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Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria. Nat Commun 2021; 12:980. [PMID: 33579917 PMCID: PMC7881107 DOI: 10.1038/s41467-021-21210-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 01/08/2021] [Indexed: 01/26/2023] Open
Abstract
Insertion sequences (IS) are ubiquitous bacterial mobile genetic elements, and the mutations they cause can be deleterious, neutral, or beneficial. The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. IS elements account for ~35% of the mutations that reached high frequency through 50,000 generations in those populations that retained the ancestral point-mutation rate. In mutator populations, IS-mediated mutations are only half as frequent in absolute numbers. In one population, an exceptionally high ~8-fold increase in IS150 copy number is associated with the beneficial effects of early insertion mutations; however, this expansion later slowed down owing to reduced IS150 activity. This population also achieves the lowest fitness, suggesting that some avenues for further adaptation are precluded by the IS150-mediated mutations. More generally, across all populations, we find that higher IS activity becomes detrimental to adaptation over evolutionary time. Therefore, IS-mediated mutations can both promote and constrain evolvability. Insertion sequences (IS) are common mobile genetic elements in bacteria, but their effects on bacterial evolution are not well understood. Here, Consuegra and colleagues investigate the dynamics and fitness consequences of IS elements in E. coli over 50,000 generations.
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52
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Birnie A, Dekker C. Genome-in-a-Box: Building a Chromosome from the Bottom Up. ACS NANO 2021; 15:111-124. [PMID: 33347266 PMCID: PMC7844827 DOI: 10.1021/acsnano.0c07397] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA-protein interactions. Here, we introduce "genome-in-a-box" (GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.
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Affiliation(s)
- Anthony Birnie
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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53
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Correlated chromosomal periodicities according to the growth rate and gene expression. Sci Rep 2020; 10:15531. [PMID: 32968121 PMCID: PMC7511328 DOI: 10.1038/s41598-020-72389-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/02/2022] Open
Abstract
Linking genetic information to population fitness is crucial to understanding living organisms. Despite the abundant knowledge of the genetic contribution to growth, the overall patterns/features connecting genes, their expression, and growth remain unclear. To reveal the quantitative and direct connections, systematic growth assays of single-gene knockout Escherichia coli strains under both rich and poor nutritional conditions were performed; subsequently, the resultant growth rates were associated with the original expression levels of the knockout genes in the parental genome. Comparative analysis of growth and the transcriptome identified not only the nutritionally differentiated fitness cost genes but also a significant correlation between the growth rates of the single-gene knockout strains and the original expression levels of these knockout genes in the parental strain, regardless of the nutritional variation. In addition, the coordinated chromosomal periodicities of the wild-type transcriptome and the growth rates of the strains lacking the corresponding genes were observed. The common six-period periodicity was somehow attributed to the essential genes, although the underlying mechanism remains to be addressed. The correlated chromosomal periodicities associated with the gene expression-growth dataset were highly valuable for bacterial growth prediction and discovering the working principles governing minimal genetic information.
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Krogh TJ, Franke A, Møller-Jensen J, Kaleta C. Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation. Front Microbiol 2020; 11:2002. [PMID: 32983020 PMCID: PMC7491251 DOI: 10.3389/fmicb.2020.02002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Both intrinsic and extrinsic mechanisms regulating bacterial expression have been elucidated and described, however, such studies have mainly focused on local effects on the two-dimensional structure of the prokaryote genome while long-range as well as spatial interactions influencing gene expression are still only poorly understood. In this paper, we investigate the association between co-expression and distance between genes, using RNA-seq data at multiple growth phases in order to illuminate whether such conserved patterns are an indication of a gene regulatory mechanism relevant for prokaryotic cell proliferation, adaption, and evolution. We observe recurrent sinusoidal patterns in correlation of pairwise expression as function of genomic distance and rule out that these are caused by transcription-induced supercoiling gradients, gene clustering in operons, or association with regulatory transcription factors (TFs). By comparing spatial proximity for pairs of genomic bins with their correlation of pairwise expression, we further observe a high co-expression proportional with the spatial proximity. Based on these observations, we propose that the observed patterns are related to nucleoid structure as a product of transcriptional spilling, where genes actively influence transcription of spatially proximal genes through increases within shared local pools of RNA polymerases (RNAP), and actively spilling transcription onto neighboring genes.
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Affiliation(s)
- Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University Kiel, Kiel, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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55
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Bettridge K, Verma S, Weng X, Adhya S, Xiao J. Single-molecule tracking reveals that the nucleoid-associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA. Mol Microbiol 2020; 115:12-27. [PMID: 32640056 DOI: 10.1111/mmi.14572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 12/31/2022]
Abstract
HU (Histone-like protein from Escherichia coli strain U93) is the most conserved nucleoid-associated protein in eubacteria, but how it impacts global chromosome organization is poorly understood. Using single-molecule tracking, we demonstrate that HU exhibits nonspecific, weak, and transitory interactions with the chromosomal DNA. These interactions are largely mediated by three conserved, surface-exposed lysine residues (triK), which were previously shown to be responsible for nonspecific binding to DNA. The loss of these weak, transitory interactions in a HUα(triKA) mutant results in an over-condensed and mis-segregated nucleoid. Mutating a conserved proline residue (P63A) in the HUα subunit, deleting the HUβ subunit, or deleting nucleoid-associated naRNAs, each previously implicated in HU's high-affinity binding to kinked or cruciform DNA, leads to less dramatically altered interacting dynamics of HU compared to the HUα(triKA) mutant, but highly expanded nucleoids. Our results suggest HU plays a dual role in maintaining proper nucleoid volume through its differential interactions with chromosomal DNA. On the one hand, HU compacts the nucleoid through specific DNA structure-binding interactions. On the other hand, it decondenses the nucleoid through many nonspecific, weak, and transitory interactions with the bulk chromosome. Such dynamic interactions may contribute to the viscoelastic properties and fluidity of the bacterial nucleoid to facilitate proper chromosome functions.
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Affiliation(s)
- Kelsey Bettridge
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Subhash Verma
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiaoli Weng
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP. Nat Commun 2020; 11:3796. [PMID: 32732900 PMCID: PMC7394560 DOI: 10.1038/s41467-020-17606-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
The ter region of the bacterial chromosome, where replication terminates, is the last to be segregated before cell division in Escherichia coli. Delayed segregation is controlled by the MatP protein, which binds to specific sites (matS) within ter, and interacts with other proteins such as ZapB. Here, we investigate the role of MatP by combining short-time mobility analyses of the ter locus with biochemical approaches. We find that ter mobility is similar to that of a non ter locus, except when sister ter loci are paired after replication. This effect depends on MatP, the persistence of catenanes, and ZapB. We characterise MatP/DNA complexes and conclude that MatP binds DNA as a tetramer, but bridging matS sites in a DNA-rich environment remains infrequent. We propose that tetramerisation of MatP links matS sites with ZapB and/or with non-specific DNA to promote optimal pairing of sister ter regions until cell division. Protein, MatP, binds to and delays segregation of the ter region of the bacterial chromosome before cell division. Here, the authors show that MatP displays multiple activities to promote optimal pairing of sister ter regions until cell division.
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57
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Espinosa E, Paly E, Barre FX. High-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts. Mol Cell 2020; 79:857-869.e3. [PMID: 32681820 DOI: 10.1016/j.molcel.2020.06.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Sister-chromatid cohesion describes the orderly association of newly replicated DNA molecules behind replication forks. It plays an essential role in the maintenance and faithful transmission of genetic information. Cohesion is created by DNA topological links and proteinaceous bridges, whose formation and deposition could be potentially affected by many processes. Current knowledge on cohesion has been mainly gained by fluorescence microscopy observation. However, the resolution limit of microscopy and the restricted number of genomic positions that can be simultaneously visualized considerably hampered progress. Here, we present a high-throughput methodology to monitor sister-chromatid contacts (Hi-SC2). Using the multi-chromosomal Vibrio cholerae bacterium as a model, we show that Hi-SC2 permits to monitor local variations in sister-chromatid cohesion at a high resolution over a whole genome.
