Predicted structure of tail‐fiber proteins of T‐even type phages

Riede, Isolde; Schwarz, Heinz; Jähnig, Fritz

doi:10.1016/0014-5793(87)80130-8

Cited by 10 publications

(6 citation statements)

References 17 publications

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“…The annotations of phage homologs vary and include “phage tail tip,” “minor phage tail,” and “putative carbohydrate-binding” proteins. The amino acid sequences of rcc01079 and rcc01080 lack any detectable conserved domains, but predicted secondary structures of both proteins are dominated by β strands, which is consistent with known structures of tail fiber proteins ( Riede et al 1987 ). The observed distribution of rcc01079 and rcc01080 homologs in bacteria and phages implies that these genes are of phage origin and have frequently been horizontally exchanged.…”

Section: Resultssupporting

confidence: 78%

Functional and Evolutionary Characterization of a Gene Transfer Agent’s Multilocus “Genome”

et al. 2016

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Gene transfer agents (GTAs) are phage-like particles that can package and transfer a random piece of the producing cell’s genome, but are unable to transfer all the genes required for their own production. As such, GTAs represent an evolutionary conundrum: are they selfish genetic elements propagating through an unknown mechanism, defective viruses, or viral structures “repurposed” by cells for gene exchange, as their name implies? In Rhodobacter capsulatus, production of the R. capsulatus GTA (RcGTA) particles is associated with a cluster of genes resembling a small prophage. Utilizing transcriptomic, genetic and biochemical approaches, we report that the RcGTA “genome” consists of at least 24 genes distributed across five distinct loci. We demonstrate that, of these additional loci, two are involved in cell recognition and binding and one in the production and maturation of RcGTA particles. The five RcGTA “genome” loci are widespread within Rhodobacterales, but not all loci have the same evolutionary histories. Specifically, two of the loci have been subject to frequent, probably virus-mediated, gene transfer events. We argue that it is unlikely that RcGTA is a selfish genetic element. Instead, our findings are compatible with the scenario that RcGTA is a virus-derived element maintained by the producing organism due to a selective advantage of within-population gene exchange. The modularity of the RcGTA “genome” is presumably a result of selection on the host organism to retain GTA functionality.

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Section: Resultssupporting

confidence: 78%

Functional and Evolutionary Characterization of a Gene Transfer Agent’s Multilocus “Genome”

et al. 2016

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“…Therefore, it can be speculated that the NS1 region containing the bipartite motif interacts with itself in homo-oligomerization. A similar type of association has previously been reported for a number of homo-oligomeric proteins (51,56,59). Additional experiments particularly with NS1 clones modified by site-directed mutagenesis are needed to assess the role of this putative ␤-strand structure in NS1-NS1 interactions.…”

Section: Discussionsupporting

confidence: 69%

Inhibition of parvovirus minute virus of mice replication by a peptide involved in the oligomerization of nonstructural protein NS1

Pujol

Deleu

Nüesch

et al. 1997

J Virol

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The large nonstructural protein NS1 of the minute virus of mice and other parvoviruses is involved in essential steps of the viral life cycle, such as DNA replication and transcriptional regulation, and is a major contributor to the toxic effect on host cells. Various biochemical functions, such as ATP binding, ATPase, site-specific DNA binding and nicking, and helicase activities, have been assigned to NS1. Homo-oligomerization is a prerequisite for a number of proteins to be fully functional. In particular, helicases generally act as homo-oligomers. Indirect evidence of NS1 self-association has been recently obtained by a nuclear cotransport assay (J. P. Nüesch and P. Tattersall, Virology 196:637-651, 1993). In order to demonstrate the oligomerizing property of NS1 in a direct way and localize the protein region(s) involved, the yeast two-hybrid system was used in combination with deletion mutagenesis across the whole NS1 molecule, followed by high-resolution mapping of the homo-oligomerization domain by a peptide enzyme-linked immunosorbent assay method. This study led to the identification of a distinct NS1 peptide that contains a bipartite domain involved in NS1 oligomerization. Furthermore, this isolated peptide was found to act as a specific competitive inhibitor and suppress NS1 helicase activity in vitro and parvovirus DNA replication in vivo, arguing for the involvement of NS1 oligomerization in these processes. Our results point to drug targeting of oligomerization motifs of viral regulatory proteins as a potentially useful antiviral strategy.

