Infection biology: Small RNA with a large impact.

Abstract

What happens when bacteria encounter or enter host cells? How does each of the species respond, the bacteria to survive in their new environ­ ment and the host cells to either tolerate non­harmful bacteria or defend against path­ ogenic ones? To answer these questions, it is imperative to understand how gene transcrip­ tion in both cells changes during the encounter. Over the years, approaches applied to this problem have ranged from in vivo gene­ expression technology to sequencing the full complement of bacterial or host­cell tran­ scripts (the transcriptome). However, such analyses have largely focused on messenger RNAs and have profiled either the bacteria or the host, not both at once. In a paper online in Nature, Westermann et al. go beyond the individual organisms by using dual RNA­ seq, an approach that simultaneously profiles bacterial and host transcriptomes throughout the course of an infection. The RNA­seq method takes advantage of the ever­increasing depth of sequencing (the num­ ber of reads for a particular sample) now pos­ sible. Westermann et al. first assessed whether the dual RNA­seq approach accurately reflected known gene regulation in human HeLa cells and in the bacterium Salmonella enterica serovar Typhimurium (hereafter Salmonella), a common cause of food poisoning, during infection. The authors’ data confirmed that, as previously reported, transcription of invasion­related genes in the genomic region known as Salmonella pathogenicity island 1 (SPI­1) was reduced after bacterial inter­ nalization, whereas transcription of SPI­2 genes, which promote intracellular survival, increased. Having validated the sensitivity of the approach, Westermann et al. focused on mRNAs and regulatory RNAs whose expres­ sion changed during the course of the 24­hour infection. In bacteria, small regulatory RNAs (sRNAs) that base­pair with target mRNAs to modulate the mRNA’s stability or translation are integral to a wide range of stress responses, including the response to host cells. Thus, the authors were intrigued by an 80­nucleo­ tide sRNA, which they denoted PinT, whose expression was highly induced during infec­ tion, and which was activated by the bacterial PhoP/Q system, known to be crucial for Salmonella survival in the intracellular environment. A striking finding of the dual RNA­seq analysis was that tens of bacterial and hun­ dreds of host­cell transcripts were affected merely by the presence or absence of PinT (Fig. 1). On the bacterial side, overproduction of PinT led to reduced levels of the mRNAs encoding SopE and SopE2, two SPI­1 effec­ tor proteins that mediate host­cell invasion by Salmonella. These mRNAs were elevated in strains lacking the pinT gene. By mutating the pinT, sopE and sopE2 sequences, the authors revealed that the inhibitory effect of PinT occurred through direct base­pairing with the mRNAs. Dual RNA­seq also revealed a role for PinT in repressing SPI­2 genes later in infection. However, control of these genes was indirect and occurred through PinT base­ pairing with the mRNA that encodes the cyclic AMP receptor protein (CRP), an activator of transcription of SPI­2 genes. These data indi­ cate that PinT, on bacterial internalization, controls the temporal expression of both SPI­1 effectors and SPI­2 virulence genes, thus facilitating the bacterium’s transition from an invasive state to a state of intracellular replication. Westermann et al. then compared the tran­ scriptomes of the host HeLa cells challenged with either wild­type Salmonella or a strain lacking PinT. They discovered numerous changes in cells infected with the PinT­lacking mutant, including altered levels of many long non­coding RNAs (lncRNAs), hyperactivation of mitochondrial genes, increased abundance of mRNAs for proteins involved in innate immune pathways (such as the interleukin­8 mRNA) and accelerated activation of SOCS3, a protein that regulates the inflammatory JAK– STAT signalling pathway. The last finding is of particular interest, because properly balanced JAK–STAT signalling is essential for optimal Salmonella infection. Too little inflammation reduces the ability of Salmonella to compete I N F E C T I O N B I O L O G Y

DOI: 10.1038/nature16872

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Cite this paper

@article{Machner2016InfectionBS, title={Infection biology: Small RNA with a large impact.}, author={Matthias P Machner and Gisela Storz}, journal={Nature}, year={2016}, volume={529 7587}, pages={472-3} }