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A Functional Study of Bacterial Orthologues of the Malarial Plastid Gene, Jc/24

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A Functional Study of Bacterial Orthologues of the Malarial Plastid Gene, Jc/24 A Functional Study of Bacterial Orthologues of the Malarial Plastid Gene, jc/24 A thesis submitted for the degree of Doctor of Philosophy b y Anna Elizabeth Law Division of Parasitology National Institute for Medical Research ProQuest Number: U642662 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U642662 Published by ProQuest LLC(2015). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Abstract Malaria parasites have two DNA containing organelles, a mitochondrion and a plastid. Most of the plastid genes are involved in gene expression however there are a number of open reading frames (ORFs) of unknown function. In Plasmodium falciparum, ORF470 is particularly interesting as it is highly conserved with an orthologue {ycf 24) in both algae and bacteria. Some annotations describe ycf 24’s product as an ABC transporter subunit but the level of significance is low. To investigate the function o îycflA , the cyanobacterium Synechocystis, strain PCC6803, was transformed with a disrupted version of the gene and allowed to undergo several rounds of replication before selection with kanamycin. Synechocystis 6803 was chosen as it carries up to 10 copies of its genome per cell, allowing the support and selection of lethal genes. Primary transformants formed “ragged” colonies attributable to the death of homoplasmic transformants (complete “knockouts”). This indicates that loss of the gene is lethal. After selection, transformants were shown to be heteroplasmic (containing both disrupted and wild type y c f 24). Furthermore, heteroplasmic cells plated in the absence of kanamycin resumed WT growth rate and colony morphology indicating that the presence of the disrupted gene was deleterious and/or that the gene product is required in stoichiometric amounts. When the gross morphology of cells fi'om ragged colonies was observed by scanning electron microscopy, a statistically significant accumulation of cells in the last stages of cell division was apparent. This suggests that disruption of y c f 24 leads to a defect in cytokinesis. Upon relaxation of kanamycin selection, the proportion of dividing cells returned to one resembling WT. Attempts were made to knock out the single copy of y c f 24 in E. coli. One approach made use of the temperature sensitive gene replacement vector pK03 that contains genes for chloramphenicol resistance and levansucrase, which is lethal to E. coli in the presence of sucrose. This protocol allowed both positive and negative selection of recombination at the y c f 24 locus. However, no viable knockouts were obtained. Over-expression of y c f 24 in E. coli using the pMAL-c2 vector resulted in moderate filamentation, the fusion protein localizing as a band on either side of the nucleoid, sometimes extending along the membrane to the cell poles. Unlike some other partition mutants, FtsZ ring formation was inhibited in such cells and the first division of nucleoids following induction resulted in their accumulation transverse to the cell’s length rather than longitudinally in the usual way. It is proposed ihdXycflA is an essential prokaryotic gene involved in cell division and/or DNA segregation. Acknowledgements Primarily I would like to thank my supervisor Iain Wilson for providing me with support and direction throughout my course of study. I would also like to thank Conrad Mullineaux at University College London for introducing me to cyanobacteria, and for all his help. For their invaluable advice, instruction and friendship I want to thank all the other members of the lab at NIMR; Barbara Clough, Katherine Ellis, Kaveri Rangachari, Peter Preiser and Don Williamson and also Malcolm Strath for his help with protein purification, for running sequencing gels and for antibody production. In addition, I thank Liz Hirst at NIMR for the electron microscopy work and acknowledge Nick Fisher (UCL) and Elaine Davis (NIMR) for their advice on my E. coli gene knockout studies. For donating the antibiotic resistance genes, as well as his help, I would like to thank Mark Ashby (UCL). Likewise I’d like to thank Daniel Emlyn-Jones (UCL) for the kanamycin resistant Synechocystis strain; Elaine Davis (NIMR) for the KM4104 E. coli strain; and George Church (Harvard University) for the pK03 vector On a more personal note I owe a lot to Pete - 1 could not have done this without him. Finally, I thank my parents for their support and encouragement through thick and thin. Contents Page Abstract 2 Acknowledgements 4 Contents 5 List of Figures 11 List of Tables 15 Abbreviations 16 Chapter 1. Introduction 1.1 Malaria 19 1.1.1 Protozoans and the phylum Apicomplexa 19 1.1.2 sp. and the disease 19 1.1.3 Treatment and eradication of malaria 21 1.1.4 Malaria genome sequencing project 22 1.2 The 35kb extrachromosomal DNA element of malaria 22 1.2.1 Discovery 24 1.2.2 Genetic evidence for a plastid origin 24 1.2.2.1 Plastid or mitochondrial? 