DNA Recognition by Quinoline Antibiotics: Use of Base-Modified DNA Molecules to Investigate Determinants of Sequence-Specific Binding of Luzopeptin

Abstract

The luzopeptin antibiotics contain a cyclic decadepsipeptide to which are attached two quinoline chromophores that bisintercalate into DNA. Although they bind DNA less tightly than the structurally related quinoxaline antibiotics echinomycin and triostin A, the molecular basis of their interaction remains unclear. We have used the PCR in conjunction with novel nucleotides to create specifically modified DNA for footprinting experiments. In order to study the influence that removal, addition or relocation of the guanine 2-amino group, which normally identifies G. C base pairs from the minor groove, has on the interaction of luzopeptin antibiotics with DNA. The presence of a purine 2-amino group is not strictly required for binding of luzopeptin to DNA, but the exact location of this group can alter the position of preferred drug binding sites. It is, however, not the sole determinant of nucleotide sequence recognition in luzopeptin-DNA interaction. Nor can the selectivity of luzopeptin be attributed to the quinoline chromophores, suggesting that an analogue mode of DNA recognition may be operative. This is in contrast to the digital readout that seems to predominate with the quinoxaline antibiotics.     

Species-Specific Association of the Cell-Aggregation Molecule Mediates Recognition in Marine Sponges

Reaggrcgation of dissociated cells of marine sponges, resulting in reformation of functional sponges, is a calcium-dependent process mediated by large, proteoglycan-like molecules termed aggregation factors (AF). During aggregation, species-specific sorting of cells is often observed. We purified and characterized AFs from three different sponge species and investigated their role in species-specific aggregation using novel approaches. The calcium-dependent association between purified AFs is species-specific in most combinations, as was shown in overlay assays and bead-sorting assays with AFs immobilized onto colored beads. Species-specific interactions of living cells and AF-beads resulted in incorporation of only homospecific AF-beads into reforming cell aggregates. Sequences from peptides obtained from the AF core proteins could all be aligned to the sequence of one species, the Microciona prolifera AFp3 core protein. In contrast to this similarity, major species-specific differences were seen in carbohydrate composition and in the response of AFs to specific carbohydrate-recognizing antibodies. In summary, our data point to a prominent role for the calcium-dependent association of AFs in recognition processes during aggregation. As this association of AFs occurs via carbohydrate -carbohydrate interactions, we speculate that the specificity of those interactions may be fundamental to recognition mechanisms required for regeneration of individuals from dissociated cells and for rejection of foreign material by sponge individuals.     

A novel pattern recognition protein of the Chinese oak silkmoth,Antheraea pernyi,is involved in the pro-PO activating system

In this paper, we firstly reported a C-type lectin cDNA clone of 1029 bps from the larvae of A. Pernyi (Ap-CTL) using PCR and RACE techniques. The full-length cDNA contains an open reading frame encoding 308 amino acid residues which has two different carbohydrate-recognition domains (CRDs) arranged in tandem. To investigate the biological activities in the innate immunity, recombinant Ap-CTL was expressed in E. coli with a 6-histidine at the amino-terminus (Ap-rCTL). Besides acted as a broad-spectrum recognition protein binding to a wide range of PAMPs and microorganisms, Ap-rCTL also had the ability to recognize and trigger the agglutination of bacteria and fungi. In the proPO activation assay, Ap-rCTL specifically restored the PO activity of hemolymph blocked by anti-Ap-rCTL antibody in the presence of different PAMPs or microorganisms. In summary, Ap-rCTL plays an important role in insect innate immunity as an pattern recognition protein. [BMB Reports 2013; 46(7): 358-363]     

Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification

Fungi belong to the large kingdom of lower eukaryotic organisms encompassing yeasts along with filamentous and dimorphic members. Microbial P450 enzymes have contributed to exploration of and adaptation to diverse ecological niches such as conversion of lipophilic compounds to more hydrophilic derivatives or degradation of a vast array of environmental toxicants. To better understand diversification of the catalytic behavior of fungal P450s, detailed insight into the molecular machinery steering oxidative attack on the distinctly structured endogenous and xenobiotic substrates is of preeminent interest. Based on a general, CYP102A1-related template the bulk of predicted substrate/inhibitor-binding determinants were shown to cluster near the distal heme face within the six known substrate recognition sites (SRSs) made up by the α-helical B′/F/G/I tetrad, the B′–C interhelical loop and strands of the β6-sheet, population density being highest in the structurally flexible SRS-1 and SRS-4 domains, showing a low degree of conservation. Reactivity toward ligands favorably coincides with the lipophilicity/hydrophilicity profile and bulkiness of critical amino acids acting as selective filters. Some decisive elements may also serve in maintenance of catalytic competence via their action as gatekeepers directing substrate access/positioning or stabilizers of the heme environment enabling dioxygen activation. Non-SRS residues seem to control spin state equilibria and attract redox partners by electrostatic forces. Of note, the inhibitory potency of azole-type fungicides is likely to arise from perturbation of the complex interplay of the mechanistic principles addressed above. Knowledge-supported exploitation of the topological data will be helpful in the manufacture of commodity/specialty chemicals as well as therapeutic agents. Also, engineered fungal P450s may be used to improve pollutant-specific bioremediation of contaminated soils.     

