Nutritional Control of Elongation of DNA Replication by (p)ppGpp

Wang, Jue D.; Sanders, Glenn M.; Grossman, Alan D.

doi:10.1016/j.cell.2006.12.043

Cited by 267 publications

(286 citation statements)

References 46 publications

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“…The position of the forks is determined by the regions of the graph where the gene dosage rises higher than one (log 2 ϭ 0). The positions of the forks were approximately symmetric from oriC; both forks replicated up to Ϸ0.5 Mbp from oriC, as observed previously (22).…”

Section: Transcription Does Not Detectably Affect Replication Elongatsupporting

confidence: 66%

“…3 A-C). There was typically a higher dosage of genes just to the right of oriC compared with the left, indicating that one replication fork was slightly ahead (10-50 kb) of the other (22). This difference was more obvious in cells grown in fumarate, where the frequency of initiation and synchrony are reduced relative to that in cells grown in glucose (compare Figs.…”

Section: Discussionmentioning

confidence: 84%

“…Microarrays contained PCR products from Ͼ99% of the annotated B. subtilis ORFs (22,23,28). Cells were collected and mixed with an equal volume of ice-cold methanol.…”

Section: Methodsmentioning

confidence: 99%

“…We monitored DNA content and replication fork progression in synchronously replicating B. subtilis cells by using microarrays to measure the relative amount of DNA for almost all ORFs (22)(23)(24). We synchronized replication in a population of cells by using a mutant (dnaB134) that was temperaturesensitive for the initiation of replication, essentially as described (25,26).…”

Section: Transcription Does Not Detectably Affect Replication Elongatmentioning

confidence: 99%

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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.

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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: Transcription Does Not Detectably Affect Replication Elongatsupporting

confidence: 66%

Section: Discussionmentioning

confidence: 84%

“…Microarrays contained PCR products from Ͼ99% of the annotated B. subtilis ORFs (22,23,28). Cells were collected and mixed with an equal volume of ice-cold methanol.…”

Section: Methodsmentioning

confidence: 99%

Section: Transcription Does Not Detectably Affect Replication Elongatmentioning

confidence: 99%

See 2 more Smart Citations

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.

Self Cite

104

119

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“…The (p)ppGpp alarmone exerts its regulatory role chiefly via direct binding to the bacterial RNA polymerase (3), provoking changes in the profile of transcribed messages. (p)ppGpp also regulates bacterial replication via binding to DNA primase (4) and inhibits translation initiation via binding to initiation factor IF2, a translational GTPase (5,6). Evidently, the stringent response is a core cellular adaptation pathway, acting as a hub in the regulatory network, where it integrates information about the nutritional status of the bacterial cell and regulates cellular metabolism on the transcription, translation, and replication levels.…”

mentioning

confidence: 99%

Single-molecule investigations of the stringent response machinery in living bacterial cells

English

Hauryliuk

Sanamrad

et al. 2011

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

262

294

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The RelA-mediated stringent response is at the heart of bacterial adaptation to starvation and stress, playing a major role in the bacterial cell cycle and virulence. RelA integrates several environmental cues and synthesizes the alarmone ppGpp, which globally reprograms transcription, translation, and replication. We have developed and implemented novel single-molecule tracking methodology to characterize the intracellular catalytic cycle of RelA. Our single-molecule experiments show that RelA is on the ribosome under nonstarved conditions and that the individual enzyme molecule stays off the ribosome for an extended period of time after activation. This suggests that the catalytically active part of the RelA cycle is performed off, rather than on, the ribosome, and that rebinding to the ribosome is not necessary to trigger each ppGpp synthesis event. Furthermore, we find fast activation of RelA in response to heat stress followed by RelA rapidly being reset to its inactive state, which makes the system sensitive to new environmental cues and hints at an underlying excitable response mechanism. cytosolic diffusion | single particle tracking | photoactivated localization microscopy | stroboscopic illumination

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Clues to transcription/replication collision‐induced DNA damage: it was RNAP, in the chromosome, with the fork

Cooke,

Herman,

Sivaramakrishnan

2024

FEBS Letters

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DNA replication and RNA transcription processes compete for the same DNA template and, thus, frequently collide. These transcription–replication collisions are thought to lead to genomic instability, which places a selective pressure on organisms to avoid them. Here, we review the predisposing causes, molecular mechanisms, and downstream consequences of transcription–replication collisions (TRCs) with a strong emphasis on prokaryotic model systems, before contrasting prokaryotic findings with cases in eukaryotic systems. Current research points to genomic structure as the primary determinant of steady‐state TRC levels and RNA polymerase regulation as the primary inducer of excess TRCs. We review the proposed mechanisms of TRC‐induced DNA damage, attempting to clarify their mechanistic requirements. Finally, we discuss what drives genomes to select against TRCs.

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Nutritional Control of Elongation of DNA Replication by (p)ppGpp

Cited by 267 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

Single-molecule investigations of the stringent response machinery in living bacterial cells

Clues to transcription/replication collision‐induced DNA damage: it was RNAP, in the chromosome, with the fork

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