Project title: Junk or not Junk? Functional characterization of a non-coding RNA regulating microbial metabolism of climate active trace gases.
Project code:
Host institution: University of Warwick
Theme: Organisms, ‘omics’ and biogeochemistry
Key words: trace gas, climate, marine microbiology, small RNA, biogeochemistry, biogeochemical cycles
Supervisory team (including institution & email address) :
Dr Yin Chen (University of Warwick) Y.Chen.25@warwick.ac.uk
Dr Hendrik Schäfer (University of Warwick) H.schaefer@warwick.ac.uk
DMS co-metabolism by TMA and fmoR has important

Climate change meets microbiology

Unique opportunity to study a ‘junk’ RNA

World-leading supervisory team on climateenvironmental significance since both DMS and TMA are common metabolites resulting from degradation of osmolytes in a wide range of marine change microbiology phytoplankton, providing an essential link between marine productivity and marine trace gas emission
Overview
Dimethylsulphide (DMS) and methylated amines (such through ecologically important marine heterotrophs as trimethylamine, TMA) are climate active trace gases emitted from the oceans. Unlike greenhouse
(such as Ruegeria pomeroyi ). Unlike many other noncoding RNAs in bacterial genomes whose biological gases, such as carbon dioxide and methane, DMS and
TMA are important in aerosol formation, subsequent functionality remains difficult to ascertain, this project provides a unique opportunity to investigate the role formation of cloud condensation nuclei and cloud droplets in the remote marine atmosphere, therefore of fmoR in regulating the co-metabolism of two globally important oceanic climate active gases. 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. 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 ( fmoR ) encoded in the antisense strand of the flavin-containing TMA monooxygenase (Tmm), which was previously characterized by our groups. This dual regulation of
Figure 1 top left: amaZon liquid chromatography-mass spectrometry. Top right: ion-exchange chromatography. Bottom left: gas chromatography.
Bottom right: Ruegeria pomeroyi under phasecontrast microscope.
Aims and Methodology:
The overall of this project is therefore to understand the regulation of TMA/DMS cometabolism 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:
The project is based on our recent unpublished observation of a novel antisense RNA in a model marine bacterium which can co-metabolize both DMA and TMA, 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.
CENTA students will attend 45 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 the student's projects and themes.
Partners and collaboration (including CASE):
The Chen and Schäfer groups at Warwick have pioneered research of microbial-mediated climateactive gas cycles in the marine environment, particularly DMS and methylated amines. Current research in the groups is funded by the Natural
Environment Research Council, and the Gordon and
Betty Moore Foundation. Further details on their research activities can be found via the links below.
Dr Chen’s group: http://www2.warwick.ac.uk/fac/sci/lifesci/people/ych en
Dr Schäfer’s group: http://www2.warwick.ac.uk/fac/sci/lifesci/people/hsc haefer
Possible timeline:
Year 1: Identification and bioinformatics characterization of the antisense RNA. fmoR mapping by 5’ and 3’ rapid amplification of cDNA ends (RACE).
Training on analytic methods including gas chromatography, ion-exchange chromatography and mass spectrometry.
Year 2: Experimental confirmation of the anti-sense
RNA through RNA-seq and qRT-PCR. Characterization of fmrR expression in TMA and DMS co-metabolism
Year 3: Establishment of a comprehensive model of regulation through antisense RNA and transcriptional regulators in TMA/DMS cometabolism.
Further reading:
Chen, Y ., Patel, N., Crombie, A., Scrivens J., Murrell,
J.C. (2011) 'Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase', Proceedings of
The National Academy Of Sciences, 108 (43), 17791 -
17796
Lidbury, I., Murrell, J.C., Chen, Y.
(2014)
'Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria', Proceedings of The
National Academy of Sciences, 111 (7), 2710 – 2715.
Lidbury, I., Murrell, J.C., Chen, Y.
(2015)
'Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling', ISME Journal 9:760–769
Y Chen (2012) 'Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers
( tmm, gmaS )', Environmental Microbiology, 14 (9),
2308 - 2322
Schäfer, H ., Myronova, N. and Boden, R. (2010)
'Microbial degradation of dimethylsulfide and related
C1-sulfur compounds: organisms and pathways controlling fluxes of sulfur in the biosphere', Journal of
Experimental Botany, 61 (2), 315 – 334.
Boden, R., Borodina, E., Wood, A.P., Kelly, D.P.,
Murrell, J.C., and H. Schäfer. (2011) Purification and characterization of dimethylsulfide monooxygenase from Hyphomicrobium sulfonivorans . Journal of
Bacteriology, 193: 1250 – 1258.
Further details:
Applicants from the UK or the EU are eligible.
Applicants should hold a BSc and/or MSc degree in relevant subjects.
Informal enquires can be made to Dr Yin Chen
( y.chen.25@warwick.ac.uk
, 00 44 24765 28976) or Dr
Hendrik Schäfer ( H.schaefer@warwick.ac.uk
, 00 44
24765 75052).