Stories of the future: manipulating RNA and Intra/Interkingdom communication

Abstract

My expertise is RNA and ribonucleases, and it has been a pleasure to observe and participate in the RNA revolution, which is rapidly changing how we interpret gene expression. Small non-coding RNAs repress or activate genes in consonance to environmental or developmental cues and they can modulate life and death of the cell. RNAs can change shapes to adapt to different temperatures (thermosensors), and this can modify their functions; for instance, changing to 37°C can lead to structural changes that trigger the translation of virulence factors (Johansson et al., 2002). Furthermore, RNAs can sequester specific molecules to halt the production of surplus levels of those products (e.g. riboswitches – McCown et al., 2017). The advance of modern technologies such as RNAseq has shown that myriad RNAs are synthesized, and elegant methods can select specific types of RNAs and their targets (RNAs, proteins or DNA). About ten years ago, Nobel Prizes were given for RNA interference studies, the structure of the ribosome and the study of RNA polymerase II during transcription. Lessons from bacteria have led to the discovery of new DNA remodelling and immunological mechanisms mediated by RNA, CRISPR and Cas proteins. Many important genetic technologies have derived from this process and this will certainly lead to another Nobel in the near future. The powerful RNAs have to exist in a balance between synthesis and degradation. Ribonucleases (RNases) actively process, degrade and monitor the quality control of all types of RNA (Arraiano et al., 2010, 2013; Saramago et al., 2014). They can recognize the sequence, structure and the terminal tails of some of their favourite targets. This process is very dynamic, and the ‘predator’ RNases have to locate their ‘prey’ RNAs in time and space. The ribonucleases have a fundamental role in the turnover of RNAs since the accumulation of degradation products and aberrant transcripts is usually quite detrimental for the cell; furthermore, they actively participate in the recycling of valuable nucleotides. Engineering and modulating the lifespan of RNAs has great potential (Viegas et al., 2018) and will certainly be one of the highlights of future science. Synthetic Biology supported by all the recent RNA-derived technologies will lead to important Biotech applications. (de Lorenzo, 2018). The investigation of new small non-coding RNAs in a symbiont bacteria gave me the inspiration for this article within the frame of the Microbial Biotechnology CrystalBall series of 2018/2019. The bacterium was the betaproteobacteria Herbaspirillum seropedicae strain SmR1, an endophyte that colonizes economically important grain crops including rice, maize and fixes nitrogen, thereby promoting plant growth (Pedrosa et al., 2001). During the laboratory experiments, it struck me that when naringenin (a plant flavonoid) is added H. seropedicaea acts as if it was inside the host plant (Tadra-Sfeir et al., 2015). This important symbiont senses it is somewhere else and behaves in conformity with the ‘fake’ environment, just like ‘virtual reality’. The exploration of this concept can have a tremendous potential for innumerous applications, and the ‘make believe’ between interkingdom communication is my Crystal Ball proposition for a future story of success! It is already known that bacteria can easily communicate by means such as quorum sensing, and the molecular messengers containing the information sometimes are only ‘translated’ by certain populations (Bassler and Losick, 2006). Besides, some bacteria can intercept and hijack the information sent by other species (Xavier and Bassler, 2005). The small noncoding RNAs are among the molecules participating in this dynamic network of communication. The studies on the microbiome will progress much faster when we learn to communicate with bacteria. Recent developments have shown that the interactions of bacteria among each other and with different organisms can also be mediated by volatile molecules (Audrain et al., 2015; Chung et al., 2016). It is certainly a powerful means, Received 5 November, 2018; accepted 9 November, 2018. *For correspondence. E-mail [email protected]; Tel. +351 214469547; Fax +351 214469549. Microbial Biotechnology (2019) 12(1), 48–50 doi:10.1111/1751-7915.13344