Autographa Californica Multicapsid Nucleopolyhedrovirus Research Articles

Serpin-4 Facilitates Baculovirus Infection by Inhibiting Melanization in Asian Corn Borer, Ostrinia furnacalis (Guenée).

Phenoloxidase (PO)–catalyzed melanization is a vital immune response in insects for defense against pathogen infection. This process is mediated by clip domain serine proteases and regulated by members of the serpin superfamily. We here revealed that the infection of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) significantly inhibited the PO activity in Ostrinia furnacalis hemolymph and induced the expression of O. furnacalis serpin–4. Addition of recombinant serpin-4 protein to O. furnacalis hemolymph resulted in a great increase of AcMNPV copies. Serpin-4 significantly suppressed the PO activity and the amidase activity in cleaving colorimetric substrate IEARpNA (IEARase activity) of hemolymph. Further experiments indicated it formed covalent complexes with three serine proteases (SP1, SP13 and SP105) and prevented them from cleaving their cognate downstream proteases in vitro. Altogether, O. furnacalis melanization restricted AcMNPV replication and serpin-4 facilitated AcMNPV infection by inhibiting serine proteases, SP1, SP13, and SP105 which were all involved in the melanization response.

Carbohydrate metabolism is a determinant for the host specificity of baculovirus infections

SummaryBaculoviruses Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) and Bombyx mori nucleopolyhedrovirus (BmNPV) have highly similar genome sequences but exhibit no overlap in their host range. After baculovirus infects nonpermissive larvae (e.g., AcMNPV infecting B. mori or BmNPV infecting Spodoptera litura), we found that stored carbohydrates, including hemolymph trehalose and fat body glycogen, are rapidly transformed into glucose; enzymes involved in glycolysis and the TCA cycle are upregulated and produce more ATP; adenosine signaling that regulates glycolytic activity is also increased. Subsequently, phagocytosis in cellular immunity and the expression of genes involved in humoral immunity increase significantly. Moreover, inhibiting glycolysis and the expression of gloverins in nonpermissive hosts increased baculovirus infectivity, indicating that the stimulated energy production is designed to support the immune response against infection. Our study highlights that alteration of the host's carbohydrate metabolism is an important factor determining the host specificity of baculoviruses, in addition to viral factors.

Ac25 in Autographa californica multiple nucleopolyhedrovirus was crucial for progeny budded virion production

To analyze the effect of Ac25 on the proliferation of AcMNPV (Autographa californica multicapsid nucleopolyhedrovirus) progeny virus and its function in virogenic stroma. AcMNPV is a model of baculovirus and is the most widely studied baculovirus. Ac25, as a single-stranded DNA-binding protein, is involved in viral genomic DNA replication. Viral proliferation assay showed that AcMNPV progeny virus could not be produced when Ac25 was knocked out, which indicated it was crucial for BV production. Absolute quantitative PCR analysis indicated that Ac25 was able to promote replication of the AcMNPV genome in host Sf9 cells. It was also found that Ac25 could increase the transcription level of 38k and vp39 late expression genes, and inhibit host cell proliferation. Ac25 is highly accumulated in the nucleus and promotes progeny virus production by stimulating viral genome replication and up-regulating the expression of late genes. Two potential applications of vAc-Ac25-EGFP were proposed: an improved bac-to-bac eukaryotic protein expression systems and biopesticides.

Baculovirus entire ORF1629 is not essential for viral replication.

It is generally accepted that ORF1629 is essential for baculovirus replication, which has enabled isolation of recombinant viruses in a baculovirus expression system using linearized viral DNA. ORF1629-defective viruses cannot replicate in insect cells; only recombinant virus with complete ORF1629 restoration by recombination can propagate, allowing for pure isolation and the development of bacmids for easy selection of recombinant viruses. We inadvertently found proliferation in insect cells of a bacmid lacking a complete ORF1629. PCR indicated no other viruses but a lack of complete ORF1629 in the proliferated bacmid, suggesting that the baculovirus propagated without a complete ORF1629. Lack of ORF1629 decreased the virus growth rate and yield; it also increased the occlusion body (OB) size but decreased its yield. These results were confirmed for Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) and Bombyx mori NPV (BmNPV). Thus, entire ORF1629 is not essential for viral replication, though it does affect the virus growth rate, yield, and size and OB production.

