SignificanceThe Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science program is an inclusive Research Education Community with centralized programmatic and scientific support, in which broad student engagement in authentic science is linked to increased accessibility to research experiences for students; increased persistence of these students in science, technology, engineering, and mathematics; and increased scientific productivity for students and faculty alike.

A challenge for chromosome segregation in all domains of life is the formation of catenated progeny chromosomes, which arise during replication as a consequence of the interwound strands of the DNA double helix. Topoisomerases play a key role in DNA unlinking both during and at the completion of replication. Here we report that chromosome unlinking can instead be accomplished by multiple rounds of site-specific recombination. We show that stepwise, site-specific recombination by XerCD-dif or Cre-loxP can unlink bacterial chromosomes in vivo, in reactions that require KOPS-guided DNA translocation by FtsK. Furthermore, we show that overexpression of a cytoplasmic FtsK derivative is sufficient to allow chromosome unlinking by XerCD-dif recombination when either subunit of TopoIV is inactivated. We conclude that FtsK acts in vivo to simplify chromosomal topology as Xer recombination interconverts monomeric and dimeric chromosomes.

The bacterial septum-located DNA translocase FtsK coordinates circular chromosome segregation with cell division. Rapid translocation of DNA by FtsK is directed by 8-base-pair DNA motifs (KOPS), so that newly replicated termini are brought together at the developing septum, thereby facilitating completion of chromosome segregation. Translocase functions reside in three domains, α, β and γ. FtsKαβ are necessary and sufficient for ATP hydrolysis-dependent DNA translocation, which is modulated by FtsKγ through its interaction with KOPS. By solving the FtsKγ structure by NMR, we show that γ is a winged-helix domain. NMR chemical shift mapping localizes the DNA-binding site on the γ domain. Mutated proteins with substitutions in the FtsKγ DNA-recognition helix are impaired in DNA binding and KOPS recognition, yet remain competent in DNA translocation and XerCD-dif site-specific recombination, which facilitates the late stages of chromosome segregation.The 4.6-million-base-pair (bp) circular Escherichia coli chromosome is replicated bidirectionally from a unique origin (oriC), with replication termination occurring in a broad ter region opposite oriC (reviewed in refs. 1,2). Therefore, replication divides the chromosome into two equal arms or replichores, which locate to separate halves of the E. coli cell and behave as units of chromosome segregation 3 . Each replichore is transcribed predominantly in the same direction as replication and contains distinctive asymmetric, base composition-skewed sequences on each strand. These have been implicated in recombination, genome stability and chromosome processing 1,2,4,5 . Separation and segregation of newly replicated sister chromosomes can be compromised by catenation and chromosome dimer formation. Site-specific recombination mediated by the XerCD recombinase occurs between newly replicated sister dif sites, located in ter, and acts in sister-chromosome segregation by converting any chromosome dimers to monomers and by © 2006 Nature Publishing Group Correspondence should be addressed to D.J.S. (sherratt@bioch.ox.ac.uk).. 4 These authors contributed equally to this work. AUTHOR CONTRIBUTIONS V.S., molecular biology and manuscript preparation. M.D.A., biochemistry, NMR and manuscript preparation. C.d.B., molecular biology. R.B., molecular biology. L.K.A., project direction and manuscript preparation. S.M.F., NMR. M.B., NMR. J.L., molecular biology, structural biology, project direction and manuscript preparation. D.J.S., project conception, project direction and manuscript preparation.Supplementary information is available on the Nature Structural & Molecular Biology website. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. Fig. 1a,b), containing helices H1, H2 and H3 and the C-terminal wing. We have not assigned or constrained secondary structure in the wing; in other WHD proteins, the wing usually has very few residues in true β-sheet conformation. WHDs are a subtype of helix-turn-helix DNA-binding proteins in ...

SummaryThe study of chromosome segregation in bacteria has gained strong insights from the use of cytology techniques. A global view of chromosome choreography during the cell cycle is emerging, highlighting as a next challenge the description of the molecular mechanisms and factors involved. Here, we review one of such factor, the FtsK DNA translocase. FtsK couples segregation of the chromosome terminus, the ter region, with cell division. It is a powerful and fast translocase that reads chromosome polarity to find the end, thereby sorting sister ter regions on either side of the division septum, and activating the last steps of segregation. Recent data have revealed the structure of the FtsK motor, how translocation is oriented by specific DNA motifs, termed KOPS, and suggests novel mechanisms for translocation and sensing chromosome polarity.

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.