Toxin Engineering

As up to now, no toxin specific to Varroa mites is known, we tried to engineer one. As basis for this, the Cry3Aa toxin – toxic to Coleoptera as the mealworm Tenebrionis molitor – has been chosen. It is also toxic to 4 different kinds of mites and has been well characterized in structure and mechanism of function, leaving us to believe to have a good basis. The engineering towards specificity has been performed in two ways:
• Binding site mutagenesis
• Phage display

Binding site mutagenesis

Design

To mutate these, the plasmid pSB1A3_Cry3Aa_TEV_HIS has been used as a template. This plasmid contains the toxin Cry3Aa as it can be found in Bacillus thuringiensis var. tenebrionis. Its expression is regulated by the arabinose inducible promotor pBAD/araC (Bb_I0500). From this, three different plasmids have been created: three plasmids with the same properties as the template, but with a series of Ns at the place of the binding sites. Thus, having cells containing one of these variants grow, a library of Cry3Aa proteins with randomly modified binding sites has been obtained.

Screening

Varroa Isolates

Staining Isolates

To provide an alternative to currently available pesticides, we wanted to adopt Cry toxins to kill Varroa destructor. Cry toxins, also known as Bt toxins, have been used commercially for decades and can limit the environmental impact of pesticide use ¹. Cry toxins are produced by the insect pathogen Bacillus thuringiensis. They are activated by the alkaline conditions of the insect gut, after which the protoxin is cleaved off. The toxin can then recognize receptors on the gut membrane and bind to them. It will form oligomers with other toxin molecules and make a pore in the gut membrane. This is what causes the insect’s death ². Their mode of action can make them highly specific to certain species of insects.

While over 800 Cry toxins are known, research on the workings of these toxins mainly focuses on conventional pests such as the Colorado potato beetle, cabbage moths and mosquitoes. Field experiments on non-target invertebrates show that Acari (mites and ticks) are not significantly affected by Bt crops³ (transgenic crops which express Cry toxins, such as Bt cotton or Bt maize), but these use only a few known Cry toxins. Other studies have shown that there are strains of B. thuringiensis which are harmful to Acari. While most of these strains or toxins were tested against herbivorous species of mites^4,5,6,7, some are known to kill species of ticks^8,9,10,11. In fact, two strains have been discovered which show toxicity to V. destructor^12,13! Unfortunately, they did not identify a particular Cry toxin.

To find our own Cry toxin, we adapted a procedure from Rampersad et al.¹⁴ and Alquisira-Ramírez et al¹². We gathered over 800 dead mites from the Dutch foundation “De Duurzame Bij”¹⁵, Bennekom, The Netherlands.

Our method of sample preparation selected for spore formation, but not the B. thuringiensis rod-shaped morphology. Therefore, 106 colonies from the mites were investigated with brightfield microscopy. They were stained with Coomassie Brilliant Blue to make Cry toxins more visible. Five isolates were identified as Bacillus-like species. Some of them, including Bacillus thuringiensis HD-350, are shown in Figure 2.

In Vivo Toxicity

We wanted to test the strains we identified for their toxicity to Varroa destructor. Protein extracts and SDS-PAGE were performed. The toxicity assay was based on the assay used by Alquisira-Ramírez et al.¹², but we faced one major problem: the assay, including the negative control, killed all of the Varroa mites. Therefore, it was not a reliable indicator of the isolates’ toxicity to Varroa. An alternative would be to use an assay where we dip honeybee larvae in protein extracts from the strains; a Varroa mite which feeds on the larvae should then ingest any toxins. Unfortunately, Varroa mites tend to share feeding sites and use them repeatedly¹⁶, which means that not all mites would consume the protein extract.

