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Understanding the genetic blueprint of photosynthetic bacteria?


Project Description

Project Highlights:
• Cutting-edge 3D chromosome reconstruction and “gene transplants” using CRISPR
• Understanding the evolution of chromosomes of photosynthetic organisms
• Redesigning bacterial chromosomes for efficient photosynthesis

Overview:

Photoautotrophic bacteria (cyanobacteria) are responsible for over a quarter of oxygen produced on Earth. They are essential for maintenance of food webs and through endosymbiosis, led to the rise of all land plants. Yet our basic understanding of their cell biology is poor. This is problematic, when, for instance, attempting to use synthetic biology to rationally engineer photosynthetic cell factories (e.g. for biofuel production).

In general, bacteria organise their genomes in operons. Genes involved in certain processes are found close to one another in the genome to allow coordinate expression in response to external stimuli. The process of photosynthesis poses a huge demand on the cell. The continuous damage to the photosynthetic apparatus by light, results in the cell dedicating a large fraction of transcription and translation to making this apparatus de novo and targeting it to the site of photosynthesis, the thylakoid membrane. We might therefore expect that genes involved with photosynthesis to be arranged in operon like structures such that regulation is coordinated and not wasteful. In reality, photosynthesis genes are sparsely distributed across the genome. Why this is the case remains a mystery.

Recently, high-resolution electron microscope images of the interior of cyanobacterial cells has revealed a high concentration of ribosomes around the area of thylakoid membrane biogenesis (Figure 1A). Since bacteria complete transcription and translation almost simultaneously, and ribosomes centre on sites of thylakoid biogenesis, we pose the hypothesis that the 3D conformation of the chromosome means photosynthesis genes are orientated to this site. You will test this hypothesis using recently developed chromosome conformation mapping, “gene transplants” via CRISPR based mutagenesis and advanced confocal microscopy imaging. Your results will have implications for the evolution of phototrophy on Earth, and how we can generate more efficient photosynthetic cell factories.

Methodology:
You will use 3D chromosome structure reconstruction techniques [2]. You will couple this with CRISPR based engineering of the cyanobacterial chromosomes to relocate photosynthesis genes in the chromosome (“gene transplants”). Lastly, you will use fluorescent in-situ hybridisation and confocal microscopy to image the location of genes in the cell.
Training and skills:
This project offers numerous technical transferable skills. These include molecular cloning; CRISPR based mutagenesis and high throughout automation using robotics. In addition, you will use high-throughput sequencing (Illumina) and become expert in confocal microscopy.

Partners and collaboration:
The supervisors are world-leading experts in cyanobacterial cell biology, as evidenced by regularly publishing in high profile interdisciplinary journals (e.g. Proc. Natl. Acad. Sci. USA, Current Biology) and field specific high impact journals (e.g. The ISME Journal). The supervisors have combined experience of >25 years. You will belong to a larger group of environmental microbiologists in the department of life sciences’ environment theme. (https://warwick.ac.uk/fac/sci/lifesci/research/envbiosci/). These groups occupy a large shared lab area and as such, there is continuous collaborations and opportunities for career development within the theme. Current research in the groups is funded by NERC and generous start-up award to Dr. Puxty.

Dr Puxty’s group: https://warwick.ac.uk/fac/sci/lifesci/people/rpuxty/
Prof Scanlan’s group http://www2.warwick.ac.uk/fac/sci/lifesci/people/dscanlan

Possible timeline:
Year 1: Generate 3D maps of cyanobacterial chromosomes. Test whether light can affect these 3D maps.
Year 2: Use fluorescent in-situ hybridisation and fluorescently labelled proteins to localise genes within the cell
Year 3: Perform “chromosome transplants” of key photosynthesis genes and test whether genome location affects the ability of the cell to perform photosynthesis.

Funding Notes

This funding provides full tuition fees at the Home/EU rate, pays an annual stipend in line with UK Research Councils (currently £15,009) and a research training support grant (RTSG) of £8,000

References

Further reading:
[1] Rast et al. 2019. Biogenic regions of cyanobacterial thylakoids form contact sites with the plasma membrane. Nature Plants, 5, 436-446.
[2] Marbouty et al. 2014. Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife:3:e03318.

How good is research at University of Warwick in Agriculture, Veterinary and Food Science?

FTE Category A staff submitted: 12.60

Research output data provided by the Research Excellence Framework (REF)

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