A New Sugar for an Old Phage:a c-di-GMP-Dependent Polysaccharide Pathway Sensitizes Escherichia coli for Bacteriophage Infection

Bacteriophages are ubiquitous parasites of bacteria and major drivers of bacterial ecology and evolution. Despite an ever-growing interest in their biotechnological and therapeutic applications, detailed knowledge of the molecular mechanisms underlying phage-host interactions remains scarce. Here, we show that bacteriophage N4 exploits a novel surface glycan (NGR) as a receptor to infect its host Escherichia coli. We demonstrate that this process is regulated by the second messenger c-di-GMP and that N4 infection is specifically stimulated by the diguanylate cyclase DgcJ, while the phosphodiesterase PdeL effectively protects E. coli from N4-mediated killing. PdeL-mediated protection requires its catalytic activity to reduce c-di-GMP and includes a secondary role as a transcriptional repressor. We demonstrate that PdeL binds to and represses the promoter of the wec operon, which encodes components of the enterobacterial common antigen (ECA) exopolysaccharide pathway. However, only the acetylglucosamine epimerase WecB but none of the other ECA components is required for N4 infection. Based on this, we postulate that NGR is an N-acetylmannosamine-based carbohydrate polymer that is produced and exported to the cell surface of E. coli in a c-di-GMP-dependent manner, where it serves as a receptor for N4. This novel carbohydrate pathway is conserved in E. coli and other bacterial pathogens, serves as the primary receptor for various bacteriophages, and is induced at elevated temperature and by specific amino acid-based nutrients. These studies provide an entry point into understanding how bacteria use specific regulatory mechanisms to balance costs and benefits of highly conserved surface structures

The importance of human dimensions research in managing harmful algal blooms

Author Posting. © Ecological Society of America, 2010. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Frontiers in Ecology and the Environment 8 (2010): 75–83, doi:10.1890/070181.Harmful algal blooms (HABs) are natural freshwater and marine hazards that impose substantial adverse impacts on the human use of coastal and marine resources. The socioeconomic and health impacts of HABs can be considerable, thereby making a case for “human dimensions” research to support HAB response. Human dimensions research is multidisciplinary, integrating social science, humanities, and other fields with natural science to enhance resource management by addressing human causes, consequences, and responses to coastal environmental problems. Case studies reported here illustrate the importance of human dimensions research. Incorporating such research into the scientific agenda – as well as into management decisions of public agencies concerned with natural resource management, environmental protection, and public health and welfare – requires the development of both strategic guidance and institutional capacity. The recent development of a multi-agency research strategy for HAB response and a strategic plan for human dimensions research represent two important steps in this direction.This paper was developed with partial support from NOAA’s National Centers for Coastal and Ocean Science

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Bimodality and local signaling in the c-di-GMP network of E. coli

