Wagner lab

Our research group is interested in the biological functions, and mechanisms of actions, of a heterogeneous class of bacterial regulatory RNAs. Most of these so-called small RNAs (sRNAs) base-pair to multiple target mRNAs to activate or repress their translation, and/or affect mRNA stability. This in turn regulates the production of proteins involved in, for instance, bacterial stress responses and lifestyle decisions.

Popular science presentation

Small RNAs regulate gene activity

In the last decade, we have witnessed a paradigm shift. The widely accepted view on how a gene's activity is controlled – by designated proteins – has become obsolete. We know now that small (and in some cases, large) RNA molecules are major players in regulating all kinds of life processes in cells and organisms.

The genetic information in all cells and organisms is written in DNA. The activity of the genes must be carefully controlled so that each protein is produced when and where it is needed. A rapid change in a bacterium's environment, or the development of a specialized nerve cell in an animal, requires that certain genes have to be turned on and others off. Earlier on, this was supposed to be the exclusive role of specific controller proteins (transcription factors), but now we know that numerous RNAs can carry out the same function. In 2001, we discovered many then unknown short RNAs (so-called small RNAs/ sRNAs) in a gut bacterium. Almost all of these turned out to regulate genes. Shortly after, a great number of very short RNAs (microRNAs) were found in animals and plants. They also regulate genes, for instance during tissue development or larval development in worms.

So how can small RNAs regulate genes? The solution is suggested by the double-stranded structure of DNA, where two strands in the spiral are held together by the pairing of nucleobases (they are "complementary"). In the same fashion, an sRNA can be complementary to an mRNA (messenger RNA, the RNA that is a copy of a gene and carries the information to produce a protein). Binding of an sRNA to a matching mRNA renders it inactive. RNAs that use such a mechanism are also called "antisense" RNAs.

This kind of antisense regulation is found in all organisms on the planet. We study a common bacterium called Escherichia coli to understand the biological roles of these new RNAs, and the molecular mechanisms of how they bind their target mRNAs and how this in turn affects the protein output. We also want to understand regulation by RNAs in a broader perspective. Bacterial sRNAs are much longer that microRNAs in animals and plants, and differ also in other properties. For instance our sRNAs need special 3D structure elements to be efficient. In terms of mechanisms, binding of an sRNA can prevent the synthesis of protein from an mRNA, but also lead to mRNA degradation. However, sRNAs – but not microRNAs – can also have the opposite effect: activation of protein synthesis.

We have in great detail studied several sRNAs and their functions. One of them can stop the synthesis of a toxic protein that bacteria produce during stress (here: when DNA is broken). Two others control the formation of "curli" which are structures that some bacteria build up on their outside to collectively attach to surfaces (=biofilm) – this often happens during bacterial infections. The cell surface is particularly important for harmful, infectious bacteria, because it is the point of first contact with the immune response of the host. We and others have seen that many of the proteins on the surface of the bacterium are exquisitely regulated by only a few sRNAs. We are therefore interested in how a single sRNA can regulate several different target mRNAs. In order to learn about the control circuits that sRNAs participate in, we use state-of-the-art methods like RNA deep-sequencing.

A fairly new story concerns phenotypic heterogeneity. This means that genetically identical bacteria in the same environment can display entirely different behaviours (like: being actively growing or falling asleep). One can see this as a strategy to not put all eggs into one basket – which may be a good idea if drastic changes often occur in the environment. Bacterial cells that for a longer time are "asleep" are called persisters, and create problems in health care since most antibiotics cannot tackle non-growing bacteria. We study an sRNA-regulated toxin that increased the number of persisters in a population. Our group is also interested in changes in bacterial lifestyles, for example swimming alone instead of forming a colony on a surface (a biofilm). Also here we have found sRNAs that affect such decisions.

In our daily experimental work, we use genetics, biochemistry, and small- and large-scale molecular biology experiments. Our main interest lies in a deep understanding of the many fascinating and important roles that sRNA play, and in how they do it in molecular detail. Internationally, research on regulatory RNAs is a very hot topic. Maybe our knowledge in antisense-type RNAs can contribute to how sRNAs affect the changing bacterial surface, stress responses, and persister formation – which is relevant beyond our bacterial lab pet and extends to nasty pathogens.

Research projects

Our group has a strong track record in the field of bacterial regulatory RNAs. In earlier years, we studied plasmid-related functions (copy number control, stability of maintenance) that are controlled by antisense RNAs. Often in international collaborations, we investigated in depth the biological aspects of control and their underlying mechanisms of action.

Subsequent projects identified many new so-called small RNAs (sRNAs), an abundant class of regulatory RNAs now known to be ubiquitously encoded by all bacterial and archaeal chromosomes. Most of these act by an antisense mechanism reminiscent of that used by their plasmid-encoded friends, and by their eukaryotic cousins, the miRNAs. We study the roles of sRNAs in stress responses and lifestyle decisions, and elucidate their modes of regulation on a molecular level. sRNAs usually but not exclusively inhibit translation of target mRNAs. As we have shown, this sometimes involves non-conventional mechanisms such as an inhibition of "ribosome stand-by". A more recent focus is on stochastic gene regulatory processes in which sRNAs play a role. This involves sometimes bistable expression patterns that govern phenotypic heterogeneity in isogenic bacterial populations.

We are also interested in the biological roles, and the mechanisms of action, of helper proteins such as the Sm-like Hfq, which is required for the activity and/or stability of most sRNAs.

Our group conducts work that involves molecular genetics, bacterial physiology, biochemistry, molecular biology, and systems biology.