamic boundary conditions driving the particle motion.
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Affiliation(s)
- Irene Abelenda-Núñez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
| | - Francisco Ortega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
- Unidad de Materia Condensada, Instituto Pluridisciplinar, Universidad Complutense de Madrid, Paseo Juan XXIII 1., Madrid, 28040, Spain
| | - Ramón G Rubio
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
| | - Eduardo Guzmán
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
- Unidad de Materia Condensada, Instituto Pluridisciplinar, Universidad Complutense de Madrid, Paseo Juan XXIII 1., Madrid, 28040, Spain
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21
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Mantovanelli L, Linnik DS, Punter M, Kojakhmetov HJ, Śmigiel WM, Poolman B. Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli. PLoS Comput Biol 2023; 19:e1011093. [PMID: 37695774 PMCID: PMC10513214 DOI: 10.1371/journal.pcbi.1011093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/21/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
We have developed Simulation-based Reconstructed Diffusion (SbRD) to determine diffusion coefficients corrected for confinement effects and for the bias introduced by two-dimensional models describing a three-dimensional motion. We validate the method on simulated diffusion data in three-dimensional cell-shaped compartments. We use SbRD, combined with a new cell detection method, to determine the diffusion coefficients of a set of native proteins in Escherichia coli. We observe slower diffusion at the cell poles than in the nucleoid region of exponentially growing cells, which is independent of the presence of polysomes. Furthermore, we show that the newly formed pole of dividing cells exhibits a faster diffusion than the old one. We hypothesize that the observed slowdown at the cell poles is caused by the accumulation of aggregated or damaged proteins, and that the effect is asymmetric due to cell aging.
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Affiliation(s)
- Luca Mantovanelli
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Dmitrii S. Linnik
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Michiel Punter
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | | | - Wojciech M. Śmigiel
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
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22
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Lv S, Wang C, Xue K, Wang J, Xiao M, Sun Z, Han L, Shi L, Zhu C. Activated alkyne-enabled turn-on click bioconjugation with cascade signal amplification for ultrafast and high-throughput antibiotic screening. Proc Natl Acad Sci U S A 2023; 120:e2302367120. [PMID: 37364107 PMCID: PMC10318996 DOI: 10.1073/pnas.2302367120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Antimicrobial susceptibility testing plays a pivotal role in the discovery of new antibiotics. However, the development of simple, sensitive, and rapid assessment approaches remains challenging. Herein, we report an activated alkyne-based cascade signal amplification strategy for ultrafast and high-throughput antibiotic screening. First of all, a novel water-soluble aggregation-induced emission (AIE) luminogen is synthesized, which contains an activated alkyne group to enable fluorescence turn-on and metal-free click bioconjugation under physiological conditions. Taking advantage of the in-house established method for bacterial lysis, a number of clickable biological substances (i.e., bacterial solutes and debris) are released from the bacterial bodies, which remarkably increases the quantity of analytes. By means of the activated alkyne-mediated turn-on click bioconjugation, the system fluorescence signal is significantly amplified due to the increased labeling sites as well as the AIE effect. Such a cascade signal amplification strategy efficiently improves the detection sensitivity and thus enables ultrafast antimicrobial susceptibility assessment. By integration with a microplate reader, this approach is further applied to high-throughput antibiotic screening.
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Affiliation(s)
- Shuyi Lv
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Chao Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Ke Xue
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Jiaxin Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Minghui Xiao
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Zhencheng Sun
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Lei Han
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong266109, China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Chunlei Zhu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
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23
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Liang T, Yang C, Song X, Feng Y, Liu Y, Chen H. Quantification of macromolecule crowding at single-molecule level. Phys Rev E 2023; 108:014406. [PMID: 37583195 DOI: 10.1103/physreve.108.014406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/19/2023] [Indexed: 08/17/2023]
Abstract
Macromolecule crowding has a prominent impact on a series of biochemical processes in the cell. It is also expected to promote macromolecular complexation induced by excluded volume effects, which conflicts with recent advances in the thermodynamic interaction between inert, synthetic polymers, and nucleic acids. Along this line, a method combining high-resolution magnetic tweezers and extended crowder-oxDNA model was applied to resolve these discrepancies by systematically studying the kinetics and thermodynamics of the folding-unfolding transition for an individual DNA hairpin in a crowded environment. More specifically, from the magnetic tweezers-based experiments, the linear dependence of the critical force of the DNA hairpin on the polyethylene glycol (PEG) concentration was demonstrated, which is consistent with the results based on the crowder-oxDNA model in which the Lennard-Jones potential was adopted to express the interaction between the crowders and the DNA hairpin. These consistencies highlight that the excluded volume effects are mainly responsible for the interaction between PEG and the DNA hairpin, which is different from the interaction between dextran and the DNA hairpin. In the meantime, the dependence of the folding rate on the molecule weight of PEG, which was different from fluorescence resonance energy transfer-based results, was identified. The proposed method opens a path to detect the interaction between an inert, synthetic molecule, and the DNA hairpin, which is important to accurately mimic the cytosolic environments using mixtures of different inert molecules.
