1
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Son JB, Kim S, Yang S, Ahn Y, Lee NK. Analysis of Fluorescent Proteins for Observing Single Gene Locus in a Live and Fixed Escherichia coli Cell. J Phys Chem B 2024; 128:6730-6741. [PMID: 38968413 PMCID: PMC11264270 DOI: 10.1021/acs.jpcb.4c01816] [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: 03/19/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Fluorescent proteins (FPs) are essential tools for advanced microscopy techniques such as super-resolution imaging, single-particle tracking, and quantitative single-molecule counting. Various FPs fused to DNA-binding proteins have been used to observe the subcellular location and movement of specific gene loci in living and fixed bacterial cells. However, quantitative assessments of the properties of FPs for gene locus measurements are still lacking. Here, we assessed various FPs to observe specific gene loci in live and fixed Escherichia coli cells using a fluorescent repressor-operator binding system (FROS), tet operator-Tet repressor proteins (TetR). Tsr-fused FPs were used to assess the intensity and photostability of various FPs (five red FPs: mCherry2, FusionRed, mRFP, mCrimson3, and dKatushka; and seven yellow FPs: SYFP2, Venus, mCitrine, YPet, mClover3, mTopaz, and EYFP) at the single-molecule level in living cells. These FPs were then used for gene locus measurements using FROS. Our results indicate that TetR-mCrimson3 (red) and TetR-EYFP (yellow) had better properties for visualizing gene loci than the other TetR-FPs. Furthermore, fixation procedures affected the clustering of diffusing TetR-FPs and altered the locations of the TetR-FP foci. Fixation with formaldehyde consistently disrupted proper DNA locus observations using TetR-FPs. Notably, the foci measured using TetR-mCrimson3 remained close to their original positions in live cells after glyoxal fixation. This in vivo study provides a cell-imaging guide for the use of FPs for gene-locus observation in E. coli and a scheme for evaluating the use of FPs for other cell-imaging purposes.
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Affiliation(s)
| | | | | | - Youmin Ahn
- Department of Chemistry, Seoul
National University, 08826 Seoul, South
Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul
National University, 08826 Seoul, South
Korea
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2
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Wu L, Zhang Y, Hong X, Wu M, Wang L, Yan X. Deciphering the Relationship between Cell Growth and Cell Cycle in Individual Escherichia coli Cells by Flow Cytometry. Anal Chem 2024. [PMID: 39015018 DOI: 10.1021/acs.analchem.4c02058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Accurate coordination of chromosome replication and cell division is essential for cellular processes, yet the regulatory mechanisms governing the bacterial cell cycle remain contentious. The lack of quantitative data connecting key cell cycle players at the single-cell level across large samples hinders consensus. Employing high-throughput flow cytometry, we quantitatively correlated the expression levels of key cell cycle proteins (FtsZ, MreB, and DnaA) with DNA content in individual bacteria. Our findings reveal distinct correlations depending on the chromosome number (CN), specifically whether CN ≤2 or ≥4, unveiling a mixed regulatory scenario in populations where CN of 2 or 4 coexist. We observed function-dependent regulations for these key proteins across nonoverlapping division cycles and various nutrient conditions. Notably, a logarithmic relationship between total protein content and replication origin number across nutrient conditions suggests a unified mechanism governing cell cycle progression, confirming the applicability of Schaechter's growth law to cells with CN ≥4. For the first time, we established a proportional relationship between the synthesis rates of key cell cycle proteins and chromosome dynamics in cells with CN ≥4. Drug experiments highlighted CN 2 and 4 as pivotal turning points influencing cellular resource allocation. This high-throughput, single-cell analysis provides interconnected quantitative insights into key molecular events, facilitating a predictive understanding of the relationship between cell growth and cell cycle.
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Affiliation(s)
- Lina Wu
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Yuzhen Zhang
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Xinyi Hong
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Mingkai Wu
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Liangan Wang
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Xiaomei Yan
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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3
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Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nat Rev Mol Cell Biol 2024; 25:534-554. [PMID: 38509203 PMCID: PMC11199108 DOI: 10.1038/s41580-024-00706-2] [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] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3'-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3'-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Morgan Shine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jackson Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dagmar Zigackova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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4
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Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q. An evolutionary optimum amid moderate heritability in prokaryotic cell size. Cell Rep 2024; 43:114268. [PMID: 38776226 DOI: 10.1016/j.celrep.2024.114268] [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: 01/04/2024] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
We investigate the distribution and evolution of prokaryotic cell size based on a compilation of 5,380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita); however, most species congregate heavily around the mean. The distribution approximates but is distinct from log normality. Comparative phylogenetics suggests that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e., fractal). Evolutionary modeling indicates the presence of an optimal cell size to which most species gravitate. The size is equivalent to a coccus of 0.70 μm in diameter. Analyses of 1,361 species with sequenced genomes show that genomic traits contribute to size evolution moderately and synergistically. Given our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.
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Affiliation(s)
- Henry Secaira-Morocho
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abhinav Chede
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Luis Gonzalez-de-Salceda
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Qiyun Zhu
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
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5
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Ciolli Mattioli C, Avraham R. Protocol for comparing ribosomal levels in single bacterial cells at different growth stages using rRNA-FISH. STAR Protoc 2024; 5:103137. [PMID: 38878285 PMCID: PMC11234016 DOI: 10.1016/j.xpro.2024.103137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 07/13/2024] Open
Abstract
Ribosome quantification in single cells is typically achieved through fluorescence tagging of ribosomal proteins. Here, we present a protocol for comparing ribosomal levels in bacteria at different growth stages using fluorescence in situ hybridization of rRNA (rRNA-FISH), eliminating the need for genetic engineering of the strain of interest. We detail the steps for preparing bacterial samples, staining with fluorescent probes, and acquiring data using flow cytometry and microscopy. Furthermore, we provide guidelines on controlling for proper labeling through signal localization analysis. For complete details on the use and execution of this protocol, please refer to Ciolli Mattioli et al.1.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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6
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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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7
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Woldringh CL. Compaction and Segregation of DNA in Escherichia coli. Life (Basel) 2024; 14:660. [PMID: 38929644 PMCID: PMC11205073 DOI: 10.3390/life14060660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/28/2024] Open
Abstract
Theoretical and experimental approaches have been applied to study the polymer physics underlying the compaction of DNA in the bacterial nucleoid. Knowledge of the compaction mechanism is necessary to obtain a mechanistic understanding of the segregation process of replicating chromosome arms (replichores) during the cell cycle. The first part of this review discusses light microscope observations demonstrating that the nucleoid has a lower refractive index and thus, a lower density than the cytoplasm. A polymer physics explanation for this phenomenon was given by a theory discussed at length in this review. By assuming a phase separation between the nucleoid and the cytoplasm and by imposing equal osmotic pressure and chemical potential between the two phases, a minimal energy situation is obtained, in which soluble proteins are depleted from the nucleoid, thus explaining its lower density. This theory is compared to recent views on DNA compaction that are based on the exclusion of polyribosomes from the nucleoid or on the transcriptional activity of the cell. These new views prompt the question of whether they can still explain the lower refractive index or density of the nucleoid. In the second part of this review, we discuss the question of how DNA segregation occurs in Escherichia coli in the absence of the so-called active ParABS system, which is present in the majority of bacteria. How is the entanglement of nascent chromosome arms generated at the origin in the parental DNA network of the E. coli nucleoid prevented? Microscopic observations of the position of fluorescently-labeled genetic loci have indicated that the four nascent chromosome arms synthesized in the initial replication bubble segregate to opposite halves of the sister nucleoids. This implies that extensive intermingling of daughter strands does not occur. Based on the hypothesis that leading and lagging replichores synthesized in the replication bubble fold into microdomains that do not intermingle, a passive four-excluding-arms model for segregation is proposed. This model suggests that the key for segregation already exists in the structure of the replication bubble at the very start of DNA replication; it explains the different patterns of chromosome arms as well as the segregation distances between replicated loci, as experimentally observed.
