Characterization of a Gene Family Encoding SEA (Sea-urchin Sperm Protein, Enterokinase and Agrin)-Domain Proteins with Lectin-Like and Heme-Binding Properties from Schistosoma japonicum

BackgroundWe previously identified a novel gene family dispersed in the genome of Schistosoma japonicum by retrotransposon-mediated gene duplication mechanism. Although many transcripts were identified, no homolog was readily identifiable from sequence information.Methodology/Principal FindingsHere, we utilized structural homology modeling and biochemical methods to identify remote homologs, and characterized the gene products as SEA (sea-urchin sperm protein, enterokinase and agrin)-domain containing proteins. A common extracellular domain in this family was structurally similar to SEA-domain. SEA-domain is primarily a structural domain, known to assist or regulate binding to glycans. Recombinant proteins from three members of this gene family specifically interacted with glycosaminoglycans with high affinity, with potential implication in ligand acquisition and immune evasion. Similar approach was used to identify a heme-binding site on the SEA-domain. The heme-binding mode showed heme molecule inserted into a hydrophobic pocket, with heme iron putatively coordinated to two histidine axial ligands. Heme-binding properties were confirmed using biochemical assays and UV-visible absorption spectroscopy, which showed high affinity heme-binding (KD = 1.605×10?6 M) and cognate spectroscopic attributes of hexa-coordinated heme iron. The native proteins were oligomers, antigenic, and are localized on adult worm teguments and gastrodermis; major host-parasite interfaces and site for heme detoxification and acquisition.ConclusionsThe results suggest potential role, at least in the nucleation step of heme crystallization (hemozoin formation), and as receptors for heme uptake. Survival strategies exploited by parasites, including heme homeostasis mechanism in hemoparasites, are paramount for successful parasitism. Thus, assessing prospects for application in disease intervention is warranted

Autoproteolysis accelerated by conformational strain - a novel biochemical mechanism

Natural fragmentation of polypeptide chains by autoproteolysis occurs in a number of protein families. It is a vital step in the maturation of several enzymes and in the formation of membrane-associated mucins that constitute a part of the protective mucus barrier lining epithelial cells. These reactions follow similar routes involving an initial N-O or N-S acyl shift starting with a nucleophilic attack by a hydroxyl or thiol group on a carbonyl carbon followed by resolution of the ester intermediate. Previous studies indicate that distortion of the scissile peptide bond may play a role in autoproteolysis. Our structural, biochemical and molecular dynamics studies of the autoproteolyzed SEA domains from human membrane-bound mucin MUC1 and human orphan receptor GPR116 confirmed this by revealing a novel biochemical mechanism where the folding free energy accelerates cleavage by imposing conformational strain in the precursor structure. This mechanism may well be general for autoproteolysis. The structure of the cleaved MUC1 SEA domain was determined using NMR spectroscopy. It consists of four alpha-helices packed against the concave surface of a four-stranded anti-parallel beta-sheet. There are no disordered loops. The site of autoproteolysis is a conserved GSVVV sequence located at the ends of beta-sheets 2 and 3 where the resulting N- and C-terminal residues become integrated parts of these sheets after cleavage. The structure does not reveal any charge-relay system or oxyanion hole as would be expected if catalysis proceeded by way of transition state stabilization. The surface of the domain contains two hydrophobic patches that may serve as sites of interaction with other proteins, giving it a potential function in the regulation of the protective mucus layer. Combined studies of autoproteolysis and adoption of native fold show that these mechanisms proceed with the same rate and that the autoproteolysis has a global effect on structure. Studies of the stability and cleavage kinetics were performed by destabilizing core mutations or addition of denaturing co-solvents. Analysis revealed that ~7 kcal mol-1 of conformational free energy is partitioned as strain in the precursor. The results corroborate a mechanism where the autoproteolysis is accelerated by the concerted action of a conserved serine residue and strain imposed on the precursor structure upon folding, that is, the catalytic mechanism is substrate destabilization. The autoproteolysis of SEA is pH dependent. This is in line with a proposed mechanism with an initial N-O acyl shift, involving transient protonation of the amide nitrogen, and subsequent hydroxyl-mediated hydrolysis of the resulting ester. The mechanistic link between strain and cleavage kinetics is that strain induces a pyramidal conformation of the amide nitrogen which results in an increase of the pKa and thereby an acceleration of the N-O acyl shift. Furthermore we propose a water hydronium as proton donor in this step. This explains the absence of conserved acid-base functionality within the SEA structure

