Phylogenomics of the Maverick Virus-Like Mobile Genetic Elements of Vertebrates

Mavericks are virus-like mobile genetic elements found in the genomes of eukaryotes. Although Mavericks encode capsid morphogenesis homologs, their viral particles have not been observed. Here, we provide new evidence supporting the viral nature of Mavericks and the potential existence of virions. To this end, we conducted a phylogenomic analysis of Mavericks in hundreds of vertebrate genomes, discovering 134 elements with an intact coding capacity in 17 host species. We reveal an extensive genomic fossil record in 143 species and date three groups of elements to the Late Cretaceous. Bayesian phylogenetic analysis using genomic fossil orthologs suggests that Mavericks have infected osteichthyans for ∼419 My. They have undergone frequent cross-species transmissions in cyprinid fish and all core genes are subject to strong purifying selection. We conclude that vertebrate Mavericks form an ancient lineage of aquatic dsDNA viruses which are probably still functional in some vertebrate lineages.     

Embryonic gene expression and pro-protein processing of proSAAS during rodent development

In vitro assays have demonstrated that peptides derived from the recently-identified proSAAS precursor inhibit prohormone convertase 1 (PC1) suggesting that this novel peptide may function as an endogenous inhibitor of PC1. To further understand the role of proSAAS in vivo, we have investigated the expression of proSAAS mRNA and processing of proSAAS during pre- and early postnatal rodent development. In situ hybridization showed that, by embryonic day 12.5 (e12.5) in the rat, proSAAS mRNA was present in essentially all differentiating neurons in the mantle layer of the myelencephalon, metencephalon, diencephalon, spinal cord and several sympathetic ganglia. During later stages of prenatal development, widespread proSAAS expression continues in post-mitotic neurons of both the CNS and PNS and begins in endocrine cells of the anterior and intermediate pituitary. Although proSAAS expression overlaps with PC1 in several regions, its overall expression pattern is significantly more extensive, suggesting that proSAAS may be multifunctional during development. Processed forms of proSAAS are present by at least mid-gestation with marked accumulation of two C-terminal forms, comprising the PC1 inhibitory fragment of proSAAS.     

Entamoeba histolytica: the serine-rich gene polymorphism-based genetic variability of clinical isolates from Georgia

It is generally accepted that a majority of individuals infected by Entamoeba histolytica do not develop symptomatic disease. However, the parasite and the host factors contributing to the development of the disease, remain undetermined. It is also unclear why certain individuals develop extra-intestinal amebiasis without exhibiting apparent intestinal symptoms. An outbreak of amebic liver abscess in Tbilisi, Georgia in 1998-1999 suggested that the causative E. histolytica strain had an unusual propensity for extra-intestinal spread. To correlate the genetic differences with pathogenic potential of the parasite, we have examined the SREHP gene polymorphisms among Georgian E. histolytica isolates. Comparison of polymorphic patterns revealed the presence of several different genotypes of E. histolytica, thus preventing an association of a single genotype with hepatic disease, but supporting the previous finding of extensive genetic diversity among E. histolytica isolates from the same geographic origin.     

Mycobacterium szulgai identification by hsp65 gene sequencing in an HIV-positive patient with non-Hodgkin's lymphoma

Mycobacterium szulgai, described for the first time in 1972, is a rare human pathogen that mainly causes pulmonary non-tubercular mycobacteriosis. We report its isolation and identification from a bronchoalveolar lavage specimen by hsp65 gene sequencing analysis in an HIV-positive patient with non-Hodgkin's lymphoma.     

Characterization of lytic Pseudomonas aeruginosa bacteriophages via biological properties and genomic sequences

Pseudomonas aeruginosa is an important cause of infections, especially in patients with immunodeficiency or diabetes. Antibiotics are effective in preventing morbidity and mortality from Pseudomonas infection, but because of spreading multidrug-resistant bacterial strains, bacteriophages are being explored as an alternative therapy. Two newly purified broad host range Pseudomonas phages, named vB_Pae-Kakheti25 and vB_Pae-TbilisiM32, were characterized as candidates for use in phage therapy. Morphology, host range, growth properties, thermal stability, serology, genomic sequence, and virion composition are reported. When phages are used as bactericides, they are used in mixtures to overcome the development of resistance in the targeted bacterial population. These two phages are representative of diverse siphoviral and podoviral phage families, respectively, and hence have unrelated mechanisms of infection and no cross-antigenicity. Composing bactericidal phage mixtures with members of different phage families may decrease the incidence of developing resistance through a common mechanism.     

