Membrane-bound mucin modular domains: From structure to function

Mucins belong to a heterogeneous family of large O-glycoproteins composed of a long peptidic chain called apomucin on which are linked hundreds of oligosaccharidic chains. Among mucins, membrane-bound mucins are modular proteins and have a structural organization usually containing Pro/Thr/Ser-rich O-glycosylated domains (PTS), EGF-like and SEA domains. Via these modular domains, the membrane-bound mucins participate in cell signalling and cell interaction with their environment in normal and pathological conditions. Moreover, the recent knowledge of these domains and their biological activities led to the development of new therapeutic approaches involving mucins. In this review, we show 3D structures of EGF and SEA domains. We also describe the functional features of the evolutionary conserved domains of membrane-bound mucins and discuss consequences of splice events.     

NOD2 gene mutations associate weakly with ulcerative colitis but not with Crohn's disease in Indian patients with inflammatory bowel disease

Background

Three mutations (two missense and one frameshift) in the NOD2 gene are associated with Crohn's disease (CD) in a proportion of patients with Crohn's disease in North America, Europe and Australia. These three mutations are not found in Indian patients with CD. We undertook new studies to identify polymorphisms in the NOD2 gene in the Indian population and to detect whether any of these were associated with inflammatory bowel disease (IBD) in this population.

Methods

Individual exons of the NOD2 gene were amplified by PCR and subjected to denaturing high performance liquid chromatography (DHPLC) to detect heteroduplex formation. All 12 exons of the NOD2 gene were amplified and Sanger-sequenced to detect polymorphisms in the NOD2 gene. 310 patients with CD, 318 patients with ulcerative colitis (UC) and 442 healthy controls (HC) were recruited for association studies. DNA from these participants was evaluated for the identified eight polymorphisms by Sequenom analysis.

Results

Heteroduplex formation was noted by DHPLC in exons 2 and 4 of the NOD2 gene. Sequencing of the entire NOD2 gene data revealed eight polymorphisms – rs2067085, rs2066842, rs2066843, rs1861759, rs2111235, rs5743266, rs2076753, and rs5743291 – of which the latter four were described for the first time in Indians. None of these polymorphisms was associated with CD. The SNPs rs2066842 and rs2066843 were in significant linkage disequilibrium. Both SNPs showed a significant association with UC (P = 0.03 and 0.04 respectively; odds ratio 1.44 and 1.41 respectively).

Conclusion

Four NOD2 polymorphisms were identified for the first time in the Indian population. Of 8 NOD2 polymorphisms, none were associated with CD but two were weakly associated with UC. NOD2 polymorphisms do not play a major role in CD genesis in India.     

A fossil stemmiulid millipede (Diplopoda: Stemmiulida) from the Miocene amber of Simojovel,Chiapas, México

A fossil millipede representative of the order Stemmiulida is described on the basis of a well-preserved adult female trapped in amber from the Miocene of Simojovel, Chiapas, south-eastern México. The fossil specimen is named as Parastemmiulus elektron, a new genus and species. As observed in extant stemmiulids, this fossil shows a reduced number of ocelli, the distal larger than the proximal, as well as a total of 46 trunk segments including 2 apodous segments in front of the telson. The head of this ancient stemmiulid has three ocelli and a Tömösváry organ, characteristics not reported before in Stemmiulida, requiring the diagnosis of the order to be emended.http://zoobank.org/urn:lsid:zoobank.org:pub:361400A8-37D4-421F-B4FD-A0AE63BE538C     

Dioxygenase from Aspergillus fumigatus MC8: molecular modelling and in silico studies on enzyme–substrate interactions

Flavoenzymes have been extensively studied for their structural and mechanistic properties because they find potential application as industrial biocatalysts. They are attractive for biocatalysis because of the selectivity, controllability and efficiency of their reactions. Some of these enzymes catalyse the oxidative modification of protein substrates. Among them oxygenases (monoxoygenases and dioxygenases) are of special interest because they are highly entantio as well as regio-selective and can be used for oxyfunctionalisation. Dioxygenase enzymes catalyse oxygenation reactions in which both di-oxygen atoms are incorporated into the product. A dioxygenase enzyme purified from Aspergillus fumigatus MC8 was subjected to protein digestion followed by peptide sequencing. The sequence analysis of the peptide fragments resulted in identifying its match with that of an extracellular dioxygenase sequence from the same species of fungus existing in the protein database. The sequence was submitted to protein homology/analogy recognition engine online server for homology modelling and the 3D structure was predicted. Subsequently, the in silico studies of the enzyme–substrate (protein–ligand) interaction were carried out by using the method of molecular docking simulations wherein the modelled dioxygenase enzyme (protein) was docked with the substrates (ligands), catechin and epicatechin.     

