1
|
Wang T, He F, He T, Lin C, Guan X, Qin Z, Xue X. Reconstruction of a robust bacterial replication module. Nucleic Acids Res 2024; 52:11394-11407. [PMID: 39271106 PMCID: PMC11472063 DOI: 10.1093/nar/gkae786] [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: 08/27/2023] [Revised: 08/25/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Chromosomal DNA replication is a fundamental process of life, involving the assembly of complex machinery and dynamic regulation. In this study, we reconstructed a bacterial replication module (pRC) by artificially clustering 23 genes involved in DNA replication and sequentially deleting these genes from their naturally scattered loci on the chromosome of Escherichia coli. The integration of pRC into the chromosome, moving from positions farther away to close to the replication origin, leads to an enhanced efficiency in DNA synthesis, varying from lower to higher. Strains containing replication modules exhibited increased DNA replication by accelerating the replication fork movement and initiating chromosomal replication earlier in the replication cycle. The minimized module pRC16, containing only replisome and elongation encoding genes, exhibited chromosomal DNA replication efficiency comparable to that of pRC. The replication module demonstrated robust and rapid DNA replication, regardless of growth conditions. Moreover, the replication module is plug-and-play, and integrating it into Mb-sized extrachromosomal plasmids improves their genetic stability. Our findings indicate that DNA replication, being a fundamental life process, can be artificially reconstructed into replication functional modules. This suggests potential applications in DNA replication and the construction of synthetic modular genomes.
Collapse
Affiliation(s)
- Tao Wang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Fan He
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ting He
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Chen Lin
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xin Guan
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Xiaoli Xue
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| |
Collapse
|
2
|
Welikala MU, Butterworth LJ, Behrmann MS, Trakselis MA. Tau-mediated coupling between Pol III synthesis and DnaB helicase unwinding helps maintain genomic stability. J Biol Chem 2024; 300:107726. [PMID: 39214305 PMCID: PMC11470591 DOI: 10.1016/j.jbc.2024.107726] [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: 04/10/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
The τ-subunit of the clamp loader complex physically interacts with both the DnaB helicase and the polymerase III (Pol III) core α-subunit through domains IV and V, respectively. This interaction is proposed to help maintain rapid and efficient DNA synthesis rates with high genomic fidelity and plasticity, facilitating enzymatic coupling within the replisome. To test this hypothesis, CRISPR-Cas9 editing was used to create site-directed genomic mutations within the dnaX gene at the C terminus of τ predicted to interact with the α-subunit of Pol III. Perturbation of the α-τ binding interaction in vivo resulted in cellular and genomic stress markers that included reduced growth rates, fitness, and viabilities. Specifically, dnaX:mut strains showed increased cell filamentation, mutagenesis frequencies, and activated SOS. In situ fluorescence flow cytometry and microscopy quantified large increases in the amount of ssDNA gaps present. Removal of the C terminus of τ (I618X) still maintained its interactions with DnaB and stimulated unwinding but lost its interaction with Pol III, resulting in significantly reduced rolling circle DNA synthesis. Intriguingly, dnaX:L635P/D636G had the largest induction of SOS, high mutagenesis, and the most prominent ssDNA gaps, which can be explained by an impaired ability to regulate the unwinding speed of DnaB resulting in a faster rate of in vitro rolling circle DNA replication, inducing replisome decoupling. Therefore, τ-stimulated DnaB unwinding and physical coupling with Pol III acts to enforce replisome plasticity to maintain an efficient rate of synthesis and prevent genomic instability.
Collapse
Affiliation(s)
- Malisha U Welikala
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | | | - Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA.
| |
Collapse
|
3
|
Verma H, Chauhan A, Kumar A, Kumar M, Kanchan K. Synchronization of Mycobacterium life cycle: A possible novel mechanism of antimycobacterial drug resistance evolution and its manipulation. Life Sci 2024; 346:122632. [PMID: 38615748 DOI: 10.1016/j.lfs.2024.122632] [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: 10/14/2023] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
Mycobacterium Tuberculosis (Mtb) causing Tuberculosis (TB) is a widespread disease infecting millions of people worldwide. Additionally, emergence of drug resistant tuberculosis is a major challenge and concern in high TB burden countries. Most of the drug resistance in mycobacteria is attributed to developing acquired resistance due to spontaneous mutations or intrinsic resistance mechanisms. In this review, we emphasize on the role of bacterial cell cycle synchronization as one of the intrinsic mechanisms used by the bacteria to cope with stress response and perhaps involved in evolution of its drug resistance. The importance of cell cycle synchronization and its function in drug resistance in cancer cells, malarial and viral pathogens is well understood, but its role in bacterial pathogens has yet to be established. From the extensive literature survey, we could collect information regarding how mycobacteria use synchronization to overcome the stress response. Additionally, it has been observed that most of the microbial pathogens including mycobacteria are responsive to drugs predominantly in their logarithmic phase, while they show resistance to antibiotics when they are in the lag or stationary phase. Therefore, we speculate that Mtb might use this novel strategy wherein they regulate their cell cycle upon antibiotic pressure such that they either enter in their low metabolic phase i.e., either the lag or stationary phase to overcome the antibiotic pressure and function as persister cells. Thus, we propose that manipulating the mycobacterial drug resistance could be possible by fine-tuning its cell cycle.
Collapse
Affiliation(s)
- Hritika Verma
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Aditi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Awanish Kumar
- Department of Bio Technology, National Institute of Technology, Raipur, India
| | - Manoj Kumar
- Amity Institute of Genome Engineering, Amity University Uttar Pradesh, Noida 201313, India
| | - Kajal Kanchan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India.
| |
Collapse
|
4
|
Niault T, Czarnecki J, Lambérioux M, Mazel D, Val ME. Cell cycle-coordinated maintenance of the Vibrio bipartite genome. EcoSal Plus 2023; 11:eesp00082022. [PMID: 38277776 PMCID: PMC10729929 DOI: 10.1128/ecosalplus.esp-0008-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
To preserve the integrity of their genome, bacteria rely on several genome maintenance mechanisms that are co-ordinated with the cell cycle. All members of the Vibrio family have a bipartite genome consisting of a primary chromosome (Chr1) homologous to the single chromosome of other bacteria such as Escherichia coli and a secondary chromosome (Chr2) acquired by a common ancestor as a plasmid. In this review, we present our current understanding of genome maintenance in Vibrio cholerae, which is the best-studied model for bacteria with multi-partite genomes. After a brief overview on the diversity of Vibrio genomic architecture, we describe the specific, common, and co-ordinated mechanisms that control the replication and segregation of the two chromosomes of V. cholerae. Particular attention is given to the unique checkpoint mechanism that synchronizes Chr1 and Chr2 replication.
Collapse
Affiliation(s)
- Théophile Niault
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Jakub Czarnecki
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Morgan Lambérioux
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Didier Mazel
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marie-Eve Val
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| |
Collapse
|
5
|
LaGree TJ, Byrd BA, Quelle RM, Schofield SL, Mok WWK. Stimulating Transcription in Antibiotic-Tolerant Escherichia coli Sensitizes It to Fluoroquinolone and Nonfluoroquinolone Topoisomerase Inhibitors. Antimicrob Agents Chemother 2023; 67:e0163922. [PMID: 36951560 PMCID: PMC10112259 DOI: 10.1128/aac.01639-22] [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: 12/08/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Antibiotic tolerant bacteria and persistent cells that remain alive after a course of antibiotic treatment can foster the chronicity of infections and the development of antibiotic resistance. Elucidating how bacteria overcome antibiotic action and devising strategies to bolster a new drug's activity can allow us to preserve our antibiotic arsenal. Here, we investigate strategies to potentiate the activities of topoisomerase inhibitors against nongrowing Escherichia coli that are often recalcitrant to existing antibiotics. We focus on sensitizing bacteria to the fluoroquinolone (FQ) levofloxacin (Levo) and to the spiropyrimidinetrione zoliflodacin (Zoli)-the first antibiotic in its class of compounds in clinical development. We found that metabolic stimulation either alone or in combination with inhibiting the AcrAB-TolC efflux pump sensitized stationary-phase E. coli to Levo and Zoli. We demonstrate that the added metabolites increased proton motive force generation and ATP production in stationary-phase cultures without restarting growth. Instead, the stimulated bacteria increased transcription and translation, which rendered the populations more susceptible to topoisomerase inhibitors. Our findings illuminate potential vulnerabilities of antibiotic-tolerant bacteria that can be leveraged to sensitize them to new and existing classes of topoisomerase inhibitors. These approaches enable us to stay one step ahead of adaptive bacteria and safeguard the efficacy of our existing antibiotics.
Collapse
Affiliation(s)
- Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
- School of Medicine, University of Connecticut, Farmington, Connecticut, USA
| | - Ryan M. Quelle
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Stephanie L. Schofield
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
| |
Collapse
|
6
|
Kannoly S, Oken G, Shadan J, Musheyev D, Singh K, Singh A, Dennehy JJ. Single-Cell Approach Reveals Intercellular Heterogeneity in Phage-Producing Capacities. Microbiol Spectr 2023; 11:e0266321. [PMID: 36541779 PMCID: PMC9927085 DOI: 10.1128/spectrum.02663-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population level, not the single-cell level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (λ) single-cell burst size mean and variance following different intracellular accumulation period durations by employing Escherichia coli lysogens bearing lysis-deficient λ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual cells. Our data showed that λ phage burst size initially increased exponentially with increased lysis time (i.e., period between induction and chemical lysis) and then saturated at longer lysis times. We also demonstrated that cell-to-cell variation, or "noise," in lysis timing did not contribute significantly to burst size noise. The burst size noise remained constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise was that cell-to-cell differences in burst size originated from intercellular heterogeneity in cellular capacities to produce phages. The mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity. IMPORTANCE Phages produce offspring by hijacking a cell's replicative machinery. Previously, it was noted that the variation in the number of phages produced by single infected cells far exceeded cell size variation. It was hypothesized that this variation is a consequence of variation in the timing of host cell lysis. Here, we show that cell-to-cell variation in lysis timing does not significantly contribute to the burst size variation. We suggest that the constant burst size variation across different host lysis times results from cell-to-cell differences in capacity to produce phages. We found that the mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity.