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Affiliation(s)
- Conrad L Woldringh
- Faculty of Science, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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8
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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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9
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Prichard A, Sy A, Meyer J, Villa E, Pogliano J. Asesino: a nucleus-forming phage that lacks PhuZ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593592. [PMID: 38766163 PMCID: PMC11100802 DOI: 10.1101/2024.05.10.593592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the proposed Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning. One clade that represents 24% of all currently known chimalliviruses lacks a PhuZ homolog. Here we show that Erwinia phage Asesino, one member of this PhuZ-less clade, shares a common overall replication mechanism with other characterized nucleus-forming phages despite lacking PhuZ. We show that Asesino replicates via a phage nucleus that encloses phage DNA and partitions proteins in the nuclear compartment and cytoplasm in a manner similar to previously characterized nucleus-forming phages. Consistent with a lack of PhuZ, however, we did not observe active positioning or rotation of the phage nucleus within infected cells. These data show that some nucleus-forming phages have evolved to replicate efficiently without PhuZ, providing an example of a unique variation in the nucleus-based replication pathway.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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10
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Nagarajan T, Gayathri MP, Mack J, Nyokong T, Govindarajan S, Babu B. Blue-Light-Activated Water-Soluble Sn(IV)-Porphyrins for Antibacterial Photodynamic Therapy (aPDT) against Drug-Resistant Bacterial Pathogens. Mol Pharm 2024; 21:2365-2374. [PMID: 38620059 DOI: 10.1021/acs.molpharmaceut.3c01162] [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] [Indexed: 04/17/2024]
Abstract
Antimicrobial resistance has emerged as a global threat to the treatment of infectious diseases. Antibacterial photodynamic therapy (aPDT) is a promising alternative approach and is highly suitable for the treatment of cutaneous bacterial infections through topical applications. aPDT relies on light-responsive compounds called photosensitizer (PS) dyes, which generate reactive oxygen species (ROS) when induced by light, thereby killing bacterial cells. Despite several previous studies in this area, the molecular details of targeting and cell death mediated by PS dyes are poorly understood. In this study, we further investigate the antibacterial properties of two water-soluble Sn(IV) tetrapyridylporphyrins that were quaternized with methyl and hexyl groups (1 and 2). In this follow-up study, we demonstrate that Sn(IV)-porphyrins can be photoexcited by blue light (a 427 nm LED) and exhibit various levels of bactericidal activity against both Gram-(+) and Gram-(-) strains of bacteria. Using localization studies through fluorescence microscopy, we show that 2 targets the bacterial membrane more effectively than 1 and exhibits comparatively higher aPDT activity. Using multiple fluorescence reporters, we demonstrate that photoactivation of 1 and 2 results in extensive collateral damage to the bacterial cells including DNA cleavage, membrane damage, and delocalization of central systems necessary for bacterial growth and division. In summary, this investigation provides deep insights into the mechanism of bacterial killing mediated by the Sn(IV)-porphyrins. Moreover, our approach offers a new method for evaluating the activity of PS, which may inspire the discovery of new PS with enhanced aPDT activity.
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Affiliation(s)
- T Nagarajan
- Department of Biological Sciences, SRM University-AP, Amaravati 522502, India
| | - M P Gayathri
- Department of Chemistry, SRM University-AP, Amaravati 522502, India
| | - John Mack
- Institute for Nanotechnology Innovation, Rhodes University, Makhanda 6140, South Africa
| | - Tebello Nyokong
- Institute for Nanotechnology Innovation, Rhodes University, Makhanda 6140, South Africa
| | | | - Balaji Babu
- Department of Chemistry, SRM University-AP, Amaravati 522502, India
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11
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Thappeta Y, Cañas-Duarte SJ, Kallem T, Fragasso A, Xiang Y, Gray W, Lee C, Cegelski L, Jacobs-Wagner C. Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590186. [PMID: 38659787 PMCID: PMC11042326 DOI: 10.1101/2024.04.19.590186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bacteria often experience nutrient limitation in nature and the laboratory. While exponential and stationary growth phases are well characterized in the model bacterium Escherichia coli, little is known about what transpires inside individual cells during the transition between these two phases. Through quantitative cell imaging, we found that the position of nucleoids and cell division sites becomes increasingly asymmetric during transition phase. These asymmetries were coupled with spatial reorganization of proteins, ribosomes, and RNAs to nucleoid-centric localizations. Results from live-cell imaging experiments, complemented with genetic and 13C whole-cell nuclear magnetic resonance spectroscopy studies, show that preferential accumulation of the storage polymer glycogen at the old cell pole leads to the observed rearrangements and asymmetric divisions. In vitro experiments suggest that these phenotypes are likely due to the propensity of glycogen to phase separate in crowded environments, as glycogen condensates exclude fluorescent proteins under physiological crowding conditions. Glycogen-associated differences in cell sizes between strains and future daughter cells suggest that glycogen phase separation allows cells to store large glucose reserves without counting them as cytoplasmic space.
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Affiliation(s)
- Yashna Thappeta
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Silvia J. Cañas-Duarte
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Till Kallem
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Alessio Fragasso
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yingjie Xiang
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - William Gray
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - Cheyenne Lee
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | | | - Christine Jacobs-Wagner
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
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12
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Kim S, Wang YH, Hassan A, Kim S. Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.588412. [PMID: 38659903 PMCID: PMC11042359 DOI: 10.1101/2024.04.18.588412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In eukaryotic cells, transcription, translation, and mRNA degradation occur in distinct subcellular regions. How these mRNA processes are organized in bacteria, without employing membrane-bound compartments, remains unclear. Here, we present generalizable principles underlying coordination between these processes in bacteria. In Escherichia coli, we found that co-transcriptional degradation is rare for mRNAs except for those encoding inner membrane proteins, due to membrane localization of the main ribonuclease, RNase E. We further found, by varying ribosome binding sequences, that translation affects mRNA stability not because ribosomes protect mRNA from degradation, but because low translation leads to premature transcription termination in the absence of transcription-translation coupling. Extending our analyses to Bacillus subtilis and Caulobacter crescentus, we established subcellular localization of RNase E (or its homolog) and premature transcription termination in the absence of transcription-translation coupling as key determinants that explain differences in transcriptional and translational coupling to mRNA degradation across genes and species.
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Affiliation(s)
- Seunghyeon Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yu-Huan Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Albur Hassan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sangjin Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801, USA
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13
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Magkiriadou S, Stepp WL, Newman DK, Manley S, Racki LR. Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2024; 121:e2313004121. [PMID: 38564631 PMCID: PMC11009631 DOI: 10.1073/pnas.2313004121] [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: 08/21/2023] [Accepted: 01/26/2024] [Indexed: 04/04/2024] Open
Abstract
Polyphosphate (polyP) synthesis is a ubiquitous stress and starvation response in bacteria. In diverse species, mutants unable to make polyP have a wide variety of physiological defects, but the mechanisms by which this simple polyanion exerts its effects remain unclear. One possibility is that polyP's many functions stem from global effects on the biophysical properties of the cell. We characterize the effect of polyphosphate on cytoplasmic mobility under nitrogen-starvation conditions in the opportunistic pathogen Pseudomonas aeruginosa. Using fluorescence microscopy and particle tracking, we quantify the motion of chromosomal loci and cytoplasmic tracer particles. In the absence of polyP and upon starvation, we observe a 2- to 10-fold increase in mean cytoplasmic diffusivity. Tracer particles reveal that polyP also modulates the partitioning between a "more mobile" and a "less mobile" population: Small particles in cells unable to make polyP are more likely to be "mobile" and explore more of the cytoplasm, particularly during starvation. Concomitant with this larger freedom of motion in polyP-deficient cells, we observe decompaction of the nucleoid and an increase in the steady-state concentration of ATP. The dramatic polyP-dependent effects we observe on cytoplasmic transport properties occur under nitrogen starvation, but not carbon starvation, suggesting that polyP may have distinct functions under different types of starvation.
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Affiliation(s)
- Sofia Magkiriadou
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Willi L. Stepp
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Lisa R. Racki
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA92037
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14
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Harju J, Broedersz CP. Physical models of bacterial chromosomes. Mol Microbiol 2024. [PMID: 38578226 DOI: 10.1111/mmi.15257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can be theoretically challenging. In this minireview, we discuss how connecting experimental observations to biophysical theory and modeling can give rise to new insights on bacterial chromosome organization. We consider three flavors of models of increasing complexity: simple polymer models that explore how physical constraints, such as confinement or plectoneme branching, can affect bacterial chromosome organization; bottom-up mechanistic models that connect these constraints to their underlying causes, for instance, chromosome compaction to macromolecular crowding, or supercoiling to transcription; and finally, data-driven methods for inferring interpretable and quantitative models directly from complex experimental data. Using recent examples, we discuss how biophysical models can both deepen our understanding of how bacterial chromosomes are structured and give rise to novel predictions about bacterial chromosome organization.