The Golgi Protein ACBD3, an Interactor for Poliovirus Protein 3A,Modulates Poliovirus Replication

We have shown that the circulating vaccine-derived polioviruses responsible for poliomyelitis outbreaks in Madagascar have recombinant genomes composed of sequences encoding capsid proteins derived from poliovaccine Sabin, mostly type 2 (PVS2), and sequences encoding nonstructural proteins derived from other human enteroviruses. Interestingly, almost all of these recombinant genomes encode a nonstructural 3A protein related to that of field coxsackievirus A17 (CV-A17) strains. Here, we investigated the repercussions of this exchange, by assessing the role of the 3A proteins of PVS2 and CV-A17 and their putative cellular partners in viral replication. We found that the Golgi protein acyl-coenzyme A binding domain-containing 3 (ACBD3), recently identified as an interactor for the 3A proteins of several picornaviruses, interacts with the 3A proteins of PVS2 and CV-A17 at viral RNA replication sites, in human neuroblastoma cells infected with either PVS2 or a PVS2 recombinant encoding a 3A protein from CV-A17 [PVS2-3A(CV-A17)]. The small interfering RNA-mediated downregulation of ACBD3 significantly increased the growth of both viruses, suggesting that ACBD3 slowed viral replication. This was confirmed with replicons. Furthermore, PVS2-3A(CV-A17) was more resistant to the replication-inhibiting effect of ACBD3 than the PVS2 strain, and the amino acid in position 12 of 3A was involved in modulating the sensitivity of viral replication to ACBD3. Overall, our results indicate that exchanges of nonstructural proteins can modify the relationships between enterovirus recombinants and cellular interactors and may thus be one of the factors favoring their emergence.     

Evaluating developmental shape changes in Homo antecessor subadult facial morphology

The fossil ATD6-69 from Atapuerca, Spain, dated to ca. 900 ka (thousands of years ago) has been suggested to mark the earliest appearance of modern human facial features. However, this specimen is a subadult and the interpretation of its morphology remains controversial, because it is unclear how developmental shape changes would affect the features that link ATD6-69 to modern humans. Here we analyze ATD6-69 in an evolutionary and developmental context. Our modern human sample comprises cross-sectional growth series from four populations. The fossil sample covers human specimens from the Pleistocene to the Upper Paleolithic, and includes several subadult Early Pleistocene humans and Neanderthals. We digitized landmarks and semilandmarks on surface and CT scans and analyzed the Procrustes shape coordinates using multivariate statistics. Ontogenetic allometric trajectories and developmental simulations were employed in order to identify growth patterns and to visualize potential adult shapes of ATD6-69. We show that facial differences between modern and archaic humans are not exclusively allometric. We find that while postnatal growth further accentuates the differences in facial features between Neanderthals and modern humans, those features that have been suggested to link ATD6-69's morphology to modern humans would not have been significantly altered in the course of subsequent development. In particular, the infraorbital depression on this specimen would have persisted into adulthood. However, many of the facial features that ATD6-69 shares with modern humans can be considered to be part of a generalized pattern of facial architecture. Our results present a complex picture regarding the polarity of facial features and demonstrate that some modern human-like facial morphology is intermittently present in Middle Pleistocene humans. We suggest that some of the facial features that characterize recent modern humans may have developed multiple times in human evolution.     

Oxidative stress in the root nodules of Phaseolus vulgaris is induced under conditions of phosphorus deficiency

One of the most adverse effects of phosphorus (P) deficiency on N₂-fixing legumes is the generation of harmful active oxygen species which cause oxidative stress. And although oxidative stress has been widely studied in roots and shoots of various plant species, it has not yet sufficiently been documented in bean nodules so far. In this study, two recombinant inbred lines RIL115 (P-deficiency tolerant) and RIL147 (P-deficiency sensitive) of common bean and Concesa (local variety) were inoculated separately with the reference strain R. tropici CIAT899, RhM₁₁ (R. gallicum) or RhM₁₄ (R. tropici); two local strains of the Marrakesh region of Morocco. Nodulated plants were grown under semi-hydroponic conditions with sufficient or deficient P supply and analyzed for their oxidative responses at the flowering stage. The results indicated that P-deficiency decreased the growth of shoots (48 %) and nodules (32 %), particularly with RhM₁₄ exhibiting the highest decrease (52 %) of nodulation. This constraint increased electrolyte leakage of nodules (40 %) as compared to leaves (20 %), especially for plants inoculated with RhM₁₄ and CIAT899. Moreover, high H₂O₂ and malondialdehyde contents were noticed in P-deficient nodules of RhM₁₄ and RhM₁₁. These variations were associated with peroxidase activity stimulation in P-deficient nodules induced by CIAT899 and RhM₁₄. In symbiosis with RIL115, these last strains exhibited the highest nodule phenol content. Overall, phenol content was mainly enhanced in P-deficient nodules (35 %) as compared to the leaves (16 %). It was concluded that the genotypes inoculated with CIAT899 and RhM₁₁ are relatively P-deficiency tolerant combinations as compared to those inoculated with RhM₁₄. Increase of oxidative stress in nodules rather than in leaves points to the need for further investigations of mechanisms that improve the root-nodule efficiency under adverse conditions.     

