theta replication of plasmid

Takechi S, Matsui H, Itoh T. Primer RNA synthesis by plasmid-specified Rep protein for initiation of ColE2 DNA replication. Next, the 5 end of RNAI (antitail) nucleates the hybridization between the two RNAs to form a duplex. Reconsidering plasmid maintenance factors for computational plasmid design. In some replicons duplex melting depends on transcription, while other replicons rely on plasmid-encoded trans-acting proteins (Reps); primers for leading-strand synthesis can be generated through processing of a transcript or in other replicons by the action of host- or plasmid-encoded primases. There are two methods for the replication of plasmids. Plasmids are transmissible by conjugation (Frost et al., 2005; Sota and Top, 2008; Frost and Koraimann, 2010 ). These dimeric circles are then resolved into individual linear plasmid DNAs with closed hairpins at the ends. Kim JW, Bugata V, Corts-Corts G, Quevedo-Martnez G, Camps M. EcoSal Plus. Microbiol Spectr. It has been shown previously that initiation of pAM1 replication requires a plasmid-encoded protein (RepE) and a short origin and is carried out by the host DNA polymerase I. Wang Z, Yuan Z, Hengge UR. A model for regulation of ColE1-like plasmid replication by uncharged tRNAs in amino acid-starved Escherichia coli cells. The .gov means its official. Like class B plasmids, however, both initiate of leading-strand synthesis by Pol I extension of a free 3-OH. Some plasmids and bacterial chromosomes are linear rather than circular. Replication initiation depends on a section of sequence known as plasmid origin of replication (ori). Mechanism of Theta Plasmid Replication: DNA unwinds at the ori site from where the replication begins. Our discussion will focus on replication initiation, which informs different biological properties of plasmids (size, host range, plasmid copy number, etc.) The last section of the chapter reviews how plasmid copy number is sensed and how this feedback modulates the frequency of replication. The endpoints, which correspond to plasmid origin and terC, were mapped with single-nucleotide precision. del Solar G, Giraldo R, Ruiz-Echevarra MJ, Espinosa M, Daz-Orejas R. Microbiol Mol Biol Rev. Learning more about the diversity of replication mechanisms present in plasmids can help understand the mechanisms that cells have available to replicate and repair their DNA. In the case of strand displacement, replication initiation is mediated by RepC, which (similar to class A theta . For stringently controlled plasmids, replication is tightly coupled to the bacterial host's cell cycle in order to maintain a stable concentration of plasmid. Origin of replication or ori to refer to the cis -ori, and replicon to refer to basic or minimal replicons. 1998 Jun;62(2):434-64. doi: 10.1128/MMBR.62.2.434-464.1998. What does the homology between E. coli tRNAs and RNAs controlling ColE1 plasmid replication mean? The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). official website and that any information you provide is encrypted and then the two daughter DNAs separate. Unable to load your collection due to an error, Unable to load your delegates due to an error. 2023 Feb 16;14:1112307. doi: 10.3389/fmicb.2023.1112307. Clipboard, Search History, and several other advanced features are temporarily unavailable. Plasmids of lactococci - genetic accessories or genetic necessities Given that the 5 end portion of RNAI does not cover the initiation codon of Rep or its immediate vicinity, inhibition in this case appears to be caused by structural disruption of secondary or tertiary structures required for translation (70). SL1-3 bear a structural resemblance to the clover-leaf structure of tRNAs and even have homology to the anticodon loops of eleven tRNAs (66). While the plasmid replicates, the FRT closer to the Ori replicates early, and the one farther replicates late. Rep binds specifically and rapidly to a unique site immediately upstream of the replication initiation site. Inclusion in an NLM database does not imply endorsement of, or agreement with, These two alternative types of plasmid replication differ from theta plasmid replication in two additional key aspects: lagging-strand synthesis is decoupled from leading strand synthesis; lagging -strand synthesis is continuous. Grabherr R, Nilsson E, Striedner G, Bayer K. Stabilizing plasmid copy number to improve recombinant protein production. Template switching is a known feature of break-induced replication in yeast and requires EXOI-dependent resection to increase ssDNA for recombination 9, 45, 46, 47. DasGupta S, Mukhopadhyay G, Papp PP, Lewis MS, Chattoraj DK. These regulatory mechanisms allow for rapid expansion when plasmids colonize a new permissive cell (establishment phase), and later tune the frequency of replication so that, on average, there is one replicative event per plasmid copy number per cell cycle (steady state phase), minimizing fluctuations in copy number (54). and transmitted securely. Hjalt TA, Wagner EG. This article discusses theta plasmid replication, which is a class of circular plasmid replication that includes ColE1-like origins of replication popular with expression vectors. doi: 10.1128/ecosalplus.ESP-0026-2019. As mentioned above, the double strand melts in response to iteron binding by Rep protein. The frequency of replication initiation is tightly regulated to facilitate establishment in permissive hosts and to achieve a steady state. This is the most common mode of DNA