Honours Projects
The projects below aim to provide a broad experimental and scientific education and experience in molecular genetics. The laboratory is concerned to provide Honours students with strong practical and intellectual support. Many previous participants have used this experience to successfully continue in many diverse areas of research.
Possible Honours projects: Endosymbiotic evolution
Mitochondria and chloroplasts contain genomes which encode only a small fraction of the proteins required for their biogenesis and function. Most of the genes that were present in the prokaryotic ancestors of these organelles have been transferred to the nucleus during endosymbiotic evolution. Genes that relocated and became functional in the nucleus were deleted from the organelle genomes, reducing organelle genome size. Early experiments, confirmed by genome sequencing revealed many large contiguous segments of mitochondrial and chloroplast DNA sequences, sometimes even complete organelle genomes that are integrated into the nuclear DNA of many organisms. The process of organellar DNA transfer and integration – that underlies endosymbiotic gene transfer - is a ubiquitous, ongoing, and natural mechanism that pervades nuclear DNA dynamics (Timmis et al., 2004). As a result of functional gene transfer to the nucleus, cytoplasmic organelle autonomy has been abolished and nuclear complexity and heterogeneity have increased. Real time experiments in tobacco show that chloroplast DNA transposes to the nucleus at an astonishingly high frequency, suggesting that the process is capable of generating a high level of nuclear and cytoplasmic genetic novelty that must have been a major driver of eukaryote-specific evolution.
The Timmis laboratory has gained international recognition for its contribution in this area.
Project 1: Evolutionary variation in the location of functional genes between nuclear and organellar genomes
Adams et al (2000) and Millen et al (2001) claimed that the functional genes rps10 and infA are present in nuclear DNA in certain Allium species whereas they are located in the mitochondrial or plastid genomes respectively in closely related genera. They further claim that the transfers are unique and independent events that occurred relatively recently in evolution and they showed good evidence that similar transfers have been common in the flowering plants. We wish to investigate two aspects of this scenario. Firstly we will determine whether this gene disposition is ubiquitous, or at least common, within the Allium genus and among the available wealth of intraspecific genetic variants of Allium. Secondly, we suspect that the gene relocation events reported may not be primary events as the authors infer, but rather the new nuclear genes may derive by the activation, by genomic rearrangements, of previous numt and nupts of greater evolutionary age. These may be searched for within the clades which show variability in gene location.Project 2: NUPT and NUMT variation within and between ecotypes of a single species
In the few instances where the complete nuclear genomic sequence is known, many NUPTs and NUMTs have been identified. In view of the dynamic insertion and deletion of nuclear organellar DNA sequences (Sheppard et al, 2008 in press; Sheppard and Timmis, manuscript submitted) it is likely that considerable variation exists between ecotypes of a species and even between individuals with a population. This project will use PCR strategies to investigate this possibility and any NUPT or NUMT variants discovered will be characterised at the molecular level.
References
Adams KL et al (2000) Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408, 354-357
Huang, CY, Ayliffe, MA and Timmis, JN (2003) Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature, 422, 72-76
Huang, CY, Ayliffe, MA and Timmis, JN (2003) Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature, 422, 72-76
Huang, CY, Ayliffe, MA and Timmis, JN (2004) Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco. Proc. Nat. Acad. Sci., USA, 101: 9710-9715
Huang, CY, Grünheit, N, Ahmadinejad, N, Timmis, JN and Martin, W (2005) Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear
Millen et al (2001) Many parallel losses of infA from chloroplast DNA during Angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell, 13, 645-659
Anna E. Sheppard, Michael A. Ayliffe, Laura Blatch, Anil Day, Sven K. Delaney, Norfarhana Khairul-Fahmy, Yuan Li, Panagiotis Madesis, Anthony J. Pryor, and Jeremy N. Timmis. (2008) Transfer of Plastid DNA to the Nucleus Is Elevated during Male Gametogenesis in Tobacco. Plant Physiology, 148, 328-336
Additional References from the Timmis Laboratory
Ralph Bock and Jeremy N. Timmis. Reconstructing evolution: gene transfer from plastids to the nucleus. (2008) BioEssays, 30, 556-566
Sheppard AE, Timmis JN (2009) Instability of Plastid DNA in the Nuclear Genome. PLoS Genet., 5(1): e1000323. doi:10.1371/journal.pgen.1000323
Timmis JN et al (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet., 5: 123-135
