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Journal articles on the topic 'Bacteria; DNA replication'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Skarstad, K., and T. Katayama. "Regulating DNA Replication in Bacteria." Cold Spring Harbor Perspectives in Biology 5, no. 4 (2013): a012922. http://dx.doi.org/10.1101/cshperspect.a012922.

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2

Majerník, A. I., E. R. Jenkinson, and J. P. J. Chong. "DNA replication in thermophiles." Biochemical Society Transactions 32, no. 2 (2004): 236–39. http://dx.doi.org/10.1042/bst0320236.

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DNA replication enzymes in the thermophilic Archaea have previously attracted attention due to their obvious use in methods such as PCR. The proofreading ability of the Pyrococcus furiosus DNA polymerase has resulted in a commercially successful product (Pfu polymerase). One of the many notable features of the Archaea is the fact that their DNA processing enzymes appear on the whole to be more like those found in eukaryotes than bacteria. These proteins also appear to be simpler versions of those found in eukaryotes. For these reasons, archaeal organisms make potentially interesting model syst

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3

Greci, Mark D., and Stephen D. Bell. "Archaeal DNA Replication." Annual Review of Microbiology 74, no. 1 (2020): 65–80. http://dx.doi.org/10.1146/annurev-micro-020518-115443.

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It is now well recognized that the information processing machineries of archaea are far more closely related to those of eukaryotes than to those of their prokaryotic cousins, the bacteria. Extensive studies have been performed on the structure and function of the archaeal DNA replication origins, the proteins that define them, and the macromolecular assemblies that drive DNA unwinding and nascent strand synthesis. The results from various archaeal organisms across the archaeal domain of life show surprising levels of diversity at many levels—ranging from cell cycle organization to chromosome

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4

Marsin, Stéphanie, Yazid Adam, Claire Cargemel, et al. "Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase." Nucleic Acids Research 49, no. 11 (2021): 6569–86. http://dx.doi.org/10.1093/nar/gkab463.

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Abstract Replicative helicases are essential proteins that unwind DNA in front of replication forks. Their loading depends on accessory proteins and in bacteria, DnaC and DnaI are well characterized loaders. However, most bacteria do not express either of these two proteins. Instead, they are proposed to rely on DciA, an ancestral protein unrelated to DnaC/I. While the DciA structure from Vibrio cholerae shares no homology with DnaC, it reveals similarities with DnaA and DnaX, two proteins involved during replication initiation. As other bacterial replicative helicases, VcDnaB adopts a toroid-

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Bazin, Alexandre, Mickaël Cherrier, and Laurent Terradot. "Structural insights into DNA replication initiation in Helicobacter pylori." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1632. http://dx.doi.org/10.1107/s2053273314083673.

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In Gram-negative bacteria, opening of DNA double strand during replication is performed by the replicative helicase DnaB. This protein allows for replication fork elongation by unwinding DNA and interacting with DnaG primase. DnaB is composed of two domains: an N-terminal domain (NTD) and a C-terminal domain (CTD) connected by a flexible linker. The protein forms two-tiered hexamers composed of a NTD-ring and a CTD-ring. In Escherichia coli, the initiator protein DnaA binds to the origin of replication oriC and induces the opening of a AT-rich region. The replicative helicase DnaB is then load

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6

Sinha, Anurag Kumar, Christophe Possoz, and David R. F. Leach. "The Roles of Bacterial DNA Double-Strand Break Repair Proteins in Chromosomal DNA Replication." FEMS Microbiology Reviews 44, no. 3 (2020): 351–68. http://dx.doi.org/10.1093/femsre/fuaa009.

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ABSTRACT It is well established that DNA double-strand break (DSB) repair is required to underpin chromosomal DNA replication. Because DNA replication forks are prone to breakage, faithful DSB repair and correct replication fork restart are critically important. Cells, where the proteins required for DSB repair are absent or altered, display characteristic disturbances to genome replication. In this review, we analyze how bacterial DNA replication is perturbed in DSB repair mutant strains and explore the consequences of these perturbations for bacterial chromosome segregation and cell viabilit

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7

Cheung, Andrew K. "Rolling-Circle Replication of an Animal Circovirus Genome in a Theta-Replicating Bacterial Plasmid in Escherichia coli." Journal of Virology 80, no. 17 (2006): 8686–94. http://dx.doi.org/10.1128/jvi.00655-06.

