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MIAMI UNIVERSITY the Graduate School Certificate for Approving The MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Erik Andrew Feldmann Candidate for the Degree: Doctor of Philosophy __________________________________________ Michael A. Kennedy, Advisor __________________________________________ Christopher A. Makaroff, Committee Chair __________________________________________ Carole Dabney-Smith, Reader __________________________________________ Michael W. Crowder, Reader __________________________________________ Richard E. Lee, Graduate School Representative ABSTRACT BIOPHYSICAL CHARACTERIZATION OF HETEROCYST DIFFERENTIATION REGULATORS, HETR AND PATS, FROM THE CYANOBACTERIUM, ANABAENA SP. STRAIN PCC 7120 AND STRUCTURAL BIOLOGY OF BACTERIAL PROTEINS FROM THE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM by Erik A. Feldmann The filamentous cyanobacterium Anabaena (Nostoc) sp. strain PCC 7120 has evolved a mechanism for isolating the two incompatible processes of photosynthesis and nitrogen fixation by differentiating specialized cells called heterocysts. The structure and metabolism of heterocysts support a microanaerobic environment allowing for the nitrogenase-dependent fixation of dinitrogen into ammonia to occur with limited inhibition by oxygen. Under conditions of nitrogen starvation, Anabaena differentiates heterocysts in regular patterned intervals in approximately one out of every ten cells. The hetR and patS genes are essential for proper heterocyst differentiation. The gene products, HetR and PatS, are regulators of heterocyst differentiation, but their specific mechanisms of activity are unclear. In the first part of this dissertation, an in depth biophysical characterization of both HetR and PatS is presented. We describe a method for over-expressing and purifying high yields of soluble HetR from Anabaena in Escherichia coli, have provided the first experimental evidence that the master regulatory HetR transcription factor is the direct binding target for the PatS inhibitor peptide, have characterized the binding stoichiometry of HetR with DNA and PatS substrates, and have quantified the binding thermodynamics of HetR-PatS complexes. The second part of this dissertation describes a detailed structural biology summary of four different bacterial protein targets of the National Institutes of Health. The first section of this second part includes an uncharacterized protein, Pspto_3016 from Pseudomonas syringae which adopts a putative DNA-binding double-wing motif. The second and third sections include two different proteins from the cyanobacterium Anabaena sp. PCC 7120: a hypothetical uncharacterized protein, Asl3597, with a novel fold and that exhibits sequence homology to the chlororespiratory reductase family of plant proteins, and another uncharacterized protein, Asr4154, annotated as a subunit of the protochlorophyllide reductase superfamily of enzymes. The fourth and final section includes an uncharacterized protein fragment, the putative mucin-binding domain of the protein LBA1460 from Lactobacillus acidophilus. We provide high resolution, three- dimensional structures of each protein, solved by solution NMR spectroscopy, to assist in future characterization of their corresponding biological and biochemical functions. BIOPHYSICAL CHARACTERIZATION OF HETEROCYST DIFFERENTIATION REGULATORS, HETR AND PATS, FROM THE CYANOBACTERIUM, ANABAENA SP. STRAIN PCC 7120 AND STRUCTURAL BIOLOGY OF BACTERIAL PROTEINS FROM THE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM A DISSERTATION Submitted to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Chemistry and Biochemistry by Erik A. Feldmann Miami University Oxford, Ohio 2012 Dissertation Director: Michael A. Kennedy Table of Contents Chapter 1: Introduction ....................................................................................................... 1 1.1 Heterocyst differentiation in cyanobacteria .............................................................. 2 1.1.1 The emergence of cyanobacteria and the evolution of heterocysts .................... 2 1.1.2 The cyanobacterium, Anabaena sp. strain PCC 7120 ........................................ 2 1.2 Regulation of heterocyst pattern formation ............................................................... 4 1.2.1 Initiation of regulatory events............................................................................. 4 1.2.2 HetR, the master regulator of heterocysts .......................................................... 5 1.2.3 PatS, a heterocyst pattern regulator .................................................................... 7 1.3 Structural Genomics .................................................................................................. 8 1.3.1 The Protein Structure Initiative .......................................................................... 8 1.3.2 The Northeast Structural Genomics Consortium................................................ 9 1.3.3 Target selection ................................................................................................. 10 1.3.4 High-throughput cloning, purification, and isotopic labeling of NESG protein targets......................................................................................................................... 10 1.3.5 Multidimensional Nuclear Magnetic Resonance (NMR) spectroscopy ........... 13 1.3.5 Three-dimensional structure calculations ......................................................... 16 1.4 Dissertation goals and specific aims ....................................................................... 18 1.6 References ............................................................................................................... 21 Chapter 2: Evidence for direct binding between HetR from Anabaena sp. strain PCC 7120 and PatS-5 ................................................................................................................ 27 2.1 Abstract ................................................................................................................... 28 2.2 Introduction ............................................................................................................. 28 2.3 Materials and Methods ............................................................................................ 31 2.3.1 Bacterial strains and growth conditions ............................................................ 32 2.3.2 Plasmid construction for making chromosomal alleles .................................... 32 2.3.3 Construction of strains containing mutant alleles ............................................. 35 2.3.4 In vivo PatS-5 sensitivity assays ....................................................................... 35 2.3.5 Cloning, overexpression and purification of recombinant soluble HetR ......... 35 ii 2.3.6 DNA binding assays ......................................................................................... 39 2.3.7 Circular dichroism spectroscopy ...................................................................... 39 2.3.8 Site-directed spin labeling ................................................................................ 40 2.3.9 Preparation of samples for electron paramagnetic resonance spectroscopy ..... 40 2.3.10 Electron paramagnetic resonance spectroscopy ............................................. 40 2.3.11 EPR spectral simulations ................................................................................ 41 2.3.12 Molecular dynamics simulations .................................................................... 42 2.3.13 Isothermal titration calorimetry ...................................................................... 42 2.4 Results ..................................................................................................................... 43 2.4.1 Conservative substitutions at HetR residues 250-256 affect heterocyst formation and sensitivity to PatS-5 ........................................................................... 43 2.4.2 Evidence for direct binding of PatS-5 to HetR ................................................. 46 2.4.3 Evidence for PatS-5 binding to the dimer form of HetR .................................. 52 2.4.4 Characterization of binding of HetR to a 29 bp inverted repeat containing DNA sequence upstream of hetP ........................................................................................ 56 2.4.5 Sensitivity of the HetR-DNA complex to PatS-5 ............................................. 58 2.4.6 Similarity of HetR and HetR-C48A ................................................................. 61 2.4.7 Determination of the stoichiometry, dissociation constant, and thermodynamic parameters for binding of PatS-5 to HetR ................................................................. 65 2.5 Discussion ............................................................................................................... 68 2.6 Acknowledgements ................................................................................................. 70 2.7 References ............................................................................................................... 70 Chapter 3: Differential binding between PatS C-terminal peptide fragments and HetR from Anabaena sp PCC 7120 ........................................................................................... 79 3.1 Abstract ..................................................................................................................
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