Collapse
Affiliation(s)
- Sherin Kannoly
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Gabriella Oken
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Jonathan Shadan
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - David Musheyev
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Kevin Singh
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA
| | - John J. Dennehy
- Biology Department, Queens College of The City University of New York, New York, New York, USA
- The Graduate Center of The City University of New York, New York, New York, USA
| |
Collapse
|
7
|
Zheng Q, Chang PV. Shedding Light on Bacterial Physiology with Click Chemistry. Isr J Chem 2023; 63:e202200064. [PMID: 37841997 PMCID: PMC10569449 DOI: 10.1002/ijch.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Indexed: 11/11/2022]
Abstract
Bacteria constitute a major lifeform on this planet and play numerous roles in ecology, physiology, and human disease. However, conventional methods to probe their activities are limited in their ability to visualize and identify their functions in these diverse settings. In the last two decades, the application of click chemistry to label these microbes has deepened our understanding of bacterial physiology. With the development of a plethora of chemical tools that target many biological molecules, it is possible to track these microorganisms in real-time and at unprecedented resolution. Here, we review click chemistry, including bioorthogonal reactions, and their applications in imaging bacterial glycans, lipids, proteins, and nucleic acids using chemical reporters. We also highlight significant advances that have enabled biological discoveries that have heretofore remained elusive.
Collapse
Affiliation(s)
- Qiuyu Zheng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Pamela V Chang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853
| |
Collapse
|
8
|
Beauchemin ET, Hunter C, Maurice CF. Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting. Gut Microbes 2023; 15:2180317. [PMID: 36823031 PMCID: PMC9980609 DOI: 10.1080/19490976.2023.2180317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria. In this study, we aimed to address this gap by adapting 5-ethynyl-2'-deoxyuridine (EdU) click chemistry (EdU-click), a metabolic labeling method, coupled with fluorescence-activated cell sorting and sequencing (FACS-Seq) to characterize replicating gut bacteria. We first used EdU-click with human gut bacterial isolates and show that many of them are amenable to this technique. We then optimized EdU-click and FACS-Seq for murine fecal bacteria and reveal that Prevotella UCG-001 and Ileibacterium are enriched in the replicating fraction. Finally, we labeled the actively replicating murine gut bacteria during exposure to cell wall-specific antibiotics in vitro. We show that regardless of the antibiotic used, the actively replicating bacteria largely consist of Ileibacterium, suggesting the resistance of this taxon to perturbations. Overall, we demonstrate how combining EdU-click and FACSeq can identify the actively replicating gut bacteria and their link with the composition of the whole community in both homeostatic and perturbed conditions. This technique will be instrumental in elucidating in situ bacterial replication dynamics in a variety of other ecological states, including colonization and species invasion, as well as for investigating the relationship between the replication and abundance of bacteria in complex communities.
Collapse
Affiliation(s)
- Eve T. Beauchemin
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Claire Hunter
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada,McGill Centre for Microbiome Research, McGill University, Montreal, Quebec, Canada,CONTACT Corinne F. Maurice Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
9
|
Teufel M, Henkel W, Sobetzko P. The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity. Front Microbiol 2023; 14:1119878. [PMID: 37152747 PMCID: PMC10157177 DOI: 10.3389/fmicb.2023.1119878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
For a coherent response to environmental changes, bacterial evolution has formed a complex transcriptional regulatory system comprising classical DNA binding proteins sigma factors and modulation of DNA topology. In this study, we investigate replication-induced gene copy numbers - a regulatory concept that is unlike the others not based on modulation of promoter activity but on replication dynamics. We show that a large fraction of genes are predominantly affected by transient copy numbers and identify cellular functions and central pathways governed by this mechanism in Escherichia coli. Furthermore, we show quantitatively that the previously observed spatio-temporal expression pattern between different growth phases mainly emerges from transient chromosomal copy numbers. We extend the analysis to the plant pathogen Dickeya dadantii and the biotechnologically relevant organism Vibrio natriegens. The analysis reveals a connection between growth phase dependent gene expression and evolutionary gene migration in these species. A further extension to the bacterial kingdom indicates that chromosome evolution is governed by growth rate related transient copy numbers.
Collapse
Affiliation(s)
- Marc Teufel
- Synthetic Microbiology Center Marburg (SYNMIKRO), Philipps Universität Marburg, Marburg, Germany
| | - Werner Henkel
- Transmission Systems Group, Jacobs University Bremen, Bremen, Germany
| | - Patrick Sobetzko
- Synthetic Microbiology Center Marburg (SYNMIKRO), Philipps Universität Marburg, Marburg, Germany
- DynAMic Department, Universitè de Lorraine, INRAE, Nancy, France
- *Correspondence: Patrick Sobetzko
| |
Collapse
|
10
|
HslO ameliorates arrested ΔrecA polA cell growth and reduces DNA damage and oxidative stress responses. Sci Rep 2022; 12:22182. [PMID: 36564489 PMCID: PMC9789031 DOI: 10.1038/s41598-022-26703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Chromosome damage combined with defective recombinase activity has been widely considered to render cells inviable, owing to deficient double-strand break repair. However, temperature-sensitive recAts polA cells grow well upon induction of DNA damage and supplementation with catalase at restrictive temperatures. These treatments reduce intracellular reactive oxygen species (ROS) levels, which suggests that recAts polA cells are susceptible to ROS, but not chronic chromosome damage. Therefore, we investigated whether polA cells can tolerate a complete lack of recombinase function. We introduced a ΔrecA allele in polA cells in the presence or absence of the hslO-encoding redox molecular chaperon Hsp33 expression plasmid. Induction of the hslO gene with IPTG resulted in increased cell viability in ΔrecA polA cells with the hslO expression plasmid. ΔrecA polA cells in the absence of the hslO expression plasmid showed rich medium sensitivity with increasing ROS levels. Adding catalase to the culture medium considerably rescued growth arrest and decreased ROS. These results suggest that hslO expression manages oxidative stress to an acceptable level in cells with oxidative damage and rescues cell growth. Overall, ROS may regulate several processes, from damage response to cell division, via ROS-sensitive cell metabolism.
Collapse
|
11
|
Kaidow A, Ishii N, Suzuki S, Shiina T, Kasahara H. Vitamin C Maintenance against Cell Growth Arrest and Reactive Oxygen Species Accumulation in the Presence of Redox Molecular Chaperone hslO Gene. Int J Mol Sci 2022; 23:12786. [PMID: 36361576 PMCID: PMC9659236 DOI: 10.3390/ijms232112786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2022] Open
Abstract
Chromosome damage combined with defective recombinase activity renders cells inviable, owing to deficient double-strand break repair. Despite this, recA polA cells grow well under either DNA damage response (SOS) conditions or catalase medium supplementation. Catalase treatments reduce intracellular reactive oxygen species (ROS) levels, suggesting that recA polA cells are susceptible to not only chronic chromosome damage but also ROS. In this study, we used a reducing agent, vitamin C, to confirm whether cell growth could be improved. Vitamin C reduced ROS levels and rescued colony formation in recAts polA cells under restrictive temperatures in the presence of hslO, the gene encoding a redox molecular chaperone. Subsequently, we investigated the role of hslO in the cell growth failure of recAts polA cells. The effects of vitamin C were observed in hslO+ cells; simultaneously, cells converged along several ploidies likely through a completion of replication, with the addition of vitamin C at restrictive temperatures. These results suggest that HslO could manage oxidative stress to an acceptable level, allowing for cell division as well as rescuing cell growth. Overall, ROS may regulate several processes, from damage response to cell division. Our results provide a basis for understanding the unsolved regulatory interplay of cellular processes.
Collapse
Affiliation(s)
- Akihiro Kaidow
- Department of Biology, School of Biological Sciences, Tokai University, Sapporo 005-8601, Japan
- Hokkaido Regional Research Center, Tokai University, Sapporo 005-8601, Japan
| | - Noriko Ishii
- Department of Biology, School of Biological Sciences, Tokai University, Sapporo 005-8601, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara 259-1193, Japan
| | - Hirokazu Kasahara
- Department of Biology, School of Biological Sciences, Tokai University, Sapporo 005-8601, Japan
| |
Collapse
|
12
|
Kaidow A, Ishii N, Suzuki S, Shiina T, Kasahara H. Reactive oxygen species accumulation is synchronised with growth inhibition of temperature-sensitive recAts polA Escherichia coli. Arch Microbiol 2022; 204:396. [PMID: 35705748 PMCID: PMC9200703 DOI: 10.1007/s00203-022-02957-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
When combined with recombinase defects, chromosome breakage and double-strand break repair deficiencies render cells inviable. However, cells are viable when an SOS response occurs in recAts polA cells in Escherichia coli. Here, we aimed to elucidate the underlying mechanisms of this process. Transposon mutagenesis revealed that the hslO gene, a redox chaperone Hsp33 involved in reactive oxidative species (ROS) metabolism, was required for the suppression of recAts polA lethality at a restricted temperature. Recently, it has been reported that lethal treatments trigger ROS accumulation. We also found that recAts polA cells accumulated ROS at the restricted temperature. A catalase addition to the medium alleviates the temperature sensitivity of recAts polA cells and decreases ROS accumulation. These results suggest that the SOS response and hslO manage oxidative insult to an acceptable level in cells with oxidative damage and rescue cell growth. Overall, ROS might regulate several cellular processes.