A sample-size calculation was performed in R with the following code to assess the feasibility of such an assay.
> p=0.66
> p0=0.5
> alpha=0.05
> beta=0.1
> (n=p*(1-p)*((qnorm(1-alpha)+qnorm(1-beta))/(p-p0))^2)

Here, p is the alternative hypothesis, p0 the null hypothesis, alpha the type I error and beta the type II error. The values of these variables were based on the following assumptions:

• The null hypothesis is 50% mite mortality. Natural mite mortality is very high in the laboratory.
• Linea Muhsal estimated during feeding experiments that approximately 16% of mites ingested the fluorophores she had dipped honeybee larvae in.
• If an effective Cry toxin is ingested, we expect to see 100% mite mortality. This is an optimistic assumption.
• 16% of mites eat a toxin which causes 100% mite mortality, so if there is a toxin, we should see 66% mite mortality.

With these assumptions, a sample size of 75 was calculated. We were generally able to gather a maximum of 40 mites per week. Gathering enough mites to test all our samples was unfeasible. Therefore, pursuit of this type of toxicity assay was cancelled in favour of further development of an in vitro assay.

16s rRNA sequencing and SDS-PAGE results

All five isolates with Bacillus-like morphology had their 16s rRNA sequenced. A search of NCBI’s 16S ribosomal RNA sequences database resulted in the following alignments, each with approximately 99% identity of their best match. The isolates and their matches are displayed in Table 1.

It can be difficult to tell Bacillus species apart with just a 16s rRNA sequence¹⁷, so an SDS-PAGE gel of the protein extracts was prepared to further analyse them. This gel is shown in Figure 3.

Proteomics analysis of isolate V82

Based on the previous results, our Lysinibacillus isolate V82 had the most potential as a putative mite pathogen. It is relatively closely related to a known insect pathogen, Lysinibacillus sphaericus, a species which is known to make a 100 kDa mosquiticidal toxin ¹⁸. Our isolate also showed a strong band at the 100 kDa region (Figure 3). A new SDS-PAGE gel was prepared with independently grown V82 cultures and bands were cut out for peptide extraction, so the 100 kDa protein could be analysed with LC-MS/MS. Negative control bands were cut out approximately ~1 cM above the 100 kDa bands. MaxQuant was used to analyze the data.

Analysis of the LC-MS/MS results resulted in Figure 5. Figure 5 is a vulcano plot; the x-axis plots the protein abundance ratio between the 100 kDa band and its respective control band, while the y-axis plots the p-value of this difference in protein abundance. Therefore, a protein in the left half of the plot is more abundant in the control bands, while the opposite goes for proteins in the right half of the plot. The higher it is on the y-axis, the more significant this difference is.

Contaminations such as keratins and the trypsin used to digest the samples should not differ significantly between the samples. This is also shown in Figure 5 as most contaminants (the orange data points) are present in the bottom half of the vulcano plot. The relative label-free quantification (LFQ) intensity of the significant proteins shown in Figure 4 was very low, in all cases lower than the LFQ intensity of trypsin. From a biological perspective, this makes sense; there is no reason for an organism to produce mass amounts of alanine tRNA ligase. However, this and the fact that only 3% of peptides could be matched indicates that the 100 kDa protein was not present in the prepared Lysinibacillus sequence database. Therefore, the peptides were also matched against a Bacillus database, but this yielded similar results. Genomic DNA was extracted from V82 and sent for sequencing so the LC-MS/MS data could be run against the isolate's own DNA. This genomic DNA was also analyzed with the Toxin Scanner.

References

 

References for Varroa isolates

1. Lacey, L. A., Grzywacz, D., Shapiro-Ilan, D. I., Frutos, R., Brownbridge, M., & Goettel, M. S. (2015). Insect pathogens as biological control agents: back to the future. Journal of invertebrate pathology, 132, 1-41. ↩

2. de Maagd, R. A., Bravo, A., & Crickmore, N. (2001). How Bacillus thuringiensis has evolved specific toxins to colonize the insect world.TRENDS in Genetics, 17(4), 193-199. ↩

3. Marvier, M., McCreedy, C., Regetz, J., & Kareiva, P. (2007). A meta-analysis of effects of Bt cotton and maize on nontarget invertebrates.science, 316(5830), 1475-1477. ↩

4. Ahmed, N., Wang, M., & Shu, S. (2016). Effect of commercial Bacillus thuringiensis toxins on Tyrophagus putrescentiae (Schrank) fed on wolfberry (Lycium barbarum L.). International Journal of Acarology, 42(1), 1-6. ↩

