Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models

RESEARCH ARTICLE Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models Kartik Subramanian1, Mark R. Paul2, John J. Tyson3,4* a11111 1 Graduate Program in Genetics, Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America, 2 Department of Mechanical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America, 3 Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America, 4 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America * Abstract OPEN ACCESS Citation: Subramanian K, Paul MR, Tyson JJ (2015) Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models. PLoS Comput Biol 11(7): e1004348. doi:10.1371/journal.pcbi.1004348 Editor: Jörg Stelling, ETH Zurich, SWITZERLAND Received: September 12, 2014 Accepted: May 20, 2015 Published: July 17, 2015 Copyright: © 2015 Subramanian et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Computer code for the model is available at https://github.com/subkar/PleC_ DivL_Spatial Funding: This work was funded by National Science Foundation (Division of Mathematical Sciences1225160). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Cell-fate asymmetry in the predivisional cell of Caulobacter crescentus requires that the regulatory protein DivL localizes to the new pole of the cell where it up-regulates CckA kinase, resulting in a gradient of CtrA~P across the cell. In the preceding stage of the cell cycle (the “stalked” cell), DivL is localized uniformly along the cell membrane and maintained in an inactive form by DivK~P. It is unclear how DivL overcomes inhibition by DivK~P in the predivisional cell simply by changing its location to the new pole. It has been suggested that co-localization of DivL with PleC phosphatase at the new pole is essential to DivL’s activity there. However, there are contrasting views on whether the bifunctional enzyme, PleC, acts as a kinase or phosphatase at the new pole. To explore these ambiguities, we formulated a mathematical model of the spatiotemporal distributions of DivL, PleC and associated proteins (DivJ, DivK, CckA, and CtrA) during the asymmetric division cycle of a Caulobacter cell. By varying localization profiles of DivL and PleC in our model, we show how the physiologically observed spatial distributions of these proteins are essential for the transition from a stalked cell to a predivisional cell. Our simulations suggest that PleC is a kinase in predivisional cells, and that, by sequestering DivK~P, the kinase form of PleC enables DivL to be reactivated at the new pole. Hence, co-localization of PleC kinase and DivL is essential to establishing cellular asymmetry. Our simulations reproduce the experimentally observed spatial distribution and phosphorylation status of CtrA in wild-type and mutant cells. Based on the model, we explore novel combinations of mutant alleles, making predictions that can be tested experimentally. Competing Interests: The authors have declared that no competing interests exist. PLOS Computational Biology | DOI:10.1371/journal.pcbi.1004348 July 17, 2015 1 / 27 DivL and PleC in the division cycle of Caulobacter Author Summary The aquatic bacterium, Caulobacter crescentus, divides asymmetrically into a non-motile “stalked” cell that stays at its place of birth, and a motile “swarmer” cell that disperses to a different locale. Prior to cell division, the cell passes through a “predivisional” stage, when it has a stalk at its “old” end and a flagellum at its “new” end. These spatiotemporal changes in morphology are driven, in part, by changes in subcellular localization of signaling proteins. To understand how the cell exploits protein localization to generate distinct cell fates, we formulated a mathematical model of the spatiotemporal dynamics of six regulatory proteins (DivJ, DivK, PleC, DivL, CckA and CtrA) during the Caulobacter cell cycle. Contrary to some suggestions, our model predicts that PleC functions as a kinase during the predivisional stage of the cell cycle. Further, we show that spatial separation of DivL and PleC kinase in the stalked stage is required for inactivation of DivL and for initiation of DNA synthesis. Later, co-localization of DivL and PleC kinase at the new pole of the cell restores DivL activity in the swarmer-half of the cell, resulting in the establishment of replicative asymmetry in the predivisional stage of the cell cycle. Introduction The asymmetric localization of proteins is critical for cell and/or tissue development in eukaryotic systems as diverse as S. cerevisiae [1], C. elegans [2], A. thaliana [3], and D. melanogaster [4]. For years, spatial organization of cellular components was thought to be an exclusive feature of eukaryotes, but advances in microscopy and protein labeling over the past two decades have dispelled this notion [5]. The localization of cellular components—including lipids, DNA, RNA and proteins–is also an integral feature of prokaryotic cells; observed to play a role in the growth, function and survival of many bacteria, including E. coli [6], B. subtilis [7,8], V. cholerae [9], S. flexnerii [10,11]. However, with roughly 10% of its proteins having the potential to localize [12], Caulobacter crescentus serves as the model bacterium to study subcellular localization of proteins in prokaryotes. In Caulobacter, the non-uniform distribution of proteins is visibly manifested in the asymmetric division cycle that gives rise to two morphologically and functionally distinct daughter cells [13–15]. Furthermore, subcellular localization of macromolecules influences many physiological attributes of Caulobacter cells, such as growth [16,17], cell shape [18,19], morphogenesis [20], differentiation [21,22], stringent response [23,24], and cell division [25]. Caulobacter shares many regulatory genes with other species of alpha-proteobacteria, including species that are of importance to agriculture and medicine, such as the nitrogen-fixing Sinorhizobium meliloti, the plant pathogen Agrobacterium tumefaciens, and the mammalian pathogens Rickettsia prowazekii and Brucella abortus [26,27]. While mounting evidences show causal links between protein localization and cell function in these bacteria [20,28–34], the underlying molecular mechanisms that enabl (...truncated)