Yeast functional genomic screens lead to identification of a role for a bacterial effector in innate immunity regulation

Numerous bacterial pathogens manipulate host cell processes to promote infection and ultimately cause disease through the action of proteins that they directly inject into host cells. Identification of the targets and molecular mechanisms of action used by these bacterial effector proteins is critical to understanding pathogenesis. We have developed a systems biological approach using the yeast Saccharomyces cerevisiae that can expedite the identification of cellular processes targeted by bacterial effector proteins. We systematically screened the viable yeast haploid deletion strain collection for mutants hypersensitive to expression of the Shigella type III effector OspF. Statistical data mining of the results identified several cellular processes, including cell wall biogenesis, which when impaired by a deletion caused yeast to be hypersensitive to OspF expression. Microarray experiments revealed that OspF expression resulted in reversed regulation of genes regulated by the yeast cell wall integrity pathway. The yeast cell wall integrity pathway is a highly conserved mitogen-activated protein kinase (MAPK) signaling pathway, normally activated in response to cell wall perturbations. Together these results led us to hypothesize and subsequently demonstrate that OspF inhibited both yeast and mammalian MAPK signaling cascades. Furthermore, inhibition of MAPK signaling by OspF is associated with attenuation of the host innate immune response to Shigella infection in a mouse model. These studies demonstrate how yeast systems biology can facilitate functional characterization of pathogenic bacterial effector proteins.     

A critical role of tropomyosins in TGF-beta regulation of the actin cytoskeleton and cell motility in epithelial cells

We have investigated transforming growth factor beta (TGF-beta)-mediated induction of actin stress fibers in normal and metastatic epithelial cells. We found that stress fiber formation requires de novo protein synthesis, p38Mapk and Smad signaling. We show that TGF-beta via Smad and p38Mapk up-regulates expression of actin-binding proteins including high-molecular-weight tropomyosins, alpha-actinin and calponin h2. We demonstrate that, among these proteins, tropomyosins are both necessary and sufficient for TGF-beta induction of stress fibers. Silencing of tropomyosins with short interfering RNAs (siRNAs) blocks stress fiber assembly, whereas ectopic expression of tropomyosins results in stress fibers. Ectopic-expression and siRNA experiments show that Smads mediate induction of tropomyosins and stress fibers. Interestingly, TGF-beta induction of stress fibers was not accompanied by changes in the levels of cofilin phosphorylation. TGF-beta induction of tropomyosins and stress fibers are significantly inhibited by Ras-ERK signaling in metastatic breast cancer cells. Inhibition of the Ras-ERK pathway restores TGF-beta induction of tropomyosins and stress fibers and thereby reduces cell motility. These results suggest that induction of tropomyosins and stress fibers play an essential role in TGF-beta control of cell motility, and the loss of this TGF-beta response is a critical step in the acquisition of metastatic phenotype by tumor cells.     

The role of hypersalinity in the persistence of the Texas 'brown tide' in the Laguna Madre

A brown tide bloom of the alga Aureoumbra lagunensis was presentwithout interruption in the Laguna Madre of Texas from January1990 through October 1997. This is the longest continual phytoplanktonbloom of which we are aware. Although the factors leading tothe initiation of this bloom have been well documented, thefactors contributing to its persistence are still being investigated.Two physical characteristics of the Laguna Madre may play animportant role: the long turnover time for waters in this coastallagoon (–1 year) and the hypersaline conditions that usuallyexist (40–60 PSU) due to evaporation exceeding precipitation.In this study, we examined the effects of salinity on the growthrates of the brown tide alga and on the growth of one of itsprotozoan grazers. Historical data from before the onset ofthe brown tide provide evidence for the suppression of microzooplanktonpopulations and mesozooplankton growth caused by hypersalinity.The brown tide alga will grow in a remarkably wide range ofsalinities ranging from 10 to 90 PSU. Maximum growth rates areachieved at salinities ranging from 20 to 60 PSU. One commongrazer on the brown tide alga, the heterotrophic dinoftagellateOxyrrhis marina, was found to grow more slowly under hypersalineconditions. The normally hypersaline conditions of the LagunaMadre may, therefore, favor the brown tide alga over other phytoplanktonspecies that do not grow well under hypersaline conditions,and also suppress the growth and feeding rates of potentialgrazers.     