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ABSTRACT A bacterial plasmid containing 1.75 copies of double-stranded porcine circovirus (PCV) DNA in tandem (0.8 copy of PCV type 1 [PCV1], 0.95 copy of PCV2) with two origins of DNA replication (Ori) yielded three different DNA species when transformed into Escherichia coli: the input construct, a unit-length chimeric PCV1Rep/PCV2Cap genome with a composite Ori but lacking the plasmid vector, and a molecule consisting of the remaining 0.75 copy PCV1Cap/PCV2Rep genome with a different composite Ori together with the bacterial plasmid. Replication of the input construct was presumably via the

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8

Pelliciari, Simone, Mei-Jing Dong, Feng Gao, and Heath Murray. "Evidence for a chromosome origin unwinding system broadly conserved in bacteria." Nucleic Acids Research 49, no. 13 (2021): 7525–36. http://dx.doi.org/10.1093/nar/gkab560.

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Abstract Genome replication is a fundamental requirement for the proliferation of all cells. Throughout the domains of life, conserved DNA replication initiation proteins assemble at specific chromosomal loci termed replication origins and direct loading of replicative helicases (1). Despite decades of study on bacterial replication, the diversity of bacterial chromosome origin architecture has confounded the search for molecular mechanisms directing the initiation process. Recently a basal system for opening a bacterial chromosome origin (oriC) was proposed (2). In the model organism Bacillus

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9

Mott, Melissa L., and James M. Berger. "DNA replication initiation: mechanisms and regulation in bacteria." Nature Reviews Microbiology 5, no. 5 (2007): 343–54. http://dx.doi.org/10.1038/nrmicro1640.

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10

Bartosik, Aneta A., and Grazyna Jagura-Burdzy. "Bacterial chromosome segregation." Acta Biochimica Polonica 52, no. 1 (2005): 1–34. http://dx.doi.org/10.18388/abp.2005_3481.

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In most bacteria two vital processes of the cell cycle: DNA replication and chromosome segregation overlap temporally. The action of replication machinery in a fixed location in the cell leads to the duplication of oriC regions, their rapid separation to the opposite halves of the cell and the duplicated chromosomes gradually moving to the same locations prior to cell division. Numerous proteins are implicated in co-replicational DNA segregation and they will be characterized in this review. The proteins SeqA, SMC/MukB, MinCDE, MreB/Mbl, RacA, FtsK/SpoIIIE playing different roles in bacterial

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11

Sarmiento, Felipe, Feng Long, Isaac Cann, and William B. Whitman. "Diversity of the DNA Replication System in theArchaeaDomain." Archaea 2014 (2014): 1–15. http://dx.doi.org/10.1155/2014/675946.

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The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the special

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12

Fukui, Kenji. "DNA Mismatch Repair in Eukaryotes and Bacteria." Journal of Nucleic Acids 2010 (2010): 1–16. http://dx.doi.org/10.4061/2010/260512.

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DNA mismatch repair (MMR) corrects mismatched base pairs mainly caused by DNA replication errors. The fundamental mechanisms and proteins involved in the early reactions of MMR are highly conserved in almost all organisms ranging from bacteria to human. The significance of this repair system is also indicated by the fact that defects in MMR cause human hereditary nonpolyposis colon cancers as well as sporadic tumors. To date, 2 types of MMRs are known: the human type andEscherichia colitype. The basic features of the former system are expected to be universal among the vast majority of organis

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13

Sobecky, Patricia A., Tracy J. Mincer, Michelle C. Chang, Aresa Toukdarian, and Donald R. Helinski. "Isolation of Broad-Host-Range Replicons from Marine Sediment Bacteria." Applied and Environmental Microbiology 64, no. 8 (1998): 2822–30. http://dx.doi.org/10.1128/aem.64.8.2822-2830.1998.

