Bioinformatic Analysis of Yeast Two-Hybrid Next-Generation Interaction Screen Data

Yeast two-hybrid next-generation interaction screening (Y2H-NGIS) uses the output of next-generation sequencing to mine for novel protein-protein interactions. Here, we outline the analytics underlying Y2H-NGIS datasets. Different systems, libraries, and experimental designs comprise Y2H-NGIS methodologies. We summarize the analysis in several layers that comprise the characterization of baits and preys, quantification, and identification of true interactions for subsequent secondary validation. We present two software designed for this purpose, NGPINT and Y2H-SCORES, which are used as front-end and back-end tools in the analysis. Y2H-SCORES software can be used and adapted to analyze different datasets not only from Y2H-NGIS but from other techniques ruled by similar biological principles.

Biochemical and computational approaches to understand venom toxin-toxin interaction

Snake venoms are mainly composed of proteins and peptides (venom toxins). The venom transcriptomes and proteomes have been extensively investigated; however, venom toxin-toxin interactions remain poorly characterized. We detected the interaction of venom Asp49-PLA₂ and 3FTx using biochemical and computational approaches. A stable structure of Asp49-PLA₂-3FTx was identified, and the interface of Asp49-PLA₂ and 3FTx was analyzed. The approaches will shed light on understanding the venom complexity and deciphering the synergistic effects of venom toxins.

Structure and function of S9 segment of grass carp reovirus Anhui strain

A highly virulent grass carp reovirus (GCRV) strain, named GCRV-AH528, was recently purified from a diseased grass carp with hemorrhage disease in Anhui, China. GCRV-AH528 S9 segment was 1320 nucleotides in length and encoded a 418 amino acid VP6 protein. BLAST search showed that the VP6 protein owned a conserved domain belonging to the reoviral σ2 family. Phylogenetic analysis of VP6 presented that GCRV-AH528 belonged to GCRV genotype II, which was more closely related to Orthoreovirus than GCRV genotype I and genotype III. Further analysis revealed that GCRV-AH528 S9 and mammalian orthoreovirus S8 might have evolved from a common ancestral precursor and have identical mechanism in virus assembly. The expression level of vp6 gene was detected by quantitative real-time PCR (qRT-PCR). Over time, the expression level of vp6 gradually increased in Ctenopharyngodon idellus kidney cells. However, the level of vp6 expression in blood sharply increased at 4-6 days, and then decreased to a low level after GCRV-AH528 challenge (P < 0.05). The vp6 gene was detected in all tissues examined, whereas at relatively higher levels in blood, kidney, and liver (P < 0.05). The yeast two-hybrid (Y2H) system was used to identify VP6 self-interaction, while no interaction was detected in VP6-VP6. This study not only revealed the S9 segment structure and expression pattern but also analyzed the VP6 mechanism by yeast hybridization method. The present study provides valuable informations for further experimental design and investigation of VP6 functions.

The interaction between host Annexin A2 and viral Nsp9 is beneficial for replication of porcine reproductive and respiratory syndrome virus

Non-structural protein 9 (Nsp9), a RNA-dependent RNA polymerase (RdRp) of the porcine reproductive and respiratory syndrome virus (PRRSV), is necessary for PRRSV replication. However, the binding partners of Nsp9 have not been identified. In this study, seven host proteins were identified as Nsp9-binding proteins using yeast two-hybrid (Y2H). Among of them, we confirmed the interaction of Nsp9 with Annexin A2 (ANXA2) using Y2H, Co-immunoprecipitation (Co-IP), GST pulldown and immunofluorescence assay (IFA). We found that only full-length ANXA2 could bind with Nsp9 in vitro and Nsp9 interacted with endogenous ANXA2 in PRRSV-infected MARC-145 cells. In addition, we found that the Nsp9-ANXA2 interaction was partially reduced by RNase A treatment. Furthermore, PRRSV growth was significantly hindered in ANXA2-knockdown MARC-145 cells. Taken together, these results indicate that Nsp9 binding partner ANXA2 is beneficial for PRRSV replication.