Department of Biological and Medical Sciences

Research Projects

  • Comparative and functional genomics to understand the genome-wide dynamics for the bacterial cell response to antibiotics, and for the discovery of novel antibiotics

    Summary

    It aims to exploit soil and marine Actinomycetes to produce knowledge and practical technologies to help in addressing the major current problem associated with the treatment of antibiotic resistant bacterial infections. It has direct implications for medicine and for pharmaceutical companies, contributing both to their efforts to understand the molecular basis of defensive responses and resistance to antibiotics in bacteria, and to developing methods to discover new antibiotic activities. The key issues that I would like to address through my research are:

    1) the molecular basis of resistance mechanism in microorganisms

    2) understanding the selection of resistant microbes and their subsequent spread

    3) identifying specific signatures and novel regulatory mechanisms associated with the ability to acquire and/or express resistance to antimicrobials in a population

    4) developing novel bioassay tools to monitor the rapidly changing patterns of drug resistance

    5) discovering and developing novel antimicrobial compounds

    Introduction

    The development of resistance against antibiotics among pathogens has become an acute public-health concern especially since the 1970’s with the appearance of MRSA (methicillin-resistant Staphylococcus aureus). This situation has been exacerbated by several factors including the inappropriate use of antibiotics and, above all, a lack of investment by big pharma in the discovery of new drugs. As a consequence, this trend will inevitably create a situation where bacterial infections re-emerge as major agents of human disease and mortality. A fundamental understanding of bacterial antibiotic resistance mechanisms in parallel with developing novel antibiotics preferably with completely new activity and action will therefore be a fundamental part of any future strategy aimed at solving the growing problems with treating microbial infections. How damage caused externally by antibiotics is communicated to the bacterial chromosome, and how the subsequent reprogramming of gene expression acts to counteract the damage is the major focus of my research. As such, any future development of new drugs with novel antibacterial activities must be underpinned by a detailed understanding of the resistance mechanisms to existing antibiotics i.e. of how the current antibiotics are failing. Because such information is usually linked intimately to the antibiotic’s mode of action this provides unique insights that can help devise novel compounds or new ways of prolonging the therapeutic usefulness of existing ones. This can be an important platform for the future development of effective antibiotics, and for prolonging the therapeutic usefulness of existing drugs.

    Past research in my group

    I use harmless, soil derived Gram positive bacteria, Actinomycetes, as a model system: Actinomycetes produce about 70% of known antibiotics and are the ultimate source of most antibiotic resistance genes. Consequently they possess many genes involved in sensing and responding to antibiotics, and are an ideal system to use for furthering the understanding of the processes involved. Also, I intend to progress this research into pathogenic strains such as Enterococci and Staphylococci which are major killer pathogens in hospital acquired infections. In particular, I have primarily been focusing on bacterial cell wall as a target. The bacterial cell wall is one of the most important key targets in antibacterial drug development as it is crucial for cell growth, and provides a physical protective barrier between the cell and its environment. Antibiotics that inhibit bacterial cell wall biosynthesis, such as penicillin and vancomycin, are clinically important in the treatment of infectious diseases. The majority of antibiotics in use have been discovered as natural products of free living bacteria resident in soil and marine environments. Antibiotics do not kill the organisms that produce them since they have co-evolved systems that make them resistant or tolerant to their effects, but it is when similar systems develop in the target pathogenic bacteria allowing them to survive drug treatments that major problems can arise. The current problem with vancomycin-resistant MRSA in hospital acquired infections is a good example of this. A major achievement of the recent work in my group in this area has been helping to define exactly how bacteria sense vancomycin, a mechanism that triggers resistance to the only antibiotic in widespread use for the treatment of MRSA. My group has expertise in molecular microbiology and a proven record in elucidating the mechanisms of bacterial antibiotic resistance, culminating in work published in BMC Genomics that characterized the dynamic genome-wide transcriptional response of a Gram-positive bacterium exposed to a number of different cell wall specific antibiotics (Hesketh et al., 2011; please note ‘Publications’ section), and also work in Nature Chemical Biology that helped to define exactly how bacteria sense vancomycin, a mechanism that triggers resistance to the only antibiotic in widespread use for the treatment of MRSA (Koteva et al., 2010). This was particularly a fruitful outcome of an international multi-disciplinary collaboration with scientists in the UK and Canada which used Streptomyces as a model for studying and understanding vancomycin resistance. It was built on research which we initiated with the discovery of a vancomycin resistance system in Streptomyces coelicolor which serves as the model Actinomycete (Hong et al., 2004) and developed over the years with several high-impact publications (Hong et al., 2002a, 2002b, 2005, 2008; Hutchings et al., 2005, 2006). These studies also yielded three patented drug screening systems, providing valuable experience in translating the outcome of research into intellectual property (Please note ‘Patents’ section).

