Modeling the ecology of parasitic plasmids

Plasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the central role they play in antibiotic resistance and modern biotechnology, our understanding of plasmids’ natural ecology is limited. Recent experiments have shown that plasmids can spread even when they are a burden to the cell, suggesting that natural plasmids may exist as parasites. Here, we use mathematical modeling to explore the ecology of such parasitic plasmids. We first develop models of single plasmids and find that a plasmid’s population dynamics and optimal infection strategy are strongly determined by the plasmid’s HGT mechanism. We then analyze models of co-infecting plasmids and show that parasitic plasmids are prone to a “tragedy of the commons” in which runaway plasmid invasion severely reduces host fitness. We propose that this tragedy of the commons is averted by selection between competing populations and demonstrate this effect in a metapopulation model. We derive predicted distributions of unique plasmid types in genomes—comparison to the distribution of plasmids in a collection of 17,725 genomes supports a model of parasitic plasmids with positive plasmid–plasmid interactions that ameliorate plasmid fitness costs or promote the invasion of new plasmids.Subject terms: Theoretical ecology, Microbial ecology     

Type III secretion system in Chlamydia species: identified members and candidates

Chlamydia trachomatis and Chlamydia pneumoniae genomes contain genes coding for type III secretion apparatuses. Like other pathogens, Chlamydia probably uses this system to secrete proteins in the host cell. With the aim of identifying such proteins, we analyzed the organization of Chlamydia type III secretion genes.     

FisB relies on homo-oligomerization and lipid binding to catalyze membrane fission in bacteria

Little is known about mechanisms of membrane fission in bacteria despite their requirement for cytokinesis. The only known dedicated membrane fission machinery in bacteria, fission protein B (FisB), is expressed during sporulation in Bacillus subtilis and is required to release the developing spore into the mother cell cytoplasm. Here, we characterized the requirements for FisB-mediated membrane fission. FisB forms mobile clusters of approximately 12 molecules that give way to an immobile cluster at the engulfment pole containing approximately 40 proteins at the time of membrane fission. Analysis of FisB mutants revealed that binding to acidic lipids and homo-oligomerization are both critical for targeting FisB to the engulfment pole and membrane fission. Experiments using artificial membranes and filamentous cells suggest that FisB does not have an intrinsic ability to sense or induce membrane curvature but can bridge membranes. Finally, modeling suggests that homo-oligomerization and trans-interactions with membranes are sufficient to explain FisB accumulation at the membrane neck that connects the engulfment membrane to the rest of the mother cell membrane during late stages of engulfment. Together, our results show that FisB is a robust and unusual membrane fission protein that relies on homo-oligomerization, lipid binding, and the unique membrane topology generated during engulfment for localization and membrane scission, but surprisingly, not on lipid microdomains, negative-curvature lipids, or curvature sensing.

Little is known about how membrane fission occurs in bacteria; this study suggests that the membrane fission protein FisB exploits the unique cellular geometry encountered during sporulation to enable its localization to the fission site through a novel mechanism, where it catalyzes membrane scission.     

Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit

Gene expression is stochastic, and noise that arises from the stochastic nature of biochemical reactions propagates through active regulatory links. Thus, correlations in gene-expression noise can provide information about regulatory links. We present what to our knowledge is a new approach to measure and interpret such correlated fluctuations at the level of single microcolonies, which derive from single cells. We demonstrated this approach mathematically using stochastic modeling, and applied it to experimental time-lapse fluorescence microscopy data. Specifically, we investigated the relationships among LuxO, LuxR, and the small regulatory RNA qrr4 in the model quorum-sensing bacterium Vibrio harveyi. Our results show that LuxR positively regulates the qrr4 promoter. Under our conditions, we find that qrr regulation weakly depends on total LuxO levels and that LuxO autorepression is saturated. We also find evidence that the fluctuations in LuxO levels are dominated by intrinsic noise. We furthermore propose LuxO and LuxR interact at all autoinducer levels via an unknown mechanism. Of importance, our new method of evaluating correlations at the microcolony level is unaffected by partition noise at cell division. Moreover, the method is first-order accurate and requires less effort for data analysis than single-cell-based approaches. This new correlation approach can be applied to other systems to aid analysis of gene regulatory circuits.     

Testing Cheverud's conjecture for behavioral correlations and behavioral syndromes

Recent research regarding correlations among behaviors--under the labels of behavioral syndromes and animal personalities--has typically assumed that phenotypic correlations between behaviors are representative of underling genetic correlations. However, for behaviors, the concordance between phenotypic and genetic correlations has not been rigorously examined. I tested this assumption using published estimates and found phenotypic and genetic correlations to be strongly related but found that the average absolute difference between the two was quite high and similar to that observed in other traits. Using absolute differences as the sole criterion, phenotypic correlations do not reliably estimate the magnitude of genetic correlations for behaviors, which is problematic for behavioral syndrome researchers. However, phenotypic correlations explained 75% of the variation in genetic correlations and their sign was typically the same as that of genetic correlations. This suggests that phenotypic correlations between behaviors reliably estimate the direction of underling genetic relationships and provide considerable information regarding the magnitude of genetic correlations. Thus, if researchers are careful about the questions they ask, phenotypic correlations between behaviors can be informative regarding underling genetic correlations and their evolutionary implications.     

