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Size Does Matter: NanoLuc® Technologies Advance Virology Research

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Abstract

Recombinant reporter viruses are vital tools for studying the pathogenicity and transmission of viruses in animal models. Here we highlight several recent studies that use NanoLuc® and NanoBiT® technologies to investigate viral life cycles in vivo.

Kyle Hooper Promega Corporation Publication Date: September 2018; tpub_202

In 2012, a new reporter enzyme called NanoLuc® Luciferase (NLuc) and its detection reagent, Nano-Glo® Luciferase Assay System, were introduced. NLuc was molecularly evolved from a 19kDa deep sea shrimp luciferase to increase stability and improve brightness. The natural substrate of the original luciferase, coelenterazine, was chemically evolved to a brighter, more stable substrate, furimazine. Together, NLuc and furimazine produce a luminescent signal >100-fold brighter than either firefly luciferase (FLuc) or Renilla luciferase (RLuc). The bonus is that the NanoLuc® luminescent signal has a long lifetime, exhibiting glow kinetics rather than a rapid flash signal like other small, bright luciferases such as Gaussia luciferase. Additionally, other key features of NLuc made it an ideal reporter. The small 19kDa enzyme was thermally stable, active over a broad pH range and required no post-translational modifications or maturation after translation to make an active enzyme. NLuc produces blue light with maximum emission at 460nm. To learn more, details of the creation, characterization and early applications of NLuc and Nano-Glo® Assay System are found in Hall et al. (1) .

Luciferase enzymes are an important tool for making recombinant reporter viruses, which are used to further understanding of viral life cycles and lethality in animal models (2) . Though luciferases come with their challenges, viruses with embedded reporters make it easier to follow infection in the same animal over time using bioluminescent imaging. FLuc is most commonly used for in vivo animal imaging due to its emission at ~600nm in live animals, which is better for deep-tissue imaging. At 61kDa, FLuc is a rather large protein, and limitations on viral capsid size mean that many viral genomes cannot incorporate an additional 1,600+ nucleotides of DNA. Viruses are more tolerant of the 34kDa RLuc reporter, but imaging is difficult because its blue light emission is easily scattered within animals. While imaging the blue light of NLuc does present a challenge in animal models, the brightness and long lifetime of the signal, as well as its small size, are significant benefits. Gaussia luciferase is also a small, bright enzyme, but is challenging to work with in vivo due to secretion from the cell and a rapid flash signal.

Figure 1. Comparison of the coding region sizes of Firefly (FLuc), Renilla (RLuc) and NanoLuc® (NLuc) luciferases and the HiBiT bioluminescent protein tag. The size of the luciferases in kilodaltons (kDa) are listed to the right of each respective bar in the graph.

This paper will review two examples of how the NLuc size produced better, more stable recombinant viruses. See Table 1 for a more extensive list of NLuc-containing viruses or virus-like particles that have been cited in peer-reviewed publications. Recently, a short 11-amino acid bioluminescent protein tag was introduced that uses structural complementation to achieve a functional luciferase, which also can be applied to viral research. A review of two early papers using this peptide tag, known as HiBiT, follows the section concerning full-length NLuc.

 

Studies with Full-Length NanoLuc® Luciferase

 

NanoLuc® Luciferase means generating a near-native, replicative reporter Influenza A virus

Generating an influenza reporter virus is difficult for several reasons (3) :

  1. All the viral genes are critical in vivo, precluding simple gene replacement with a reporter.
  2. Compact genome does not tolerate large insertions, which are destabilized and lost over time.
  3. Insertions can severely attenuate replication.
  4. Insertions at the end of coding regions can disrupt packaging.

An influenza reporter virus would allow real-time analysis of the infection process in live animals rather than cell culture models, which is important for determining the pathogenicity and transmission potential of emerging influenza viruses.

Tran et al. overcame these challenges by using the small, bright NLuc and clever approaches to recombinant virus design. The polymerase subunit gene PA was known to tolerate insertions at the C terminus and was chosen as the integration site. Though PA-NLuc fusions were deemed as active as wild-type PA, the viral construct chosen used the self-cleaving 2A peptide from porcine teschovirus as a linker (ultimately producing separate PA and NLuc proteins) to avoid any problems with other PA functions like trafficking and assembly.

