The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

Effect of low temperature on the resistance of Listeria monocytogenes and Escherichia coli O157:H7 to acid electrolyzed water

Low temperature can affect the resistance of pathogenic bacteria to other external stress. The present study was envisaged to assess the tolerance of L. monocytogenes and E. coli O157:H7 to acidic electrolyzed water (AEW) under low temperature stress. AEW treatment caused a damage to cell membrane of the pathogenic bacteria, which led to protein leakage and DNA damage. Compared with the pathogenic bacteria cultured at 37 °C (pure culture), the L. monocytogenes and E. coli O157:H7 cells cultivated at low temperature presented a less damage and had a higher survival rate when exposed to AEW. Therefore, 4 °C or 10 °C grown bacteria were less susceptible to AEW than those cultured at 37 °C. And this phenomenon was verified when AEW was used to treat the pathogenic bacteria inoculated in salmon. In addition, transcriptomic sequencing technology (RNA-seq) was used to reveal the mechanism of AEW tolerance of L. monocytogenes under low temperature stress. Transcriptomic analysis showed the expression of the cold shock protein, regulation of DNA-templated transcription, ribosome pathway, phosphotransferase system (PTS), bacteria chemotaxis, SOS response and DNA repair were involved in the resistance of L. monocytogenes to AEW. We speculated that the direct modulation of the expression of cold shock protein CspD, the indirect effect on the expression of cspD by inhibiting the expression of Crp/Fnr family transcriptional regulator or enhancing the level of cAMP by regulating PTS could reduce the resistance of L. monocytogenes cultivated at 4 °C to AEW. Our study contributes to solving the problem of the reduced bacteriostatic effect in cold storage environment.

Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes

Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transcriptional repressor, which controls genes involved in DNA repair, mutagenesis and cell-cycle control. To date, the SOS response has been characterized in most major bacterial groups, with the notable exception of the Bacteroidetes. No LexA homologs had been identified in this large, diverse and ecologically important phylum, suggesting that it lacked an inducible mechanism to address DNA damage. Here, we report the identification of a novel family of transcriptional repressors in the Bacteroidetes that orchestrate a canonical response to DNA damage in this phylum. These proteins belong to the S24 peptidase family, but are structurally different from LexA. Their N-terminal domain is most closely related to CI-type bacteriophage repressors, suggesting that they may have originated from phage lytic phase repressors. Given their role as SOS regulators, however, we propose to designate them as non-canonical LexA proteins. The identification of a new class of repressors orchestrating the SOS response illuminates long-standing questions regarding the origin and plasticity of this transcriptional network.

The effect of atrazine on intestinal histology, microbial community and short chain fatty acids in Pelophylax nigromaculatus tadpoles

The intestine is the main organ for nutrient absorption in amphibians. It is sensitive to atrazine, which is a herbicide widely used in agricultural areas. At present, there is a lack of systematic research on the effect of atrazine on the amphibian intestine. In this study, we evaluated the effects of atrazine exposure (0, 50 μg/L, 100 μg/L, and 500 μg/L) for 20 days on intestinal histology, microbiota and short chain fatty acids in Pelophylax nigromaculatus tadpoles. Our research showed that 500 μg/L atrazine exposure significantly decreased the height of microvilli and epithelial cells, and altered the composition and diversity of intestinal microbiota in P. nigromaculatus tadpoles compared to the control. At the phylum level, the abundance of Bacteroidetes and Fusobacteria increased significantly, while that of Verrucomicrobia and Firmicutes decreased significantly in the 500 μg/L atrazine treatment group. At the genus level, Akkermansia and Lactococcus had significantly lower abundance in the 100 μg/L and 500 μg/L atrazine exposure group, while Cetobacterium was only detected in the 100 μg/L and 500 μg/L atrazine treated group. Also, function prediction of intestinal microbiota showed that atrazine treatment significantly changed the metabolism pathways of P. nigromaculatus tadpoles. In addition, 500 μg/L atrazine exposure changed the content of short chain fatty acids by significantly increasing the content of total SFCAs, butyric acid, and valeric acid, and decreasing the content of isovaleric acid in the intestine. Taken together, atrazine exposure could affect the intestinal histology and induce intestinal microbiota imbalance and metabolic disorder in amphibian tadpoles.

Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria

Transcriptional rewiring is the regulation of different target genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances.