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Affiliation(s)
- Elena Espinosa
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Evelyne Paly
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - François-Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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58
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Walker DM, Harshey RM. Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli. Mob DNA 2020; 11:26. [PMID: 32670425 PMCID: PMC7350765 DOI: 10.1186/s13100-020-00217-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/18/2020] [Indexed: 01/12/2023] Open
Abstract
Background The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the E. coli genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (cis-immunity) as well as the entire ~ 37 kb genome of Mu (Mu genome immunity). Paradoxically, MuB is responsible for cis-immunity and is also implicated in Mu genome immunity, but via different mechanisms. This study was undertaken to dissect the role of MuB in target choice in vivo. Results We tracked Mu transposition from six different starting locations on the E. coli genome, in the presence and absence of MuB. The data reveal that Mu’s ability to sample the entire genome during a single hop in a clonal population is independent of MuB, and that MuB is responsible for cis-immunity, plays a minor role in Mu genome immunity, and facilitates insertions into transcriptionally active regions. Unexpectedly, transposition patterns in the absence of MuB have helped extend the boundaries of the insular Ter segment of the E. coli genome. Conclusions The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.
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Affiliation(s)
- David M Walker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712 USA
| | - Rasika M Harshey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712 USA
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59
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Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M. Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling. Nat Commun 2020; 11:2905. [PMID: 32518228 PMCID: PMC7283360 DOI: 10.1038/s41467-020-16724-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/19/2020] [Indexed: 01/26/2023] Open
Abstract
Bacterial nucleoid remodeling dependent on conserved histone-like protein, HU is one of the determining factors in global gene regulation. By imaging of near-native, unlabeled E. coli cells by soft X-ray tomography, we show that HU remodels nucleoids by promoting the formation of a dense condensed core surrounded by less condensed isolated domains. Nucleoid remodeling during cell growth and environmental adaptation correlate with pH and ionic strength controlled molecular switch that regulated HUαα dependent intermolecular DNA bundling. Through crystallographic and solution-based studies we show that these effects mechanistically rely on HUαα promiscuity in forming multiple electrostatically driven multimerization interfaces. Changes in DNA bundling consequently affects gene expression globally, likely by constrained DNA supercoiling. Taken together our findings unveil a critical function of HU–DNA interaction in nucleoid remodeling that may serve as a general microbial mechanism for transcriptional regulation to synchronize genetic responses during the cell cycle and adapt to changing environments. HU is among the most conserved and abundant nucleoid-associated proteins in eubacteria. Here the authors investigate the role of histone-like proteins (HU) in the 3D organization of the bacteria DNA and show via soft X-ray tomography the process of nucleoid remodeling.
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Affiliation(s)
- Soumya G Remesh
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Subhash C Verma
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Axel A Ekman
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Carolyn A Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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60
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Nagai M, Kurokawa M, Ying BW. The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli. DNA Res 2020; 27:5899727. [PMID: 32866232 PMCID: PMC7508348 DOI: 10.1093/dnares/dsaa018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/24/2020] [Indexed: 11/12/2022] Open
Abstract
The growth rate, representing the fitness of a bacterial population, is determined by the transcriptome. Chromosomal periodicity, which is known as the periodic spatial pattern of a preferred chromosomal distance in microbial genomes, is a representative overall feature of the transcriptome; however, whether and how it is associated with the bacterial growth rate are unknown. To address these questions, we analysed a total of 213 transcriptomes of multiple Escherichia coli strains growing in an assortment of culture conditions varying in terms of temperature, nutrition level and osmotic pressure. Intriguingly, Fourier transform analyses of the transcriptome identified a common chromosomal periodicity of transcriptomes, which was independent of the variation in genomes and environments. In addition, fitting of the data to a theoretical model, we found that the amplitudes of the periodic transcriptomes were significantly correlated with the growth rates. These results indicated that the amplitude of periodic transcriptomes is a parameter representing the global pattern of gene expression in correlation with the bacterial growth rate. Thus, our study provides a novel parameter for evaluating the adaptiveness of a growing bacterial population and quantitatively predicting the growth dynamics according to the global expression pattern.
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Affiliation(s)
- Motoki Nagai
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Masaomi Kurokawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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61
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Abstract
Over the past decade, advances in methodologies for the determination of chromosome conformation have provided remarkable insight into the local and higher-order organization of bacterial and eukaryotic chromosomes. Locally folded domains are found in both bacterial and eukaryotic genomes, although they vary in size. Importantly, genomes of metazoans also possess higher-order organization into A- and B-type compartments, regions of transcriptionally active and inactive chromatin, respectively. Until recently, nothing was known about the organization of genomes of organisms in the third domain of life - the archaea. However, despite archaea possessing simple circular genomes that are morphologically reminiscent of those seen in many bacteria, a recent study of archaea of the genus Sulfolobus has revealed that it organizes its genome into large-scale domains. These domains further interact to form defined A- and B-type compartments. The interplay of transcription and localization of a novel structural maintenance of chromosomes (SMC) superfamily protein, termed coalescin, defines compartment identity. In this Review, we discuss the mechanistic and evolutionary implications of these findings.
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Affiliation(s)
- Naomichi Takemata
- Biology Department, Indiana University, Bloomington, USA.,Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, USA
| | - Stephen D Bell
- Biology Department, Indiana University, Bloomington, USA .,Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, USA
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62
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Joyeux M. Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling. Biophys J 2020; 118:2141-2150. [PMID: 31629479 PMCID: PMC7202931 DOI: 10.1016/j.bpj.2019.09.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 01/17/2023] Open
Abstract
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this work, we investigate the interplay of these two mechanisms with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime in which the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixing.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
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63
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Syeda AH, Dimude JU, Skovgaard O, Rudolph CJ. Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics. Front Microbiol 2020; 11:534. [PMID: 32351461 PMCID: PMC7174701 DOI: 10.3389/fmicb.2020.00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022] Open
Abstract
Each cell division requires the complete and accurate duplication of the entire genome. In bacteria, the duplication process of the often-circular chromosomes is initiated at a single origin per chromosome, resulting in two replication forks that traverse the chromosome in opposite directions. DNA synthesis is completed once the two forks fuse in a region diametrically opposite the origin. In some bacteria, such as Escherichia coli, the region where forks fuse forms a specialized termination area. Polar replication fork pause sites flanking this area can pause the progression of replication forks, thereby allowing forks to enter but not to leave. Transcription of all required genes has to take place simultaneously with genome duplication. As both of these genome trafficking processes share the same template, conflicts are unavoidable. In this review, we focus on recent attempts to add additional origins into various ectopic chromosomal locations of the E. coli chromosome. As ectopic origins disturb the native replichore arrangements, the problems resulting from such perturbations can give important insights into how genome trafficking processes are coordinated and the problems that arise if this coordination is disturbed. The data from these studies highlight that head-on replication–transcription conflicts are indeed highly problematic and multiple repair pathways are required to restart replication forks arrested at obstacles. In addition, the existing data also demonstrate that the replication fork trap in E. coli imposes significant constraints to genome duplication if ectopic origins are active. We describe the current models of how replication fork fusion events can cause serious problems for genome duplication, as well as models of how such problems might be alleviated both by a number of repair pathways as well as the replication fork trap system. Considering the problems associated both with head-on replication-transcription conflicts as well as head-on replication fork fusion events might provide clues of how these genome trafficking issues have contributed to shape the distinct architecture of bacterial chromosomes.
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Affiliation(s)
- Aisha H Syeda
- Department of Biology, University of York, York, United Kingdom
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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64
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Hołówka J, Zakrzewska-Czerwińska J. Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress. Front Microbiol 2020; 11:590. [PMID: 32373086 PMCID: PMC7177045 DOI: 10.3389/fmicb.2020.00590] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
The bacterial chromosome must be efficiently compacted to fit inside the small and crowded cell while remaining accessible for the protein complexes involved in replication, transcription, and DNA repair. The dynamic organization of the nucleoid is a consequence of both intracellular factors (i.e., simultaneously occurring cell processes) and extracellular factors (e.g., environmental conditions, stress agents). Recent studies have revealed that the bacterial chromosome undergoes profound topological changes under stress. Among the many DNA-binding proteins that shape the bacterial chromosome structure in response to various signals, NAPs (nucleoid associated proteins) are the most abundant. These small, basic proteins bind DNA with low specificity and can influence chromosome organization under changing environmental conditions (i.e., by coating the chromosome in response to stress) or regulate the transcription of specific genes (e.g., those involved in virulence).