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Affiliation(s)
- Ting Liang
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Chao Yang
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Xiaoya Song
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Yuyu Feng
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Yanhui Liu
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
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24
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Kitahara Y, van Teeffelen S. Bacterial growth - from physical principles to autolysins. Curr Opin Microbiol 2023; 74:102326. [PMID: 37279609 DOI: 10.1016/j.mib.2023.102326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 06/08/2023]
Abstract
For bacteria to increase in size, they need to enzymatically expand their cell envelopes, and more concretely their peptidoglycan cell wall. A major task of growth is to increase intracellular space for the accumulation of macromolecules, notably proteins, RNA, and DNA. Here, we review recent progress in our understanding of how cells coordinate envelope growth with biomass growth, focusing on elongation of rod-like bacteria. We first describe the recent discovery that surface area, but not cell volume, increases in proportion to mass growth. We then discuss how this relation could possibly be implemented mechanistically, reviewing the role of envelope insertion for envelope growth. Since cell-wall expansion requires the well-controlled activity of autolysins, we finally review recent progress in our understanding of autolysin regulation.
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Affiliation(s)
- Yuki Kitahara
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Sven van Teeffelen
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada.
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25
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Morra R, Pratama F, Butterfield T, Tomazetto G, Young K, Lopez R, Dixon N. arfA antisense RNA regulates MscL excretory activity. Life Sci Alliance 2023; 6:e202301954. [PMID: 37012050 PMCID: PMC10070815 DOI: 10.26508/lsa.202301954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Excretion of cytoplasmic protein (ECP) is a commonly observed phenomenon in bacteria, and this partial extracellular localisation of the intracellular proteome has been implicated in a variety of stress response mechanisms. In response to hypoosmotic shock and ribosome stalling in Escherichia coli, ECP is dependent upon the presence of the large-conductance mechanosensitive channel and the alternative ribosome-rescue factor A gene products. However, it is not known if a mechanistic link exists between the corresponding genes and the respective stress response pathways. Here, we report that the corresponding mscL and arfA genes are commonly co-located on the genomes of Gammaproteobacteria and display overlap in their respective 3' UTR and 3' CDS. We show this unusual genomic arrangement permits an antisense RNA-mediated regulatory control between mscL and arfA, and this modulates MscL excretory activity in E. coli These findings highlight a mechanistic link between osmotic, translational stress responses and ECP in E. coli, further elucidating the previously unknown regulatory function of arfA sRNA.
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Affiliation(s)
- Rosa Morra
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Fenryco Pratama
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Institut Teknologi Bandung, Bandung, Indonesia
| | - Thomas Butterfield
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Geizecler Tomazetto
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Kate Young
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Ruth Lopez
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Neil Dixon
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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26
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Wagner L, Jules M, Borkowski O. What remains from living cells in bacterial lysate-based cell-free systems. Comput Struct Biotechnol J 2023; 21:3173-3182. [PMID: 37333859 PMCID: PMC10275740 DOI: 10.1016/j.csbj.2023.05.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Because they mimic cells while offering an accessible and controllable environment, lysate-based cell-free systems (CFS) have emerged as valuable biotechnology tools for synthetic biology. Historically used to uncover fundamental mechanisms of life, CFS are nowadays used for a multitude of purposes, including protein production and prototyping of synthetic circuits. Despite the conservation of fundamental functions in CFS like transcription and translation, RNAs and certain membrane-embedded or membrane-bound proteins of the host cell are lost when preparing the lysate. As a result, CFS largely lack some essential properties of living cells, such as the ability to adapt to changing conditions, to maintain homeostasis and spatial organization. Regardless of the application, shedding light on the black-box of the bacterial lysate is necessary to fully exploit the potential of CFS. Most measurements of the activity of synthetic circuits in CFS and in vivo show significant correlations because these only require processes that are preserved in CFS, like transcription and translation. However, prototyping circuits of higher complexity that require functions that are lost in CFS (cell adaptation, homeostasis, spatial organization) will not show such a good correlation with in vivo conditions. Both for prototyping circuits of higher complexity and for building artificial cells, the cell-free community has developed devices to reconstruct cellular functions. This mini-review compares bacterial CFS to living cells, focusing on functional and cellular process differences and the latest developments in restoring lost functions through complementation of the lysate or device engineering.
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27
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Dong H, Yang X, Shi J, Xiao C, Zhang Y. Exploring the Feasibility of Cell-Free Synthesis as a Platform for Polyhydroxyalkanoate (PHA) Production: Opportunities and Challenges. Polymers (Basel) 2023; 15:polym15102333. [PMID: 37242908 DOI: 10.3390/polym15102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The extensive utilization of traditional petroleum-based plastics has resulted in significant damage to the natural environment and ecological systems, highlighting the urgent need for sustainable alternatives. Polyhydroxyalkanoates (PHAs) have emerged as promising bioplastics that can compete with petroleum-based plastics. However, their production technology currently faces several challenges, primarily focused on high costs. Cell-free biotechnologies have shown significant potential for PHA production; however, despite recent progress, several challenges still need to be overcome. In this review, we focus on the status of cell-free PHA synthesis and compare it with microbial cell-based PHA synthesis in terms of advantages and drawbacks. Finally, we present prospects for the development of cell-free PHA synthesis.