The recombinant NLuc virus replicated with near-native properties in culture and in vivo. Treatment with ribavirin demonstrated that the luminescence from NLuc was due to gene expression and not fortuitous carryover or packaging of NLuc. Cell-based assays comparing plaque forming units versus luminescence correlated well (r2 = 0.99), with the benefit that the NLuc assay takes 8 hours compared to the 48–72 hour plaque assay.

The NLuc virus exhibited pathogenicity and lethality in mice indistinguishable from the parental virus. The virus was used to perform in vivo imaging and to track viral load and spread of infection into mouse lungs. A known mutation that restricts replication of Influenza A strains to avian species was shown to produce the same phenotype with the NLuc virus. Thus, this reporter virus could evaluate emerging viruses as well as assess antivirals in animal models. Later work by the lab also demonstrated contact and airborne transmission of a different NLuc-expressing H1N1 influenza A virus in a ferret model (4) .

 

Integration of NanoLuc® Luciferase generates stable, replicative reporter alphaviruses

While reporter alphaviruses for tracking viral replication in vitro and in animals do exist, inserting the FLuc reporter gene has several disadvantages, namely:

  1. Potential for rapid transgene loss.
  2. Replication attenuation.

Sun, et al(5) sought to address these problems by choosing a different integration site and using NLuc.

Previous work directed reporter fusions to the poorly conserved carboxy-terminal half of nonstructural protein 3 (nsP3). Sun et al. targeted that site in Sindbis, Chikungunya, and both Eastern and Venezuelan equine encephalitis viruses with FLuc (61kDa; 1,650 nucleotides) or NLuc (19kDa; 513 nucleotides). Other sites and strategies were examined as well. An insertion site between the capsid and PE2 protein was used for both FLuc and NLuc with the Trosea asigna virus (TaV) peptide 2A sequence included to create the reporter without protein fusion. Recombinant viruses were also created expressing either NLuc or FLuc from a subgenomic promoter not fused to any viral protein, but still part of the viral genome.

Inserts with FLuc were rapidly lost, no matter which insertion method used, as judged by diminished luminescence over cell passages and Western blots demonstrating loss of expressed protein. The NLuc constructs were very stable. The nsP3 fusion, whether to FLuc or NLuc, showed lower expression compared to the nsP3 gene alone. Lethality studies confirmed that the TaV-NLuc constructs were just as lethal as the parent viruses. Imaging of animal models verified that the NLuc-expressing viruses replicated in vivo and spread throughout the animal whereas luminescence from FLuc-expressing viruses was localized to the site of injection due to loss of the FLuc insert after repeated replication.

 

Studies with HiBiT Bioluminescent Protein Tag

In 2016, we introduced a protein structural complementation technology called NanoLuc Binary Technology or NanoBiT® (6) . The initial peer-reviewed paper focused on how NLuc was divided between amino acids 156 and 157 to produce a 156aa subunit and a 13aa subunit. The larger subunit was molecularly evolved to improve stability and expression, yielding the LgBiT subunit. LgBiT has little inherent enzymatic activity. Over 350 peptide variants of the 13aa subunit were made in vitro and tested for both binding properties to LgBiT and structural complementation of LgBiT to produce a new functional enzyme (NanoBiT® Luciferase). Two peptides stood out: One that had minimal affinity for LgBiT, termed SmBiT; and one that had extremely high affinity for LgBiT, termed HiBiT. LgBiT and SmBiT subunits were employed to measure protein:protein interactions where the affinity of the proteins under study brings LgBiT and SmBiT into close enough proximity to interact. This intramolecular study of protein:protein interactions is performed using the NanoBiT® Protein:Protein Interaction System.

HiBiT could spontaneously complement LgBiT to form a NanoBiT® luciferase enzyme that is nearly as bright as NLuc. Work by Schwinn, et al. (7)  examined the utility of the HiBiT subunit as a bioluminescent protein tag. The HiBiT tag (11 amino acids) can be appended to a protein, and this fusion can be recognized by reagents containing the LgBiT subunit and furimazine substrate. Three detection reagents for HiBiT-tagged proteins are available: Nano-Glo® HiBiT Lytic Detection System, Nano-Glo® HiBiT Extracellular Detection System and a unique reagent for detecting HiBiT-tagged proteins on Western blots, the Nano-Glo® HiBiT Blotting System.