Biofilms protect bacteria from environmental threats, such as predators, antibiotics, or attacks by host immune systems. The second messenger c-di-GMP is a key regulator of bacterial behavior and biofilm formation, orchestrating the transition from a solitary and motile to a sessile community lifestyle. The cellular concentration of c-di-GMP is regulated by diguanylate cyclases (DGCs) that produce and phosphodiesterases (PDEs) that degrade c-di-GMP in response to intra- and extracellular stimuli. Many bacteria have evolved multiple DGCs and PDEs to broaden their sensing capabilities and to respond to a large variety of signals. However, it remains poorly understood how multiple signaling pathways converge into specific and robust cellular readouts and how the hypersensitive c-di-GMP network absorbs noise emerging from stochastic expression or activation of DGCs and PDEs. Here, I use Escherichia coli as a model to study how gradual changes and fluctuation of c-di-GMP are converted into deterministic cellular responses. In the first chapter of my thesis, I describe a novel molecular mechanism through which bacteria convert gradual changes of c-di-GMP into binary signaling outcomes. Together with my collaborators, I present genetic, biochemical, and structural evidence to demonstrate that the E. coli PDE PdeL operates as a hypersensitive switch to quench noise and to install robust bimodal c-di-GMP regimes. We show that PdeL is both a c-di-GMP degrading catalyst and a transcription factor that stimulates its own expression. In addition, PdeL is a c-di-GMP sensor as both transcriptional and enzymatic activities are high at low c-di-GMP but curbed at high intracellular c-di-GMP concentrations. PdeL adopts an inert dimer conformation at high c-di-GMP levels but switches into a highly active tetramer conformation when c-di-GMP is lowered. We show that with its highly cooperative behavior, PdeL converts populations experiencing gradual changes of c-di-GMP into bimodal populations where individual cells exhibit either high or low c-di-GMP. Based on the observation that pdeL expression is strongly hysteretic, we propose that this switch provides E. coli with a short-term memory which entails robustness to costly lifestyle transitions. Finally, I observed that PdeL effectively protects E. coli against specific bacteriophage predators, indicating that this simple molecular switch also serves as a bet-hedging device to minimize risks associated with biofilm formation. In the second chapter of my thesis, I describe a novel regulatory pathway responsible for the synthesis and secretion of an as yet unknown extracellular glycan polymer in E. coli. Starting from the observation that bacteriophage N4 can only infect E. coli if PdeL is in its off state and c-di-GMP levels high, this part investigates how c-di-GMP contributes to phage entry. I could demonstrate that N4 infection requires two DGCs, DgcQ and DgcJ, which sense arginine and an as yet unidentified component of complex media, respectively. Genetic data suggest that DgcJ and DgcQ expedite N4 infection by stimulating the synthesis of a novel surface-associated glycan polymer, which is used by N4 as a primary surface receptor. Genetic data combined with homology modeling identified NfrB and NfrA as inner and outer membrane components of the N4-specific polysaccharide secretion system. NfrB not only shows strong homologies to glycosyltransferases but also harbors a C-terminal MshE-like c-di-GMP binding domain. Based on this, and based on the observation that the UDP-N-acetylglucosamine 2-epimerase WecB is also essential for N4 infection, we propose that c-di-GMP activates NfrB to polymerize a glycan polymer containing N-acetylmannosamine (ManNAc), which is then secreted through the NfrA outer membrane porin to the cell surface where it serves as the primary receptor for bacteriophage N4. Preliminary data indicate that DgcJ specifically activates the NfrBA pathway by acting as a «local pacemaker» while DgcQ acts globally and stimulates this pathway by functionally interacting with DgcJ activity. Overall, this work uncovers novel mechanistic principles, which bacteria use to convert changes of a small diffusible signaling molecules into deterministic, precise, and irreversible cellular responses. The finding that bacteria can use spatially localized signaling domains to stimulate specific cellular processes and that they are able to convert graded into binary frequency-based responses greatly expands our knowledge on the extensive signaling repertoire that bacteria have evolved to maximize their fitness in constantly changing environments. While the nature and the function of the novel glycan are yet to be understood, it is evident that E. coli has evolved the regulatory interface allowing for precise utilization of the glycan to mitigate the risk of phage invasion and other adverse effects

Forschung und Entwicklung in Krisenzeiten

Im Zuge von Wirtschaftskrisen nehmen finanzielle Beschränkungen für Unternehmen häufig zu. Diese Liquiditätsengpässe dämpfen auch F&E-Investitionen, die gerade in ökonomisch schwierigen Zeiten, aufgrund der geringeren Opportunitätskosten, verstärkt unternommen werden sollten. Daher empfehlen sich stärker antizyklisch ausgerichtete wirtschaftspolitische Maßnahmen im Bereich der Liquidität und der direkten Forschungsförderung. Dadurch bleiben bei liquiditätsbeschränkten Unternehmen F&E-Kapazitäten erhalten und bei liquiden Unternehmen wird die Wirksamkeit der F&E-Förderungen erhöht

Wettbewerbsfähigkeit und Digitalisierung

Die Digitalisierung der Gesellschaft und Wirtschaft stellt neben dem Klimawandel, der Globalisierung und dem demographischen Wandel einen der treibenden Trends unserer Zeit dar. Der digitale Wandel wird stark durch den technologischen Fortschritt und die Adaptions- bzw. Absorptionsfähigkeit der Gesellschaft vorangetrieben. Mit der Digitalisierung einhergehend werden massive Transformationsprozesse innerhalb des Arbeitsmarkts, Bildungssystems, der Produktionsprozesse der Unternehmen und bei den Präferenzen der Konsumenten erwartet. Globalisierte und wettbewerbsorientierte Märkte tragen dazu bei die Innovation und den Diffusionsprozess der neuen Technologien und deren Anwendungen zu verstärken

Werden die Folgen der Robotisierung überschätzt?

Mit neuen Technologien gehen häufig überzogene Ängste und Hoffnungen einher. So findet eine viel zitierte Studie, dass die Robotisierung ähnliche Produktivitätseffekte zur Folge hat wie die Einführung der Dampfmaschine. Im Gegensatz dazu zeigt unser Beitrag, dass die disruptive Kraft der Roboter wohl deutlich geringer ist als bisher angenommen

Robots at Work? Pitfalls of Industry Level Data

In a seminal paper Graetz and Michaels (2018) find that robots increase labor productivity and TFP, lower output prices and adversely affect the employment share of low-skilled labor. We show that these effects hold only, when comparing hardly-robotizing with highly-robotizing sectors and collapse, when only the latter are analyzed. Controlling for demographic workforce variables reestablishes the productivity effects, but still rejects positive wage effects and skill-biased technological change. Additionally, we find no effects, when the investigation period is extended to the most recent data (2008-2015) and document non-monotonicity in one of the instruments, which calls the respective results into question