scholarly journals From phages to mammalian viruses: viral receptors play a central role in protein-protein interaction network

2019 ◽  
Author(s):  
Fen Yu ◽  
Zheng Zhang ◽  
Yuanqiang Zou ◽  
Ye Qiu ◽  
Aiping Wu ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Protein Interaction ◽  
Outer Membrane Proteins ◽  
Host Cells ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Virus Receptors ◽  
Protein Receptors ◽  
Mammalian Virus

AbstractMotivationReceptors on host cells play a critical role in viral infection. How phages select receptors is still unknown.ResultsHere, we manually curated a high-quality database named phageReceptor, including 355 pairs of phage-host receptor interactions, 280 unique viral species or sub-species and 64 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The protein receptors were highly diverse in their structures, and had little homology with mammalian virus receptors. Further functional characterization of phage protein receptors in Escherichia coli showed that they had larger node degrees and betweennesses in the protein-protein interaction (PPI) network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins, or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors, suggesting that viral protein receptors play a central role in the host’s PPI network. The study deepens our understanding of virus-host interactions.AvailabilityThe database of phageReceptor is publicly accessible at http://www.computationalbiology.cn/viralRecepetor/index.html.

scholarly journals Phage protein receptors have multiple interaction partners and high expressions

2020 ◽  
Vol 36 (10) ◽  
pp. 2975-2979 ◽  
Author(s):  
Zheng Zhang ◽  
Fen Yu ◽  
Yuanqiang Zou ◽  
Ye Qiu ◽  
Aiping Wu ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Host Cells ◽  
Supplementary Information ◽  
Interaction Partners ◽  
Virus Receptors ◽  
Phage Protein ◽  
Protein Receptors ◽  
Mammalian Virus ◽  
Multiple Interaction

Abstract Motivation Receptors on host cells play a critical role in viral infection. How phages select receptors is still unknown. Results Here, we manually curated a high-quality database named phageReceptor, including 427 pairs of phage–host receptor interactions, 341 unique viral species or sub-species and 69 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The phage protein receptors (PPRs) were highly diverse in their structures, and had little sequence identity and no common protein domain with mammalian virus receptors. Further functional characterization of PPRs in Escherichia coli showed that they had larger node degrees and betweennesses in the protein–protein interaction network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors reported in previous studies, suggesting that viral protein receptors tend to have multiple interaction partners and high expressions. The study deepens our understanding of virus–host interactions. Availability and implementation phageReceptor is publicly available from: http://www.computationalbiology.cn/phageReceptor/index.html. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Physical Linkage of Naturally Complexed Bacterial Outer Membrane Proteins Enhances Immunogenicity

2007 ◽  
Vol 76 (3) ◽  
pp. 1223-1229 ◽  
Author(s):  
Henriette Macmillan ◽  
Junzo Norimine ◽  
Kelly A. Brayton ◽  
Guy H. Palmer ◽  
Wendy C. Brown
Keyword(s):  
T Cell ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Outer Membrane Proteins ◽  
Surface Protein ◽  
Host Cells ◽  
Effective Vaccine ◽  
T Cell Epitopes ◽  
Carrier Effect ◽  
Major Surface

ABSTRACTThe outer membrane proteins (OMPs) of bacterial pathogens are essential for their growth and survival and especially for attachment and invasion of host cells. Since the outer membrane is the interface between the bacterium and the host cell, outer membranes and individual OMPs are targeted for development of vaccines against many bacterial diseases. Whole outer membrane fractions often protect against disease, and this protection cannot be fully reproduced by using individual OMPs. Exactly how the interactions among individual OMPs influence immunity is not well understood. We hypothesized that one OMP rich in T-cell epitopes can act as a carrier for an associated OMP which is poor in T-cell epitopes to generate T-dependent antibody responses, similar to the hapten-carrier effect. Major surface protein 1a (MSP1a) and MSP1b1 occur as naturally complexed OMPs in theAnaplasma marginaleouter membrane. Previous studies demonstrated that immunization with the native MSP1 heteromer induced strong immunoglobulin G (IgG) responses to both proteins, but only MSP1a stimulated strong CD4+T-cell responses. Therefore, to test our hypothesis, constructs of CD4+T-cell epitopes from MSP1a linked to MSP1b1 were compared with individually administered MSP1a and MSP1b1 for induction of MSP1b-specific IgG. By linking the T-cell epitopes from MSP1a to MSP1b1, significantly higher IgG titers against MSP1b1 were induced. Understanding how the naturally occurring intermolecular interactions between OMPs influence the immune response may lead to more effective vaccine design.

