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Variability of Photosynthesis Genes in Purple Bacteria and Molecular Determinants of Their Spectral Properties

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Variability of Photosynthesis Genes in Purple Bacteria and Molecular Determinants of Their Spectral Properties Variability of photosynthesis genes in purple bacteria and molecular determinants of their spectral properties Von der Fakultät für Mathematik und Naturwissenschaften der Carl von Ossietzky Universität Oldenburg zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften angenommene Dissertation von Christian Tuschak geboren am 12. Dezember 1969 in Recklinghausen Oldenburg, September 2003 Erstreferent: Prof. Dr. Heribert Cypionka Korreferent: Prof. Dr. Jörg Overmann Tag der Disputation: 17.12.2003 Für meine Eltern Für Judit List of Abbreviations [32P]dCTP deoxy cytidine triphosphate, labled with radioactive phosphor 32P aa amino acids ATCC American type culture collection ATP adenosine triphosphate bp base pairs bch bacteriochlorophyll biosynthesis genes BChl bacteriochlorophyll crt carontenoid biosynthesis genes DSM / DSMZ Deutsche Sammlung für Mikroorganismen und Zellkulturen EDTA ethylendiamine tetraacetic acid iPCR inverse polymerase chain reaction LH1 light harvesting complex 1 (core antenna) LH2, LH3 light harvesting complexes 2 and 3 (peripheral antennae) MOPS 3-(N-morpholino)propanesulfonic acid NIR near infrared nt nucleotides orf open reading frame PCR polymerase chain reaction PDB protein database PS I, PS II photosystem I and II puc structural and regulatory genes for the peripheral antenna puf photosynthetic unit forming genes (reaction center + light harvesting core antenna) puh structural gene for the reaction center H subunit (photosynthetic unit H protein) QA, QB acceptor quinones A and B in the purple bacterial reaction center Qy long wavelength transition of bacteriochlorophylls RC reaction center SDS sodium dodecyl sulfate SSC sodium chloride-sodium citrate TBE Tris-boric acid-EDTA TE Tris-EDTA Tris Tris(hydroxymethyl)aminomethane i Abbreviations of genus names Acp. Acidiphilium Alc. Allochromatium Amb. Amoebobacter Blc. Blastochloris Blm. Blastomonas Cfx. Chloroflexus Ery. Erythrobacter Ect. Ectothiorhodospira Hlr. Halorhodospira Psp. Phaeospirillum Rbc. Rhodobacter Rbi. Rhodobium Rbl. Rhodoblastus Rcy. Rhodocyclus Rdv. Rhodovulum Rps. Rhodopseudomonas Rsb. Roseobacter Rss. Roseospirillum Rsp. Rhodospirillum Rst. Roseateles Rvi. Rubrivivax Thc. Thermochromatium ii CONTENTS Table of Contents List of Abbreviations............................................................................................................i Abbreviations of genus names............................................................................................ii Table of Contents................................................................................................................iii Chapter I Introduction ......................................................................................................................... 1 1 PHOTOSYNTHESIS ............................................................................................................ 1 2 ANOXYGENIC PHOTOTROPHIC BACTERIA......................................................................... 2 3 PURPLE BACTERIA ........................................................................................................... 5 3.1 Photochemical processes in purple bacteria........................................................... 6 3.2 Structure of the pigment binding proteins and architecture of the purple bacterial photosynthetic apparatus....................................................................................... 7 3.3 Photosynthesis genes of the purple bacteria ........................................................ 11 4 AIMS OF THIS STUDY...................................................................................................... 12 5 THIS WORK .................................................................................................................... 15 6 REFERENCES.................................................................................................................. 16 CHAPTER II The puf operon of the Purple Sulfur Bacterium Amoebobacter purpureus: Structure, Transcription and Phylogenetic Analysis........................................................................ 24 1 ABSTRACT ..................................................................................................................... 25 2 INTRODUCTION .............................................................................................................. 26 3 MATERIALS AND METHODS........................................................................................... 29 Cell cultivation........................................................................................................... 29 PCR ............................................................................................................................ 29 Cloning and Sequencing ............................................................................................ 31 Generation of hybridization probes............................................................................ 32 Extraction of RNA, gel electrophoresis, blotting and hybridization.......................... 32 Sequence analyses...................................................................................................... 33 Nucleotide sequence accession number..................................................................... 34 4 RESULTS........................................................................................................................ 35 Structure and organization of puf genes in Amb. purpureus...................................... 35 Analysis of puf transcripts in Amb. purpureus........................................................... 40 iii CONTENTS Analysis of amino acid sequences ............................................................................. 43 Phylogenetic relationships of LH1 genes................................................................... 43 5 DISCUSSION................................................................................................................... 49 Structure and organization of the puf operon............................................................. 49 Phylogenetic and functional aspects of the multiplicity of LH1 antenna genes ........ 49 Transcription and regulation ...................................................................................... 51 Concluding remarks ................................................................................................... 52 6 ACKNOWLEDGEMENTS .................................................................................................. 53 7 REFERENCE ................................................................................................................... 54 CHAPTER III Photosynthesis genes and LH1 proteins of Roseospirillum parvum 930I, a purple non- sulfur bacterium with unusual spectral properties ........................................................ 60 1 ABSTRACT ..................................................................................................................... 61 2 INTRODUCTION .............................................................................................................. 62 3 MATERIALS AND METHODS........................................................................................... 65 Cultivation and DNA extraction ................................................................................ 65 PCR amplification of photosynthesis genes............................................................... 65 Generation of nucleotide probes ................................................................................ 67 Cloning and Sequencing ............................................................................................ 67 Sequence analyses...................................................................................................... 67 Modeling of three-dimensional structures ................................................................. 69 Nucleotide sequence accession number..................................................................... 70 4 RESULTS........................................................................................................................ 71 Structure of the puf operon in Roseospirillum parvum .............................................. 71 Analysis of amino acid sequences ............................................................................. 74 Structural models of the LH1 polypeptides ............................................................... 77 Phylogenetic relationships of LH1 sequences ........................................................... 79 5 DISCUSSION................................................................................................................... 86 Structure of the Rss. parvum puf operon.................................................................... 86 Significance of amino acid substitutions in the Rss. parvum LH1 polypeptides....... 86 Phylogenetic aspects .................................................................................................. 89 Summary and outlook ................................................................................................ 89 6 ACKNOWLEDGEMENTS .................................................................................................. 90 7 REFERENCES.................................................................................................................. 91 iv CONTENTS IV Summary......................................................................................................................
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