R01ES019625/ES/NIEHS NIH HHS/United States. 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). Patel PH, Suzuki M, Adman E, Shinkai A, Loeb LA. 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). Plasmids: Biology and Impact in Biotechnology and Discovery. eCollection 2019. Since the structure resembles the Greek letter theta (), its name has been derived from it. There are two methods for the replication of plasmids. Since DNA polymerases cannot initiate the synthesis of a new strand of the DNA, this has been the primer problem. The endpoints, which correspond to plasmid origin and terC, were mapped with single-nucleotide precision. Competitive hybridization between tRNA and RNAI or RNAII appears to interfere with RNAI/RNAII hybrid formation (66). The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). 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. The best known medium to large plasmids are circular and use a form of replication called "theta replication" because of the formation of characteristic replication intermediates whose structure resembles the Greek letter . In a linear DNA, there is no upstream primer on this strand from which to grow. Microbial Genetics Finally, maintaining a stable plasmid copy number is critical for the host, as loss of the plasmid entails losing the adaptive functions carried in plasmid sequence, and runaway plasmid replication is lethal. Class C and D theta plasmid replication is based on the evolution of more efficient ways to prime replication initiation. Conformation of the origin of P1 plasmid replication. Theta replication of the lactococcal plasmid pWVO2 - DeepDyve Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. del Solar G, Alonso JC, Espinosa M, Diaz-Orejas R. Broad-host-range plasmid replication: an open question. PriA promotes both the unwinding of the lagging-strand arm and assembly of two additional proteins (PriB, and DnaT) to load DnaB onto the lagging strand template. Theta replication of the lactococcal plasmid pWVO2 - PubMed 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). The replicase extends a free 3-OH of an RNA primer, which can be generated by DnaG primase (in Gram bacteria), by the concerted action of DnaE and DnaG primase (in Gram + bacteria), or by alternative plasmid-encoded primases. Maki H, Bryan SK, Horiuchi T, Moses RE. In these plasmids, iterons are located in the promoter of the Rep operon, outside the plasmid ori. Both mechanisms of autoregulation could be working together for initiators that are limiting (81). The nature of another replication mechanism utilized by HPV18 involves most likely recombination-dependent replication. Rep proteins are plasmid-encoded initiators of replication, although some theta plasmids rely exclusively on host initiation factors for replication. Class C replication is unidirectional, as the 3 end of the lagging-strand DNA fragment was mapped to a specific site at the end of the ori region. Wagner EG, Altuvia S, Romby P. Antisense RNAs in bacteria and their genetic elements. The site is secure. 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. Under a steady-state condition, the plasmids replicate by theta mode of replication, thus duplicating the plasmid number during the S phase. Rakowski SA, Filutowicz M. Plasmid R6K replication control. This is shown as areas where one of the strands has no hydrogen bonding. Bookshelf 1 Panels III and IV). When these two sites are exposed in single-stranded configuration, base-pair complementarity favors the formation of two hairpins, one for each strand, (Fig. Bruand C, Ehrlich SD. In pIP501 plasmids, RNAIII hybridization to its complementary sequence induces folding of RNA into a transcriptional terminator structure that prevents transcription of repR. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted Class D plasmids have a cop-ctRNA-rep modular structure. The copy number of pLP60 was measured as 5 copies per cell by qPCR. Zzaman S, Bastia D. Oligomeric initiator protein-mediated DNA looping negatively regulates plasmid replication in vitro by preventing origin melting. In this case, PriA (initiator of primosome assembly) can be recruited to the forked structure of the D-loop; alternatively, PriA can be recruited to a hairpin structure that forms when the double-stranded DNA opens (6). A fourth class of theta-replicating plasmids: the pAM beta 1 family Brantl S. Antisense-RNA mediated control of plasmid replication - pIP501 revisited. . These dimeric circles are then resolved into individual linear plasmid DNAs with closed hairpins at the ends. Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host. Mutational analysis of the specific priming signal essential for DNA replication of the broad host-range plasmid RSF1010. 