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Affiliation(s)
- Janni Harju
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Chase P Broedersz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilian-University Munich, Munich, Germany
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15
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Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN. Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587083. [PMID: 38585850 PMCID: PMC10996671 DOI: 10.1101/2024.03.27.587083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The crowded bacterial cytoplasm is comprised of biomolecules that span several orders of magnitude in size and electrical charge. This complexity has been proposed as the source of the rich spatial organization and apparent anomalous diffusion of intracellular components, although this has not been tested directly. Here, we use biplane microscopy to track the 3D motion of self-assembled bacterial Genetically Encoded Multimeric nanoparticles (bGEMs) with tunable size (20 to 50 nm) and charge (-2160 to +1800 e) in live Escherichia coli cells. To probe intermolecular details at spatial and temporal resolutions beyond experimental limits, we also developed a colloidal whole-cell model that explicitly represents the size and charge of cytoplasmic macromolecules and the porous structure of the bacterial nucleoid. Combining these techniques, we show that bGEMs spatially segregate by size, with small 20-nm particles enriched inside the nucleoid, and larger and/or positively charged particles excluded from this region. Localization is driven by entropic and electrostatic forces arising from cytoplasmic polydispersity, nucleoid structure, geometrical confinement, and interactions with other biomolecules including ribosomes and DNA. We observe that at the timescales of traditional single molecule tracking experiments, motion appears sub-diffusive for all particle sizes and charges. However, using computer simulations with higher temporal resolution, we find that the apparent anomalous exponents are governed by the region of the cell in which bGEMs are located. Molecular motion does not display anomalous diffusion on short time scales and the apparent sub-diffusion arises from geometrical confinement within the nucleoid and by the cell boundary.
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Affiliation(s)
- Diana Valverde-Mendez
- Department of Physics, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Alp M. Sunol
- Department of Chemical Engineering, Stanford University, , Stanford, CA 94305, USA
| | - Benjamin P. Bratton
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Department of Pathology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection, Inflammation and Immunology, Vanderbilt University, Nashville, TN 37235, USA
| | - Morgan Delarue
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Jennifer L. Hofmann
- Department of Chemical Engineering, Stanford University, , Stanford, CA 94305, USA
| | - Joseph P. Sheehan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Liam J. Holt
- Institute for Systems Genetics, New York University School of Medicine, 435 E 30th St, NY 10016, USA
| | - Joshua W. Shaevitz
- Department of Physics, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Roseanna N. Zia
- Department of Chemical Engineering, Stanford University, , Stanford, CA 94305, USA
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16
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Tišma M, Bock FP, Kerssemakers J, Antar H, Japaridze A, Gruber S, Dekker C. Direct observation of a crescent-shape chromosome in expanded Bacillus subtilis cells. Nat Commun 2024; 15:2737. [PMID: 38548820 PMCID: PMC10979009 DOI: 10.1038/s41467-024-47094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Bacterial chromosomes are folded into tightly regulated three-dimensional structures to ensure proper transcription, replication, and segregation of the genetic information. Direct visualization of chromosomal shape within bacterial cells is hampered by cell-wall confinement and the optical diffraction limit. Here, we combine cell-shape manipulation strategies, high-resolution fluorescence microscopy techniques, and genetic engineering to visualize the shape of unconfined bacterial chromosome in real-time in live Bacillus subtilis cells that are expanded in volume. We show that the chromosomes predominantly exhibit crescent shapes with a non-uniform DNA density that is increased near the origin of replication (oriC). Additionally, we localized ParB and BsSMC proteins - the key drivers of chromosomal organization - along the contour of the crescent chromosome, showing the highest density near oriC. Opening of the BsSMC ring complex disrupted the crescent chromosome shape and instead yielded a torus shape. These findings help to understand the threedimensional organization of the chromosome and the main protein complexes that underlie its structure.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Florian Patrick Bock
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jacob Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Hammam Antar
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
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17
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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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18
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Kannaiah S, Goldberger O, Alam N, Barnabas G, Pozniak Y, Nussbaum-Shochat A, Schueler-Furman O, Geiger T, Amster-Choder O. MinD-RNase E interplay controls localization of polar mRNAs in E. coli. EMBO J 2024; 43:637-662. [PMID: 38243117 PMCID: PMC10897333 DOI: 10.1038/s44318-023-00026-9] [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: 02/03/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The E. coli transcriptome at the cell's poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.
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Affiliation(s)
- Shanmugapriya Kannaiah
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Georgina Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Pathology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yair Pozniak
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100001, Rehovot, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
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19
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Govers SK, Campos M, Tyagi B, Laloux G, Jacobs-Wagner C. Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle. Cell Syst 2024; 15:19-36.e5. [PMID: 38157847 DOI: 10.1016/j.cels.2023.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; de Duve Institute, UCLouvain, Brussels, Belgium; Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Toulouse, France
| | - Bhavyaa Tyagi
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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20
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [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: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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21
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Ciolli Mattioli C, Eisner K, Rosenbaum A, Wang M, Rivalta A, Amir A, Golding I, Avraham R. Physiological stress drives the emergence of a Salmonella subpopulation through ribosomal RNA regulation. Curr Biol 2023; 33:4880-4892.e14. [PMID: 37879333 PMCID: PMC10843543 DOI: 10.1016/j.cub.2023.09.064] [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: 06/08/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Bacteria undergo cycles of growth and starvation to which they must adapt swiftly. One important strategy for adjusting growth rates relies on ribosomal levels. Although high ribosomal levels are required for fast growth, their dynamics during starvation remain unclear. Here, we analyzed ribosomal RNA (rRNA) content of individual Salmonella cells by using fluorescence in situ hybridization (rRNA-FISH) and measured a dramatic decrease in rRNA numbers only in a subpopulation during nutrient limitation, resulting in a bimodal distribution of cells with high and low rRNA content. During nutritional upshifts, the two subpopulations were associated with distinct phenotypes. Using a transposon screen coupled with rRNA-FISH, we identified two mutants, DksA and RNase I, acting on rRNA transcription shutdown and degradation, which abolished the formation of the subpopulation with low rRNA content. Our work identifies a bacterial mechanism for regulation of ribosomal bimodality that may be beneficial for population survival during starvation.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kfir Eisner
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aviel Rosenbaum
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mengyu Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andre' Rivalta
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ariel Amir
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Golding
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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22
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Mortier J, Govers SK, Cambré A, Van Eyken R, Verheul J, den Blaauwen T, Aertsen A. Protein aggregates act as a deterministic disruptor during bacterial cell size homeostasis. Cell Mol Life Sci 2023; 80:360. [PMID: 37971522 PMCID: PMC11072981 DOI: 10.1007/s00018-023-05002-4] [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: 05/02/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
Mechanisms underlying deviant cell size fluctuations among clonal bacterial siblings are generally considered to be cryptic and stochastic in nature. However, by scrutinizing heat-stressed populations of the model bacterium Escherichia coli, we uncovered the existence of a deterministic asymmetry in cell division that is caused by the presence of intracellular protein aggregates (PAs). While these structures typically locate at the cell pole and segregate asymmetrically among daughter cells, we now show that the presence of a polar PA consistently causes a more distal off-center positioning of the FtsZ division septum. The resulting increased length of PA-inheriting siblings persists over multiple generations and could be observed in both E. coli and Bacillus subtilis populations. Closer investigation suggests that a PA can physically perturb the nucleoid structure, which subsequently leads to asymmetric septation.
