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Pountain AW, Jiang P, Yao T, Homaee E, Guan Y, McDonald KJC, Podkowik M, Shopsin B, Torres VJ, Golding I, Yanai I. Transcription-replication interactions reveal bacterial genome regulation. Nature 2024; 626:661-669. [PMID: 38267581 PMCID: PMC10923101 DOI: 10.1038/s41586-023-06974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024]
Abstract
Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. In bacteria, the relationship between the regulatory architecture of a gene and its expression is well understood for individual model gene circuits2,3. However, a broader perspective of these dynamics at the genome scale is lacking, in part because bacterial transcriptomics has hitherto captured only a static snapshot of expression averaged across millions of cells4. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on the transcriptional response of each gene to its own replication, which we term the transcription-replication interaction profile (TRIP). Analysing single-bacterium RNA-sequencing data, we found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal the local regulatory context of a gene. Whereas the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, and this is shaped by factors such as intra-operon position and repression state. By revealing the underlying mechanistic drivers of gene expression heterogeneity, this work provides a quantitative, biophysical framework for modelling replication-dependent expression dynamics.
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Affiliation(s)
- Andrew W Pountain
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Peien Jiang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Ehsan Homaee
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yichao Guan
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Kevin J C McDonald
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Bo Shopsin
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Victor J Torres
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ido Golding
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Itai Yanai
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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2
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Pflug FG, Bhat D, Pigolotti S. Genome replication in asynchronously growing microbial populations. PLoS Comput Biol 2024; 20:e1011753. [PMID: 38181054 PMCID: PMC10796026 DOI: 10.1371/journal.pcbi.1011753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/18/2024] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and genome stability. In a growing cell culture, genomic regions that are replicated early should be more abundant than regions that are replicated late. This abundance pattern can be experimentally measured using deep sequencing. However, a general quantitative theory linking this pattern to the replication program is still lacking. In this paper, we predict the abundance of DNA fragments in asynchronously growing cultures from any given stochastic model of the DNA replication program. As key examples, we present stochastic models of the DNA replication programs in budding yeast and Escherichia coli. In both cases, our model results are in excellent agreement with experimental data and permit to infer key information about the replication program. In particular, our method is able to infer the locations of known replication origins in budding yeast with high accuracy. These examples demonstrate that our method can provide insight into a broad range of organisms, from bacteria to eukaryotes.
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Affiliation(s)
- Florian G. Pflug
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Deepak Bhat
- Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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3
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Goodall DJ, Warecka D, Hawkins M, Rudolph CJ. Interplay between chromosomal architecture and termination of DNA replication in bacteria. Front Microbiol 2023; 14:1180848. [PMID: 37434703 PMCID: PMC10331603 DOI: 10.3389/fmicb.2023.1180848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Faithful transmission of the genome from one generation to the next is key to life in all cellular organisms. In the majority of bacteria, the genome is comprised of a single circular chromosome that is normally replicated from a single origin, though additional genetic information may be encoded within much smaller extrachromosomal elements called plasmids. By contrast, the genome of a eukaryote is distributed across multiple linear chromosomes, each of which is replicated from multiple origins. The genomes of archaeal species are circular, but are predominantly replicated from multiple origins. In all three cases, replication is bidirectional and terminates when converging replication fork complexes merge and 'fuse' as replication of the chromosomal DNA is completed. While the mechanics of replication initiation are quite well understood, exactly what happens during termination is far from clear, although studies in bacterial and eukaryotic models over recent years have started to provide some insight. Bacterial models with a circular chromosome and a single bidirectional origin offer the distinct advantage that there is normally just one fusion event between two replication fork complexes as synthesis terminates. Moreover, whereas termination of replication appears to happen in many bacteria wherever forks happen to meet, termination in some bacterial species, including the well-studied bacteria Escherichia coli and Bacillus subtilis, is more restrictive and confined to a 'replication fork trap' region, making termination even more tractable. This region is defined by multiple genomic terminator (ter) sites, which, if bound by specific terminator proteins, form unidirectional fork barriers. In this review we discuss a range of experimental results highlighting how the fork fusion process can trigger significant pathologies that interfere with the successful conclusion of DNA replication, how these pathologies might be resolved in bacteria without a fork trap system and how the acquisition of a fork trap might have provided an alternative and cleaner solution, thus explaining why in bacterial species that have acquired a fork trap system, this system is remarkably well maintained. Finally, we consider how eukaryotic cells can cope with a much-increased number of termination events.
