Prediction of Bacterial microRNAs and possible targets in human cell transcriptome

Abstract

Recent studies have examined gene transfer from bacteria to humans that would result in vertical inheritance. Bacterial DNA appears to integrate into the human somatic genome through an RNA intermediate, and such integrations are detected more frequently in tumors than normal samples and in RNA than DNA samples. Also, vertebrate viruses encode products that interfere with the RNA silencing machinery, suggesting that RNA silencing may indeed be important for antiviral responses in vertebrates. RNA silencing in response to virus infection could be due to microRNAs encoded by either the virus or the host. We hypothesized that bacterial expression of RNA molecules with secondary structures is potentially able to generate miRNA molecules that can interact with the human host mRNA during bacterial infection. To test this hypothesis, we developed a pipeline-based bioinformatics approach to identify putative micro-RNAs derived from bacterial RNAs that may have the potential to regulate gene expression of the human host cell. Our results suggest that 68 bacterial RNAs predicted from 37 different bacterial genomes have predicted secondary structures potentially able to generate putative microRNAs that may interact with messenger RNAs of genes involved in 47 different human diseases. As an example, we examined the effect of transfecting three putative microRNAs into human embryonic kidney 293 (HEK293) cells. The results show that the bacterially derived microRNA sequence can significantly regulate the expression of the respective target human gene. We suggest that the study of these predicted microRNAs may yield important clues as to how the human host cell processes involved in human diseases like cancer, diabetes, rheumatoid arthritis, and others may respond to a particular bacterial environment.

A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles

“…marinum , but intracellular levels of the sRNA were too low to repress target mRNA in cultured cells [ 39 ]. Moreover, a high-throughput bioinformatics approach predicted possible targets of bacterial sRNAs in the human transcriptome, and in vitro transfection of host cells with a selection of these putative sRNAs decreased target mRNA abundance [ 43 ]. However, the actual expression levels of the predicted sRNAs or their effect on a biological response, such as cytokine secretion, were not reported.…”

Wolbachia small noncoding RNAs and their role in cross-kingdom communications

“…However, recent studies suggest that bacteria could also produce functional miRNA or miRNA-like snRNAs (12,13). In this study, we found that Wolbachia, as endosymbiotic bacteria, are able to encode snRNAs that act as effectors to modulate the expression of Wolbachia and mosquito host genes.…”

MicroRNA expression profiles of bovine monocyte-derived macrophages infected in vitro with two strains of Streptococcus agalactiae

“…This suggests that it may be a bacterial-derived miRNA released by infection of the macrophages. Bacterial-derived miRNAs have recently been extensively studied [ 39 , 40 ]. It is likely that these small RNA molecules may repress the ability of the host cell to resist bacterial invasion, as has been shown for viruses and fungi [ 41 – 43 ].…”