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Affiliation(s)
- Julien Mortier
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Sander K Govers
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Alexander Cambré
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Ronald Van Eyken
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Jolanda Verheul
- Swammerdam Institute for Life Sciences, Bacterial Cell Biology and Physiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Tanneke den Blaauwen
- Swammerdam Institute for Life Sciences, Bacterial Cell Biology and Physiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
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23
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Roller BRK, Hellerschmied C, Wu Y, Miettinen TP, Gomez AL, Manalis SR, Polz MF. Single-cell mass distributions reveal simple rules for achieving steady-state growth. mBio 2023; 14:e0158523. [PMID: 37671861 PMCID: PMC10653891 DOI: 10.1128/mbio.01585-23] [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: 06/27/2023] [Accepted: 07/14/2023] [Indexed: 09/07/2023] Open
Abstract
IMPORTANCE Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates from optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells. Here, we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for individual cell mass accumulation and cell number increase via cell division to balance out. Steady-state growth is important for reliable cell mass distributions and experimental reproducibility. We discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.
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Affiliation(s)
- Benjamin R. K. Roller
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Cathrine Hellerschmied
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Yanqi Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Teemu P. Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Annika L. Gomez
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Scott R. Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Martin F. Polz
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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24
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Sundermeyer L, Folkerts JG, Lückel B, Mack C, Baumgart M, Bott M. Cellular localization of the hybrid pyruvate/2-oxoglutarate dehydrogenase complex in the actinobacterium Corynebacterium glutamicum. Microbiol Spectr 2023; 11:e0266823. [PMID: 37754766 PMCID: PMC10581250 DOI: 10.1128/spectrum.02668-23] [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: 06/27/2023] [Accepted: 08/05/2023] [Indexed: 09/28/2023] Open
Abstract
For many bacterial proteins, specific localizations within the cell have been demonstrated, but enzymes involved in central metabolism are usually considered to be homogenously distributed within the cytoplasm. Here, we provide an example for a spatially defined localization of a unique enzyme complex found in actinobacteria, the hybrid pyruvate/2-oxoglutarate dehydrogenase complex (PDH-ODH). In non-actinobacterial cells, PDH and ODH form separate multienzyme complexes of megadalton size composed of three different subunits, E1, E2, and E3. The actinobacterial PDH-ODH complex is composed of four subunits, AceE (E1p), AceF (E2p), Lpd (E3), and OdhA (E1oE2o). Using fluorescence microscopy, we observed that in Corynebacterium glutamicum, all four subunits are co-localized in distinct spots at the cell poles, and in larger cells, additional spots are present at mid-cell. These results further confirm the existence of the hybrid complex. The unphosporylated OdhI protein, which binds to OdhA and inhibits ODH activity, was co-localized with OdhA at the poles, whereas phosphorylated OdhI, which does not bind OdhA, was distributed in the entire cytoplasm. Isocitrate dehydrogenase and glutamate dehydrogenase, both metabolically linked to ODH, were evenly distributed in the cytoplasm. Based on the available structural data for individual PDH-ODH subunits, a novel supramolecular architecture of the hybrid complex differing from classical PDH and ODH complexes has to be postulated. Our results suggest that localization at the poles or at mid-cell is most likely caused by nucleoid exclusion and results in a spatially organized metabolism in actinobacteria, with consequences yet to be studied. IMPORTANCE Enzymes involved in the central metabolism of bacteria are usually considered to be distributed within the entire cytoplasm. Here, we provide an example for a spatially defined localization of a unique enzyme complex of actinobacteria, the hybrid pyruvate dehydrogenase/2-oxoglutarate dehydrogenase (PDH-ODH) complex composed of four different subunits. Using fusions with mVenus or mCherry and fluorescence microscopy, we show that all four subunits are co-localized in distinct spots at the cell poles, and in larger cells, additional spots were observed at mid-cell. These results clearly support the presence of the hybrid PDH-ODH complex and suggest a similar localization in other actinobacteria. The observation of a defined spatial localization of an enzyme complex catalyzing two key reactions of central metabolism poses questions regarding possible consequences for the availability of substrates and products within the cell and other bacterial enzyme complexes showing similar behavior.
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Affiliation(s)
- Lea Sundermeyer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Jan-Gerrit Folkerts
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Benita Lückel
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Christina Mack
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
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25
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Mortier J, Cambré A, Schack S, Christie G, Aertsen A. Impact of Protein Aggregates on Sporulation and Germination of Bacillus subtilis. Microorganisms 2023; 11:2365. [PMID: 37764209 PMCID: PMC10536567 DOI: 10.3390/microorganisms11092365] [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: 06/30/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
In order to improve our general understanding of protein aggregate (PA) management and impact in bacteria, different model systems and processes need to be investigated. As such, we developed an inducible synthetic PA model system to investigate PA dynamics in the Gram-positive model organism Bacillus subtilis. This confirmed previous observations that PA segregation in this organism seems to follow the Escherichia coli paradigm of nucleoid occlusion governing polar localization and asymmetric segregation during vegetative growth. However, our findings also revealed that PAs can readily persist throughout the entire sporulation process after encapsulation in the forespore during sporulation. Moreover, no deleterious effects of PA presence on sporulation, germination and spore survival against heat or UV stress could be observed. Our findings therefore indicate that the sporulation process is remarkably robust against perturbations by PAs and misfolded proteins.
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Affiliation(s)
- Julien Mortier
- Department of Microbial and Molecular Systems, KU Leuven, B-3000 Leuven, Belgium; (J.M.); (A.C.)
| | - Alexander Cambré
- Department of Microbial and Molecular Systems, KU Leuven, B-3000 Leuven, Belgium; (J.M.); (A.C.)
| | - Sina Schack
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; (S.S.); (G.C.)
| | - Graham Christie
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; (S.S.); (G.C.)
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, KU Leuven, B-3000 Leuven, Belgium; (J.M.); (A.C.)
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26
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Matamouros S, Gensch T, Cerff M, Sachs CC, Abdollahzadeh I, Hendriks J, Horst L, Tenhaef N, Tenhaef J, Noack S, Graf M, Takors R, Nöh K, Bott M. Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli. Nat Commun 2023; 14:5611. [PMID: 37699882 PMCID: PMC10497606 DOI: 10.1038/s41467-023-41176-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h-1 in C. glutamicum and the fraction of active ribosomes is kept above 70% while the translation elongation rate declines 5-fold. Mathematical modelling indicates that the decrease in the translation elongation rate can be explained by a depletion of translation precursors.
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Affiliation(s)
- Susana Matamouros
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christian C Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Iman Abdollahzadeh
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Johnny Hendriks
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Lucas Horst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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27
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Kaljević J, Tesseur C, Le TBK, Laloux G. Cell cycle-dependent organization of a bacterial centromere through multi-layered regulation of the ParABS system. PLoS Genet 2023; 19:e1010951. [PMID: 37733798 PMCID: PMC10547168 DOI: 10.1371/journal.pgen.1010951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/03/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023] Open
Abstract
The accurate distribution of genetic material is crucial for all organisms. In most bacteria, chromosome segregation is achieved by the ParABS system, in which the ParB-bound parS sequence is actively partitioned by ParA. While this system is highly conserved, its adaptation in organisms with unique lifestyles and its regulation between developmental stages remain largely unexplored. Bdellovibrio bacteriovorus is a predatory bacterium proliferating through polyploid replication and non-binary division inside other bacteria. Our study reveals the subcellular dynamics and multi-layered regulation of the ParABS system, coupled to the cell cycle of B. bacteriovorus. We found that ParA:ParB ratios fluctuate between predation stages, their balance being critical for cell cycle progression. Moreover, the parS chromosomal context in non-replicative cells, combined with ParB depletion at cell division, critically contribute to the unique cell cycle-dependent organization of the centromere in this bacterium, highlighting new levels of complexity in chromosome segregation and cell cycle control.
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Affiliation(s)
| | | | - Tung B. K. Le
- John Innes Centre, Department of Molecular Microbiology, Norwich, United Kingdom
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28
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Fan J, El Sayyed H, Pambos OJ, Stracy M, Kyropoulos J, Kapanidis AN. RNA polymerase redistribution supports growth in E. coli strains with a minimal number of rRNA operons. Nucleic Acids Res 2023; 51:8085-8101. [PMID: 37351576 PMCID: PMC10450203 DOI: 10.1093/nar/gkad511] [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: 02/02/2022] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Bacterial transcription by RNA polymerase (RNAP) is spatially organized. RNAPs transcribing highly expressed genes locate in the nucleoid periphery, and form clusters in rich medium, with several studies linking RNAP clustering and transcription of rRNA (rrn). However, the nature of RNAP clusters and their association with rrn transcription remains unclear. Here we address these questions by using single-molecule tracking to monitor the subcellular distribution of mobile and immobile RNAP in strains with a heavily reduced number of chromosomal rrn operons (Δrrn strains). Strikingly, we find that the fraction of chromosome-associated RNAP (which is mainly engaged in transcription) is robust to deleting five or six of the seven chromosomal rrn operons. Spatial analysis in Δrrn strains showed substantial RNAP redistribution during moderate growth, with clustering increasing at cell endcaps, where the remaining rrn operons reside. These results support a model where RNAPs in Δrrn strains relocate to copies of the remaining rrn operons. In rich medium, Δrrn strains redistribute RNAP to minimize growth defects due to rrn deletions, with very high RNAP densities on rrn genes leading to genomic instability. Our study links RNAP clusters and rrn transcription, and offers insight into how bacteria maintain growth in the presence of only 1-2 rrn operons.
