Investigation of the Influence of Pase Variable Restriction-Modification Systems on Resistance of Haemophilus influenzae to Infection by Bateriophage

The Department of Genetics is pleased to offer a funded studentship for October 2012 entry to its Doctor of Philosophy (PhD) programme. The studentship will pay full-time University UK/EU tuition fees for 3.5 years (with the possibility of funding for a further six months subject to performance) and include a tax-free annual maintenance grant worth at least £13,590 a year.

Research Areas and Supervision

H. influenzae is a commensal of the human respiratory tract with the potential to cause diseases such as otitis media and meningitis. Many surface structures of this species are subject to stochastic, reversible ON and OFF switches in gene expression (Moxon et al. 2007; Bayliss, 2009). This process, termed phase variation, is mediated by mutations or changes in the length of tandem DNA repeat tracts (also termed microsatellites). These changes in repeat number cause switches in gene expression by altering the reading frame or the relative positions of promoter elements. Intriguingly two of the restriction-modification (R-M) systems of H. influenzae strain Rd are subject to phase variation. One is a type I R-M system called HindI and consists of three proteins:- HsdM, HsdS and HsdR. Changes in a pentanucleotide repeat located within the reading frame of the hsdM gene cause ON/OFF switches in expression of restriction and methylation activity (Zaleski et al., 2005). Phase variation of this system alters susceptibility to infection by HP1, an H. influenzae specific bacteriophage. The other system is a type III R-M system and has a tetranucleotide repeat tract within the Mod gene (De Bolle et al., 2000). Phase variation of this latter system alters expression of several other genes in the genome suggesting the phase variable R-M systems are a stochastic mechanism for adaptation to environmental challenge (Srikhanta et al. 2005). An alternate view is that phase variable R-M systems are a population-based mechanism for preventing the development of resistance to restriction among bacteriophages (Bayliss et al., 2006).

The importance of bacteriophages is being increasingly realized and they have been shown to play key roles in bacterial evolution (Clokie et al., 2011). Establishing a genetic basis for these roles can often be challenging but this well characterised system gives us an ideal opportunity to decipher how phages may control bacterial population dynamics. Switching OFF of HindI renders H. influenzae strain Rd susceptibility to infection by HP1. However replication of the bacteriophage in an ON phase variant of HindI results in methylation of the phage genome and insensitivity to restriction by this RM system (Zaleski et al., 2005). We speculate that phase variation of HindI prevents development of phage resistance and reduces spread of the phage through H. influenzae populations. Resistance to phage infection is also mediated by phase variation of the lic2A gene, which encodes a glycosyltransferase involved in biosynthesis of the receptor for this phage (Zaleski et al., 2005).

The specific aims of this project are:

1. to investigate the diversity and phase variation rates of the R-M systems present in different H. influenzae strains
2. to develop a protocol for investigating the spread of bacteriophage through a bacterial population
3. to investigate whether alterations in phase variation rate of R-M systems change the susceptibility of bacterial populations to spread of
   bacteriophage
4. to investigate whether the presence of multiple phase variable R-M systems increases resistance to bacteriophage spread
5. development of computer models for predicting the spread of phage through a phase variable bacterial population

The successful applicant will be supervised by Dr Chris Bayliss (Department of Genetics) and Dr Martha Clokie (Department of Infection, Immunity, and Inflammation).

References

Moxon ER, Bayliss CD and Hood DW (2007). Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation. Annual Review of Genetics. 40:307-333.

Bayliss CD (2009). Determinants of phase variation rate and the fitness implications of differing rates for bacterial pathogens and commensals. FEMS Microbiological Reviews 33: 504-520.

Clokie, MRJ, Millard AD, Letarov, AV and Heaphy, S. (2011). Phages in nature. Bacteriophage. 1: 31-45.

Zaleski P, Wojciechowski M. and Piekarowicz, A. (2005) The role of Dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infection. Microbiology, 151, 3361-3369.

De Bolle X, Bayliss CD, Field D, van de Ven T, Saunders NJ, Hood DW, and Moxon ER (2000). The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases.
Molecular Microbiology, 35:211-222.

Srikhanta YN, Maguire TL, Stacey KJ, Grimmond SM and Jennings MP (2005) The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes. Proc Natl Acad Sci U S A, 102, 5547-5551.

Bayliss CD, Callaghan MJ and Moxon ER (2006). High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae. Nucl. Acids Res. 34 4046-4059.

Entry Requirements

Applicants must have a first-class or high upper second-class honours degree (or equivalent qualification) in a relevant discipline and meet the University's standard English language entry requirements.

This studentship is open to suitable UK/EU and International (i.e., outside the EU) applicants. Please note though that the award covers tuition fees at the UK/EU rate only. International applicants (and those not eligible to pay UK/EU tuition fees) must demonstrate at the time of their application that they can fund the difference in tuition fee rates.

The studentship is for full-time study only and applicants must be able to commence their studies in October 2012.

Informal Enquiries

Informal enquiries are welcomed - please contact:

• Dr Chris Bayliss
• cdb12@le.ac.uk  
• Tel. +44 (0)116 252 3465

Apply Now

To apply, simply follow our three-point checklist:

1. Draft a brief personal statement explaining why you would like to work in this area and describing any relevant research experience (including any research projects that you have undertaken - for example, as part of a previous degree - and listing any academic work you have published or which is currently in press awaiting publication). Your personal statement should be no more than 1,000 words.
2. Prepare your supporting documents - including a full Curriculum Vitae
3. Submit your online application or apply by post

The studentship will remain open until filled - however early application is encouraged.

IMPORTANT - In the Fees and Financial Support section of the application, you must state that you wish to be considered for this "PhD Studentship Genetics Ref. MBSP-12/04"

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