Collapse
Affiliation(s)
- Akihiro Kaidow
- Department of Biology, School of Biology, Tokai University, Sapporo, 005-8601, Japan.
| | - Noriko Ishii
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
| | - Sinngo Suzuki
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Hirokazu Kasahara
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
| |
Collapse
|
13
|
Iyengar BR, Wagner A. GroEL/S overexpression helps to purge deleterious mutations and reduce genetic diversity during adaptive protein evolution. Mol Biol Evol 2022; 39:6540901. [PMID: 35234895 PMCID: PMC9188349 DOI: 10.1093/molbev/msac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chaperones are proteins that help other proteins fold. They also affect the adaptive evolution of their client proteins by buffering the effect of deleterious mutations and increasing the genetic diversity of evolving proteins. We study how the bacterial chaperone GroE (GroEL + GroES) affects the evolution of green fluorescent protein (GFP). To this end we subjected GFP to multiple rounds of mutation and selection for its color phenotype in four replicate E. coli populations, and studied its evolutionary dynamics through high-throughput sequencing and mutant engineering. We evolved GFP both under stabilizing selection for its ancestral (green) phenotype, and to directional selection for a new (cyan) phenotype. We did so both under low and high expression of the chaperone GroE. In contrast to previous work, we observe that GroE does not just buffer but also helps purge deleterious (fluorescence reducing) mutations from evolving populations. In doing so, GroE helps reduce the genetic diversity of evolving populations. In addition, it causes phenotypic heterogeneity in mutants with the same genotype, helping to enhance their fluorescence in some cells, and reducing it in others. Our observations show that chaperones can affect adaptive evolution in more than one way.
Collapse
|
14
|
Conin B, Billault-Chaumartin I, El Sayyed H, Quenech'Du N, Cockram C, Koszul R, Espéli O. Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome. Nucleic Acids Res 2022; 50:2635-2650. [PMID: 35212387 PMCID: PMC8934667 DOI: 10.1093/nar/gkac105] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/07/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022] Open
Abstract
In bacteria, chromosome segregation occurs progressively from the origin to terminus within minutes of replication of each locus. Between replication and segregation, sister loci are held in an apparent cohesive state by topological links. The decatenation activity of topoisomerase IV (Topo IV) is required for segregation of replicated loci, yet little is known about the structuring of the chromosome maintained in a cohesive state. In this work, we investigated chromosome folding in cells with altered decatenation activities. Within minutes after Topo IV inactivation, massive chromosome reorganization occurs, associated with increased in contacts between nearby loci, likely trans-contacts between sister chromatids, and in long-range contacts between the terminus and distant loci. We deciphered the respective roles of Topo III, MatP and MukB when TopoIV activity becomes limiting. Topo III reduces short-range inter-sister contacts suggesting its activity near replication forks. MatP, the terminus macrodomain organizing system, and MukB, the Escherichia coli SMC, promote long-range contacts with the terminus. We propose that the large-scale conformational changes observed under these conditions reveal defective decatenation attempts involving the terminus area. Our results support a model of spatial and temporal partitioning of the tasks required for sister chromosome segregation.
Collapse
Affiliation(s)
- Brenna Conin
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France.,Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France.,Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Ingrid Billault-Chaumartin
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Hafez El Sayyed
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Nicole Quenech'Du
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Charlotte Cockram
- Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France
| | - Romain Koszul
- Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France
| | - Olivier Espéli
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| |
Collapse
|
15
|
Tan Y, Agustin RVC, Stein LY, Sauvageau D. Transcriptomic analysis of synchrony and productivity in self-cycling fermentation of engineered yeast producing shikimic acid. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00691. [PMID: 34934640 PMCID: PMC8660916 DOI: 10.1016/j.btre.2021.e00691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 05/25/2023]
Abstract
Industrial fermentation provides a wide variety of bioproducts, such as food, biofuels and pharmaceuticals. Self-cycling fermentation (SCF), an advanced automated semi-continuous fermentation approach, has shown significant advantages over batch reactors (BR); including cell synchrony and improved production. Here, Saccharomyces cerevisiae engineered to overproduce shikimic acid was grown under SCF operation. This led to four-fold increases in product yield and volumetric productivity compared to BR. Transcriptomic analyses were performed to understand the cellular mechanisms leading to these increases. Results indicate an up-regulation of a large number of genes related to the cell cycle and DNA replication in the early stages of SCF cycles, inferring substantial synchronization. Moreover, numerous genes related to gluconeogenesis, the citrate cycle and oxidative phosphorylation were significantly up-regulated in the late stages of SCF cycles, consistent with significant increases in shikimic acid yield and productivity.
Collapse
Key Words
- BR, Batch reactor
- CER, Carbon dioxide evolution rate
- DDT, Dithiothreitol
- DNA, Deoxyribonucleic acid
- EDTA, Ethylenediaminetetraacetic acid
- FC, Fold change
- OD600, Optical density at 600 nm
- RNA, Ribonucleic acid
- SCF, Self-cycling fermentation
- STP, Standard temperature and pressure
- Saccharomyces cerevisiae
- Self-cycling fermentation (SCF)
- Shikimic acid
- Synchrony
- Transcriptomics
- cDNA, Complementary deoxyribonucleic acid
- mRNA, Messenger ribonucleic acid
- qPCR, Quantitative polymerase chain reaction
Collapse
Affiliation(s)
- Yusheng Tan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Roman Vincent C. Agustin
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Lisa Y. Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
16
|
Rashid FZM, Mahlandt E, van der Vaart M, Boer DEC, Varela Alvarez M, Henneman B, Brocken DJW, Voskamp P, Blok A, Shimizu T, Meijer A, Luijsterburg M, Goedhart J, Crémazy FGE, Dame R. HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein. Nucleic Acids Res 2021; 50:e10. [PMID: 34734265 PMCID: PMC8789088 DOI: 10.1093/nar/gkab993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 02/02/2023] Open
Abstract
The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.
Collapse
Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Eike Mahlandt
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Michiel van der Vaart
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Monica Varela Alvarez
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Bram Henneman
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Daan J W Brocken
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Anneloes J Blok
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Thomas S Shimizu
- Systems Biology, AMOLF Institute, Amsterdam 1098XG, The Netherlands
| | - Annemarie H Meijer
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Joachim Goedhart
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
| |
Collapse
|
17
|
Barr DA, Omollo C, Mason M, Koch A, Wilkinson RJ, Lalloo DG, Meintjes G, Mizrahi V, Warner DF, Davies G. Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria. Sci Rep 2021; 11:18661. [PMID: 34545154 PMCID: PMC8452731 DOI: 10.1038/s41598-021-98176-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022] Open
Abstract
Detection and accurate quantitation of viable Mycobacterium tuberculosis is fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology—including the tendency to clump, and “differential” culturability—and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). During exponential growth CA + cell counts are highly correlated with CFU counts and can be used as a real-time alternative to simplify the accurate standardisation of inocula for experiments. In contrast to CFU counting, this method can detect and enumerate cell aggregates in samples, which we show are a potential source of variance and bias when using established methods. We show that CFUs comprise a sub-population of intact, metabolically active mycobacterial cells in liquid cultures, with CFU-proportion varying by growth conditions. A pharmacodynamic application of the flow cytometry method, exploring kinetics of fluorescent probe defined subpopulations compared to CFU is demonstrated. Flow cytometry derived Mycobacterium bovis bacillus Calmette-Guérin (BCG) time-kill curves differ for rifampicin and kanamycin versus isoniazid and ethambutol, as do the relative dynamics of discrete morphologically-distinct subpopulations of bacilli revealed by this high-throughput single-cell technique.
Collapse
Affiliation(s)
- David A Barr
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, L7 3EA, UK. .,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Charles Omollo
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mandy Mason
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Anastasia Koch
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,Department of Medicine, University of Cape Town, Cape Town, South Africa.,The Francis Crick Institute, London, NW11AT, UK.,Department of Medicine, Imperial College, London, W12 0NN, UK
| | - David G Lalloo
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Valerie Mizrahi
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Gerry Davies
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L7 3EA, UK
| |
Collapse
|
18
|
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
Collapse
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.
| |
Collapse
|
19
|
Murawski AM, Brynildsen MP. Ploidy is an important determinant of fluoroquinolone persister survival. Curr Biol 2021; 31:2039-2050.e7. [PMID: 33711253 PMCID: PMC8183807 DOI: 10.1016/j.cub.2021.02.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 02/04/2023]
Abstract
Genetic mutants have demonstrated the importance of homologous recombination (HR) to fluoroquinolone (FQ) persistence, which suggests that single-cell chromosome (Chr) abundance might be a phenotypic variable of importance to persisters. Here, we sorted stationary-phase E. coli based on ploidy and subjected the subpopulations to tolerance assays. Subpopulations sorted to contain diploid cells harbored up to ∼40-fold more FQ persisters than those sorted to contain monoploid cells. This association was observed with distinct FQs, in independent environmental conditions, and with more than one strain of E. coli (MG1655; uropathogenic CFT073) but was abolished in HR-deficient strains (ΔrecA and ΔrecB). It was observed that the persister level of monoploid subpopulations exceeded those of ΔrecA and ΔrecB by 10-fold or more, and subsequent high-purity sorting confirmed that observation. Those data suggested the existence of distinct FQ persister subtypes: those that are and are not proficient with HR. Time-lapse microscopy revealed significant differences in initial size and growth dynamics during the post-antibiotic recovery period for persisters from monoploid- and diploid-enriched subpopulations. In addition, non-persisters in monoploid-enriched subpopulations elongated minimally following FQ treatment, resembling previous observations of HR-deficient strains, whereas non-persisters in diploid-enriched subpopulations on average filamented extensively. Together, these results identify a phenotypic variable with a significant impact on FQ persistence, establish the existence of more than one type of persister to the same antibiotic in an isogenic culture, and reveal roles for RecA and RecB in FQ persistence, even in the absence of homologous chromosomes.