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Affiliation(s)
- Huaming Dong
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jingjing Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Chunqiao Xiao
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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28
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van Zanten TS, S GP, Mayor S. Quantitative fluorescence emission anisotropy microscopy for implementing homo-fluorescence resonance energy transfer measurements in living cells. Mol Biol Cell 2023; 34:tp1. [PMID: 37144969 DOI: 10.1091/mbc.e22-09-0446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Quantitative fluorescence emission anisotropy microscopy reveals the organization of fluorescently labeled cellular components and allows their characterization in terms of changes in either rotational diffusion or homo-Förster's energy transfer characteristics in living cells. These properties provide insights into molecular organization, such as orientation, confinement, and oligomerization in situ. Here we elucidate how quantitative measurements of anisotropy using multiple microscope systems may be made by bringing out the main parameters that influence the quantification of fluorescence emission anisotropy. We focus on a variety of parameters that contribute to errors associated with the measurement of emission anisotropy in a microscope. These include the requirement for adequate photon counts for the necessary discrimination of anisotropy values, the influence of extinction ratios of the illumination source, the detector system, the role of numerical aperture, and excitation wavelength. All these parameters also affect the ability to capture the dynamic range of emission anisotropy necessary for quantifying its reduction due to homo-FRET and other processes. Finally, we provide easily implementable tests to assess whether homo-FRET is a cause for the observed emission depolarization.
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Affiliation(s)
- Thomas S van Zanten
- Cell Biology Group, National Centre for Biological Sciences, UAS-GKVK Campus, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Greeshma Pradeep S
- Cell Biology Group, National Centre for Biological Sciences, UAS-GKVK Campus, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Satyajit Mayor
- Cell Biology Group, National Centre for Biological Sciences, UAS-GKVK Campus, Tata Institute for Fundamental Research, Bangalore 560065, India
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29
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Huang DQ, Wu Q, Yang JH, Jiang Y, Li ZY, Fan NS, Jin RC. Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system. WATER RESEARCH 2023; 239:120061. [PMID: 37201375 DOI: 10.1016/j.watres.2023.120061] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.
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Affiliation(s)
- Dong-Qi Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Qian Wu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jia-Hui Yang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuan Jiang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zi-Yue Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Nian-Si Fan
- Laboratory of Water Pollution Remediation, School of Engineering, Hangzhou Normal University, Hangzhou 310018, China; School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Ren-Cun Jin
- Laboratory of Water Pollution Remediation, School of Engineering, Hangzhou Normal University, Hangzhou 310018, China; School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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30
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Scott M, Hwa T. Shaping bacterial gene expression by physiological and proteome allocation constraints. Nat Rev Microbiol 2023; 21:327-342. [PMID: 36376406 PMCID: PMC10121745 DOI: 10.1038/s41579-022-00818-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Abstract
Networks of molecular regulators are often the primary objects of focus in the study of gene regulation, with the machinery of protein synthesis tacitly relegated to the background. Shifting focus to the constraints imposed by the allocation of protein synthesis flux reveals surprising ways in which the actions of molecular regulators are shaped by physiological demands. Using carbon catabolite repression as a case study, we describe how physiological constraints are sensed through metabolic fluxes and how flux-controlled regulation gives rise to simple empirical relations between protein levels and the rate of cell growth.
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Affiliation(s)
- Matthew Scott
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada.
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA, USA.
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31
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Sakamoto S, Hamachi I. Ligand‐Directed Chemistry for Protein Labeling for Affinity‐Based Protein Analysis. Isr J Chem 2023. [DOI: 10.1002/ijch.202200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
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32
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Connecting the Dots: Macromolecular Crowding and Protein Aggregation. J Fluoresc 2023; 33:1-11. [PMID: 36417150 DOI: 10.1007/s10895-022-03082-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
Proteins are one of the dynamic macromolecules that play a significant role in many physiologically important processes to sustain life on the earth. Proteins need to be properly folded into their active conformation to perform their function. Alteration in the protein folding process may lead to the formation of misfolded conformers. Accumulation of these misfolded conformers can result in the formation of protein aggregates which are attributed to many human pathological conditions including neurodegeneration, cataract, neuromuscular disorders, and diabetes. Living cells naturally have heterogeneous crowding environments with different concentrations of various biomolecules. Macromolecular crowding condition has been found to alter the protein conformation. Here in this review, we tried to show the relation between macromolecular crowding, protein aggregation, and its consequences.