Effects of Karenia brevis diet on RNA:DNA ratios and egg production of Acartia tonsa

Karenia brevis is a harmful alga associated with deleterious effects on zooplankton, but the exact cause (e.g. toxin, nutritional inadequacy or starvation) of these adverse effects is not clear. RNA:DNA ratios, fecundity and fecal pellet production of Acartia tonsa were measured on mono-algal and mixed-algal culture diets of K. brevis and Peridinium foliaceum to examine the usefulness of RNA:DNA ratios as an indicator of nutrition and to determine if adverse effects of K. brevis are due to the presence of toxins, poor nutritional quality or starvation. RNA:DNA ratios and egg production values were significantly higher for 100% P. foliaceum diet compared to 100% K. brevis diet. Significant differences in egg production, but not RNA:DNA ratios, were found between the various mixed diets, suggesting egg production is a more sensitive indicator of nutritional quality than RNA:DNA ratios. Changes in RNA:DNA ratios, fecundity and fecal pellet production of copepods fed two different toxic K. brevis strains were nearly identical, indicating that the presence of brevetoxins has little affect on A. tonsa. The similarity in RNA:DNA ratios, egg production, percent hatching and fecal production between the 100% K. brevis diet and starved copepods suggests that A. tonsa does not consume K. brevis when offered as its sole food source.     

FIRST HARMFUL DINOPHYSIS (DINOPHYCEAE,DINOPHYSIALES) BLOOM IN THE U.S. IS REVEALED BY AUTOMATED IMAGING FLOW CYTOMETRY1

Imaging FlowCytobot (IFCB) combines video and flow cytometric technology to capture images of nano‐ and microplankton (～10 to >100 μm) and to measure the chlorophyll fluorescence associated with each image. The images are of sufficient resolution to identify many organisms to genus or even species level. IFCB has provided >200 million images since its installation at the entrance to the Mission‐Aransas estuary (Port Aransas, TX, USA) in September 2007. In early February 2008, Dinophysis cells (1–5 · mL^?1) were detected by manual inspection of images; by late February, abundance estimates exceeded 200 cells · mL^?1. Manual microscopy of water samples from the site confirmed that D. cf. ovum F. Schütt was the dominant species, with cell concentrations similar to those calculated from IFCB data, and toxin analyses showed that okadaic acid was present, which led to closing of shellfish harvesting. Analysis of the time series using automated image classification (extraction of image features and supervised machine learning algorithms) revealed a dynamic phytoplankton community composition. Before the Dinophysis bloom, Myrionecta rubra (a prey item of Dinophysis) was observed, and another potentially toxic dinoflagellate, Prorocentrum, was observed after the bloom. Dinophysis cell‐division rates, as estimated from the frequency of dividing cells, were the highest at the beginning of the bloom. Considered on a daily basis, cell concentration increased roughly exponentially up to the bloom peak, but closer inspection revealed that the increases generally occurred when the direction of water flow was into the estuary, suggesting the source of the bloom was offshore.     

GEF-H1 Mediated Control of NOD1 Dependent NF-κB Activation by Shigella Effectors

Shigella flexneri has evolved the ability to modify host cell function with intracellular active effectors to overcome the intestinal barrier. The detection of these microbial effectors and the initiation of innate immune responses are critical for rapid mucosal defense activation. The guanine nucleotide exchange factor H1 (GEF-H1) mediates RhoA activation required for cell invasion by the enteroinvasive pathogen Shigella flexneri. Surprisingly, GEF-H1 is requisite for NF-κB activation in response to Shigella infection. GEF-H1 interacts with NOD1 and is required for RIP2 dependent NF-κB activation by H-Ala-D-γGlu-DAP (γTriDAP). GEF-H1 is essential for NF-κB activation by the Shigella effectors IpgB2 and OspB, which were found to signal in a NOD1 and RhoA Kinase (ROCK) dependent manner. Our results demonstrate that GEF-H1 is a critical component of cellular defenses forming an intracellular sensing system with NOD1 for the detection of microbial effectors during cell invasion by pathogens.     