 

 

Figure 2. Schematic of HiBiT Detection with Nano-Glo® Detection Systems (top). Linearity of luminescent signal generated by the HiBiT/LgBiT NanoBiT® Luciferase (bottom). Luminescent signal generated either by full-length recombinant NanoLuc® Luciferase or by HaloTag®-HiBiT incubated with saturating LgBiT is shown in the graph.

Just as NLuc accelerated virology research due to its small size, the effect of HiBiT looks promising. Rather than contend with a 169aa (~500 nucleotides) reporter like NLuc, a small 11aa (33 nucleotide) insertion is now sufficient. Early examples of how the HiBiT tag could be used in virology have already been published.

 

HiBiT tagging simplifies research on West Nile Virus entry and release

Flaviviruses such as West Nile virus typically require biocontainment facilities to do conventional virology work. Investigations into the attachment of the virus to target cells and release of viral particles do not require the whole genome of the virus. Simply providing a cell with a plasmid containing the structural proteins results in budding of viral-like particles from the endoplasmic reticulum and secretion from the cell. These subviral particles (SVP) can be used to study the attachment of the virus to cells without the need of a biocontainment facility.

Sasaki et al. (8)  have developed a system to look for inhibitors of West Nile virus entry. These experiments depended upon an ELISA-based assay to quantitate the number of viral particles. Under the best conditions, the assay takes at least 2 hours with a limited range of quantitation (~twofold). HiBiT was incorporated into the intra-SVP loop of the E protein and used to make HiBiT-subviral particles (SVP-HiBiT). Plasmids containing the viral M protein and the HiBiT-E protein were transfected into 293T cells and the appearance of HiBiT-SVP in samples of the culture medium over a 48-hour period could be monitored using the Nano-Glo® HiBiT Extracellular Detection System. The Nano-Glo® HiBiT Assay took only 10 minutes to perform and showed a large linear quantitation range (~fivefold). The presence of the HiBiT sequence was confirmed by Western blot using the Nano-Glo® HiBiT Blotting System. An siRNA knockdown of the Rab11 G-protein greatly reduces secretion of conventional West Nile SVP and likewise inhibited release of the HiBiT-SVP.

Including the West Nile virus capsid protein with E and M proteins, along with a construct to make a subgenomic RNA with the packaging sequences, creates West Nile virus virus-like particles (VLPs). These VLPs can deliver a gene to target cells for expression. In addition, VLPs allow examination of cell attachment, and the subgenomic RNA can contain a reporter to demonstrate viral internalization. The HiBiT sequence was added to the C-terminus of the capsid protein and attachment and internalization of VLP-HiBiT was monitored using a Vero cell line stably expressing the LgBiT protein. The formation of the NanoBiT® enzyme that occurs when VLP-HiBiT was internalized was monitored using the Nano-Glo® Live Cell Assay System. The NLuc-VLP was used to demonstrate how the system could be used to screen for inhibitors of virus entry—in this case, an antibody to the West Nile virus E protein or inhibitors of clathrin-coated pit formation.

 

HiBiT tagging produces better reporter flaviviruses with near-native replication

Reporter viruses are useful for determining the viral life cycle and discovering required host cell proteins. A recombinant NLuc-hepatitis C virus (HCV) helped Puig-Basagoiti et al. (9)  determine the importance of host apolipoprotein E in secretion of the virus. The lab was concerned about the difference in replication of the virus that contained the full-length NLuc. Therefore, they tested the HiBiT tag to obtain better replication dynamics (10) . The lab produced HiBiT-tagged HCV, Dengue (DENV), Japanese encephalitis (JEV) and bovine viral diarrhea (BVDV) viruses and recovered stable HiBiT reporter viruses with better replication, significantly higher than viruses containing full-length reporters.

In vitro work to determine recombinant viral infectivity and replication rates was performed either in cells stably expressing the LgBiT or using the Nano-Glo® HiBiT Lytic Detection Reagent. The HiBiT-HCV was able to confirm the importance of apolipoprotein E to viral secretion. The HiBiT-JEV replicated in a variety of host cells including hamster (BHK21), human (HeLa, A549, Huh7), monkey (Vero E6) and mosquito (C6/36). The HiBiT-DENV was tested only in human and mosquito cells and found to replicate. With BVDV, HiBiT was fused to an envelope protein and the lab was concerned that the HiBiT fusion would alter viral particle formation. However, the fusion was found to have no effect in comparison to wild-type virus.