Insect-resistant Mechanism of Recombinant Baculovirus AcMNPV-PK2-EGFP against Spodoptera exigua Larvae

Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) is a kind of potential biological insecticide. Ac-PK2 protein encoded by orf123 in AcMNPV genome can inhibit eIF2α family kinases to increase viral adaptation in vivo. In our previous study, it was found that recombinant AcMNPV-PK2-EGFP showed high virulence and anti-insect activity against Sf9 cells and Spodoptera exigua larvae. In this study, we investigated the function of Ac-PK2 protein in the insecticidal activity of AcMNPV and the anti-insect mechanism. AcMNPV-PK2-EGFP up-regulated the expression of Ac-pk2 gene in midgut and nerve cord in infected Spodoptera exigua larvae, compared with these in wild-type treatment group. Transcriptional level of BmK IT and detoxication related genes in epidermis, midgut and nerve cord was detected by quantitative PCR. Phenoloxidase activity assay showed that the insect’s humoral immunity was affected by AcMNPV-PK2-EGFP in a time-effect relationship. Western blot analysis of P53 protein indicated the apoptotic level in the midgut tissue was higher in AcMNPV-BmK IT and AcMNPV-PK2-EGFP co-infeced Spodoptera exigua larvae than that in other treatment groups at 4 h and 8 h postinfection. These results provided a theoretical basis to study the application of AcMNPV-PK2-EGFP as a biological insecticide.

Sequential deletion of AcMNPV homologous regions leads to reductions in budded virus production and late protein expression

Homologous regions (hrs) have been predicted to act as origins of baculovirus DNA replication. Hrs have also been shown to function as enhancers of virus transcription. Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) carries eight hrs. In order to assess the role of hrs in virus replication in vivo, we applied a two-step RED recombination system for site-specific mutagenesis to sequentially delete each hr from a bacmid copy of AcMNPV. We then characterized the ability of the bacmids carrying different numbers of hrs or no hr to produce polyhedra and budded virus in transfected cells. We also investigated the ability of virus supernatants from transfected cells to produce budded virus and polyhedra when used to infect cells. We also characterized the expression of specific early and late virus proteins in transfected cells. The results demonstrated that removal of five hrs had little or no effect on virus infection but deleting all eight hrs compromised budded virus production and delayed early and late gene expression but did not completely eliminate assembly of infectious virus. We conclude that multiple hrs ensure an effective virus infection cycle with production of high titers of budded virus and polyhedra.

The Functional Oligomeric State of Tegument Protein GP41 Is Essential for Baculovirus Budded Virion and Occlusion-Derived Virion Assembly.

gp41, one of the baculovirus core genes, encodes the only recognized tegument (O-glycosylated) protein of the occlusion-derived virion (ODV) phenotype so far. A previous study using a temperature-sensitive Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) mutant showed that GP41 plays a crucial role in budded virion (BV) formation. However, the precise function of GP41 in the baculovirus replication cycle remains unclear. In this study, AcMNPV GP41 was found to accumulate around the ring zone (RZ) region within the infected nucleus and finally assembled into both BVs and ODVs. Deletion of gp41 from the AcMNPV genome showed that BVs were no longer formed and ODVs were no longer assembled, suggesting the essential role of this gene in baculovirus virion morphogenesis. In infected cells, besides the 42-kDa monomers, dimers and trimers were detected under nonreducing conditions, whereas only trimeric GP41 forms were selectively incorporated into BVs or ODVs. Mutations of all five cysteines in GP41 individually had minor effects on GP41 oligomer formation, albeit certain mutations impaired infectious BV production, suggesting flexibility in the intermolecular disulfide bonding. Single mutations of key leucines within two predicted leucine zipper-like motifs did not interfere with GP41 oligomerization or BV and ODV formation, but double leucine mutations completely blocked oligomerization of GP41 and progeny BV production. In the latter case, the usual subcellular localization, especially RZ accumulation, of GP41 was abolished. The above findings clearly point out a close correlation between GP41 oligomerization and function and therefore highlight the oligomeric state as the functional form of GP41 in the baculovirus replication cycle.IMPORTANCE The tegument, which is sandwiched between the nucleocapsid and the virion envelope, is an important substructure of many enveloped viruses. It is composed of one or more proteins that have important functions during virus entry, replication, assembly, and egress. Unlike another large DNA virus (herpesvirus) that encodes an extensive set of tegument components, baculoviruses very likely exploit the major tegument protein, GP41, to execute functions in baculovirus virion morphogenesis and assembly. However, the function of this O-glycosylated baculovirus tegument protein remains largely unknown. In this study, we identified trimers as the functional structure of GP41 in baculovirus virion morphogenesis and showed that both disulfide bridging and protein-protein interactions via the two leucine zipper-like domains are involved in the formation of different oligomeric states. This study advances our understanding of the unique viral tegument protein GP41 participating in the life cycle of baculoviruses.

