PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/26996 Please be advised that this information was generated on 2021-10-08 and may be subject to change. Origin and evolution of the mitochondrial proteome Applications for protein function prediction in the eukaryotes Toni Gabaldón A mis Padres, por hacer de mis ilusiones las suyas. A Marta, por nuestra bonita simbiosis. Cover: Der Baum des Lebens (Gustav Klimt) ISBN: 90‐9019731‐1 (ISBN‐13: 9789090197319) Printed by PrintPartners Ipskamp, Nijmegen. Origin and evolution of the mitochondrial proteome. Applications for protein function prediction in the eukaryotes Een wetenschappelijke proeve op het gebied van de Medische Wetenschappen Proefschrift ter verkrijging van de graad van doctor aan de Radboud Universiteit Nijmegen op gezag van de Rector Magnificus prof. Dr. C.W.P.M. Blom, volgens besluit van het College van Decanen in het openbaar te verdedigen op dinsdag, 11 oktober 2005 des namiddags om 1:30 uur precies door Juan Antonio Gabaldón Estevan Geboren op 8 november 1973 Te Valencia (Spanje) Promotor: prof. dr . Martijn A. Huynen Manuscriptcommissie: prof. dr. Wilfried de Jong dr. Frank Holstege UMC-Utrecht prof dr. Charles Kurland. Lund Univ. (Sweden) Origin and evolution of the mitochondrial proteome. Applications for protein function prediction in the eukaryotes A scientific essay in the medical sciences Doctoral thesis to obtain the degree of doctor from Radboud University Nijmegen on the authority of the Rector, Prof. C.W.P.M. Blom, according to the decision of the Council of Deans to be defended in public on Tuesday, 11 October 2005 at 13:30 p.m. precisely by Juan Antonio Gabaldón Estevan Born in Valencia (Spain) On the 8th of November 1973 Index of contents Chapter 1 General Introduction 9 Chapter 2 Prediction of protein functions and pathways in the genome era 23 Chapter 3 Reconstruction of the proto‐mitochondrial metabolism 51 Chapter 4 Lineage‐specific gene loss following mitochondrial endosymbiosis and its applications for function prediction in the eukaryotes 57 Chapter 5 Tracing the evolution of a large protein complex in the eukaryotes, NADH:Ubiquinone oxidoreductase (Complex I) 73 Chapter 6 Evolution of mitochondrial metabolism 97 Chapter 7 Shaping the mitochondrial proteome 119 Chapter 8 The evolutionary origin of the peroxisome 135 Chapter 9 Summarizing discussion 151 Nederlandse samenvatting en discusie 156 Resumen y discusión 160 Appendix 1 An aerobic mitochondrion that produces hydrogen 167 Appendix 2 Color figures 179 Acknowledgements 195 Curriculum Vitae 199 List of publications 201 Chapter 1 Uno no es lo que es por lo que escribe, sino por lo que ha leído*. Jorge Luis Borges *One is not what he is because of what he writes, but because of what he has read 8 General introduction Chapter 1 General introduction 9 Chapter 1 1. Mitochondria as eukaryotic organelles 1.1 The Eukaryotic cell All known cellular life on earth can be divided into three major domains, namely Bacteria, Archaea and Eukaryota. The first two differ in many features such as the structure and chemistry of their cell walls and membranes and their molecular biology. However, both Bacterial and Archaeal domains share the absence of a cell nucleus and are therefore referred to as prokaryotes, from the Greek “before the nucleus”. On the contrary, Eukaryotes, “true nucleus” in Greek, do posses a nucleus. This membrane‐bound structure confines the genome and the processes of replication, transcription and RNA maturation. Besides the presence of a nucleus, eukaryotic cells display several other distinctive characteristics, some of which I will briefly mention here. Eukaryotes have much larger cells than prokaryotes, commonly by a factor of a thousand or more. To regulate the shape and movement of such large cells, as well as to control the place of the internal structures, eukaryotes posses a network of protein filaments that is called the cytoskeleton. Embedded within this cytoskeleton are several membranous structures or organelles (Figure 1). These include, among others, the Endoplasmic Reticulum (ER), the Golgi apparatus, peroxisomes, hydrogenosomes, choloroplasts and mitochondria. Remarkably, the presence of some of these organelles is restricted to specific phyla. This is the case of chloroplasts in photosynthetic eukaryotes and the hydrogenosomes in some anaerobic protozoa and fungi. By targeting specific enzymes to different organelles, eukaryotes have achieved a high level of compartmentalization of their metabolism. For example, in the Golgi apparatus occurs the synthesis of lipids for the cell membrane while the ER is responsible for the synthesis and insertion of cell membrane proteins. Other