Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections

Astroviruses (AstVs) are positive sense, single-stranded RNA viruses transmitted to a wide range of hosts via the fecal-oral route. The number of AstV-infected animal hosts has rapidly expanded in recent years with many more likely to be discovered because of the advances in viral surveillance and next generation sequencing. Yet no study to date has identified human AstV genotypes in animals, although diverse AstV genotypes similar to animal-origin viruses have been found in children with diarrhea and in one instance of encephalitis. Here we provide important new evidence that non-human primates (NHP) can harbor a wide variety of mammalian and avian AstV genotypes, including those only associated with human infection. Serological analyses confirmed that >25% of the NHP tested had antibodies to human AstVs. Further, we identified a recombinant AstV with parental relationships to known human AstVs. Phylogenetic analysis suggests AstVs in NHP are on average evolutionarily much closer to AstVs from other animals than are AstVs from bats, a frequently proposed reservoir. Our studies not only demonstrate that human astroviruses can be detected in NHP but also suggest that NHP are unique in their ability to support diverse AstV genotypes, further challenging the paradigm that astrovirus infection is species-specific.     

Expanded RNA-binding activities of mammalian Argonaute 2

Mammalian Argonaute 2 (Ago2) protein associates with microRNAs (miRNAs) or small interfering RNAs (siRNAs) forming RNA-induced silencing complexes (RISCs/miRNPs). In the present work, we characterize the RNA-binding and nucleolytic activity of recombinant mouse Ago2. Our studies show that recombinant mouse Ago2 binds efficiently to miRNAs forming active RISC. Surprisingly, we find that recombinant mouse Ago2 forms active RISC using pre-miRNAs or long unstructured single stranded RNAs as guides. Furthermore, we demonstrate that, in vivo, endogenous human Ago2 binds directly to pre-miRNAs independently of Dicer, and that Ago2:pre-miRNA complexes are found both in the cytoplasm and in the nucleus of human cells.     

Comparison and evaluation of RNA quantification methods using viral, prokaryotic, and eukaryotic RNA over a 10 concentration range

Quantification of RNA is essential for various molecular biology studies. In this work, three quantification methods were evaluated: ultraviolet (UV) absorbance, microcapillary electrophoresis (MCE), and fluorescence-based quantification. Viral, bacterial, and eukaryotic RNA were measured in the 500 to 0.05-ng μl⁻¹ range via an ND-1000 spectrophotometer (UV), Agilent RNA 6000 kits (MCE), and Quant-iT RiboGreen assay (fluorescence). The precision and accuracy of each method were assessed and compared with a concentration derived independently using inductively coupled plasma-optical emission spectroscopy (ICP-OES). Cost, operator time and skill, and required sample volumes were also considered in the evaluation. Results indicate an ideal concentration range for each quantification technique to optimize accuracy and precision. The ND-1000 spectrophotometer exhibits high precision and accurately quantifies a 1-μl sample in the 500 to 5-ng μl⁻¹ range. The Quant-iT RiboGreen assay demonstrates high precision in the 1 to 0.05-ng μl⁻¹ range but is limited to lower RNA concentrations and is more costly than the ND-1000 spectrophotometer. The Agilent kits exhibit less precision than the ND-1000 spectrophotometer and Quant-iT RiboGreen assays in the 500 to 0.05-ng μl⁻¹ range. However, the Agilent kits require 1 μl of sample and can determine the integrity of the RNA, a useful feature for verifying whether the isolation process was successful.     

A Second-Site Noncomplementation Screen for Modifiers of Rho1 Signaling during Imaginal Disc Morphogenesis in Drosophila

Background

Rho1 is a small GTPase of the Ras superfamily that serves as the central component in a highly conserved signaling pathway that regulates tissue morphogenesis during development in all animals. Since there is tremendous diversity in the upstream signals that can activate Rho1 as well as the effector molecules that carry out its functions, it is important to define relevant Rho1-interacting genes for each morphogenetic event regulated by this signaling pathway. Previous work from our lab and others has shown that Rho signaling is necessary for the morphogenesis of leg imaginal discs during metamorphosis in Drosophila, although a comprehensive identification of Rho1-interacting genes has not been attempted for this process.