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Affiliation(s)
- Joanna Hołówka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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65
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Yubero P, Poyatos JF. The Impact of Global Transcriptional Regulation on Bacterial Gene Order. iScience 2020; 23:101029. [PMID: 32283521 PMCID: PMC7155222 DOI: 10.1016/j.isci.2020.101029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/15/2019] [Accepted: 03/27/2020] [Indexed: 12/04/2022] Open
Abstract
Bacterial gene expression depends on the allocation of limited transcriptional resources provided a particular growth rate and growth condition. Early studies in a few genes suggested this global regulation to generate a unifying hyperbolic expression pattern. Here, we developed a large-scale method that generalizes these experiments to quantify the response to growth of over 700 genes that a priori do not exhibit any specific control. We distinguish a core subset following a promoter-specific hyperbolic response. Within this group, we sort genes with regard to their responsiveness to the global regulatory program to show that those with a particularly sensitive linear response are located near the origin of replication. We then find evidence that this genomic architecture is biologically significant by examining position conservation of E. coli genes in 100 bacteria. The response to the transcriptional resources of the cell results in an additional feature contributing to bacterial genome organization. Cell physiology determines a global transcriptional regulatory program Constitutive genes show a differential response to this global regulation The most responsive constitutive genes are located near the origin of replication Global transcriptional regulation acts as a gene position conservation force
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Affiliation(s)
- Pablo Yubero
- Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain.
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66
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Veetil RT, Malhotra N, Dubey A, Seshasayee ASN. Laboratory Evolution Experiments Help Identify a Predominant Region of Constitutive Stable DNA Replication Initiation. mSphere 2020; 5:e00939-19. [PMID: 32102945 PMCID: PMC7045392 DOI: 10.1128/msphere.00939-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/06/2020] [Indexed: 01/06/2023] Open
Abstract
The bacterium Escherichia coli can initiate replication in the absence of the replication initiator protein DnaA and/or the canonical origin of replication oriC in a ΔrnhA background. This phenomenon, which can be primed by R-loops, is called constitutive stable DNA replication (cSDR). Whether DNA replication during cSDR initiates in a stochastic manner through the length of the chromosome or at specific sites and how E. coli can find adaptations to loss of fitness caused by cSDR remain inadequately answered. We use laboratory evolution experiments of ΔrnhA-ΔdnaA strains followed by deep sequencing to show that DNA replication preferentially initiates within a broad region located ∼0.4 to 0.7 Mb clockwise of oriC. This region includes many bisulfite-sensitive sites, which have been previously defined as R-loop-forming regions, and includes a site containing sequence motifs that favor R-loop formation. Initiation from this region would result in head-on replication-transcription conflicts at rRNA loci. Inversions of these rRNA loci, which can partly resolve these conflicts, help the bacterium suppress the fitness defects of cSDR. These inversions partially restore the gene expression changes brought about by cSDR. The inversion, however, increases the possibility of conflicts at essential mRNA genes, which would utilize only a minuscule fraction of RNA polymerase molecules, most of which transcribe rRNA genes. Whether subsequent adaptive strategies would attempt to resolve these conflicts remains an open question.IMPORTANCE The bacterium E. coli can replicate its DNA even in the absence of the molecules that are required for canonical replication initiation. This often requires the formation of RNA-DNA hybrid structures and is referred to as constitutive stable DNA replication (cSDR). Where on the chromosome does cSDR initiate? We answer this question using laboratory evolution experiments and genomics and show that selection favors cSDR initiation predominantly at a region ∼0.6 Mb clockwise of oriC. Initiation from this site will result in more head-on collisions of DNA polymerase with RNA polymerase operating on rRNA loci. The bacterium adapts to this problem by inverting a region of the genome including several rRNA loci such that head-on collisions between the two polymerases are minimized. Understanding such evolutionary strategies in the context of cSDR can provide insights into the potential causes of resistance to antibiotics that target initiation of DNA replication.
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Affiliation(s)
- Reshma T Veetil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bengaluru, Karnataka, India
- School of Life Science, The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bengaluru, Karnataka, India
| | - Nitish Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bengaluru, Karnataka, India
| | - Akshara Dubey
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bengaluru, Karnataka, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bengaluru, Karnataka, India
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67
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Walker DM, Freddolino PL, Harshey RM. A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition. Cell 2020; 180:703-716.e18. [PMID: 32059782 DOI: 10.1016/j.cell.2020.01.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 10/21/2019] [Accepted: 01/22/2020] [Indexed: 02/06/2023]
Abstract
The three-dimensional structures of chromosomes are increasingly being recognized as playing a major role in cellular regulatory states. The efficiency and promiscuity of phage Mu transposition was exploited to directly measure in vivo interactions between genomic loci in E. coli. Two global organizing principles have emerged: first, the chromosome is well-mixed and uncompartmentalized, with transpositions occurring freely between all measured loci; second, several gene families/regions show "clustering": strong three-dimensional co-localization regardless of linear genomic distance. The activities of the SMC/condensin protein MukB and nucleoid-compacting protein subunit HU-α are essential for the well-mixed state; HU-α is also needed for clustering of 6/7 ribosomal RNA-encoding loci. The data are explained by a model in which the chromosomal structure is driven by dynamic competition between DNA replication and chromosomal relaxation, providing a foundation for determining how region-specific properties contribute to both chromosomal structure and gene regulation.
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Affiliation(s)
- David M Walker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Peter L Freddolino
- Department of Biological Chemistry and Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Rasika M Harshey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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68
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Travers A, Muskhelishvili G. Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0016-2019. [PMID: 32056535 PMCID: PMC11168577 DOI: 10.1128/ecosalplus.esp-0016-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/22/2022]
Abstract
In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.
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Affiliation(s)
- Andrew Travers
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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69
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Planchenault C, Pons MC, Schiavon C, Siguier P, Rech J, Guynet C, Dauverd-Girault J, Cury J, Rocha EPC, Junier I, Cornet F, Espéli O. Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells. J Mol Biol 2020; 432:745-761. [PMID: 31931015 DOI: 10.1016/j.jmb.2019.11.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/04/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023]
Abstract
Bacterial genomes, organized intracellularly as nucleoids, are composed of the main chromosome coexisting with different types of secondary replicons. Secondary replicons are major drivers of bacterial adaptation by gene exchange. They are highly diverse in type and size, ranging from less than 2 to more than 1000 kb, and must integrate with bacterial physiology, including to the nucleoid dynamics, to limit detrimental costs leading to their counter-selection. We show that large DNA circles, whether from a natural plasmid or excised from the chromosome tend to localize in a dynamic manner in a zone separating the nucleoid from the cytoplasm at the edge of the nucleoid. This localization is in good agreement with silico simulations of DNA circles in the nucleoid volume. Subcellular positioning systems counteract this tendency, allowing replicons to enter the nucleoid space. In enterobacteria, these systems are found in replicons above 25 kb, defining the limit with small randomly segregated plasmids. Larger replicons carry at least one of the three described family of systems, ParAB, ParRM, and StbA. Replicons above 180 kb all carry a ParAB system, suggesting this system is specifically required in the cases of large replicons. Simulations demonstrated that replicon size profoundly affects localization, compaction, and dynamics of DNA circles in the nucleoid volume. The present work suggests that presence of partition systems on the larger plasmids or chromids is not only due to selection for accurate segregation but also to counteract their unmixing with the chromosome and consequent exclusion from the nucleoid.