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. The complete sequence of plasmid pLP60 was obtained by plasmid DNA libraries and iPCR. Frontiers | Genomics of microbial plasmids: classification and The pMBL6842 origin shares a high similarity of organization with the P1 origin and contains multiple iterons. Several ctRNAs (ColE1 and ColE2 RNAI, and R1 copA) have a short half-life due to the presence of an RNase E cleavage site, which consists of the U-rich sequence and a hairpin structure at the 3 end. Unidirectional theta replication of the structurally stable Next, the 5 end of RNAI (antitail) nucleates the hybridization between the two RNAs to form a duplex. A second replication arrest site can be found 230 nt downstream from the plasmid ori; in this case arrest is caused by collision with a site-specific resolvase, Resb, which is a plasmid-borne gene responsible for plasmid segregation stability (47). doi: 10.1128/microbiolspec.PLAS-0035-2014. 2023 Feb 16;14:1112307. doi: 10.3389/fmicb.2023.1112307. Example: Plasmids, phage DNA, chromosomes. sharing sensitive information, make sure youre on a federal 2015 Feb;3(1):PLAS-0029-2014. Plasmid 2022 May 31;10(6):1132. doi: 10.3390/microorganisms10061132. This is solved, in circular plasmids, by two main strategies: (i) opening of the strands followed by RNA priming (theta and strand displacement replication) or (ii) cleavage of one of the DNA strands to generate a 3'-OH end (rolling-circle replication). The pWVO2 minimal replicon is strongly related to that of several other lactococcal plasmid replicons. Allen JM, Simcha DM, Ericson NG, Alexander DL, Marquette JT, Van Biber BP, Troll CJ, Karchin R, Bielas JH, Loeb LA, et al. Processing of plasmid DNA with ColE1-like replication origin. In ColE1, the ctRNA (RNAI) is transcribed from P1, a promoter located 108 bp downstream from the sense promoter P2. DNA repair and genome maintenance in Bacillus subtilis. Plasmids are autonomously replicating pieces of DNA. Yavachev L, Ivanov I. Filutowicz M, Dellis S, Levchenko I, Urh M, Wu F, York D. Regulation of replication of an iteron-containing DNA molecule. They have the 5 and 3 ends joined to each other. It then creates the structure where the whole replicational machinery assembles. Discontinuous lagging-strand synthesis involves repeated priming and elongation of Okazaki fragments and is comparable in plasmids and chromosome, although Okazaki fragments were found to be smaller in a ColE1-like plasmid, approximately 1/3 the length of Okazaki fragments in the chromosome (13). 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 Mar 22;9(1):92. doi: 10.1038/s41597-022-01179-8. There are clear differences between different modalities of theta plasmid replication in mechanisms of DNA duplex melting and in priming of leading- and lagging-strand synthesis. 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. The last section of the chapter reviews how plasmid copy number is sensed and how this feedback modulates the frequency of replication. Detection and characterization of a theta-replicating plasmid pLP60 This chapter discusses theta plasmid replication, which is class of circular plasmid replication that includes ColE1-like origins of replication popular with expression vectors. . (33). Characterization of a theta-replicating plasmid from III) The base of the hairpin is recognized by RepB, which initiates the synthesis of an RNA primer (light grey dashed line). 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. Then the Rep protein can make a nick in the sequence. Front Microbiol. Wickner S, Skowyra D, Hoskins J, McKenney K. DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step. In the known cases, a specialised protein (the initiator) binds to its recognition site(s) adjacent to an AT-rich region within a replication origin. By contrast, RK2's TrfA was shown to mediate open complex formation and DnaB helicase loading in the absence of dnaA boxes, although the presence of DnaA protein was still required (22). Our discussion will focus on replication initiation, which informs different biological properties of plasmids (size, host range, plasmid copy number, etc.) In some cases, monomerization can be assisted by chaperones or by the allosteric effect of binding iterons at the ori (74-77). Gowrishankar J, Harinarayanan R. Why is transcription coupled to translation in bacteria? Theta structures are produced during the replication of circular DNA molecules (prokaryote DNA). Sandler SJ, Marians KJ. Accordingly, titration of R loop-suppressing factors through uncoupling transcription from translation (by starvation, temperature shift or chloramphenicol treatment) results in increased ColE1 plasmid copy number (36) whereas RecG overexpression dramatically suppresses replication initiation (37). Vertical lines show hybridization between DNA strands. This work was partially supported by a National Cancer Institute Award [K08CA116429], by a National Institute of Environmental Health Sciences grant [R01ES019625] award, and by a NSF Advances in Biological Informatics Innovation Grant [ABI1262435]. In addition to being short-lived, ColE1 RNA I has a short window of action, because as soon as RNAII is transcribed past position 200 downstream of the RNA/DNA switch, hybridization of the domain with another sequence domain () forms a new loop (SL4), which makes RNAII refractory to RNA I inhibition. Kogoma T. