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author:("Wang, indan")
1.  Spatio-Temporal Organization of Replication in Bacteria and Eukaryotes (Nucleoids and Nuclei) 
Here we discuss the spatio-temporal organization of replication in eubacteria and eukaryotes. Although there are significant differences in how replication is organized in cells that contain nuclei from those that do not, you will see that organization of replication in all organisms is principally dictated by the structured arrangement of the chromosome. We will begin with how replication is organized in eubacteria with particular emphasis on three well studied model organisms. We will then discuss spatial and temporal organization of replication in eukaryotes highlighting the similarities and differences between these two domains of life.
Compared to bacteria, eukaryotes face three challenges when replicating their genomes: the replication of many chromosomes, the compaction of DNA into higher-order chromatin, and the preservation of epigenetic information.
PMCID: PMC3405862  PMID: 22855726
2.  Organization and segregation of bacterial chromosomes 
Nature reviews. Genetics  2013;14(3):10.1038/nrg3375.
The bacterial chromosome must be compacted over 1000-fold to fit into its cellular compartment. How it is condensed, organized and ultimately segregated has been a puzzle for over half a century. Recent advances in live-cell imaging and genome-scale analyses have led to new insights into these problems. We argue that the key feature of compaction is orderly folding of DNA along adjacent segments, and that this organization provides easy and efficient access for protein-DNA transactions and plays a central role in driving segregation. Similar principles and common proteins are used in eukaryotes to condense and resolve sister chromatids at metaphase.
PMCID: PMC3869393  PMID: 23400100
3.  Bypass of a protein roadblock by a replicative DNA helicase 
Nature  2012;492(7428):205-209.
Replicative DNA helicases generally unwind DNA as a single hexamer that encircles and translocates along one strand of the duplex while excluding the complementary strand (“steric exclusion”). In contrast, large T antigen (T-ag), the replicative DNA helicase of the Simian Virus 40 (SV40), is reported to function as a pair of stacked hexamers that pumps double-stranded DNA through its central channel while laterally extruding single-stranded DNA. Here, we use single-molecule and ensemble assays to show that T-ag assembled on the SV40 origin unwinds DNA efficiently as a single hexamer that translocates on single-stranded DNA in the 3′ to 5′ direction. Unexpectedly, T-ag unwinds DNA past a DNA-protein crosslink on the translocation strand, suggesting that the T-ag ring can open to bypass bulky adducts. Together, our data underscore the profound conservation among replicative helicase mechanisms while revealing a new level of plasticity in their interactions with DNA damage.
PMCID: PMC3521859  PMID: 23201686
4.  Independent Segregation of the Two Arms of the Escherichia coli ori Region Requires neither RNA Synthesis nor MreB Dynamics ▿ § ‡  
Journal of Bacteriology  2010;192(23):6143-6153.
The mechanism of Escherichia coli chromosome segregation remains elusive. We present results on the simultaneous tracking of segregation of multiple loci in the ori region of the chromosome in cells growing under conditions in which a single round of replication is initiated and completed in the same generation. Loci segregated as expected for progressive replication-segregation from oriC, with markers placed symmetrically on either side of oriC segregating to opposite cell halves at the same time, showing that sister locus cohesion in the origin region is local rather than extensive. We were unable to observe any influence on segregation of the proposed centromeric site, migS, or indeed any other potential cis-acting element on either replication arm (replichore) in the AB1157 genetic background. Site-specific inhibition of replication close to oriC on one replichore did not prevent segregation of loci on the other replichore. Inhibition of RNA synthesis and inhibition of the dynamic polymerization of the actin homolog MreB did not affect ori and bulk chromosome segregation.
PMCID: PMC2981198  PMID: 20889756
5.  Replication-directed sister chromosome alignment in Escherichia coli 
Molecular Microbiology  2009;75(5):1090-1097.
Non-replicating Escherichia coli chromosomes are organized as sausage-shaped structures with the left (L) and the right (R) chromosome arms (replichores) on opposite cell halves and the replication origin (oriC) close to midcell. The replication termination region (ter) therefore passes between the two outer edges of the nucleoid. Four alignment patterns of the two sister chromosomes within a cell have been detected in an asynchronous population, with the pattern predominating. We test the hypothesis that the minority and patterns arise because of pausing of DNA replication on the right and left replichores respectively. The data resulting from transient pausing or longer-term site-specific blocking of replication show that paused/blocked loci remain close to midcell and the normally replicated-segregated loci locate to the outer regions of the nucleoid, therefore providing experimental support for a direct mechanistic link between DNA replication and chromosome organization.
PMCID: PMC2859247  PMID: 20487299

Results 1-5 (5)