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ABSTRACT Naturally occurring plasmids isolated from heterotrophic bacterial isolates originating from coastal California marine sediments were characterized by analyzing their incompatibility and replication properties. Previously, we reported on the lack of DNA homology between plasmids from the culturable bacterial population of marine sediments and the replicon probes specific for a number of well-characterized incompatibility and replication groups (P. A. Sobecky, T. J. Mincer, M. C. Chang, and D. R. Helinski, Appl. Environ. Microbiol. 63:888–895, 1997). In the present study we isolated 1.

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14

Anand, Syam P., Poulami Mitra, Asma Naqvi, and Saleem A. Khan. "Bacillus anthracis and Bacillus cereus PcrA Helicases Can Support DNA Unwinding and In Vitro Rolling-Circle Replication of Plasmid pT181 of Staphylococcus aureus." Journal of Bacteriology 186, no. 7 (2004): 2195–99. http://dx.doi.org/10.1128/jb.186.7.2195-2199.2004.

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ABSTRACT Replication of rolling-circle replicating (RCR) plasmids in gram-positive bacteria requires the unwinding of initiator protein-nicked plasmid DNA by the PcrA helicase. In this report, we demonstrate that heterologous PcrA helicases from Bacillus anthracis and Bacillus cereus are capable of unwinding Staphylococcus aureus plasmid pT181 from the initiator-generated nick and promoting in vitro replication of the plasmid. These helicases also physically interact with the RepC initiator protein of pT181. The ability of PcrA helicases to unwind noncognate RCR plasmids may contribute to the

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15

Angert, Esther R. "DNA Replication and Genomic Architecture of Very Large Bacteria." Annual Review of Microbiology 66, no. 1 (2012): 197–212. http://dx.doi.org/10.1146/annurev-micro-090110-102827.

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16

Arjes, Heidi A., Allison Kriel, Nohemy A. Sorto, Jared T. Shaw, Jue D. Wang, and Petra Anne Levin. "Failsafe Mechanisms Couple Division and DNA Replication in Bacteria." Current Biology 24, no. 18 (2014): 2149–55. http://dx.doi.org/10.1016/j.cub.2014.07.055.

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17

Fijalkowska, I. J., R. L. Dunn, and R. M. Schaaper. "Mutants of Escherichia coli with increased fidelity of DNA replication." Genetics 134, no. 4 (1993): 1023–30. http://dx.doi.org/10.1093/genetics/134.4.1023.

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Abstract To improve our understanding of the role of DNA replication fidelity in mutagenesis, we undertook a search for Escherichia coli antimutator strains with increased fidelity of DNA replication. The region between 4 and 5 min of the E. coli chromosome was mutagenized using localized mutagenesis mediated by bacteriophage P1. This region contains the dnaE and dnaQ genes, which encode, respectively, the DNA polymerase (alpha subunit) and 3' exonucleolytic proofreading activity (epsilon subunit) of DNA polymerase III holoenzyme, the enzyme primarily responsible for replicating the bacterial

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18

Lo, Chen-Yu, and Yang Gao. "DNA Helicase–Polymerase Coupling in Bacteriophage DNA Replication." Viruses 13, no. 9 (2021): 1739. http://dx.doi.org/10.3390/v13091739.

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Bacteriophages have long been model systems to study the molecular mechanisms of DNA replication. During DNA replication, a DNA helicase and a DNA polymerase cooperatively unwind the parental DNA. By surveying recent data from three bacteriophage replication systems, we summarized the mechanistic basis of DNA replication by helicases and polymerases. Kinetic data have suggested that a polymerase or a helicase alone is a passive motor that is sensitive to the base-pairing energy of the DNA. When coupled together, the helicase–polymerase complex is able to unwind DNA actively. In bacteriophage T

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19

Bonilla, Carla Y., and Alan D. Grossman. "The Primosomal Protein DnaD Inhibits Cooperative DNA Binding by the Replication Initiator DnaA in Bacillus subtilis." Journal of Bacteriology 194, no. 18 (2012): 5110–17. http://dx.doi.org/10.1128/jb.00958-12.

