Translation reinitiation relies on the interaction between eIF3a/TIF32 and progressively folded cis-acting mRNA elements preceding short uORFs

Reinitiation is a gene-specific translational control mechanism characterized by the ability of some short upstream uORFs to retain post-termination 40S subunits on mRNA. Its efficiency depends on surrounding cis-acting sequences, uORF elongation rates, various initiation factors, and the intercistronic distance. To unravel effects of cis-acting sequences, we investigated previously unconsidered structural properties of one such a cis-enhancer in the mRNA leader of GCN4 using yeast genetics and biochemistry. This leader contains four uORFs but only uORF1, flanked by two transferrable 5' and 3' cis-acting sequences, and allows efficient reinitiation. Recently we showed that the 5' cis-acting sequences stimulate reinitiation by interacting with the N-terminal domain (NTD) of the eIF3a/TIF32 subunit of the initiation factor eIF3 to stabilize post-termination 40S subunits on uORF1 to resume scanning downstream. Here we identify four discernible reinitiation-promoting elements (RPEs) within the 5' sequences making up the 5' enhancer. Genetic epistasis experiments revealed that two of these RPEs operate in the eIF3a/TIF32-dependent manner. Likewise, two separate regions in the eIF3a/TIF32-NTD were identified that stimulate reinitiation in concert with the 5' enhancer. Computational modeling supported by experimental data suggests that, in order to act, the 5' enhancer must progressively fold into a specific secondary structure while the ribosome scans through it prior uORF1 translation. Finally, we demonstrate that the 5' enhancer's stimulatory activity is strictly dependent on and thus follows the 3' enhancer's activity. These findings allow us to propose for the first time a model of events required for efficient post-termination resumption of scanning. Strikingly, structurally similar RPE was predicted and identified also in the 5' leader of reinitiation-permissive uORF of yeast YAP1. The fact that it likewise operates in the eIF3a/TIF32-dependent manner strongly suggests that at least in yeasts the underlying mechanism of reinitiation on short uORFs is conserved.     

Non-detection of human herpesvirus 8 (HHV-8) DNA in HHV-8-seropositive blood donors from three Brazilian regions

Human herpesvirus 8 (HHV-8), also known as Kaposi''s sarcoma-associated herpesvirus (KSHV), is the etiologic agent of all forms of Kaposi''s sarcoma, primary effusion lymphoma and the plasmablastic cell variant of multicentric Castleman disease. In endemic areas of sub-Saharan Africa, blood transfusions have been associated with a substantial risk of HHV-8 transmission. By contrast, several studies among healthy blood donors from North America have failed to detect HHV-8 DNA in samples of seropositive individuals. In this study, using a real-time PCR assay, we investigated the presence of HHV-8 DNA in whole-blood samples of 803 HHV-8 blood donors from three Brazilian states (São Paulo, Amazon, Bahia) who tested positive for HHV-8 antibodies, in a previous multicenter study. HHV-8 DNA was not detected in any sample. Our findings do not support the introduction of routine HHV-8 screening among healthy blood donors in Brazil. (WC = 140).     

Structure and diversity of intertidal benthic diatom assemblages in contrasting shores: a case study from the Tagus estuary1

The structure of intertidal benthic diatoms assemblages in the Tagus estuary was investigated during a 2‐year survey, carried out in six stations with different sediment texture. Nonparametric multivariate analyses were used to characterize spatial and temporal patterns of the assemblages and to link them to the measured environmental variables. In addition, diversity and other features related to community physiognomy, such as size‐class or life‐form distributions, were used to describe the diatom assemblages. A total of 183 diatom taxa were identified during cell counts and their biovolume was determined. Differences between stations (analysis of similarity (ANOSIM), R = 0.932) were more evident than temporal patterns (R = 0.308) and mud content alone was the environmental variable most correlated to the biotic data (BEST, ρ = 0.863). Mudflat stations were typically colonized by low diversity diatom assemblages (H′ ~ 1.9), mainly composed of medium‐sized motile epipelic species (250–1,000 μm³), that showed species‐specific seasonal blooms (e.g., Navicula gregaria Donkin). Sandy stations had more complex and diverse diatom assemblages (H′ ~ 3.2). They were mostly composed by a large set of minute epipsammic species (<250 μm³) that, generally, did not show temporal patterns. The structure of intertidal diatom assemblages was largely defined by the interplay between epipelon and epipsammon, and its diversity was explained within the framework of the Intermediate Disturbance Hypothesis. However, the spatial distribution of epipelic and epipsammic life‐forms showed that the definition of both functional groups should not be over‐simplified.     

