
@article {27276,
	title = {Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic rac Prophage of Escherichia coli K-12.},
	journal = {mSphere},
	volume = {2},
	year = {2017},
	month = {2017 Nov-Dec},
	abstract = {<p>Horizontal gene transfer is a major driving force behind the genomic diversity seen in prokaryotes. The cryptic rac prophage in Escherichia\&nbsp;coli K-12 carries the gene for a putative transcription factor RacR, whose deletion is lethal. We have shown that the essentiality of racR in E.\&nbsp;coli K-12 is attributed to its role in transcriptionally repressing toxin gene(s) called ydaS and ydaT, which are adjacent to and coded divergently to racR. IMPORTANCE Transcription factors in the bacterium E.\&nbsp;coli are rarely essential, and when they are essential, they are largely toxin-antitoxin systems. While studying transcription factors encoded in horizontally acquired regions in E.\&nbsp;coli, we realized that the protein RacR, a putative transcription factor encoded by a gene on the rac prophage, is an essential protein. Here, using genetics, biochemistry, and bioinformatics, we show that its essentiality derives from its role as a transcriptional repressor of the ydaS and ydaT genes, whose products are toxic to the cell. Unlike type II toxin-antitoxin systems in which transcriptional regulation involves complexes of the toxin and antitoxin, repression by RacR is sufficient to keep ydaS transcriptionally silent.</p>
},
	issn = {2379-5042},
	doi = {10.1128/mSphere.00392-17},
	author = {Krishnamurthi, Revathy and Ghosh, Swagatha and Khedkar, Supriya and Seshasayee, Aswin Sai Narain}
}
@article {5304,
	title = {Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology?},
	journal = {G3 (Bethesda)},
	volume = {6},
	year = {2016},
	month = {2016},
	pages = {1597-606},
	abstract = {<p>Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across \~{}250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences.</p>
},
	issn = {2160-1836},
	doi = {10.1534/g3.116.028274},
	author = {Khedkar, Supriya and Seshasayee, Aswin Sai Narain}
}