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ABSTRACTDnaA is an AAA+ ATPase and the conserved replication initiator in bacteria. Bacteria control the timing of replication initiation by regulating the activity of DnaA. DnaA binds to multiple sites in the origin of replication (oriC) and is required for recruitment of proteins needed to load the replicative helicase. DnaA also binds to other chromosomal regions and functions as a transcription factor at some of these sites.Bacillus subtilisDnaD is needed during replication initiation for assembly of the replicative helicase atoriCand during replication restart at stalled replication forks

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20

Gallay, Clement, Stefano Sanselicio, Mary E. Anderson, et al. "CcrZ is a pneumococcal spatiotemporal cell cycle regulator that interacts with FtsZ and controls DNA replication by modulating the activity of DnaA." Nature Microbiology 6, no. 9 (2021): 1175–87. http://dx.doi.org/10.1038/s41564-021-00949-1.

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AbstractMost bacteria replicate and segregate their DNA concomitantly while growing, before cell division takes place. How bacteria synchronize these different cell cycle events to ensure faithful chromosome inheritance by daughter cells is poorly understood. Here, we identify Cell Cycle Regulator protein interacting with FtsZ (CcrZ) as a conserved and essential protein in pneumococci and related Firmicutes such as Bacillus subtilis and Staphylococcus aureus. CcrZ couples cell division with DNA replication by controlling the activity of the master initiator of DNA replication, DnaA. The absenc

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21

Druzhinin, Vladimir G., Elizaveta D. Baranova, Vladislav Yu Buslaev, Lyudmila V. Matskova, and Alina V. Tolstikova. "Bacterial DNA damage effectors in host cells." Ecological genetics 16, no. 3 (2018): 26–36. http://dx.doi.org/10.17816/ecogen16326-36.

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The microbiota has a significant, and sometimes decisive, effect on the host's homeostasis. The results of recent metagenomic studies confirm the importance of microbiota in maintaining health or its impact on the development of acute, chronic and neoplastic diseases. One of the important aspects of microbiota exposure is the ability of many bacterial species to induce mutations or modulate a mutation process in the cells of the host organism. This review summarizes the main experimental data revealing various mechanisms of genotoxic action of a bacterial microbiota, including direct damage to

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22

Saint-Dic, Djenann, Jason Kehrl, Brian Frushour, and Lyn Sue Kahng. "Excess SeqA Leads to Replication Arrest and a Cell Division Defect in Vibrio cholerae." Journal of Bacteriology 190, no. 17 (2008): 5870–78. http://dx.doi.org/10.1128/jb.00479-08.

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ABSTRACT Although most bacteria contain a single circular chromosome, some have complex genomes, and all Vibrio species studied so far contain both a large and a small chromosome. In recent years, the divided genome of Vibrio cholerae has proven to be an interesting model system with both parallels to and novel features compared with the genome of Escherichia coli. While factors influencing the replication and segregation of both chromosomes have begun to be elucidated, much remains to be learned about the maintenance of this genome and of complex bacterial genomes generally. An important aspe

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23

Menzel, Thomas M., Maximilian Tischer, Patrice François, et al. "Mode-of-Action Studies of the Novel Bisquaternary Bisnaphthalimide MT02 againstStaphylococcus aureus." Antimicrobial Agents and Chemotherapy 55, no. 1 (2010): 311–20. http://dx.doi.org/10.1128/aac.00586-10.

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ABSTRACTScreening of various bisquaternary bisnaphthalimides against a variety of human pathogens revealed one compound, designated MT02, with strong inhibitory effects against Gram-positive bacteria. The MICs ranged from 0.31 μg/ml against community-acquired methicillin-resistantStaphylococcus aureus(MRSA) lineage USA300 to 20 μg/ml againstStreptococcus pneumoniae. Radioactive whole-cell labeling experiments indicated a strong impact of MT02 on bacterial DNA replication. DNA microarray studies generated a transcriptional signature characterized by stronger expression of genes involved in DNA

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Hill, Norbert S., Ryosuke Kadoya, Dhruba K. Chattoraj, and Petra Anne Levin. "Cell Size and the Initiation of DNA Replication in Bacteria." PLoS Genetics 8, no. 3 (2012): e1002549. http://dx.doi.org/10.1371/journal.pgen.1002549.

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25

Nešvera, J., and J. Hochmannová. "DNA — protein interactions during replication of Genetic elements of bacteria." Folia Microbiologica 30, no. 2 (1985): 154–76. http://dx.doi.org/10.1007/bf02922209.