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Affiliation(s)
- Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Mathew Stracy
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jingwen Kyropoulos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
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29
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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30
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Li Y, Liang W, Li C. Exogenous adenosine and/or guanosine enhances tetracycline sensitivity of persister cells. Microbiol Res 2023; 270:127321. [PMID: 36773473 DOI: 10.1016/j.micres.2023.127321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Vibrio splendidus is an opportunistic pathogen, its pathogenicity continues to be a major aquaculture disease infection problem in many parts of the world. Bacteria can form dormant and persister cells, which may be responsible for the difficulty in treating latent infections. Bacterial persister cells are a small subpopulation with high phenotypic heterogeneity that have the ability to persist in response to high concentrations of antibiotics. In our previous work, we have confirmed tetracycline could induce V. splendidus AJ01 persister cells formation. Here, we show that exogenous adenosine and/or guanosine supply restores susceptibility of AJ01 persister cells to tetracycline, leading to effective killing of this persist subpopulation upon wake-up. Mechanistically, exogenous adenosine and/or guanosine promotes the intracellular ATP level, reduces percentage of cells with protein aggresomes, and destroys membrane stability. In addition, when cells were exposed to tetracycline, we found that cells with small nucleocytoplasmic ratio is easy to survive. Overall, our results support that exogenous adenosine or guanosine could be an effective strategy for treating infections with antibiotic-persist bacteria via regulating persisters cells formation.
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Affiliation(s)
- Yanan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Weikang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.
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31
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Garner RM, Molines AT, Theriot JA, Chang F. Vast heterogeneity in cytoplasmic diffusion rates revealed by nanorheology and Doppelgänger simulations. Biophys J 2023; 122:767-783. [PMID: 36739478 PMCID: PMC10027447 DOI: 10.1016/j.bpj.2023.01.040] [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: 07/28/2022] [Revised: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The cytoplasm is a complex, crowded, actively driven environment whose biophysical characteristics modulate critical cellular processes such as cytoskeletal dynamics, phase separation, and stem cell fate. Little is known about the variance in these cytoplasmic properties. Here, we employed particle-tracking nanorheology on genetically encoded multimeric 40 nm nanoparticles (GEMs) to measure diffusion within the cytoplasm of individual fission yeast (Schizosaccharomyces pombe) cellscells. We found that the apparent diffusion coefficients of individual GEM particles varied over a 400-fold range, while the differences in average particle diffusivity among individual cells spanned a 10-fold range. To determine the origin of this heterogeneity, we developed a Doppelgänger simulation approach that uses stochastic simulations of GEM diffusion that replicate the experimental statistics on a particle-by-particle basis, such that each experimental track and cell had a one-to-one correspondence with their simulated counterpart. These simulations showed that the large intra- and inter-cellular variations in diffusivity could not be explained by experimental variability but could only be reproduced with stochastic models that assume a wide intra- and inter-cellular variation in cytoplasmic viscosity. The simulation combining intra- and inter-cellular variation in viscosity also predicted weak nonergodicity in GEM diffusion, consistent with the experimental data. To probe the origin of this variation, we found that the variance in GEM diffusivity was largely independent of factors such as temperature, the actin and microtubule cytoskeletons, cell-cyle stage, and spatial locations, but was magnified by hyperosmotic shocks. Taken together, our results provide a striking demonstration that the cytoplasm is not "well-mixed" but represents a highly heterogeneous environment in which subcellular components at the 40 nm size scale experience dramatically different effective viscosities within an individual cell, as well as in different cells in a genetically identical population. These findings carry significant implications for the origins and regulation of biological noise at cellular and subcellular levels.
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Affiliation(s)
- Rikki M Garner
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Arthur T Molines
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Julie A Theriot
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts
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32
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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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33
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Carpousis AJ, Campo N, Hadjeras L, Hamouche L. Compartmentalization of RNA Degradosomes in Bacteria Controls Accessibility to Substrates and Ensures Concerted Degradation of mRNA to Nucleotides. Annu Rev Microbiol 2022; 76:533-552. [PMID: 35671533 DOI: 10.1146/annurev-micro-041020-113308] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA degradosomes are multienzyme complexes composed of ribonucleases, RNA helicases, and metabolic enzymes. RNase E-based degradosomes are widespread in Proteobacteria. The Escherichia coli RNA degradosome is sequestered from transcription in the nucleoid and translation in the cytoplasm by localization to the inner cytoplasmic membrane, where it forms short-lived clusters that are proposed to be sites of mRNA degradation. In Caulobacter crescentus, RNA degradosomes localize to ribonucleoprotein condensates in the interior of the cell [bacterial ribonucleoprotein-bodies (BR-bodies)], which have been proposed to drive the concerted degradation of mRNA to nucleotides. The turnover of mRNA in growing cells is important for maintaining pools of nucleotides for transcription and DNA replication. Membrane attachment of the E. coli RNA degradosome is necessary to avoid wasteful degradation of intermediates in ribosome assembly. Sequestering RNA degradosomes to C. crescentus BR-bodies, which exclude structured RNA, could have a similar role in protecting intermediates in ribosome assembly from degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Agamemnon J Carpousis
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , , .,TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nathalie Campo
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , ,
| | - Lydia Hadjeras
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , , .,Current affiliation: IMIB, University of Würzburg, Würzburg, Germany;
| | - Lina Hamouche
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , ,
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34
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Bera P, Wasim A, Mondal J. Hi-C embedded polymer model of Escherichia coli reveals the origin of heterogeneous subdiffusion in chromosomal loci. Phys Rev E 2022; 105:064402. [PMID: 35854496 DOI: 10.1103/physreve.105.064402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Underneath its apparently simple architecture, the circular chromosome of Escherichia coli is known for displaying complex dynamics in its cytoplasm, with past investigations hinting at inherently diverse mobilities of chromosomal loci across the genome. To decipher its origin, we simulate the dynamics of genome-wide spectrum of E. coli chromosomal loci, via integrating its experimentally derived Hi-C interaction matrix within a polymer-based model. Our analysis demonstrates that, while the dynamics of the chromosome is subdiffusive in a viscoelastic media, the diffusion constants are strongly dependent of chromosomal loci coordinates and diffusive exponents (α) are widely heterogenous with α ≈ 0.36-0.60. The loci-dependent heterogeneous dynamics and mean first-passage times of interloci encounter were found to be modulated via genetically distant interloci communications and is robust even in the presence of active, ATP-dependent noises. Control investigations reveal that the absence of Hi-C-derived interactions in the model would have abolished the traits of heterogeneous loci diffusion, underscoring the key role of loci-specific genetically distant interaction in modulating the underlying heterogeneity of the loci diffusion.