replication. VI) Segregation: the two daughter strands are ligated, resulting in two DNA duplexes, each containing a parental strand (solid black line) and daughter strand (dashed black line). Similarly, in R6K plasmids, binding of its cognate iterons bends the DNA and generates a wrapped nucleoprotein structure (18). Arch Microbiol. Role of PriA in replication fork reactivation in Escherichia coli. Thus, and oris are still dependent on the multiple iterons present in ori . Rep binding of cognate sequence in the plasmid ori mediates the earliest step in replication initiation: duplex DNA melting. Both hairpins and forked structures recruit PriA, which is the first step in the replisome initiation complex. Those DNA molecules which can replicate autonomously are known as replicons. Basic replicon refers to the minimal sequence that supports replication preserving the regulatory circuitry. Multiple homeostatic mechanisms in the control of P1 plasmid replication. 2019 Jan 8;47(D1):D74-D77. Of the plasmids found in Mycobacterium, only the low copy number plasmid pAL5000 has been widely used (Labidi et al., 1985). Following R-loop formation, the RNA pre-primer is processed by RNAse H (which recognizes the AAAAA motif in RNAII) producing a free 3 -OH end. The first contact between sense and antisense RNAs occurs by pairing between complementary sequences at the loop portion of stem-loops, a rate-limiting step known as kissing complex formation(58). First, the Rep protein recognizes and binds to the strand that contains the double-strand origin (DSO) on the DNA. Brantl S. Antisense-RNA mediated control of plasmid replication - pIP501 revisited. Rep protein is the dimer that is formed of the two monomers. . BMC Microbiol. None of these processes require DNA breaks. The 3 end of the pre-primer RNA forms a stable hybrid with 5 end of the lagging-strand DNA template of ori. Filutowicz M, Dellis S, Levchenko I, Urh M, Wu F, York D. Regulation of replication of an iteron-containing DNA molecule. Since DNA polymerases cannot initiate the synthesis of a new strand of the DNA, this has been the primer problem. In plasmids that instead rely on transcription for duplex melting, the transcript itself can be processed and become the primer for extension. mSystems. 8600 Rockville Pike Drolet M. Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology. Int J Mol Sci. Loftie-Eaton W, Rawlings DE. Plasmids that replicate using the strand-displacement mode of replication include E. coli incompatibility group Q (IncQ) plasmids of-proteobacteria such as RSF1010. The https:// ensures that you are connecting to the 2015 Feb; 3(1): PLAS-0029-2014. Tauch et al. Among the two mechanisms, replication can occur by any one of the mechanisms: theta mode for both unidirectional and bi-directional pathways rolling circle mode. Decreased plasmid copy number leads to pII derepression resulting in increased RepR expression. Diaz-Lopez T, Lages-Gonzalo M, Serrano-Lopez A, Alfonso C, Rivas G, Diaz-Orejas R, Giraldo R. Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. Kim JW, Bugata V, Corts-Corts G, Quevedo-Martnez G, Camps M. EcoSal Plus. The ori site like theta-type could be located upstream of repB, which contains a short tandem repeats (sTR) and a long tandem repeats (lTR). It has been shown previously that initiation of pAM1 replication requires a plasmidencoded protein (RepE) and a short origin and is carried out by the host DNA polymerase I. Rep loci, when present, are typically upstream of the plasmid ori, immediately adjacent or in close proximity to it. It contains one open reading frame encoding the replication protein, which is preceded by a 22 bp sequence tandemly repeated three and a half times. The plasmid replication origin is often named. del Solar G, Alonso JC, Espinosa M, Diaz-Orejas R. Broad-host-range plasmid replication: an open question. RNAIII is transcribed in the opposite orientation relative to its target DNA (5 end of rep) from promoter pIII, whereas pI and pII control CopR and Rep expression, respectively, in the sense orientation. The site is secure. These dual mechanisms may represent an advantage during the establishment phase, particularly for mobilizable plasmids such as class D plasmids. The same reaction is used to re-form a circular plasmid after conjugational transfer. 1997 Dec;61(4):442-55. doi: 10.1128/mmbr.61.4.442-455.1997. Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC. Both mechanisms of autoregulation could be working together for initiators that are limiting (81). Lee EH, Kornberg A. Replication deficiencies in priA mutants of Escherichia coli lacking the primosomal replication n' protein. Plasmid copy number regulation needs mechanisms to monitor plasmid copy number through a sensor and mechanisms to modulate replication initiation in response to feedback through an effector (55). Molecular Characterization of the Minimal Replicon and the A second problem with linear plasmids and chromosomes has to do with replicating the lagging-strand template. Replication starts at the ori site that is the origin of replication where the Rep protein attaches one of the strands. Plasmid replication initiation requires specific proteins encoded by the plasmid and its host. Bookshelf By 2D agarose gel electrophoresis of replication intermediates, it was shown that pWVO2 replicates via a theta mechanism. Plasmids are autonomously replicating pieces of DNA. In any case, ori acts as an enhancer, favoring the long-range activation of and oris by transfer