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26

Titok, Marina, Catherine Suski, Bérengère Dalmais, S. Dusko Ehrlich, and Laurent Jannière. "The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72." Microbiology 152, no. 5 (2006): 1471–78. http://dx.doi.org/10.1099/mic.0.28693-0.

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Plasmids are the tools of choice for studying bacterial functions involved in DNA maintenance. Here a genetic study on the replication of a novel, low-copy-number, Bacillus subtilis plasmid, pBS72, is reported. The results show that two plasmid elements, the initiator protein RepA and an iteron-containing origin, and at least nine host-encoded replication proteins, the primosomal proteins DnaB, DnaC, DnaD, DnaG and DnaI, the DNA polymerases DnaE and PolC, and the polymerase cofactors DnaN and DnaX, are required for pBS72 replication. On the contrary, the cellular initiators DnaA and PriA, the

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Mirkin, Ekaterina V., and Sergei M. Mirkin. "Mechanisms of Transcription-Replication Collisions in Bacteria." Molecular and Cellular Biology 25, no. 3 (2005): 888–95. http://dx.doi.org/10.1128/mcb.25.3.888-895.2005.

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ABSTRACT While collisions between replication and transcription in bacteria are deemed inevitable, the fine details of the interplay between the two machineries are poorly understood. In this study, we evaluate the effects of transcription on the replication fork progression in vivo, by using electrophoresis analysis of replication intermediates. Studying Escherichia coli plasmids, which carry constitutive or inducible promoters in different orientations relative to the replication origin, we show that the mutual orientation of the two processes determines their mode of interaction. Replicatio

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Li, Huilin, Nina Y. Yao, and Michael E. O'Donnell. "Anatomy of a twin DNA replication factory." Biochemical Society Transactions 48, no. 6 (2020): 2769–78. http://dx.doi.org/10.1042/bst20200640.

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The replication of DNA in chromosomes is initiated at sequences called origins at which two replisome machines are assembled at replication forks that move in opposite directions. Interestingly, in vivo studies observe that the two replication forks remain fastened together, often referred to as a replication factory. Replication factories containing two replisomes are well documented in cellular studies of bacteria (Escherichia coli and Bacillus subtilis) and the eukaryote, Saccharomyces cerevisiae. This basic twin replisome factory architecture may also be preserved in higher eukaryotes. Des

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Lestienne, Patrick P. "Priming DNA Replication from Triple Helix Oligonucleotides: Possible Threestranded DNA in DNA Polymerases." Molecular Biology International 2011 (September 14, 2011): 1–9. http://dx.doi.org/10.4061/2011/562849.

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Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs) are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second homologous duplex sequence through the formation of a triple helix, which is able to prime further DNA r

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30

Bolt, E. L., and C. P. Guy. "Homologous recombination in Archaea: new Holliday junction helicases." Biochemical Society Transactions 31, no. 3 (2003): 703–5. http://dx.doi.org/10.1042/bst0310703.

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Homologous recombination (HR) maintains genome stability by promoting high fidelity DNA repair. Several recent reports have established that the primary function of HR enzymes is to underpin DNA replication, resetting forks that are blocked or collapsed at sites of DNA damage remote from replication origins. These functions are crucial to ensuring that genomes are transmitted successfully into subsequent generations of cells. Enzymes of HR have been unearthed in all three domains of life: bacteria, Archaea and eukarya. Helicases that specifically unwind branched DNA molecules are pivotal in li

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Krause, Klaudyna, Monika Maciąg-Dorszyńska, Anna Wosinski, et al. "The Role of Metabolites in the Link between DNA Replication and Central Carbon Metabolism in Escherichia coli." Genes 11, no. 4 (2020): 447. http://dx.doi.org/10.3390/genes11040447.

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A direct link between DNA replication regulation and central carbon metabolism (CCM) has been previously demonstrated in Bacillus subtilis and Escherichia coli, as effects of certain mutations in genes coding for replication proteins could be specifically suppressed by particular mutations in genes encoding CCM enzymes. However, specific molecular mechanism(s) of this link remained unknown. In this report, we demonstrate that various CCM metabolites can suppress the effects of mutations in different replication genes of E. coli on bacterial growth, cell morphology, and nucleoid localization. T

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Barnes, Marjorie H., Shelley D. Miller, and Neal C. Brown. "DNA Polymerases of Low-GC Gram-Positive Eubacteria: Identification of the Replication-Specific Enzyme Encoded by dnaE." Journal of Bacteriology 184, no. 14 (2002): 3834–38. http://dx.doi.org/10.1128/jb.184.14.3834-3838.2002.

