- Opens: Monday 17 February 2020
- Number of places: 1
- Duration: 36 Months
OverviewMicrobiology and Industrial Biotechnology, antibiotic-producing bacteria, genomics, genetics
Over the last 60 years actinobacteria, especially from the genus Streptomyces have been the most important source of biologically-derived bioactive molecules to reach the clinic. These natural products include antibiotics (tetracyclines, streptomycins, & erythromycins), immunosuppressants (FK506/520 & rapamycin) and anti-cancer drugs (doxorubicin). Now, in this post-genomic era, they provide a valuable opportunity for drug discovery - using a combination of data mining, molecular biology and analytical chemistry.
A key component of the identification of novel antibiotics is through the application of genome mining to sequenced streptomycetes (Corre and Challis, 2009, Blin et al., 2016). Despite this, the genomes of many streptomycetes are incomplete due to difficulties in sequencing the telomeric regions on their linear chromosomes. As such, the aim of this project is to characterise these regions of a number of streptomycete strains and their cognate telomeric proteins responsible for priming the synthesis of the chromosome ends (Tsai et al., 2012, Huang et al., 2013, Yang et al., 2013). We will complete the genome sequences and establish the presence of giant linear plasmids (GLPS) of these strains. In addition, we will the clone the telomeres of both the chromosome and any GLPs (Fan et al., 2012). Furthermore we will generate deletions in the genes predicted to encode telomeric proteins and determine the effect of this on chromosome and plasmid linearity. Finally we will purify the telomeric proteins in order to establish their interactions with the telomeres in vitro. This will lead to a better understanding of chromosome architecture and chromosome segregation (Kois-Ostrowska et al., 2016) in this important antibiotic-producing group of bacteria.
Genome sequencing, protein purification, gene cloning, Pulsed Field Gel Electrophoresis
BLIN, K., MEDEMA, M. H., KOTTMANN, R., LEE, S. Y. & WEBER, T. 2016. The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters. Nucleic Acids Research, gkw960.
CORRE, C. & CHALLIS, G. L. 2009. New natural product biosynthetic chemistry discovered by genome mining. Nat Prod Rep, 26, 977-86.
FAN, Y., DAI, Y., CHENG, Q., ZHANG, G., ZHANG, D., FANG, P., WU, H., BAI, L., DENG, Z. & QIN, Z. 2012. A self-ligation method for PCR-sequencing the telomeres of Streptomyces and Mycobacterium linear replicons. J Microbiol Methods, 90, 105-7.
HUANG, T. W., HSU, C. C., YANG, H. Y. & CHEN, C. W. 2013. Topoisomerase IV is required for partitioning of circular chromosomes but not linear chromosomes in Streptomyces. Nucleic Acids Res, 41, 10403-13.
KOIS-OSTROWSKA, A., STRZAŁKA, A., LIPIETTA, N., TILLEY, E., ZAKRZEWSKA-CZERWIŃSKA, J., HERRON, P. & JAKIMOWICZ, D. 2016. Unique Function of the Bacterial Chromosome Segregation Machinery in Apically Growing Streptomyces - Targeting the Chromosome to New Hyphal Tubes and its Anchorage at the Tips. PLOS Genetics, 12, e1006488.
TSAI, H. H., SHU, H. W., YANG, C. C. & CHEN, C. W. 2012. Translesion-synthesis DNA polymerases participate in replication of the telomeres in Streptomyces. Nucleic Acids Res, 40, 1118-30.
YANG, C. C., SUN, W. C., WANG, W. Y., HUANG, C. H., LU, F. S., TSENG, S. M. & CHEN, C. W. 2013. Mutational analysis of the terminal protein Tpg of Streptomyces chromosomes: identification of the deoxynucleotidylation site. PLoS One, 8, e56322.
Applicant will need to self-fund, find sponsorship for tuition and bench fees of £5000 per annum for duration of studies
Applicants can apply using the University PEGASUS Application System https://www.strath.ac.uk/science/strathclydeinstituteofpharmacybiomedicalsciences/studywithus-postgraduate/phd/
This project is also suitable for PhD Plus https://www.strath.ac.uk/science/strathclydeinstituteofpharmacybiomedicalsciences/studywithus-postgraduate/phdplus/