Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in Bacillus cereus strains

Abstract

Bacillus cereus is a food contaminant with widely varying enterotoxic potential due to its virulence proteins. In this article, phylogenetic analysis of the amino acid sequences from the whole-genomes of 41 strains, evolutionary distance calculation of the amino acid sequences of the virulence genes, and functional and structural predictions of the virulence proteins were performed to reveal the taxonomically diverse distribution of virulence factors. The genome evolution of the strains showed a clustering trend based on the protein-coding virulence genes. The strains of B. cereus have evolved into non-toxic risk and toxic risk clusters with medium-high- and medium-low-risk subclusters. The evolutionary transfer distances of incomplete virulence genes relative to housekeeping genes were greater than those of complete virulence genes, and the distance values of HblACD were higher than those of nheABC and CytK among the complete virulence genes. Cytoplasmic localization was impossible for all the virulence proteins, and NheB, NheC, Hbl-B, and Hbl-L1 were predicted to be extracellular. Nhe and Hbl proteins except CytK had similar spatial structures. The predicted structures of Nhe and Hbl mainly showed ‘head’ and ‘tail’ domains. The ‘head’ of NheA and Hbl-B, including two α-helices separated by β-tongue strands, might play a special role in the formation of Nhe trimers and Hbl trimers, respectively. The ‘cap’ of CytK, which includes two ‘latches’ with many β-sheets, formed a β-barrel structure with pores, and a ‘rim’ balanced the structure. The evolution of B. cereus strains showed a clustering tendency based on the protein-coding virulence genes, and the complete virulence-gene operon combination had higher relative genetic stability. The beta-tongue or latch associated with β-sheet folding might play an important role in the binding of virulence structures and pore-forming toxins in B. cereus.

Characterization of the Toxigenic Potential of Bacillus cereus sensu lato Isolated from Raw Berries and Their Products

“…The complex Twenty-three different toxin profiles were found among the B. cereus isolates and their prevalence and distribution are shown in Tables 4 and 5 and in Figure 2. Consistent reports indicate the presence of multiple toxin profiles [14,[42][43][44]; however, the most prevalent profile varies between studies. Enterotoxin genes were found more frequently in blackberry, raspberry, and strawberry samples than in blueberries.…”

“…In addition, three distinct biovars were created: Emeticus, Anthracis, and Thuringiensis, based on the presence of genes associated with specific characteristics. More recently, Zhang et al [14] conducted a study that examined the species diversity of B. cereus strains and their phylogenetic relationships concerning virulence factors. The aim of the research was to systematically evaluate the distribution of virulence genes and analyze the structures and functions of virulence proteins.…”

Role of Bacilli in phytohormone production in rice and grain under different doses of vegetative and generative fertilizer

“…Despite being mainly reported in widely recognized as 'not-safe' species of Bacillus cereus, several species of Bacillus have also been reported to have these genes (From et al, 2005;Yu et al, 2023). Owing to the diversity of genomic structure between Bacillus species and strains, the presence of one gene may existent in one species and be non-existent in another or even between strains within the same species (Rossi et al, 2018;de Magalhães, 2019;Zhang et al, 2022) with the possible presence of multiple toxin-encoding genes in a Bacillus strain (Jeżewska-Frąckowiak et al, 2017). Thus, multi toxin gene loci detection based on PCR has been chosen as an effective way to ensure the toxicity potential of a Bacillus strain, and so one cannot simply rely on a single gene (Hwang and Park, 2015;Jeżewska-Frąckowiak et al, 2017;Bianco et al, 2023).…”