Which only has RNA

The sense of antisense RNA

The discovery of thousands of unknown RNA molecules in every imaginable organism has given a new impetus to RNA research. In the past, RNA was seen primarily as a link to the gene expression between DNA and proteins. But now one can find more and more molecular circuits in which RNA operates as a regulator. Such RNA molecules are not translated into proteins, so they are called non-coding. The RNA Biology working group at the Max Planck Institute for Infection Biology researches the function of such RNA molecules in bacteria that are pathogenic to humans.

RNA is being rediscovered

The last few years have clearly shown that RNA molecules have far more biological functions than previously assumed. Traditionally, RNA was only assigned three basic roles, namely i.) As a messenger substance for genetic information in the form of messenger RNAs (mRNAs), ii.) As genetic material of certain viruses and iii.) As an essential part of the protein synthesis machinery, the ribosomes, there in the form of transfer RNA (tRNA) and ribosomal RNA (rRNA). It has long been known that RNA itself, like enzymes, can be catalytically active and that small, untranslated RNAs have other important functions in the cell, for example when splicing mRNAs, as well as that non-coding RNA molecules themselves act as regulators of gene expression. Nevertheless, such regulatory functions appeared to be limited mainly to bacterial plasmids, phages or transposons. That changed about five years ago, however, when a systematic search in bacteria and higher living things unearthed a whole microcosm of non-coding, small RNAs. Soon afterwards, the use of small RNAs for the targeted switching off of genes in higher organisms, the so-called RNAi (RNA interference) technology, gained enormous momentum.

Goods in the model bacteria Escherichia coli only ten small non-coding RNAs (sRNAs) were known, their number rose to over eighty within a very short time. Hundreds more sRNAs have been predicted so far, but have yet to be detected. The function of most of the newly discovered sRNAs is still unknown, but there is evidence that they form a new class of regulators in bacterial stress responses.

sRNAs in pathogenic bacteria

So far, only a few sRNAs have been described in pathogenic bacteria. In contrast to the systematic search in the non-pathogenic E. coli-Tribe K12, they were mostly only discovered by chance and little is known about their function. The successful search in E. coli was largely based on the discovery that the sRNA-coding genes of this bacterium are also present in a conserved form in closely related pathogenic enterobacteria such as Salmonella, Klebsiella and Yersinia species.

The focus of the working group on RNA biology is the functional characterization of sRNAs with regard to bacterial virulence and the interaction of pathogenic bacteria with infected host cells. A whole spectrum of molecular, biochemical, genetic and bioinformatic methods is used. Since only a few cases have so far been investigated in depth how such small RNAs intervene in bacterial gene expression in a regulatory manner, the working group is particularly interested in the molecular mechanisms of this regulation.

Most sRNAs operate as something called a antisense RNAs, i.e. they can bind to messenger RNAs via base complementarity and thus control the synthesis of certain proteins. The pairings between these molecules are, however, quite short in length, imperfect and therefore difficult to predict, which means that the greatest challenge for research is to assign one or more target molecules to the sRNAs.

Small RNAs control the condition of the Salmonella cell envelope

Together with British scientists, the mechanism was recently described how non-coding RNA molecules in Salmonella bacteria monitor the condition of the cell envelope [1]. Salmonella are bacteria that infest humans and animals, and as pathogens, they must be able to continuously and quickly adapt to new environmental conditions in order to survive inside and outside their hosts. Such adaptations cause stress, against which salmonella protect themselves, for example with their cell envelope. Keeping the cell envelope intact and reorganizing it again and again is extremely important for the survival of Salmonella under the most adverse conditions. For example, if Salmonella infects a host, it must be able to withstand the low pH value of the stomach as well as the low-oxygen and salty environment in the intestine. In order to be able to adapt, Salmonella must be able to incorporate new and different membrane proteins into their cell envelope over and over again. These outer membrane proteins form pores and allow the bacteria to absorb nutrients and salts from their environment - a double-edged sword, because at the same time these pore proteins are also recognized by the host's immune system, so their synthesis must be precisely controlled by the bacterium, so that not too many of them accumulate in the envelope.

It has now been found that salmonellae can use a kind of monitoring loop to precisely register whether misfolded membrane proteins accumulate as a sign of damage to their shell. As soon as this is registered, small non-coding sRNAs immediately switch off the biosynthesis of membrane proteins (Fig. 1). Since, in contrast to regulatory proteins, the synthesis of such sRNAs is completed in a few seconds, this protective reaction can take place at an extremely high speed.

The regulatory sRNAs solve a second problem, namely that of the extremely stable, membrane protein-coding messenger RNAs. These RNAs have biological half-lives of around a quarter of an hour - compared to other messenger RNAs with half-lives of a few minutes. Whatever the reason for this great stability, it means that even if the corresponding gene is switched off quickly, the synthesis of the corresponding membrane protein by the messenger RNA will continue for a long time - too long for Salmonella, which, as I said, often have to rearrange their shell within seconds. The regulatory sRNAs can solve this problem by directly inactivating the messenger RNAs that encode membrane proteins and thus completely switching off the production of envelope proteins.

A special feature of the newly discovered, regulatory sRNAs is that they can recognize the membrane protein-encoding messenger RNAs in a highly specific manner, although these themselves are very different from one another. How exactly this detection works will have to be found out in the coming years.

Original publications

Papenfort, K ​​.; Pfeiffer, V .; Mika, F .; Lucchini, S .; Hinton, J. C .; Vogel, J .:
SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating globally omp mRNA decay.
Molecular Microbiology 62, 1674–1688 (2006)