Whole-genome sequence analysis of multidrug-resistant uropathogenic strains of Escherichia coli from Mexico

Background: Escherichia coli is the main bacterium associated with urinary tract infections (UTIs), including cystitis and pyelonephritis. Uropathogenic E. coli (UPEC) harbors numerous genes that encode diverse virulence factors contributing to its pathogenicity. The treatment of UTIs has become complicated due to the natural selection of E. coli strains that are multiresistant to several groups of antibiotics regularly used in clinical settings such as hospitals. Genomic reports of the global composition and distribution of the antibiotic resistance and virulence genes of these pathogenic strains are lacking in the Mexican population.

Purpose and methods: The aim of this study was to globally characterize the genomes of a group of UPEC strains by massive parallel sequencing to determine the prevalence and distribution of virulence and antibiotic resistance genes associated with different serotypes and phylogenetic groups.

Results: The strains exhibited 138-197 virulence genes and 29 antibiotic resistance genes related to antibiotics that are commonly used in clinical practice. 

Conclusions: These findings are relevant to the definition of new strategies for treating urinary tract infections in public hospitals and private practice. To further define the epidemiological distribution and composition of these virulence and antibiotic resistance genes, larger studies are needed.

Neural circuits for sexually dimorphic and sexually divergent behaviors in Caenorhabditis elegans

Increasing interest in sex differences in Caenorhabditis elegans neurobiology is resulting from several advances, including the completion of the male tail connectome and the surprising discovery of two 'new' neurons in the male head. In this species, sex-specific circuits in the hermaphrodite and male control reproductive behaviors such as egg-laying and copulation, respectively. Studies of these systems are revealing interesting similarities and contrasts, particularly in the mechanisms by which nutritional status influences reproductive behaviors. Other studies have highlighted the importance of sexual modulation of shared neurons and circuits in optimizing behavioral strategies. Together, these findings indicate that C. elegans uses intertwined, distributed sex differences in circuit structure and function to implement sex-specific as well as sexually divergent, shared behaviors.

Developmental alterations of the C. elegans male anal depressor morphology and function require sex-specific cell autonomous and cell non-autonomous interactions

We studied the Caenorhabditis elegans anal depressor development in larval males and hermaphrodites to address how a differentiated cell sex-specifically changes its morphology prior to adulthood. In both sexes, the larval anal depressor muscle is used for defecation behavior. However in the adult males, the muscle's sarcomere is reorganized to facilitate copulation. To address when the changes occur in the anal depressor, we used YFP:actin to monitor, and mutant analysis, laser-ablation and transgenic feminization to perturb the cell's morphological dynamics. In L1 and L2 stage larva, the muscle of both sexes has similar sarcomere morphology, but the hermaphrodite sex-determination system promotes more growth. The male anal depressor begins to change in the L3 stage, first by retracting its muscle arm from the neurons of the defecation circuit. Then the muscle's ventral region develops a slit that demarcates an anterior and posterior domain. This demarcation is not dependent on the anal depressor's intrinsic genetic sex, but is influenced by extrinsic interactions with the developing male sex muscles. However, subsequent changes are dependent on the cell's sex. In the L4 stage, the anterior domain first disassembles the dorsal-ventral sarcomere region and develops filopodia that elongates anteriorly towards the spicule muscles. Later, the posterior domain dissembles the remnants of its sarcomere, but still retains a vestigial attachment to the ventral body wall. Finally, the anterior domain attaches to the sex muscles, and then reassembles an anterior-posteriorly oriented sarcomere. Our work identifies key steps in the dimorphic re-sculpting of the anal depressor that are regulated by genetic sex and by cell-cell signaling.

Caenorhabditis elegans male sensory-motor neurons and dopaminergic support cells couple ejaculation and post-ejaculatory behaviors

The circuit structure and function underlying post-coital male behaviors remain poorly understood. Using mutant analysis, laser ablation, optogenetics, and Ca²⁺ imaging, we observed that following C. elegans male copulation, the duration of post-coital lethargy is coupled to cellular events involved in ejaculation. We show that the SPV and SPD spicule-associated sensory neurons and the spicule socket neuronal support cells function with intromission circuit components, including the cholinergic SPC and PCB and the glutamatergic PCA sensory-motor neurons, to coordinate sex muscle contractions with initiation and continuation of sperm movement. Our observations suggest that the SPV and SPD and their associated dopamine-containing socket cells sense the intrauterine environment through cellular endings exposed at the spicule tips and regulate both sperm release into the hermaphrodite and the recovery from post-coital lethargy.

DOI:http://dx.doi.org/10.7554/eLife.02938.001

The nematode worm, C. elegans, is roughly 1 mm long, made up of around 1000 cells and has two sexes: male and hermaphrodite. Hermaphrodite worms produce both eggs and sperm and can self-fertilize to generate around 300 offspring each time. Fertilization by a male, on the other hand, results in three times as many progeny and introduces genetic diversity into the population. However, it also reduces the lifespan of the hermaphrodite.