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Affiliation(s)
- Daniel J. Goodall
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | | | - Christian J. Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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4
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Huang D, Johnson AE, Sim BS, Lo TW, Merrikh H, Wiggins PA. The in vivo measurement of replication fork velocity and pausing by lag-time analysis. Nat Commun 2023; 14:1762. [PMID: 36997519 PMCID: PMC10063678 DOI: 10.1038/s41467-023-37456-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractAn important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell. To capture these dynamics, we develop lag-time analysis, a method for measuring in vivo dynamics. Using this approach, we provide quantitative locus-specific measurements of fork velocity, in units of kilobases per second, as well as replisome pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In this work, we quantitatively characterize known phenomena, detect brief, locus-specific pauses at ribosomal DNA loci in wild-type cells, and observe temporal fork velocity oscillations in three highly-divergent bacterial species.
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Hamilton NA, Jehru AE, Samples WN, Wendel BM, Mokhtari PD, Courcelle CT, Courcelle J. chi sequences switch the RecBCD helicase-nuclease complex from degradative to replicative modes during the completion of DNA replication. J Biol Chem 2023; 299:103013. [PMID: 36781123 PMCID: PMC10025158 DOI: 10.1016/j.jbc.2023.103013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
Accurately completing DNA replication when two forks converge is essential to genomic stability. The RecBCD helicase-nuclease complex plays a central role in completion by promoting resection and joining of the excess DNA created when replisomes converge. chi sequences alter RecBCD activity and localize with cross-over hotspots during sexual events in bacteria, yet their functional role during chromosome replication remains unknown. Here, we use two-dimensional agarose gel analysis to show that chi induces replication on substrates containing convergent forks. The induced-replication is processive, but uncoupled with respect to leading and lagging strand synthesis, and can be suppressed by ter sites which limit replisome progression. Our observations demonstrate that convergent replisomes create a substrate that is processed by RecBCD, and that chi, when encountered, switches RecBCD from a degradative to replicative function. We propose that chi serves to functionally differentiate DNA ends created during completion, which require degradation, from those created by chromosomal double-strand breaks, which require resynthesis.
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Affiliation(s)
| | - Avery E. Jehru
- Department of Biology, Portland State University, Portland, Oregon, USA
| | | | - Brian M. Wendel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | | | | | - Justin Courcelle
- Department of Biology, Portland State University, Portland, Oregon, USA
- For correspondence: Justin Courcelle
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Escherichia coli cell factories with altered chromosomal replication scenarios exhibit accelerated growth and rapid biomass production. Microb Cell Fact 2022; 21:125. [PMID: 35729580 PMCID: PMC9210752 DOI: 10.1186/s12934-022-01851-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/21/2022] [Indexed: 11/24/2022] Open
Abstract
Background Generally, bacteria have a circular genome with a single replication origin for each replicon, whereas archaea and eukaryotes can have multiple replication origins in a single chromosome. In Escherichia coli, bidirectional DNA replication is initiated at the origin of replication (oriC) and arrested by the 10 termination sites (terA–J). Results We constructed E. coli derivatives with additional or ectopic replication origins, which demonstrate the relationship between DNA replication and cell physiology. The cultures of E. coli derivatives with multiple replication origins contained an increased fraction of replicating chromosomes and the cells varied in size. Without the original oriC, E. coli derivatives with double ectopic replication origins manifested impaired growth irrespective of growth conditions and enhanced cell size, and exhibited excessive and asynchronous replication initiation. The generation time of an E. coli strain with three replication origins decreased in a minimal medium supplemented with glucose as the sole carbon source. As well as cell growth, the introduction of additional replication origins promoted increased biomass production. Conclusions Balanced cell growth and physiological stability of E. coli under rapid growth condition are affected by changes in the position and number of replication origins. Additionally, we show that, for the first time to our knowledge, the introduction of replication initiation sites to the chromosome promotes cell growth and increases protein production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01851-z.
