Genetic Dark Matter? Functional characterization of a non-coding RNA regulation of microbial metabolism of climate active trace gases.

Project Highlights
• Climate change meets microbiology
• Unique opportunity to study a ‘junk’ RNA
• World-leading supervisory team on climate-change microbiology

Overview
Dimethylsulphide (DMS) and methylated amines (such as trimethylamine, TMA) are climate active trace gases emitted from the oceans. Unlike greenhouse gases, such as carbon dioxide and methane, DMS and TMA are important in aerosol formation, subsequent formation of cloud condensation nuclei and cloud droplets in the remote marine atmosphere, therefore potentially acting as climate cooling gases.
Surface oceanic waters are the major sink of marine trace gases before they can reach the atmosphere. Microorganisms inhabiting the surface oceans can utilize these compounds as carbon/nitrogen/sulfur sources, thereby affecting their biogeochemical cycles in the marine environment. However, little is known of the marine microbes involved in these biogeochemical cycles, let alone the regulation of metabolism of these climate-active trace gases.

Using a model marine bacterium, Ruegeria pomeroyi, we have recently revealed the presence of a unique antisense RNA in the regulation of DMS/TMA metabolism in this bacterium (Lidbury et al 2016). R. pomeroyi can utilize TMA as a sole nitrogen source. It can also oxidise DMS, but only if TMA is present. This regulation is achieved through a non-coding RNA (also known as genetic dark matter), fmoR, encoded in the antisense strand of the flavin-containing TMA monooxygenase (Tmm), which was previously characterized by our groups. This dual regulation of DMS co-metabolism by TMA and fmoR has important environmental significance since both DMS and TMA are common metabolites resulting from degradation of osmolytes in a wide range of marine phytoplankton, providing an essential link between marine productivity and marine trace gas emission through ecologically important marine heterotrophs (such as Ruegeria pomeroyi). Unlike many other non-coding RNAs in bacterial genomes whose biological functionality remains difficult to ascertain, this project provides a unique opportunity to investigate the role of fmoR in regulating the co-metabolism of two globally important oceanic climate active gases.

Methodology
The overall aim of this project is therefore to understand the regulation of TMA/DMS co-metabolism by fmoR in order to establish a comprehensive model of the role of fmoR in regulating trace gas metabolism in R. pomeroyi.
Growth of R. pomeroyi will be achieved using both defined synthetic medium as well as nutrient broth. DMS/TMA will be quantified by gas chromatography and ion-exchange chromatography respectively. Metabolites of DMS/TMA catabolism will be identified and quantified using LC/MS.

Training and skills
CENTA students are required to complete 50 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes.
The Supervisory team has an excellent record in PhD supervision. The last two PhD students completed from the Chen group has published 4 and 3 first-authored papers respectively, including 2 in PNAS, 1 in the ISME Journal, 3 in Environmental Microbiology and 1 in the FEBS Journal.

The project is based on our recent published observation of a novel antisense RNA in a model marine bacterium which can co-metabolize both DMA and TMA (Lidbury et al 2016), therefore providing a unique opportunity to use contemporary bioinformatics with biology.

This exciting project provides cutting-edge training on genome-wide bioinformatic identification of novel regulatory RNAs. It will also provide excellent training in wider aspects of marine microbiology, biogeochemistry and molecular biology using cutting edge biochemical, molecular and ‘omic approaches’, as well as in a variety of analytical techniques currently available in the Chen/Schäfer group, including gas chromatography, ion-exchange chromatography, liquid chromatography-mass spectrometry.

Partners and collaboration
The Chen and Schäfer groups at Warwick have pioneered research of microbial-mediated climate-active gas cycles in the marine environment, particularly DMS and methylated amines. Current research in the groups is funded by NERC, BBSRC and the Gordon and Betty Moore Foundation.
Dr Chen’s group: http://www2.warwick.ac.uk/fac/sci/lifesci/people/ychen
Dr Schäfer’s group: http://www2.warwick.ac.uk/fac/sci/lifesci/people/hschaefer