Identification and characterization of ZapC, a stabilizer of the FtsZ ring in Escherichia coli

In Escherichia coli, spatiotemporal control of cell division occurs at the level of the assembly/disassembly process of the essential cytoskeletal protein FtsZ. A number of regulators interact with FtsZ and modulate the dynamics of the assembled FtsZ ring at the midcell division site. In this article, we report the identification of an FtsZ stabilizer, ZapC (Z-associated protein C), in a protein localization screen conducted with E. coli. ZapC colocalizes with FtsZ at midcell and interacts directly with FtsZ, as determined by a protein-protein interaction assay in yeast. Cells lacking or overexpressing ZapC are slightly elongated and have aberrant FtsZ ring morphologies indicative of a role for ZapC in FtsZ regulation. We also demonstrate the ability of purified ZapC to promote lateral bundling of FtsZ in a sedimentation reaction visualized by transmission electron microscopy. While ZapC lacks sequence similarity with other nonessential FtsZ regulators, ZapA and ZapB, all three Zap proteins appear to play an important role in FtsZ regulation during rapid growth. Taken together, our results suggest a key role for lateral bundling of the midcell FtsZ polymers in maintaining FtsZ ring stability during division.     

Use of the FlowCAM for semi-automated recognition and enumeration of red tide cells (Karenia brevis) in natural plankton samples

Early detection is the most effective way to mitigate the effects of harmful algal blooms (HAB). Cell counts based on examination of microplankton samples using settling chambers and visual inspection with an inverted microscope are tedious and time consuming, and counting precision is generally poor at low cell densities. The FlowCAM is a continuous imaging flow cytometer designed to characterize particles in the microplankton size range (20–200 μm diameter). In this study we examined the ability of the FlowCAM to improve routine monitoring protocols for HAB species by automatically recording information on size and fluorescence per cell. This will eliminate the need to examine cells outside the ranges of these measurements for our target species, Karenia brevis. We also tested the ability of image comparison software to match images of cells in mixed assemblages to images of the target species. For simple mixtures of cultured dinoflagellates, the ability of the image matching software to discriminate target cells varied greatly depending on how similar the two species were in size and shape. When target cells were added to natural plankton samples, the image recognition software correctly identified 80–90% of the target cells, but misidentified 20–50% of non-target cells in the size range of the target species. We conclude that the FlowCAM is less tedious and time-consuming than microscopy, allowing for examination of more cells for greater counting precision. The cell recognition software helps reduce the numbers of cells that must be screened, but images must still be examined by a trained operator to identify the HAB species of interest.     

The Chlamydia effector chlamydial outer protein N (CopN) sequesters tubulin and prevents microtubule assembly

Chlamydia species are obligate intracellular pathogens that utilize a type three secretion system to manipulate host cell processes. Genetic manipulations are currently not possible in Chlamydia, necessitating study of effector proteins in heterologous expression systems and severely complicating efforts to relate molecular strategies used by Chlamydia to the biochemical activities of effector proteins. CopN is a chlamydial type three secretion effector that is essential for virulence. Heterologous expression of CopN in cells results in loss of microtubule spindles and metaphase plate formation and causes mitotic arrest. CopN is a multidomain protein with similarity to type three secretion system "plug" proteins from other organisms but has functionally diverged such that it also functions as an effector protein. We show that CopN binds directly to αβ-tubulin but not to microtubules (MTs). Furthermore, CopN inhibits tubulin polymerization by sequestering free αβ-tubulin, similar to one of the mechanisms utilized by stathmin. Although CopN and stathmin share no detectable sequence identity, both influence MT formation by sequestration of αβ-tubulin. CopN displaces stathmin from preformed stathmin-tubulin complexes, indicating that the proteins bind overlapping sites on tubulin. CopN is the first bacterial effector shown to disrupt MT formation directly. This recognition affords a mechanistic understanding of a strategy Chlamydia species use to manipulate the host cell cycle.