Imprecision of Adaptation in Escherichia coli Chemotaxis

Adaptability is an essential property of many sensory systems, enabling maintenance of a sensitive response over a range of background stimulus levels. In bacterial chemotaxis, adaptation to the preset level of pathway activity is achieved through an integral feedback mechanism based on activity-dependent methylation of chemoreceptors. It has been argued that this architecture ensures precise and robust adaptation regardless of the ambient ligand concentration, making perfect adaptation a celebrated property of the chemotaxis system. However, possible deviations from such ideal adaptive behavior and its consequences for chemotaxis have not been explored in detail. Here we show that the chemotaxis pathway in Escherichia coli shows increasingly imprecise adaptation to higher concentrations of attractants, with a clear correlation between the time of adaptation to a step-like stimulus and the extent of imprecision. Our analysis suggests that this imprecision results from a gradual saturation of receptor methylation sites at high levels of stimulation, which prevents full recovery of the pathway activity by violating the conditions required for precise adaptation. We further use computer simulations to show that limited imprecision of adaptation has little effect on the rate of chemotactic drift of a bacterial population in gradients, but hinders precise accumulation at the peak of the gradient. Finally, we show that for two major chemoeffectors, serine and cysteine, failure of adaptation at concentrations above 1 mM might prevent bacteria from accumulating at toxic concentrations of these amino acids.     

Measurement and verification of rates of sediment phosphorus release for a hypereutrophic urban lake

The contribution of sediment release to the phosphorus budget of hypereutrophic Onondaga Lake was determined through laboratory measurements made on intact cores. Rates ranged from 9–21 mg P m^–2 d^–1 with a mean of 13 mg P m^–2 d^–1, values similar to those observed in other lakes of comparable trophic state. There was no statistically significant trend in rates in time (July versus September) or in space (location along the major N/S axis of the lake). Rates of sediment phosphorus release measured in the laboratory compared favorably with the observed rate of soluble reactive phosphorus accumulation in the lake's hypolimnion. The sediments are the second largest source of phosphorus for Onondaga Lake, contributing 24% of the overall phosphorus load to the system.     

Spa32 regulates a switch in substrate specificity of the type III secreton of Shigella flexneri from needle components to Ipa proteins

Type III secretion systems (TTSS) are essential virulence determinants of many gram-negative bacteria and serve, upon physical contact with target cells, to translocate bacterial proteins directly across eukaryotic cell membranes. The Shigella TTSS is encoded by the mxi/spa loci located on its virulence plasmid. By electron microscopy secretons are visualized as tripartite with an external needle, a transmembrane domain, and a cytoplasmic bulb. In the present study, we generated a Shigella spa32 mutant and studied its phenotype. The spa32 gene shows low sequence homology to Salmonella TTSS1 invJ/spaN and to flagellar fliK. The spa32 mutant, like the wild-type strain, secreted the Ipas and IpgD, which are normally secreted via the TTSS, at low levels into the growth medium. However, unlike the wild-type strain, the spa32 mutant could neither be induced to secrete the Ipas and IpgD instantaneously upon addition of Congo red nor penetrate HeLa cells in vitro. Additionally, the Spa32 protein is secreted in large amounts by the TTSS during exponential growth but not upon Congo red induction. Interestingly, electron microscopy analysis of the spa32 mutant revealed that the needle of its secretons were up to 10 times longer than those of the wild type. In addition, in the absence of induction, the spa32 mutant secreted normal levels of MxiI but a large excess of MxiH. Taken together, our data indicate that the spa32 mutant presents a novel phenotype and that the primary defect of the mutant may be its inability to regulate or control secretion of MxiH.     

Effect of CO2-enrichnient on seedling physiology and growth of two tropical tree species

Seedlings of two tree species from the Atlantic lowlands of Costa Rica, Ochroma la-gopus Swartz, a fast-growing pioneer species, and Pentaclethra macroloba (Willd.) Kuntze, a slower-growing climax species, were grown under enriched atmospheric CO₂ in controlled environment chambers. Carbon dioxide concentrations were maintained at 350 and 675 μl 1⁻¹ under photosynthetic photon flux densities of 500 μol m⁻² s⁻¹ and temperatures of 26°C day and 20°C night. Total biomass of both species increased significantly in the elevated CO₂ treatment; the increase in biomass was greatest for the pioneer species, O. lagopus . Both species had greater leaf areas and specific leaf weights with increased atmospheric CO₂. However, the ratio of non-pho-tosynthetic tissue to leaf area also increased in both species leading to decreased leaf area ratios. Plants of both species grown at 675 μl 1⁻¹ CO₂ had lower chlorophyll contents and photosynthesis on a leaf area basis than those grown at 350 μl 1⁻¹. Reductions in net photosynthesis occurred despite increased internal CO₂ concentrations in the CO₂-enriched treatment. Stomatal conductances of both species decreased with CO₂-enrichment resulting in significant increases in water use efficiency.