All four HiBiT viruses were tested for susceptibility to known flavivirus inhibitors and behaved like the parental viruses. HiBiT-HCV and HiBiT-JEV were used to screen a panel of 69 protease inhibitors and identified inhibitory compounds using the luciferase readout, rather than viral titers. The screen identified known HCV inhibitors and turned up a compound that was effective against HiBiT-JEV that, in turn, was effective against HiBiT-DENV. The HiBiT-HCV replicated in a human liver chimeric mouse model and responded to HCV inhibitor treatments.

 

Conclusions

Virus research is necessary to understand how viral diseases emerge and spread. Recombinant reporter viruses can help researchers uncover the inner workings of viruses. Viruses, however, have evolved minimal genomes to infect, replicate and spread, and do not tolerate extra genomic baggage very well. NLuc is a small, bright luciferase with a minimal effect on genomic size for many viruses of interest, making it an important research tool. The HiBiT bioluminescent protein tag further decreases the burden that must be carried by a recombinant reporter virus and offers a luminescent signal approaching NLuc when paired with its LgBiT binding partner in detection arrangements.

Table 1. Recombinant Virus or Virus-Like Particles Created with NanoLuc® Luciferase.

Adenovirus Zhang, W. et al. (2017) An engineered virus library as a resource for the spectrum-wide exploration of virus and vector diversity. Cell Rep. 19, 1698–709.
Bovine viral diarrhea virus Büning, M.K. et al. (2017) Nonreplicative RNA recombination of an animal plus-strand RNA virus in the absence of efficient translation of viral proteins. Genome Biol. Evol. 9, 817–29.
Chikungunya virus Wada, Y. et al. (2017) Discovery of a novel antiviral agent targeting the nonstructural protein 4 (nsP4) of chikungunya virus. Virology 505, 102–12.
Coronavirus (SARS) Agostini, M.L. et al. (2018) Coronavirus susceptibility to the antiviral Remdesivir (GS-5734) Is mediated by the viral polymerase and the proofreading exoribonuclease. mBio 9, e00221–18.
Crimean-Congo hemorrhagic fever virus Schotte, F.E.M. et al. (2017) Crimean-Congo hemorrhagic fever virus suppresses innate immune responses via a ubiquitin and ISG15 specific protease. Cell Rep. 20, 2396–407.
Dengue virus Eyre, N.S. et al. (2017) Genome-wide mutagenesis of Dengue virus reveals plasticity of the NS1 protein and enables generation of infectious tagged reporter viruses. J. Virol. 91, e01455–17.
Eilat virus Reynaud, J.M. et al. (2015) IFIT1 differentially interferes with translation and replication of alphavirus genomes and promotes induction of type I interferon. PLoS Pathog. 11, e1004863.
Enterovirus Wu, K.X. and Chu, J.J.-H. (2017) Antiviral screen identifies EV71 inhibitors and reveals camptothecin-target, DNA topoisomerase 1 as a novel EV71 host factor. Antivir. Res. 143, 122–33.
Equine encephalitis virus (Venezuelan) Reynaud, J.M. et al. (2015) IFIT1 differentially interferes with translation and replication of alphavirus genomes and promotes induction of type I interferon. PLoS Pathog. 11, e1004863.
Foot and Mouth Disease virus Zhang, F. et al. (2017) A replication-competent foot-and-mouth disease virus expressing a luciferase reporter. J. Virol. Meth. 247, 38–44.
Hepatitis B Nishitsuji, H. et al. (2018) TIP60 complex inhibits HBV transcription. J. Virol. 92, e01788–17.
Hepatitis C Eyre, N.S. et al. (2017) Sensitive luminescent reporter viruses reveal appreciable release of hepatitis C virus NS5A protein into the extracellular environment. Virology 507, 20–31.
HIV-1 Astronomo, R.D. et al. (2017) Neutralization takes precedence over IgG or IgA isotype-related functions in mucosal HIV-1 antibody-mediated protection. EbioMedicine 14, 97–111.
Influenza A Diot, C. et al. (2016) Influenza A virus polymerase recruits the RNA helicase DDX19 to promote the nuclear export of viral mRNAs. Sci. Reports 6, 33763.
Influenza B Fulton, B.O. Palese, P. and Heaton, N.S. (2015) Replication-competent influenza B reporter viruses as tools for screening antivirals and antibodies. J. Virol. 89, 12226–31.
JC Polyomavirus Geoghegan, E.M., et al. (2017) Infectious entry and neutralization of pathogenic JC polyomaviruses. Cell Rep. 21, 1169–79.
Rabies virus Nakagawa, K., et al. (2017) Molecular function analysis of rabies virus RNA polymerase L protein by using an L gene-deficient virus. J. Virol. 91, e00826–17.
Rotavirus Kanai, Y., et al. (2017) Entirely plasmid-based reverse genetics system for rotaviruses. PNAS 114, 2349–54.
Semliki Forest virus Sarén, T., et al. (2017) Insertion of the type-I IFN decoy receptor B18R in a miRNA-tagged Semliki Forest virus improves oncolytic capacity but results in neurotoxicity. Mol. Ther. Oncolytics 7, 67–75.
Sendai virus Goto, H., et al. (2016) Evidence that receptor destruction by the Sendai virus hemagglutinin-neuraminidase protein is responsible for homologous interference. J. Virol. 90, 7640–6.
Sindbis virus Sokoloski, K.J., et al. (2017) Identification of interactions between Sindbis virus capsid protein and cytoplasmic vRNA as novel virulence determinants. PLoS Pathog. 13, e1006473.
Vesicular Stomatitis virus Halbherr, S.J., et al. (2015) Biological and protective properties of immune sera directed to the influenza virus neuraminidase. J. Virol. 89, 1550–63.
West Nile virus Setoh, Y.X., et al. (2017) Helicase domain of West Nile virus NS3 protein plays a role in inhibition of type I interferon signalling. Viruses 9, 326.
Zika virus Mutso, M., et al. (2017) Reverse genetic system, genetically stable reporter viruses and packaged subgenomic replicon based on a Brazilian Zika virus isolate. J. Gen. Virol. 98, 2712-24