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Affiliation(s)
- Palash Bera
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Abdul Wasim
- Tata Institute of Fundamental Research, Hyderabad 500046, India
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35
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Garner RM, Theriot JA. Leading edge maintenance in migrating cells is an emergent property of branched actin network growth. eLife 2022; 11:74389. [PMID: 35275060 PMCID: PMC9033267 DOI: 10.7554/elife.74389] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 03/09/2022] [Indexed: 11/17/2022] Open
Abstract
Animal cell migration is predominantly driven by the coordinated, yet stochastic, polymerization of thousands of nanometer-scale actin filaments across micron-scale cell leading edges. It remains unclear how such inherently noisy processes generate robust cellular behavior. We employed high-speed imaging of migrating neutrophil-like HL-60 cells to explore the fine-scale shape fluctuations that emerge and relax throughout the process of leading edge maintenance. We then developed a minimal stochastic model of the leading edge that reproduces this stable relaxation behavior. Remarkably, we find lamellipodial stability naturally emerges from the interplay between branched actin network growth and leading edge shape – with no additional feedback required – based on a synergy between membrane-proximal branching and lateral spreading of filaments. These results thus demonstrate a novel biological noise-suppression mechanism based entirely on system geometry. Furthermore, our model suggests that the Arp2/3-mediated ~70–80° branching angle optimally smooths lamellipodial shape, addressing its long-mysterious conservation from protists to mammals. In every human cell, there are tens of millions of proteins which work together to control everything from the cell’s shape to its behavior. One of the most abundant proteins is actin, which organizes itself into filaments that mechanically support the cell and help it to move. These filaments are very dynamic, with individual actin molecules constantly being added or removed. This allows the cell to build large structures with distinct shapes and properties. Many motile cells, for example, have a structure called a lamellipodium which protrudes at their ‘leading edge’ and pushes them forward. The lamellipodium has a very robust shape that does not vary much between different cell types, or change significantly as cells migrate. But how the tens of thousands of actin molecules inside the lamellipodium organize themselves into this large, stable structure is not fully understood. To investigate, Garner and Theriot used high-speed video microscopy to track the shape of human cells cultured in the laboratory. As the cells crawled along a glass surface, their leading edge undulated like strings being plucked on a guitar. A computer simulation showed that these ripples can be caused by filaments randomly adding and removing actin molecules. While these random movements could destabilize the structure of the leading edge, the simulation suggests that another aspect of actin filament growth smooths out any fluctuations in the lamellipodium’s shape. Actin networks in the lamellipodium have a branched configuration, with new strands emerging off each other at an angle like branches in a tree. Garner and Theriot found that the specific angle in which new filaments are added smooths out the lamellipodium’s shape, which may explain why this geometry has persisted throughout evolution. These findings suggest that the way in which actin filaments join together helps to maintain the shape of large cellular structures. In the future, scientists could use this design principle to build molecular machines that can self-organize into microstructures. These engineered constructs could be used to modulate the activity of living cells that have been damaged by disease.
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Affiliation(s)
- Rikki M Garner
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Julie A Theriot
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, United States
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36
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Lemière J, Real-Calderon P, Holt LJ, Fai TG, Chang F. Control of nuclear size by osmotic forces in Schizosaccharomyces pombe. eLife 2022; 11:76075. [PMID: 35856499 PMCID: PMC9410708 DOI: 10.7554/elife.76075] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The size of the nucleus scales robustly with cell size so that the nuclear-to-cell volume ratio (N/C ratio) is maintained during cell growth in many cell types. The mechanism responsible for this scaling remains mysterious. Previous studies have established that the N/C ratio is not determined by DNA amount but is instead influenced by factors such as nuclear envelope mechanics and nuclear transport. Here, we developed a quantitative model for nuclear size control based upon colloid osmotic pressure and tested key predictions in the fission yeast Schizosaccharomyces pombe. This model posits that the N/C ratio is determined by the numbers of macromolecules in the nucleoplasm and cytoplasm. Osmotic shift experiments showed that the fission yeast nucleus behaves as an ideal osmometer whose volume is primarily dictated by osmotic forces. Inhibition of nuclear export caused accumulation of macromolecules in the nucleoplasm, leading to nuclear swelling. We further demonstrated that the N/C ratio is maintained by a homeostasis mechanism based upon synthesis of macromolecules during growth. These studies demonstrate the functions of colloid osmotic pressure in intracellular organization and size control.
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Affiliation(s)
- Joël Lemière
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
| | - Paula Real-Calderon
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States,Centro Andaluz de Biología del DesarrolloSevillaSpain
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone HealthNew YorkUnited States
| | - Thomas G Fai
- Department of Mathematics and Volen Center for Complex Systems, Brandeis UniversityWalthamUnited States
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
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37
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Spatiotemporal localization of proteins in mycobacteria. Cell Rep 2021; 37:110154. [PMID: 34965429 PMCID: PMC8861988 DOI: 10.1016/j.celrep.2021.110154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 01/10/2023] Open
Abstract
Although prokaryotic organisms lack traditional organelles, they must still organize cellular structures in space and time, challenges that different species solve differently. To systematically define the subcellular architecture of mycobacteria, we perform high-throughput imaging of a library of fluorescently tagged proteins expressed in Mycobacterium smegmatis and develop a customized computational pipeline, MOMIA and GEMATRIA, to analyze these data. Our results establish a spatial organization network of over 700 conserved mycobacterial proteins and reveal a coherent localization pattern for many proteins of known function, including those in translation, energy metabolism, cell growth and division, as well as proteins of unknown function. Furthermore, our pipeline exploits morphologic proxies to enable a pseudo-temporal approximation of protein localization and identifies previously uncharacterized cell-cycle-dependent dynamics of essential mycobacterial proteins. Collectively, these data provide a systems perspective on the subcellular organization of mycobacteria and provide tools for the analysis of bacteria with non-standard growth characteristics. Zhu et al. develop a two-stage image analysis pipeline, MOMIA and GEMATRIA, that efficiently models the spatial and temporal dynamics of over 700 conserved proteins in M. smegmatis. Through the analysis they report spatial constraints of mycobacterial ribosomes and membrane complexes and reconstruct temporal dynamics from still image data.
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38
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Fisunov GY, Zubov AI, Pobeguts OV, Varizhuk AM, Galyamina MA, Evsyutina DV, Semashko TA, Manuvera VA, Kovalchuk SI, Ziganshin RK, Barinov NA, Klinov DV, Govorun VM. The Dynamics of Mycoplasma gallisepticum Nucleoid Structure at the Exponential and Stationary Growth Phases. Front Microbiol 2021; 12:753760. [PMID: 34867875 PMCID: PMC8637272 DOI: 10.3389/fmicb.2021.753760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
The structure and dynamics of bacterial nucleoids play important roles in regulating gene expression. Bacteria of class Mollicutes and, in particular, mycoplasmas feature extremely reduced genomes. They lack multiple structural proteins of the nucleoid, as well as regulators of gene expression. We studied the organization of Mycoplasma gallisepticum nucleoids in the stationary and exponential growth phases at the structural and protein levels. The growth phase transition results in the structural reorganization of M. gallisepticum nucleoid. In particular, it undergoes condensation and changes in the protein content. The observed changes corroborate with the previously identified global rearrangement of the transcriptional landscape in this bacterium during the growth phase transition. In addition, we identified that the glycolytic enzyme enolase functions as a nucleoid structural protein in this bacterium. It is capable of non-specific DNA binding and can form fibril-like complexes with DNA.
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Affiliation(s)
- Gleb Y Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander I Zubov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Olga V Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Mariya A Galyamina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria V Evsyutina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valentin A Manuvera
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Sergey I Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Rustam K Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nicolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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39
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Cantwell H, Dey G. Nuclear size and shape control. Semin Cell Dev Biol 2021; 130:90-97. [PMID: 34776332 DOI: 10.1016/j.semcdb.2021.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/27/2022]
Abstract
The nucleus displays a wide range of sizes and shapes in different species and cell types, yet its size scaling and many of the key structural constituents that determine its shape are highly conserved. In this review, we discuss the cellular properties and processes that contribute to nuclear size and shape control, drawing examples from across eukaryotes and highlighting conserved themes and pathways. We then outline physiological roles that have been uncovered for specific nuclear morphologies and disease pathologies associated with aberrant nuclear morphology. We argue that a comparative approach, assessing and integrating observations from different systems, will be a powerful way to help us address the open questions surrounding functional roles of nuclear size and shape in cell physiology.
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Affiliation(s)
- Helena Cantwell
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Meyerhofstr.1, 69117 Heidelberg, Germany.
