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Title: Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics
Authors: Adeniji A, Chukwuneme C, Conceição E, Ayangbenro A, Wilkinson E, Maasdorp E, de Oliveira T, Babalola O.
Journal: Microbiology Spectrum,doi: 10.1128/spectrum.01466-24.: (2025)

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Abstract

Priestia megaterium strain AB-S79 isolated from active gold mine soil previously expressed in vitro heavy metal resistance and has a 5.7 Mb genome useful for biotechnological exploitation. This study used web-based bioinformatic resources to analyze P. megaterium AB-S79 genomic relatedness, decipher its secondary metabolite biosynthetic gene clusters (BGCs), and better comprehend its taxa. Genes were highly conserved across the 14 P. megaterium genomes examined here. The pangenome reflected a total of 61,397 protein-coding genes, 59,745 homolog protein family hits, and 1,652 singleton protein family hits. There were also 7,735 protein families, including 1,653 singleton families and 6,082 homolog families. OrthoVenn3 comparison of AB-S79 protein sequences with 13 other P. megaterium strains, 7 other Priestia spp., and 6 other Bacillus spp. highlighted AB-S79’s unique genomic and evolutionary trait. antiSMASH identified two key transcription factor binding site regulators in AB-S79’s genome: zinc-responsive repressor (Zur) and antibiotic production activator (AbrC3), plus putative enzymes for the biosynthesis of terpenes and ranthipeptides. AB-S79 also harbors BGCs for two unique siderophores (synechobactins and schizokinens), phosphonate, dienelactone hydrolase family protein, and phenazine biosynthesis protein (phzF), which is significant for this study. Phosphonate particularly showed specificity for the P. megaterium sp. validating the effect of gene family expansion and contraction. P. megaterium AB-S79 looks to be a viable source for value-added compounds. Thus, this study contributes to the theoretical framework for the systematic metabolic and genetic exploitation of the P. megaterium sp., particularly the value-yielding strains. Priestia megaterium strain AB-S79 isolated from active gold mine soil previously expressed in vitro heavy metal resistance and has a 5.7 Mb genome useful for biotechnological exploitation. This study used web-based bioinformatic resources to analyze P. megaterium AB-S79 genomic relatedness, decipher its secondary metabolite biosynthetic gene clusters (BGCs), and better comprehend its taxa. Genes were highly conserved across the 14 P . megaterium genomes examined here. The pangenome reflected a total of 61,397 protein-coding genes, 59,745 homolog protein family hits, and 1,652 singleton protein family hits. There were also 7,735 protein families, including 1,653 singleton families and 6,082 homolog families. OrthoVenn3 comparison of AB-S79 protein sequences with 13 other P. megaterium strains, 7 other Priestia spp., and 6 other Bacillus spp. highlighted AB-S79’s unique genomic and evolutionary trait. antiSMASH identified two key transcription factor binding site regulators in AB-S79’s genome: zinc-responsive repressor (Zur) and antibiotic production activator (AbrC3), plus putative enzymes for the biosynthesis of terpenes and ranthipeptides. AB-S79 also harbors BGCs for two unique siderophores (synechobactins and schizokinens), phosphonate, dienelactone hydrolase family protein, and phenazine biosynthesis protein (phzF), which is significant for this study. Phosphonate particularly showed specificity for the P. megaterium sp. validating the effect of gene family expansion and contraction. P. megaterium AB-S79 looks to be a viable source for value-added compounds. Thus, this study contributes to the theoretical framework for the systematic metabolic and genetic exploitation of the P. megaterium sp., particularly the value-yielding strains. IMPORTANCE This study explores microbial natural product discovery using genome mining, focusing on Priestia megaterium . Key findings highlight the potential of P. megaterium , particularly strain AB-S79, for biotechnological applications. The research shows a limited output of P. megaterium genome sequences from Africa, emphasizing the importance of the native strain AB-S79. Additionally, the study underlines the strain’s diverse metabolic capabilities, reinforcing its suitability as a model for microbial cell factories and its foundational role in future biotechnological exploitation.

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Citation: Adeniji A, Chukwuneme C, Conceição E, Ayangbenro A, Wilkinson E, Maasdorp E, de Oliveira T, Babalola O. Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics Microbiology Spectrum,doi: 10.1128/spectrum.01466-24.: (2025).