Traits reveal how habitat‐quality gradients structure small mammal communities in a fragmented tropical landscape

Understanding the relationships among community structure, vegetation structure and availability of food resources are a key to unravelling the ecological processes that structure biological communities. In this study, we tested (i) whether the composition of small mammal communities changed across gradients in habitat quality in tropical forest fragments, and (ii) whether any observed change could be explained by the functional traits of species. We sampled 24 trapping grids in fragments of semi‐deciduous forest, in each of two 6‐month periods. We considered each trapping grid as a sampling unit, for which we collected three datasets: an environmental matrix (vegetation structure and food resource availability), the abundance of small mammal species (community structure) and a matrix of functional traits (ecological and morphological traits which express tolerance to habitat disturbance and trophic guild). We used an RLQ approach to evaluate the association between traits and environmental gradients. Forest‐specialist and scansorial–arboreal species were associated with more complex habitat that had greater litter and canopy cover and more fallen logs. In relation to trophic guilds, granivore (fruit seeds), insectivorous and omnivorous species were also associated with higher complexity habitat, while frugivores were associated with shrub cover and availability of fruits. We conclude that functional traits (habitat use, use of vertical strata and diet) provide valuable insights into the distribution of small mammals along gradients of habitat quality in tropical forest fragments. We highlight that communities studies in fragmented landscapes should investigate the different components of biodiversity not only in landscape‐scale but also in habitat scale. Abstract in Portuguese is available with online material.     

Identification of five major and two minor genotypes of varicella-zoster virus strains: a practical two-amplicon approach used to genotype clinical isolates in Australia and New Zealand

Whole genome phylogenetic analysis in this study resolved a total of five major genotypes among the 22 varicella-zoster virus (VZV) strains or isolates for which complete genomic sequences are available. Consistent with earlier publications we have designated these genotypes European 1 (E1), European 2 (E2), Japanese (J), mosaic 1 (M1), and mosaic 2 (M2). Single nucleotide polymorphism (SNP) analysis performed in a whole-genome alignment revealed that VZV isolates of all five genotypes can be accurately genotyped using SNPs from two amplicons: open reading frame 22 (ORF22) and either ORF21 or ORF50. This modified approach identifies all of the genotypes observed using any of the published genotyping protocols. Of 165 clinical varicella and zoster isolates from Australia and New Zealand typed using this approach, 67 of 127 eastern Australian isolates were E1, 30 were E2, 16 were J, 10 were M1, and 4 were M2; 25 of 38 New Zealand isolates were E1, 8 were E2, and 5 were M1. VZV strain diversity in eastern Australia is thus broader than has been described for any other region, including Europe, Africa, and North America. J strains were far more prevalent than previously observed in countries other than Japan. Two-amplicon typing was in complete accord with genotypes derived using SNP in multiple ORFs (ORFs 1, 21, 22, 38, 50, 54, and 62). Two additional minor genotypes, M3 and M4, could also be resolved using two-amplicon typing.     