Political mobilization of a regional minority: Han Chinese settlers in Xinjiang

The tumultuous events of summer 2009 have brought Uighur protests and minority mobilization in the Xinjiang Uighur Autonomous Region (XUAR) to the forefront. But this focus overlooks similar protests organized by various groups of Han Chinese settlers over the years. This paper contributes to the body of literature on minority mobilization and ethnic relations in Xinjiang by illustrating how the political mobilization of a group that is simultaneously a national majority and a regional minority differs substantially from ‘traditional’ minority mobilization. Reviewing the main instances of Han Chinese political mobilization since the XUAR was created in 1955, I argue that two factors are particularly important in enabling their mobilization: the Han Chinese's subjective perception of discrimination and their close ethnic ties to the state. This paper concludes with a discussion on the presence of a cycle of protests between Han settlers and the Uighurs in Xinjiang.     

Role of Glycoside Phosphorylases in Mannose Foraging by Human Gut Bacteria

To metabolize both dietary fiber constituent carbohydrates and host glycans lining the intestinal epithelium, gut bacteria produce a wide range of carbohydrate-active enzymes, of which glycoside hydrolases are the main components. In this study, we describe the ability of phosphorylases to participate in the breakdown of human N-glycans, from an analysis of the substrate specificity of UhgbMP, a mannoside phosphorylase of the GH130 protein family discovered by functional metagenomics. UhgbMP is found to phosphorolyze β-d-Manp-1,4-β-d-GlcpNAc-1,4-d-GlcpNAc and is also a highly efficient enzyme to catalyze the synthesis of this precious N-glycan core oligosaccharide by reverse phosphorolysis. Analysis of sequence conservation within family GH130, mapped on a three-dimensional model of UhgbMP and supported by site-directed mutagenesis results, revealed two GH130 subfamilies and allowed the identification of key residues responsible for catalysis and substrate specificity. The analysis of the genomic context of 65 known GH130 sequences belonging to human gut bacteria indicates that the enzymes of the GH130_1 subfamily would be involved in mannan catabolism, whereas the enzymes belonging to the GH130_2 subfamily would rather work in synergy with glycoside hydrolases of the GH92 and GH18 families in the breakdown of N-glycans. The use of GH130 inhibitors as therapeutic agents or functional foods could thus be considered as an innovative strategy to inhibit N-glycan degradation, with the ultimate goal of protecting, or restoring, the epithelial barrier.     

Inverted Repeats and Genome Architecture Conversions of Terrestrial Isopods Mitochondrial DNA

Mitochondrial DNA (mtDNA) is usually depicted as a circular molecule, however, there is increasing evidence that linearization of mtDNA evolved independently many times in organisms such as fungi, unicellular eukaryotes, and animals. Recent observations in various models with linear mtDNA revealed the presence of conserved inverted repeats (IR) at both ends that, when they become single-stranded, may be able to fold on themselves to create telomeric-hairpins involved in genome architecture conversions. The atypical mtDNA of terrestrial isopods (Crustacea: Oniscidea) composed of linear monomers and circular dimers is an interesting model to study genome architecture conversions. Here, we present the mtDNA control region sequences of two species of the genus Armadillidium: A. vulgare and A. pelagicum. All features of arthropods mtDNA control regions are present (origin of replication, poly-T stretch, GA and TA-rich blocks and one variable domain), plus a conserved IR. This IR can potentially fold into a hairpin structure and is present in two different orientations among the A. vulgare populations: either in one sense or in its reverse complement. This polymorphism, also observed in a single individual (heteroplasmy), might be a signature of genome architecture conversions from linear to circular monomeric mtDNA via successive opening and closing of the molecules.