Expression and Characterisation ofa Gene Enc oding RbpD, an RNA- Bind ing Protein in Anabaena sp. strain PeC 7120 by Rob in lee Tremblay A lhesis submitted to the Scltool of Graduale Studies in partial fulfilment of the requirements fOl" the degree of Master of Science Department of BiochemistrylFacultyof Science Memorial University of Newfoundland January 2000 SI.JOM'S Newfoun dland Abs t ra ct The RNA-binding protein RbpD, from the cyano bacterium Anaba ena sp, strain Pe C 7120 was expressed in £Sch~ ric h ia coli and successfully purified using me IMPACT I system (New England Biolabs). The rbp D gene was cloned into the pCYBt expre ssion vector by using polymerase chain reaction to introduce Ndel and SapI restriction sites at the 5' end 3' ends of the gene respect ively. The 3'.-end mutagenesis also chan ged the stop codon into a cysteine codon. The resulting gene encoded a fusion protein consisting of RbpD, the Saccharomyces cerev isiae VMA intein and a chitin binding domain.. Expressi on of the fusion protein was observed in £ coli strain MCI061 but Western blot analysis using an intein-directed ant ibody indicated that significant in vivo fmeln-direcred splicing of the fusion protein occurred. We were unable to eliminate this problem; no fusion protein expression was observed in 8 other E coli strains tested. Wild -type RbpD was purified following binding of the fusion protein 10 a chitin column and overnight cleavage in the presence of a reducing agent, dlthicthrehc l. A number of modifications to the manufacturer' s purification protocol were found to be necessary for success ful purification. The NaCI concentration in the cleavage and elution buffe r was increased from SOmM to 500 ruM to eliminate problems of RbpD solubility. An inC~ in the dithi othreirol concentration of the cleavage buffer from 30 mM to SOmM was required for full cleavage. A modified form of RbpD containing an hexa-histidine tag in loop 3 of the RNA recognition motif,RbpD I, was also successful!y purified. The rbpD/ gene, previously constructed by Cynthia Slade, was cloned info the p'ffiC99A expression vector. An Nee! site was introduced at the S'-end of the gene using site-directed mutagenesis. This modification also changed the second codon of the gene from serine to alanine . The RbpDl protein was expressed in £ coli strain BUI(DEJ )PlysS following induction with IPTG and purified using a nickel-NfA agarose affi nity column. The protein was eluted with l Oa roM imidazole and appeared to be pure upon analysis using polyacrylamide gel electrophoresis. The RNA-binding activity of RbpO and RbpD I ....ere first determi ned using Sepharose-4 B-, polyacrylhydrazid.o-agarose-. or agarose-bound RNA homopolymers. Both proteins bound strongly to poly(U),less strongly to poly(O ), weakly to poly(A). and not at all to pely(e). This pattern is consist ent with that observed for other cyanobacterial RNA-bin din g proteins. Th ere was no apparent difference in the binding affinit ies of RbpD and Rbp DI indicating tha t the presence of the 6x-hist idine tag had no effect. Experiments to de tect binding betwee n RbpD and a conserved sequence element in the S' - untranslared region of rbpD using both electro phoretic mo bility shift assays and nitrocellulose filter binding were unsuccessful. Similarly, attempts to detect binding between RbpD and size-fractionated radioacti vely labelled poly(U) by electrophoretic mobility shift assays were unsuccessful. Two SElEX experiments were also unsuccess ful. In both cases, no increase in specific binding over background was detected through four rounds of selection. iii This thesis is dedica ted to my parents. Kerry and Lee Tremblay who have always supported me in anything I have put my mind to . I wou ld like to thank Dr. Martin Mulligan. my supervisor on this project. for all the belp be has provided. and also for the emotio nal support. I'd also like to thank Tom Belbin for question answering, Kerry Tremblay for editing the writing in this thesis (and learning lots ofbiochemistry white doing so!) , Lee Tremblay for computer support, and Dr.lohn Brosnan who has gone