 

References

  1. Hall, M.P. et al. (2012) Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate. ACS Chem. Biol. 7, 1848–57.
  2. Ma, H. et al. (2008) The challenge of selecting protein kinase assays for lead discovery optimization. Expert Opin. Drug Discov. 3, 607–21.
  3. Tran, V. et al. (2013) Highly sensitive real-time in vivo imaging of an influenza reporter virus reveals dynamics of replication and spread. J. Virol. 87, 13321–9.
  4. Kao, C. et al. (1999) A simple and efficient method to reduce nontemplated nucleotide addition at the 3´ terminus of RNAs transcribed by T7 RNA polymerase. RNA 5, 1268–72.
  5. Sun, C. et al. (2014) Stable, high-level expression of reporter proteins from improved alphavirus expression vectors to track replication and dissemination during encephalitic and arthritogenic disease. J. Virol. 88, 2035–46.
  6. Dixon, A.S. et al. (2016) NanoLuc complementation reporter optimized for accurate measurement of protein interactions in cells. ACS Chem. Biol. 11, 400–8.
  7. Schwinn, M. et al. (2018) CRISPR-mediated tagging of endogenous proteins with a luminescent peptide. ACS Chem. Biol. 13, 467–74.
  8. Sasaki, M. et al. (2018) Development of a rapid and quantitative method for the analysis of viral entry and release using a NanoLuc luciferase complementation assay. Virus Res. 243, 69–74.
  9. Puig-Basagoiti, F. et al. (2016) Human cathelicidin compensates for the role of apolipoproteins in hepatitis C virus infectious particle formation. J. Virol. 90, 8464–77.
  10. Tamura, T. et al. (2018) Characterization of recombinant Flaviviridae viruses possessing a small reporter tag. J. Virol. 92, e01582–17.

How to Cite This Article

Hooper, K. Size Does Matter: NanoLuc® Technologies Advance Virology Research. [Internet] September 2018; tpub_202. [cited: year, month, date]. Available from: http://www.promega.com/resources/pubhub/2018/tpub-202-size-does-matter-nanoluc-technologies-applied-to-virology/

Hooper, K. Size Does Matter: NanoLuc® Technologies Advance Virology Research. Promega Corporation Web site. http://www.promega.com/resources/pubhub/2018/tpub-202-size-does-matter-nanoluc-technologies-applied-to-virology/ Updated September 2018; tpub_202. Accessed Month Day, Year.