Methodology/Principal Findings

We characterized an amorphic allele of Rho1 that displays a poorly penetrant dominant malformed leg phenotype and is capable of being strongly enhanced by Rho1-interacting heterozygous mutations. We then used this allele in a second-site noncomplementation screen with the Exelixis collection of molecularly defined deficiencies to identify Rho1-interacting genes necessary for leg morphogenesis. In a primary screen of 461 deficiencies collectively uncovering ∼50% of the Drosophila genome, we identified twelve intervals harboring Rho1-interacting genes. Through secondary screening we identified six Rho1-interacting genes including three that were previously identified (RhoGEF2, broad, and stubbloid), thereby validating the screen. In addition, we identified Cdc42, Rheb and Sc2 as novel Rho1-interacting genes involved in adult leg development.

Conclusions/Significance

This screen identified well-known and novel Rho1-interacting genes necessary for leg morphogenesis, thereby increasing our knowledge of this important signaling pathway. We additionally found that Rheb may have a unique function in leg morphogenesis that is independent of its regulation of Tor.     

The Neovolcanic Axis Is a Barrier to Gene Flow among Aedes aegypti Populations in Mexico That Differ in Vector Competence for Dengue 2 Virus

Background

Aedes aegypti is the main mosquito vector of the four serotypes of dengue virus (DENV). Previous population genetic and vector competence studies have demonstrated substantial genetic structure and major differences in the ability to transmit dengue viruses in Ae. aegypti populations in Mexico.

Methodology/Principal Findings

Population genetic studies revealed that the intersection of the Neovolcanic axis (NVA) with the Gulf of Mexico coast in the state of Veracruz acts as a discrete barrier to gene flow among Ae. aegypti populations north and south of the NVA. The mosquito populations north and south of the NVA also differed in their vector competence (VC) for dengue serotype 2 virus (DENV2). The average VC rate for Ae. aegypti mosquitoes from populations from north of the NVA was 0.55; in contrast the average VC rate for mosquitoes from populations from south of the NVA was 0.20. Most of this variation was attributable to a midgut infection and escape barriers. In Ae. aegypti north of the NVA 21.5% failed to develop midgut infections and 30.3% of those with an infected midgut failed to develop a disseminated infection. In contrast, south of the NVA 45.2% failed to develop midgut infections and 62.8% of those with an infected midgut failed to develop a disseminated infection.

Conclusions

Barriers to gene flow in vector populations may also impact the frequency of genes that condition continuous and epidemiologically relevant traits such as vector competence. Further studies are warranted to determine why the NVA is a barrier to gene flow and to determine whether the differences in vector competence seen north and south of the NVA are stable and epidemiologically significant.     

Occurrence of Tetracycline Resistance Genes in Aquaculture Facilities with Varying Use of Oxytetracycline

The contribution of human activities to environmental reservoirs of antibiotic resistance is poorly understood. The purpose of this study was to determine if oxytetracycline (OTC) use in aquaculture facilities increased the detection frequency (i.e., prevalence) of tetracycline resistance (tet^R) genes relative to facilities with no recent OTC treatment. We used polymerase chain reaction to screen water and sediment from four noncommercial fish farms in northwestern Wisconsin for the presence of ten tet^R determinants: tet(A), tet(B), tet(D), tet(E), tet(G), tet(M), tet(O), tet(Q), tet(S), and tet(W). Water from farms with recent OTC use had significantly higher tet^R detection frequencies than did water from farms without recent OTC use, with prevalence in raceways and rearing ponds of farms with recent OTC use exceeding by more than twofold that of farms not using OTC. Effluent from all farms, regardless of treatment regime, had higher tet^R detection frequencies than their corresponding influent for all genes, but the specific combinations of tet^R genes detected in a sample were not different from their corresponding influent. Although OTC use was associated with the increased occurrence and diversity of tet^R genes in water samples, it was not found to relate to tet^R gene occurrence in sediment samples. Sediment samples from facilities with no recent OTC use had significantly higher frequencies of tet^R gene detection than did samples from facilities with recent OTC use. All of the tet^R genes were detected in both the medicated and nonmedicated feed samples analyzed in this study. These findings suggest that both OTC treatment in aquaculture facilities and the farms themselves may be sources of tet^R gene introduction to the environment. To our knowledge, this is the first study to use genotypic and cultivation-independent methods to examine tet^R gene occurrence associated with OTC use in aquaculture.     