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ABSTRACT dnaE, the gene encoding one of the two replication-specific DNA polymerases (Pols) of low-GC-content gram-positive bacteria (E. Dervyn et al., Science 294:1716-1719, 2001; R. Inoue et al., Mol. Genet. Genomics 266:564-571, 2001), was cloned from Bacillus subtilis, a model low-GC gram-positive organism. The gene was overexpressed in Escherichia coli. The purified recombinant product displayed inhibitor responses and physical, catalytic, and antigenic properties indistinguishable from those of the low-GC gram-positive-organism-specific enzyme previously named DNA Pol II after the polB-e

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Mei, Qian, Devon M. Fitzgerald, Jingjing Liu, et al. "Two mechanisms of chromosome fragility at replication-termination sites in bacteria." Science Advances 7, no. 25 (2021): eabe2846. http://dx.doi.org/10.1126/sciadv.abe2846.

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Chromosomal fragile sites are implicated in promoting genome instability, which drives cancers and neurological diseases. Yet, the causes and mechanisms of chromosome fragility remain speculative. Here, we identify three spontaneous fragile sites in the Escherichia coli genome and define their DNA damage and repair intermediates at high resolution. We find that all three sites, all in the region of replication termination, display recurrent four-way DNA or Holliday junctions (HJs) and recurrent DNA breaks. Homology-directed double-strand break repair generates the recurrent HJs at all of these

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Acharya, Sandesh, Amol Dahal, and Hitesh Kumar Bhattarai. "Evolution and origin of sliding clamp in bacteria, archaea and eukarya." PLOS ONE 16, no. 8 (2021): e0241093. http://dx.doi.org/10.1371/journal.pone.0241093.

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The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains

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Moriya, Shigeki, Yoshikazu Kawai, Sakiko Kaji, Adrian Smith, Elizabeth J. Harry, and Jeffery Errington. "Effects of oriC relocation on control of replication initiation in Bacillus subtilis." Microbiology 155, no. 9 (2009): 3070–82. http://dx.doi.org/10.1099/mic.0.030080-0.

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In bacteria, DNA replication initiation is tightly regulated in order to coordinate chromosome replication with cell growth. In Escherichia coli, positive factors and negative regulatory mechanisms playing important roles in the strict control of DNA replication initiation have been reported. However, it remains unclear how bacterial cells recognize the right time for replication initiation during the cell cycle. In the Gram-positive bacterium Bacillus subtilis, much less is known about the regulation of replication initiation, specifically, regarding negative control mechanisms which ensure r

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Pérez-Arnaiz, Patricia, Ambika Dattani, Victoria Smith, and Thorsten Allers. "Haloferax volcanii —a model archaeon for studying DNA replication and repair." Open Biology 10, no. 12 (2020): 200293. http://dx.doi.org/10.1098/rsob.200293.

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The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii , a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, gen

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O'Donnell, M., L. Langston, and B. Stillman. "Principles and Concepts of DNA Replication in Bacteria, Archaea, and Eukarya." Cold Spring Harbor Perspectives in Biology 5, no. 7 (2013): a010108. http://dx.doi.org/10.1101/cshperspect.a010108.

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Munoz-Espin, D., R. Daniel, Y. Kawai, et al. "The actin-like MreB cytoskeleton organizes viral DNA replication in bacteria." Proceedings of the National Academy of Sciences 106, no. 32 (2009): 13347–52. http://dx.doi.org/10.1073/pnas.0906465106.

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39

Casadesús, Josep, and David Low. "Epigenetic Gene Regulation in the Bacterial World." Microbiology and Molecular Biology Reviews 70, no. 3 (2006): 830–56. http://dx.doi.org/10.1128/mmbr.00016-06.