Collapse
Affiliation(s)
- Allison M Murawski
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA.
| |
Collapse
|
20
|
Vitelli M, Budman H, Pritzker M, Tamer M. Applications of flow cytometry sorting in the pharmaceutical industry: A review. Biotechnol Prog 2021; 37:e3146. [PMID: 33749147 DOI: 10.1002/btpr.3146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
The article reviews applications of flow cytometry sorting in manufacturing of pharmaceuticals. Flow cytometry sorting is an extremely powerful tool for monitoring, screening and separating single cells based on any property that can be measured by flow cytometry. Different applications of flow cytometry sorting are classified into groups and discussed in separate sections as follows: (a) isolation of cell types, (b) high throughput screening, (c) cell surface display, (d) droplet fluorescent-activated cell sorting (FACS). Future opportunities are identified including: (a) sorting of particular fractions of the cell population based on a property of interest for generating inoculum that will result in improved outcomes of cell cultures and (b) the use of population balance models in combination with FACS to design and optimize cell cultures.
Collapse
Affiliation(s)
- Michael Vitelli
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Hector Budman
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Mark Pritzker
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Melih Tamer
- Department of Manufacturing Technology, Sanofi Pasteur, Toronto, Canada
| |
Collapse
|
21
|
Murawski AM, Rittenbach K, DeCoste CJ, Laevsky G, Brynildsen MP. Counting Chromosomes in Individual Bacteria to Quantify Their Impacts on Persistence. Methods Mol Biol 2021; 2357:125-146. [PMID: 34590256 DOI: 10.1007/978-1-0716-1621-5_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] [Indexed: 06/13/2023]
Abstract
Persisters are phenotypic variants within bacterial populations that tolerate antibiotic treatments considerably better than the majority of cells. A phenotypic quality that varies within bacterial populations is the chromosome number of individual cells. One, two, four, or more chromosomes per cell have been observed previously, and the impact of genome copy number can range from gene dosage effects to an inability to perform specific DNA repair functions, such as homologous recombination. We hypothesize that chromosome abundance is an underappreciated phenotypic variable that could impact persistence to antibiotics. Here, we describe methodologies to segregate bacterial populations based on chromosome number, assess the purity of those subpopulations, and suggest assays that could be used to quantify the impacts of genome abundance on persistence.
Collapse
Affiliation(s)
- Allison M Murawski
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | | | | | - Gary Laevsky
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
22
|
Gross MH, Konieczny I. Polyphosphate induces the proteolysis of ADP-bound fraction of initiator to inhibit DNA replication initiation upon stress in Escherichia coli. Nucleic Acids Res 2020; 48:5457-5466. [PMID: 32282902 PMCID: PMC7261185 DOI: 10.1093/nar/gkaa217] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 11/29/2022] Open
Abstract
The decision whether to replicate DNA is crucial for cell survival, not only to proliferate in favorable conditions, but also to adopt to environmental changes. When a bacteria encounters stress, e.g. starvation, it launches the stringent response, to arrest cell proliferation and to promote survival. During the stringent response a vast amount of polymer composed of phosphate residues, i.e. inorganic polyphosphate (PolyP) is synthesized from ATP. Despite extensive research on PolyP, we still lack the full understanding of the PolyP role during stress. It is also elusive what is the mechanism of DNA replication initiation arrest in starved Escherichia coli cells. Here, we show that during stringent response PolyP activates Lon protease to degrade selectively the replication initiaton protein DnaA bound to ADP, but not ATP. In contrast to DnaA-ADP, the DnaA-ATP does not interact with PolyP, but binds to dnaA promoter to block dnaA transcription. The systems controlling the ratio of nucleotide states of DnaA continue to convert DnaA-ATP to DnaA-ADP, which is proteolysed by Lon, thereby resulting in the DNA replication initiation arrest. The uncovered regulatory mechanism interlocks the PolyP-dependent protease activation with the ATP/ADP cycle of dual-functioning protein essential for bacterial cell proliferation.
Collapse
Affiliation(s)
- Marta H Gross
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Igor Konieczny
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| |
Collapse
|
23
|
Organization of the Escherichia coli Chromosome by a MukBEF Axial Core. Mol Cell 2020; 78:250-260.e5. [PMID: 32097603 PMCID: PMC7163298 DOI: 10.1016/j.molcel.2020.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/03/2019] [Accepted: 02/03/2020] [Indexed: 01/22/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes organize chromosomes ubiquitously, thereby contributing to their faithful segregation. We demonstrate that under conditions of increased chromosome occupancy of the Escherichia coli SMC complex, MukBEF, the chromosome is organized as a series of loops around a thin (<130 nm) MukBEF axial core, whose length is ∼1,100 times shorter than the chromosomal DNA. The linear order of chromosomal loci is maintained in the axial cores, whose formation requires MukBEF ATP hydrolysis. Axial core structure in non-replicating chromosomes is predominantly linear (1 μm) but becomes circular (1.5 μm) in the absence of MatP because of its failure to displace MukBEF from the 800 kbp replication termination region (ter). Displacement of MukBEF from ter by MatP in wild-type cells directs MukBEF colocalization with the replication origin. We conclude that MukBEF individualizes and compacts the chromosome lengthwise, demonstrating a chromosome organization mechanism similar to condensin in mitotic chromosome formation. MukBEF forms a chromosome axial core dependent on ATP hydrolysis MukBEF compacts the chromosome lengthwise while avoiding links between replichores MatP determines the shape of the axial core by displacing MukBEF from ter The displacement by MatP directs MukBEF colocalization with the replication origin
Collapse
|
24
|
Hofmann A, Mäkelä J, Sherratt DJ, Heermann D, Murray SM. Self-organised segregation of bacterial chromosomal origins. eLife 2019; 8:e46564. [PMID: 31397672 PMCID: PMC6701925 DOI: 10.7554/elife.46564] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/09/2019] [Indexed: 01/12/2023] Open
Abstract
The chromosomal replication origin region (ori) of characterised bacteria is dynamically positioned throughout the cell cycle. In slowly growing Escherichia coli, ori is maintained at mid-cell from birth until its replication, after which newly replicated sister oris move to opposite quarter positions. Here, we provide an explanation for ori positioning based on the self-organisation of the Structural Maintenance of Chromosomes complex, MukBEF, which forms dynamically positioned clusters on the chromosome. We propose that a non-trivial feedback between the self-organising gradient of MukBEF complexes and the oris leads to accurate ori positioning. We find excellent agreement with quantitative experimental measurements and confirm key predictions. Specifically, we show that oris exhibit biased motion towards MukBEF clusters, rather than mid-cell. Our findings suggest that MukBEF and oris act together as a self-organising system in chromosome organisation-segregation and introduces protein self-organisation as an important consideration for future studies of chromosome dynamics.
Collapse
Affiliation(s)
- Andreas Hofmann
- Institute for Theoretical PhysicsHeidelberg UniversityHeidelbergGermany
| | - Jarno Mäkelä
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - David J Sherratt
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Dieter Heermann
- Institute for Theoretical PhysicsHeidelberg UniversityHeidelbergGermany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology, LOEWE Centre for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| |
Collapse
|
25
|
Two-step chromosome segregation in the stalked budding bacterium Hyphomonas neptunium. Nat Commun 2019; 10:3290. [PMID: 31337764 PMCID: PMC6650430 DOI: 10.1038/s41467-019-11242-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/28/2019] [Indexed: 12/11/2022] Open
Abstract
Chromosome segregation typically occurs after replication has finished in eukaryotes but during replication in bacteria. Here, we show that the alphaproteobacterium Hyphomonas neptunium, which proliferates by bud formation at the tip of a stalk-like cellular extension, segregates its chromosomes in a unique two-step process. First, the two sister origin regions are targeted to opposite poles of the mother cell, driven by the ParABS partitioning system. Subsequently, once the bulk of chromosomal DNA has been replicated and the bud exceeds a certain threshold size, the cell initiates a second segregation step during which it transfers the stalk-proximal origin region through the stalk into the nascent bud compartment. Thus, while chromosome replication and segregation usually proceed concurrently in bacteria, the two processes are largely uncoupled in H. neptunium, reminiscent of eukaryotic mitosis. These results indicate that stalked budding bacteria have evolved specific mechanisms to adjust chromosome segregation to their unusual life cycle.