In vitro effect of pesticides (dichlofluanid, endosulfan, simazine, tolylfluanid and triallate) on proliferative activity of animal derived cell cultures

In this study pesticides with different chemical structures (dichlofluanid, endosulfan, simazine, tolylfluanid and triallate) were examined for their potential cytotoxic effect on proliferative activity of cell cultures of mammalian origin. Cell lines Madin-Darby Bovine Kidney (MDBK), Rabbit Kidney (RK13), Porcine Kidney (PK15), and semicontinual line of Bovine Embryonic Pulmonary Cells (BEPC) were used in the study. From these cell cultures cell proliferative activity was suppressed most intensively in PK15 culture by endosulfan (10(-1) - 10(-6) M). The least effect on cell proliferation in all cell cultures tested, with the exception PK 15 (10(-1) - 10(-2) M), was recorded after simazine exposure. On the basis of IC50 values the cytotoxic effect was: dichlofluanid (IC50 = 10(-3.94) M) > tolylfluanid (IC50 = 10(-3.69) M) > endosulfan (IC50 = 10(-3.24) M) > triallate (IC50 = 10(-3.12) M) > simazine (IC50 = 10(-1.78) M). The comparison of average IC50 values of cell cultures revealed that the most sensitive cell lines were PK15 (IC50 = 10(-3.27) M) and RK13 (IC50 = 10(-3.21) M), whereas MDBK (IC50 = 10(-2.55) M) and BEPC (IC50 = 10(-2.52) M) were less sensitive to pesticide exposure.     

Microtubule motors transport phagosomes in the RPE,and lack of KLC1 leads to AMD-like pathogenesis

The degradation of phagosomes, derived from the ingestion of photoreceptor outer segment (POS) disk membranes, is a major role of the retinal pigment epithelium (RPE). Here, POS phagosomes were observed to associate with myosin-7a, and then kinesin-1, as they moved from the apical region of the RPE. Live-cell imaging showed that the phagosomes moved bidirectionally along microtubules in RPE cells, with kinesin-1 light chain 1 (KLC1) remaining associated in both directions and during pauses. Lack of KLC1 did not inhibit phagosome speed, but run length was decreased, and phagosome localization and degradation were impaired. In old mice, lack of KLC1 resulted in RPE pathogenesis that was strikingly comparable to aspects of age-related macular degeneration (AMD), with an excessive accumulation of RPE and sub-RPE deposits, as well as oxidative and inflammatory stress responses. These results elucidate mechanisms of POS phagosome transport in relation to degradation, and demonstrate that defective microtubule motor transport in the RPE leads to phenotypes associated with AMD.     

Arabidopsis Glutathione Transferases U24 and U25 Exhibit a Range of Detoxification Activities with the Environmental Pollutant and Explosive, 2,4,6-Trinitrotoluene