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33
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Quinn SD, Dresser L, Graham S, Conteduca D, Shepherd J, Leake MC. Crowding-induced morphological changes in synthetic lipid vesicles determined using smFRET. Front Bioeng Biotechnol 2022; 10:958026. [PMID: 36394015 PMCID: PMC9650091 DOI: 10.3389/fbioe.2022.958026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Lipid vesicles are valuable mesoscale molecular confinement vessels for studying membrane mechanics and lipid-protein interactions, and they have found utility among bio-inspired technologies, including drug delivery vehicles. While vesicle morphology can be modified by changing the lipid composition and introducing fusion or pore-forming proteins and detergents, the influence of extramembrane crowding on vesicle morphology has remained under-explored owing to a lack of experimental tools capable of capturing morphological changes on the nanoscale. Here, we use biocompatible polymers to simulate molecular crowding in vitro, and through combinations of FRET spectroscopy, lifetime analysis, dynamic light scattering, and single-vesicle imaging, we characterize how crowding regulates vesicle morphology. We show that both freely diffusing and surface-tethered vesicles fluorescently tagged with the DiI and DiD FRET pair undergo compaction in response to modest concentrations of sorbitol, polyethylene glycol, and Ficoll. A striking observation is that sorbitol results in irreversible compaction, whereas the influence of high molecular weight PEG-based crowders was found to be reversible. Regulation of molecular crowding allows for precise control of the vesicle architecture in vitro, with vast implications for drug delivery and vesicle trafficking systems. Furthermore, our observations of vesicle compaction may also serve to act as a mechanosensitive readout of extramembrane crowding.
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Affiliation(s)
- Steven D. Quinn
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Lara Dresser
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Sarah Graham
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Donato Conteduca
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Jack Shepherd
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Mark C. Leake
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
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34
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Water Stress-Driven Changes in Bacterial Cell Surface Properties. Appl Environ Microbiol 2022; 88:e0073222. [PMID: 36226960 PMCID: PMC9642014 DOI: 10.1128/aem.00732-22] [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: 11/20/2022] Open
Abstract
Increased drought intensity and frequency exposes soil bacteria to prolonged water stress. While numerous studies reported on behavioral and physiological mechanisms of bacterial adaptation to water stress, changes in bacterial cell surface properties during adaptation are not well researched. We studied adaptive changes in cell surface hydrophobicity (CSH) after exposure to osmotic (NaCl) and matric stress (polyethylene glycol 8000 [PEG 8000]) for six typical soil bacteria (Bacillus subtilis, Arthrobacter chlorophenolicus, Pseudomonas fluorescens, Novosphingobium aromaticivorans, Rhodococcus erythropolis, and Mycobacterium pallens) covering a wide range of cell surface properties. Additional physicochemical parameters (surface chemical composition, surface charge, cell size and stiffness) of B. subtilis and P. fluorescens were analyzed to understand their possible contribution to CSH development. Changes in CSH caused by osmotic and matric stress depend on strain and stress type. CSH of B. subtilis and P. fluorescens increased with stress intensity, R. erythropolis and M. pallens exhibited a generally high but constant contact angle, while the response of A. chlorophenolicus and N. aromaticivorans depended on growth conditions and stress type. Osmotically driven changes in CSH of B. subtilis and P. fluorescens are accompanied by increasing surface N/C ratio, suggesting an increase in protein concentration within the cell wall. Cell envelope proteins thus presumably control bacterial CSH in two ways: (i) by increases in the relative density of surface proteins due to efflux of cytoplasmic water and subsequent cell shrinkage, and (ii) by destabilization of cell wall proteins, resulting in conformational changes which render the surface more hydrophobic. IMPORTANCE Changes in precipitation frequency, intensity, and temporal distribution are projected to result in increased frequency and intensity of droughts and heavy rainfall events. Prolonged droughts can promote the development of soil water repellency (SWR); this impacts the infiltration and distribution of water in the soil profile, exposing soil microorganisms to water stress. Exposure to water stress has recently been reported to result in increased cell surface hydrophobicity. However, the mechanism of this development is poorly understood. This study investigates the changes in the physicochemical properties of bacterial cell surfaces under water stress as a possible mechanism of increased surface hydrophobicity. Our results improve understanding of the microbial response to water stress in terms of surface properties, the variations in stress response depending on cell wall composition, and its contribution to the development of SWR.