Collapse
|
26
|
Chang Z, Shen Y, Lang Q, Zheng H, Tokuyasu TA, Huang S, Liu C. Microfluidic Synchronizer Using a Synthetic Nanoparticle-Capped Bacterium. ACS Synth Biol 2019; 8:962-967. [PMID: 30964646 DOI: 10.1021/acssynbio.9b00058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conventional techniques to synchronize bacterial cells often require manual manipulations and lengthy incubation lacking precise temporal control. An automated microfluidic device was recently developed to overcome these limitations. However, it exploits the stalk property of Caulobacter crescentus that undergoes asymmetric stalked and swarmer cell cycle stages and is therefore restricted to this species. To address this shortcoming, we have engineered Escherichia coli cells to adhere to microchannel walls via a synthetic and inducible "stalk". The pole of E. coli is capped by magnetic fluorescent nanoparticles via a polar-localized outer membrane protein. A mass of cells is immobilized in a microfluidic chamber by an externally applied magnetic field. Daughter cells are formed without the induced stalk and hence are flushed out, yielding a synchronous population of "baby" cells. The stalks can be tracked by GFP and nanoparticle fluorescence; no fluorescence signal is detected in the eluted cell population, indicating that it consists solely of daughters. The collected daughter cells display superb synchrony. The results demonstrate a new on-chip method to synchronize the model bacterium E. coli and likely other bacterial species, and also foster the application of synthetic biology to the study of the bacterial cell cycle.
Collapse
Affiliation(s)
- Zhiguang Chang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Shenzhen, 518120, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China
| | - Qi Lang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Hai Zheng
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Taku A. Tokuyasu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
| | - Shuqiang Huang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Chenli Liu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| |
Collapse
|
27
|
Barrett TC, Mok WWK, Murawski AM, Brynildsen MP. Enhanced antibiotic resistance development from fluoroquinolone persisters after a single exposure to antibiotic. Nat Commun 2019; 10:1177. [PMID: 30862812 PMCID: PMC6414640 DOI: 10.1038/s41467-019-09058-4] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial persisters are able to tolerate high levels of antibiotics and give rise to new populations. Persister tolerance is generally attributed to minimally active cellular processes that prevent antibiotic-induced damage, which has led to the supposition that persister offspring give rise to antibiotic-resistant mutants at comparable rates to normal cells. Using time-lapse microscopy to monitor Escherichia coli populations following ofloxacin treatment, we find that persisters filament extensively and induce impressive SOS responses before returning to a normal appearance. Further, populations derived from fluoroquinolone persisters contain significantly greater quantities of antibiotic-resistant mutants than those from untreated controls. We confirm that resistance is heritable and that the enhancement requires RecA, SOS induction, an opportunity to recover from treatment, and the involvement of error-prone DNA polymerase V (UmuDC). These findings show that fluoroquinolones damage DNA in persisters and that the ensuing SOS response accelerates the development of antibiotic resistance from these survivors. Fluoroquinolone (FQ)-induced DNA damage in persisters could promote antibiotic resistance. Here, using time-lapse microscopy and genetic analyses, the authors show that after a single round of FQ treatment, SOS response in persisters accelerates the development of resistance to unrelated antibiotics.
Collapse
Affiliation(s)
- Theresa C Barrett
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Wendy W K Mok
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06032-3305, USA
| | - Allison M Murawski
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
| |
Collapse
|
28
|
Noise in bacterial gene expression. Biochem Soc Trans 2018; 47:209-217. [PMID: 30578346 DOI: 10.1042/bst20180500] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/25/2022]
Abstract
The expression level of a gene can fluctuate significantly between individuals within a population of genetically identical cells. The resultant phenotypic heterogeneity could be exploited by bacteria to adapt to changing environmental conditions. Noise is hence a genome-wide phenomenon that arises from the stochastic nature of the biochemical reactions that take place during gene expression and the relatively low abundance of the molecules involved. The production of mRNA and proteins therefore occurs in bursts, with alternating episodes of high and low activity during transcription and translation. Single-cell and single-molecule studies demonstrated that noise within gene expression is influenced by a combination of both intrinsic and extrinsic factors. However, our mechanistic understanding of this process at the molecular level is still rather limited. Further investigation is necessary that takes into account the detailed knowledge of gene regulation gained from biochemical studies.
Collapse
|
29
|
Spahn CK, Glaesmann M, Grimm JB, Ayala AX, Lavis LD, Heilemann M. A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels. Sci Rep 2018; 8:14768. [PMID: 30282984 PMCID: PMC6170473 DOI: 10.1038/s41598-018-33052-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/21/2018] [Indexed: 11/09/2022] Open
Abstract
Maintenance of the bacterial homeostasis initially emanates from interactions between proteins and the bacterial nucleoid. Investigating their spatial correlation requires high spatial resolution, especially in tiny, highly confined and crowded bacterial cells. Here, we present super-resolution microscopy using a palette of fluorescent labels that bind transiently to either the membrane or the nucleoid of fixed E. coli cells. The presented labels are easily applicable, versatile and allow long-term single-molecule super-resolution imaging independent of photobleaching. The different spectral properties allow for multiplexed imaging in combination with other localisation-based super-resolution imaging techniques. As examples for applications, we demonstrate correlated super-resolution imaging of the bacterial nucleoid with the position of genetic loci, of nascent DNA in correlation to the entire nucleoid, and of the nucleoid of metabolically arrested cells. We furthermore show that DNA- and membrane-targeting labels can be combined with photoactivatable fluorescent proteins and visualise the nano-scale distribution of RNA polymerase relative to the nucleoid in drug-treated E. coli cells.
Collapse
Affiliation(s)
- Christoph K Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Anthony X Ayala
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA.
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| |
Collapse
|
30
|
Köller M, Ziegler N, Sengstock C, Schildhauer TA, Ludwig A. Bacterial cell division is involved in the damage of gram-negative bacteria on a nano-pillar titanium surface. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aad2c1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
31
|
Timing of DNA damage responses impacts persistence to fluoroquinolones. Proc Natl Acad Sci U S A 2018; 115:E6301-E6309. [PMID: 29915065 DOI: 10.1073/pnas.1804218115] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial persisters are subpopulations of phenotypic variants in isogenic cultures that can survive lethal doses of antibiotics. Their tolerances are often attributed to reduced activities of antibiotic targets, which limit corruption and damage in persisters compared with bacteria that die from treatment. However, that model does not hold for nongrowing populations treated with ofloxacin, a fluoroquinolone, where antibiotic-induced damage is comparable between cells that live and those that die. To understand how those persisters achieve this feat, we employed a genetic system that uses orthogonal control of MazF and MazE, a toxin and its cognate antitoxin, to generate model persisters that are uniformly tolerant to ofloxacin. Despite this complete tolerance, MazF model persisters required the same DNA repair machinery (RecA, RecB, and SOS induction) to survive ofloxacin treatment as their nongrowing, WT counterparts and exhibited similar indicators of DNA damage from treatment. Further investigation revealed that, following treatment, the timing of DNA repair was critical to MazF persister survival because, when repair was delayed until after growth and DNA synthesis resumed, survival was compromised. In addition, we found that, with nongrowing, WT planktonic and biofilm populations, stalling the resumption of growth and DNA synthesis after the conclusion of fluoroquinolone treatment with a prevalent type of stress at infection sites (nutrient limitation) led to near complete survival. These findings illustrate that the timing of events, such as DNA repair, following fluoroquinolone treatment is important to persister survival and provide further evidence that knowledge of the postantibiotic recovery period is critical to understanding persistence phenotypes.
Collapse
|
32
|
Gutiérrez-Ramos S, Hoyos M, Ruiz-Suárez JC. Induced clustering of Escherichia coli by acoustic fields. Sci Rep 2018; 8:4668. [PMID: 29549342 PMCID: PMC5856742 DOI: 10.1038/s41598-018-22960-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/26/2018] [Indexed: 11/21/2022] Open
Abstract
Brownian or self-propelled particles in aqueous suspensions can be trapped by acoustic fields generated by piezoelectric transducers usually at frequencies in the megahertz. The obtained confinement allows the study of rich collective behaviours like clustering or spreading dynamics in microgravity-like conditions. The acoustic field induces the levitation of self-propelled particles and provides secondary lateral forces to capture them at nodal planes. Here, we give a step forward in the field of confined active matter, reporting levitation experiments of bacterial suspensions of Escherichia coli. Clustering of living bacteria is monitored as a function of time, where different behaviours are clearly distinguished. Upon the removal of the acoustic signal, bacteria rapidly spread, impelled by their own swimming. Nevertheless, long periods of confinement result in irreversible bacteria entanglements that could act as seeds for levitating bacterial aggregates.
Collapse
Affiliation(s)
- Salomé Gutiérrez-Ramos
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH UMR 7636) CNRS, ESPCI Paris, PSL Research University, Sorbonne Université, Université Paris Diderot, 10 rue Vauquelin, 75005 Paris, France.,Centro de Investigación y de Estudios Avanzados, Unidad Monterrey, PIIT Autopista al Aeropuerto Km. 9.5, Apodaca, Nuevo León, 66600, Mexico
| | - Mauricio Hoyos
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH UMR 7636) CNRS, ESPCI Paris, PSL Research University, Sorbonne Université, Université Paris Diderot, 10 rue Vauquelin, 75005 Paris, France
| | - J C Ruiz-Suárez
- Centro de Investigación y de Estudios Avanzados, Unidad Monterrey, PIIT Autopista al Aeropuerto Km. 9.5, Apodaca, Nuevo León, 66600, Mexico.
| |
Collapse
|
33
|
Kemter FS, Messerschmidt SJ, Schallopp N, Sobetzko P, Lang E, Bunk B, Spröer C, Teschler JK, Yildiz FH, Overmann J, Waldminghaus T. Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae. PLoS Genet 2018; 14:e1007251. [PMID: 29505558 PMCID: PMC5854411 DOI: 10.1371/journal.pgen.1007251] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae, the causative agent of the cholera disease, is commonly used as a model organism for the study of bacteria with multipartite genomes. Its two chromosomes of different sizes initiate their DNA replication at distinct time points in the cell cycle and terminate in synchrony. In this study, the time-delayed start of Chr2 was verified in a synchronized cell population. This replication pattern suggests two possible regulation mechanisms for other Vibrio species with different sized secondary chromosomes: Either all Chr2 start DNA replication with a fixed delay after Chr1 initiation, or the timepoint at which Chr2 initiates varies such that termination of chromosomal replication occurs in synchrony. We investigated these two models and revealed that the two chromosomes of various Vibrionaceae species terminate in synchrony while Chr2-initiation timing relative to Chr1 is variable. Moreover, the sequence and function of the Chr2-triggering crtS site recently discovered in V. cholerae were found to be conserved, explaining the observed timing mechanism. Our results suggest that it is beneficial for bacterial cells with multiple chromosomes to synchronize their replication termination, potentially to optimize chromosome related processes as dimer resolution or segregation.
