Genome sequencing of Bacillus thuringiensis isolate T414 toxic to pink bollworm (Pectinophora gossypiella Saunders) and its insecticidal genes

Genome mining of Bacillus thuringiensis strain SY49.1 reveals novel candidate pesticidal and bioactive compounds

BACKGROUND

Bacillus thuringiensis SY49.1 (Bt SY49.1) strain has promising insecticidal and fungicidal activity against phytopathogens and pests. Therefore, we selected this strain for whole-genome sequencing (WGS), annotation and analysis, with the aim of identifying genes responsible for producing putative pesticidal toxins, antimicrobial metabolites and plant growth-promoting features.

RESULTS

Our results showed that the SY49.1 genome is 6. 32 Mbp long with a GC content of 34.68%. Genome mining revealed the presence of multiple gene inventories for the biosynthesis of bioactive compounds such as insecticidal delta endotoxins, secondary metabolites, and several plant growth-promoting proteins. Multiple sequence alignment revealed residue variations in the toxic core of Cry1Ab when compared with known Cry1Ab sequences from Bt nomenclature databases. This suggests that the cry1Ab of SY49.1 is a new kind of its group. Among the predicted secondary metabolites, we found a kurstakin with a predicted peptide that differs from the known kurstakin peptide available in the NORINE database. In addition, lipopeptides extracted from SY49.1 suppressed the growth of Verticillium dahliae and Fusarium oxysporum.

CONCLUSION

We anticipate that the complete genome of Bt SY49.1 may provide a model for properly understanding and studying antimicrobial compound mining, genetic diversity among the B. cereus group, and pathogenicity against insects. This is the first report on the WGS and mining of the Bt strain isolated from Turkey. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genome profiling of an indigenous Bacillus thuringiensis isolate, T405 toxic against the fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae)

In this study, we present the molecular and insecticidal characteristics of an indigenous Bt isolate T405 toxic against the maize fall armyworm (FAW), Spodoptera frugiperda. The presence of cry1, cry2 (cry2Aa & cry2Ab) and vip3A1 genes in T405 was confirmed. The SDS-PAGE gel analysis confirmed the occurrence of Cry and Vip proteins with molecular masses of 130, ∼88 and 65 kDa in T405. LC₅₀ estimates of T405 and HD1 were 161.37 and 910.73 μg ml^-1 for neonates whereas, 412.29 and 1014.95 μg ml^-1 correspondingly for 2^nd instar FAW larvae. Scanning Electron Microscopy depicted the existence of bipyramidal, spherical and cubic crystals in T405 spore suspension. The whole genome sequencing and assembly of T405 produced a total of 563 scaffolds with a genome size of 6,673,691 bp. The BLAST similarity search showed that 12 plasmids were distributed in this genome. Genome annotation revealed the presence of 6174 protein coding genes, 13 rRNA and 98 tRNA, in which 6126 genes were completely annotated for their functions through sequence similarity search, domains/motifs identification and gene ontology studies. Further analysis of these genes identified the presence of many insecticidal toxin protein coding genes viz., cry1Ac32, cry1Ab9, cry1Aa6, cry1Ac5, cry1Aa18, cry1Ab8, cry1Ab11, cry2Aa9, cry1Ia40, cry2Aa9, cry1Ia40, cry2Ab35, cyt, vip3Aa7 and tpp80Aa and several additional virulence assisted factors viz., immune inhibitor A, phospholipase C, sphingomyelinase, cell wall hydrolases, chitinase, hemolysin XhlA and seven urease subunit coding genes (ureA, ureB, ureC, ureD, ureE, ureF, ureG) in the annotated genome.

BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis

SUMMARY

Bacillus thuringiensis (Bt) has been used as the most successful microbial pesticide for decades. Its toxin genes are used for the development of genetically modified crops against pests. We previously developed a web-based insecticidal gene mining tool BtToxin_scanner. It has been frequently used by many researchers worldwide. However, it can only handle the genome one by one online. To facilitate efficiently mining toxin genes from large-scale sequence data, we re-designed this tool with a new workflow and the novel bacterial pesticidal protein database. Here, we present BtToxin_Digger, a comprehensive and high-throughput Bt toxin mining tool. It can be used to predict Bt toxin genes from thousands of raw genome and metagenome data, and provides accurate results for downstream analysis and experiment testing. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the replacement of the database.

AVAILABILITY AND IMPLEMENTATION

The BtToxin_Digger codes and web services are freely available at https://github.com/BMBGenomics/BtToxin_Digger and https://bcam.hzau.edu.cn/BtToxin_Digger, respectively.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A novel Bacillus thuringiensis isolate toxic to cotton pink bollworm (Pectinophora gossypiella Saunders)

In this study, we report a novel indigenous Bacillus thuringiensis (Bt) isolate, T26, which showed spores and crystals under scanning electron microscope and pathogenicity against the pink bollworm (Pectinophora gossypiella Saunders) in artificial diet based bioassay. SDS-PAGE analysis of the spore-crystal mixture of the Bt isolate, T26 revealed presence of three major protein bands of approximate molecular weights of 80, 55 and 40 kDa. The draft genome assembly consists of 56 scaffolds with an entire draft genome size of 5,054,095 bp. NCBI blast analysis revealed that assembled draft genome is spread over in a chromosome (4,818,543 bp) and one plasmid (235,552 bp). NCBI Prokaryotic Genome Annotation Pipeline (PGAP) showed presence of 5033 coding gene sequences and 159 RNAs genes. None of the known lepidopteran active genes (cry1, cry2 and cry9) could be detected with PCR or with whole genome sequence analysis using Bt toxin scanner tool or CryProcessor tool. Thus, presence of protein crystals and toxicity towards cotton pink bollworm and absence of any known cry/vip/cyt type of genes in draft genome indicates it is a novel type of Bt isolate. Further investigation of this genome sequence along with protein sequencing will lead to understand the novel factors responsible for its virulence and could be a useful tool for the insect resistance management in pink bollworm.

Modulation of Cas9 level for efficient CRISPR-Cas9-mediated chromosomal and plasmid gene deletion in Bacillus thuringiensis

OBJECTIVES

To set up an efficient gene editing system in Bacillus thuringiensis (Bt) using CRISPR-Cas9 by demonstrating deletion of chromosomal and plasmid genes.

RESULTS

CRISPR-Cas9 from Streptococcus pyogenes was found to function in Bt cells, resulting in DNA cleavage that is lethal to the cells. The system was assessed for its ability to mediate gene editing by knock-out of the protease genes nprA (neutral protease A) and aprA (alkaline protease A). Gene editing was not detected when the Bacillus-derived pBCX was used to carry CRISPR-Cas9 elements and a DNA repair template. When the Cas9 promoter was replaced with the sporulation-specific promoter cyt2A, a Bt ∆nprA clone was obtained, but this plasmid construct did not give reproducible results. Bt ∆nprA ∆aprA and Bt ∆aprA deletion mutants were finally generated when the Lactobacillus plantarum-derived plasmid pLPPR9 was used, likely due to its lower copy number reducing Cas9 toxicity. Only three to four clones each needed to be screened to identify the desired gene-modified mutants. Conversely, efficient editing of the plasmid vip3A gene required the use of pBCX and longer homology sequences for the repair template.

CONCLUSIONS

Capitalizing on the differential impact of plasmid copy number and homology arm length, we devised distinct yet simple and efficient approaches to chromosomal and plasmid gene deletion for Bt that condense the screening process, minimize screening, and facilitate multiple consecutive gene editing steps.