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SUMMARY Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and coupl

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Lang, Kevin S., and Houra Merrikh. "The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria." Annual Review of Microbiology 72, no. 1 (2018): 71–88. http://dx.doi.org/10.1146/annurev-micro-090817-062514.

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Within the last decade, it has become clear that DNA replication and transcription are routinely in conflict with each other in growing cells. Much of the seminal work on this topic has been carried out in bacteria, specifically, Escherichia coli and Bacillus subtilis; therefore, studies of conflicts in these species deserve special attention. Collectively, the recent findings on conflicts have fundamentally changed the way we think about DNA replication in vivo. Furthermore, new insights on this topic have revealed that the conflicts between replication and transcription significantly influen

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Oh, Jangsuk, John G. Julias, Andrea L. Ferris, and Stephen H. Hughes. "Construction and Characterization of a Replication-Competent Retroviral Shuttle Vector Plasmid." Journal of Virology 76, no. 4 (2002): 1762–68. http://dx.doi.org/10.1128/jvi.76.4.1762-1768.2002.

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ABSTRACT We constructed two versions of an RCASBP-based retroviral shuttle vector, RSVP (RCASBP shuttle vector plasmid), containing either the zeocin or blasticidin resistance gene. In this vector, the drug resistance gene is expressed in avian cells from the long terminal repeat (LTR) promoter, whereas in bacteria the resistance gene is expressed from a bacterial promoter. The vector contains a bacterial origin of replication (ColE1) to allow circular viral DNA to replicate as a plasmid in bacteria. The vector also contains the lac operator sequence, which binds to the lac repressor protein,

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Raia, Pierre, Marc Delarue, and Ludovic Sauguet. "An updated structural classification of replicative DNA polymerases." Biochemical Society Transactions 47, no. 1 (2019): 239–49. http://dx.doi.org/10.1042/bst20180579.

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AbstractReplicative DNA polymerases are nano-machines essential to life, which have evolved the ability to copy the genome with high fidelity and high processivity. In contrast with cellular transcriptases and ribosome machines, which evolved by accretion of complexity from a conserved catalytic core, no replicative DNA polymerase is universally conserved. Strikingly, four different families of DNA polymerases have evolved to perform DNA replication in the three domains of life. In Bacteria, the genome is replicated by DNA polymerases belonging to the A- and C-families. In Eukarya, genomic DNA

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Windgassen, Tricia A., Maxime Leroux, Kenneth A. Satyshur, Steven J. Sandler, and James L. Keck. "Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase." Proceedings of the National Academy of Sciences 115, no. 39 (2018): E9075—E9084. http://dx.doi.org/10.1073/pnas.1809842115.

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DNA replication restart, the essential process that reinitiates prematurely terminated genome replication reactions, relies on exquisitely specific recognition of abandoned DNA replication-fork structures. The PriA DNA helicase mediates this process in bacteria through mechanisms that remain poorly defined. We report the crystal structure of a PriA/replication-fork complex, which resolves leading-strand duplex DNA bound to the protein. Interaction with PriA unpairs one end of the DNA and sequesters the 3′-most nucleotide from the nascent leading strand into a conserved protein pocket. Cross-li

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Mocanu, Camelia, and Kok-Lung Chan. "Mind the replication gap." Royal Society Open Science 8, no. 6 (2021): 201932. http://dx.doi.org/10.1098/rsos.201932.

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Unlike bacteria, mammalian cells need to complete DNA replication before segregating their chromosomes for the maintenance of genome integrity. Thus, cells have evolved efficient pathways to restore stalled and/or collapsed replication forks during S-phase, and when necessary, also to delay cell cycle progression to ensure replication completion. However, strong evidence shows that cells can proceed to mitosis with incompletely replicated DNA when under mild replication stress (RS) conditions. Consequently, the incompletely replicated genomic gaps form, predominantly at common fragile site reg

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Mohr, I. J., Y. Gluzman, M. P. Fairman, et al. "Production of simian virus 40 large tumor antigen in bacteria: altered DNA-binding specificity and dna-replication activity of underphosphorylated large tumor antigen." Proceedings of the National Academy of Sciences 86, no. 17 (1989): 6479–83. http://dx.doi.org/10.1073/pnas.86.17.6479.