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Jameson KH, Rudolph CJ, Hawkins M. Termination of DNA replication at Tus-ter barriers results in under-replication of template DNA. J Biol Chem 2021; 297:101409. [PMID: 34780717 DOI: 10.1016/j.jbc.2021.101409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 02/05/2023] Open
Abstract
The complete and accurate duplication of genomic information is vital to maintain genome stability in all domains of life. In Escherichia coli, replication termination, the final stage of the duplication process, is confined to the 'replication fork trap' region by multiple unidirectional fork barriers formed by the binding of Tus protein to genomic ter sites. Termination typically occurs away from Tus-ter complexes, but they become part of the fork fusion process when a delay to one replisome allows the second replisome to travel more than halfway around the chromosome. In this instance, replisome progression is blocked at the non-permissive interface of the Tus-ter complex, termination then occurs when a converging replisome meets the permissive interface. To investigate the consequences of replication fork fusion at Tus-ter complexes, we established a plasmid-based replication system where we could mimic the termination process at Tus-ter complexes in vitro. We developed a termination mapping assay to measure leading strand replication fork progression and demonstrate that the DNA template is under-replicated by 15-24 bases when replication forks fuse at Tus-ter complexes. This gap could not be closed by the addition of lagging strand processing enzymes or by the inclusion of several helicases that promote DNA replication. Our results indicate that accurate fork fusion at Tus-ter barriers requires further enzymatic processing, highlighting large gaps that still exist in our understanding of the final stages of chromosome duplication and the evolutionary advantage of having a replication fork trap.
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Affiliation(s)
- Katie H Jameson
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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Goodall DJ, Jameson KH, Hawkins M, Rudolph CJ. A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups. Int J Mol Sci 2021; 22:ijms22157928. [PMID: 34360694 PMCID: PMC8347550 DOI: 10.3390/ijms22157928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/26/2022] Open
Abstract
Termination of DNA replication, the final stage of genome duplication, is surprisingly complex, and failures to bring DNA synthesis to an accurate conclusion can impact genome stability and cell viability. In Escherichia coli, termination takes place in a specialised termination area opposite the origin. A 'replication fork trap' is formed by unidirectional fork barriers via the binding of Tus protein to genomic ter sites. Such a fork trap system is found in some bacterial species, but it appears not to be a general feature of bacterial chromosomes. The biochemical properties of fork trap systems have been extensively characterised, but little is known about their precise physiological roles. In this study, we compare locations and distributions of ter terminator sites in E. coli genomes across all phylogenetic groups, including Shigella. Our analysis shows that all ter sites are highly conserved in E. coli, with slightly more variability in the Shigella genomes. Our sequence analysis of ter sites and Tus proteins shows that the fork trap is likely to be active in all strains investigated. In addition, our analysis shows that the dif chromosome dimer resolution site is consistently located between the innermost ter sites, even if rearrangements have changed the location of the innermost termination area. Our data further support the idea that the replication fork trap has an important physiological role that provides an evolutionary advantage.
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Affiliation(s)
- Daniel J. Goodall
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
| | - Katie H. Jameson
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (K.H.J.); (M.H.)
| | - Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (K.H.J.); (M.H.)
| | - Christian J. Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
- Correspondence:
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9
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Integration of the pSLT Plasmid into the Salmonella Chromosome Results in a Temperature-Sensitive Growth Defect Due to Aberrant DNA Replication. J Bacteriol 2020; 202:JB.00380-20. [PMID: 32747428 DOI: 10.1128/jb.00380-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/16/2020] [Indexed: 11/20/2022] Open
Abstract
A mutant of Salmonella enterica serovar Typhimurium was isolated that simultaneously affected two metabolic pathways as follows: NAD metabolism and DNA repair. The mutant was isolated as resistant to a nicotinamide analog and as temperature-sensitive for growth on minimal glucose medium. In this mutant, Salmonella's 94-kb virulence plasmid pSLT had recombined into the chromosome upstream of the NAD salvage pathway gene pncA This insertion blocked most transcription of pncA, which reduced uptake of the nicotinamide analog. The pSLT insertion mutant also exhibited phenotypes associated with induction of the SOS DNA repair system, including an increase in filamentous cells, higher exonuclease III and catalase activities, and derepression of SOS gene expression. Genome sequencing revealed increased read coverage extending out from the site of pSLT insertion. The two pSLT replication origins are likely initiating replication of the chromosome near the normal replication terminus. Too much replication initiation at the wrong site is probably causing the observed growth defects. Accordingly, deletion of both pSLT replication origins restored growth at higher temperatures.IMPORTANCE In studies that insert a second replication origin into the chromosome, both origins are typically active at the same time. In contrast, the integrated pSLT plasmid initiated replication in stationary phase after normal chromosomal replication had finished. The gradient in read coverage extending out from a single site could be a simple but powerful tool for studying replication and detecting chromosomal rearrangements. This technique may be of particular value when a genome has been sequenced for the first time to verify correct assembly.
