Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 961 Mitochondrial Evolution Turning Bugs into Features BY OLOF KARLBERG ACTA UNIVERSITATIS UPSALIENSIS UPPSALA 2004 ! "# $%%# "&'"( ) * ) ) + , - . *, * /, $%%#, ! , - * * , 0 , 12", &3 , , 456 1"7((#7(1&&7" - * ) ) . * * 87 , - * ) ) . ) ) * ) * ) , - ) . . * * ) * * * 87 , - . 9 * ) * ) 7 ) . 87 . , / ** )7 ) * * *, : ) 87 * ) ) ) ) ) 87 , ) ) . ) * . ) * ) 87 ) ) * 7 , ! " # " $ " % # " &!' ()" " #*+,- ./ " 0 ; / ) * $%%# 4556 ""%#7$&$< 456 1"7((#7(1&&7" ' ''' 7#$"2 = '>> ,,> ? @ ' ''' 7#$"2A List of Papers This thesis is based on the following papers, which will be referred to in the text by their roman numerals. I Karlberg O, Canbäck B, Kurland CG, Andersson SGE (2000) The dual origin of the yeast mitochondrial proteome. Yeast 17, 170-187. II Amiri H, Karlberg O, Andersson SGE (2003) Deep origin of plastid/parasite ATP/ADP translocases. J Mol Evol 56, 137-150. III Alsmark CM*, Frank AC*, Karlberg EO*, Legault B, Ardell DH, Canbäck B, Eriksson A-S, Näslund AK, Handley SA, Huvet M, La Scola B, Holmberg M, Andersson SGE (2004) The louse- borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proc Natl Acad Sci U S A. in press. IV Bousseau B, Karlberg EO, Frank AC, Legault B, Andersson SGE (2004) Inferring the Į-proteobacterial ancestor. Proc Natl Acad Sci U S A in revision. Reprints were made with the permission of the publishers. * Shared first authorship Contents 1. Introduction.................................................................................................1 1.1 Eukaryota .............................................................................................1 1.2 Mitochondria – heart of the cell ...........................................................3 1.2.1 The Serial Endosymbiosis Theory................................................3 1.2.2 Reduced and restructured .............................................................4 1.3 Mitochondrial ancestor(s).....................................................................4 1.3.1 The host ........................................................................................5 1.3.2 The endosymbiont ........................................................................5 1.3.3 Į-Proteobacteria............................................................................5 1.3.4 Rickettsia prowazekii....................................................................7 1.3.5 Bartonella henselae and Bartonella quintana ..............................8 2. Aims............................................................................................................9 3. Methodological considerations .................................................................10 3.1 Determining the genome sequence (paper III) ...................................10 3.1.1 Solving repeats............................................................................10 3.2 Defining the mitochondrial proteome (paper I)..................................13 3.3 Phylogenetic methods (papers I-IV)...................................................14 3.3.1 Large scale phylogenies (papers I and IV) .................................14 3.4 Reconstructing the ancestor (paper IV)..............................................16 3.4.1 Clustering genes..........................................................................16 4. Results.......................................................................................................18 4.1 Evolution in Į-proteobacteria.............................................................18 4.1.1 Genome dynamics ......................................................................18 4.1.2 From multi- to single-host pathogen...........................................18 4.2 Mitochondrial evolution.....................................................................19 4.2.1 Origin of the mitochondrial proteome ........................................19 4.2.2 Fate of the mitochondrial ancestor..............................................20 5. Discussion.................................................................................................21 5.1 Evolution in Į-proteobacteria.............................................................21 5.1.1 From free-living to obligate parasitism ......................................22 5.2 Mitochondrial evolution.....................................................................23 5.2.1 The yeast mitochondrial proteome .............................................23 5.2.2 The mitochondrial ancestor ........................................................24 5.3 ATP/ADP-translocases.......................................................................25 6. Concluding remarks and future perspectives ............................................27 7. Summary in Swedish ................................................................................28 Mitokondriens evolution ..........................................................................28 8. Acknowledgments.....................................................................................31 9. References.................................................................................................32 Abbreviations AIDS Aquired Immunodeficiency Syndrome ADP Adenosine 5’-diphosphate ATP Adenosine 5’-triphosphate bp Base pairs COG Clusters of Orthologous Groups DNA Deoxyribonucleic acid EMBL The European Molecular Biology Laboratory Mb Mega bases NADH Nicotinamide adenine dinucleotide NCBI National Center for Biotechnology Information (USA) PCR Polymerase Chain Reaction RNA Ribonucleic acid rRNA Ribosomal RNA SET Serial Endosymbiosis Theory SSU Small Subunit tRNA Transfer RNA TrEMBL Protein translation of the EMBL nucleotide database TrEMBLnew Additions to trEMBL since the last release 1. Introduction Man has always been interested in dividing his environment into different categories. Carl von Linné is probably the most famous taxonomist ever, and much of his 18th century work is still valid. The idea that life can be categorized into increasingly larger groups of similar organisms was further fueled by Charles Darwin’s theory on the origin of the species. Modern evolutionary biology has provided a framework for classification of organisms by their evolutionary relationships. Based on the observation that all life has the same basic structure – in the form of DNA for information storage, RNA for information transfer and proteins as executive units – it is generally assumed that all extant life has a common ancestor: LUCA, the Last Universal Common Ancestor. As taxonomic classification originally had to rely on features that could be observed by eye, under the microscope or in biochemical assays, the taxonomy of microorganisms was for long a problematic field. Until Carl Woese presented his pioneering work on molecular based taxonomy, life was divided into two top-level domains: prokaryota and eukaryota. By constructing phylogenies on the slow-evolving gene for small subunit (SSU) ribosomal RNA, Woese could demonstrate that prokaryota contained two substantially different groups (Woese and Fox, 1977). The result was the split of prokaryota into archaea and bacteria (Woese et al., 1990). Previously overlooked in microbiology, archaea are specialists at surviving in extreme environments and though having a cellular organization similar to bacteria, they share many molecular features with the eukaryotes. 1.1 Eukaryota When talking about life, most people think about human life or animals and plants. These are also the best known representatives of eukaryota. All individual organisms that we can see by eye are multi-cellular eukaryotes. But eukaryotes are much more than what we can see by eye and includes also unicellular organisms as amoebas and yeasts (fig. 1). The main feature that separates eukaryotes from bacteria and archaea is the containment of the chromosomes in a nucleus. Eukaryotes are distinct from bacteria and archaea in other ways as well; the presence of various specialized cellular compartments, organelles, is only observed in eukaryotes (fig. 2). 1 Animalia Choanozoa Fungi Microsporidia* Amoebozoa* Apusozoa Loukozoa Metamonada* Parabasalia* Discicristata Rhizaria Alveolata Chromobiota Cryptophyta Plantae Figure 1 Schematic view of the eukaryotic taxonomy based on the work by Cavalier-Smith and Stechmann (Cavalier-Smith, 2002; Stechmann and Cavalier- Smith, 2002). Groups marked with * are those originally suggested as primitively amitochondrial in the Archezoa hypothesis. Figure 2 Schematic drawing of the eukaryote cell. Adopted from (Alberts et al., 1994) 2 1.2 Mitochondria – heart of the cell Mitochondria are essential organelles to all respiring eukaryotes. Often described as the powerhouse of the eukaryotic cell, it is the cellular compartment where organic compounds are oxidized to carbon dioxide and water with a high yield of chemical energy in the form of ATP. This process, called oxidative phosphorylation, is such an effective process