Collapse
Affiliation(s)
- Franziska S. Kemter
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Sonja J. Messerschmidt
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Elke Lang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jennifer K. Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Centre of Infection Research (DZIF), Partner Site Hannover–Braunschweig, Braunschweig, Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
| |
Collapse
|
34
|
Abstract
The widespread interest in cell synchronization is maintained by the studies of control mechanism involved in cell cycle regulation. During the synchronization distinct subpopulations of cells are obtained representing different stages of the cell cycle. These subpopulations are then used to study regulatory mechanisms of the cycle at the level of macromolecular biosynthesis (DNA synthesis, gene expression, protein synthesis), protein phosphorylation, development of new drugs, etc. Although several synchronization methods have been described, it is of general interest that scientists get a compilation and an updated view of these synchronization techniques. This introductory chapter summarizes: (1) the basic concepts and principal criteria of cell cycle synchronizations, (2) the most frequently used synchronization methods, such as physical fractionation (flow cytometry, dielectrophoresis, cytofluorometric purification), chemical blockade, (3) synchronization of embryonic cells, (4) synchronization at low temperature, (5) comparison of cell synchrony techniques, (6) synchronization of unicellular organisms, and (7) the effect of synchronization on transfection.
Collapse
|
35
|
Zou C, Wei X, Zhang Q. Visual synchronization of two 3-variable Lotka–Volterra oscillators based on DNA strand displacement. RSC Adv 2018; 8:20941-20951. [PMID: 35542339 PMCID: PMC9080848 DOI: 10.1039/c8ra01393d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/21/2018] [Indexed: 01/30/2023] Open
Abstract
DNA strand displacement as a theoretic foundation is helpful in constructing reaction networks and DNA circuits.
Collapse
Affiliation(s)
- Chengye Zou
- School of Computer Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Xiaopeng Wei
- School of Computer Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Qiang Zhang
- School of Computer Science and Engineering
- Dalian University of Technology
- Dalian 116024
- China
- Key Laboratory of Advanced and Intelligent Computing
| |
Collapse
|
36
|
Martel M, Balleydier A, Brochu J, Drolet M. Detection of oriC-Independent Replication in Escherichia coli Cells. Methods Mol Biol 2018; 1703:131-138. [PMID: 29177738 DOI: 10.1007/978-1-4939-7459-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In bacteria, replication of the chromosome is normally initiated following the binding of DnaA proteins to the oriC region. However, under certain circumstances, replication can also be initiated independent of the oriC/DnaA system. This is the case, for example, in Escherichia coli cells lacking RNase HI (rnha mutants) or type 1A topoisomerase activity (topA topB mutants). Here, we present a protocol in which replication from the oriC/DnaA system is first inhibited by the addition of the protein synthesis inhibitor, spectinomycin, to exponentially growing bacterial cell cultures. The thymidine analog, 5-ethynyl-2'-deoxyurdine (EdU) is then added to the cells, and after 1 h the cells are fixed and the Alexa Fluor® 488 dye is conjugated to EdU by the click-iT® reaction. The oriC-independent replication is detected in fixed cells by flow cytometry and can be visualized by fluorescence microscopy.
Collapse
Affiliation(s)
- Makisha Martel
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec, Canada, H3C 3J7
| | - Aurélien Balleydier
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec, Canada, H3C 3J7
| | - Julien Brochu
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec, Canada, H3C 3J7
| | - Marc Drolet
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec, Canada, H3C 3J7.
| |
Collapse
|
37
|
Abstract
Genes of the Rel/Spo homolog (RSH) superfamily synthesize and/or hydrolyse the modified nucleotides pppGpp/ ppGpp (collectively referred to as (p)ppGpp) and are prevalent across diverse bacteria and in plant chloroplasts. Bacteria accumulate (p)ppGpp in response to nutrient deprivation (generically called the stringent response) and elicit appropriate adaptive responses mainly through the regulation of transcription. Although at different concentrations (p)ppGpp affect the expression of distinct set of genes, the two well-characterized responses are reduction in expression of the protein synthesis machinery and increase in the expression of genes coding for amino acid biosynthesis. In Escherichia coli, the cellular (p)ppGpp level inversely correlates with the growth rate and increasing its concentration decreases the steady state growth rate in a defined growth medium. Since change in growth rate must be accompanied by changes in cell cycle parameters set through the activities of the DNA replication and cell division apparatus, (p)ppGpp could coordinate protein synthesis (cell mass increase) with these processes. Here we review the role of (p)ppGpp in bacterial cell cycle regulation.
Collapse
|
38
|
Colangelo-Lillis J, Wing BA, Raymond-Bouchard I, Whyte LG. Viral Induced Microbial Mortality in Arctic Hypersaline Spring Sediments. Front Microbiol 2017; 7:2158. [PMID: 28167930 PMCID: PMC5253365 DOI: 10.3389/fmicb.2016.02158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/22/2016] [Indexed: 12/30/2022] Open
Abstract
Viruses are a primary influence on microbial mortality in the global ocean. The impacts of viruses on their microbial hosts in low-energy environments are poorly explored and are the focus of this study. To investigate the role of viruses in mediating mortality in low-energy environments where contacts between viruses and microbes are infrequent, we conducted a set of in situ time series incubations in the outlet and channel sediments of two cold, hypersaline springs of the Canadian High Arctic. We found microbial and viral populations in dynamic equilibrium, indicating approximately equal birth and death rates for each population. In situ rates of microbial growth were low (0.5–50 × 103 cells cm-3 h-1) as were rates of viral decay (0.09–170 × 104 virions cm-3 h-1). A large fraction of the springs’ viral communities (49–100%) were refractory to decay over the timescales of our experiments. Microcosms amended with lactate or acetate exhibited increased microbial growth rates (up to three-fold) indicating organic carbon as one limiting resource for the microbial communities in these environments. A substantial fraction (15–71%) of the microbial populations contained inducible proviruses that were released- occasionally in multiple pulses- over the eight monitored days following chemical induction. Our findings indicate that viruses in low-energy systems maintain low rates of production and activity, have a small but notable impact on microbial mortality (8–29% attenuation of growth) and that successful viral replication may primarily proceed by non-lethal strategies. In cold, low biomass marine systems of similar character (e.g., subsurface sediments), viruses may be a relatively minor driver of community mortality compared to less energy-limited environments such as the marine water column or surface sediments.
Collapse
Affiliation(s)
- Jesse Colangelo-Lillis
- Department of Earth and Planetary Science, McGill University, MontrealQC, Canada; McGill Space Institute, McGill University, MontrealQC, Canada
| | - Boswell A Wing
- Department of Earth and Planetary Science, McGill University, MontrealQC, Canada; McGill Space Institute, McGill University, MontrealQC, Canada
| | | | - Lyle G Whyte
- McGill Space Institute, McGill University, MontrealQC, Canada; Department of Natural Resource Science, McGill University, MontrealQC, Canada
| |
Collapse
|
39
|
Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Transcription leads to pervasive replisome instability in bacteria. eLife 2017; 6. [PMID: 28092263 PMCID: PMC5305214 DOI: 10.7554/elife.19848] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/15/2017] [Indexed: 12/19/2022] Open
Abstract
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%). Furthermore, many of the observed complexes have short lifetimes (<8 min), suggesting that replisome disassembly is quite prevalent, possibly occurring several times per cell cycle. The instability of the replisome complex is conflict-induced: transcription inhibition stabilizes these complexes, restoring the second replisome in many of the cells. Our results suggest that, in contrast to the canonical model, DNA replication is a largely discontinuous process in vivo due to pervasive replication-transcription conflicts. DOI:http://dx.doi.org/10.7554/eLife.19848.001
Collapse
Affiliation(s)
| | | | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, United States.,Department of Microbiology, University of Washington, Seattle, United States.,Department of Bioengineering, University of Washington, Seattle, United States
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| |
Collapse
|
40
|
Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Transcription leads to pervasive replisome instability in bacteria. eLife 2017; 6. [PMID: 28092263 DOI: 10.7554/elife.19848.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/15/2017] [Indexed: 05/21/2023] Open
Abstract
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%). Furthermore, many of the observed complexes have short lifetimes (<8 min), suggesting that replisome disassembly is quite prevalent, possibly occurring several times per cell cycle. The instability of the replisome complex is conflict-induced: transcription inhibition stabilizes these complexes, restoring the second replisome in many of the cells. Our results suggest that, in contrast to the canonical model, DNA replication is a largely discontinuous process in vivo due to pervasive replication-transcription conflicts.
