@article {32028, title = {Using stochastic cell division and death to probe minimal units of cellular replication}, journal = {New Journal of Physics}, volume = {20}, year = {2018}, month = {03/2018}, abstract = {

The invariant cell initiation mass measured in bacterial growth experiments has been interpreted as a minimal unit of cellular replication. Here we argue that the existence of such minimal units induces a coupling between the rates of stochastic cell division and death. To probe this coupling we tracked live and dead cells in Escherichia coli populations treated with a ribosome-targeting antibiotic. We find that the growth exponent from macroscopic cell growth or decay measurements can be represented as the difference of microscopic first-order cell division and death rates. The boundary between cell growth and decay, at which the number of live cells remains constant over time, occurs at the minimal inhibitory concentration (MIC) of the antibiotic. This state appears macroscopically static but is microscopically dynamic: division and death rates exactly cancel at MIC but each is remarkably high, reaching 60\% of the antibiotic-free division rate. A stochastic model of cells as collections of minimal replicating units we term {\textquoteright}widgets{\textquoteright} reproduces both steady-state and transient features of our experiments. Sub-cellular fluctuations of widget numbers stochastically drive each new daughter cell to one of two alternate fates, division or death. First-order division or death rates emerge as eigenvalues of a stationary Markov process, and can be expressed in terms of the widget{\textquoteright}s molecular properties. High division and death rates at MIC arise due to low mean and high relative fluctuations of widget number. Isolating cells at the threshold of irreversible death might allow molecular characterization of this minimal replication unit.

}, doi = {10.1088/1367-2630/aab197}, author = {Chib, Savita and Das, Suman and Venkatesan, S and Seshasayee, Aswin S N and Thattai, Mukund} } @article {3566, title = {Genome scale patterns of supercoiling in a bacterial chromosome.}, journal = {Nat Commun}, volume = {7}, year = {2016}, month = {2016}, pages = {11055}, abstract = {

DNA in bacterial cells primarily exists in a negatively supercoiled state. The extent of supercoiling differs between regions of the chromosome, changes in response to external conditions and regulates gene expression. Here we report the use of trimethylpsoralen intercalation to map the extent of supercoiling across the Escherichia coli chromosome during exponential and stationary growth phases. We find that stationary phase E. coli cells display a gradient of negative supercoiling, with the terminus being more negatively supercoiled than the origin of replication, and that such a gradient is absent in exponentially growing cells. This stationary phase pattern is correlated with the binding of the nucleoid-associated protein HU, and we show that it is lost in an HU deletion strain. We suggest that HU establishes higher supercoiling near the terminus of the chromosome during stationary phase, whereas during exponential growth DNA gyrase and/or transcription equalizes supercoiling across the chromosome.

}, issn = {2041-1723}, doi = {10.1038/ncomms11055}, author = {Lal, Avantika and Dhar, Amlanjyoti and Trostel, Andrei and Kouzine, Fedor and Seshasayee, Aswin S N and Adhya, Sankar} } @article {1006, title = {Restriction modification systems as engines of diversity.}, journal = {Front Microbiol}, volume = {6}, year = {2015}, month = {2015}, pages = {528}, abstract = {

Restriction modification (RM) systems provide protection against a broad spectrum of phages. However, the likelihood of a phage permanently bypassing this can be as high as 0.1 per infection (Korona et al., 1993) which makes for a relatively weak defense. Here we argue that, apart from providing such transient defenses, RM systems can facilitate long-term coexistence of many bacterial strains. We show that this diversity can be as large as the burst size of the phage but no larger-a curious correspondence between a number at the level of species and another number at the level of individuals. Such a highly diverse and stably coexisting ecosystem is robust to substantial variation in both bacterial growth rates and strength of their RM systems, which might be one reason why quite weak RM systems exist in the wild.

}, issn = {1664-302X}, doi = {10.3389/fmicb.2015.00528}, author = {Sneppen, Kim and Semsey, Szabolcs and Seshasayee, Aswin S N and Krishna, Sandeep} }