Identification and characterization of two novel C-type lectins from the larvae of housefly, Musca domestica L.

Lectins and antimicrobial peptides (AMPs) are widely distributed in various insects and play crucial roles in primary host defense against pathogenic microorganisms. Two AMPs (cecropin and attacin) have been identified and characterized in the larvae of housefly. In this study, two novel C-type lectins (CTLs) were obtained from Musca domestica, while their agglutinating and antiviral properties were evaluated. Real-time PCR analysis showed that the mRNA levels of four immune genes (MdCTL1, MdCTL2, Cecropin, and Attacin) from M. domestica were significantly upregulated after injection with killed Gram-negative Escherichia coli. Moreover, purified MdCTL1-2 proteins can agglutinate E. coli and Staphylococcus aureus in the presence of calcium ions, suggesting their immune function is Ca2+ dependent. Sequence analysis indicated that typical WND and QPD motifs were found in the Ca2+ -binding site 2 of carbohydrate recognition domain from MdCTL1-2, which was consistent with their agglutinating activities. Subsequently, antiviral experiments indicated that MdCTL1-2 proteins could significantly reduce the infection rate of Spodoptera frugiperda 9 cells by the baculovirus Autographa californica multicapsid nucleopolyhedrovirus, indicating they might play important roles in insect innate immunity against microbial pathogens. In addition, MdCTL1-2 proteins could effectively inhibit the replication of influenza H1 N1 virus, which was similar to the effect of ribavirin. These results suggested that two novel CTLs could be considered a promising drug candidate for the treatment of influenza. Moreover, it is believed that the discovery of the CTLs with antiviral effects in M. domestica will improve our understanding of the molecular mechanism of insect immune response against viruses.

Production of GP64-free virus-like particles from baculovirus-infected insect cells

The retroviral Gag protein is frequently used to generate 'virus-like particles' (VLPs) for a variety of applications. Retroviral Gag proteins self-assemble and bud at the plasma membrane to form enveloped VLPs that resemble natural retrovirus virions, but contain no viral genome. The baculovirus expression vector system has been used to express high levels of the retroviral Gag protein to produce VLPs. However, VLP preparations produced from baculovirus-infected insect cells typically contain relatively large concentrations of baculovirus budded virus (BV) particles, which are similar in size and density to VLPs, and thus may be difficult to separate when purifying VLPs. Additionally, these enveloped VLPs may have substantial quantities of the baculovirus-encoded GP64 envelope protein in the VLP envelope. Since VLPs are frequently produced for vaccine development, the presence of the GP64 envelope protein in VLPs, and the presence of Autographa californica multicapsid nucleopolyhedrovirus BVs in VLP preparations, is undesirable. In the current studies, we developed a strategy for reducing BVs and eliminating GP64 in the production of VLPs, by expressing the human immunodeficiency virus type 1 gag gene in the absence of the baculovirus gp64 gene. Using a GP64null recombinant baculovirus, we demonstrate Gag-mediated VLP production and an absence of GP64 in VLPs, in the context of reduced BV production. Thus, this approach represents a substantially improved method for producing VLPs in insect cells.

Baculoviruses require an intact ODV entry-complex to resist proteolytic degradation of per os infectivity factors by co-occluded proteases from the larval host.