The degree to which genetic or physiological systems evolve over evolutionary distance is often untested. One can assume that the same system in different organisms will change very little if 1) the evolutionary distance between the organisms is small, 2) the systems perform critical functions, and 3) the organisms have been under similar selective pressures (i.e. the organisms inhabited the same ecological niche). The Alphaproteobacteria offer an excellent opportunity to test this assertion as several critical global transcriptional regulators are conserved throughout this clade. In this study, the regulons of two such global regulators, GcrA and CcrM, in two closely related Alphaproteobacteria that inhabit the same ecological niche were compared and it was found that they regulate vastly different genes. In many cases, genes were present in both organisms, but targeted by a regulator in one organism and not in the other. These results suggest that significant transcriptional rewiring can occur even in a core regulatory system over small evolutionary distances and indicate that conservation of genes and genetic regulators may not be a complete indicator of their physiological function in an organism.

Improving Alzheimer's disease by altering gut microbiota in tree shrews with ginsenoside Rg1

Ginsenoside Rg1 (GRg1) has neuroprotective effects on Alzheimer's disease (AD). The occurrence and progression of AD are closely related to gut microbiota. Few studies have learned the direct relationship between GRg1 and gut microbiota. In this study, we found an original way to research this relationship by using GRg1 in the AD model of tree shrews. Morris water maze and immunohistochemistry were performed to test the cognition repairing function of GRg1 by tree shrews and 16S ribosomal RNA sequencing was used to explore the composition and abundance of gut microbiota. After GRg1 treatment, the result of Morris water maze showed an improvement in cognitive function, and immunohistochemistry revealed a decrease in tau protein. Moreover, 16SrRNA sequencing results showed the abundances of Proteobacteria and Verrucomicrobia were significantly different, and Lactobacillaceae was significantly increased in the GRg1 treatment group. It also showed that the gut microbiome with middle and high doses of GRg1 was close to the normal group. In conclusion, this study suggests that GRg1 at middle and high doses may change the abundance of gut microbiota to improve AD, and thatProteobacteria and Verrucomicrobia are key microbiota. This is the first report that has ever studied the relationship between GRg1 and gut microbiota in tree shrews.

Flexible comparative genomics of prokaryotic transcriptional regulatory networks

Background

Comparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evolution of bacterial regulons, few comparative genomics suites have been developed for the automated analysis of these regulatory systems. Available solutions typically rely on precomputed databases for operon and ortholog predictions, limiting the scope of analyses to processed complete genomes, and several key issues such as the transfer of experimental information or the integration of regulatory information in a probabilistic setting remain largely unaddressed.

Results

Here we introduce CGB, a flexible platform for comparative genomics of prokaryotic regulons. CGB has few external dependencies and enables fully customized analyses of newly available genome data. The platform automates the merging of experimental information and uses a gene-centered, Bayesian framework to generate and integrate easily interpretable results. We demonstrate its flexibility and power by analyzing the evolution of type III secretion system regulation in pathogenic Proteobacteria and by characterizing the SOS regulon of a new bacterial phylum, the Balneolaeota.

Conclusions

Our results demonstrate the applicability of the CGB pipeline in multiple settings. CGB’s ability to automatically integrate experimental information from multiple sources and use complete and draft genomic data, coupled with its non-reliance on precomputed databases and its easily interpretable display of gene-centered posterior probabilities of regulation provide users with an unprecedented level of flexibility in launching comparative genomics analyses of prokaryotic transcriptional regulatory networks. The analyses of type III secretion and SOS response regulatory networks illustrate instances of convergent and divergent evolution of these regulatory systems, showcasing the power of formal ancestral state reconstruction at inferring the evolutionary history of regulatory networks.

Evaluation of gene expression and protein structural modeling involved in persister cell formation in Salmonella Typhimurium

Persisters are phenotypic variants of the bacterial population that survive against lethal doses of bactericidal antibiotics.These phenotypes are created in numerous bacterial species, including those of clinical significance, such as Salmonella Typhimurium. Since persister cells are associated with the failure of antibiotic treatment and infection recurrence, it is crucial to identify the mechanisms that influence the formation of these cells. The aim of this study is to investigate the persister cell formation and expression analysis as well as to predict the 3D structure of the genes involved in the production of persister cells. The presence of persisters in S. Typhimurium was determined by time dependent killing of different types of bactericidal antibiotics and expression of genes associated with persister cell formation which was assessed five hours after the addition of antibiotics by the qRT-PCR. Indeed, the 3D structural model of the proteins studied was predicted by performing several computational methods of retrieved primary protein sequences. The results of the study showed that the S. Typhimurium produced high levels of persister cells in the exposure of bactericidal antibiotics. Furthermore, qRT-PCR resulted in the fact that the expression of related genes was different depending on the type of antibiotic. Overall, this study provides information on the creation of persister cells and the role of different genes in the formation of these cells and structure of proteins involved in the production of persister cells in S. Typhimurium.