The explosive 2,4,6-trinitrotoluene (TNT) is a major worldwide military pollutant. The presence of this toxic and highly persistent pollutant, particularly at military sites and former manufacturing facilities, presents various health and environmental concerns. Due to the chemically resistant structure of TNT, it has proven to be highly recalcitrant to biodegradation in the environment. Here, we demonstrate the importance of two glutathione transferases (GSTs), GST-U24 and GST-U25, from Arabidopsis (Arabidopsis thaliana) that are specifically up-regulated in response to TNT exposure. To assess the role of GST-U24 and GST-U25, we purified and characterized recombinant forms of both enzymes and demonstrated the formation of three TNT glutathionyl products. Importantly, GST-U25 catalyzed the denitration of TNT to form 2-glutathionyl-4,6-dinitrotoluene, a product that is likely to be more amenable to subsequent biodegradation in the environment. Despite the presence of this biochemical detoxification pathway in plants, physiological concentrations of GST-U24 and GST-U25 result in only a limited innate ability to cope with the levels of TNT found at contaminated sites. We demonstrate that Arabidopsis plants overexpressing GST-U24 and GST-U25 exhibit significantly enhanced ability to withstand and detoxify TNT, properties that could be applied for in planta detoxification of TNT in the field. The overexpressing lines removed significantly more TNT from soil and exhibited a corresponding reduction in glutathione levels when compared with wild-type plants. However, in the absence of TNT, overexpression of these GSTs reduces root and shoot biomass, and although glutathione levels are not affected, this effect has implications for xenobiotic detoxification.The containment and cleanup of environmental pollutants is increasingly both a legal requirement and a responsible action in many developed countries. The most commonly used explosives in military weapons are 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and their continual use, along with production and decommissioning, are progressively contaminating millions of hectares of military land (Rylott and Bruce, 2009). Bioremediation of TNT is particularly challenging, as the electron-withdrawing properties of the three nitro groups render the aromatic ring particularly resistant to oxidative attack and ring cleavage by microbial oxygenases, which in the environment are normally central to the biodegradation of aromatic compounds (Qasim et al., 2007). In the United States, the Environmental Protection Agency and the military are addressing methods by which toxic TNT and RDX can be contained and detoxified on active military training ranges. One way this problem might be tackled is through the use of plants that are adapted to detoxify these compounds. This could be achieved either by traditional breeding programs or by genetic modification, as has been demonstrated previously for both RDX and TNT (Hannink et al., 2001; Rylott et al., 2006; Jackson et al., 2007).In the majority of species tested so far (tobacco [Nicotiana tabacum], bean [Phaseolus vulgaris], wheat [Triticum aestivum], poplar [Populus spp.], and switchgrass [Panicum virgatum]), with the exception of some conifer trees (Schoenmuth and Pestemer, 2004), TNT is located almost entirely in the roots (Sens et al., 1998, 1999; Hannink et al., 2007; Van Dillewijn et al., 2008; Brentner et al., 2010). Endogenous metabolism of TNT by plants has been characterized (Rylott and Bruce, 2009; Rylott et al., 2011b), with recent research focusing on the model plant species Arabidopsis (Arabidopsis thaliana; Hannink et al., 2001; Van Dillewijn et al., 2008; Rylott et al., 2011a). First, TNT is transformed by nitroreductases to hydroxylamino dinitrotoluenes (HADNTs), with a varying portion further reduced to amino dinitrotoluenes (ADNTs). In Arabidopsis, oxophytodienoate reductases are known to catalyze these steps (Beynon et al., 2009). Plants engineered to express bacterial nitroreductases, which also perform this transformation step, have increased TNT transformation activity and show dramatically enhanced resistance to TNT (Hannink et al., 2001; Rylott et al., 2011a). The additional functionality of HADNTs and ADNTs permits their subsequent conjugation to amino acids, organic acids, and sugars (Bhadra et al., 1999, 2001), and conjugation of HADNT and ADNT isomers to Glc by Arabidopsis glucosyltransferases has been characterized (Gandia-Herrero et al., 2008), with research suggesting that these conjugates are subsequently sequestered within the cell walls (Rylott and Bruce, 2009).Glutathione transferases (GSTs) are a multigene family of proteins known to conjugate glutathione to electrophilic molecules and, in plants, are involved in the detoxification of herbicide xenobiotics (Cummins et al., 2011). Since GSTs have evolved the ability to catalyze glutathione-linked reactions with thousands of different chemical structures, it has been hypothesized that GSTs should play a central role, alongside glucosyltransferases, in the detoxification of TNT (Mezzari et al., 2005; Brentner et al., 2008). Gene expression studies in poplar (Tanaka et al., 2007; Brentner et al., 2008) and Arabidopsis (Ekman et al., 2003; Mezzari et al., 2005; Gandia-Herrero et al., 2008) have identified GSTs up-regulated in response to TNT; however, to date, the biochemical response of GSTs toward TNT has not been investigated. The overexpression of plant GSTs has been shown to increase resistance to a range of stresses, with some τ class GSTs shown to detoxify herbicides via a conjugation activity (Dixon and Edwards, 2010; Cummins et al., 2011). Many Arabidopsis GSTs (in common with some mammalian and other plant GSTs) exhibit a glutathione-dependent peroxide (GPOX) activity (Dixon and Edwards, 2010), catalyzing the reduction of lipid hydroperoxides to the respective monohydroxyalcohols, an activity that confers tolerance to a number of oxidative stresses (Dixon et al., 1998; Dixon and Edwards, 2010). Here, we expressed, purified, and characterized TNT-responsive Arabidopsis GSTs and investigated their contribution toward the detoxification of TNT in Arabidopsis.