DETERMINANTS OF COMPARTMENTALIZATION OF GENE EXPRESSION DURING SPORULATION IN BACILLUS SUBTILIS ________________________________________________________________________ A Dissertation Submitted to The Temple University Graduate Board _____________________________________________________________________ In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ________________________________________________________________________ By Francis Di Donato August 2008 ii ABSTRACT Determinants of compartmentalization of gene expression during sporulation in Bacillus subtilis Francis Anthony Di Donato Temple University, 2008 Doctor of Philosophy Doctoral Advisory Committee Chair: Patrick J. Piggot, Ph.D. Bacillus subtilis, a benign gram-positive bacterium, utilizes the strategy of sporulation, which enables it to survive stresses such as starvation, desiccation, and UV irradiation. The spore provides greatly heightened safety to heat and noxious chemicals and remains dormant until conditions become favorable to growth. Sporulation by Bacillus subtilis is a primitive example of cell differentiation. The study of sporulation by Bacillus subtilis has become a paradigm for the study of differentiation in prokaryotes. Central to this process is the establishment of distinct patterns of gene expression in the cell types involved. Our laboratory has developed a two-part sacB/SacY probe to study the temporal and spatial compartmentalization of gene expression. It utilizes the anti-terminator protein SacY to control the transcription of reporter lacZ, (cloned downstream of the sacB gene,) which is regulated by anti-termination. Expression of sacB and SacY is regulated by a pair of promoters specific for σF (prespore specific) and σE (mother cell specific.) Both SacY and sacB must be in the same compartment of the sporulating cell in order to obtain β-galactosidase activity. Mutagenesis of Bacillus subtilis was employed to identify determinants of compartmentalization of gene expression during sporulation. Mutants were screened for loss of compartmentalization using the two-part probe. iii In addition to the two-part sacB/SacY probe, a second method was developed; transposon mutagenesis was performed on strains where expression of gfp was regulated by promoters recognized by either σF or σE. Cells deficient in sporulation were isolated and evaluated by fluorescence microscopy for uncompartmentalized gfp expression. A rescue vector was developed that allowed for efficient cloning of Tn10 insertions. This plamid, pJP17, proved to be an essential tool. Mutations causing uncompartmentalized σF activity were identified in spoIIIE, spoIIIAA, spoIIIAB, spoIIIJ, spoIIE, spoIIAA, spoIID, spoIIM, kinA and ald. The spoIIIE mutation provides the most dramatic phenotype, and was the only mutation, that resulted in 100% loss of compartmentalization during stage II of sporulation. In contrast to all other mutants, the dramatic stage II loss of compartmentalized activity of σF indicates a regulatory role for SpoIIIE, which has yet to be elucidated. Taken together, these results indicate a central role for SpoIIIE in preventing activation of σF in the mother cell in addition to its DNA translocation activity. iv ACKNOWLEDGEMENTS AND DEDICATION This work is dedicated with great affection and admiration to my friend and mentor, Patrick Piggot, Ph.D. I would also like to acknowledge Andi, Max and Luna, my dear family. I believe a leaf of grass is no less than the journey-work of the stars. -Walt Whitman v TABLE OF CONTENTS Page ABSTRACT iii ACKNOWLEDGEMENTS AND DEDICATION v LIST OF TABLES x LIST OF FIGURES xi LIST OF ABBREVIATIONS xii CHAPTER 1. INTRODUCTION......................................................................................1 A Paradigm for Study of Differentiation 1 Morphological Stages of Sporulation 3 Initiation of Sporulation 6 Spo0A Regulon 10 Transition-State Sigma Factor σH 11 Spo- Mutants and spo Loci 11 Axial Filament Formation 12 Asymmetric Division 13 Chromosome Segregation 15 Compartmentalization of Gene Expression 17 Evidence for Compartmentalized Gene Expression 18 Activation of σF 19 Compartmentalization of σF Activity 21 ATP/ADP Ratio 21 SpoIIE Localization 23 Transient Genetic Asymmetry 24 SpoIIAB Sink 27 Mathematical Model 29 The σF Regulon 41 Activation of σE 41 Compartmentalization of σE Activity 42 The σE Regulon 43 Engulfment of the Prespore by The Mother Cell 44 The Late Prespore-Specific Transcription Factor σG 45 The σG Regulon 46 The Late Mother Cell-Specific Transcription Factor σK 47 vi The σK Regulon 48 Late Stages of Sporulation 49 Project Aims 50 2. MATERIAL AND METHODS ..................................................................54 Bacterial Strains 54 Media 54 DNA Manipulations 57 