Baculoviruses orally infect caterpillars in the form of occlusion-derived viruses (ODVs). The ODV-envelope contains a number of proteins which are essential for oral infectivity, called per os infectivity factors (PIFs). Most of these PIFs are involved in the formation of an ODV-entry complex that consists of a stable core, formed by PIF1, PIF2, PIF3 and PIF4, and the more loosely associated PIFs P74 (PIF0) and P95 (PIF8). PIF1, PIF2 and PIF3 are essential for formation of the stable core, whereas deletion of the pif4 gene results in the formation of a smaller complex. P74 is not needed for formation of the stable core. We show here in larva-derived ODVs of the Autographa californica multicapsid nucleopolyhedrovirus that PIF-proteins are degraded by host-derived proteases after deletion of a single pif-gene. Constituents of the stable core-complex appeared to be more resistant to proteases as part of the complex than as monomer, as in ODVs of a p74 deletion mutant only the stable core was found but no PIF monomers. When the stable core lacks PIF4, it lost its proteolytic resistance as the resulting smaller core complex was degraded in a pif4 deletion mutant. We also identified PIF6 as a loosely associated component of the entry complex that appeared nevertheless important for the proteolytic resistance of the stable core, which was degraded after deletion of pif6. We conclude from these results that an intact entry-complex in the ODV-envelope is prerequisite for proteolytic resistance of PIF-proteins under the alkaline conditions of the larval midgut.

Gene delivery and gene expression in vertebrate using baculovirus Bombyx mori nucleopolyhedrovirus vector.

The baculovirus Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) has been investigated as a possible tool for gene therapy, but its inhibition by complement proteins in human serum limits its applicability. Here, we used the baculovirus Bombyx mori nucleopolyhedrovirus (BmNPV) to construct a gene delivery vector in which a reporter gene is driven by a cytomegalovirus IE promoter. Enhanced green fluorescent protein (EGFP) and luciferase reporter genes were used to test the efficiency of gene delivery. In vitro complement inactivation data showed that the recombinant BmNPV vector was more stable in human serum than the recombinant AcMNPV vector. The recombinant BmNPV vector successfully delivered the reporter genes into different tissues and organs in mice and chicks. These results demonstrate that the BmNPV vector is more stability against complement inactivation in human serum than the AcMNPV vector, and indicate that it may be useful as an effective gene delivery vector for gene therapy in vertebrates.

SfP53 and filamentous actin (F-actin) are the targets of viral pesticide AcMNPV-BmK IT (P10/PH) in host Spodoptera frugiperda 9 cells.

To analyze the anti-insect mechanism of viral pesticide AcMNPV-BmK IT(P10/PH) in the host Spodoptera frugiperda 9 (Sf9) cells. Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV)- mediated expression of BmK IT, regulated by P10 protein promoter (P10) and polyhedrosis promoter (PH), promoted the replication of progeny virus in host Sf9 cells. AcMNPV-BmK IT(P10) could accelerate the budding process (or speed) of budded virus (BV) in Sf9 cells. The impact of AcMNPV-BmK IT(P10) on the nuclear polymerization of filamentous actin (F-actin) participated in regulating the accelerated budding process. Unexpectedly, both AcMNPV-BmK IT(P10) and AcMNPV-BmK IT(PH) delayed the nuclear polymerization of F-actin and promoted the clearance of F-actin in the nucleus. SfP53, an important apoptosis factor, was involved in the regulation of AcMNPV-BmK IT(P10/PH) in Sf9 cells. AcMNPV-BmK IT(P10/PH) could also delay and promote the nuclear recruitment of SfP53 after 27h post infection (h p.i.). SfP53 and F-actin are the targets of viral pesticide AcMNPV-BmK IT (P10/PH) in host Sf9 cells, which provides the experimental basis for the development of recombinant baculovirus biopesticides.

Synthesis and Functional Characterization of MAF-1A Peptide Derived From the Larvae of Housefly, Musca domestica (Diptera: Muscidae).

