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Molecular Characterization and Evolution of Α-Actinin: from Protozoa to Vertebrates

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Molecular Characterization and Evolution of Α-Actinin: from Protozoa to Vertebrates Molecular characterization and evolution of α-actinin: from protozoa to vertebrates av Ana Virel Akademisk avhandling Som med vederbörligt tillstånd av rektor vid Umeå universitet för avläggande av filosofie doktorsexamen vid teknisk–naturvetenskaplig fakultet kommer att offentligen försvaras på Kemiska institutionen i sal KB3A9, KBC, lördagen den 9 december 2006, kl. 10.00. Fakultetsopponent: Dr. Kristina Djinovic-Carugo, Department for Biomolecular Structural Chemistry, Faculty of Chemistry, University of Vienna. Department of Chemistry, Biochemistry, Umeå University Umeå 2006 Organization Document name UMEÅ UNIVERSITY DOCTORAL DISSERTATION Department of Chemistry Biochemistry SE-901 87 Umeå, Sweden Date of issue November 2006 Author Ana Virel Title Molecular characterization and evolution of α-actinin: from protozoa to vertebrates Abstract α-actinin is a ubiquitous protein found in most eukaryotic organisms. The ability to form dimers allows α-actinin to cross-link actin in different structures. In muscle cells α-actinin is found at the Z-disk of sarcomeres. In non-muscle cells α-actinin is found in zonula adherens or focal adhesion sites where it can bind actin to the plasma membrane. α-actinin is the shortest member of the spectrin superfamily of proteins which also includes spectrin, dystrophin and utrophin. Several hypotheses suggest that α-actinin is the ancestor of this superfamily. The structure of α-actinin in higher organisms has been well characterized consisting of three main domains: an N-terminal actin-binding domain with two calponin homology domains, a central rod domain with four spectrin repeats and a C-terminal calcium-binding domain. Data mining of genomes from diverse organisms has made possible the discovery of new and atypical α-actinin isoforms that have not been characterized yet. Invertebrates contain a single α-actinin isoform, whereas most of the vertebrates contain four. These four isoforms can be broadly classified in two groups, muscle isoforms and non-muscle isoforms. Muscle isoforms bind actin in a calcium- independent manner whereas non-muscle isoforms bind actin in a calcium-dependent manner. Some of the protozoa and fungi isoforms are atypical in that they contain fewer spectrin repeats in the rod domain. We have purified and characterized two ancestral α-actinins from the parasite Entamoeba histolytica. Our results show that despite the shorter rod domain they conserve the most important functions of modern α-actinin such as actin-bundling formation and calcium-binding regulation. Therefore it is suggested that they are genuine α-actinins. The phylogenetic tree of α-actinin shows that the four different α-actinin isoforms appeared after the vertebrate-invertebrate split as a result of two rounds of genome duplication. The atypical α-actinin isoforms are placed as the most divergent isoforms suggesting that they are ancestral isoforms. We also propose that the most ancestral α-actinin contained a single repeat in its rod domain. After a first intragene duplication α-actinin with two spectrin repeats were created and a second intragene duplication gave rise to modern α-actinins with four spectrin repeats. Key words: α-actinin, evolution, spectrin repeat, intragene duplication, phylogenetic tree, spectrin superfamily. Language: English ISBN: 91-7264-204-1 Number of pages: 52 + 4 papers Molecular characterization and evolution of -actinin: from protozoa to vertebrates Ana Virel Department of Chemistry, Biochemistry, Umeå University Umeå 2006 Department of Chemistry, Biochemistry Umeå University SE-901 87 Umeå, Sweden • COPYRIGHT © 2006 BY ANA VIREL ISBN: 91-7264-204-1 PRINTED IN SWEDEN BY PRINT OCH MEDIA: 2002524 UMEÅ UNIVERSITY, UMEÅ 2006 Organization Document name UMEÅ UNIVERSITY DOCTORAL DISSERTATION Department of Chemistry Biochemistry SE-901 87 Umeå, Sweden Date of issue December 2006 Author Ana Virel Title Molecular characterization and evolution of -actinin: from protozoa to vertebrates Abstract -actinin is a ubiquitous protein found in most eukaryotic organisms. The ability to form dimers allows -actinin to cross-link actin in different structures. In muscle cells -actinin is found at the Z-disk of sarcomeres. In non-muscle cells -actinin is found in zonula adherens or focal adhesion sites where it can bind actin to the plasma membrane. -actinin is the shortest member of the spectrin superfamily of proteins which also includes spectrin, dystrophin and utrophin. Several hypotheses suggest that -actinin is the ancestor of this superfamily. The structure of -actinin in higher organisms has been well characterized consisting of three main domains: an N-terminal actin-binding domain with two