The effect of C-terminal domain deletion on the catalytic activity of Leishmania donovani surface proteinase GP63: Role of Ser446 in proteolysis

The kinetoplastid protozoan Leishmania encodes major surface glycoprotein GP63, a zinc metallo-peptidase (EC.3.4.24.36) expressed both in promastigote and amastigote life stages. In the present study, we explored for the first time the role of C-terminal domain (CTD) in proteinase activity by serial truncation of Leishmania donovani GP63 (LdGP63) from carboxyl terminal end (CTend). Deletion of 180–211 amino acids from CTend (Δ420 and Δ389) resulted in almost 50% loss of catalytic activity against azocasein, casein and gelatin. Moreover, all the truncated constructs showed reduced activity towards immunoglobulin (IgG). Upon homology modeling, we identified two residues, S446, and F448 in CTD, conserved in different Leishmania species, which were positioned 6.8–11 Å apart from the active site. To ascertain the role of S446 and F448 in catalysis, we replaced S446 with Ala and Thr, and F448 with Val and Tyr by site-directed mutagenesis. The variant enzymes (S446T, F448V, and F448Y) maintained near wild-type activity, whereas S446A demonstrated 50% loss of catalytic activity towards the cleavage of various biological substrates. Kinetic analysis of S446A resulted in a 2.6-fold decrease in the affinity, 10-fold decrease in turn-over rates, and large increase in transition-state binding energy (1.4 kcal/mol) for the quenched peptide substrates. These results emphasize the relevance of CTD in the proteolytic activity of LdGP63. Fluorescence spectroscopy, and CD analysis however, indicated that the reduced activities showed by Δ389 and S446A were not due to global changes in the enzyme structures. Indeed, identification of S446 and its possible role in the stabilization of transition-state binding between enzyme and substrate can be exploited towards understanding of structure–function relationship of GP63.     

Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes

N-linked glycosylation is one of the most frequent post-translational modifications of proteins with a profound impact on their biological function. Besides other functions, N-linked glycosylation assists in protein folding, determines protein orientation at the cell surface, or protects proteins from proteases. The N-linked glycans attach to asparagines in the sequence context Asn-X-Ser/Thr, where X is any amino acid except proline. Any variation (e.g. non-synonymous single nucleotide polymorphism or mutation) that abolishes the N-glycosylation sequence motif will lead to the loss of a glycosylation site. On the other hand, variations causing a substitution that creates a new N-glycosylation sequence motif can result in the gain of glycosylation. Although the general importance of glycosylation is well known and acknowledged, the effect of variation on the actual glycoproteome of an organism is still mostly unknown. In this study, we focus on a comprehensive analysis of non-synonymous single nucleotide variations (nsSNV) that lead to either loss or gain of the N-glycosylation motif. We find that 1091 proteins have modified N-glycosylation sequons due to nsSNVs in the genome. Based on analysis of proteins that have a solved 3D structure at the site of variation, we find that 48% of the variations that lead to changes in glycosylation sites occur at the loop and bend regions of the proteins. Pathway and function enrichment analysis show that a significant number of proteins that gained or lost the glycosylation motif are involved in kinase activity, immune response, and blood coagulation. A structure-function analysis of a blood coagulation protein, antithrombin III and a protease, cathepsin D, showcases how a comprehensive study followed by structural analysis can help better understand the functional impact of the nsSNVs.     

Complete nucleotide sequence of a quinolone resistance gene (qnrS2) carrying plasmid of Aeromonas hydrophila isolated from fish

Aeromonas hydrophila strain AO1 isolated from an infected fish was found to be resistant to several quinolones. A plasmid isolated from the strain AO1, termed pBRST7.6, was cloned and sequenced and shown to be 7621 bp in length with a GC content of 60%. Further analysis confirmed that it contained a gene with 100% identity to qnrS2 genes described in plasmids associated with other Aeromonas species, the product of which usually confers increased resistance to quinolones. The plasmid backbone contained a replication initiation module (repA repC) belonging to the IncQ-family and two genes (mobC and mobB), the products of which are putatively involved in plasmid mobilization. Putative iteron-based origin of replication and characteristic oriT like sequences were also present in the plasmid. The result suggests that Aeromonas spp. carrying plasmids with quinolone resistance genes are potential reservoirs of antimicrobial resistance determinants in the environment.     

Site-Specific 13C Labeling of DNA to Deduce DNA Repair Mechanisms of Uracil-DNA Glycosyiase and UV Endonuclease V

Abstract

The oligodeoxynucleotide d(GCGUGCG) was synthesized with [1′,3′ -¹³C₂)U labeling. The uracil unit was removed with uracil-DNA glycosylase to generate an abasic site and the resulting oligonucleotide was paired with the possible d(CGCNCGC) structures. One of these heteroduplexes was a substrate for W endonuclease V. The ¹³C NMR spectra of these heteroduplexes describe the structure of the abasic site and the mechanism of the endonuclease reaction.     