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Affiliation(s)
- Charlène Planchenault
- Center for Interdisciplinary Research in Biology - Collège de France, CNRS UMR7241, INSERM U1050, PSL University, France
| | - Marine C Pons
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Caroline Schiavon
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Patricia Siguier
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Jérôme Rech
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Catherine Guynet
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Julie Dauverd-Girault
- Center for Interdisciplinary Research in Biology - Collège de France, CNRS UMR7241, INSERM U1050, PSL University, France
| | - Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Ivan Junier
- CNRS, Univ. Grenoble Alpes, TIMC-IMAG, F-38000 Grenoble, France
| | - François Cornet
- Centre de Biologie Intégrative de Toulouse (CBI Toulouse), Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Université de Toulouse, UPS, CNRS, France
| | - Olivier Espéli
- Center for Interdisciplinary Research in Biology - Collège de France, CNRS UMR7241, INSERM U1050, PSL University, France.
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70
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Kawalek A, Wawrzyniak P, Bartosik AA, Jagura-Burdzy G. Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes. Microorganisms 2020; 8:E105. [PMID: 31940850 PMCID: PMC7022226 DOI: 10.3390/microorganisms8010105] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
The segregation of newly replicated chromosomes in bacterial cells is a highly coordinated spatiotemporal process. In the majority of bacterial species, a tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target(s) parS sequence(s), facilitates the initial steps of chromosome partitioning. ParB nucleates around parS(s) located in the vicinity of newly replicated oriCs to form large nucleoprotein complexes, which are subsequently relocated by ParA to distal cellular compartments. In this review, we describe the role of ParB in various processes within bacterial cells, pointing out interspecies differences. We outline recent progress in understanding the ParB nucleoprotein complex formation and its role in DNA segregation, including ori positioning and anchoring, DNA condensation, and loading of the structural maintenance of chromosome (SMC) proteins. The auxiliary roles of ParBs in the control of chromosome replication initiation and cell division, as well as the regulation of gene expression, are discussed. Moreover, we catalog ParB interacting proteins. Overall, this work highlights how different bacterial species adapt the DNA partitioning ParAB-parS system to meet their specific requirements.
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Affiliation(s)
| | | | | | - Grazyna Jagura-Burdzy
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (A.K.); (P.W.); (A.A.B.)
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71
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Kivisaar M. Mutation and Recombination Rates Vary Across Bacterial Chromosome. Microorganisms 2019; 8:microorganisms8010025. [PMID: 31877811 PMCID: PMC7023495 DOI: 10.3390/microorganisms8010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure which is established by binding of the nucleoid-associated proteins (NAPs) and other proteins. This review gives an overview of recent findings indicating that the mutagenic and recombination processes in bacteria vary at different chromosomal positions. Involvement of NAPs and other possible mechanisms in these regional differences are discussed. Variations in mutation and recombination rates across the bacterial chromosome may have implications in the evolution of bacteria.
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Affiliation(s)
- Maia Kivisaar
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
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72
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Abstract
How genomes are organized within cells and how the 3D architecture of a genome influences cellular functions are significant questions in biology. A bacterial genomic DNA resides inside cells in a highly condensed and functionally organized form called nucleoid (nucleus-like structure without a nuclear membrane). The Escherichia coli chromosome or nucleoid is composed of the genomic DNA, RNA, and protein. The nucleoid forms by condensation and functional arrangement of a single chromosomal DNA with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. Although a high-resolution structure of a bacterial nucleoid is yet to come, five decades of research has established the following salient features of the E. coli nucleoid elaborated below: 1) The chromosomal DNA is on the average a negatively supercoiled molecule that is folded as plectonemic loops, which are confined into many independent topological domains due to supercoiling diffusion barriers; 2) The loops spatially organize into megabase size regions called macrodomains, which are defined by more frequent physical interactions among DNA sites within the same macrodomain than between different macrodomains; 3) The condensed and spatially organized DNA takes the form of a helical ellipsoid radially confined in the cell; and 4) The DNA in the chromosome appears to have a condition-dependent 3-D structure that is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent, influencing each other reciprocally. Current advents of high-resolution microscopy, single-molecule analysis and molecular structure determination of the components are expected to reveal the total structure and function of the bacterial nucleoid.
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Affiliation(s)
- Subhash C. Verma
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (SCV); (SLA)
| | - Zhong Qian
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sankar L. Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (SCV); (SLA)
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73
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A gatekeeping function of the replicative polymerase controls pathway choice in the resolution of lesion-stalled replisomes. Proc Natl Acad Sci U S A 2019; 116:25591-25601. [PMID: 31796591 DOI: 10.1073/pnas.1914485116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA lesions stall the replisome and proper resolution of these obstructions is critical for genome stability. Replisomes can directly replicate past a lesion by error-prone translesion synthesis. Alternatively, replisomes can reprime DNA synthesis downstream of the lesion, creating a single-stranded DNA gap that is repaired primarily in an error-free, homology-directed manner. Here we demonstrate how structural changes within the Escherichia coli replisome determine the resolution pathway of lesion-stalled replisomes. This pathway selection is controlled by a dynamic interaction between the proofreading subunit of the replicative polymerase and the processivity clamp, which sets a kinetic barrier to restrict access of translesion synthesis (TLS) polymerases to the primer/template junction. Failure of TLS polymerases to overcome this barrier leads to repriming, which competes kinetically with TLS. Our results demonstrate that independent of its exonuclease activity, the proofreading subunit of the replisome acts as a gatekeeper and influences replication fidelity during the resolution of lesion-stalled replisomes.
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74
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Qin L, Erkelens AM, Ben Bdira F, Dame RT. The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins. Open Biol 2019; 9:190223. [PMID: 31795918 PMCID: PMC6936261 DOI: 10.1098/rsob.190223] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/08/2019] [Indexed: 12/15/2022] Open
Abstract
Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns- phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.
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Affiliation(s)
- L. Qin
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - A. M. Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - F. Ben Bdira
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - R. T. Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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75
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Rhodoccoccus erythropolis Is Different from Other Members of Actinobacteria: Monoploidy, Overlapping Replication Cycle, and Unique Segregation Pattern. J Bacteriol 2019; 201:JB.00320-19. [PMID: 31570531 DOI: 10.1128/jb.00320-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/24/2019] [Indexed: 11/20/2022] Open
Abstract
Among actinomycetes, chromosome organization and segregation studies have been limited to Streptomyces coelicolor, Corynebacterium glutamicum, and Mycobacterium spp. There are differences with respect to ploidy and chromosome organization pattern in these bacteria. Here, we report on chromosome replication, organization, and segregation in Rhodococcus erythropolis PR4, which has a circular genome of 6.5 Mbp. The origin of replication of R. erythropolis PR4 was identified, and the DNA content in the cell under different growth conditions was determined. Our results suggest that the number of origins increases as the growth medium becomes rich, suggesting an overlapping replication cell cycle in this bacterium. Subcellular localization of the origin region revealed polar positioning in minimal and rich media. The terminus, which is the last region to be replicated and segregated, was found to be localized at the cell center in large cells. The middle markers corresponding to the 1.5-Mb and 4.7-Mb loci did not overlap, suggesting discontinuity in the segregation of the two arms of the chromosome. Chromosome segregation was not affected by inhibiting cell division. Deletion of parA or parB affected chromosome segregation. Unlike in C. glutamicum and Streptomyces spp., diploidy or polyploidy was not observed in R. erythropolis PR4. Our results suggest that R. erythropolis is different from other members of Actinobacteria; it is monoploid and has a unique chromosome segregation pattern. This is the first report on chromosome organization, replication, and segregation in R. erythropolis PR4.IMPORTANCE Rhodococci are highly versatile Gram-positive bacteria with high bioremediation potential. Some rhodococci are pathogenic and have been suggested as emerging threats. No studies on the replication, segregation, and cell cycle of these bacteria have been reported. Here, we demonstrate that the genus Rhodococcus is different from other actinomycetes, such as members of the genera Corynebacterium, Mycobacterium, and Streptomyces, with respect to ploidy and chromosome organization and segregation. Such studies will be useful not only in designing better therapeutics pathogenic strains in the future but also for studying genome maintenance in strains used for bioremediation.
