Zheng Zhang1, Fen Yu1, Yuanqiang Zou2, Ye Qiu1, Aiping Wu3,4, Taijiao Jiang3,4, Yousong Peng1. 1. College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China. 2. Changsha Qiangze Biotech Co., Ltd, Changsha 410000, China. 3. Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China. 4. Suzhou Institute of Systems Medicine, Suzhou, Jiangsu 215123, China.
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.
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.