calponin homology domains, a central rod domain with four spectrin repeats and a C-terminal calcium-binding domain. Data mining of genomes from diverse organisms has made possible the discovery of new and atypical -actinin isoforms that have not been characterized yet. Invertebrates contain a single -actinin isoform, whereas most of the vertebrates contain four. These four isoforms can be broadly classified in two groups, muscle isoforms and non-muscle isoforms. Muscle isoforms bind actin in a calcium- independent manner whereas non-muscle isoforms bind actin in a calcium-dependent manner. Some of the protozoa and fungi isoforms are atypical in that they contain fewer spectrin repeats in the rod domain. We have purified and characterized two ancestral -actinins from the parasite Entamoeba histolytica. Our results show that despite the shorter rod domain they conserve the most important functions of modern -actinin such as actin-bundling formation and calcium-binding regulation. Therefore it is suggested that they are genuine -actinins. The phylogenetic tree of -actinin shows that the four different -actinin isoforms appeared after the vertebrate-invertebrate split as a result of two rounds of genome duplication. The atypical -actinin isoforms are placed as the most divergent isoforms suggesting that they are ancestral isoforms. We also propose that the most ancestral -actinin contained a single repeat in its rod domain. After a first intragene duplication -actinin with two spectrin repeats were created and a second intragene duplication gave rise to modern -actinins with four spectrin repeats. Key words: -actinin, evolution, spectrin repeat, intragene duplication, phylogenetic tree, spectrin superfamily. Language: English ISBN: 91-7264-204-1 Number of pages: 52 + 4 papers The only true wisdom is in knowing you know nothing. • Socrates Why and how to study protein evolution? Many times people ask me why do I study protein evolution? What is the important thing with it? Protein evolution is the study of how proteins have changed and evolved as a result of selection or specialization. The tools to study protein evolution are among others sequence comparison, structure prediction and phylogenetic trees. The publishing of diverse genomes give us the opportunity to identify proteins with unknown structure or function. By knowing the evolutionary story of different proteins we can predict the structure and function of these unknown proteins simply by comparison. The knowledge about function and structure of one protein will accelerate the understanding of related proteins. We can track evolution and predict how topology and functionality changed over time. We will be able to predict how mutations can affect protein structure, or which sequences are essential for the functionality of a particular domain. The study of protein evolution allows to recognize relations among proteins. Understanding how proteins evolve can be also useful to design effective and long lasting vaccines or drugs. Prologue When I first came to Umeå my project was to study the evolution of the spectrin superfamily of proteins. We decided to start studying -actinin since it was believed to be the ancestor of this superfamily. During this time I realized that little was known about the evolution of -actinin. At that point, I found myself immersed in a new unexplored world with lots of helpful information and uncharacterized -actinin isoforms. Now, 5 years later, I have collected in this thesis all my research about -actinin. The first part is a general introduction that shows the relevance of -actinin and its related proteins. The second part will discuss more in detail the structure, function and evolution of -actinin. Although my research has been more focus on the evolution of -actinin, it has also contributed to other relevant aspects associated with this protein. • List of Contents LIST OF PAPERS .....................................................................................................1 ABREVIATIONS ......................................................................................................2 PART I INTRODUCTION .......................................................................................3 1. THE CYTOSKELETON ......................................................................................3 2. ACTIN ....................................................................................................................4 2.1 Actin Structure ..................................................................................................5 2.2 Actin polymerization.........................................................................................5 3. ACTIN-BINDING PROTEINS ............................................................................8 3.1 Proteins regulating actin polymerization...........................................................8
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