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10
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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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11
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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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12
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Hawkins M, Dimude JU, Howard JAL, Smith AJ, Dillingham MS, Savery NJ, Rudolph CJ, McGlynn P. Direct removal of RNA polymerase barriers to replication by accessory replicative helicases. Nucleic Acids Res 2019; 47:5100-5113. [PMID: 30869136 PMCID: PMC6547429 DOI: 10.1093/nar/gkz170] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/22/2019] [Accepted: 03/08/2019] [Indexed: 11/24/2022] Open
Abstract
Bacterial genome duplication and transcription require simultaneous access to the same DNA template. Conflicts between the replisome and transcription machinery can lead to interruption of DNA replication and loss of genome stability. Pausing, stalling and backtracking of transcribing RNA polymerases add to this problem and present barriers to replisomes. Accessory helicases promote fork movement through nucleoprotein barriers and exist in viruses, bacteria and eukaryotes. Here, we show that stalled Escherichia coli transcription elongation complexes block reconstituted replisomes. This physiologically relevant block can be alleviated by the accessory helicase Rep or UvrD, resulting in the formation of full-length replication products. Accessory helicase action during replication-transcription collisions therefore promotes continued replication without leaving gaps in the DNA. In contrast, DinG does not promote replisome movement through stalled transcription complexes in vitro. However, our data demonstrate that DinG operates indirectly in vivo to reduce conflicts between replication and transcription. These results suggest that Rep and UvrD helicases operate on DNA at the replication fork whereas DinG helicase acts via a different mechanism.
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Affiliation(s)
- Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | | | - Abigail J Smith
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Mark S Dillingham
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Nigel J Savery
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Peter McGlynn
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
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13
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Midgley-Smith SL, Dimude JU, Rudolph CJ. A role for 3' exonucleases at the final stages of chromosome duplication in Escherichia coli. Nucleic Acids Res 2019; 47:1847-1860. [PMID: 30544222 PMCID: PMC6393302 DOI: 10.1093/nar/gky1253] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/25/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
Chromosome duplication initiates via the assembly of replication fork complexes at defined origins, from where they proceed in opposite directions until they fuse with a converging fork. Recent work highlights that the completion of DNA replication is highly complex in both pro- and eukaryotic cells. In this study we have investigated how 3' and 5' exonucleases contribute towards the successful termination of chromosome duplication in Escherichia coli. We show that the absence of 3' exonucleases can trigger levels of over-replication in the termination area robust enough to allow successful chromosome duplication in the absence of oriC firing. Over-replication is completely abolished if replication fork complexes are prevented from fusing by chromosome linearization. Our data strongly support the idea that 3' flaps are generated as replication fork complexes fuse. In the absence of 3' exonucleases, such as ExoI, these 3' flaps can be converted into 5' flaps, which are degraded by 5' exonucleases, such as ExoVII and RecJ. Our data support the idea that multiple protein activities are required to process fork fusion intermediates. They highlight the complexity of fork fusions and further support the idea that the termination area evolved to contain fork fusion-mediated pathologies.