High-Resolution Cryo-Electron Microscopy Structures of Murine Norovirus 1 and Rabbit Hemorrhagic Disease Virus Reveal Marked Flexibility in the Receptor Binding Domains

Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. Here, the three-dimensional (3D) reconstructions of recombinant rabbit hemorrhagic disease virus (rRHDV) virus-like particles (VLPs) and intact MNV-1 were determined to ∼8-Å resolution. rRHDV also has a raised P domain, and therefore, this conformation is independent of infectivity and genus. The atomic structure of the MNV-1 P domain was used to interpret the MNV-1 reconstruction. Connections between the P and shell domains and between the floating P domains were modeled. This observed P-domain flexibility likely facilitates virus-host receptor interactions.Murine norovirus 1 (MNV-1) (3, 14, 15) and rabbit hemorrhagic disease virus (RHDV) are members of the genera Norovirus and Lagovirus of the family Caliciviridae that offer a comparison to recombinant human norovirus (rNV) virus-like particles (VLPs) for assessing the structures and roles of domains within the capsid proteins of this family of viruses. Calicivirus particles contain 180 copies of the 56- to 76-kDa major capsid protein (Orf2), which is comprised of the internal/buried N terminus (N), shell (S), and protruding (P) domains (9, 10). The S domain, an eight-stranded β-barrel, forms an ∼300-Å contiguous shell around the RNA genome. A flexible hinge connects the shell to a “protruding” (P) domain at the C-terminal half of the capsid protein, which can be further divided into a globular head region (P2) and a stem region (P1) that connects the shell domain to P2. The accompanying article (13) describes the determination of the structure of the P domain of MNV-1 to a resolution of 2.0 Å.We recently determined the cryo-transmission electron microscopy (TEM) structure of MNV-1 to ∼12-Å resolution (4) and found that, compared to rNV VLPs (10) and San Miguel sea lion virus (SMSV) (1, 2), the protruding domains are rotated by ∼40° in a clockwise fashion and lifted up by ∼16 Å. To better understand the unusual conformation of MNV-1 and whether it is unique to this particular member of the calicivirus family, the ∼8-Å cryo-TEM structures of infectious MNV-1 and the VLPs of RHDV were determined.MNV-1 was produced as previously described (4). Three liters of cell culture yielded 0.5 to 1.0 mg of purified virus with a particle/PFU ratio of less than 100. Baculovirus expression and purification of recombinant RHDV (rRHDV) VLPs were performed as previously described (8). Cryo-electron microscopy (EM) data were collected at the National Resource for Automated Molecular Microscopy (NRAMM) facility in San Diego, CA (4). Images were collected at a nominal magnification of ×50,000 at a pixel size of 0.1547 nm at the specimen level using Leginon software (12) and processed with Appion software (5). The contrast transfer function for each set of particles from each image was estimated and corrected using ACE2 (a variation of ACE [7]). Particle images were automatically selected (11). The final stacks of particle images contained 20,425 MNV virions and 7,856 rRHDV VLPs, and EMAN 3D (6) was used for the reconstructions. Resolutions were estimated by Fourier shell correlations (FSC) of the three-dimensional (3D) reconstructions and application of a cutoff of 0.5. An amplitude correction of the final electron density was performed using GroEL small-angle X-ray scattering (SAXS) data.3D reconstructions of MNV-1 and rRHDV were calculated to resolutions of 8 Å and 8.1 Å, respectively (Fig. ​(Fig.1).1). The P domains of rNV VLPs rest directly on top of the shell domain (10) (Fig. ​(Fig.1A).1A). In contrast, the P domains of MNV-1 are lifted and rotated above the shell of the capsid (4) (Fig. ​(Fig.1B).1B). At this higher resolution, there was a clear connection between the P1 domain and the shell domain in all three capsid subunits (Fig. ​(Fig.1B,1B, arrow A). Unlike the smooth protruding domains of rNV, MNV-1 has two clear “horns” (arrow B), not dissimilar to those observed for the sapoviruses (1, 2). There also are islands of density in the interior of the shell, directly beneath the 5-fold axes, that may represent ordered regions of RNA.Open in a separate windowFIG. 1.Stereo diagrams (left) and thin sections (right), with radius coloring, of rNV (A), MNV-1 (B), and an rRHDV VLP (C). For rNV, the atomic coordinates (10) were used. In MNV, arrow A indicates the thin connector between the P1 and S domains. Arrow B denotes the horns found at the tips of the P2 domains. Arrow C denotes the large gap between the P1 and S domains in the rRHDV VLP. Arrow D denotes the false connectivity in rRHDV VLPs between the P1 domain and the S domain near the 5-fold axes.As with MNV-1, there is a marked gap between the P and S domains in the rRHDV VLP (Fig. ​(Fig.1C,1C, arrow C). This gap is not as pronounced as in MNV-1 because the P domains are not rotated as in MNV-1. In this electron density map, the A/B dimers appear to be touching the shell domain near the 5-fold axes. This contact difference