MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella

Krishnendu Mukherjee,Andre Billion,Andreas Vilcinskas,Daniel Amsel,Miriam Kalsy,Ulrich Dobrindt

doi:10.1038/s41598-020-59407-3

Abstract

Uropathogenic Escherichia coli (UPEC) strains cause symptomatic urinary tract infections in humans whereas commensal-like E. coli strains in the urinary bladder cause long-term asymptomatic bacteriuria (ABU). We previously reported that UPEC and ABU strains differentially regulate key DNA methylation and histone acetylation components in the surrogate insect host Galleria mellonella to epigenetically modulate innate immunity-related gene expression, which in turn controls bacterial growth. In this follow-up study, we infected G. mellonella larvae with UPEC strain CFT073 or ABU strain 83972 to identify differences in the expression of microRNAs (miRNAs), a class of non-coding RNAs that regulate gene expression at the post-transcriptional level. Our small RNA sequencing analysis showed that UPEC and ABU infections caused significant changes in the abundance of miRNAs in the larvae, and highlighted the differential expression of 147 conserved miRNAs and 95 novel miRNA candidates. We annotated the G. mellonella genome sequence to investigate the miRNA-regulated expression of genes encoding antimicrobial peptides, signaling proteins, and enzymatic regulators of DNA methylation and histone acetylation in infected larvae. Our results indicate that miRNAs play a role in the epigenetic reprograming of innate immunity in G. mellonella larvae to distinguish between pathogenic and commensal strains of E. coli.

Highlights

Uropathogenic Escherichia coli (UPEC) strains cause symptomatic urinary tract infections in humans whereas commensal-like E. coli strains in the urinary bladder cause long-term asymptomatic bacteriuria (ABU)
We previously found that DNA methylation and histone acetylation were differentially regulated in larvae infected with UPEC and ABU strains, underpinning the reprogramming of innate immunity at the level of transcriptional initiation[23]
We carried out miRNA sequencing in G. mellonella larvae infected with UPEC strain CFT073 or ABU strain 83972 to investigate strain-dependent expression of novel and conserved miRNAs, to identify the messenger RNAs (mRNAs) targets of these miRNAs, and to analyze co-expression of miRNAs and their mRNA targets in infected larvae

Summary

Introduction

Uropathogenic Escherichia coli (UPEC) strains cause symptomatic urinary tract infections in humans whereas commensal-like E. coli strains in the urinary bladder cause long-term asymptomatic bacteriuria (ABU). We previously reported that UPEC and ABU strains differentially regulate key DNA methylation and histone acetylation components in the surrogate insect host Galleria mellonella to epigenetically modulate innate immunity-related gene expression, which in turn controls bacterial growth. In this follow-up study, we infected G. mellonella larvae with UPEC strain CFT073 or ABU strain 83972 to identify differences in the expression of microRNAs (miRNAs), a class of non-coding RNAs that regulate gene expression at the post-transcriptional level. We carried out miRNA sequencing in G. mellonella larvae infected with UPEC strain CFT073 or ABU strain 83972 to investigate strain-dependent expression of novel and conserved miRNAs, to identify the mRNA targets of these miRNAs, and to analyze co-expression of miRNAs and their mRNA targets in infected larvae

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Discussion

Conclusion