Collapse
Affiliation(s)
| | | | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, United States
- Department of Microbiology, University of Washington, Seattle, United States
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, United States
- Department of Genome Sciences, University of Washington, Seattle, United States
| |
Collapse
|
41
|
Spahn C, Glaesmann M, Gao Y, Foo YH, Lampe M, Kenney LJ, Heilemann M. Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells. Methods Mol Biol 2017; 1624:269-289. [PMID: 28842890 DOI: 10.1007/978-1-4939-7098-8_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Despite their small size and the lack of compartmentalization, bacteria exhibit a striking degree of cellular organization, both in time and space. During the last decade, a group of new microscopy techniques emerged, termed super-resolution microscopy or nanoscopy, which facilitate visualizing the organization of proteins in bacteria at the nanoscale. Single-molecule localization microscopy (SMLM) is especially well suited to reveal a wide range of new information regarding protein organization, interaction, and dynamics in single bacterial cells. Recent developments in click chemistry facilitate the visualization of bacterial chromatin with a resolution of ~20 nm, providing valuable information about the ultrastructure of bacterial nucleoids, especially at short generation times. In this chapter, we describe a simple-to-realize protocol that allows determining precise structural information of bacterial nucleoids in fixed cells, using direct stochastic optical reconstruction microscopy (dSTORM). In combination with quantitative photoactivated localization microscopy (PALM), the spatial relationship of proteins with the bacterial chromosome can be studied. The position of a protein of interest with respect to the nucleoids and the cell cylinder can be visualized by super-resolving the membrane using point accumulation for imaging in nanoscale topography (PAINT). The combination of the different SMLM techniques in a sequential workflow maximizes the information that can be extracted from single cells, while maintaining optimal imaging conditions for each technique.
Collapse
Affiliation(s)
- Christoph Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Yunfeng Gao
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Otto-Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Linda J Kenney
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore.
- University of Illinois, Chicago, Chicago, IL, 60612, USA.
- Jesse Brown VA Medical Center, Chicago, IL, 60612, USA.
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| |
Collapse
|
42
|
Diekmann R, Wolfson DL, Spahn C, Heilemann M, Schüttpelz M, Huser T. Nanoscopy of bacterial cells immobilized by holographic optical tweezers. Nat Commun 2016; 7:13711. [PMID: 27958271 PMCID: PMC5159804 DOI: 10.1038/ncomms13711] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/26/2016] [Indexed: 01/19/2023] Open
Abstract
Imaging non-adherent cells by super-resolution far-field fluorescence microscopy is currently not possible because of their rapid movement while in suspension. Holographic optical tweezers (HOTs) enable the ability to freely control the number and position of optical traps, thus facilitating the unrestricted manipulation of cells in a volume around the focal plane. Here we show that immobilizing non-adherent cells by optical tweezers is sufficient to achieve optical resolution well below the diffraction limit using localization microscopy. Individual cells can be oriented arbitrarily but preferably either horizontally or vertically relative to the microscope's image plane, enabling access to sample sections that are impossible to achieve with conventional sample preparation and immobilization. This opens up new opportunities to super-resolve the nanoscale organization of chromosomal DNA in individual bacterial cells.
Collapse
Affiliation(s)
- Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Deanna L. Wolfson
- NSF Center for Biophotonics, University of California, 2700 Stockton Boulevard, Suite 1400, Davis, Sacramento, California 95817, USA
- Department of Physics and Technology, UiT The Arctic University of Norway, Klokkargårdsbakken 35, 9019 Tromsø, Norway
| | - Christoph Spahn
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- NSF Center for Biophotonics, University of California, 2700 Stockton Boulevard, Suite 1400, Davis, Sacramento, California 95817, USA
| |
Collapse
|
43
|
A Magic Spot in Genome Maintenance. Trends Genet 2016; 33:58-67. [PMID: 27931778 DOI: 10.1016/j.tig.2016.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 01/02/2023]
Abstract
Nucleotide excision repair (NER) is the key DNA repair system that eliminates the majority of DNA helix-distorting lesions. RNA polymerase (RNAP) expedites the recognition of DNA damage by NER components via transcription-coupled DNA repair (TCR). In bacteria, a modified nucleotide ppGpp ('magic spot') is a pleiotropic second messenger that mediates the response to nutrient deficiencies by altering the initiation properties of RNAP. In this review, we discuss newly elucidated roles of guanosine 5'-diphosphate 3'-diphosphate (ppGpp) in transcription elongation that couple this alarmone to DNA damage repair and maintenance.
Collapse
|
44
|
Luo Y, Yang X, Tan X, Xu L, Liu Z, Xiao J, Peng R. Functionalized graphene oxide in microbial engineering: An effective stimulator for bacterial growth. CARBON 2016; 103:172-180. [PMID: 35431318 PMCID: PMC9012453 DOI: 10.1016/j.carbon.2016.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Whether graphene and graphene oxide (GO) would affect the activities of bacteria has been under debate. Nevertheless, how graphene derivatives with biocompatible coatings interact with microorganisms and the underlying mechanisms are important issues for nanobiotechnology, and remain to be further explored. Herein, three new types of nano-GOs functionalized with polyethylene glycol (nGO-PEGs) were synthesized by varying the PEGylation degree, and their effects on Escherichia coli (E. coli) were carefully investigated. Interestingly, nGO-PEG (1:1), the one with relatively lower PEGylation degree, could significantly stimulate bacterial growth, whereas as-made GO and the other two nGO-PEGs showed no effect. Further analysis revealed that nGO-PEG (1:1) treatment significantly accelerated FtsZ-ring assembly, shortening Phase 1 in the bacterial cell cycle. Both DNA synthesis and extracellular polymeric substance (EPS) secretion were also dramatically increased. This unique phenomenon suggests promising potentials in microbial engineering as well as in clinical detection of bacterial pathogens. As a proof-of-concept, nGO-PEG (1:1) treatment could remarkably enhance (up to 6-fold) recombinant protein production in engineered bacteria cells. To our best knowledge, this is the first demonstration of functionalized GO as a novel, positive regulator in microbial engineering. Moreover, our work highlights the critical role of surface chemistry in modulating the interactions between nanomaterials and microorganisms.
Collapse
Affiliation(s)
- Yinchan Luo
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu 215123, China
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, WBSB 708, Baltimore, MD 21205, USA
| | - Xiaofang Tan
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu 215123, China
| | - Ligeng Xu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu 215123, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu 215123, China
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, WBSB 708, Baltimore, MD 21205, USA
| | - Rui Peng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu 215123, China
| |
Collapse
|
45
|
Wiktor J, Lesterlin C, Sherratt DJ, Dekker C. CRISPR-mediated control of the bacterial initiation of replication. Nucleic Acids Res 2016; 44:3801-10. [PMID: 27036863 PMCID: PMC4857001 DOI: 10.1093/nar/gkw214] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 12/20/2022] Open
Abstract
Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is accurately regulated by the DnaA protein, which promotes the unwinding of DNA at oriC We demonstrate that the binding of CRISPR/dCas9 to any position within origin or replication blocks the initiation of replication. Serial-dilution plating, single-cell fluorescence microscopy, and flow-cytometry experiments show that ongoing rounds of chromosome replication are finished upon CRISPR/dCas9 binding, but no new rounds are initiated. Upon arrest, cells stay metabolically active and accumulate cell mass. We find that elevating the temperature from 37 to 42°C releases the CRISR/dCas9 replication inhibition, and we use this feature to recover cells from the arrest. Our simple and robust method of controlling the bacterial cell cycle is a useful asset for synthetic biology and DNA-replication studies in particular. The inactivation of CRISPR/dCas9 binding at elevated temperatures may furthermore be of wide interest for CRISPR/Cas9 applications in genomic engineering.
Collapse
Affiliation(s)
- Jakub Wiktor
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628CJ Delft, The Netherlands
| | | | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628CJ Delft, The Netherlands
| |
Collapse
|
46
|
Inácio ÂS, Domingues NS, Nunes A, Martins PT, Moreno MJ, Estronca LM, Fernandes R, Moreno AJM, Borrego MJ, Gomes JP, Vaz WLC, Vieira OV. Quaternary ammonium surfactant structure determines selective toxicity towards bacteria: mechanisms of action and clinical implications in antibacterial prophylaxis. J Antimicrob Chemother 2015; 71:641-54. [PMID: 26679255 DOI: 10.1093/jac/dkv405] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/02/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Broad-spectrum antimicrobial activity of quaternary ammonium surfactants (QAS) makes them attractive and cheap topical prophylactic options for sexually transmitted infections and perinatal vertically transmitted urogenital infections. Although attributed to their high affinity for biological membranes, the mechanisms behind QAS microbicidal activity are not fully understood. We evaluated how QAS structure affects antimicrobial activity and whether this can be exploited for use in prophylaxis of bacterial infections. METHODS Acute toxicity of QAS to in vitro models of human epithelial cells and bacteria were compared to identify selective and potent bactericidal agents. Bacterial cell viability, membrane integrity, cell cycle and metabolism were evaluated to establish the mechanisms involved in selective toxicity of QAS. RESULTS QAS toxicity normalized relative to surfactant critical micelle concentration showed n-dodecylpyridinium bromide (C12PB) to be the most effective, with a therapeutic index of ∼10 for an MDR strain of Escherichia coli and >20 for Neisseria gonorrhoeae after 1 h of exposure. Three modes of QAS antibacterial action were identified: impairment of bacterial energetics and cell division at low concentrations; membrane permeabilization and electron transport inhibition at intermediate doses; and disruption of bacterial membranes and cell lysis at concentrations close to the critical micelle concentration. In contrast, toxicity to mammalian cells occurs at higher concentrations and, as we previously reported, results primarily from mitochondrial dysfunction and apoptotic cell death. CONCLUSIONS Our data show that short chain (C12) n-alkyl pyridinium bromides have a sufficiently large therapeutic window to be good microbicide candidates.