between the A/B dimers and the C/C dimers could be the reason why the tops of the C/C dimers appear to be markedly disordered compared to the A/B dimers in rRHDV and the C/C dimers in MNV-1.Shown in Fig. ​Fig.22 is the fitting of the atomic structures of the MNV-1 P domain (13) and the rNV S domains into the MNV-1 3D reconstruction electron density. The horns (arrow A, loops A′-B′ and E′-F′) observed at the tips of the P domain match exceedingly well with the electron density. As discussed in the accompanying publication (13), the A′-B′ and E′-F′ loops displayed two discrete conformations, a closed structure, where the two loops were tightly associated, and an open structure, where the loops were splayed apart. The horns of the closed conformation fit better into the reconstruction, as the E′-F′ loop in the open form jutted out of the density at the base of the horns. The unmodified density in the lower panel of Fig. ​Fig.22 shows fine features in the shell domain and a very clear connection between the shell and P1 domains. The connections between the P1 and S domains were of sufficient quality to build a basic backbone model by uncoiling the linker region (arrow B). The P domain in the unfiltered 3D reconstruction was far less ordered than the S domain (Fig. ​(Fig.2).2). This was likely due to movement of the entire P domain with respect to the shell.Open in a separate windowFIG. 2.Fitting of the MNV-1 P domain and the rNV shell domain into the MNV-1 electron density. A, B, and C subunits are represented by blue, green, and red, respectively. The electron density is shown in transparent gray. The top panel is the 8.0-Å-resolution 3D reconstruction modified using a low-pass filter. The bottom panel is the reconstruction without modification. The horns on the tops of the P domains are denoted by arrow A. Arrow B denotes the connection between the S and P domains.Using the structure of rNV VLP P domains for modeling, the rRHDV P domains are lifted off the surface of the shell, but not rotated as with MNV-1. This places the bottom edge of the A subunit P1 domain near the S domain at the 5-fold axes. The P-domain dimers of rNV and rRHDV have a more “arch-like” shape than MNV-1. Unlike in MNV-1, the electron densities of the C/C dimers in rRHDV are far more diffuse than those of the A/B dimers (Fig. ​(Fig.3B)3B) and the connector between the S and P1 domains is not clear. During fitting, the connector region was not as extended as with MNV-1. This may afford greater flexibility, leading to more diffuse electron density.Open in a separate windowFIG. 3.Fitting of the rNV atomic structure into the rRHDV VLP electron density. The upper stereo image shows the 8.1-Å-resolution 3D reconstruction after modification by a low-pass filter. Below is the same reconstruction prior to density modification.When the atomic models for the MNV-1 P domains (13) were placed into the cryo-TEM electron density (Fig. ​(Fig.4),4), the C termini extended deep into the cores of adjacent P domains. Possible connections not accounted for by the P-domain structures were also observed in the electron density between the P domains. A bulge between the P1 and P2 domains in the 3D reconstruction indicated a possible interaction between the C termini and the adjacent P domains. These same interactions were observed in the crystal lattice. This highly mobile C terminus may be a flexible tether between the P domains in the intact virion.Open in a separate windowFIG. 4.Possible carboxyl-terminus interactions between the P domains of MNV-1. (A) Stereo image of MNV-1 calculated to 12-Å resolution with (red) and without (yellow) the last 10 residues of the P domain. (B) The calculated MNV-1 density with the carboxyl terminus removed (yellow) overlaid onto the 3D reconstruction of MNV-1 (blue). Note the strands of difference density that roughly correspond to the C terminus in panel A. (C) The C-terminus interactions observed in the structure of the MNV-1 P domains. Shown in blue and green are ribbon diagrams of an A/B P-domain dimer. In mauve is a surface rendering of the C terminus from a crystallographically related dimer. (D) Surface rendering of the final MNV-1 model with possible interactions between the P domains in MNV-1. The carboxyl termini of the A subunits (blue) interact with the counterclockwise-related B subunits around the 5-fold axes (white arrows). Around the 3-fold (quasi-6-fold) axes, the C subunits interact with the A subunits and the B subunits interact with the C subunits (orange arrows).It is absolutely clear that the hinge region between the S and P domains affords a remarkable degree of flexibility in the P domains that is not genus specific or related to differences between rVLPs and authentic virions. The simplest explanation for the role of this transition is that it gives the P domains flexibility that may be used to optimize interactions with cell receptors during attachment and entry. In this way, the P domains can increase their avidity for the cell surface by being more facile in adapting to the presentation of cellular recognition motifs.     