Mating also incurs a cost for males: it requires a lot of energy, which prevents male works from engaging in other activities, such as feeding, and it also increases their risk of predation. In many species, including C. elegans, the frequency with which a male can mate is limited by a period of reduced mating drive and ability that follows each instance of successful mating. However, the molecular and cellular basis of this ‘refractory period’ remains largely unclear.

Using a range of techniques, LeBoeuf et al. have now identified the circuits that regulate male mating behavior in C. elegans. When male worms were introduced into a Petri dish containing 15 hermaphrodites, most males initiated mating within about 2 min. The length of the refractory period varied between worms, but averaged roughly 12 min. This consisted of a period of disinterest, in which males did not approach hermaphrodites, followed by a period in which males attempted mating but were slower and less efficient, suggesting that the neural circuits controlling mating behaviors had yet to recover completely.

Males with longer refractory periods produced more progeny in their second mating than those with shorter refractory periods, suggesting that the interval also enables males to replenish their sperm levels. Further experiments revealed that a chemical transmitter called dopamine promotes ejaculation and then immediately reduces the worm's activity levels, giving rise to the refractory period.

By enforcing a delay between matings, the refractory period may also increase the likelihood that successive matings will be with different hermaphrodites, helping to maximize the number and diversity of offspring. Some aspects of the neural circuitry that controls the refractory period in C. elegans resemble those seen in mammals, suggesting that insights gained from an animal with 1000 cells could also be relevant to more complex species.

DOI:http://dx.doi.org/10.7554/eLife.02938.002

SIR-2.1 integrates metabolic homeostasis with the reproductive neuromuscular excitability in early aging male Caenorhabditis elegans

The decline of aging C. elegans male's mating behavior is correlated with the increased excitability of the cholinergic circuitry that executes copulation. In this study, we show that the mating circuits' functional durability depends on the metabolic regulator SIR-2.1, a NAD(+)-dependent histone deacetylase. Aging sir-2.1(0) males display accelerated mating behavior decline due to premature hyperexcitability of cholinergic circuits used for intromission and ejaculation. In sir-2.1(0) males, the hypercontraction of the spicule-associated muscles pinch the vas deferens opening, thus blocking sperm release. The hyperexcitability is aggravated by reactive oxygen species (ROS). Our genetic, pharmacological, and behavioral analyses suggest that in sir-2.1(0) and older wild-type males, enhanced catabolic enzymes expression, coupled with the reduced expression of ROS-scavengers contribute to the behavioral decline. However, as a compensatory response to reduce altered catabolism/ROS production, anabolic enzymes expression levels are also increased, resulting in higher gluconeogenesis and lipid synthesis. DOI: http://dx.doi.org/10.7554/eLife.01730.001.

C. elegans dopaminergic D2-like receptors delimit recurrent cholinergic-mediated motor programs during a goal-oriented behavior

Caenorhabditis elegans male copulation requires coordinated temporal-spatial execution of different motor outputs. During mating, a cloacal circuit consisting of cholinergic sensory-motor neurons and sex muscles maintains the male's position and executes copulatory spicule thrusts at his mate's vulva. However, distinct signaling mechanisms that delimit these behaviors to their proper context are unclear. We found that dopamine (DA) signaling directs copulatory spicule insertion attempts to the hermaphrodite vulva by dampening spurious stimulus-independent sex muscle contractions. From pharmacology and genetic analyses, DA antagonizes stimulatory ACh signaling via the D2-like receptors, DOP-2 and DOP-3, and Gα(o/i) proteins, GOA-1 and GPA-7. Calcium imaging and optogenetics suggest that heightened DA-expressing ray neuron activities coincide with the cholinergic cloacal ganglia function during spicule insertion attempts. D2-like receptor signaling also attenuates the excitability of additional mating circuits to reduce the duration of mating attempts with unproductive and/or inappropriate partners. This suggests that, during wild-type mating, simultaneous DA-ACh signaling modulates the activity threshold of repetitive motor programs, thus confining the behavior to the proper situational context.

The effects of transient starvation persist through direct interactions between CaMKII and ether-a-go-go K+ channels in C. elegans males

Prolonged nutrient limitation has been extensively studied due to its positive effects on life span. However, less is understood of how brief periods of starvation can have lasting consequences. In this study, we used genetics, biochemistry, pharmacology and behavioral analysis to show that after a limited period of starvation, the synthesis of egl-2-encoded ether-a-go-go (EAG) K+ channels and its C-terminal modifications by unc-43-encoded CaMKII have a perduring effect on C. elegans male sexual behavior. EGL-2 and UNC-43 interactions, induced after food deprivation, maintain reduced excitability in muscles involved in sex. In young adult males, spastic contractions occur in cholinergic-activated sex muscles that lack functional unc-103-encoded ERG-like K+ channels. Promoting EGL-2 and UNC-43 interactions in unc-103 mutant adult males by starving them for a few hours reduce spastic muscle contractions over multiple days. Although transient starvation during early adulthood has a hormetic effect of suppressing mutation-induced muscle contractions, the treatment reduces the ability of young wild-type (WT) males to compete with well-fed cohorts in siring progeny.

Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoKI

Infection of Escherichia coli containing the type I restriction enzyme EcoKI by bacteriophage T7 0.3 mutants leads to restriction during the late stages of genome entry and during DNA replication. Patterns of cleavage in vivo suggest that some cutting occurs near the midpoint of two recognition sites, consistent with the idea that EcoKI translocates DNA bidirectionally through itself and cuts when two enzyme molecules collide. Rapid ejection of a 0.3(+) T7 genome from a bacteriophage lambda particle results in degradation of the infecting DNA by EcoKI, showing that the normal T7 DNA translocation process delays restriction. A unique recognition site inserted at the genomic left end allows EcoKI to function as a molecular motor and to translocate the remaining 39 kilobases of T7 DNA into the cell.

Transcription-independent DNA translocation of bacteriophage T7 DNA into Escherichia coli

Penetration of wild-type T7 DNA into the host cell occurs in two steps. The phage particle ejects a few hundred base pairs of the left end of the genome into the host. Translocation of the remainder of the DNA is then coupled to transcription. In a normal infection, transcription-coupled translocation of wild-type T7 DNA is initiated at the major A1, A2, and A3 promoters for Escherichia coli RNA polymerase. At 37 degrees C, various deletion mutants lacking these three promoters grow at the same efficiency as wild-type T7 because the minor B promoter is efficiently transferred from the phage head into the cell. As the temperature of the phage infection decreases, the latent periods of (A1, A2, A3)- phages increase relative to that of wild-type T7; nevertheless, (A1, A2, A3)- phages have normal plating efficiencies at reduced temperatures. Lengthening of the latent period at low temperatures is due to a delay in transferring the complete (A1, A2, A3)- genome into the host cell. The (A1, A2, A3)- phages eject the leading end of their genome into the host, but at low temperature, insufficient DNA is transferred into the cell to allow RNA polymerase immediate access the B promoter. However, by an inefficient transcription-independent process, the B promoter eventually translocates into the cell. Mutant derivatives of (A1, A2, A3)- phages that have growth profiles at low temperatures similar to that of wild-type T7 have been isolated. The mutations allow both (A1, A2, A3)- and (A1, A2, A3)+ phages to translocate their entire genomes into the cell by a transcription-independent mechanism. The mutations are located in gene 16, a gene that encodes a component of the internal virion core. We postulate that gp16 is directly involved with the process of DNA translocation from the virion into the cell.

Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia coli

Translocation of bacteriophage T7 DNA from the capsid into the cell has been assayed by measuring the time after infection that each GATC site on the phage genome is methylated by cells containing high levels of DNA adenine methylase. Methylation at GATC sites on T7 DNA renders both the infecting genome and any newly synthesized molecules sensitive to the restriction enzyme DpnI. In a normal infection at 30 degrees C, translocation of the T7 genome into the cell takes between 9 and 12 min. In contrast, translocation of the entire phage lambda genome or of a T7 genome ejected from a lambda capsid can be detected within the first minute of infection. Entry of the leading end of the T7 genome occurs by a transcription-independent mechanism that brings both Escherichia coli and T7 promoters into the cell. Further translocation of the genome normally involves transcription by the RNA polymerases of both E. coli and T7; the rates of DNA translocation into the cell when catalyzed by each enzyme are comparable to the estimated rates of transcription of the respective enzymes. A GATC site located between the early E. coli promoters and the coding sequences of the first T7 protein made after infection is not methylated before the protein is synthesized, a result supporting the idea (B. A. Moffatt and F. W. Studier, J. Bacteriol. 170:2095-2105, 1988) that only certain proteins are permitted access to the entering T7 DNA. In the absence of transcription, the genomes of most T7 strains do not completely enter the cell. However, the entire genome of a mutant that lacks bp 3936 to 808 of T7 DNA enters the cell in a transcription-independent process at an average overall rate of 50 bp per s.

Incomplete entry of bacteriophage T7 DNA into F plasmid-containing Escherichia coli

The penetration of bacteriophage T7 DNA into F plasmid-containing Escherichia coli cells was determined by measuring Dam methylation of the entering genome. T7 strains that cannot productively infect F-containing cells fail to completely translocate their DNA into the cell before the infection aborts. The entry of the first 44% of the genome occurs normally in an F-containing cell, but the entry of the remainder is aberrant. Bypassing the normal mode of entry of the T7 genome by transfecting naked DNA into competent cells fails to suppress F exclusion of phage development. However, overexpression of various nontoxic T7 1.2 alleles from a high-copy-number plasmid or expression of T3 1.2 from a T7 genome allows phage growth in the presence of F.