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76
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Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens. mSystems 2019; 4:4/6/e00702-19. [PMID: 31744907 PMCID: PMC6867878 DOI: 10.1128/msystems.00702-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Whooping cough (pertussis), primarily caused by Bordetella pertussis, has resurged in the United States, and circulating strains exhibit considerable chromosome structural fluidity in the form of rearrangement and deletion. The genus Bordetella includes additional pathogenic species infecting various animals, some even causing pertussis-like respiratory disease in humans; however, investigation of their genome evolution has been limited. We studied chromosome structure in complete genome sequences from 167 Bordetella species isolates, as well as 469 B. pertussis isolates, to gain a generalized understanding of rearrangement patterns among these related pathogens. Observed changes in gene order primarily resulted from large inversions and were only detected in species with genomes harboring multicopy insertion sequence (IS) elements, most notably B. holmesii and B. parapertussis While genomes of B. pertussis contain >240 copies of IS481, IS elements appear less numerous in other species and yield less chromosome structural diversity through rearrangement. These data were further used to predict all possible rearrangements between IS element copies present in Bordetella genomes, revealing that only a subset is observed among circulating strains. Therefore, while it appears that rearrangement occurs less frequently in other species than in B. pertussis, these clinically relevant respiratory pathogens likely experience similar mutation of gene order. The resulting chromosome structural fluidity presents both challenges and opportunity for the study of Bordetella respiratory pathogens.IMPORTANCE Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable structural rearrangement, but insufficient data have prevented comparable investigation in related species. In this study, we analyze chromosome structure variation in several Bordetella species to gain a generalized understanding of rearrangement patterns in this genus. Just as in B. pertussis, we observed inversions in other species that likely result from common mutational processes. We used these data to further predict additional, unobserved inversions, suggesting that specific genome structures may be preferred in each species.
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77
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Kisner JR, Kuwada NJ. Nucleoid-mediated positioning and transport in bacteria. Curr Genet 2019; 66:279-291. [PMID: 31691024 DOI: 10.1007/s00294-019-01041-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/28/2022]
Abstract
Precise management of the spatiotemporal position of subcellular components is critical to a number of essential processes in the bacterial cell. The bacterial nucleoid is a highly structured yet dynamic object that undergoes significant reorganization during the relatively short cell cycle, e.g. during gene expression, chromosome replication, and segregation. Although the nucleoid takes up a large fraction of the volume of the cell, the mobility of macromolecules within these dense regions is relatively high and recent results suggest that the nucleoid plays an integral role of dynamic localization in a host of seemingly disparate cellular processes. Here, we review a number of recent reports of nucleoid-mediated positioning and transport in the model bacteria Escherichia coli. These results viewed as a whole suggest that the dynamic, cellular-scale structure of the nucleoid may be a key driver of positioning and transport within the cell. This model of a global, default positioning and transport system may help resolve many unanswered questions about the mechanisms of partitioning and segregation in bacteria.
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Affiliation(s)
- Jessica R Kisner
- Department of Physics, Central Washington University, Ellensburg, WA, 98926, USA
| | - Nathan J Kuwada
- Department of Physics, Central Washington University, Ellensburg, WA, 98926, USA.
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78
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Shen BA, Landick R. Transcription of Bacterial Chromatin. J Mol Biol 2019; 431:4040-4066. [PMID: 31153903 PMCID: PMC7248592 DOI: 10.1016/j.jmb.2019.05.041] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Decades of research have probed the interplay between chromatin (genomic DNA associated with proteins and RNAs) and transcription by RNA polymerase (RNAP) in all domains of life. In bacteria, chromatin is compacted into a membrane-free region known as the nucleoid that changes shape and composition depending on the bacterial state. Transcription plays a key role in both shaping the nucleoid and organizing it into domains. At the same time, chromatin impacts transcription by at least five distinct mechanisms: (i) occlusion of RNAP binding; (ii) roadblocking RNAP progression; (iii) constraining DNA topology; (iv) RNA-mediated interactions; and (v) macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and, in combination, mediate gene regulation. Here, we review the current understanding of these mechanisms with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. The myriad questions about transcription of bacterial chromatin are increasingly answerable due to methodological advances, enabling a needed paradigm shift in the field of bacterial transcription to focus on regulation of genes in their native state. We can anticipate answers that will define how bacterial chromatin helps coordinate and dynamically regulate gene expression in changing environments.
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Affiliation(s)
- Beth A Shen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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79
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Stoof R, Wood A, Goñi-Moreno Á. A Model for the Spatiotemporal Design of Gene Regulatory Circuits †. ACS Synth Biol 2019; 8:2007-2016. [PMID: 31429541 DOI: 10.1021/acssynbio.9b00022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mathematical modeling assists the design of synthetic regulatory networks by providing a detailed mechanistic understanding of biological systems. Models that can predict the performance of a design are fundamental for synthetic biology since they minimize iterations along the design-build-test lifecycle. Such predictability depends crucially on what assumptions (i.e., biological simplifications) the model considers. Here, we challenge a common assumption when it comes to the modeling of bacterial-based gene regulation: considering negligible the effects of intracellular physical space. It is commonly assumed that molecules, such as transcription factors (TF), are homogeneously distributed inside a cell, so there is no need to model their diffusion. We describe a mathematical model that accounts for molecular diffusion and show how simulations of network performance are decisively affected by the distance between its components. Specifically, the model focuses on the search by a TF for its target promoter. The combination of local searches, via one-dimensional sliding along the chromosome, and global searches, via three-dimensional diffusion through the cytoplasm, determine TF-promoter interplay. Previous experimental results with engineered bacteria in which the distance between TF source and target was minimized or enlarged were successfully reproduced by the spatially resolved model we introduce here. This suggests that the spatial specification of the circuit alone can be exploited as a design parameter in synthetic biology to select programmable output levels.
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Affiliation(s)
- Ruud Stoof
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
| | - Alexander Wood
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
| | - Ángel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
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80
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Lorenzi JN, Lespinet O, Leblond P, Thibessard A. Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome. Microb Genom 2019; 7:000525. [PMID: 33749576 PMCID: PMC8627663 DOI: 10.1099/mgen.0.000525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/11/2021] [Indexed: 01/14/2023] Open
Abstract
Streptomyces possess a large linear chromosome (6-12 Mb) consisting of a conserved central region flanked by variable arms covering several megabases. In order to study the evolution of the chromosome across evolutionary times, a representative panel of Streptomyces strains and species (125) whose chromosomes are completely sequenced and assembled was selected. The pan-genome of the genus was modelled and shown to be open with a core-genome reaching 1018 genes. The evolution of Streptomyces chromosome was analysed by carrying out pairwise comparisons, and by monitoring indexes measuring the conservation of genes (presence/absence) and their synteny along the chromosome. Using the phylogenetic depth offered by the chosen panel, it was possible to infer that within the central region of the chromosome, the core-genes form a highly conserved organization, which can reveal the existence of an ancestral chromosomal skeleton. Conversely, the chromosomal arms, enriched in variable genes evolved faster than the central region under the combined effect of rearrangements and addition of new information from horizontal gene transfer. The genes hosted in these regions may be localized there because of the adaptive advantage that their rapid evolution may confer. We speculate that (i) within a bacterial population, the variability of these genes may contribute to the establishment of social characters by the production of 'public goods' (ii) at the evolutionary scale, this variability contributes to the diversification of the genetic pool of the bacteria.
