Award details

Investigations into unprecedented reactions associated with the biosynthesis of hemes

Reference	BB/N006445/1
Principal Investigator / Supervisor	Professor Stuart John Ferguson
Co-Investigators / Co-Supervisors	Dr Shilpa Bali
Institution	University of Oxford
Department	Biochemistry
Funding type	Research
Value (£)	366,687
Status	Completed
Type	Research Grant
Start date	01/06/2016
End date	31/10/2019
Duration	41 months

Abstract

Tetrapyrroles and modified tetrapyrroles have essential roles in a large of range of different molecular processes. We have a far from complete understanding of the reactions, some unprecedented, that biology uses to synthesise these molecules. Recently we discovered an alternative biosynthetic route to heme via double decarboxylation of siroheme, to give didecarboxysiroheme (DDSH), followed by two S-adenosylmethionine (SAM)-dependent reactions that lead to heme via Fe-coproporphyrin IX. Even more recently it has been reported that Fe-coproporphyrin IX can be produced, not from siroheme but from an intermediate, coproporphyrinogen III, on the long established heme synthesis pathway. In this case the required replacement of two propionate groups by two vinyl groups, to give heme, is SAM-independent. Either route for forming the vinyl groups poses novel mechanistic challenges and we shall use a range of contemporary methods to elucidate these unprecedented reaction mechanisms, along with simultaneous interrogation of how coproporphyrinogen III is converted to coproporphyrin IX. Our discovery of a pathway to heme via siroheme and DDSH stemmed from showing that this reaction sequence was also on the pathway to the modified tetrapyrrole, d1 heme, of the periplasmic bacterial cytochrome cd1 nitrite reductase that catalyses the reduction of nitrite to nitric oxide. We now intend to elucidate how the cytoplasmic NirJ protein, a radical SAM enzyme, generates two carbonyl groups at the expense of two propionates and how the periplasmic NirN protein complete the synthesis of the d1 cofactor by introducing a double bond into a propionate side chain. NirN is able to remove two hydrogens from a saturated carbon-carbon bond without dehydrogenation specific cofactors and allows the electrons from the oxidation to flow to heme centre irons in NirN. We will apply a multidisciplinary approach ranging from regiospecific labelling studies through to structural biology and EPR.

Summary

The project aims to have a major impact on our understanding of how heme and heme-like molecules are made within bacteria. In so doing the research will impinge upon several important priority areas of BBSRC, including antimicrobial resistance and strategic approaches to industrial biotechnology. This is because in the course of our previous research we have discovered that heme, a major life pigment, is synthesized by at least three distinct routes. The research in this application highlights strategies that can be used to underpin the development of novel antimicrobials through the exploitation of these biochemical differences. Moreover, the transformations involved in the biosyntheses of these hemes involve some very novel chemistry, which if redesigned could be applied to industrial biotechnology. In this respect the research programme involves cross-disciplinary technologies, with the potential to permit the translation of basic discoveries into new products and processes through the development of new biocatalytic entities and pathways. Our previous research has demonstrated that heme is not made by a single "classic" pathway, rather it can be made either by an "alternative" or a "transitional" pathway. In particular we wish to look at the role of HemY, a recently identified coproporphyrin synthase, that oxidises coprporphyrinogen through the removal of 6 electrons and 6 protons. We have identified a number of inhibitors of this enzyme through specific searches of chemical libraries, but to enhance their development we need to know more about the action of the enzyme. Similarly, two separate enzymes have been identified that convert Fe-coproporphyrin into heme through the decarboxylation of propionic acid side chains into vinyl groups. Such chemistry is, of course, very significant in biotechnology for the conversion of fatty acids into alkenes and thus redesigning these enzyme for fatty acid substrates would have significant industrial relevance. However, toachieve this we must first understand the molecular processes that drive substrate recognition, specificity and catalytic mechanism. The final part of the research is tailored towards an understanding of d1 heme synthesis, where we have make huge progress in delineating the various steps at the molecular level. Of particular interest is the reaction of NirN, which is able to catalyse the introduction of a double bond into one of the propionate side chains within the confines of the periplasm and without the assistance of any flavin or nicotinamide cofactors. Again such chemistry would be of broad interest to the biotechnology sector, especially as a potentially cheap way of reducing alkanes for high-value and platform chemicals. To achieve this long-term goal again we need to determine the precise nature of the reaction and then redesign the system to allow it to be used in other contexts. Overall, the research addresses basic biochemical questions concerning the biosynthesis of important metabolites within the cell by painting a molecular portrait of events at the molecular level. In so doing it will provide a neodarwinistic understanding of the evolution ofcomplex biosynthetic pathways. It will also help maintain the UK at the cutting edge of biomolecular science research and maintain the position our groups have as world leaders in this field.

Impact Summary

The beneficiaries of this research will be researchers in academia and industry who are interested in synthetic biology and its applications. The research will show how pathways and enzymes can be investigated by a multi-disciplinary approaches to challenging pathways and will also provide greater insight into the biosynthesis of both a modified tetrapyrrole d1 heme, as well as heme itself. The novel enzyme activities that are involved in the d1 assembly pathway and in newly recognised alternative heme biosynthesis pathways are expected also to be relevant to assembling other kinds of cyclic molecules that can be of interest to the pharmaceutical industry. Thus we will ensure that our findings are widely disseminated, through for example timely short review articles. Notably there is no doubt that d1 heme is vital for the operation of the bacterial Anammox process which is key for waste water treatment because it removes dissolved amonium under anaerobic conditions. Thus we will ensure that our findings are disseminated to those working in waste water treatment. Knowledge of d1 assembly is important for that field as if it were inadvertently inhibited then clearly the process would be blocked. On the other hand, blocking this activity would be relevant to understanding how Pseudomonas aeruginosa, which forms anaerobic biofilms, might be controlled during infections. Thus we will also publicise our findings to the medical field by presenting work at meetings dealing with infection. Thus nation's health could benefit in the longer term from this research. The Warren and Ferguson groups are heavily involved in outreach programmes, through interactions with local schools and community groups and offering placements to 6th formers which are much in demand from local schools. The skills acquired by those involved in this project include not only a wide range of important biological techniques ranging from spectroscopy and structural biology through to microbiology and recombinant DNA technology but also the opportunity to contribute towards a basic understanding of bacterial physiology. The latter is an area in which there is an increasing knowlege gap in the UK which this type of project will contribute to closing. The knowledge and techniques will provide those employed with skills that can be used across education and industry. The intellectual property resulting from this project will be protected and used via the Innovation and Enterprise Offices. The research will be published in high impact journals and oral communications given at international conferences. Using the infrastructure of the Isis Office at Oxford and the new Centre for Molecular Processing within the University of Kent, the research will be brought to the attention of many leading industrial companies.

Committee	Research Committee D (Molecules, cells and industrial biotechnology)
Research Topics	Microbiology, Structural Biology
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

Associated awards:

BB/N00924X/1 Investigations into the unprecedented reactions associated with the biosyntheses of hemes

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