Suppression of initiation defects of chromosome replication in Bacillus subtilis dnaA and oriC-deleted mutants by integration of a plasmid replicon into the chromosomes

Hassan, Anwarul K. M.; Moriya, Shigeki; Ogura, Mitsuo; Tanaka, Toshiaki; Kawamura, Fujio; Ogasawara, Nagahisa

doi:10.1128/jb.179.8.2494-2502.1997

Cited by 58 publications

(82 citation statements)

References 46 publications

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“…We used strains (27) that have oriC inactivated and that initiate replication from the dnaAindependent heterologous origin oriN (29,30). In asynchronous growth, the amount of replication initiation from oriN at 359° ( Fig.…”

Section: Inhibition Of Replication Elongation In the Head-onmentioning

confidence: 99%

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

Wang

Berkmen

Grossman

2007

Proc. Natl. Acad. Sci. U.S.A.

104

119

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In many bacteria, there is a strong bias for genes to be encoded on the leading strand of DNA, resulting in coorientation of replication and transcription. In Bacillus subtilis, transcription of the majority of genes (75%) is cooriented with replication. By using genomewide profiling of replication with DNA microarrays, we found that this coorientation bias reduces adverse effects of transcription on replication. We found that in wild-type cells, transcription did not appear to affect the rate of replication elongation. However, in mutants with reversed transcription bias for an extended region of the chromosome, replication elongation was slower. This reduced replication rate depended on transcription and was limited to the region in which the directions of replication and transcription are opposed. These results support the hypothesis that the strong bias to coorient transcription and replication is due to selective pressure for processive, efficient, and accurate replication.DNA microarrays ͉ elongation of replication ͉ genomic organization ͉ genomic stability ͉ origin of replication M any aspects of the organization of bacterial genomes are conserved and important for cell survival. DNA rearrangements, including large chromosomal inversions, can lead to inviability, decreased fitness, and impaired development (1-4). It has been proposed that genomic organization affects replication, transcription, and segregation of genomes (5).One benefit of proper genomic organization may be the reduction of potential conflicts between replication and transcription (5-7). The same DNA template is used by RNA polymerase (RNAP) for transcription and by the replisome (DNA polymerase and associated proteins) for replication. Transcription complexes that are stalled, initiating, or terminating can slow or block replication (8, 9). RNAP and the replisome can collide when moving toward each other (head-on), or when the replisome, which moves faster than RNAP, catches up with RNAP moving in the same direction (codirectional). Head-on and codirectional collisions can occur when genes are on the lagging and leading strands, respectively.The consequences of head-on and codirectional collisions are different. In Escherichia coli, high levels of transcription can effectively slow or block progression of replication forks if transcription and replication are head-on, but not if they are codirectional (10). In French's landmark study, an inducible plasmid-derived origin of replication was positioned on either side of an rRNA operon, one of the most highly transcribed operons. Replication fork progression, monitored by EM, was much slower when running against, rather than with, the direction of transcription. Plasmid DNA replication in E. coli can also be hindered by head-on transcription from a strong inducible promoter, probably because of collisions between the replisome and RNAP (ref.

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Section: Inhibition Of Replication Elongation In the Head-onmentioning

confidence: 99%

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

Wang

Berkmen

Grossman

2007

Proc. Natl. Acad. Sci. U.S.A.

104

119

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“…The factors required for pBS72 initiation of replication are two plasmid elements, the origin and the RepA protein, and four host-encoded replication factors, namely DnaD, DnaB, DnaI and DnaC. It is, however, surprisingly independent of the initiator proteins DnaA and PriA (so far, only orib from R6K, R1, pLS32, pAMb1 and RSF1010 have been shown to be DnaA-independent; Bernander et al, 1991;Espinosa et al, 2000;Hassan et al, 1997;Kelley & Bastia, 1992;Scherzinger et al, 1991;Tang et al, 1989). This suggests that the recruitment of the DnaD-driven cascade to the RepA/ origin complex might differ from that occurring at the DnaA/oriC and PriA/DNA complexes.…”

Section: Discussionmentioning

confidence: 99%

“…CN values presented in Table 1 were calculated from three independent measurements. Control experiments showed that the integrated plasmid replicon (pLS32) that directs chromosomal replication in the DdnaA strain (Hassan et al, 1997) does not affect pBS72 derivative CN values (not shown). CN measurement in the DpriA strain was carried out in LB with fresh transformants isolated in a poor medium.…”