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35
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Li W, Whitcomb KL, Warncke K. Confinement dependence of protein-associated solvent dynamics around different classes of proteins, from the EPR spin probe perspective. Phys Chem Chem Phys 2022; 24:23919-23928. [PMID: 36165617 PMCID: PMC10371532 DOI: 10.1039/d2cp03047k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein function is modulated by coupled solvent fluctuations, subject to the degree of confinement from the surroundings. To identify universal features of the external confinement effect, the temperature dependence of the dynamics of protein-associated solvent over 200-265 K for proteins representative of different classes and sizes is characterized by using the rotational correlation time (detection bandwidth, 10-10-10-7 s) of the electron paramagnetic resonance (EPR, X-band) spin probe, TEMPOL, which is restricted to regions vicinal to protein in frozen aqueous solution. Weak (protein surrounded by aqueous-dimethylsulfoxide cryosolvent mesodomain) and strong (no added crysolvent) conditions of ice boundary confinement are imposed. The panel of soluble proteins represents large and small oligomeric (ethanolamine ammonia-lyase, 488 kDa; streptavidin, 52.8 kDa) and monomeric (myoglobin, 16.7 kDa) globular proteins, an intrinsically disordered protein (IDP, β-casein, 24.0 kDa), an unstructured peptide (protamine, 4.38 kDa) and a small peptide with partial backbone order (amyloid-β residues 1-16, 1.96 kDa). Expanded and condensate structures of β-casein and protamine are resolved by the spin probe under weak and strong confinement, respectively. At each confinement condition, the soluble globular proteins display common T-dependences of rotational correlation times and normalized weights, for two mobility components, protein-associated domain, PAD, and surrounding mesodomain. Strong confinement induces a detectable PAD component and emulation of globular protein T-dependence by the amyloid-β peptide. Confinement uniformly impacts soluble globular protein PAD dynamics, and is therefore a generic control parameter for modulation of soluble globular protein function.
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Affiliation(s)
- Wei Li
- Department of Physics, Emory University, Atlanta, Georgia, 30322.
| | | | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia, 30322.
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36
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Figueroa B, Xu FX, Hu R, Men S, Fu D. Quantitative Imaging of Intracellular Density with Ratiometric Stimulated Raman Scattering Microscopy. J Phys Chem B 2022; 126:7595-7603. [PMID: 36135097 DOI: 10.1021/acs.jpcb.2c04355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell size and density are tightly controlled in mammalian cells. They impact a wide range of physiological functions, including osmoregulation, tissue homeostasis, and growth regulation. Compared to size, density variation for a given cell type is typically much smaller, implying that cell-type-specific density plays an important role in cell function. However, little is known about how cell density affects cell function or how it is regulated. Current tools for intracellular cell density measurements are limited to either suspended cells or cells grown on 2D substrates, neither of which recapitulate the physiology of single cells in intact tissue. While optical measurements have the potential to noninvasively measure cell density in situ, light scattering in multicellular systems prevents direct quantification. Here, we introduce an intracellular density imaging technique based on ratiometric stimulated Raman scattering microscopy (rSRS). It uses intrinsic vibrational information from intracellular macromolecules to quantify dry mass density. Moreover, water is used as an internal standard to correct for aberration and light scattering effects. We demonstrate real-time measurement of intracellular density and show that density is tightly regulated across different cell types and can be used to differentiate cell types as well as cell states. We further demonstrate dynamic imaging of density change in response to osmotic challenge as well as intracellular density imaging of a 3D tumor spheroid. Our technique has the potential for imaging intracellular density in intact tissue and understanding density regulation and its role in tissue homeostasis.
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Affiliation(s)
- Benjamin Figueroa
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Fiona Xi Xu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ruoqian Hu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Shuaiqian Men
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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37
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Czech L, Gertzen C, Smits SHJ, Bremer E. Guilty by association: importers, exporters and
MscS
‐type mechanosensitive channels encoded in biosynthetic gene clusters for the stress‐protectant ectoine. Environ Microbiol 2022; 24:5306-5331. [DOI: 10.1111/1462-2920.16203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Czech
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
- Department of Chemistry and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Christoph Gertzen
- Center for Structural Studies (CSS) Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
- Institute of Pharmaceutical and Medicinal Chemistry Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
| | - Sander H. J. Smits
- Center for Structural Studies (CSS) Heinrich‐Heine‐University Düsseldorf Düsseldorf Germany
- Institute of Biochemistry Heinrich Heine University Düsseldorf Düsseldorf Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
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38
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Śmigiel WM, Mantovanelli L, Linnik DS, Punter M, Silberberg J, Xiang L, Xu K, Poolman B. Protein diffusion in Escherichia coli cytoplasm scales with the mass of the complexes and is location dependent. SCIENCE ADVANCES 2022; 8:eabo5387. [PMID: 35960807 PMCID: PMC9374337 DOI: 10.1126/sciadv.abo5387] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/28/2022] [Indexed: 05/30/2023]
Abstract
We analyze the structure of the cytoplasm by performing single-molecule displacement mapping on a diverse set of native cytoplasmic proteins in exponentially growing Escherichia coli. We evaluate the method for application in small compartments and find that confining effects of the cell membrane affect the diffusion maps. Our analysis reveals that protein diffusion at the poles is consistently slower than in the center of the cell, i.e., to an extent greater than the confining effect of the cell membrane. We also show that the diffusion coefficient scales with the mass of the used probes, taking into account the oligomeric state of the proteins, while parameters such as native protein abundance or the number of protein-protein interactions do not correlate with the mobility of the proteins. We argue that our data paint the prokaryotic cytoplasm as a compartment with subdomains in which the diffusion of macromolecules changes with the perceived viscosity.