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A bacterial expression system was used to produce simian virus 40 large tumor antigen (T antigen) in the absence of the extensive posttranslational modifications that occur in mammalian cells. Wild-type T antigen produced in bacteria retained a specific subset of the biochemical activities displayed by its mammalian counterpart. Escherichia coli T antigen functioned as a helicase and bound to DNA fragments containing either site I or the wild-type origin of replication in a manner identical to mammalian T antigen. However, T antigen purified from E. coli did not efficiently bind to site II, an

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Hoover, Sharon E., Weihong Xu, Wenzhong Xiao, and William F. Burkholder. "Changes in DnaA-Dependent Gene Expression Contribute to the Transcriptional and Developmental Response of Bacillus subtilis to Manganese Limitation in Luria-Bertani Medium." Journal of Bacteriology 192, no. 15 (2010): 3915–24. http://dx.doi.org/10.1128/jb.00210-10.

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ABSTRACT The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that pert

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Akashi, Motohiro, and Masaharu Takemura. "Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus." Viruses 11, no. 3 (2019): 267. http://dx.doi.org/10.3390/v11030267.

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The detailed mechanisms of replication initiation, termination and segregation events were not yet known in Acanthamoeba polyphaga mimivirus (APMV). Here, we show detailed bioinformatics-based analyses of chromosomal replication in APMV from initiation to termination mediated by proteins bound to specific DNA sequences. Using GC/AT skew and coding sequence skew analysis, we estimated that the replication origin is located at 382 kb in the APMV genome. We performed homology-modeling analysis of the gamma domain of APMV-FtsK (DNA translocase coordinating chromosome segregation) related to FtsK-o

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Duckworth, Alexander T., Tricia A. Windgassen, and James L. Keck. "Examination of the roles of a conserved motif in the PriA helicase in structure-specific DNA unwinding and processivity." PLOS ONE 16, no. 7 (2021): e0255409. http://dx.doi.org/10.1371/journal.pone.0255409.

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DNA replication complexes (replisomes) frequently encounter barriers that can eject them prematurely from the genome. To avoid the lethality of incomplete DNA replication that arises from these events, bacteria have evolved “DNA replication restart” mechanisms to reload replisomes onto abandoned replication forks. The Escherichia coli PriA DNA helicase orchestrates this process by recognizing and remodeling replication forks and recruiting additional proteins that help to drive replisome reloading. We have identified a conserved sequence motif within a linker region of PriA that docks into a g

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Myka, Kamila K., and Kenneth J. Marians. "Two components of DNA replication-dependent LexA cleavage." Journal of Biological Chemistry 295, no. 30 (2020): 10368–79. http://dx.doi.org/10.1074/jbc.ra120.014224.

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Induction of the SOS response, a cellular system triggered by DNA damage in bacteria, depends on DNA replication for the generation of the SOS signal, ssDNA. RecA binds to ssDNA, forming filaments that stimulate proteolytic cleavage of the LexA transcriptional repressor, allowing expression of > 40 gene products involved in DNA repair and cell cycle regulation. Here, using a DNA replication system reconstituted in vitro in tandem with a LexA cleavage assay, we studied LexA cleavage during DNA replication of both undamaged and base-damaged templates. Only a ssDNA–RecA filament supported LexA

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O'Neil, Pierce, Scott Lovell, Nurjahan Mehzabeen, Kevin Battaile, and Indranil Biswas. "Crystal structure of histone-like protein fromStreptococcus mutansrefined to 1.9 Å resolution." Acta Crystallographica Section F Structural Biology Communications 72, no. 4 (2016): 257–62. http://dx.doi.org/10.1107/s2053230x1600217x.

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Nucleoid-associated proteins (NAPs) in prokaryotes play an important architectural role in DNA bending, supercoiling and DNA compaction. In addition to architectural roles, some NAPs also play regulatory roles in DNA replication and repair, and act as global transcriptional regulators in many bacteria. Bacteria encode multiple NAPs and some of them are even essential for survival.Streptococcus mutans, a dental pathogen, encodes one such essential NAP called histone-like protein (HLP). Here, the three-dimensional structure ofS. mutansHLP has been determined to 1.9 Å resolution. The HLP structur

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