Loss of Par-1a/MARK3/C-TAK1 Kinase Leads to Reduced Adiposity,Resistance to Hepatic Steatosis,and Defective Gluconeogenesis

Par-1 is an evolutionarily conserved protein kinase required for polarity in worms, flies, frogs, and mammals. The mammalian Par-1 family consists of four members. Knockout studies of mice implicate Par-1b/MARK2/EMK in regulating fertility, immune homeostasis, learning, and memory as well as adiposity, insulin hypersensitivity, and glucose metabolism. Here, we report phenotypes of mice null for a second family member (Par-1a/MARK3/C-TAK1) that exhibit increased energy expenditure, reduced adiposity with unaltered glucose handling, and normal insulin sensitivity. Knockout mice were protected against high-fat diet-induced obesity and displayed attenuated weight gain, complete resistance to hepatic steatosis, and improved glucose handling with decreased insulin secretion. Overnight starvation led to complete hepatic glycogen depletion, associated hypoketotic hypoglycemia, increased hepatocellular autophagy, and increased glycogen synthase levels in Par-1a^−/− but not in control or Par-1b^−/− mice. The intercrossing of Par-1a^−/− with Par-1b^−/− mice revealed that at least one of the four alleles is necessary for embryonic survival. The severity of phenotypes followed a rank order, whereby the loss of one Par-1b allele in Par-1a^−/− mice conveyed milder phenotypes than the loss of one Par-1a allele in Par-1b^−/− mice. Thus, although Par-1a and Par-1b can compensate for one another during embryogenesis, their individual disruption gives rise to distinct metabolic phenotypes in adult mice.Cellular polarity is a fundamental principle in biology (6, 36, 62). The prototypical protein kinase originally identified as a regulator of polarity was termed partitioning defective (Par-1) due to early embryonic defects in Caenorhabditis elegans (52). Subsequent studies revealed that Par-1 is required for cellular polarity in worms, flies, frogs, and mammals (4, 17, 58, 63, 65, 71, 89). An integral role for Par-1 kinases in multiple signaling pathways has also been established, and although not formally addressed, multifunctionality for individual Par-1 family members is implied in reviews of the list of recognized upstream regulators and downstream substrates (Table ​(Table1).1). Interestingly, for many Par-1 substrates the phosphorylated residues generate 14-3-3 binding sites (25, 28, 37, 50, 59, 61, 68, 69, 78, 95, 101, 103). 14-3-3 binding in turn modulates both nuclear/cytoplasmic as well as cytoplasmic/membrane shuttling of target proteins, thus allowing Par-1 activity to establish intracellular spatial organization (15, 101). The phosphorylation of Par-1 itself promotes 14-3-3 binding, thereby regulating its subcellular localization (37, 59, 101).

TABLE 1.

Multifunctionality of Par-1 polarity kinase pathways^a