Collapse
Affiliation(s)
- Ângela S Inácio
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Neuza S Domingues
- CEDOC, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Alexandra Nunes
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Patrícia T Martins
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
| | - Maria J Moreno
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
| | - Luís M Estronca
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Rui Fernandes
- IBMC/HEMS - Instituto de Biologia Molecular e Celular/Histology and Electron Microscopy Service, Universidade do Porto, Porto, Portugal
| | | | - Maria J Borrego
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João P Gomes
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Winchil L C Vaz
- CEDOC, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Otília V Vieira
- CEDOC, NOVA Medical School
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| |
Collapse
|
47
|
Sumares JAP, Morão LG, Martins PMM, Martins DAB, Gomes E, Belasque J, Ferreira H. Temperature stress promotes cell division arrest in Xanthomonas citri subsp. citri. Microbiologyopen 2015; 5:244-53. [PMID: 26663580 PMCID: PMC4831469 DOI: 10.1002/mbo3.323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 11/10/2022] Open
Abstract
Citrus canker is an economically important disease that affects orange production in some of the most important producing areas around the world. It represents a great threat to the Brazilian and North American citriculture, particularly to the states of São Paulo and Florida, which together correspond to the biggest orange juice producers in the world. The etiological agent of this disease is the Gram‐negative bacterium Xanthomonas citri subsp. citri (Xcc), which grows optimally in laboratory cultures at ~30°C. To investigate how temperatures differing from 30°C influence the development of Xcc, we subjected the bacterium to thermal stresses, and afterward scored its recovery capability. In addition, we analyzed cell morphology and some markers of essential cellular processes that could indicate the extent of the heat‐induced damage. We found that the exposure of Xcc to 37°C for a period of 6 h led to a cell cycle arrest at the division stage. Thermal stress might have also interfered with the DNA replication and/or the chromosome segregation apparatuses, since cells displayed an increased number of sister origins side‐by‐side within rods. Additionally, Xcc treated at 37°C was still able to induce citrus canker symptoms, showing that thermal stress did not affect the ability of Xcc to colonize the host citrus. At 40–42°C, Xcc lost viability and became unable to induce disease symptoms in citrus. Our results provide evidence about essential cellular mechanisms perturbed by temperature, and can be potentially explored as a new method for Xanthomonas citri synchronization in cell cycle studies, as well as for the sanitation of plant material.
Collapse
Affiliation(s)
- Júlia A P Sumares
- Faculdade de Ciências Farmacêuticas, Depto. de Ciências Biológicas, Universidade Estadual Paulista, Rodovia Araraquara/Jaú Km 1, CP 502, Araraquara, SP, 14801-902, Brazil
| | - Luana Galvão Morão
- Depto. Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, Rio Claro, SP, 13506-900, Brazil
| | - Paula M M Martins
- Depto. Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, Rio Claro, SP, 13506-900, Brazil
| | - Daniela A B Martins
- Depto. de Bioquímica e Tecnologia Química, Instituto de Química, Universidade Estadual Paulista, R. Prof. Francisco Degni, 55, Araraquara, SP, 14800-060, Brazil
| | - Eleni Gomes
- Depto. de Biologia, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265 Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - José Belasque
- Depto. de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, SP, 13418-900, Brazil
| | - Henrique Ferreira
- Depto. Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, Rio Claro, SP, 13506-900, Brazil
| |
Collapse
|
48
|
The Consequences of Replicating in the Wrong Orientation: Bacterial Chromosome Duplication without an Active Replication Origin. mBio 2015; 6:e01294-15. [PMID: 26530381 PMCID: PMC4631800 DOI: 10.1128/mbio.01294-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Chromosome replication is regulated in all organisms at the assembly stage of the replication machinery at specific origins. In Escherichia coli, the DnaA initiator protein regulates the assembly of replication forks at oriC. This regulation can be undermined by defects in nucleic acid metabolism. In cells lacking RNase HI, replication initiates independently of DnaA and oriC, presumably at persisting R-loops. A similar mechanism was assumed for origin-independent synthesis in cells lacking RecG. However, recently we suggested that this synthesis initiates at intermediates resulting from replication fork fusions. Here we present data suggesting that in cells lacking RecG or RNase HI, origin-independent synthesis arises by different mechanisms, indicative of these two proteins having different roles in vivo. Our data support the idea that RNase HI processes R-loops, while RecG is required to process replication fork fusion intermediates. However, regardless of how origin-independent synthesis is initiated, a fraction of forks will proceed in an orientation opposite to normal. We show that the resulting head-on encounters with transcription threaten cell viability, especially if taking place in highly transcribed areas. Thus, despite their different functions, RecG and RNase HI are both important factors for maintaining replication control and orientation. Their absence causes severe replication problems, highlighting the advantages of the normal chromosome arrangement, which exploits a single origin to control the number of forks and their orientation relative to transcription, and a defined termination area to contain fork fusions. Any changes to this arrangement endanger cell cycle control, chromosome dynamics, and, ultimately, cell viability. IMPORTANCE Cell division requires unwinding of millions of DNA base pairs to generate the template for RNA transcripts as well as chromosome replication. As both processes use the same template, frequent clashes are unavoidable. To minimize the impact of these clashes, transcription and replication in bacteria follow the same directionality, thereby avoiding head-on collisions. This codirectionality is maintained by a strict regulation of where replication is started. We have used Escherichia coli as a model to investigate cells in which the defined location of replication initiation is compromised. In cells lacking either RNase HI or RecG, replication initiates away from the defined replication origin, and we discuss the different mechanisms by which this synthesis arises. In addition, the resulting forks proceed in a direction opposite to normal, thereby inducing head-on collisions between transcription and replication, and we show that the resulting consequences are severe enough to threaten the viability of cells.
Collapse
|
49
|
Martel M, Balleydier A, Sauriol A, Drolet M. Constitutive stable DNA replication in Escherichia coli cells lacking type 1A topoisomerase activity. DNA Repair (Amst) 2015; 35:37-47. [PMID: 26444226 DOI: 10.1016/j.dnarep.2015.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 01/12/2023]
Abstract
Type 1A topoisomerases (topos) are ubiquitous enzymes involved in supercoiling regulation and in the maintenance of genome stability. Escherichia coli possesses two type 1A enzymes, topo I (topA) and topo III (topB). Cells lacking both enzymes form very long filaments and have severe chromosome segregation and growth defects. We previously found that RNase HI overproduction or a dnaT::aph mutation could significantly correct these phenotypes. This leads us to hypothesize that they were related to unregulated replication originating from R-loops, i.e. constitutive stable DNA replication (cSDR). cSDR, first observed in rnhA (RNase HI) mutants, is characterized by its persistence for several hours following protein synthesis inhibition and by its requirement for primosome components, including DnaT. Here, to visualize and measure cSDR, the incorporation of the nucleotide analog ethynyl deoxyuridine (EdU) during replication in E. coli cells pre-treated with protein synthesis inhibitors, was revealed by "click" labeling with Alexa Fluor(®) 488 in fixed cells, and flow cytometry analysis. cSDR was detected in rnhA mutants, but not in wild-type strains, and the number of cells undergoing cSDR was significantly reduced by the introduction of the dnaT::aph mutation. cSDR was also found in topA, double topA topB but not in topB null cells. This result is consistent with the established function of topo I in the inhibition of R-loop formation. Moreover, our finding that topB rnhA mutants are perfectly viable demonstrates that topo III is not uniquely required during cSDR. Thus, either topo I or III can provide the type 1A topo activity that is specifically required during cSDR to allow chromosome segregation.
Collapse
Affiliation(s)
- Makisha Martel
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec H3C 3J7, Canada
| | - Aurélien Balleydier
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec H3C 3J7, Canada
| | - Alexandre Sauriol
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec H3C 3J7, Canada
| | - Marc Drolet
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec H3C 3J7, Canada.
| |
Collapse
|
50
|
Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli. Genetics 2015; 200:619-31. [PMID: 25911659 DOI: 10.1534/genetics.115.176677] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 04/23/2015] [Indexed: 11/18/2022] Open
Abstract
Twelve replicate populations of Escherichia coli have been evolving in the laboratory for >25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara-1. By tracking 42 known mutations in these samples, we reconstructed the history of this population's genotypic evolution over this period. The evolutionary dynamics of Ara-1 show strong evidence of selective sweeps as well as clonal interference between competing lineages bearing different beneficial mutations. In some cases, sets of several mutations approached fixation simultaneously, often conveying no information about their order of origination; we present several possible explanations for the existence of these mutational cohorts. Against a backdrop of rapid selective sweeps both earlier and later, two genetically diverged clades coexisted for >6000 generations before one went extinct. In that time, many additional mutations arose in the clade that eventually prevailed. We show that the clades evolved a frequency-dependent interaction, which prevented the immediate competitive exclusion of either clade, but which collapsed as beneficial mutations accumulated in the clade that prevailed. Clonal interference and frequency dependence can occur even in the simplest microbial populations. Furthermore, frequency dependence may generate dynamics that extend the period of coexistence that would otherwise be sustained by clonal interference alone.
Collapse
|