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Affiliation(s)
- Wojciech M. Śmigiel
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Luca Mantovanelli
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Dmitrii S. Linnik
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Michiel Punter
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Jakob Silberberg
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Limin Xiang
- Department of Chemistry, UC Berkeley, Stanley Hall, Berkeley, CA 94720, USA
| | - Ke Xu
- Department of Chemistry, UC Berkeley, Stanley Hall, Berkeley, CA 94720, USA
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
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39
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Joshi A, Kishore N. Macromolecular crowding and preferential exclusion counteract the effect of protein denaturant: Biophysical aspects. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Structure-Function Relationships in Temperature Effects on Bacterial Luciferases: Nothing Is Perfect. Int J Mol Sci 2022; 23:ijms23158119. [PMID: 35897698 PMCID: PMC9332260 DOI: 10.3390/ijms23158119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
The evaluation of temperature effects on the structure and function of enzymes is necessary to understand the mechanisms underlying their adaptation to a constantly changing environment. In the current study, we investigated the influence of temperature variation on the activity, structural dynamics, thermal inactivation and denaturation of Photobacterium leiognathi and Vibrio harveyi luciferases belonging to different subfamilies, as well as the role of sucrose in maintaining the enzymes functioning and stability. We used the stopped-flow technique, differential scanning calorimetry and molecular dynamics to study the activity, inactivation rate, denaturation and structural features of the enzymes under various temperatures. It was found that P. leiognathi luciferase resembles the properties of cold-adapted enzymes with high activity in a narrow temperature range and slightly lower thermal stability than V. harveyi luciferase, which is less active, but more thermostable. Differences in activity at the studied temperatures can be associated with the peculiarities of the mobile loop conformational changes. The presence of sucrose does not provide an advantage in activity but increases the stability of the enzymes. Differential scanning calorimetry experiments showed that luciferases probably follow different denaturation schemes.
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41
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Morimoto R, Horita M, Yamaguchi D, Nakai H, Nakano SI. Evaluation of Weak Interactions of Proteins and Organic Cations with DNA Duplex Structures. Biophys J 2022; 121:2873-2881. [PMID: 35791875 PMCID: PMC9388550 DOI: 10.1016/j.bpj.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/02/2022] Open
Abstract
Molecular interactions and reactions in living cells occur with high background concentrations of organic compounds including proteins. Uncharged water-soluble polymers are commonly used cosolutes in studies on molecular crowding, and most studies argue about the effects of intracellular crowding based on results obtained using polymer cosolutes. Further investigations using protein crowders and organic cations are important in understanding the effects of cellular environments on nucleic acids with negatively charged surfaces. We assessed the effects of using model globular proteins, serum proteins, histone proteins, structurally flexible polypeptides, di- and polyamines, and uncharged polymers. Thermal stability analysis of DNA oligonucleotide structures revealed that unlike conventional polymer cosolutes, basic globular proteins (lysozyme and cytochrome c) at high concentrations stabilized long internal and bulge loop structures but not fully matched duplexes. The selective stabilization of long loop structures suggests preferential binding to unpaired nucleotides in loops through weak electrostatic interactions. Furthermore, the ability of the proteins to stabilize the loop structures was enhanced under macromolecular crowding conditions. Remarkably, the effects of basic proteins on the stability of fully matched duplexes were dissimilar to those of basic amino-acid-rich polypeptides and polyamines. This study provides new insights into the interaction of nucleic acid structures with organic cations.
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Stecker D, Hoffmann T, Link H, Commichau FM, Bremer E. L-Proline Synthesis Mutants of Bacillus subtilis Overcome Osmotic Sensitivity by Genetically Adapting L-Arginine Metabolism. Front Microbiol 2022; 13:908304. [PMID: 35783388 PMCID: PMC9245794 DOI: 10.3389/fmicb.2022.908304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
The accumulation of the compatible solute L-proline by Bacillus subtilis via synthesis is a cornerstone in the cell’s defense against high salinity as the genetic disruption of this biosynthetic process causes osmotic sensitivity. To understand how B. subtilis could potentially cope with high osmolarity surroundings without the functioning of its natural osmostress adaptive L-proline biosynthetic route (ProJ-ProA-ProH), we isolated suppressor strains of proA mutants under high-salinity growth conditions. These osmostress-tolerant strains carried mutations affecting either the AhrC transcriptional regulator or its operator positioned in front of the argCJBD-carAB-argF L-ornithine/L-citrulline/L-arginine biosynthetic operon. Osmostress protection assays, molecular analysis and targeted metabolomics showed that these mutations, in conjunction with regulatory mutations affecting rocR-rocDEF expression, connect and re-purpose three different physiological processes: (i) the biosynthetic pathway for L-arginine, (ii) the RocD-dependent degradation route for L-ornithine, and (iii) the last step in L-proline biosynthesis. Hence, osmostress adaptation without a functional ProJ-ProA-ProH route is made possible through a naturally existing, but inefficient, metabolic shunt that allows to substitute the enzyme activity of ProA by feeding the RocD-formed metabolite γ-glutamate-semialdehyde/Δ1-pyrroline-5-carboxylate into the biosynthetic route for the compatible solute L-proline. Notably, in one class of mutants, not only substantial L-proline pools but also large pools of L-citrulline were accumulated, a rather uncommon compatible solute in microorganisms. Collectively, our data provide an example of the considerable genetic plasticity and metabolic resourcefulness of B. subtilis to cope with everchanging environmental conditions.