above and beyo nd the call of duty in his role as Head of the Department. I also thank Dr. Margaret Brosnan and Dr. David Heeley who were on my advisory committee. r wou ld like to thank my fiance Jaso n Church ill for being there through al l the stress. iv T able of Co nte nts StttiOD Pagr: Abs tnci Ac:kn owl rd gem en u iv T a ble or C ontents Lisl or Ta bles viii Lisl or Figu re s ix Lisl or Abb rev iations a nd Symbol! xii CHAPTERI : INTR OD UCTI ON 1.1 Cyanobacteria 1.2 Anabae na sp. strain PCC 7120 1.2.1 General t .2.2 Heterocysts 1.2.3 Mechani sm of Heterocyst Formation t.3. RNA·Binding Proteins 10 t.3 .1 RNP·Type RNA-Binding Proteins 10 1.3.2 RNA-Binding Proleins in Cyanobacteria l3 1.3.3 RbpD in Anab aena 7120 15 1.3.4 UIA 18 1.3.5 Heterogeneous Nuclear R..i bonucteoproteins 21 13 .6 Glycine Loops 24 13 .7 Evolutionary Trends in RNA-Binding 26 Proteins 1.4 Cold -Shock Proteins 28 1.5 lnteias 30 1.5. 1 General 30 1.52 Rationale for the Placement of Irueins 31 1.5.3 Mechanism of Intein Excision 32 1.5.4 Inteins in Cyanobac teria 33 1.5.5 Inreins for Protein Expression Systems 36 S«tion Pa ge 1.6 SELEX 37 1.7 Aims 43 CHAPTER 2: MATERIALS AND METHO DS 2.1 Materials 45 2.2 Culturing and Cloning 45 2.2.1 Media 45 2.2.2 Competent Cells 50 2.2.3 Transfonn ations 50 2.2.4 lsclatlon of Plasmid DNA 51 2.2.5 Cloning of DNA 52 2.3 Sequencing of ONA 53 2.4 Detection of Proteins 55 2.5 Expression of RbpD 56 2.5.1 Cloningo f rbpD lntopCYBI 56 2.5.2 Expression and Purification of RbpD 57 2.5.3 Western Blotting of Fusion Protein 60 2.6 Expression of RbpDI 61 2.6.1 Site Directed M utagenesis o fr bpDl a 6 1 2.6.2 Expression of RbpD1 65 2.7 Storage of proteins 66 2.8 Binding Experiments 66 2.8.1 Polymer Bindi ng 66 2.8.2 Binding of S' -Untranslated Region -DNA 67 2.8.3 Binding of 5'-Unuans lated Region - RNA 68 2.8.4 Binding of Poly(U) 70 2.9 SELEX 71 CHAPTE R 3: RESULTS AND DISCUSSIO N - PROTEIN EXPRESSION 3.1 Expression ofRbpD 76 3.1.1 Cloning ofrbp D Into pCYBI 76 vi Page 3.1.2 Expression of the Fusion Protein in £. coli 79 MCI061 3.1.3 Expression o flheFusion Prote in inE. coli 84 BL2 1(DEJ)pLysS 3.1.4 Western Blotting 92 3.1.5 Expression of RbpD in Other Strains of 96 E. coli 3.1.6 Purification of RbpD 99 3.2 Expression and Purifi cation of RbpD 1 102 3.2.1 Background 102 3.2.2 Site-Dire cted Mu tagenesis 110 3.2.3 Affects o f the Nco l Site in r bpD / 113 3.2 .4 Expression and Purifica tion of Rbp Dl 114 CHAPTE R 4: RES ULT S AND DISC USSION - CHARACTERJSAnos OFRbpD 4.1 Bind ing to Agarose -Bound Po lymers 123 42 Binding to 5'-Untransla te<lRegion ofrbpD -DNA 127 4.3 Bindi ng to 5' - Untrans lated Region ofrbpD - RN A 131 4.4 Binding of RbpD to Poly(U) 139 4.5 SELEX 140 CHAPTER 5: GENERAL DlSCUSIOS 5.\ General Disc ussion lS I 5.2 Future Work 1S6 1S8 Appendil I : C lon ing and Seque nci n g of nifH* from 174 ChlorogloeopsiJ sp. PCC 6192 vii List of Tab les Table Page 2.1 Plasmids used in this work 46 2.2 Bacterial Suains usedin thiswork 48 2.3 Oligonucleotides synthesisedin thiswork 54 viii List o f Figures Figun C ha plcr I 1.1 Photo of Anaba ena 7 120 1.2 VIA RNA-Recognition motif bound 10an RNA hairpin 12 1.3 Nucleo tide seq uence ofthe rbpD gene from Anaba ena 7120 17 and its inferred am ino acid sequence 1.4 Schematic diagram of the mechanism ofintein splicing 3S 1.5 Schematic dia gram illustrating the theory o f SEL EX 40 C ha pter 2 2. 1 Protocol for express ion and purification of RbpD 59 2.2 Schematic dia gram of the Altered Sites II mutagenesis proc edure 63 3. I Schematic drawing of the splicing mechanism cf the [MPACT [ 78 system 3.2 C loningrbpD in pC YB I 81 3.3 pRLTl dige sted with Ndel and Kpnl 83 3.4 Induction of RbpD fusion protein expression in £. coli MCI 06 1 86 3.5 Expression of the RbpD fusion protein from pRLTl in E. coli 88 strain MC I06 1 3.6 Expression of the RbpD fusion protein in E. coli 91 BL2I(DE3)pL ysS 3.7 Western blot anal ysis o f the RbpD fusion protein in E. coli 94 strain MC I06 1 ix Figure Pa ge 3.S Expression of the Rbp D fusio n protein from pRLTl in eight 9S strainsof£ coli 3.9 RbpD elution wi th 0.1% Triuln*X IOOin Cleavage Buffer 101 3.