The Musca domestica antifungal peptide-1A (MAF-1A peptide) from housefly larvae was synthesized by solid-phase synthesis technique, and antiviral, antioxidant, and antifungal properties were evaluated in this study. Present results indicated that it could significantly inhibit the infection of influenza virus H1N1, Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV), and Bombyx mori nuclear polyhydrosis virus (BmNPV), which displayed excellent virucidal activities. Antioxidant results demonstrated that the MAF-1A peptide had effective scavenging activity for hydroxyl and superoxide radicals, which were similar to that of ascorbic acid. Besides, antifungal results showed that it can also significantly inhibit the growth of four fungi, and the half inhibitory concentrations (IC50) values were ∼59.3, 84.2, 144.9, and 48.5 μg/ml, respectively, highlighting an important role of MAF-1A peptide in the defense of M domestica against pathogenic microorganisms. These results revealed that the MAF-1A peptide from housefly larvae has great potential as a natural ingredient for the exploitation of antiviral and antifungal therapeutic agents, avoiding abuse of chemical agents and environmental pollution.

AcMNPV-BmK IT improves the progeny virus production via baculovirus GP64 envelope fusion protein.

To analyze the mechanisms underlying the impact of recombinant Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV)-mediated BmK IT expression on the function of baculovirus GP64 envelope fusion protein and progeny virus production. Viral propagation assay indicated that overexpression GP64 could promote replication of AcMNPV. AcMNPV-mediated expression of BmK IT also promoted replication of AcMNPV. Immunofluorescence analysis showed BmK IT, which was regulated by very early promoter IE1 in AcMNPV, could make the GP64 protein move to the cytomembrane soon after transfection. BmK IT, which is regulated by P10 protein promoter (P10) and polyhedrosis promoter (PH), could promote the expression of GP64. BmK IT, regulated by very early promoter IE1, P10 protein promoter (P10) and PH, accelerated the expression of GP64 protein, promoted its early cytomembrane localization and then triggered virus budding and progeny virus production.

A New Continuous Cell Line of Spodoptera exigua and Its Susceptibility to Autographa californica Multicapsid Nucleopolyhedrovirus

A New Continuous Cell Line of Spodoptera exigua and Its Susceptibility to Autographa californica Multicapsid Nucleopolyhedrovirus

Budded baculovirus particle structure revisited

Baculoviruses are a group of enveloped, double-stranded DNA insect viruses with budded (BV) and occlusion-derived (ODV) virions produced during their infection cycle. BVs are commonly described as rod shaped particles with a high apical density of protein extensions (spikes) on the lipid envelope surface. However, due to the fragility of BVs the conventional purification and electron microscopy (EM) staining methods considerably distort the native viral structure. Here, we use cryo-EM analysis to reveal the near-native morphology of two intensively studied baculoviruses, Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) and Spodoptera exigua MNPV (SeMNPV), as models for BVs carrying GP64 and F as envelope fusion protein on the surface. The now well-preserved AcMNPV and SeMNPV BV particles have a remarkable elongated, ovoid shape leaving a large, lateral space between nucleocapsid (NC) and envelope. Consistent with previous findings the NC has a distinctive cap and base structure interacting tightly with the envelope. This tight interaction may explain the partial retaining of the envelope on both ends of the NC and the disappearance of the remainder of the BV envelope in the negative-staining EM images. Cryo-EM also reveals that the viral envelope contains two layers with a total thickness of ≈6–7nm, which is significantly thicker than a usual biological membrane (<4nm) as measured by X-ray scanning. Most spikes are densely clustered at the two apical ends of the virion although some envelope proteins are also found more sparsely on the lateral regions. The spikes on the surface of AcMNPV BVs appear distinctly different from those of SeMNPV. Based on our observations we propose a new near-native structural model of baculovirus BVs.

A simple plasmid-based transient gene expression method using High Five cells

The High Five (H5) cell line, derived from the lepidopteran Trichoplusia ni, is one of the major insect cell hosts for the production of recombinant proteins using the baculovirus expression vector system (BEVS). Here, we describe a simple polyethylenimine (PEI)-based transient gene expression (TGE) process for the rapid production of recombinant proteins from suspension-adapted H5 cells. The method was optimized using two model proteins, enhanced green fluorescent protein (EGFP) and human tumor necrosis factor receptor-Fc fusion protein (TNFR-Fc). After screening several promoter and enhancer combinations for high levels of TNFR:Fc production, an expression vector containing the Autographa californica multicapsid nucleopolyhedrovirus immediate early 1 (ie1) promoter and homologous region 5 (hr5) enhancer was selected. Cells were transfected at a density of 2×106 cells/mL by direct addition of DNA and PEI. Under optimized conditions, a 90% transfection efficiency (percentage of EGFP-positive cells) was obtained. In addition, we observed volumetric TNFR-Fc yields over 150μg/mL within 4 days of transfection. The method was found to be reproducible and scalable to 300mL. This plasmid-based transient transfection process is a simple and efficient alternative to the BEVS for recombinant protein production in H5 cells.

