Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2022.01.11.475806

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

Zhang, M.·Liu, J.·Yin, Z.·Zhang, L.
View original source ↗Export metadata ↓

Abstract

Bacillus cereus is a food contaminant with widely varying enterotoxic potential of its virulence proteins. In this article, phylogenetic analysis of the whole-genome amino acid sequences of 41 strains, evolutionary distance calculation of the amino acid sequences of the virulence genes, and functional and structural prediction 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 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 clusters. The distances of evolutionary transfer relative to housekeeping genes of incomplete virulence 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 extracellular according to predictive analysis. 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 -helices separated by {beta}-tongue strands, might play a special role in Nhe trimers and Hbl trimers, respectively. The cap of CytK, which includes two latches with many {beta}-sheets, formed a {beta}-barrel structure with pores, and a rim balanced the structure. The evolution of B. cereus strains showed a clustering tendency based on the coding virulence genes, and the complete virulence-gene operon combination had higher relative genetic stability. The beta-tongue or latch associated with {beta}-sheet folding might play an important role in the binding of virulence structures and pore-forming toxins in B. cereus.

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Zhang, M., Liu, J., Yin, Z., Zhang, L.. 2022-01-11. Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in the Bacillus cereus group. https://doi.org/10.1101/2022.01.11.475806

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Darwinian and Wallacean evolution both explain sexual dichromatism in avian iridescence.

One of the longest-standing arguments in evolutionary biology is that between Darwin and Wallace on the evolution of sexual dichromatism, and which sex changed colour over time. While Darwin argued that males became more colourful over time, Wallace argued that females became less colourful, and numerous studies have lent support to each hypothesis over time. Iridescent colouration provides a particularly interesting system for studying sexual dichromatism because its conspicuousness is often associated with sexual selection and it has evolved multiple times. Here, using a dataset on iridescent colouration of 25,432 patches from 3,151 bird species, we provide one of the most comprehensive tests to date of the evolutionary origins of sexual dichromatism. We show that both hypotheses explain the evolution of iridescent sexual dichromatism in birds, but that Darwin's hypothesis is more strongly supported with males contributing stronger to evolutionary changes in dichromatism. Furthermore, our analyses support Darwin's prediction that sexual selection is associated to the evolution of dichromatism, but also Wallace's prediction that safer nests facilitate more colourful females (and males), and mostly in patches exposed during incubation.

evolutionary biology↗
bioRxiv2026

Evolutionary dynamics of RNA viruses during persistent infection in Drosophila melanogaster

Persistent viral infections provide an extended window for viral evolution, yet their intra-host trajectories across the host lifespan remain underexplored. Here, we tracked the longitudinal evolution of three single-stranded RNA (ssRNA) viruses (Drosophila A virus [DAV], Drosophila C virus [DCV], and Nora virus) and one double-stranded RNA (dsRNA) virus (Bloomfield virus) during persistent infection in Drosophila melanogaster. By analyzing viral populations across early, intermediate, and late infection stages, we mapped dynamic shifts in the viral quasispecies and the emergence of adaptive mutations. These data demonstrate that long-term persistence drives viral evolution in a viral species-specific manner. DAV evolution was defined by clonal interference, driven by the continuous turnover of competing haplotypes. Nora virus exhibited prolonged evolutionary stasis punctuated by a late-stage sweep, suggesting adaptation to the senescing host environment. In contrast, standard DCV populations were locked under strong purifying selection, where no adaptive mutations were detected. However, this constraint collapsed in high-titer DCV infections, triggering extensive mutational diversification. Distinct from the ssRNA dynamics, the multi-segmented dsRNA Bloomfield virus maintained higher sequence fidelity and a stable genomic formula. Ultimately, these results demonstrate that viral evolution during persistent infection is governed by the interplay between specific host-pathogen interactions and the physiological decline of the host.

evolutionary biology↗
bioRxiv2026

A new cell type facilitated live-bearing and multiple independent origins of placentation in fish

The origin of new organs has fascinated biologists since Darwin. Yet the molecular and evolutionary steps that give rise to new organs remain difficult to resolve, largely because most organs have ancient origins. The fish family Poeciliidae offers a rare exception. Within poeciliids, placentas have independently evolved at least nine times, including within the last ~10 million years. Here, we study the molecular and cellular drivers of five independent origins of a placenta, using pairs of sister species with and without a placenta. We identified a new maternal cell type that emerged in the common ancestor of poeciliids and likely enabled the family to transition from egg-laying to live-bearing through egg retention. This new cell type originated by partly co-opting the existing gene regulatory network of another ovarian cell type. Subsequently, this same new maternal cell type, together with the embryonic yolk sac, was repeatedly and independently co-opted to form a placenta in all five origins. The evolution of these placentas involved high levels of convergence at the pathway level (e.g., lipid metabolism and vesicle-mediated transport), although these functional changes relied primarily on distinct genes across species. Our analyses show how the evolution and modification of a new cell type enabled the evolution of live birth and placentation, providing the cellular and genetic foundations for the repeated evolution of a new organ.

evolutionary biology↗