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Affiliation(s)
- Jean-Noël Lorenzi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Olivier Lespinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
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81
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Mehta SB, Kumar A, Radhakrishna M. Role of confinement, molecular connectivity and flexibility in entropic driven surface segregation of polymer-colloid mixtures. SOFT MATTER 2019; 15:6495-6503. [PMID: 31342047 DOI: 10.1039/c9sm00883g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Relative surface affinity between polymers and colloids is leveraged in many applications like filtration, adhesion, bio-sensing, etc. The surface affinity is governed by both enthalpic (relative interactions between the species and surface) and entropic (excluded volume) effects. Neglecting enthalpic effects, i.e. for purely athermal systems, entropy is the only driving force that controls the surface affinity of the species in a binary or multi-component mixture. Many intensive (relative size of colloids, chain length, equilibrium bond angle, chain flexibility) and extensive (confinement, temperature) factors can dramatically change the entropy of the system and thus enhance or decrease the surface affinities of the constituent species. In this article, we use coarse grained metropolis Monte Carlo simulations to delineate the role of these factors in entropic surface segregation in a binary mixture of polymers and colloids. At low number densities, excluded volume effects are negligible and we do not observe any entropic driven surface segregation. Therefore our system of interest is binary polymer-colloid mixtures at moderate to high number densities where excluded volume effects are predominant. Our results indicate that for flexible polymer chains, the surface is always enriched with colloids compared to polymers and this effect is enhanced for longer polymer chains. The configurational entropy of the flexible polymers is significantly reduced near the surface and therefore they prefer to stay in the bulk (away from the surface). However this behavior can be completely reversed by introducing a large degree of confinement and making the chains relatively rigid (less flexible). Our results show that polymer segregation of long stiff chains in slit pore geometry is driven by nematization near the surface while looping of polymers is observed under a large degree of confinement. We observe that for longer polymer chains with an equilibrium bond angle (θ = π), both confinement and chain stiffness enhance the surface segregation of polymers relative to colloids. However, the segregation behavior within a confinement is dependent on the polymer chain length. The surface segregation of polymers is dramatically decreased for chains with equilibrium bond angles independent of chain length and flexibility due to excluded volume effects and inefficient packing near the surface.
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Affiliation(s)
- Spand Bharat Mehta
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat- 382355, India.
| | - Avishek Kumar
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat- 382355, India.
| | - Mithun Radhakrishna
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat- 382355, India.
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82
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Niccum BA, Lee H, MohammedIsmail W, Tang H, Foster PL. The Symmetrical Wave Pattern of Base-Pair Substitution Rates across the Escherichia coli Chromosome Has Multiple Causes. mBio 2019; 10:e01226-19. [PMID: 31266871 PMCID: PMC6606806 DOI: 10.1128/mbio.01226-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/28/2019] [Indexed: 01/28/2023] Open
Abstract
Mutation accumulation experiments followed by whole-genome sequencing have revealed that, for several bacterial species, the rate of base-pair substitutions (BPSs) is not constant across the chromosome but varies in a wave-like pattern that is symmetrical about the origin of replication. The experiments reported here demonstrated that, in Escherichia coli, several interacting factors determine the wave. The origin is a major driver of BPS rates. When it is relocated, the BPS rates in a 1,000-kb region surrounding the new origin reproduce the pattern that surrounds the normal origin. However, the pattern across distant regions of the chromosome is unaltered and thus must be determined by other factors. Increasing the deoxynucleoside triphosphate (dNTP) concentration shifts the wave pattern away from the origin, supporting the hypothesis that fluctuations in dNTP pools coincident with replication firing contribute to the variations in the mutation rate. The nucleoid binding proteins (HU and Fis) and the terminus organizing protein (MatP) are also major factors. These proteins alter the three-dimensional structure of the DNA, and results suggest that mutation rates increase when highly structured DNA is replicated. Biases in error correction by proofreading and mismatch repair, both of which may be responsive to dNTP concentrations and DNA structure, also are major determinants of the wave pattern. These factors should apply to most bacterial and, possibly, eukaryotic genomes and suggest that different areas of the genome evolve at different rates.IMPORTANCE It has been found in several species of bacteria that the rate at which single base pairs are mutated is not constant across the genome but varies in a wave-like pattern that is symmetrical about the origin of replication. Using Escherichia coli as our model system, we show that this pattern is the result of several interconnected factors. First, the timing and progression of replication are important in determining the wave pattern. Second, the three-dimensional structure of the DNA is also a factor, and the results suggest that mutation rates increase when highly structured DNA is replicated. Finally, biases in error correction, which may be responsive both to the progression of DNA synthesis and to DNA structure, are major determinants of the wave pattern. These factors should apply to most bacterial and, possibly, eukaryotic genomes and suggest that different areas of the genome evolve at different rates.
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Affiliation(s)
- Brittany A Niccum
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Heewook Lee
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - Wazim MohammedIsmail
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - Haixu Tang
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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83
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Position effects on promoter activity in Escherichia coli and their consequences for antibiotic-resistance determinants. Biochem Soc Trans 2019; 47:839-845. [PMID: 31189732 DOI: 10.1042/bst20180503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023]
Abstract
The activity of any bacterial promoter is generally supposed to be set by its base sequence and the different transcription factors that bind in the local vicinity. Here, we review recent data indicating that the activity of the Escherichia coli lac operon promoter also depends upon its chromosomal location. Factors that affect promoter activity include the binding of nucleoid-associated proteins to neighbouring sequences, supercoiling and the activity of neighbouring promoters. We suggest that many bacterial promoters might be susceptible to similar position-dependent effects and we review recent data showing that the expression of mobile genes encoding antibiotic-resistance determinants is also location-dependent, both when carried on a bacterial chromosome or a conjugative plasmid.
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84
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Wu F, Japaridze A, Zheng X, Wiktor J, Kerssemakers JWJ, Dekker C. Direct imaging of the circular chromosome in a live bacterium. Nat Commun 2019; 10:2194. [PMID: 31097704 PMCID: PMC6522522 DOI: 10.1038/s41467-019-10221-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 04/26/2019] [Indexed: 01/08/2023] Open
Abstract
Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower-density origin of replication and an ultrathin flexible string of DNA at the terminus of replication. At the single-cell level, the torus is strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. Our data show a domain organization underlying the chromosome structure of E. coli, where MatP proteins induce site-specific persistent domain boundaries at Ori/Ter, while transcription regulators HU and Fis induce weaker transient domain boundaries throughout the genome. These findings provide an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells.
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MESH Headings
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- DNA Replication
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- DNA, Circular/chemistry
- DNA, Circular/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Genome, Bacterial
- Intravital Microscopy/instrumentation
- Intravital Microscopy/methods
- Microscopy, Fluorescence/instrumentation
- Microscopy, Fluorescence/methods
- Nucleic Acid Conformation
- Single-Cell Analysis/instrumentation
- Single-Cell Analysis/methods
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Affiliation(s)
- Fabai Wu
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Xuan Zheng
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jakub Wiktor
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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85
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Sutormin D, Rubanova N, Logacheva M, Ghilarov D, Severinov K. Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome. Nucleic Acids Res 2019; 47:1373-1388. [PMID: 30517674 PMCID: PMC6379681 DOI: 10.1093/nar/gky1222] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022] Open
Abstract
An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate. By exploiting the ability of several topoisomerase poisons to stabilize this intermediate we developed a ChIP-Seq-based approach to locate, with single nucleotide resolution, DNA gyrase cleavage sites (GCSs) throughout the Escherichia coli genome. We identified an extended gyrase binding motif with phased 10-bp G/C content variation, indicating that bending ability of DNA contributes to gyrase binding. We also found that GCSs are enriched in extended regions located downstream of highly transcribed operons. Transcription inhibition leads to redistribution of gyrase suggesting that the enrichment is functionally significant. Our method can be applied for precise mapping of prokaryotic and eukaryotic type II topoisomerases cleavage sites in a variety of organisms and paves the way for future studies of various topoisomerase inhibitors.