Evaluation of unbound free heme in plant cells by differential acetone extraction

Heme functions not only as a prosthetic group of hemoproteins but also as a regulatory molecule, suggesting the presence of 'free' heme. Classically, total non-covalently bound heme is extracted from plant samples with acidic acetone after removal of pigments with basic and neutral acetone. Earlier work proposed that free heme can be selectively extracted into basic acetone. Using authentic hemoproteins, we confirmed that acidic acetone can quantitatively extract heme, while no heme was extracted into neutral acetone. Meanwhile, a certain amount of heme was extracted into basic acetone from hemoglobin and myoglobin. Moreover, basic acetone extracted loosely bound heme from bovine serum albumin, implying that the nature of hemoproteins largely influences heme extraction into basic acetone. Using a highly sensitive heme assay, we found that basic and neutral acetone can extract low levels of heme from plant samples. In addition, neutral acetone quantitatively extracted free heme when it was externally added to plant homogenates. Furthermore, the level of neutral acetone-extractable heme remained unchanged by precursor (5-aminolevulinic acid) feeding, while increased by norflurazon treatment which abolishes chloroplast biogenesis. However, changes in these heme levels did not correlate to genomes uncoupled phenotypes, suggesting that the level of unbound free heme would not affect retrograde signaling from plastids to the nucleus. The present data demonstrate that the combination of single-step acetone extraction following a sensitive heme assay is the ideal method for determining total and free heme in plants.     

Putative Glycosyltransferases and Other Plant Golgi Apparatus Proteins Are Revealed by LOPIT Proteomics

The Golgi apparatus is the central organelle in the secretory pathway and plays key roles in glycosylation, protein sorting, and secretion in plants. Enzymes involved in the biosynthesis of complex polysaccharides, glycoproteins, and glycolipids are located in this organelle, but the majority of them remain uncharacterized. Here, we studied the Arabidopsis (Arabidopsis thaliana) membrane proteome with a focus on the Golgi apparatus using localization of organelle proteins by isotope tagging. By applying multivariate data analysis to a combined data set of two new and two previously published localization of organelle proteins by isotope tagging experiments, we identified the subcellular localization of 1,110 proteins with high confidence. These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method, as well as the localization of 304 endoplasmic reticulum and 208 plasma membrane proteins. Comparison of the hydrophobic domains of the localized proteins showed that the single-span transmembrane domains have unique properties in each organelle. Many of the novel Golgi-localized proteins belong to uncharacterized protein families. Structure-based homology analysis identified 12 putative Golgi glycosyltransferase (GT) families that have no functionally characterized members and, therefore, are not yet assigned to a Carbohydrate-Active Enzymes database GT family. The substantial numbers of these putative GTs lead us to estimate that the true number of plant Golgi GTs might be one-third above those currently annotated. Other newly identified proteins are likely to be involved in the transport and interconversion of nucleotide sugar substrates as well as polysaccharide and protein modification.The Golgi apparatus is the central organelle in the secretory pathway, and in higher plants it is involved in the biosynthesis and transport of cell wall matrix polysaccharides, glycoproteins, proteoglycans, and glycolipids as well as in protein trafficking to different subcellular compartments. The last decade has produced substantial findings on the function of the Golgi apparatus: insights into the protein trafficking at the endoplasmic reticulum (ER)/Golgi interface, Golgi structural maintenance, its involvement in endocytosis, and its behavior during cell division (for review, see Faso et al., 2009). However, despite its importance, only a small proportion of the Golgi proteome has been studied: relatively few Golgi proteins have been localized, and even fewer have been functionally characterized.The Golgi apparatus is thought to contain a large and diverse group of membrane-bound glycosyltransferases (GTs). The current view is that different GT activities are required for synthesis of the linkage between different donor and acceptor sugars. Having in mind the diversity of linkage types found in cell wall polysaccharides, the number of different GTs involved is likely to be very large. For instance, it has been estimated that for the biosynthesis of pectin alone, the action of 65 different enzymatic activities is needed (Caffall and Mohnen, 2009). By the end of the year 2011, 468 Arabidopsis (Arabidopsis thaliana) sequences had been annotated in the Carbohydrate-Active EnZymes (CAZy) GT database (Cantarel et al., 2009; http://www.cazy.org). We estimate that two-thirds of these CAZy-classified GTs may be targeted to the Golgi. The remaining one-third are cytosolic or plastidic enzymes involved in processes including, secondary metabolism or starch synthesis. The reported sequences are classified into 43 CAZy families based on amino acid sequence similarities within which at least one member has been biochemically characterized. Each family is likely to have a common structural fold, and three-dimensional (3-D) structures have been resolved for 20 of these 43 families. These are divided mostly into two structural classes, having either a GT-A fold or a GT-B fold (Unligil and Rini, 2000; Bourne and Henrissat, 2001). Moreover, most of the structurally uncharacterized GT families are predicted to adopt either the GT-A or GT-B fold based on 3-D structural homology modeling (Coutinho et al., 2003; Lairson et al., 2008). Despite this conserved 3-D structure, different GT families have very low or undetectable sequence similarities. Consequently, predicting novel GTs based solely on their amino acid sequence similarities is not always achievable, and structural homology searches have also proven useful (Hansen et al., 2009).The length and properties of the transmembrane domain (TMD) of endomembrane proteins appear to play a role in protein sorting and location within the secretory pathway and can be used to predict protein localization (Hanton et al., 2005; Sharpe et al., 2010). In order to perform such predictions, a high number of experimentally localized proteins is required, but only limited data sets have been available for plants to date.In order to identify the most abundant CAZy-classified GTs as well as novel putative GTs, in this work we rigorously extended our proteomic studies of the Golgi apparatus. We have previously developed a high-throughput mass spectrometry (MS)-based quantitative proteomics technique for localization of organelle proteins by isotope tagging (LOPIT; Dunkley et al., 2004, 2006). Here, we report new LOPIT data sets and apply a new method of combining them with published LOPIT data sets, localizing an unprecedented number of plant organelle proteins. We have analyzed the TMD properties of the proteins assigned to the ER, Golgi, and plasma membrane (PM) and determined the organelle-specific features. Structural prediction analysis of the Golgi-localized proteins with unknown functions assessed the protein sequences for the potential to fold similarly to known GT structures. We found that the Golgi contains a substantial number of candidate GT families that have no characterized functions. These results yield a broader understanding of the Golgi function and its biochemical properties.     