Section: Methodsmentioning

confidence: 99%

“…B. subtilis strains used were: 168 (trpC2) (Costa Anagnostopoulos); L1430 (ilvA metC lys-21), L1432 (dnaB19 metC ilvA), L1433 (dnaC14 metC lys-21), L1434 (dnaD23 metC lys-21), L1435 (dnaE20 metC ilvA), L1437 (dnaG5 metC lys-21) and L1439 (dnaI2 metC ilvA) (Mauel & Karamata, 1984); 1A74 (dnaX8132 hisA1 thr-5), 1A224 (hisH2 pheA1 trpC2) and 1A226 (polA5 hisH2 pheA1 trpC2) (Bacillus Genetic Stock Center); EDJ51 (168 dnaE2.10 ins-phl), EDJ58 (168 dnaE2.6 ins-phl), HVS609 (168 spac-I : : polC emr containing pMAP65) and HVS614 (168 spac-I : : dnaE emr containing pMAP65) (Dervyn et al, 2001); PB1669 (168 dnaF69) (Attolini et al, 1976); CRK6000 (purA16 metB5 hisA3 guaB) and NIS6200 (CRK6000 proA : : pBPA21 : : cat) (Hassan et al, 1997); NIS6311 [CRK6000 spoIIIJ : : pBPA21 : : cat dnaA(ochre)] (Shigeki Moriya, University of Technology, Sydney, Australia); HVS606 (168 pcrA3 ins of pMAP55 in pBR322-Cm R inserted at the metD locus) (Petit et al, 1998); PPBJ120 (168 priA1 : : pAPJ11 : : erm) and PPBJ65 (168 priA : : pAPJ12 : : erm, PriA + ) (Polard et al, 2002). Hosts for plasmid constructions were regular E. coli strains.…”

Section: Methodsmentioning

confidence: 99%

“…These factors are hence not required for pBS72 replication. As the DnaA and PriA null strains filament (Hassan et al, 1997;Polard et al, 2002;our observations), the CN increase observed in these contexts might result from dilution of negative factors in enlarged cells allowing plasmid amplification. However, in the DnaA context, it cannot be ruled out that the CN increase results from alleviation of a negative effect of DnaA on plasmid replication, because DnaA might bind to dnaA boxes of the plasmid origin or to host-encoded factors limiting for plasmid replication.…”

Section: Host-encoded Replication Functionsmentioning

confidence: 99%

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The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72

et al. 2006

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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 helicase PcrA and DNA polymerase I are dispensable. From this, it is inferred that pBS72 replication is of the theta type and is initiated by an original mechanism. Indirect evidence suggests that during this process the DnaC helicase might be delivered to the plasmid origin by the weakly active DnaD pathway stimulated by a predicted interaction between DnaC and a domain of RepA homologous to the major DnaC-binding domain of the cellular initiator DnaA. The plasmid pBS72 replication fork appears to require the same functions as the bacterial chromosome and the unrelated plasmid pAMb1. Most importantly, this replication machinery contains the two type C polymerases, PolC and DnaE. As the mechanism of initiation of the three genomes is substantially different, this suggests that both type C polymerases might be required in any Cairns replication in B. subtilis and presumably in other bacteria encoding PolC and DnaE. INTRODUCTIONDNA replication is a ubiquitous biological process carried out by proteins that have evolved profoundly since the last common ancestor. For key elements like initiators, helicases, primases, catalytic DNA polymerases and processivity factors, their evolution has been so extensive that they are postulated to originate from peptides that diverged beyond recognition or from different proteins (Edgell & Doolittle, 1997;Giraldo, 2003;Leipe et al., 1999). Surprisingly, this diversity, obvious when comparing Eubacteria to Archaea and Eukarya, is also manifest among bacterial species. For instance, in the well characterized eubacteria Escherichia coli and Bacillus subtilis, the primosomes required for initiating replication at origins or collapsed replication forks have been shown to greatly differ in their constitution and mechanism of helicase loading (Bruand et al., 1995;Cox et al., 2000;Davey & O'Donnell, 2003;Lemon et al., 2002;Marsin et al., 2001;Polard et al., 2002; Velten et al., 2003). Differences have also been documented in the DNA polymerase III (Pol III) holoenzyme, a subassembly of the replication machinery where DNA synthesis is catalysed. In E. coli this element contains 10 different subunits of which four (h, c, x and y) are missing in B. subtilis (Bruck & O'Donnell, 2000;Bruck et al., 2002;Lemon et al., 2002; MartinezJimenez et al., 2002;McHenry, 2003).Based on systems for which a Pol III holoenzyme has been isolated and/or reconstructed in vitro, it is generally thought that both DNA strands...

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Integrative Suppression

Ogasawara¹

2002

Encyclopedia of Molecular Biology

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Suppression of initiation defects of chromosome replication in Bacillus subtilis dnaA and oriC-deleted mutants by integration of a plasmid replicon into the chromosomes

Cited by 58 publications

References 46 publications

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72

Integrative Suppression

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