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“…Reed et al, proposed a model to predict the three-dimensional structure of t-even phage-type tail fibrin. Their finding were more likely consistent with electron microscopic data [17]. Over computational approach, several models have been developed for phage T7 [13], [18]- [21].…”

Section: Introductionsupporting

confidence: 52%

DeepEnzyPred: A Bi-Layered Deep Learning Framework for prediction of Bacteriophage Enzymes and their Sub-Hydrolases Enzymes via Novel Multi Level- Multi Thresholds Feature Selection technique

Wang¹,

Khan

Ali

et al. 2020

Preprint

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BackgroundBacteriophage or phage is a type of virus that replicates itself inside bacteria. It consist of genetic material surrounded by a protein structure. Bacteriophage plays a vital role in the domain of phage therapy and genetic engineering. Phage and hydrolases enzyme proteins have a significant impact on the cure of pathogenic bacterial infections and disease treatment. Accurate identification of bacteriophage proteins is important in the host subcellular localization for further understanding of the interaction between phage, hydrolases, and in designing antibacterial drugs. Looking at the significance of Bacteriophage proteins, besides wet laboratory-based methods several computational models have been developed so far. However, the performance was not considerable due to inefficient feature schemes, redundancy, noise, and lack of an intelligent learning engine. Therefore we have developed an anovative bi-layered model name DeepEnzyPred. A Hybrid feature vector was obtained via a novel Multi-Level Multi-Threshold subset feature selection (MLMT-SFS) algorithm. A two-dimensional convolutional neural network was adopted as a baseline classifier.ResultsA conductive hybrid feature was obtained via a serial combination of CTD and KSAACGP features. The optimum feature was selected via a Novel Multi-Level Multi-Threshold Subset Feature selection algorithm. Over 5-fold jackknife cross-validation, an accuracy of 91.6 %, Sensitivity of 63.39%, Specificity 95.72%, MCC of 0.6049, and ROC value of 0.8772 over Layer-1 were recorded respectively. Similarly, the underline model obtained an Accuracy of 96.05%, Sensitivity of 96.22%, Specificity of 95.91%, MCC of 0.9219, and ROC value of 0.9899 over layer-2 respectivily.ConclusionThis paper presents a robust and effective classification model was developed for bacteriophage and their types. Primitive features were extracted via CTD and KSAACGP. A novel method (MLMT-SFS ) was devised for yielding optimum hybrid feature space out of primitive features. The result drew over hybrid feature space and 2D-CNN shown an excellent classification. Based on the recorded results, we believe that the developed predictor will be a valuable resource for large scale discrimination of unknown Phage and hydrolase enzymes in particular and new antibacterial drug design in pharmaceutical companies in general.

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Predicted structure of tail‐fiber proteins of T‐even type phages

Cited by 10 publications

References 17 publications

Functional and Evolutionary Characterization of a Gene Transfer Agent’s Multilocus “Genome”

Functional and Evolutionary Characterization of a Gene Transfer Agent’s Multilocus “Genome”

Inhibition of parvovirus minute virus of mice replication by a peptide involved in the oligomerization of nonstructural protein NS1

DeepEnzyPred: A Bi-Layered Deep Learning Framework for prediction of Bacteriophage Enzymes and their Sub-Hydrolases Enzymes via Novel Multi Level- Multi Thresholds Feature Selection technique

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Predicted structure of tail‐fiber proteins of T‐even type phages

Cited by 10 publications

References 17 publications

Functional and Evolutionary Characterization of a Gene Transfer Agent’s Multilocus “Genome”

Functional and Evolutionary Characterization of a Gene Transfer Agent’s Multilocus “Genome”

Inhibition of parvovirus minute virus of mice replication by a peptide involved in the oligomerization of nonstructural protein NS1

DeepEnzyPred: A Bi-Layered Deep Learning Framework for prediction of Bacteriophage Enzymes and their&nbsp;Sub-Hydrolases Enzymes via Novel Multi Level- Multi Thresholds Feature Selection technique

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Product

Resources

About

DeepEnzyPred: A Bi-Layered Deep Learning Framework for prediction of Bacteriophage Enzymes and their Sub-Hydrolases Enzymes via Novel Multi Level- Multi Thresholds Feature Selection technique