MUS81 promotes common fragile site expression

Fragile sites are chromosomal loci with a propensity to form gaps or breaks during early mitosis, and their instability is implicated as being causative in certain neurological disorders and cancers. Recent work has demonstrated that the so-called common fragile sites (CFSs) often impair the faithful disjunction of sister chromatids in mitosis. However, the mechanisms by which CFSs express their fragility, and the cellular factors required to suppress CFS instability, remain largely undefined. Here, we report that the DNA structure-specific nuclease MUS81-EME1 localizes to CFS loci in early mitotic cells, and promotes the cytological appearance of characteristic gaps or breaks observed at CFSs in metaphase chromosomes. These data indicate that CFS breakage is an active, MUS81-EME1-dependent process, and not a result of inadvertent chromatid rupturing during chromosome condensation. Moreover, CFS cleavage by MUS81-EME1 promotes faithful sister chromatid disjunction. Our findings challenge the prevailing view that CFS breakage is a nonspecific process that is detrimental to cells, and indicate that CFS cleavage actually promotes genome stability

Mapping the Protein Domain Structures of the Respiratory Mucins: A Mucin Proteome Coverage Study

Mucin genes encode a family of the largest expressed proteins in the human genome. The proteins are highly substituted with O-linked oligosaccharides which greatly restrict access to the peptide backbones. The genomic organization of the N-terminal, O-glycosylated, and C-terminal regions of most of the mucins has been established and is available in the sequence databases. However, much less is known about the fate of their exposed protein regions after translation and secretion, and, to date, detailed proteomic studies complementary to the genomic studies are rather limited. Using mucins isolated from cultured human airway epithelial cell secretions, trypsin digestion and mass spectrometry, we investigated the proteome coverage of the mucins responsible for the maintenance and protection of the airway epithelia. Excluding the heavily glycosylated mucin domains, up to 85% coverage of the N-terminal region of the gel forming mucins MUC5B and MUC5AC was achieved, and up to 60% of the C-terminal regions were covered, suggesting that more N- and sparsely O-glycosylated regions as well as possible other modifications are available at the C-terminus. All possible peptides from the cysteine-rich regions that interrupt the heavily glycosylated mucin domains were identified. Interestingly, 43 cleavage sites from ten different domains of MUC5B and MUC5AC were identified, which possessed a non-tryptic cleavage site on the N-terminal end of the peptide, indicating potential exposure to proteolytic and/or “spontaneous cleavages”. Some of these non-tryptic cleavages may be important for proper maturation of the molecule, before and/or after secretion. Most of the peptides identified from MUC16 were from the SEA region. Surprisingly, three peptides were clearly identified from its heavily glycosylated regions. Up to 25% coverage of MUC4 was achieved covering seven different domains of the molecule. All peptides from the MUC1 cytoplasmic domain were detected along with the three non-tryptic cleavages in the region. Only one peptide was identified from MUC20 which led us to successful antisera raised against the molecule. Taken together, this report represents our current efforts to dissect the complexities of mucin macromolecules. Identification of regions accessible to proteolysis can help in the design of effective antibodies and points to regions that might be available for mucin-protein interactions and identification of cleavage sites will enable understanding of their pre- and post-secretory processing in normal and disease environments

New interplay between interstitial and alveolar macrophages explains pulmonary alveolar proteinosis (PAP) induced by indium tin oxide particles

Occupational exposure to indium tin oxide (ITO) particles has been associated with the development of severe lung diseases, including pulmonary alveolar proteinosis (PAP). The mechanisms of this lung toxicity remain unknown. Here, we reveal the respective roles of resident alveolar (Siglec-Fhigh AM) and recruited interstitial (Siglec-Flow IM) macrophages contributing in concert to the development of PAP. In mice treated with ITO particles, PAP is specifically associated with IL-1α (not GM-CSF) deficiency and Siglec-Fhigh AM (not Siglec-Flow IM) depletion. Mechanistically, ITO particles are preferentially phagocytosed and dissolved to soluble In3+ by Siglec-Flow IM. In contrast, Siglec-Fhigh AM weakly phagocytose or dissolve ITO particles, but are sensitive to released In3+ through the expression of the transferrin receptor-1 (TfR1). Blocking pulmonary Siglec-Flow IM recruitment in CCR2-deficient mice reduces ITO particle dissolution, In3+ release, Siglec-Fhigh AM depletion, and PAP formation. Restoration of IL-1-related Siglec-Fhigh AM also prevented ITO-induced PAP. We identified a new mechanism of secondary PAP development according to which metal ions released from inhaled particles by phagocytic IM disturb IL-1α-dependent AM self-maintenance and, in turn, alveolar clearance