Head and Neck Squamous Cell Carcinoma: Prognosis using molecular approach

Head and neck squamous cell carcinoma (HNSCC) is the fifth most prevalent cancer worldwide. Apart from various known clinicopathogical factors, it is still a major concern as many genetic and epigenetic alterations bring about the possibility of this deadly disease. The aim of this review is to explore the possible role of DNA repair pathways and the polymorphic status of DNA repair genes (XPA, XPC, XPD, XRCC1 and XRCC3) in the onset of HNSCC, along with sequence variations in genes such as Glutathione S-transferases (GSTT1, M1 and P1) that are significantly associated with HNSCC risk. We also focus on the p53 gene mutation induced by various etiological agents and threat factors with its implications towards HNSCC, and emphasise the current therapeutic interventions in treating HNSCC.     

The Association between Provider Practice and Knowledge of ORS and Zinc Supplementation for the Treatment of Childhood Diarrhea in Bihar,Gujarat and Uttar Pradesh,India: A Multi-Site Cross-Sectional Study

Introduction

Programs aimed at reducing the burden of diarrhea among children under-five in low-resource settings typically allocate resources to training community-level health workers, but studies have suggested that provider knowledge does not necessarily translate into adequate practice. A diarrhea management program implemented in Bihar, Gujarat and Uttar Pradesh, India trained private sector rural medical practitioners (RMPs) and public sector Accredited Social Health Activists (ASHAs) and Anganwadi workers (AWWs) in adequate treatment of childhood diarrhea with oral rehydration salts (ORS) and zinc. We used cross-sectional program evaluation data to determine the association between observed diarrhea treatment practices and reported knowledge of ORS and zinc among each provider cadre.

Methods

We conducted principal components analysis on providers’ responses to diarrhea treatment questions in order to generate a novel scale assessing ORS/zinc knowledge. We subsequently regressed a binary indicator of whether ORS/zinc was prescribed during direct observation onto the resulting knowledge scores, controlling for other relevant knowledge predictors.

Results

There was a positive association between ORS/zinc knowledge score and prescribing ORS and zinc to young children with diarrhea among private sector RMPs (aOR: 2.32; 95% CI: 1.29-4.17) and public sector ASHAs and AWWs (aOR 2.48; 95% CI: 1.90-3.24). Controlling for knowledge score, receipt of training in the preceding 6 months was a good predictor of adequate prescribing in the public but not the private sector. In the public sector, direct access to ORS and zinc supplies was also highly associated with prescribing.

Conclusions

To enhance the management of childhood diarrhea in India, programmatic activities should center on increasing knowledge of ORS and zinc among public and private sector providers through biannual trainings but should also focus on ensuring sustained access to an adequate supply chain.     

Mechanism of complement-independent and antibody-mediated killing of Leishmania donovani promastigotes

Immune serum raised against flagellar fraction of Leishmania donovani isolate UR6 has profound lethal effect on the in vitro growth of the parasite. Lethal effect of immune serum was also examined using two other isolates of L. donovani, namely DD8 and AG83. It was observed that immune serum is equally effective against UR6 and DD8 but has no effect on AG83 promastigotes. Parasite killing is mediated by Leishmania-specific antibodies in the absence of complement or any other factors present in rabbit serum. Results indicate that the lethal effect of immune serum is due to impairment in membrane function leading to inhibition in uptake of essential nutrients needed for growth and survival of parasites.     

EGFP-tagged core and linker histones diffuse via distinct mechanisms within living cells

The effect of chromatin organization on EGFP-tagged histone protein dynamics within the cell nucleus has been probed using fluorescence correlation and recovery measurements on single living HeLa cells. Our studies reveal that free fraction of core-particle histones exist as multimers within the cell nucleus whereas the linker histones exist in monomeric forms. The multimeric state of core histones is found to be invariant across mammalian and polytene chromosomes and this is ATP dependent. In contrast, the dynamics of the linker histones exhibits two distinct diffusion timescales corresponding to its transient binding and unbinding to chromatin governed by the tail domain residues. Under conditions of chromatin condensation induced by apoptosis, the free multimeric fraction of core histones is found to become immobile, while the monomeric linker histone mobility is partially reduced. In addition, we observe differences in nuclear colocalization of linker and core particle histones. These results are validated through Brownian dynamics simulation of core and linker histone mobility. Our findings provide a framework to understand the coupling between the state of chromatin assembly and histone protein dynamics that is central to accessing regulatory sites on the genome.