24 1.2.2.2 Red or green? 28 1.2.3 Questioning the evolution of apicomplexans 29 1.3 The plastid organelle 30 1.3.1 Discovery 30 1.3.2 Replication and division 35 1.4 Endosymbiosis and beyond: the acquisition and maintenance of a 37 vestigial plastid genome in malaria 1.4.1 The “Mr Gobbler” hypothesis 37 1.4.2 Translocation of plastid-encoded genes 38 1.4.2.1 The fate of “promiscuous” DNA 38 1.4.2.2 What type of genes have been lost to the nucleus and why 40 1.4.2.3 Evidence for translocation to the nucleus in secondary endosymbionts 41 1.4.3 Importation of nuclear-encoded proteins into plastids 42 1.4.3.1 Chloroplast import 43 1.4.3.2 Protein import into the apicomplexan plastid 45 1.5 Function 47 1.5.1 Is the plastid essential? 47 1.5.1.1 Active transcription, translation and the tRNA genes 47 1.5.1.2 Selective retention of genes across diverse genera of apicomplexans 49 1.5.1.3 Sensitivity to antibiotics 49 1.5.2 What might the plastid do? 5 0 1.5.2.1 General functions of plastids 50 1.5.2.2 Fatty acid biosynthesis? 51 1.5.2.3 Amino acid biosynthesis? 52 1.5.2.4 Plastid encoded open reading frames 53 1.6 Open reading frame ORF 470 {ycf24i) 53 1.6.1 Distribution 53 1.6.2 Unusual features of the y c f 24 orthologues 5 5 1.6.3 Function ofyc/'24 56 1.6.3.1 Metabolic role? 56 1.6.3.2 ABC transporter? 57 1.6.4 yc/"16 57 1.6.5 Co-transcription of yc/'24 and ycf 16: the yc/'24 operon 58 1.6.6 «//genes 59 1.6.7 Is y c f 24 an essential plastid gene? 59 1.7 Synechocystis PCC6803 60 1.7.1 Cyanobacteria 60 1.7.2 Natural competence to exogenous DNA 61 1.7.3 Transformation of *Sy«cc//ocy5^/5 PCC6803 61 1.8 Escherichia coli 63 1.8 1 Gene replacement using linear DNA 64 1.8.2 Gene replacement using pK03 65 1.8.2.1 Non-essential gene knockout 65 1.8.2.2 Essential gene knockout 66 1.9 Summary 66 Aims 68 Chapter 2. Materials and methods 2.1 General buffers and solutions 69 2.2 Growth media 69 2.2.1 £. co/z growth medium 69 2.2.2 Synechocystis growth medium 69 2.3 Bacterial strains and growth conditions 70 2.4 Analysis of growth of Synechocystis by colony area 71 2.5 DNA isolation 71 2.5.1 Synechocystis 71 2.5.2 E. coli 71 2.6 Agarose gel electrophoresis 72 2.7 Estimation of DNA concentration 72 2.8 Restriction enzyme digestion of DNA 72 2.9 Primer design 73 2.10 Amplification of DNA by PCR 73 2.11 Isolation of plasmid DNA 74 2.12 Purification of the kanamycin resistance and aadA genes 75 2.13 Cloning into plasmid vectors 75 2.13.1 Purification of insert DNA 75 2.13.2 Ligations 75 2.13.3 Transformation and selection of recombinants 76 2.\2>3.\ Synechocystis VCC6%02> 76 2.13.3.2 E. coli 76 2.13.4 Analysis of recombinants 78 2.14 Sequencing 78 2.1.4.1 Manual DNA sequencing 78 2.1.4.2 Automated DNA sequencing 79 2.15 Southern analysis 79 2.15.1 Southern transfer 79 2.15.2 Template preparation for hybridization 80 2.15.3 Labelling reaction 80 2.15.4 Purification of the radiolabelled probe 80 2.15.5 Pre-hybridization and hybridization to the radiolabelled probe 80 2.15.6 Post-hybridization 80 2.16 Stripping of Southern blots 81 2.17 Copy number analysis of inactivated Synechocystis yc f 24 81 2.18 Transmission electron microscopy 81 2.18.1 Fixation 81 2.18.2 Agarose embedding 81 2.18.3 Refixation and staining 82 2.18.4 Dehydration 82 2.18.5 Further staining 82 2.19 Scanning electron microscopy 82 2.19.1 Fixation 82 2.19.2 Post fixation 83 2.20 DAPI staining 83 2.21 Giemsa staining 83 2.22 Autofluorescence of Synechocystis 83 2.23 Statistical analysis of SEM data- the Chi-square test 84 2.24 Analysis of Synechocystis cell cycle 84 2.25 PAGE 84 2.26 Western blotting 85 2.26.1 Protein transfer to nitrocellulose membrane 85 2.26.2 Probing and developing the membrane 86 2.27 Immunofluorescence 86 2.28 Purification and cleavage of maltose binding protein (MBP) 87 2.29 Purification of polyhistidine-containing recombinant proteins 87 2.30 Over-expression and cleavage of glutathione-S-transferase (GST) 88 fusion protein Chapter 3.
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