Enzyme Treatments 57 Agarose Gel Electrophoresis for DNA Separation 57 DNA Fragment Isolation and Ligation 57 Synthetic Oligonucleotides and DNA Sequencing 58 Polymerase Chain Reaction (PCR) 58 Southern Blot 60 Transformation 61 E. coli Transformation 61 B. subtilis Transformation 62 Plasmids 62 DNA Isolation 64 Plasmid Isolation from E. coli 64 B. subtilis Total DNA Isolation 64 Construction of a Tn10 Library 65 Recovery of Tn10 flanking DNA Using pZS139 65 Recovery of Tn10 flanking DNA Using pJP17 67 Inverse PCR 68 Sporulation 69 Fluorescence Microscopy 69 3. RESULTS 71 Loss of Compartmentalization in SpoIIIA and SpoIIIJ Mutants 71 Stage III Loss of Compartmentalization in Mutants 73 Construction of a Tn10 Library 77 Pilot Test of Screening Strategy 79 Large-Scale Screening 79 Use of pZS139 to Clone Tn10 Inserts 83 Attempted Use of pIC216 to Clone Tn10 Flanking DNA 88 Construction of pJP17 89 Pilot Test of pJP17: Cloning Of the SpoIIAA::Tn10 Insert 92 Most Mutants Loss of Compartmentalization is Post-Stage II 94 pJP17 Efficiently Clones Tn10 Inserts 96 vii 4. DISCUSSION ...............................................................................................94 spoIIIE::Tn10 99 spoIIAA::Tn10 100 spoIIAA::Tn10 and spoIIAA::Tn10 101 spoIIE::Tn10 102 spoIIM::Tn10 and spoIIM::Tn10 103 spoIIIJ::Tn10 103 kinA::Tn10 103 ald::Tn10 104 Conclusion 105 REFERENCES 102 APPENDIX 122 A. MEDIA AND SOLUTIONS 122 B. THE COMPLETE SEQUENCE OF pJP17 126 viii LIST OF TABLES Table 1. B. subtilis strains 55 2. Oligonucleotides 59 3. Plasmids 63 4. Compartmentaliztion of σF and σE in mutant B. subtilis Strains 74 5. Compartmentaliztion of mutants 7 hours after initiation of sporulation 76 6. Large scale screening for loss of compartmentalized σE and σF activity 84 7. Phenotype of backcrossed Tn10mutants 95 8. The sites of Tn10 Insertions, and their respective phenotype 98 ix LIST OF FIGURES Figure Page 1. Schematic representation of the stages of sporulation 4 2. Phosophorelay activation of SpoOA 7 3. B. subtilis division 16 4. The spoIIA operon 22 5. Mathematical model for activation of σF 33 6. Total DNA isolated from our transposon library 80 7. Transformants of the Tn10 library 81 8. Fluorescent image of SLl0280 transformed with the Tn10 library 82 9. Fluorescent images of spoIIE, spoIIAA and spoIIAB mutants 86 10. A map of pJP17 90 11. A map of pJP17 inserted into Tn10 91 12. Sequencing data for the rescued pJP17 plasmid 93 x LIST OF ABBREVIATIONS bp Base pairs DNA deoxyribonucleic acid EDTA ethylenediaminetetraactic acid IPTG isopropyl-β-D-thiogalactoside Kb kilobase pairs LA Luria-Bertani agar LB Luria-Bertani broth M Moles mg milligrams ml milliliter mm millimolar MSSM modified Schaffer’s sporulation medium PCR polymerase chain reaction rpm revolutions per minute SDS Sodium dodecyl sulfate SSA Schaeffer’s Sporulation Agar μg micrograms μl microliters μM micromolar X-Gal 5-bromo-4-chloro-2-indolyl-β- galactoside xi CHAPTER 1 INTRODUCTION A Paradigm for Study of Differentiation Bacillus subtilis is a benign Gram-positive bacterium commonly found in soil. Originally named Vibrio subtilis in 1835, it is one of the first bacterial species to be studied. When nutrients become scarce or in response to high cell-density, B. subtilis can divide asymmetrically, producing a tough, protective endospore that can protect it against extreme environmental conditions such as heat, salt, radiation and desiccation. This allows B. subtilis to survive until environmental conditions become favorable to growth. Endospore formation by B. subtilis is considered a very early example of differentiation, and has become a paradigm for the study of cellular differentiation. B. subtilis has gained popularity as a model organism for the laboratory study of gram positive bacteria. There are several characteristics which make working with B. subtilis attractive at the bench, and in particular for the study of sporulation. Laboratory strains of B. subtilis are easy to manipulate genetically due to a natural competence to the uptake of foreign DNA along with high rates of homologous recombination. (Dubnau and Lovett, 2002). B. subtilis viability does not depend on its ability to sporulate, and mutant strains deficient in the ability to sporulate are easy to generate and identify (Piggot and Coote, 1976). B. subtilis is not considered a human pathogen, and was used for the study of biological warfare in 1966, when the U.S. Army dispensed B. subtilis variant niger throughout the New York City subway system (Cole, 1995; Carlton, 2001). More than a million civilians where harmlessly exposed when army scientists dropped light bulbs 1 filled with the bacteria onto ventilation grates (Cole, 1995; Carlton, 2001). Similar to Escherichia coli, the prevailing