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Affiliation(s)
- Dmitry Sutormin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Natalia Rubanova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Maria Logacheva
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Malopolska Centre of Biotechnology, Jagiellonian University, 30387 Cracow, Poland
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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86
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Taniguchi S, Kasho K, Ozaki S, Katayama T. Escherichia coli CrfC Protein, a Nucleoid Partition Factor, Localizes to Nucleoid Poles via the Activities of Specific Nucleoid-Associated Proteins. Front Microbiol 2019; 10:72. [PMID: 30792700 PMCID: PMC6374313 DOI: 10.3389/fmicb.2019.00072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/15/2019] [Indexed: 12/17/2022] Open
Abstract
The Escherichia coli CrfC protein is an important regulator of nucleoid positioning and equipartition. Previously we revealed that CrfC homo-oligomers bind the clamp, a DNA-binding subunit of the DNA polymerase III holoenzyme, promoting colocalization of the sister replication forks, which ensures the nucleoid equipartition. In addition, CrfC localizes at the cell pole-proximal loci via an unknown mechanism. Here, we demonstrate that CrfC localizes to the distinct subnucleoid structures termed nucleoid poles (the cell pole-proximal nucleoid-edges) even in elongated cells as well as in wild-type cells. Systematic analysis of the nucleoid-associated proteins (NAPs) and related proteins revealed that HU, the most abundant NAP, and SlmA, the nucleoid occlusion factor regulating the localization of cell division apparatus, promote the specific localization of CrfC foci. When the replication initiator DnaA was inactivated, SlmA and HU were required for formation of CrfC foci. In contrast, when the replication initiation was inhibited with a specific mutant of the helicase-loader DnaC, CrfC foci were sustained independently of SlmA and HU. H-NS, which forms clusters on AT-rich DNA regions, promotes formation of CrfC foci as well as transcriptional regulation of crfC. In addition, MukB, the chromosomal structure mainetanice protein, and SeqA, a hemimethylated nascent DNA region-binding protein, moderately stimulated formation of CrfC foci. However, IHF, a structural homolog of HU, MatP, the replication terminus-binding protein, Dps, a stress-response factor, and FtsZ, an SlmA-interacting factor in cell division apparatus, little or only slightly affected CrfC foci formation and localization. Taken together, these findings suggest a novel and unique mechanism that CrfC localizes to the nucleoid poles in two steps, assembly and recruitment, dependent upon HU, MukB, SeqA, and SlmA, which is stimulated directly or indirectly by H-NS and DnaA. These factors might concordantly affect specific nucleoid substructures. Also, these nucleoid dynamics might be significant in the role for CrfC in chromosome partition.
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Affiliation(s)
- Saki Taniguchi
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazutoshi Kasho
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shogo Ozaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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87
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Dewachter L, Verstraeten N, Fauvart M, Michiels J. An integrative view of cell cycle control in Escherichia coli. FEMS Microbiol Rev 2018; 42:116-136. [PMID: 29365084 DOI: 10.1093/femsre/fuy005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/19/2018] [Indexed: 11/14/2022] Open
Abstract
Bacterial proliferation depends on the cells' capability to proceed through consecutive rounds of the cell cycle. The cell cycle consists of a series of events during which cells grow, copy their genome, partition the duplicated DNA into different cell halves and, ultimately, divide to produce two newly formed daughter cells. Cell cycle control is of the utmost importance to maintain the correct order of events and safeguard the integrity of the cell and its genomic information. This review covers insights into the regulation of individual key cell cycle events in Escherichia coli. The control of initiation of DNA replication, chromosome segregation and cell division is discussed. Furthermore, we highlight connections between these processes. Although detailed mechanistic insight into these connections is largely still emerging, it is clear that the different processes of the bacterial cell cycle are coordinated to one another. This careful coordination of events ensures that every daughter cell ends up with one complete and intact copy of the genome, which is vital for bacterial survival.
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Affiliation(s)
- Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium.,Department of Life Sciences and Imaging, Smart Electronics Unit, imec, B-3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
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88
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Trojanowski D, Hołówka J, Zakrzewska-Czerwińska J. Where and When Bacterial Chromosome Replication Starts: A Single Cell Perspective. Front Microbiol 2018; 9:2819. [PMID: 30534115 PMCID: PMC6275241 DOI: 10.3389/fmicb.2018.02819] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022] Open
Abstract
Bacterial chromosomes have a single, unique replication origin (named oriC), from which DNA synthesis starts. This study describes methods of visualizing oriC regions and the chromosome replication in single living bacterial cells in real-time. This review also discusses the impact of live cell imaging techniques on understanding of chromosome replication dynamics, particularly at the initiation step, in different species of bacteria.
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Affiliation(s)
- Damian Trojanowski
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Joanna Hołówka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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89
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Abstract
Coordination between chromosome replication and segregation is essential for equal partitioning of genetic material between daughter cells. In bacteria, this is achieved through the proximity of the origin of replication, oriC, and the chromosome partitioning site, parS We report here that in Pseudomonas aeruginosa, segregation but not replication is also controlled at the terminus region of the chromosome. Using the fluorescent repressor operator system (FROS), we investigated chromosome segregation in P. aeruginosa strain PAO1-UW, wherein the chromosome dimer resolution site, dif, is asymmetrically positioned relative to oriC In these cells, segregation proceeded sequentially along the two chromosomal arms and terminated at dif In contrast, chromosome replication terminated elsewhere, opposite from oriC We further found two large domains on the longer arm of the chromosome, wherein DNA segregated simultaneously. Notably, GC-skew, which reflects a bias in nucleotide usage between the leading and lagging strands of the chromosome, switches polarity at the dif locus but not necessarily at the terminus of replication. These data demonstrate that termination of chromosome replication and segregation can be physically separated without adverse effects on bacterial fitness. They also reveal the critical role of the dif region in defining the global layout of the chromosome and the progression of chromosome segregation and suggest that chromosome packing adapts to its subcellular layout.IMPORTANCE Segregation of genetic information is a central event in cellular life. In bacteria, chromosome segregation occurs concurrently with replication, sequentially along the two arms from oriC to dif How the two processes are coordinated is unknown. We explored here chromosome segregation in an opportunistic human pathogen, Pseudomonas aeruginosa, using its strain with markedly unequal chromosomal arms. We found that replication and segregation diverge in this strain and terminate at very different locations, whereas the longer chromosomal arm folds into large domains to align itself with the shorter arm. The significance of this research is in establishing that segregation and replication of bacterial chromosomes are largely uncoupled from each other and that the large-scale structure of the chromosome adapts to its subcellular layout.
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90
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Joyeux M. A segregative phase separation scenario of the formation of the bacterial nucleoid. SOFT MATTER 2018; 14:7368-7381. [PMID: 30204212 DOI: 10.1039/c8sm01205a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a volume about a thousand times larger outside the cell. Here, by performing numerical simulations using coarse-grained models, we elaborate on the conjecture that the formation of the nucleoid may result from a segregative phase separation mechanism driven by the demixing of the DNA coil and non-binding globular macromolecules present in the cytoplasm, presumably functional ribosomes. Simulations performed with crowders having a spherical, dumbbell or octahedral geometry highlight the sensitive dependence of the level of DNA compaction on the dissymmetry of DNA/DNA, DNA/crowder, and crowder/crowder repulsive interactions, thereby supporting the segregative phase separation scenario. Simulations also consistently predict a much stronger DNA compaction close to the jamming threshold. Moreover, simulations performed with crowders of different sizes suggest that the final density distribution of each species results from the competition between thermodynamic forces and steric hindrance, so that bigger crowders are expelled selectively from the nucleoid only at moderate total crowder concentrations. This work leads to several predictions, which may eventually be tested experimentally.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
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91
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Krogh TJ, Møller-Jensen J, Kaleta C. Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. Front Microbiol 2018; 9:2019. [PMID: 30210483 PMCID: PMC6119826 DOI: 10.3389/fmicb.2018.02019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.
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Affiliation(s)
- Thøger J Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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92
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Lioy VS, Boccard F. Conformational Studies of Bacterial Chromosomes by High-Throughput Sequencing Methods. Methods Enzymol 2018; 612:25-45. [PMID: 30502944 DOI: 10.1016/bs.mie.2018.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The development of next-generation sequencing technologies has allowed the application of different methods dedicated to the study of DNA-protein interactions and chromosome conformation to entire bacterial genome. By combining these approaches, the role of various parameters and factors involved in gene expression and chromosome organization can be disclosed at the molecular level over the full genome. Here we describe two methods that profoundly revolutionized our vision of DNA-protein interactions and spatial organization of chromosomes. Chromosome conformation capture (3C) coupled to deep sequencing (3C-seq) enables studies of the genome-wide chromosome folding and its control by different parameters and structural factors. Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) revealed the extent and regulation of DNA-protein interactions in vivo and highlight the role of structural factors in the control of chromosome organization. In this chapter, we describe a detailed protocol of 3C-seq and ChIP-seq experiments that, when combined, allows the spatial study of the chromosome and the factors that promote specific folding. Data processing and analysis for both experiments are also discussed.