5. Chapman, M. H., & Hoy, M. A. (1991). Relative toxicity of Bacillus thuringiensis var. tenebrionis to the two‐spotted spider mite (Tetranychus urticae Koch) and its predator Metaseiulus occidentalis (Nesbitt)(Acari, Tetranychidae and Phytoseiidae). Journal of Applied Entomology, 111(1‐5), 147-154. ↩

6. Dunstand-Guzmán, E., Peña-Chora, G., Hallal-Calleros, C., Pérez-Martínez, M., Hernández-Velazquez, V. M., Morales-Montor, J., & Flores-Pérez, F. I. (2015). Acaricidal effect and histological damage induced by Bacillus thuringiensis protein extracts on the mite Psoroptes cuniculi. Parasites & vectors, 8(1), 1. ↩

7. Erban, T., Nesvorna, M., Erbanova, M., & Hubert, J. (2009). Bacillus thuringiensis var. tenebrionis control of synanthropic mites (Acari: Acaridida) under laboratory conditions. Experimental and Applied Acarology, 49(4), 339-346. ↩

8. Fernández-Ruvalcaba, M., Peña-Chora, G., Romo-Martínez, A., Hernández-Velázquez, V., de la Parra, A. B., & De La Rosa, D. P. (2010). Evaluation of Bacillus thuringiensis pathogenicity for a strain of the tick, Rhipicephalus microplus, resistant to chemical pesticides. Journal of Insect Science, 10(1), 186. ↩

9. Hassanain, M. A., Garhy, M. E., Abdel-Ghaffar, F. A., El-Sharaby, A., & Megeed, K. N. A. (1997). Biological control studies of soft and hard ticks in Egypt. Parasitology research, 83(3), 209-213. ↩

10. Neethu, K. B., Priji, P., Unni, K. N., Sajith, S., Sreedevi, S., Ramani, N., ... & Benjamin, S. (2015). New Bacillus thuringiensis strain isolated from the gut of Malabari goat is effective against Tetranychus macfarlanei. Journal of Applied Entomology. ↩

11. Zhioua, E., Heyer, K., Browning, M., Ginsberg, H. S., & LeBrun, R. A. (1999). Pathogenicity of Bacillus thuringiensis variety kurstaki to Ixodes scapularis (Acari: Ixodidae). Journal of medical entomology, 36(6), 900-902. ↩

12. Neethu, K. Alquisira-Ramírez, E. V., Paredes-Gonzalez, J. R., Hernández-Velázquez, V. M., Ramírez-Trujillo, J. A., & Peña-Chora, G. (2014). In vitro susceptibility of varroa destructor and Apis mellifera to native strains of Bacillus thuringiensis. Apidologie, 45(6), 707-718. ↩

13. Tsagou, V., Lianou, A., Lazarakis, D., Emmanouel, N., & Aggelis, G. (2004). Newly isolated bacterial strains belonging to Bacillaceae (Bacillus sp.) and Micrococcaceae accelerate death of the honey bee mite, varroa destructor (V. jacobsoni), in laboratory assays. Biotechnology letters, 26(6), 529-532. ↩

14. Rampersad, J., & Ammons, D. (2005). A Bacillus thuringiensis isolation method utilizing a novel stain, low selection and high throughput produced atypical results. BMC microbiology, 5(1), 1. ↩

15. This is the homepage of “De Duurzame Bij”. They want to stop treating Varroa with pesticides. ↩

16. Kanbar, G., & Engels, W. (2005). Communal use of integumental wounds in honey bee (Apis mellifera) pupae multiply infested by the ectoparasitic mite Varroa destructor. Genetics and Molecular Research, 4(3), 465-472. ↩

17. Bavykin, S. G., Lysov, Y. P., Zakhariev, V., Kelly, J. J., Jackman, J., Stahl, D. A., & Cherni, A. (2004). Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. Journal of clinical microbiology, 42(8), 3711-3730. ↩

18. Berry, C. (2012). The bacterium, Lysinibacillus sphaericus, as an insect pathogen. Journal of invertebrate pathology, 109(1), 1-10. ↩