From monomer to fibril: Abeta-amyloid binding to Aducanumab antibody studied by molecular dynamics simulation

Alzheimer's disease is one of the most common causes of dementia. It is believed that the aggregation of short Aβ -peptides to form oligomeric and protofibrillar amyloid assemblies plays a central role for disease-relevant neurotoxicity. In recent years, passive immunotherapy has been introduced as a potential treatment strategy with anti-amyloid antibodies binding to Aβ -amyloids and inducing their subsequent degradation by the immune system. Although so far mostly unsuccessful in clinical studies, the high-dosed application of the monoclonal antibody Aducanumab has shown therapeutic potential that might be attributed to its much greater affinity to Aβ -aggregates vs monomeric Aβ -peptides. In order to better understand how Aducanumab interacts with aggregated Aβ -forms compared to monomers, we have generated structural model complexes based on the known structure of Aducanumab in complex with an Aβ_{2 − 7} -eptitope. Structural models of Aducanumab bound to full-sequence Aβ_{1 − 40} -monomers, oligomers, protofilaments and mature fibrils were generated and investigated using extensive molecular dynamics simulations to characterize the flexibility and possible additional interactions. Indeed, an aggregate-specific N-terminal binding motif was found in case of Aducanumab binding to oligomers, protofilaments and fibrils that is located next to but not overlapping with the epitope binding site found in the crystal structure with Aβ_{2 − 7} . Analysis of binding energetics indicates that this motif binds weaker than the epitope but likely contributes to Aducanumab's preference for aggregated Aβ -species. The predicted aggregate-specific binding motif could potentially serve as a basis to reengineer Aducanumab for further enhanced preference to bind Aβ -aggregates vs monomers.     

C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N-terminal

Mixed lineage leukemia protein (MLL1 protein) recognizes the CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation, which also prevents MLL-related leukemia. In this paper, multiple molecular dynamic (MD) simulations were performed to investigate the mechanism of recognition and influences of C1188D mutation. Started from fully dissociated DNA and MLL1-CXXC domain, remarkably, the center of mass (COM) of MLL1-CXXC domain quickly concentrates on the vicinity of the CpG site in all 53 short MD simulations. Extended simulations of the wild type showed that the native complex formed in 500 ns among 4 of 53 simulations. In contrast, the C1188D mutant COM distributed broadly around the DNA and the native complex was not observed in any of the extended simulations. Simulations on the apo MLL1-CXXC domain further suggest that the wild type protein remained predominantly in an open form that closely resembles its structure in the native complex whereas C1188D mutant formed predominantly compact structures in which the N- terminal bends to D1188. This conformational switch hinders the formation of encounter complex, thus abolishes the recognition. Our study also provides clues to the study mechanism of recognition, by the CXXC domain from proteins like DNA methyltransferase and ten-eleven translocation enzymes.     

The role of partial incubation and egg repositioning within the clutch in hatching asynchrony and subsequent effects on breeding success

The main mechanism to achieve hatching asynchrony (HA) for incubating birds is to start heating the eggs before clutch completion. This might be achieved through partial incubation and/or early incubation. Even in the absence of incubation behaviour during the laying phase, clutches still experience a certain degree of asynchrony. Recent studies have shown that eggs located in the centre of the nest receive more heat than peripheral ones during incubation. As eggs receiving more heat would develop faster, we hypothesized that HA should be shorter in nests where eggs were moved homogeneously along the centre–periphery space during incubation than in those nests where eggs repeatedly remained in the same locations, either centrally or peripherally. We explored the relative roles of egg repositioning and partial incubation in determining HA in wild birds by (1) removing eggs from 20 Great Tit Parus major nests on the day of laying and replacing them with fake eggs to avoid partial incubation, and returning them when full incubation began; (2) monitoring twice a day the position of each individually marked egg relative to the clutch centre during incubation, and estimating the coefficient of variation of the distances; and (3) determining HA in each nest. Preventing partial incubation reduced HA by 51% days in experimental nests. It also caused negative effects for the incubating females (lengthening the full incubation period) and positive effects for the brood (increasing fledging success). However, our hypothesis about the role of egg repositioning on HA was not supported: all the females moved the eggs with remarkable consistency, generally attaining a coefficient of variation of the distances around 33%, and it was not related to the HA experienced. We therefore conclude that partial incubation is an important factor regulating HA, and females compensate for the potential effects of differential heating by moving the eggs homogeneously within the clutch.     

Ligand and pathogen specificity of the Atlantic salmon serum C-type lectin

Background

An Atlantic salmon (Salmo salar) C-type lectin (SSL) binds to mannose and related sugars as well as to the surface of Aeromonas salmonicida. To characterize this lectin as a pathogen recognition receptor in salmon, aspects of its interaction with molecules and with intact pathogens were investigated.

Methods

SSL was isolated using whole-yeast-affinity and mannan-affinity chromatography. The binding of SSL to the two major surface molecules of A. salmonicida, lipopolysaccharide (LPS) and A-layer protein was investigated by western blotting and enzyme-linked immunosorbent assays. Microbial binding specificity of SSL was examined by whole cell binding assays using a range of species. Carbohydrate ligand specificity of SSL was examined using glycan array analysis and frontal affinity chromatography.

Results

SSL showed binding to bacteria and yeast including, Pseudomonas fluorescens, A. salmonicida, A. hydrophila, Pichia pastoris, and Saccharomyces cerevisiae, but there was no detectable binding to Yersinia ruckeri. In antimicrobial assays, SSL showed no activity against Escherichia coli, Bacillus subtilis, S. cerevisiae, or A. salmonicida, but it was found to agglutinate E. coli. The major surface molecule of A. salmonicida recognized by SSL was shown to be LPS and not the A-layer protein. LPS binding was mannose-inhibitable. Glycans containing N-acetylglucosamine were shown to be predominant ligands.

Conclusion

SSL has a distinct ligand preference while allowing recognition of a wide variety of related carbohydrate structures.

General Significance

SSL is likely to function as a wide-spectrum pattern recognition protein.