Characterization of the RNA-binding domain in the Dendrolimus punctatus cytoplasmic polyhedrosis virus nonstructural protein p44

WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

The most powerful approach to detect distant homologues of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we applied a powerful sequence-based procedure to identify distant homologues of viral proteins. It relies on three principles: (1) traces of sequence similarity can persist beyond the significance cutoff of homology detection programmes; (2) candidate homologues can be identified among proteins with weak sequence similarity to the query by using 'contextual' information, e.g. taxonomy or type of host infected; (3) these candidate homologues can be validated using highly sensitive profile-profile comparison. As a test case, this approach was applied to a protein without known homologues, encoded by ORF4 of Lake Sinai viruses (which infect bees). We discovered that the ORF4 protein contains a domain that has homologues in proteins from >20 taxa of viruses infecting arthropods. We called this domain 'widespread, intriguing, versatile' (WIV), because it is found in proteins with a wide variety of functions and within varied domain contexts. For example, WIV is found in the NSs protein of tospoviruses, a global threat to food security, which infect plants as well as their arthropod vectors; in the RNA2 ORF1-encoded protein of chronic bee paralysis virus, a widespread virus of bees; and in various proteins of cypoviruses, which infect the silkworm Bombyx mori. Structural modelling with AlphaFold indicated that the WIV domain has a previously unknown fold, and bibliographical evidence suggests that it facilitates infection of arthropods.

The RNA Directed DNA Methylation (RdDM) Pathway Regulates Anthocyanin Biosynthesis in Crabapple (Malus cv. spp.) Leaves by Methylating the McCOP1 Promoter

The synthesis of anthocyanin pigments in plants is known to be regulated by multiple mechanisms, including epigenetic regulation; however, the contribution of the RNA-directed DNA methylation (RdDM) pathway is not well understood. Here, we used bisulfite sequencing and Real Time (RT)-quantitative (q) PCR to analyze the methylation level of the promoter of constitutively photomorphogenic 1 (McCOP1) from Malus cv. spp, a gene involved in regulating anthocyanin biosynthesis. The CHH methylation level of the McCOP1 promoter was negatively correlated with McCOP1 RNA expression, and inhibiting DNA methylation caused decreased methylation of the McCOP1 promoter and asymmetric cytosine CHH methylation. We observed that the McCOP1 promoter was a direct target of the RdDM pathway argonaute RISC component 4 (McAGO4) protein, which bound to a McCOP1 promoter GGTTCGG site. Bimolecular fluorescence complementation (BIFC) analysis showed that RNA-directed DNA methylation (McRDM1) interacted with McAGO4 and another RdDM protein, domains rearranged methyltransferase 2 (McDRM2), to regulate the CHH methylation of the McCOP1 promoter. Detection of CHH methylation and COP1 gene expression in the Arabidopsis thalianaatago4, atdrm2 and atrdm1 mutants showed that RDM1 is the effector of the RdDM pathway. This was confirmed by silencing McRDM1 in crabapple leaves or apple fruit, which resulted in a decrease in McCOP1 CHH methylation and an increase in McCOP1 transcript levels, as well as in anthocyanin accumulation. In conclusion, these results show that the RdDM pathway is involved in regulating anthocyanin accumulation through CHH methylation of the McCOP1 promoter.

Using non-smooth models to determine thresholds for microbial pest management

Releasing infectious pests could successfully control and eventually maintain the number of pests below a threshold level. To address this from a mathematical point of view, two non-smooth microbial pest-management models with threshold policy are proposed and investigated in the present paper. First, we establish an impulsive model with state-dependent control to describe the cultural control strategies, including releasing infectious pests and spraying chemical pesticide. We examine the existence and stability of an order-1 periodic solution, the existence of order-k periodic solutions and chaotic phenomena of this model by analyzing the properties of the Poincaré map. Secondly, we establish and analyze a Filippov model. By examining the sliding dynamics, we investigate the global stability of both the pseudo-equilibria and regular equilibria. The findings suggest that we can choose appropriate threshold levels and control intensity to maintain the number of pests at or below the economic threshold. The modelling and control outcomes presented here extend the results for the system with impulsive interventions at fixed moments.

Molecular characterization of protein p50 of Dendrolimus punctatus cytoplasmic polyhedrosis virus

Genome segment 7 of the 10-segmented RNA genomes of Dendrolimus punctatus cytoplasmic polyhedrosis virus (DpCPV) comprises 1502 nucleotides with one ORF of 1347 bp. This ORF was predicted to encode a protein of 448 amino acids with a molecular mass of 49,756 Da (p50). Antisera against both p50 and an antigen domain (AD) near the N-terminus of p50 specifically bound to a viral structural protein of ca. 33 kDa (V5), indicating that V5 was an N-terminal product of p50. Immunoblotting analysis with anti-p50 antibodies detected p50 and V5 molecules in the host midguts three days and five days post infection, respectively. The intracellular localization of p50 protein was examined by expressing truncations of p50 fused with GFP in recombinant baculovirus-infected Sf9 cells. The p50 protein was present in the cytoplasm of the cells, and the N-terminal portion (67-135 aa) of the protein played a key role in this localization.

Characterization of the RNA-binding regions in protein p36 of Heliothis armigera cypovirus 14

Some proteins of cypovirus (CPV) bind to RNA, probably contributing to the replication of viral genome. However, little is known about whether any protein from Heliothis armigera cypovirus (HaCPV) could bind to RNA. In this study, we cloned the ORF of segment 9 (S9) of HaCPV, serotype 14, into pMAL-c2X for the generation and purification of maltose binding protein (MBP) fused protein p36 (MBP-p36). The analysis of the RNA-binding properties of MBP-p36 revealed that p36, but not MBP alone, bound to ssRNA of CPV. Furthermore, the ssRNA-binding activities of p36 were significantly inhibited or completely eliminated by protein denaturants or unsuitable concentrations of NaCl. Importantly, the formation of ssRNA/p36 was only competitively inhibited by a heavy dose of competitive non-viral ssRNA or dsRNA, but not by ssDNA and dsDNA, suggesting that p36 bound to both ssRNA and dsRNA, but not DNA. Moreover, the characterization of different mutants of p36 revealed that the regions 1-26aa, 154-170aa, and 229-238aa, but not region 291-320aa, may be crucial for the ssRNA-binding ability of p36. Conceivably, the sensitivity of p36 to denaturants and the synergetic effect of different regions suggest that the RNA-binding ability of p36 may be conformation-dependent. Thus, our findings provide new insights into understanding the genomic function of HaCPV-14.

Identification of Transmembrane Domain of a Membrane Associated Protein NS5 of Dendrolimus punctatus Cytoplasmic Polyhedrosis Virus

We examined the intracellular localization of NS5 protein of Dendrolimus punctatus cytoplasmic polyhedrosis virus (DpCPV) by expressing NS5-GFP fusion protein and proteins from deletion mutants of NS5 in baculovirus recombinant infected insect Spodoptera frugiperda (Sf-9) cells. It was found that the NS5 protein was present at the plasma membrane of the cells, and that the N-terminal portion of the protein played a key role in the localization. A transmembrane region was identified to be present in the N-terminal portion of the protein, and the detailed transmembrane domain (SQIHMVWVKSGLVFF, 57-71aa) of N-terminal portion of NS5 was further determined, which was accorded with the predicted results, these findings suggested that NS5 might have an important function in viral life cycle.