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40
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Steric interactions and out-of-equilibrium processes control the internal organization of bacteria. Proc Natl Acad Sci U S A 2021; 118:2106014118. [PMID: 34675077 DOI: 10.1073/pnas.2106014118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is typically condensed into a compact body-the nucleoid. This compaction influences the localization and dynamics of many cellular processes including transcription, translation, and cell division. Here, we develop a model that takes into account steric interactions among the components of the Escherichia coli transcriptional-translational machinery (TTM) and out-of-equilibrium effects of messenger RNA (mRNA) transcription, translation, and degradation, to explain many observed features of the nucleoid. We show that steric effects, due to the different molecular shapes of the TTM components, are sufficient to drive equilibrium phase separation of the DNA, explaining the formation and size of the nucleoid. In addition, we show that the observed positioning of the nucleoid at midcell is due to the out-of-equilibrium process of mRNA synthesis and degradation: mRNAs apply a pressure on both sides of the nucleoid, localizing it to midcell. We demonstrate that, as the cell grows, the production of these mRNAs is responsible for the nucleoid splitting into two lobes and for their well-known positioning to 1/4 and 3/4 positions on the long cell axis. Finally, our model quantitatively accounts for the observed expansion of the nucleoid when the pool of cytoplasmic mRNAs is depleted. Overall, our study suggests that steric interactions and out-of-equilibrium effects of the TTM are key drivers of the internal spatial organization of bacterial cells.
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41
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Belliveau NM, Chure G, Hueschen CL, Garcia HG, Kondev J, Fisher DS, Theriot JA, Phillips R. Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. Cell Syst 2021; 12:924-944.e2. [PMID: 34214468 PMCID: PMC8460600 DOI: 10.1016/j.cels.2021.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/12/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Despite abundant measurements of bacterial growth rate, cell size, and protein content, we lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we estimate the basic requirements and physical constraints on steady-state growth by considering key processes in cellular physiology across a collection of Escherichia coli proteomic data covering ≈4,000 proteins and 36 growth rates. Our analysis suggests that cells are predominantly tuned for the task of cell doubling across a continuum of growth rates; specific processes do not limit growth rate or dictate cell size. We present a model of proteomic regulation as a function of nutrient supply that reconciles observed interdependences between protein synthesis, cell size, and growth rate and propose that a theoretical inability to parallelize ribosomal synthesis places a firm limit on the achievable growth rate. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Nathan M Belliveau
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Griffin Chure
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina L Hueschen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hernan G Garcia
- Department of Molecular Cell Biology and Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Daniel S Fisher
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Julie A Theriot
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA.
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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42
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Abstract
Since the nucleoid was isolated from bacteria in the 1970s, two fundamental questions emerged and are still in the spotlight: how bacteria organize their chromosomes to fit inside the cell and how nucleoid organization enables essential biological processes. During the last decades, knowledge of bacterial chromosome organization has advanced considerably, and today, such chromosomes are considered to be highly organized and dynamic structures that are shaped by multiple factors in a multiscale manner. Here we review not only the classical well-known factors involved in chromosome organization but also novel components that have recently been shown to dynamically shape the 3D structuring of the bacterial genome. We focus on the different functional elements that control short-range organization and describe how they collaborate in the establishment of the higher-order folding and disposition of the chromosome. Recent advances have opened new avenues for a deeper understanding of the principles and mechanisms of chromosome organization in bacteria. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
| | - Ivan Junier
- Université Grenoble Alpes, CNRS, TIMC-IMAG, 38000 Grenoble, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
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43
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Malerba ME, Marshall DJ. Larger cells have relatively smaller nuclei across the Tree of Life. Evol Lett 2021; 5:306-314. [PMID: 34367657 PMCID: PMC8327945 DOI: 10.1002/evl3.243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/13/2021] [Accepted: 06/07/2021] [Indexed: 01/13/2023] Open
Abstract
Larger cells have larger nuclei, but the precise relationship between cell size and nucleus size remains unclear, and the evolutionary forces that shape this relationship are debated. We compiled data for almost 900 species - from yeast to mammals - at three scales of biological organisation: among-species, within-species, and among-lineages of a species that was artificially selected for cell size. At all scales, we showed that the ratio of nucleus size to cell size (the 'N: C' ratio) decreased systematically in larger cells. Size evolution appears more constrained in nuclei than cells: cell size spans across six orders of magnitude, whereas nucleus size varies by only three. The next important challenge is to determine the drivers of this apparently ubiquitous relationship in N:C ratios across such a diverse array of organisms.
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Affiliation(s)
- Martino E. Malerba
- Centre of Geometric Biology, School of Biological SciencesMonash UniversityMelbourneAustralia
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityVictoriaAustralia
| | - Dustin J. Marshall
- Centre of Geometric Biology, School of Biological SciencesMonash UniversityMelbourneAustralia
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44
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Bergkessel M. Bacterial transcription during growth arrest. Transcription 2021; 12:232-249. [PMID: 34486930 PMCID: PMC8632087 DOI: 10.1080/21541264.2021.1968761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/12/2022] Open
Abstract
Bacteria in most natural environments spend substantial periods of time limited for essential nutrients and not actively dividing. While transcriptional activity under these conditions is substantially reduced compared to that occurring during active growth, observations from diverse organisms and experimental approaches have shown that new transcription still occurs and is important for survival. Much of our understanding of transcription regulation has come from measuring transcripts in exponentially growing cells, or from in vitro experiments focused on transcription from highly active promoters by the housekeeping RNA polymerase holoenzyme. The fact that transcription during growth arrest occurs at low levels and is highly heterogeneous has posed challenges for its study. However, new methods of measuring low levels of gene expression activity, even in single cells, offer exciting opportunities for directly investigating transcriptional activity and its regulation during growth arrest. Furthermore, much of the rich structural and biochemical data from decades of work on the bacterial transcriptional machinery is also relevant to growth arrest. In this review, the physiological changes likely affecting transcription during growth arrest are first considered. Next, possible adaptations to help facilitate ongoing transcription during growth arrest are discussed. Finally, new insights from several recently published datasets investigating mRNA transcripts in single bacterial cells at various growth phases will be explored. Keywords: Growth arrest, stationary phase, RNA polymerase, nucleoid condensation, population heterogeneity.
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45
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Labarde A, Jakutyte L, Billaudeau C, Fauler B, López-Sanz M, Ponien P, Jacquet E, Mielke T, Ayora S, Carballido-López R, Tavares P. Temporal compartmentalization of viral infection in bacterial cells. Proc Natl Acad Sci U S A 2021; 118:e2018297118. [PMID: 34244425 PMCID: PMC8285916 DOI: 10.1073/pnas.2018297118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Virus infection causes major rearrangements in the subcellular architecture of eukaryotes, but its impact in prokaryotic cells was much less characterized. Here, we show that infection of the bacterium Bacillus subtilis by bacteriophage SPP1 leads to a hijacking of host replication proteins to assemble hybrid viral-bacterial replisomes for SPP1 genome replication. Their biosynthetic activity doubles the cell total DNA content within 15 min. Replisomes operate at several independent locations within a single viral DNA focus positioned asymmetrically in the cell. This large nucleoprotein complex is a self-contained compartment whose boundaries are delimited neither by a membrane nor by a protein cage. Later during infection, SPP1 procapsids localize at the periphery of the viral DNA compartment for genome packaging. The resulting DNA-filled capsids do not remain associated to the DNA transactions compartment. They bind to phage tails to build infectious particles that are stored in warehouse compartments spatially independent from the viral DNA. Free SPP1 structural proteins are recruited to the dynamic phage-induced compartments following an order that recapitulates the viral particle assembly pathway. These findings show that bacteriophages restructure the crowded host cytoplasm to confine at different cellular locations the sequential processes that are essential for their multiplication.
