The replication-related organization of bacterial genomes

Rocha, Eduardo P. C.

doi:10.1099/mic.0.26974-0

Cited by 245 publications

(315 citation statements)

References 181 publications

Supporting

Mentioning

293

Contrasting

Unclassified

Order By: Relevance

“…However, it is possible that head-on collisions between SpoIIIE and RNA polymerase might affect the rate of chromosome transport. Interestingly, the majority (∼75%) of the genes in the B. subtilis genome are transcribed toward the terminus and this unusually high bias is found in all endospore formers (Rocha 2004). It has been proposed that this coorientation with replisome movement has been selected to avoid collisions between RNA and DNA polymerases (Brewer 1988;French 1992).…”

Section: Discussionmentioning

confidence: 99%

SpoIIIE strips proteins off the DNA during chromosome translocation

Marquis¹,

Nollmann²,

Ptacin³

et al. 2008

Genes Dev.

View full text Add to dashboard Cite

The FtsK/SpoIIIE family of DNA transporters are responsible for translocating missegregated chromosomes after the completion of cell division. An extreme example of this post-cytokinetic DNA segregation occurs during spore formation in the bacterium Bacillus subtilis, where SpoIIIE pumps three-quarters of the chromosome (>3 megabases) into one of the two daughter cells. Here, we investigate the fate of the proteins associated with the translocated DNA. Taking advantage of several unique features of Bacillus sporulation, we demonstrate that RNA polymerase, transcription factors, and chromosome remodeling proteins are stripped off the DNA during translocation of the chromosome into the forespore compartment. Furthermore, we show that in vitro the soluble ATPase domain of SpoIIIE can displace RNA polymerase bound to DNA, suggesting that SpoIIIE alone is capable of this wire-stripping activity. Our data suggest that the bulk of the forespore chromosome is translocated naked into the forespore compartment. We propose that the translocation-stripping activity of SpoIIIE plays a key role in reprogramming developmental gene expression in the forespore.[Keywords: Chromosome segregation; chromosome translocation; sporulation; FtsK; AAA+ ATPase] Supplemental material is available at http://www.genesdev.org.

show abstract

Section: Discussionmentioning

confidence: 99%

SpoIIIE strips proteins off the DNA during chromosome translocation

Marquis¹,

Nollmann²,

Ptacin³

et al. 2008

Genes Dev.

View full text Add to dashboard Cite

show abstract

“…However, tumor cells often have a variable haplotype and actively replicating bacteria can contain up to 8 Â more copies of certain loci than nonreplicating cells. 11 Another major problem with using this strategy is that RNA extraction procedures are usually not designed to purify DNA, so the extraction rate may vary between different samples, with DNA yields often being low.…”

Section: Normalisation; Rna Quantificationmentioning

confidence: 99%

Real-time RT-PCR normalisation; strategies and considerations

et al. 2005

View full text Add to dashboard Cite

Real-time RT-PCR has become a common technique, no longer limited to specialist core facilities. It is in many cases the only method for measuring mRNA levels of vivo low copy number targets of interest for which alternative assays either do not exist or lack the required sensitivity. Benefits of this procedure over conventional methods for measuring RNA include its sensitivity, large dynamic range, the potential for high throughout as well as accurate quantification. To achieve this, however, appropriate normalisation strategies are required to control for experimental error introduced during the multistage process required to extract and process the RNA. There are many strategies that can be chosen; these include normalisation to sample size, total RNA and the popular practice of measuring an internal reference or housekeeping gene. However, these methods are frequently applied without appropriate validation. In this review we discuss the relative merits of different normalisation strategies and suggest a method of validation that will enable the measurement of biologically meaningful results.

show abstract

“…After two more IWe on BEST7155, all further IWe attempts involving the resultant 980 kb proved unsuccessful (data not shown). Although the reason(s) for this failure was not obvious, it suggests that the symmetry of the B. subtilis genome architecture may be involved (24)(25)(26). All B. subtilis 168 derivatives (24,27) and related species (28) have circular genomes that manifest excellent symmetry with respect to the two distances between the origin of DNA replication (oriC) and its termination (terC).…”

Section: Three Megacloning Procedures For the Rest Of The Synechocystismentioning

confidence: 99%

Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome

Itaya

Tsuge²,

Koizumi³

et al. 2005

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

172

165

View full text Add to dashboard Cite

Cloning the whole 3.5-megabase (Mb) genome of the photosynthetic bacterium Synechocystis PCC6803 into the 4.2-Mb genome of the mesophilic bacterium Bacillus subtilis 168 resulted in a 7.7-Mb composite genome. We succeeded in such unprecedented largesize cloning by progressively assembling and editing contiguous DNA regions that cover the entire Synechocystis genome. The strain containing the two sets of genome grew only in the B. subtilis culture medium where all of the cloning procedures were carried out. The high structural stability of the cloned Synechocystis genome was closely associated with the symmetry of the bacterial genome structure of the DNA replication origin (oriC) and its termination (terC) and the exclusivity of Synechocystis ribosomal RNA operon genes (rrnA and rrnB). Given the significant diversity in genome structure observed upon horizontal DNA transfer in nature, our stable laboratory-generated composite genome raised fundamental questions concerning two complete genomes in one cell. Our megasize DNA cloning method, designated megacloning, may be generally applicable to other genomes or genome loci of free-living organisms.bacterial genomes ͉ DNA assembly ͉ genome symmetry

show abstract

The replication-related organization of bacterial genomes

Cited by 245 publications

References 181 publications

SpoIIIE strips proteins off the DNA during chromosome translocation

SpoIIIE strips proteins off the DNA during chromosome translocation

Real-time RT-PCR normalisation; strategies and considerations

Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome

Contact Info

Product

Resources

About