Marine virus metabolomics: dissecting subversion of host metabolism

Project title: Marine virus metabolomics: dissecting subversion of host metabolism
Project code:
Host institution: University of Warwick
Theme: Organisms, ‘omics and biogeochemistry
Key words: Cyanobacteria; Viruses; metabolomics; marine microbiology
Supervisory team : Prof Dave Scanlan (University of Warwick) [email protected];
Prof Mark Viant (University of Birmingham) [email protected]
Dr Martha Clokie (University of Leicester) [email protected]
Overview: The oceans play a major role in
determining world climate via the production of
oxygen and the consumption of carbon dioxide
largely by tiny, single celled organisms, the
photosynthetic picoplankton. These organisms, which
are numerically dominated by the cyanobacterial
genera Prochlorococcus and Synechococcus can be
responsible for up to 70% of CO2 fixation in some
oceanic regions [1]. Marine cyanophages infecting
both Synechococcus and Prochlorococcus [2] appear
to be extremely abundant (up to 106 ml-1 [2]) in most
aquatic ecosystems, and a key current question is to
what extent viruses drive the structure and function
of these marine picophytoplankton communities, and
in so doing dictate the fate of fixed carbon.
Cyanophages are exceptional in that they also appear
to play a direct role in CO2 fixation since they carry
genes (psbA and psbD, encoding core photosystem II
reaction centre polypeptides) that are essential for
photosynthesis [3, 4, 5]. In addition, many other genes
not normally found in phage genomes have been
identified [6].
specifically focuses on how these viruses might subvert
Synechococcus host metabolism during infection.
These include the zwf, gnd, and talC genes encoding
components of central C metabolism (glucose-6phosphate dehydrogenase, 6-phosphogluconate
dehydrogenase and transaldolase, respectively) as
well as genes encoding components of the
photosynthetic electron transport machinery (petE,
petF, ptoX), nucleotide metabolism (nrdAB encoding
ribonucleotide reductase) and phosphate acquisition
(pstS, phoH).
Aims & Methodology: We hypothesise that these
viral versions of ‘host’ genes play a critical role in
subverting host metabolism so that it is re-wired
towards producing the building blocks required for
cyanophage DNA replication and ultimately new
progeny viruses. This exciting PhD project will test
this hypothesis using a metabolomics approach [7]
capable of not only detecting changes in central
carbon metabolism but also revealing any novel or
unexpected changes associated with cyanophageinduced metabolic rewiring. In so doing, we will
greatly advance our understanding of lytic phage-host
interactions.
Training and skills: The project will provide excellent
Figure 1: a) and b) Synechococcus cyanobacteria
dominate marine primary production. c) A major loss
factor is biotic control via viral lysis d) This project
training in marine microbiology and microbial
physiology, as well as cutting edge analytical
chemistry (e.g. Q Exactive LC-MS and TSQ Vantage LCMS/MS) and ‘omic approaches (both non-targeted
and targeted metabolomics), whilst at the same time
developing a range of research skills.
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 student will be assisted by the wide array of
scientific expertise already available in the Scanlan
lab. In addition the project will greatly benefit from
having Prof Mark Viant, Professor of Metabolomics at
the University of Birmingham, and Dr Martha Clokie a
cyanophage molecular biologist at the University of
Leicester as co-supervisors.
Possible timeline:
Years 1 and 2: Measurement of the metabolic profiles
of viral infected versus uninfected host cells by LC-MS
(at time points during the infection cycle), allowing for
up-regulation of the viral genes and subsequent
effects on host metabolism; subsequently conduct
supervised multivariate analysis to reveal the
metabolic differences between treatment groups. The
metabolic differences identified (both in targeted
compounds as well as the non-targeted profile) will be
overlaid onto metabolic pathway maps. Subsequent
experimentation would target specific more detailed
analysis of particularly metabolic pathways dependent
on the results obtained.
Year 3: Studies will be extended to measure fluxes
through specific pathways e.g. the Calvin cycle using
13
C labelling. These studies would extend and
complement findings from the non-targeted
metabolomics above, i.e. those metabolites that
appear most elevated in (static) concentration can be
inferred to be associated with phage induced changes
in metabolism, and this will be evaluated in terms of
altered 13C abundances.
Further reading:
1. Jardillier L et al., (2010) ISME J 4 : 1180-1192.
2. Mann, NH (2003) FEMS Microbiol Rev 27 : 17-34.
3. Mann, NH et al. (2003) Nature 424: 741.
4. Millard A et al. (2004) PNAS 101: 11007-11012.
5. Clokie, MRJ et al (2006) Env Microbiol 8: 827-835.
6. Millard A et al. (2009) Env Microbiol 11: 2370-2387.
7. Viant MR & Sommer U (2013) Metabolomics 9 :
S144-158.
Further details: APPLICANTS should possess a BSc or
MSc in Microbiology/Biochemistry with some
experience and interest in analytical chemistry and
computational techniques.
Informal enquiries can be made to Prof Dave Scanlan
([email protected]), Prof Mark Viant
([email protected]) or Dr Martha Clokie
([email protected]). Further details of research
in the supervisors labs can be obtained from
http://www2.warwick.ac.uk/fac/sci/lifesci/people/ds
canlan,
http://www.bioscienceslabs.bham.ac.uk/viant/,
and
http://www2.le.ac.uk/departments/iii/people/drmartha-clokie.

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