Temporal characterization of protein production levels from baculovirus vectors coding for GFP and RFP genes under non-conventional promoter control.

The ease of use and versatility of the Baculovirus Expression Vector System (BEVS) has made it one of the most widely used systems for recombinant protein production However, co-expression systems currently in use mainly make use of the very strong very late p10 and polyhedron (polh) promoters to drive expression of foreign genes, which does not provide much scope for tailoring expression ratios within the cell. This work demonstrates the use of different Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) promoters to control the timing and expression of two easily traceable fluorescent proteins, the enhanced green fluorescent protein (eGFP), and a red fluorescent protein (DsRed2) in a BEVS co-expression system. Our results show that gene expression levels can easily be controlled using this strategy, and also that modulating the expression level of one protein can influence the level of expression of the other protein within the system, thus confirming the concept of genes "competing" for limited cellular resources. Plots of "expression ratios" of the two model genes over time were obtained, and may be used in future work to tightly control timing and levels of foreign gene expression in an insect cell co-expression system.

Regulation analysis of AcMNPV-mediated expression of a Chinese scorpion neurotoxin under the IE1, P10 and PH promoter in vivo and its use as a potential bio-insecticide.

To analyze the regulation mechanism of AcMNPV (Autographa californica multicapsid nucleopolyhedrovirus)-mediated expression of BmK IT under IE1, P10 and PH promoters in the larva of Heliothis armigera.. The transcription level of BmK IT gene in midgut and epidermal tissue was analyzed by quantitative PCR. The start time of transcription of recombinant BmK IT gene was early under the regulation of IE promoter, whereas transcription of BmK IT was high under the regulation of P10 promoter in the midgut tissue of infected larvae. TdT-UTP nick-end labeling (TUNEL) assay showed the degree of apoptotic cell death in the midgut tissue of AcMNPV-BmK IT-transfected insect larvae was higher than that in the AcMNPV treatment group at 8h post-infection. The time-effect relationship between the insect's humoral immunity and regulation of promoters was confirmed in the phenoloxidase activity assay. The anti-insect mechanism and regulation of different promoters in AcMNPV-BmK IT at molecular and cellular levels provide an experimental basis for the development of recombinant baculovirus biopesticides.

Tightly regulated expression of Autographa californica multicapsid nucleopolyhedrovirus immediate early genes emerges from their interactions and possible collective behaviors.

To infect their hosts, DNA viruses must successfully initiate the expression of viral genes that control subsequent viral gene expression and manipulate the host environment. Viral genes that are immediately expressed upon infection play critical roles in the early infection process. In this study, we investigated the expression and regulation of five canonical regulatory immediate-early (IE) genes of Autographa californica multicapsid nucleopolyhedrovirus: ie0, ie1, ie2, me53, and pe38. A systematic transient gene-expression analysis revealed that these IE genes are generally transactivators, suggesting the existence of a highly interactive regulatory network. A genetic analysis using gene knockout viruses demonstrated that the expression of these IE genes was tolerant to the single deletions of activator IE genes in the early stage of infection. A network graph analysis on the regulatory relationships observed in the transient expression analysis suggested that the robustness of IE gene expression is due to the organization of the IE gene regulatory network and how each IE gene is activated. However, some regulatory relationships detected by the genetic analysis were contradictory to those observed in the transient expression analysis, especially for IE0-mediated regulation. Statistical modeling, combined with genetic analysis using knockout alleles for ie0 and ie1, showed that the repressor function of ie0 was due to the interaction between ie0 and ie1, not ie0 itself. Taken together, these systematic approaches provided insight into the topology and nature of the IE gene regulatory network.