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Affiliation(s)
- Virginia S Lioy
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Frédéric Boccard
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.
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93
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Katayama T. Initiation of DNA Replication at the Chromosomal Origin of E. coli, oriC. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:79-98. [PMID: 29357054 DOI: 10.1007/978-981-10-6955-0_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Escherichia coli chromosomal origin consists of a duplex-unwinding region and a region bearing a DNA-bending protein, IHF-binding site, and clusters of binding sites for the initiator protein DnaA. ATP-DnaA molecules form highly organized oligomers in a process stimulated by DiaA, a DnaA-binding protein. The resultant ATP-DnaA complexes promote local unwinding of oriC with the aid of IHF, for which specific interaction of DnaA with the single-stranded DNA is crucial. DnaA complexes also interact with DnaB helicases bound to DnaC loaders, promoting loading of DnaB onto the unwound DNA strands for bidirectional replication. Initiation of replication is strictly regulated during the cell cycle by multiple regulatory systems for oriC and DnaA. The activity of oriC is regulated by its methylation state, whereas that of DnaA depends on the form of the bound nucleotide. ATP-DnaA can be yielded from initiation-inactive ADP-DnaA in a timely manner depending on specific chromosomal DNA elements termed DARS (DnaA-reactivating sequences). After initiation, DnaA-bound ATP is hydrolyzed by two systems, yielding ADP-DnaA. In this review, these and other mechanisms of initiation and its regulation in E. coli are described.
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Affiliation(s)
- Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan.
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94
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Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain. Antimicrob Agents Chemother 2018. [PMID: 29530862 PMCID: PMC5923176 DOI: 10.1128/aac.00209-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Antimicrobial resistance is a major health care problem, with the intensive use of heavy metals and biocides recently identified as a potential factor contributing to the aggravation of this situation. The present study investigated heavy metal susceptibility and genetic resistance determinants in Escherichia coli isolated from clinical urine samples from Sweden, Germany, and Spain. A total of 186 isolates were tested for their sodium arsenite, silver nitrate, and copper(II) sulfate MICs. In addition, 88 of these isolates were subjected to whole-genome sequencing for characterization of their genetic resistance determinants and epidemiology. For sodium arsenite, the isolates could be categorized into a resistant and a nonresistant group based on MIC values. Isolates of the resistant group exhibited the chromosomal ars operon and belonged to non-B2 phylogenetic groups; in contrast, within the B2 phylogroup, no ars operon was found, and the isolates were susceptible to sodium arsenite. Two isolates also harbored the silver/copper resistance determinant pco/sil, and they belonged to sequence types ST10 (phylogroup A) and ST295 (phylogroup C). The ST295 isolate had a silver nitrate MIC of ≥512 mg/liter and additionally produced extended-spectrum beta-lactamases. To our knowledge, this is the first study to describe the distribution of the arsenic resistance ars operon within phylogroups of E. coli strains isolated from patients with urinary tract infections. The arsenic resistance ars operon was present only in all non-B2 clades, which have previously been associated with the environment and commensalism in both humans and animals, while B2 clades lacked the ars operon.
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95
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Brocken DJ, Tark-Dame M, Dame RT. The organization of bacterial genomes: Towards understanding the interplay between structure and function. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2018.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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96
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Balikó G, Vernyik V, Karcagi I, Györfy Z, Draskovits G, Fehér T, Pósfai G. Rational Efforts to Streamline the Escherichia coliGenome. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gabriella Balikó
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Viktor Vernyik
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Ildikó Karcagi
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Zsuzsanna Györfy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Gábor Draskovits
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Tamás Fehér
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - György Pósfai
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
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97
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Junier I, Frémont P, Rivoire O. Universal and idiosyncratic characteristic lengths in bacterial genomes. Phys Biol 2018; 15:035001. [PMID: 29512518 DOI: 10.1088/1478-3975/aab4ac] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10-20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures.
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Affiliation(s)
- Ivan Junier
- CNRS, TIMC-IMAG, Grenoble, France. Univ. Grenoble Alpes, TIMC-IMAG, Grenoble, France
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98
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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.
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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:
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99
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Lioy VS, Cournac A, Marbouty M, Duigou S, Mozziconacci J, Espéli O, Boccard F, Koszul R. Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins. Cell 2018; 172:771-783.e18. [PMID: 29358050 DOI: 10.1016/j.cell.2017.12.027] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/02/2017] [Accepted: 12/19/2017] [Indexed: 12/26/2022]
Abstract
As in eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionally toward the opposite terminus region. Here, we investigate the higher-order architecture of the Escherichia coli genome, showing its partition into two structurally distinct entities by a complex and intertwined network of contacts: the replication terminus (ter) region and the rest of the chromosome. Outside of ter, the condensin MukBEF and the ubiquitous nucleoid-associated protein (NAP) HU promote DNA contacts in the megabase range. Within ter, the MatP protein prevents MukBEF activity, and contacts are restricted to ∼280 kb, creating a domain with distinct structural properties. We also show how other NAPs contribute to nucleoid organization, such as H-NS, which restricts short-range interactions. Combined, these results reveal the contributions of major evolutionarily conserved proteins in a bacterial chromosome organization.
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Affiliation(s)
- Virginia S Lioy
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Axel Cournac
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France
| | - Martial Marbouty
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France
| | - Stéphane Duigou
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Julien Mozziconacci
- Sorbonne Universités, Laboratoire de Physique Théorique de la Matière Condensée, UMR 7600, Université Pierre et Marie Curie, 75005 Paris, France
| | - Olivier Espéli
- Centre Interdisciplinaire de Recherche en Biologie, Collège de France, UMR-CNRS 7241, INSERM U1050, Paris, France
| | - Frédéric Boccard
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Romain Koszul
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France.
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100
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Cameron ADS, Dillon SC, Kröger C, Beran L, Dorman CJ. Broad-scale redistribution of mRNA abundance and transcriptional machinery in response to growth rate in Salmonella enterica serovar Typhimurium. Microb Genom 2017; 3:e000127. [PMID: 29177086 PMCID: PMC5695205 DOI: 10.1099/mgen.0.000127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
We have investigated the connection between the four-dimensional architecture of the bacterial nucleoid and the organism's global gene expression programme. By localizing the transcription machinery and the transcriptional outputs across the genome of the model bacterium Salmonella enterica serovar Typhimurium at different stages of the growth cycle, a surprising disconnection between gene dosage and transcriptional output was revealed. During exponential growth, gene output occurred chiefly in the Ori (origin), Ter (terminus) and NSL (non-structured left) domains, whereas the Left macrodomain remained transcriptionally quiescent at all stages of growth. The apparently high transcriptional output in Ter was correlated with an enhanced stability of the RNA expressed there during exponential growth, suggesting that longer mRNA half-lives compensate for low gene dosage. During exponential growth, RNA polymerase (RNAP) was detected everywhere, whereas in stationary phase cells, RNAP was concentrated in the Ter macrodomain. The alternative sigma factors RpoE, RpoH and RpoN were not required to drive transcription in these growth conditions, consistent with their observed binding to regions away from RNAP and regions of active transcription. Specifically, these alternative sigma factors were found in the Ter macrodomain during exponential growth, whereas they were localized at the Ori macrodomain in stationary phase.
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Affiliation(s)
- Andrew D S Cameron
- 1Institute of Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada.,2Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Shane C Dillon
- 3School of Biological Sciences, Dublin Institute of Technology, Kevin Street, Dublin 8, Ireland
| | - Carsten Kröger
- 4Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Laurens Beran
- 1Institute of Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Charles J Dorman
- 4Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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