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Omega 3 Fatty Acids: Identification of Novel Omega 3 Fatty Acids: Identification of Novel Fungal and Chromistal Sources Richard Broughton This thesis is submitted for the degree of Doctor of Philosophy at Royal Holloway, University of London, September 2011 2 Declaration of Authorship I, Richard Broughton, hereby declare that this thesis and the work presented in it is entirely my own. Where I have consulted the work of others, this is always clearly stated. Signed: ____________________________ Date: _______________ 3 Abstract There is a wealth of scientific evidence associating the dietary intake of omega 3 long-chain polyunsaturated fatty acids with beneficial health properties. In this study, alternative natural sources of these polyunsaturated fatty acids are sought from novel low temperature isolated fungi. Over 100 low temperature isolated fungi were screened for very long chain polyunsaturated fatty acids (VLCPUFAs), such as C 20:5 n3 and C 22:6 n3. Of those screened, only ten fungi were capable of VLCPUFA production, with Mortierella the predominant VLCPUFA producing species. Four Oomycete species were also capable of VLCPUFA production. It is thought that only basal fungal lineages, such as species from the Chytridiomycota and Zygomycota, are capable of VLCPUFA production. It was also found that VLCPUFAs are not essential for growth at low temperatures, as Penicillium rugulosum , capable of producing fatty acids no longer or more unsaturated than C 18:3 n3, demonstrated over 2 g of biomass per 100 ml of broth when grown at 5°C. This indicates that trienoic fatty acids are sufficient for maintaining membrane fluidity, although other factors may play a role in P. rugulosum ’s low temperature growth. Comparatively, VLCPUFA producing Mortierella species produced 200-250 mg of biomass, whereas the majority of non- VLCPUFA producing isolates produced 106-115 mg of biomass per 100 ml of broth. The total lipid unsaturation indices of nine isolates grown under three temperature regimes showed that the lowest growth temperature, 5°C, produced the highest unsaturation index value in six of the organisms. 15°C produced the highest unsaturation index value in two of the isolates. This suggests that temperature has an effect on fungal lipid composition, and that lower temperatures may increase lipid unsaturation levels. It was also found that the ∆6 elongase, initially identified from Mortierella alpina , is indicative for VLCPUFA producing fungi. The genomic conserved sequence found within ∆6 elongases was used to develop primer sets that could be used with a PCR based methodology to screen fungal isolates for VLCPUFA production. The method successfully identified VLCPUFA producing Mortierella and Allomyces species, and was not found to amplify non-∆6 elongases. Finally, recombinant Phaffia rhodozyma strains were developed using the ∆5 desaturase and ∆6 elongase from Mortierella alpina . The fatty acid profiles of the recombinant strains displayed novel fatty acids such as C 20:2 n6 and C 20:3 n3, and putatively, C 18:2 ∆5, 9 and C18:3 ∆5, 9, 12 which correlated with the inserted genes. 4 Table of Contents Abstract........................................................................................................ 3 Table of Contents ........................................................................................ 4 List of Figures.............................................................................................. 7 List of Tables ............................................................................................. 10 Abbreviations............................................................................................. 12 Nomenclature used.................................................................................... 15 Acknowledgements.................................................................................... 16 1 Introduction.......................................................................................................17 1.1 Structure and nomenclature ........................................................................18 1.2 The role of PUFAs in health and disease....................................................19 1.3 Introduction to fungi ...................................................................................24 1.3.1 Oomycota............................................................................................25 1.3.2 Chytridiomycota..................................................................................26 1.3.3 Zygomycota.........................................................................................26 1.3.4 Glomeromycota...................................................................................27 1.3.5 Ascomycota and Basidiomycota; the sub-Kingdom Dikarya .............27 1.3.6 The role of PUFAs within the fungi....................................................28 1.3.7 Fatty acid biosynthesis within the fungi .............................................33 1.3.7.1 Elongation .......................................................................................33 1.3.7.2 Desaturation ....................................................................................37 1.3.8 Oleaginicity.........................................................................................42 1.3.9 Genetic engineering ............................................................................45 1.4 Fungal PUFA producers..............................................................................47 1.4.1 Market.................................................................................................47 1.4.2 Currently known producers.................................................................50 1.5 Objectives and strategy...............................................................................56 1.5.1 Objectives............................................................................................56 1.5.2 Strategy ...............................................................................................57 2 Materials and Methods.....................................................................................58 2.1 Materials......................................................................................................58 2.1.1 Chemicals and Kits .............................................................................58 2.1.1.1 Media...............................................................................................58 2.1.1.2 Biochemical reagents ......................................................................58 2.1.1.3 Molecular biology reagents.............................................................58 2.1.2 Fungal isolates.....................................................................................58 2.1.3 Media...................................................................................................65 2.1.3.1 Potato dextrose (PD) media ............................................................65 2.1.3.2 Malt extract (MA) broth media.......................................................65 2.1.3.3 Yeast extract sucrose (YES) broth media .......................................65 2.1.3.4 Lysogeny broth (LB) media............................................................66 2.1.3.5 Antibiotic media additions..............................................................66 2.1.4 Buffers and Solutions..........................................................................67 2.1.4.1 DNA gel electrophoresis buffers and solutions ..............................67 2.1.4.2 Primers ............................................................................................69 2.1.4.3 His-tagged protein purification buffers...........................................69 2.1.4.4 SDS-PAGE buffers and solutions...................................................70 2.1.4.5 Western blot buffers and solutions..................................................72 5 2.1.4.6 Software used..................................................................................73 2.2 Methods.......................................................................................................74 2.2.1 Fungal growth for fatty acid and genomic screening..........................74 2.2.1.1 Plate growth ....................................................................................74 2.2.1.2 Broth inoculation for fatty acid screening.......................................74 2.2.1.3 Mycelial broth extraction................................................................74 2.2.2 Fungal growth for temperature and its effect on fatty acids ...............75 2.2.3 Analytical methods..............................................................................76 2.2.3.1 Fatty acid extraction........................................................................76 2.2.3.2 Fatty acid trans-methylation............................................................76 2.2.4 TLC purification procedure ................................................................77 2.2.4.1 Separation of phospholipid fractions ..............................................77 2.2.4.2 Elution of TLC fractions.................................................................77 2.2.5 GC-FID analysis .................................................................................78 2.2.6 GC-MS analysis..................................................................................78 2.2.7 Molecular biology methods ................................................................79
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