scholarly journals Mutagenesis and Functional Reconstitution of Chlamydial Major Outer Membrane Proteins: VS4 Domains Are Not Required for Pore Formation but Modify Channel Function

2001 ◽  
Vol 69 (3) ◽  
pp. 1671-1678 ◽  
Author(s):  
E. S. Hughes ◽  
K. M. Shaw ◽  
R. H. Ashley
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Single Channel ◽  
Outer Membrane Proteins ◽  
Host Cells ◽  
Chimeric Proteins ◽  
Functional Differences ◽  
And Function ◽  
Bacterial Porins ◽  
Medical Interest

ABSTRACT Chlamidial organisms are obligate intracellular pathogens containing highly antigenic porin-like major outer membrane proteins (MOMPs). MOMP epitopes are of substantial medical interest, and they cluster within four relatively short variable (VS) domains. If MOMPs adopt a β-barrel fold, like bacterial porins, the VS domains may form extramembranous loops and the conserved regions of the protein may correspond to predicted membrane-located β-strands. However, molecular studies on native MOMPs have been hampered by the need to culture chlamydiae in eukaryotic host cells and purification and reconstitution remain problematic. In addition, the organisms are difficult to manipulate genetically, and it has also been difficult to functionally reconstitute recombinant MOMPs. To help overcome these problems and improve our understanding of MOMP structure and function, we cloned and expressed C. trachomatis and C. psittaci MOMPs and functionally reconstituted them at the single-channel level. We measured significant functional differences between the two proteins, and by removing and exchanging VS4, we tested the hypothesis that the largest variable domain forms an extramembranous loop that contributes to these differences. Proteins in which VS4 was deleted continued to form functional ion channels, consistent with the idea that the domain forms an extramembranous protein loop and incompatible with models in which it contributes to predicted membrane-located β-strands. Additionally, the properties of the chimeric proteins strongly suggested that the VS4 domain interacts closely with other regions of the protein to form the channel entrance or vestibule. Our approach can be used to probe structure-function relationships in chlamydial MOMPs and may have implications for the generation of effective antichlamydial vaccines.

Protein-Protein Interaction (PPI) Network: Recent Advances in Drug Discovery

2017 ◽  
Vol 18 (1) ◽  
pp. 5-10 ◽  
Author(s):  
Alexiou Athanasios ◽  
Vairaktarakis Charalampos ◽  
Tsiamis Vasileios ◽  
Ghulam Ashraf
Keyword(s):  
Drug Discovery ◽  
Protein Interaction ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Recent Advances

scholarly journals The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 451
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Subcellular Location ◽  
Low Complexity ◽  
Extracellular Proteins ◽  
Bacterial Strains ◽  
Bacterial Proteins ◽  
Protein Subcellular Location

Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence in eukaryotes. Studying their conservation could help provide hypotheses about their function. To obtain the appropriate evolutionary focus for this rapidly evolving feature, here we study the conservation of LCRs in bacterial strains and compare their high variability to the closeness of the strains. For this, we selected 20 taxonomically diverse bacterial species and obtained the completely sequenced proteomes of two strains per species. We calculated all orthologous pairs for each of the 20 strain pairs. Per orthologous pair, we computed the conservation of two types of LCRs: compositionally biased regions (CBRs) and homorepeats (polyX). Our results show that, in bacteria, Q-rich CBRs are the most conserved, while A-rich CBRs and polyA are the most variable. LCRs have generally higher conservation when comparing pathogenic strains. However, this result depends on protein subcellular location: LCRs accumulate in extracellular and outer membrane proteins, with conservation increased in the extracellular proteins of pathogens, and decreased for polyX in the outer membrane proteins of pathogens. We conclude that these dependencies support the functional importance of LCRs in host–pathogen interactions.

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