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Affiliation(s)
- Daniela Stecker
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Hannes Link
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Fabian M. Commichau
- Insitute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
- Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Erhard Bremer
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
- *Correspondence: Erhard Bremer,
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43
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Li C, Zhang X, Dong M, Han X. Progress on Crowding Effect in Cell-like Structures. MEMBRANES 2022; 12:593. [PMID: 35736300 PMCID: PMC9228500 DOI: 10.3390/membranes12060593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022]
Abstract
Several biological macromolecules, such as proteins, nucleic acids, and polysaccharides, occupy about 30% of the space in cells, resulting in a crowded macromolecule environment. The crowding effect within cells exerts an impact on the functions of biological components, the assembly behavior of biomacromolecules, and the thermodynamics and kinetics of metabolic reactions. Cell-like structures provide confined and independent compartments for studying the working mechanisms of cells, which can be used to study the physiological functions arising from the crowding effect of macromolecules in cells. This article mainly summarizes the progress of research on the macromolecular crowding effects in cell-like structures. It includes the effects of this crowding on actin assembly behavior, tubulin aggregation behavior, and gene expression. The challenges and future trends in this field are presented at the end of the paper.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
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44
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Morawska LP, Detert Oude Weme RGJ, Frenzel E, Dirkzwager M, Hoffmann T, Bremer E, Kuipers OP. Stress-induced activation of the proline biosynthetic pathway in Bacillus subtilis: a population-wide and single-cell study of the osmotically controlled proHJ promoter. Microb Biotechnol 2022; 15:2411-2425. [PMID: 35593133 PMCID: PMC9437891 DOI: 10.1111/1751-7915.14073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 12/01/2022] Open
Abstract
Bacillus subtilis, in its natural habitat, is regularly exposed to rapid changes in the osmolarity of its surrounding. As its primary survival strategy, it accumulates large amounts of the compatible solute proline by activating the de novo proline biosynthesis pathway and exploiting the glutamate pools. This osmotically‐induced biosynthesis requires activation of a SigA‐type promoter that drives the expression of the proHJ operon. Population‐wide studies have shown that the activity of the proHJ promoter correlates with the increased osmotic pressure of the environment. Therefore, the activation of the proHJ transcription should be an adequate measure of the adaptation to osmotic stress through proline synthesis in the absence of other osmoprotectants. In this study, we investigate the kinetics of the proHJ promoter activation and the early adaptation to mild osmotic upshift at the single‐cell level. Under these conditions, we observed a switching point and heterogeneous proline biosynthesis gene expression, where the subpopulation of cells showing active proHJ transcription is able to continuously divide, and those unresponsive to osmotic stress remain dormant. Additionally, we demonstrate that bactericidal antibiotics significantly upregulate proHJ transcription in the absence of externally imposed osmotic pressure, suggesting that the osmotically‐controlled proline biosynthesis pathway is also involved in the antibiotic‐mediated stress response.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Ruud G J Detert Oude Weme
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Elrike Frenzel
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Maarten Dirkzwager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps University Marburg, Karl-von-Frisch-Str.8, D-35032, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch Strasse 14, 35043, Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps University Marburg, Karl-von-Frisch-Str.8, D-35032, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch Strasse 14, 35043, Marburg, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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Abstract
The hypervariable residues that compose the major part of proteins’ surfaces are generally considered outside evolutionary control. Yet, these “nonconserved” residues determine the outcome of stochastic encounters in crowded cells. It has recently become apparent that these encounters are not as random as one might imagine, but carefully orchestrated by the intracellular electrostatics to optimize protein diffusion, interactivity, and partner search. The most influential factor here is the protein surface-charge density, which takes different optimal values across organisms with different intracellular conditions. In this study, we examine how far the net-charge density and other physicochemical properties of proteomes will take us in terms of distinguishing organisms in general. The results show that these global proteome properties not only follow the established taxonomical hierarchy, but also provide clues to functional adaptation. In many cases, the proteome–property divergence is even resolved at species level. Accordingly, the variable parts of the genes are not as free to drift as they seem in sequence alignment, but present a complementary tool for functional, taxonomic, and evolutionary assignment.
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46
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Density fluctuations, homeostasis, and reproduction effects in bacteria. Commun Biol 2022; 5:397. [PMID: 35484403 PMCID: PMC9050864 DOI: 10.1038/s42003-022-03348-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 04/10/2022] [Indexed: 12/02/2022] Open
Abstract
Single-cells grow by increasing their biomass and size. Here, we report that while mass and size accumulation rates of single Escherichia coli cells are exponential, their density and, thus, the levels of macromolecular crowding fluctuate during growth. As such, the average rates of mass and size accumulation of a single cell are generally not the same, but rather cells differentiate into increasing one rate with respect to the other. This differentiation yields a density homeostasis mechanism that we support mathematically. Further, we observe that density fluctuations can affect the reproduction rates of single cells, suggesting a link between the levels of macromolecular crowding with metabolism and overall population fitness. We detail our experimental approach and the “invisible” microfluidic arrays that enabled increased precision and throughput. Infections and natural communities start from a few cells, thus, emphasizing the significance of density-fluctuations when taking non-genetic variability into consideration. Quantitative imaging, invisible microfluidics, and mathematical models demonstrate how the density of single E. coli cells fluctuates during the cell cycle, unmasking key homeostasis and population fitness effects.