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Gasset-Rosa F, Diaz-Lopez T, Lurz R, Prieto A, Fernandez-Tresguerres ME, Giraldo R. Negative regulation of pPS10 plasmid replication: origin pairing by zipping-up DNA-bound RepA monomers. Cross-talk between ctRNA and tRNAs may also explain the conservation of the 5-UUGGCG-3 sequence at the loop region of many of the antisense RNAs and their targets involved in regulation of replication, suggesting this sequence is under common and strong selective pressure (70). Unable to load your collection due to an error, Unable to load your delegates due to an error. 1998 Jun;62(2):434-64. doi: 10.1128/MMBR.62.2.434-464.1998. Keywords: . This type of plasmid is found in the largest groups of bacteria, as well as in archaea. In ColE1 and ColE1-like plasmids, Pol I can extend a primer to initiate leading-strand synthesis and open the DNA duplex; this process can expose a hairpin structure in the lagging-strand, known as single strand initiation (ssi) site or primosome assembly (pas) site, and/or generate a D-loop. As replication progresses, facilitated by the RepA helicase, a theta-type intermediate forms (Fig. For the separation of the strand, it may use a host helicase. Transcription-driven DNA replication of plasmid pAM1 in DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. PMC eCollection 2023. Single-molecule studies of fork dynamics in Escherichia coli DNA replication. While the plasmid replicates, the FRT closer to the Ori replicates early, and the one farther replicates late. With this mechanism, a special enzyme called a terminal protein attaches to the 5 ends of the plasmid DNA. 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. Control of primer formation for ColE1 plasmid replication: conformational change of the primer transcript. Janniere L, Bidnenko V, McGovern S, Ehrlich SD, Petit MA. K08 CA116429/CA/NCI NIH HHS/United States, R01 ES019625/ES/NIEHS NIH HHS/United States. Frontiers | Analysis of the Replication Mechanisms of the Human Plasmids that replicate using the strand-displacement mode of replication include E. coli incompatibility group Q (IncQ) plasmids of-proteobacteria such as RSF1010. The pWVO2 minimal replicon is strongly related to that of several other lactococcal plasmid replicons. Rep binding to these cognate sequences inhibits Rep expression, and thus acts as an autoregulatory mechanism. In the case of ColE1 and ColE2, these pRNAI cleavage intermediates are polyadenylated by PAPI, facilitating exonucleotidic digestion by PNPase (60,61). This mechanism only operates on nascent (<260 nt-long) RNAs, as longer rep transcripts form an alternative secondary structure that is refractory to repR-induced transcriptional attenuation (72). 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). This binding denatures an AT-rich sequence immediately downstream of the binding site to form an open complex (44). Accessibility To our knowledge, this is the first unidirectional theta replication plasmid experimentally identified in the domain of archaea. Many encode only one of the proteins needed for initiation at the. Mechanism of Theta Plasmid Replication: DNA unwinds at the ori site from where the replication begins. In addition to opening of the double strand, RepE appears to have an active role in primer processing, as melting increases RepE binding and RepE can cleave transcripts from the repE operon in close proximity to the RNA/DNA switch (45). A completely different mechanism is also used to maintain linear plasmids in some systems. Would you like email updates of new search results? A model for regulation of ColE1-like plasmid replication by uncharged tRNAs in amino acid-starved Escherichia coli cells. government site. At the 3 end, there is the presence of OH group while at the 5 end there is the presence of phosphate group. Bookshelf Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. In this method, one strand comes out while the other strand is being synthesized. PolC is a processive polymerase responsible for leading-strand synthesis, while DnaE extends DnaG-synthesized primers before handoff to PolC at the lagging strand (11,12). 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. Rep binding of two alternative binding sites (Rep promoter and plasmid ori) involves changes in conformation and oligomerization status of the Rep protein. Some linear plasmids have hairpin ends. 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). RNase III has also been reported to degrade ColE1 RNA I upstream of RNAse E (63). CopB expression is under the control of P1 but not P2. Extension of the free 3-OH of the primer by Pol III (assisted by the RepA helicase) is shown as dashed, black arrows. Before Such specificity is not possible when multiple primers are needed, as in the case of lagging-strand synthesis in the chromosome. 1997 Dec;61(4):442-55. doi: 10.1128/mmbr.61.4.442-455.1997. Also, the evolution of specialized priming mechanisms broadens the host range of these plasmids by reducing dependence on host factors (38).