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List of Contents Biochemical and biophysical characterization of various cell wall channel-forming proteins By Nafiseh Soltanmohammadi Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemical Engineering Approved, thesis committee Prof. Dr. Roland Benz Prof. Dr. Mathias Winterhalter Prof. Dr. Miquel Viñas Ciordia Date of defense: March 22, 2013 School of engineering and science Abstract The mycolic-acid layer of certain gram-positive bacteria, the mycolata, represents an additional permeability barrier for the permeation of small water-soluble solutes. Consequently, it was shown in recent years that the mycolic acid layer of individual bacteria of the group mycolata contains pores, called porins, for the passage of hydrophilic solutes. Corynebacterium amycolatum, a pathogenic Corynebacterium species, belongs to the Corynebacteriaceae family but it lacks corynomycolic acids in its cell wall. Despite the absence of corynomycolic acids the cell wall of C. amycolatum contains a cation-selective cell wall channel, which may be responsible for the limited permeability of the cell wall of C. amycolatum. In the first project of this thesis and based on partial sequencing of the protein responsible for channel formation derived from C. amycolatum ATCC 49368 we were able to identify the corresponding gene coram0001_1986 within the known genome sequence of C. amycolatum SK46 that codes for the cell wall channel. The corresponding gene of C. amycolatum ATCC 49368 was cloned into the plasmid pXHis for its expression in Corynebacterium glutamicum ∆porA∆porH. Biophysical characterization of the purified protein (PorAcoram) suggested that coram0001_1986 is indeed the gene coding for the pore-forming protein PorAcoram in C. amycolatum ATCC 49368. The protein belongs to the DUF3068 superfamily of proteins, mainly found in bacteria from the family Corynebacteriaceae. The nearest relative to PorAcoram within this family is an ORF which codes for PorAcres, which was also recognized in reconstitution experiments as a channel-forming protein in Corynebacterium resistens. More general view of the distribution of this pore-forming proteins within the genus Corynebacterium was performed by extending the search for the homologous proteins to PorAcoram to pathogenic representatives of Corynebacteriales, the C. jeikeium strain K411, the C. urealyticum strain DSM 7109 and C. variabile DSM 44702. A further objective of this thesis was to elucidate the presence of the human VDAC I–like protein in the gram-negative pathogen Legionella pneumophila. Genome sequence screening of different strains such as Paris, Lens and Philadelphia has revealed the arrangement of eukaryotic-like proteins which is unique in Legionella. It is hypothesized that these eukaryotic-like proteins likely contribute in adaptation to the eukaryotic host cells. The existence of protein sequences forming a multi-protein complex comparable to the mammalian mitochondrial permeability transition pore (MPTP) of eukaryotes contributing in the cell apoptosis has been recently described. The most abundant protein in the outer membrane of mitochondria forming the core of (MPTP) is the voltage-dependent anion- selective channel (VDAC) which transports metabolites through the outer membrane as the major conduit. Blast alignment research has shown homologous sequence (Lpg1974) in the genome of L. pneumophila with 22% identity and 35% conservative replacement with the human mitochondrial VDAC 1 protein which has unknown function up to now. To consider the hypothesize whether or not the Lpg1974 is a VDAC-like protein, the lpg1974 was cloned in pGEX-2T vector and expressed in E. coli KS26 which lacks major porins. Biophysical characterization of this protein after purification exhibited that the Lpg1974 has a channel forming activity with a single-channel conductance around 5.5 nS. LIST OF CONTENTS 1 INTRODUCTION.................................................................................................. 1 1.1 THE BACTERIAL CELL ENVELOPE ............................................................................... 2 1.1.1 The cytoplasmic membrane ............................................................................................ 2 1.1.2 The periplasm .................................................................................................................. 3 1.1.3 The peptidoglycan layer .................................................................................................. 4 1.2 THE GRAM-POSITIVE CELL ENVELOPE ......................................................................... 6 1.3 THE GRAM-NEGATIVE CELL ENVELOPE ........................................................................ 8 1.4 THE CELL WALL OF GRAM-POSITIVE MYCOLATA ..........................................................11 1.4.1 The arabinogalactan moiety .......................................................................................... 13 1.4.2 The mycolic acid moiety ................................................................................................ 14 1.4.3 Porins penetrate the mycolic acid layer ......................................................................... 16 2 OBJECTIVES OF THE PHD-THESIS ................................................................ 18 3 IDENTIFICATION AND CHARACTERIZATION OF CELL WALL CHANNEL IN CORYNEBACTERIUM AMYCOLATUM .................................................................. 19 3.1 INTRODUCTION ........................................................................................................20 3.2 MATERIAL AND METHODS ..........................................................................................21 3.2.1 Bacterial strains and growth conditions ......................................................................... 21 3.2.2 Purification of the 45 kDa channel-forming protein of C. amycolatum .......................... 22 3.2.3 Tryptic digestion and peptide sequencing ..................................................................... 22 3.2.4 Cloning of porAcoram of C. amycolatum ATCC 49368 .................................................... 22 3.2.5 Extraction of RNA and reverse transcription (RT) PCR ................................................ 23 3.2.6 Expression and purification of recombinant proteins ..................................................... 24 3.2.7 Sucrose density gradient ............................................................................................... 24 3.2.8 Protein electrophoresis and immunoblotting ................................................................. 25 3.2.9 Test for susceptibility to antibiotics ................................................................................ 25 3.2.10 Susceptibility to antibiotics by MIC (Minimal inhibitory concentration) .......................... 26 3.2.11 Black lipid bilayer assay ................................................................................................ 26 3.3 RESULTS .................................................................................................................27 3.3.1 Identification of the gene coding for the cell wall channel of C. amycolatum ................ 27 3.3.2 Cloning procedure of coram0001_1986 ........................................................................ 30 3.3.3 Expression of PorAcoram in C. glutamicum ATCC 13032∆porA∆porH and purification .. 31 3.3.4 Promotion of efficient cleavage of a fusion tag .............................................................. 33 3.3.5 RT-PCR analysis confirmed the transcription of porAcoram in C. glutamicum ∆HA pXHisPorAcoram ............................................................................................................................... 35 3.3.6 Sucrose-step-gradient density centrifugation ................................................................ 36 [I] 3.3.7 Antibiotic resistance ....................................................................................................... 36 3.3.8 Study of channel-forming ability of PorAcoram ................................................................. 38 3.3.9 Ion selectivity ................................................................................................................. 39 3.4 DISCUSSION ............................................................................................................40 3.4.1 Identification of the gene coding for the cell wall channel of C. amycolatum ATCC 49368 40 3.4.2 Isolation and purification of channel forming protein ..................................................... 42 3.4.3 Interaction of PorAcoram with lipid bilayer membranes .................................................... 44 4 STUDY OF PROTEINS HOMOLOGOUS TO PORACORAM IN C. UREALYTICUM DSM 7109, C. RESISTENS DSM 45100 AND C. JEIKEIUM K411 ......................... 45 4.1 INTRODUCTION ........................................................................................................45 4.2 MATERIAL AND METHODS ..........................................................................................47 4.2.1 Bacterial strains and growth condition ........................................................................... 47 4.2.2 Cloning of porcres of Corynebacterium resistens DSM 45100 ........................................ 47 4.2.3 Site directed mutagenesis ............................................................................................. 47 4.2.4 Cloning of porjk of Corynebacterium
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