Overview

Cells of the major marine cyanobacterial genera Synechococcus and Prochlorococcus are numerically the most abundant phototrophs on Earth. These organisms are responsible for up to 90% of primary production in various oceanic regions, with their numbers likely increasing in the future, so are vital to understanding the functioning of, and controls on, the global carbon cycle which is intrinsically linked to global warming. Their co-occurring viruses (cyanophages) are known to be equally widespread in their distribution. However, cyanophages are unique compared to other phages, because they maintain copies of photosynthetic genes within their genomes and likely play a direct role in modulating the fixation of CO2 and the production of the oxygen that we breathe.

Whilst it is clear that the photosynthetic ability of Synechococcus is maintained during phage infection, there is no direct evidence that CO2 fixation is maintained. Our preliminary data demonstrates that cyanophage infection causes a decrease in host CO2 fixation, the magnitude of which varies in different phage. We hypothesise that variation in cyanophage-encoded homologues of bacterial genes, that alter host metabolism and are designated as Auxiliary Metabolic Genes (AMGs), cause this difference. This research project will thus focus on the frequency of AMGs in cyanophage isolates from different environmental niches with the aim to understand how AMGs provide cyanophage with a fitness advantage in a specific environment. This will be complemented by functional characterisation of cyanophage AMGs specifically involved in carbon metabolism, to determine their physiological role and how they may alter host CO2 fixation capacity. 

Proposed mechanism of phage encoded proteins to alter the flow of carbon(2)⁠ . CP12 is thought to inhibit the Calvin cycle, with phage-encoded transaldolase shunting carbon towards fructose-6-phosphate, whilst G6PDH and 6PGDH increase flux through the pentose phosphate pathway. This will result in increased NADPH production, and ribose-5-phosphate for DNA biosynthesis.

Methodology

This PhD Project aims to answer the key question: How do CO2 fixation rates vary in globally important primary producers, Synechococcus and Prochlorococcus, infected by cyanophages. The successful applicant will isolate and analyse a range of cyanophages to determine their ability to alter host  CO2 fixation. Furthermore, gain a mechanisitic understanding of this by determining the function of specific genes. This project is multidisciplinary in that it emcompasses both traditional microbiology, molecular biology and bioinformatics, with supervisors in both the Medical School and Life Sciences.

Training and Skills

CENTA students will benefit from 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. 

This PhD project will offer the student a unique opportunity to learn cutting edge genomics skills including: High throughput sequencing of cyanophage isolates alongside advanced bioinformatics analysis of bacteriophage genomes. This will be combined with the opportunity to isolate a range of novel cyanophages, construction of Synechococcus mutants and experience of modern molecular/biochemical techniques including protein over-expression and enzyme assays.

Timeline

Year 1: Isolation of cyanophages from different oceanic provinces

Construction of Synechococcus mutants to express phage AMGs

CO2 fixation rates of Synechococcus cells infected with different cyanophage isolates

Year 2: Genome sequencing and bioinformatic analysis of genomes

Over expression of selected AMGs in E. coli

CO2 fixation rates of Synechococcus mutants

Year 3: CO2 fixation rates of Synechococcus mutants infected with specific cyanophages

Functional characterisation of AMGs expressed in E. coli
Enzyme Assays

Partners and collaboration (including CASE)

Dr Andrew Millard has >10 years’ experience working with marine cyanophages and bioinformatic analysis of large microbial datasets. In addition the project will greatly benefit from having Prof Scanlan, a marine microbiologist who has >20 years expertise working with marine cyanobacteria from ecology to genomics, and especially defining nutrient acquisition mechanisms and the role of P in limiting marine production.

Further Details

Applicants should possess a BSc or MSc in Microbiology/Biochemistry with a particular interest in molecular biology and bioinformatics techniques.

Informal enquiries can be made to Dr Andrew Millard (a.d.millard@warwick.ac.uk). Further details of research in each of the supervisors labs can be obtained from

http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/millardlab

http://www2.warwick.ac.uk/fac/sci/lifesci/people/dscanlan