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Affiliation(s)
- Sarah L Midgley-Smith
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
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Raghunathan N, Goswami S, Leela JK, Pandiyan A, Gowrishankar J. A new role for Escherichia coli Dam DNA methylase in prevention of aberrant chromosomal replication. Nucleic Acids Res 2019; 47:5698-5711. [PMID: 30957852 PMCID: PMC6582345 DOI: 10.1093/nar/gkz242] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Accepted: 03/26/2019] [Indexed: 01/20/2023] Open
Abstract
The Dam DNA methylase of Escherichia coli is required for methyl-directed mismatch repair, regulation of chromosomal DNA replication initiation from oriC (which is DnaA-dependent), and regulation of gene expression. Here, we show that Dam suppresses aberrant oriC-independent chromosomal replication (also called constitutive stable DNA replication, or cSDR). Dam deficiency conferred cSDR and, in presence of additional mutations (Δtus, rpoB*35) that facilitate retrograde replication fork progression, rescued the lethality of ΔdnaA mutants. The DinG helicase was required for rescue of ΔdnaA inviability during cSDR. Viability of ΔdnaA dam derivatives was dependent on the mismatch repair proteins, since such viability was lost upon introduction of deletions in mutS, mutH or mutL; thus generation of double strand ends (DSEs) by MutHLS action appears to be required for cSDR in the dam mutant. On the other hand, another DSE-generating agent phleomycin was unable to rescue ΔdnaA lethality in dam+ derivatives (mutS+ or ΔmutS), but it could do so in the dam ΔmutS strain. These results point to a second role for Dam deficiency in cSDR. We propose that in Dam-deficient strains, there is an increased likelihood of reverse replication restart (towards oriC) following recombinational repair of DSEs on the chromosome.
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Affiliation(s)
- Nalini Raghunathan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India
| | - Sayantan Goswami
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India
| | - Jakku K Leela
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Apuratha Pandiyan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
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15
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Abstract
Bacterial chromosomes harbour a unique origin of bidirectional replication, oriC. They are almost always circular, with replication terminating in a region diametrically opposite to oriC, the terminus. The oriC-terminus organisation is reflected by the orientation of the genes and by the disposition of DNA-binding protein motifs implicated in the coordination of chromosome replication and segregation with cell division. Correspondingly, the E. coli and B. subtilis model bacteria possess a replication fork trap system, Tus/ter and RTP/ter, respectively, which enforces replication termination in the terminus region. Here, we show that tus and rtp are restricted to four clades of bacteria, suggesting that tus was recently domesticated from a plasmid gene. We further demonstrate that there is no replication fork system in Vibrio cholerae, a bacterium closely related to E. coli. Marker frequency analysis showed that replication forks originating from ectopic origins were not blocked in the terminus region of either of the two V. cholerae chromosomes, but progressed normally until they encountered an opposite fork. As expected, termination synchrony of the two chromosomes is disrupted by these ectopic origins. Finally, we show that premature completion of the primary chromosome replication did not modify the choreography of segregation of its terminus region.
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16
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Hamilton NA, Wendel BM, Weber EA, Courcelle CT, Courcelle J. RecBCD, SbcCD and ExoI process a substrate created by convergent replisomes to complete DNA replication. Mol Microbiol 2019; 111:1638-1651. [PMID: 30883946 DOI: 10.1111/mmi.14242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/11/2022]
Abstract
The accurate completion of DNA replication on the chromosome requires RecBCD and structure specific SbcCD and ExoI nucleases. However, the substrates and mechanism by which this reaction occurs remains unknown. Here we show that these completion enzymes operate on plasmid substrates containing two replisomes, but are not required for plasmids containing one replisome. Completion on the two-replisome plasmids requires RecBCD, but does not require RecA and no broken intermediates accumulate in its absence, indicating that the completion reaction occurs normally in the absence of any double-strand breaks. Further, similar to the chromosome, we show that when the normal completion reaction is prevented, an aberrant RecA-mediated recombination process leads to amplifications that drive most of the instabilities associated with the two-replisome substrates. The observations imply that the substrate SbcCD, ExoI and RecBCD act upon in vivo is created specifically by two convergent replisomes, and demonstrate that the function of RecBCD in completing replication is independent of double-strand break repair, and likely promotes joining of the strands of the convergent replication forks.
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Affiliation(s)
- Nicklas A Hamilton
- Department of Biology, Portland State University, Portland, OR, 97201, USA
| | - Brian M Wendel
- Department of Biology, Portland State University, Portland, OR, 97201, USA
| | - Emma A Weber
- Department of Biology, Portland State University, Portland, OR, 97201, USA
| | | | - Justin Courcelle
- Department of Biology, Portland State University, Portland, OR, 97201, USA
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