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47
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Oh S, Lee C, Yang W, Li A, Mukherjee A, Basan M, Ran C, Yin W, Tabin CJ, Fu D, Xie XS, Kirschner MW. Protein and lipid mass concentration measurement in tissues by stimulated Raman scattering microscopy. Proc Natl Acad Sci U S A 2022; 119:e2117938119. [PMID: 35452314 PMCID: PMC9169924 DOI: 10.1073/pnas.2117938119] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/21/2022] [Indexed: 01/10/2023] Open
Abstract
Cell mass and chemical composition are important aggregate cellular properties that are especially relevant to physiological processes, such as growth control and tissue homeostasis. Despite their importance, it has been difficult to measure these features quantitatively at the individual cell level in intact tissue. Here, we introduce normalized Raman imaging (NoRI), a stimulated Raman scattering (SRS) microscopy method that provides the local concentrations of protein, lipid, and water from live or fixed tissue samples with high spatial resolution. Using NoRI, we demonstrate that protein, lipid, and water concentrations at the single cell are maintained in a tight range in cells under the same physiological conditions and are altered in different physiological states, such as cell cycle stages, attachment to substrates of different stiffness, or by entering senescence. In animal tissues, protein and lipid concentration varies with cell types, yet an unexpected cell-to-cell heterogeneity was found in cerebellar Purkinje cells. The protein and lipid concentration profile provides means to quantitatively compare disease-related pathology, as demonstrated using models of Alzheimer’s disease. This demonstration shows that NoRI is a broadly applicable technique for probing the biological regulation of protein mass, lipid mass, and water mass for studies of cellular and tissue growth, homeostasis, and disease.
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Affiliation(s)
- Seungeun Oh
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - ChangHee Lee
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Wenlong Yang
- Center for Advanced Imaging, Harvard University, Cambridge, MA 20138
| | - Ang Li
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Avik Mukherjee
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Markus Basan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129
| | - Wei Yin
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129
| | | | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - X. Sunney Xie
- Biomedical Pioneering Innovation Center, Peking University, Beijing 100871; China
| | - Marc W. Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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48
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Cubuk J, Soranno A. Macromolecular crowding and intrinsically disordered proteins: a polymer physics perspective. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202100051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Cubuk
- Washington University in St Louis Biochemistry and Molecular Biophysics UNITED STATES
| | - Andrea Soranno
- Washington University in St Louis Biochemistry and Molecular Biophysics 660 St Euclid Ave 63110 St Louis UNITED STATES
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49
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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50
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Landon C, Zhu Y, Mustafi M, Madinier JB, Lelièvre D, Aucagne V, Delmas AF, Weisshaar JC. Real-Time Fluorescence Microscopy on Living E. coli Sheds New Light on the Antibacterial Effects of the King Penguin β-Defensin AvBD103b. Int J Mol Sci 2022; 23:ijms23042057. [PMID: 35216173 PMCID: PMC8880245 DOI: 10.3390/ijms23042057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
(1) Antimicrobial peptides (AMPs) are a promising alternative to conventional antibiotics. Among AMPs, the disulfide-rich β-defensin AvBD103b, whose antibacterial activities are not inhibited by salts contrary to most other β-defensins, is particularly appealing. Information about the mechanisms of action is mandatory for the development and approval of new drugs. However, data for non-membrane-disruptive AMPs such as β-defensins are scarce, thus they still remain poorly understood. (2) We used single-cell fluorescence imaging to monitor the effects of a β-defensin (namely AvBD103b) in real time, on living E. coli, and at the physiological concentration of salts. (3) We obtained key parameters to dissect the mechanism of action. The cascade of events, inferred from our precise timing of membrane permeabilization effects, associated with the timing of bacterial growth arrest, differs significantly from the other antimicrobial compounds that we previously studied in the same physiological conditions. Moreover, the AvBD103b mechanism does not involve significant stereo-selective interaction with any chiral partner, at any step of the process. (4) The results are consistent with the suggestion that after penetrating the outer membrane and the cytoplasmic membrane, AvBD103b interacts non-specifically with a variety of polyanionic targets, leading indirectly to cell death.
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Affiliation(s)
- Céline Landon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
- Correspondence:
| | - Yanyu Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
| | - Mainak Mustafi
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
| | - Jean-Baptiste Madinier
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - Dominique Lelièvre
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - Vincent Aucagne
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - Agnes F. Delmas
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - James C. Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
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