Plasma and exhaled breath condensate nitrite-nitrate level in relation to environmental exposures in adults in the EGEA study

This study evaluated the associations between biological markers in the nitrate-nitrite-NO pathway and four environmental exposures among subjects examined in the second survey (2003-2007) of the French Epidemiological study on Genetics and Environment of Asthma (EGEA). Total nitrite and nitrate (NO(2)(-) /NO(3)(-)) levels were measured both in plasma and in exhaled breath condensate (EBC) in 949 adults. Smoking, diet and exposure to chlorine products were assessed using standardized questionnaires. Exposure to air pollutants was estimated by using geostatistical models. All estimates were obtained with generalized estimating equations for linear regression models. Median levels of NO(2)(-)/NO(3)(-) were 36.3μM (1st-3rd quartile: 25.7, 51.1) in plasma and 2.0μmol/mg proteins (1st-3rd quartile 0.9, 3.9) in EBC. After adjustment for asthma, age, sex and menopausal status, plasma NO(2)(-)/NO(3)(-) level increased with leafy vegetable consumption (above versus below median=0.04 (95%CI: 0.001, 0.07)) and decreased in smokers (versus non/ex-smokers=-0.08 (95%CI: -0.11, -0.04). EBC NO(2)(-)/NO(3)(-) level decreased in smokers (-0.08 (95%CI: -0.16, -0.001)) and with exposure to ambient O(3) concentration (above versus below median=-0.10 (95%CI: -0.17, -0.03)). Cured meat, chlorine products, PM(10) and NO(2) concentrations were not associated with NO(2)(-)/NO(3)(-) levels. Results suggest that potential modifiable environmental and behavioral risk factors may modify NO(2)(-)/NO(3)(-) levels in plasma and EBC according to the route of exposure.     

Naturally occurring IgM anti-leukocyte autoantibodies (IgM-ALA) inhibit T cell activation and chemotaxis

The physiological relevance of naturally occurring IgM-ALA remains to be elucidated. These autoantibodies are present from birth and increase in diverse inflammatory states that are both infectious and noninfectious. Clinical observations showing significantly less acute allograft rejections in recipients having high IgM-ALA levels, led us to investigate whether IgM-ALA could have a functional role in attenuating T cell mediated inflammatory responses. In pursuit of this hypothesis, we did studies using IgM purified from the serum of normal individuals, patients with end stage renal disease, and HIV-1 infection. All preparations of IgM immunoprecipitated certain receptors e.g., CD3, CD4, CCR5, and CXCR4 from whole cell lysates but failed to immunoprecipitate IL-2R and HLA Ags. In physiological doses IgM down-regulated CD4, CD2 and CD86 but not CD8 and CD28, inhibited T cell proliferation, decreased production of certain proinflammatory cytokines e.g., TNF-alpha, IL-13 and IL-2, but not IFN- gamma, IL-1beta, GM-CSF, IL-6 and IL-8 and inhibited leukocyte chemotaxis. These inhibitory effects were more pronounced when using IgM from patients with high levels of IgM-ALA and these inhibitory effects were significantly reduced after using IgM preabsorbed with leukocytes. IgM-ALA binding to leukocytes was found to be highly specific, as <10% of IgM secreting B cell clones had IgM-ALA specificity with some clones having specificity for either T cells or monocytes. These findings support the concept that IgM-ALA provides an innate mechanism to regulate T cell mediated inflammatory responses.