of . The hairpin ends are previously not recognized as DNA double-strand breaks. Class B theta plasmids include ColE1 and ColE1-like plasmids, which are frequently used for recombinant gene expression. Lagging-strand replication by Pol III appears to end a few hundred nucleotides upstream of the terH site (33), leaving a gap that is filled by Pol I (16). Extension of this RNA primer by Pol I initiates leading-strand synthesis. Once the circle is complete, the 5 phosphate is transferred from the tyrosine on the Rep protein to the 3 hydroxyl on the other end of the strand. government site. An additional plasmid-encoded protein (a helicase, RepA) helps melt the DNA, recruit Pol III and support continuous replication of one strand. It provides a novel plasmid system to conduct research on archaeal DNA replication. Bruand C, Ehrlich SD. The last section of the article reviews how plasmid copy number is sensed and how this feedback modulates the frequency of replication. We further provided evidence that this plasmid applied a new mode of theta-type replication mechanism: (1) the size of this plasmid was > 10-kb; (2) the minireplicon consisted of AT-rich (directed repeat, iteron) and DnaA sequences; (3) the minireplicon did not contain double-strand origin (DSO) and essential rep genes, and it also showed no sin. 2022 Oct 7;23(19):11910. doi: 10.3390/ijms231911910. An antisense/target RNA duplex or a strong intramolecular RNA structure 5' of a translation initiation signal blocks ribosome binding: the case of plasmid R1. It appears that the ori is an establishment origin, allowing replication initiation immediately following mobilization, when levels of protein are low, whereas and oris would be maintenance origins in cells inheriting the plasmid by vertical transmission (19). 0. This condition could be lethal to the cell and must quickly be repaired. Plasmid DNA replication and regulation. Detection and characterization of a theta-replicating plasmid pLP60 Nakasu S, Tomizawa J. In the theta and strand-displacement plasmid replication types, the replication is initiated by RNA priming, while in the rolling-circle replication, replication is initiated by the cleavage of plasmid DNA strands to generate a free 3-OH end. Unauthorized use of these marks is strictly prohibited. HHS Vulnerability Disclosure, Help In theta plasmids, lagging-strand synthesis is discontinuous and coordinated with leading-strand synthesis. (b) The R6K plasmid, which has three origins of replication, only one of which has multiple iterons: (with 7 iterons); a second origin () features a single iteron; and a third origin () only has half an iteron. In some class A theta plasmids, a different mechanism of regulation involves inhibiting Rep transcription by Rep itself. See this image and copyright information in PMC. Theta Model Of Replication - Definition, Mechanism Rep proteins are plasmid-encoded initiators of replication, although some theta plasmids rely exclusively on host initiation factors for replication. 2018 Dec 15;17:70-81. doi: 10.1016/j.csbj.2018.12.001. The plasmid replication may start at many locations, as observed in many eukaryotic systems (Santamaria et al., 2000). During this double . SSB is recruited to exposed areas of single-stranded DNA, stabilizing them. Then the Rep protein can make a nick in the sequence. The primer problem is solved by the different linear DNA in different ways. Replication starts at a cis site, designated ori, and proceeds by one of the two major DNA replication modes described for circular plasmids, rolling circle (RC) or theta (Thomas, 2000). the contents by NLM or the National Institutes of Health. Many encode only one of the proteins needed for initiation at the. In addition, plasmids are key facilitators for the evolution and dissemination of drug resistance and for the evolution of complex interactions with animal or plant hosts. doi: 10.1128/msystems.00191-22. Plasmid genomes can be circular or linear and can vary in size from as little as 1 kb in size to as large as hundreds of kilobases. Theta Plasmid Replication An official website of the United States government. Fukuoh A, Iwasaki H, Ishioka K, Shinagawa H. ATP-dependent resolution of R-loops at the ColE1 replication origin by Escherichia coli RecG protein, a Holliday junction-specific helicase. Melting occurs at an AT-rich region. IV) Synthesis continues in both directions, extending the area of D-loop formation. Mukhopadhyay G, Chattoraj DK. The last section of the chapter reviews how plasmid copy number is sensed and how this feedback modulates the frequency of replication. pAM1 is a plasmid isolated from Enterococcus faecalis which replicates in Bacillus subtilis by a unidirectional theta mechanism. Federal government websites often end in .gov or .mil. This chapter discusses theta plasmid replication, which is class of circular plasmid replication that includes ColE1-like origins of replication popular with expression vectors. 2022 Dec 12;22(1):298. doi: 10.1186/s12866-022-02718-4. pAM beta 1 minimal replicon shares no homology with highly conserved ColE1 . In ColE2 plasmids the ctRNA is also known as RNAI and has a complex secondary structure. Given that target pre-primer and ctRNA sequence are complementary, higher order structures for both RNAs are mirror images of each other. Accessibility Mechanism of Plasmid replication: theta and rolling circle DNA
Wako Weight Categories, Colorado Auction Horses, 752 Ocean Ave, Long Branch, Nj, 60 School Street, Boston, Articles T