    On-going and future research

    As I mentioned above, my group has already undertaken an extensive transcriptome study when exponentially growing bacterial cultures are challenged with a range of antibacterial agents (including vancomycin) that target distinct stages of cell wall biosynthesis and have different modes of action and the summary of work has been published in BMC Genomics (Hesketh et al., 2011). In this work, we were initially focusing on the identification and characterization of the most interesting subset of genes expressed in response to these antibiotics. In addition to genes that we have already described in the publication, there are more interesting genes identified from the study which will be further characterized to define their precise role in cell envelope structure, subsequently, the mechanism by which the signal is sensed and communicated to the chromosome will be determined. To complement the transcriptome data, we are currently undertaking an analysis of changes in the proteome (in collaboration with Professor Kathryn Lilley at the Cambridge Centre for Proteomics and Dr. Andy Hesketh at the Cambridge Systems Biology Centre) and metabolome (in collaboration with Dr. James Mason at the King’s College London) in response to treatment with the same antibiotics. This information will be integrated with the existing transcriptome data to produce a more complete picture of the response to cell wall damage by the antibiotics. As such, the functional genomics including transcriptome, proteome and metabolome profiling study to characterize the response when growing cultures of bacterial cells challenged with wide variety of antibiotics. Ultimately, understanding the dynamic link between transcriptional, translational and metabolic processes will extend our knowledge of the functions and systems that are important for bacterial cell wall homeostasis, and open ways by which these can be exploited in future antibiotic therapies. In addition, I aim to actively discover or develop novel antibiotics through information gathered from the outcome of the study described above. I have developed a number of simple but effective bioassay systems useful for screening for a broad range of antibiotics, some of which have been published as international patents. Using one such system I have recently screened, in collaboration with Professor Joo-Won Suh’s group at Myong-Ji University in South Korea, a library of natural product extracts derived from over 5000 different Actinomycete strains and discovered a previously undefined Actinomycete strain producing a glycopeptide antibiotic. We have sequenced and annotated the genome of the producer strain and the work has been published (Truman et al., 2014). The collaboration is still on-going and we are currently developing a high-throughput screening system to identify novel glycopeptide antibiotics from the Myong-Ji Library. The full extract library currently consists of approximately 150,000 natural product extracts from over 15,000 different Actinomycete strains. As soon as we identify a novel antibiotic, we will perform molecular genetic studies to characterize and exploit the biosynthesis of this new antibiotic with the aim of moving towards possible use in future clinical trials. I have also just initiated a new collaboration with Dr. Dana Ulanova’s group in Kochi University in Japan. Dr. Ulanova’s group have established a similar natural product extract library but isolated only from marine microbes. Although it hasn’t been long since I have been involved in this area of research, I have also recently developed an interest into how the soil microbiome helps to protect crops from disease. In collaboration with Dr. Youn-Sig Kwak’s group at the Gyeongsang National University in South Korea, we have undertaken a metagenome analysis on a soil sample from the field which displayed a strawberry disease suppressiveness, and we were able to identify several interesting Actinomycete strains which were responsible for defending strawberries from Fusarium wilt, a common crop disease caused by a fungal pathogen, Fusarium oxysporum. We have then carried out further genetic and biochemical analysis including mutagenesis and secondary metabolite profiling study to elucidate the defensive mechanism of one particular Actinomycete strain against the fungal disease and the work has also been published (Cha et al., 2016). We are currently continuing the collaboration to work on few more other Actinomycete strains that we isolated along with the one already characterised. We are also beginning to investigate more soil samples collected from other crop disease-suppressive fields.

    All these on-going researches will help cement interesting and close collaborations between my group and current collaborators. As the work progresses, we will also assess the potential to broaden the collaboration and involve expertise from other fields, notably structural biologists, chemists, and bioinformaticians. It is likely that some results arising from the current collaborations will merit more detailed investigation than can be achieved in the next few years, and these will be targeted for exploitation in long-term future collaborations and funding proposals.