Technique for simultaneous study of small RNA of bacteria and host cells reveals changes to both transcript profiles

January 21, 2016 by Bob Yirka report
Colonies of pathogenic bacteria growing on an agar culture plate - Salmonella enterica (serovar typhimurium) Credit: Centers for Disease Control and Prevention

(Phys.org)—A team of researchers with members from Germany, Austria and the U.S. has found that using a technique that allows for studying small RNA of both bacteria and a host during an infection, can reveal changes to the transcript profiles of both of them. In their paper published in the journal Nature, the team describes their technique, why it is useful in learning more about how bacterial infections work and what they found in their study. Matthias Machner and Gisela Storz, with the Eunice Kennedy Shriver National Institute of Child Health and Human Development, offer a News & Views piece on the work done by the team in the same journal issue.

As Machner and Stortz note, most prior studies conducted to better understand what happens when bacteria infect a have been focused on messenger RNAs in the bacteria, or the host. In this new effort, the researchers use a technique that allows for focusing on both at the same time, allowing for a more complete picture of what occurs during the initial and later stages of the infection process.

The approach, called dual RNA-seq allowed the researchers to study host transcripts and pathogen messenger RNAs at the same time—in this case, Salmonella infecting a human cell line. More particularly, they focused on a small RNA called PinT, which is known to become activated when the bacteria begins to infect a host cell. A closer look revealed that it also regulated S. enterica genes and showed signs of influencing host transcriptional patterns, which in turn led to changes in some long, non-coding RNAs and activation of other signaling pathways in host cells.

Dual RNA-seq, the researchers explain, is a method that involves using green fluorescent tagging of bacteria to allow for identifying parts of host cells as they become infected. The technique allows for studying transcripts representing messenger RNA and non-coding RNAs from both of the organisms as the infection progressed, offering an unprecedented view of the process. They group also note how their study also showed how small changes in the process of infection could propagate through to host systems possibly leading to different outcomes for the infected host.

Explore further: Transcription of host noncoding DNA elements signals viral intrusion but is hijacked by gammaherpesvirus

More information: Alexander J. Westermann et al. Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions, Nature (2016). DOI: 10.1038/nature16547

Abstract
Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK–STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.

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