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Affiliation(s)
- Audrey Labarde
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lina Jakutyte
- Laboratoire de Virologie Moléculaire et Structurale, CNRS Unité Propre de Recherche 3296 and Institut Fédératif de Recherche 115, 91198 Gif-sur-Yvette, France
| | - Cyrille Billaudeau
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Beatrix Fauler
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Maria López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Prishila Ponien
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Rut Carballido-López
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
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46
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Kaljević J, Saaki TNV, Govers SK, Remy O, van Raaphorst R, Lamot T, Laloux G. Chromosome choreography during the non-binary cell cycle of a predatory bacterium. Curr Biol 2021; 31:3707-3720.e5. [PMID: 34256020 PMCID: PMC8445325 DOI: 10.1016/j.cub.2021.06.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022]
Abstract
In bacteria, the dynamics of chromosome replication and segregation are tightly coordinated with cell-cycle progression and largely rely on specific spatiotemporal arrangement of the chromosome. Whereas these key processes are mostly investigated in species that divide by binary fission, they remain mysterious in bacteria producing larger number of descendants. Here, we establish the predatory bacterium Bdellovibrio bacteriovorus as a model to investigate the non-binary processing of a circular chromosome. We found that its single chromosome is highly compacted in a polarized nucleoid that excludes freely diffusing proteins during the non-proliferative stage of the cell cycle. A binary-like cycle of DNA replication and asymmetric segregation is followed by multiple asynchronous rounds of replication and progressive ParABS-dependent partitioning, uncoupled from cell division. Finally, we provide the first evidence for an on-off behavior of the ParB protein, which localizes at the centromere in a cell-cycle-regulated manner. Altogether, our findings support a model of complex chromosome choreography leading to the generation of variable, odd, or even numbers of offspring and highlight the adaptation of conserved mechanisms to achieve non-binary reproduction. The Bdellovibrio chromosome is polarized, with ori located near the invasive pole The highly compacted nucleoid excludes cytosolic proteins in non-replicative cells Replication and segregation of chromosomes are uncoupled from cell division The centromeric protein ParB localizes at parS in a cell-cycle-dependent manner
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Affiliation(s)
- Jovana Kaljević
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Terrens N V Saaki
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Sander K Govers
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ophélie Remy
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | | | - Thomas Lamot
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium.
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47
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Xiang Y, Surovtsev IV, Chang Y, Govers SK, Parry BR, Liu J, Jacobs-Wagner C. Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli. Cell 2021; 184:3626-3642.e14. [PMID: 34186018 DOI: 10.1016/j.cell.2021.05.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/09/2020] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
All cells fold their genomes, including bacterial cells, where the chromosome is compacted into a domain-organized meshwork called the nucleoid. How compaction and domain organization arise is not fully understood. Here, we describe a method to estimate the average mesh size of the nucleoid in Escherichia coli. Using nucleoid mesh size and DNA concentration estimates, we find that the cytoplasm behaves as a poor solvent for the chromosome when the cell is considered as a simple semidilute polymer solution. Monte Carlo simulations suggest that a poor solvent leads to chromosome compaction and DNA density heterogeneity (i.e., domain formation) at physiological DNA concentration. Fluorescence microscopy reveals that the heterogeneous DNA density negatively correlates with ribosome density within the nucleoid, consistent with cryoelectron tomography data. Drug experiments, together with past observations, suggest the hypothesis that RNAs contribute to the poor solvent effects, connecting chromosome compaction and domain formation to transcription and intracellular organization.
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Affiliation(s)
- Yingjie Xiang
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT 06520, USA; Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Ivan V Surovtsev
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Yunjie Chang
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA
| | - Bradley R Parry
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA.
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48
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Kremling A. A counting-strategy together with a spatial structured model describes RNA polymerase and ribosome availability in Escherichia coli. Metab Eng 2021; 67:145-152. [PMID: 34174424 DOI: 10.1016/j.ymben.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 05/06/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
The allocation of resources during bacterial growth is strongly related to the availability of ribosomes and RNA polymerase molecules. Here, coarse-grained models offer a promising start due to their simple structure and the limited number of kinetic parameters. Based on published data sets for proteome and mRNA data in Escherichia coli, and together with mass balance equations describing gene expression, we are able to calculate the number of active molecules (that is, the number of ribosomes that are currently translating nascent and mature mRNA, as well as the number of RNA polymerase molecules on the DNA). This information is a prerequisite for meaningful coarse-grained models. In our approach, the cellular compartment is structured into a cytosolic region and a nucleoid region, and the processes of transcription and translation are assigned accordingly. The theoretical study reveals a quadratic relationship between the number of active ribosomes and the growth rate μ. While the overall available number of ribosomes follows the linear "bacterial growth law", the approach allows us to determine the growth limit for the chosen experimental environment (minimal medium, only one C source). The new approach is in good agreement with published experimental data, and, with a simple rule of thumb can be applied to other cellular systems.
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Affiliation(s)
- Andreas Kremling
- Systems Biotechnology, Technical University of Munich, Boltzmannstr. 15, Garching b, München, Germany.
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49
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Hamouche L, Poljak L, Carpousis AJ. Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin. RNA (NEW YORK, N.Y.) 2021; 27:rna.078776.121. [PMID: 34099575 PMCID: PMC8284325 DOI: 10.1261/rna.078776.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/03/2021] [Indexed: 05/12/2023]
Abstract
Rifampicin, a broad-spectrum antibiotic, inhibits bacterial RNA polymerase. Here we show that rifampicin treatment of Escherichia coli results in a 50% decrease in cell size due to a terminal cell division. This decrease is a consequence of inhibition of transcription as evidenced by an isogenic rifampicin-resistant strain. There is also a 50% decrease in total RNA due mostly to a 90% decrease in 23S and 16S rRNA levels. Control experiments showed this decrease is not an artifact of our RNA purification protocol and therefore due to degradation in vivo. Since chromosome replication continues after rifampicin treatment, ribonucleotides from rRNA degradation could be recycled for DNA synthesis. Rifampicin-induced rRNA degradation occurs under different growth conditions and in different strain backgrounds. However, rRNA degradation is never complete thus permitting the re-initiation of growth after removal of rifampicin. The orderly shutdown of growth under conditions where the induction of stress genes is blocked by rifampicin is noteworthy. Inhibition of protein synthesis by chloramphenicol resulted in a partial decrease in 23S and 16S rRNA levels whereas kasugamycin treatment had no effect. Analysis of temperature-sensitive mutant strains implicate RNase E, PNPase and RNase R in rifampicin-induced rRNA degradation. We cannot distinguish between a direct role for RNase E in rRNA degradation versus an indirect role involving a slowdown of mRNA degradation. Since mRNA and rRNA appear to be degraded by the same ribonucleases, competition by rRNA is likely to result in slower mRNA degradation rates in the presence of rifampicin than under normal growth conditions.
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Affiliation(s)
- Lina Hamouche
- LMGM, CBI, Universite de Toulouse, CNRS, UPS, Toulouse, France
| | - Leonora Poljak
- LMGM, CBI, Universite de Toulouse, CNRS, UPS, Toulouse, France
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50
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Kleinwächter IS, Pannwitt S, Centi A, Hellmann N, Thines E, Bereau T, Schneider D. The Bacteriostatic Activity of 2-Phenylethanol Derivatives Correlates with Membrane Binding Affinity. MEMBRANES 2021; 11:membranes11040254. [PMID: 33807437 PMCID: PMC8067230 DOI: 10.3390/membranes11040254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022]
Abstract
The hydrophobic tails of aliphatic primary alcohols do insert into the hydrophobic core of a lipid bilayer. Thereby, they disrupt hydrophobic interactions between the lipid molecules, resulting in a decreased lipid order, i.e., an increased membrane fluidity. While aromatic alcohols, such as 2-phenylethanol, also insert into lipid bilayers and disturb the membrane organization, the impact of aromatic alcohols on the structure of biological membranes, as well as the potential physiological implication of membrane incorporation has only been studied to a limited extent. Although diverse targets are discussed to be causing the bacteriostatic and bactericidal activity of 2-phenylethanol, it is clear that 2-phenylethanol severely affects the structure of biomembranes, which has been linked to its bacteriostatic activity. Yet, in fungi some 2-phenylethanol derivatives are also produced, some of which appear to also have bacteriostatic activities. We showed that the 2-phenylethanol derivatives phenylacetic acid, phenyllactic acid, and methyl phenylacetate, but not Tyrosol, were fully incorporated into model membranes and affected the membrane organization. Furthermore, we observed that the propensity of the herein-analyzed molecules to partition into biomembranes positively correlated with their respective bacteriostatic activity, which clearly linked the bacteriotoxic activity of the substances to biomembranes.
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Affiliation(s)
- Isabel S. Kleinwächter
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
| | - Stefanie Pannwitt
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
| | - Alessia Centi
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany; (A.C.); (T.B.)
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
| | - Eckhard Thines
- Institute of Molecular Physiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany;
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany; (A.C.); (T.B.)
- Van ‘t Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany; (A.C.); (T.B.)
- Correspondence: ; Tel.: +49-6131-39-25833; Fax: +49-6131-39-25348
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