vesicles are devoted to specific biochemical pathways such as intracellular digestion in the lysosomes or peroxide degradation and fatty acid oxidation in the peroxisomes. Nevertheless, despite this high compartmentalization, all organellar functions are ultimately orchestrated by the cell nucleus because, with only a handful of exceptions, the proteins that are targeted to the organelles are encoded by the nuclear DNA. Mitochondria, which are introduced in more detail in the following section, play a central role in the eukaryotic cell and are widely distributed among eukaryotes. Indeed, it seems that all known eukaryotic species posses either mitochondria or one of their evolutionary related organelles such as mitosomes or hydrogenosomes. Thus, mitochondria are essential to understand the function and evolution of the eukaryotic cell. 1.2 Mitochondria as diverse organelles Mitochondria are organelles surrounded by a double membrane system and are found in virtually all eukaryotic cells. They show a striking heterogeneity in terms of their number, location, and shape in the different cell types and conditions [1]. In addition, mitochondria are constantly moving, fusing and dividing and can often be regarded as a highly interconnected network [2]. Regardless of their morphology, the structure of mitochondria defines various functional spaces within the organelle (Figure 1). Firstly, each of the two lipid bi‐layers that surround the 10 General introduction mitochondrion, the inner and outer mitochondrial membranes, has different permeability properties and contains a unique collection of proteins. Secondly, these membranes define two separate compartments, the mitochondrial matrix and the narrower inter‐membrane space, which constitute distinct microenvironments in which soluble proteins perform their functions. In addition, the inner membrane is usually highly convoluted with a series of invaginations, or cristae, that maximize its surface. M L P N ER G Figure 1 – Schematic representation of a eukaryotic cell. Surrounding the nucleus (N), and embedded in the cytoplasm, several organellar structures can be seen. These include the Endoplasmic Reticulum (ER), the Golgi apparatus (G), peroxisomes (P), lysosomes (L) and mitochondria (M). A mitochondrion is scaled‐up and illustrated in greater detail (see description in the text). Note that parts of the outer and inner membrane are not drawn to show the mitochondrial interior. (Drawn by T. Gabaldón) The structure and number of these cristae also varies greatly between different tissues. For instance, cristae from brown fat tissue mitochondria display a lamellar structure [3], whereas those from steroidogenic tissue mitochondria are tubular [4]. In terms of their function, mitochondria are often described in the textbooks as the “power plants” of the cell. Indeed, they produce more than 80% of the ATP needed by a normal human adult [5]. In most eukaryotic organisms, the end products of glycolysis and other catabolic pathways are transported to mitochondria in order to be further oxidized in the krebs cycle and the oxidative phosphorylation (OXPHOS) pathway (Figure 2). OXPHOS pathway is often considered the hallmark of mitochondria and consists of the transfer of electrons from NADH or FADH2 to O2 through a series of membrane‐embedded protein complexes, the so‐called electron transport chain (ETC). The transfer of electrons through the ETC is coupled to the pumping of protons across the mitochondrial inner membrane and the generation of a membrane potential, which provides the required energy for the synthesis of ATP. The evolution of some components of this pathway, and specifically of the first 11 Chapter 1 multi‐protein complex of the ETC, the mitochondrial NADH:ubiquinone oxidoreductase or Complex I, is analyzed in detail in chapter 5 of the present thesis. Variations from the canonical aerobic mitochondria electron transport chain described above, can be found in various eukaryotic lineages. In some species, such as the yeasts Sacharomyces cerevisiae and Schizosaccharomyces pombe, some of the ETC components have been lost. Other lineages harbor fully anaerobically functioning mitochondria, which carry an alternative terminal oxidase that allows them to use substrates other than oxygen as final electron acceptor [6]. Figure 2 – Schematic representation of the mitochondrial electron transport chain. The five multi‐protein complexes (I to V) are embedded in the mitochondrial inner membrane. The electron flux from NADH or succinate to O2 is indicated by small arrows. Protons are pumped‐out from the mitochondrial matrix by Complexes I, III and IV and enter back through Complex V (long