Abstract Lysyl hydroxylases (E.C. 1.14.11.4, LHs) have three isoenzymes that are found in humans and mice, and they hydroxylate lysine residues in collagens and other proteins containing collagenous sequences. The hydroxylysines formed are crucial for the intermolecular collagen crosslinks that stabilise collagen fibres, thereby providing the stiffness and stability required by various tissues. In addition, hydroxylysines serve as attachment sites for carbohydrates, whose functions on collagen molecules are not completely understood yet. In humans, lack of LH1 causes Ehlers-Danlos syndrome (EDS) VIA, which is characterised, for example, by severe progressive kyphoscoliosis and muscular hypotonia with joint laxity. Mutations in the LH2 gene are associated with Bruck syndrome, which is characterised by fragile bones with congenital joint contractures. In the present work recombinant human lysyl hydroxylases were produced in insect cells and purified to homogeneity. Limited proteolysis revealed that LHs consist of at least three structural domains. The N-terminal domain plays no role in the lysyl hydroxylase activity, but instead, is responsible for the recently reported glucosyltransferase activity of LH3, and the galactosyltransferase activity reported here for the first time. The LH polypeptide lacking the N-terminal domain is a fully active LH with Km values identical to those of full-length enzyme. In addition, direct evidence is shown that LH2, but not LH1 or LH3, hydroxylates the telopeptide lysine residues of fibrillar collagens. All three recombinant LHs were able to hydroxylate the synthetic peptides representing the helical hydroxylation sites in types I and IV collagens, with some differences in the Vmax and Km values. In addition, all three LHs hydroxylated the collagenous domain of coexpressed type I procollagen chain to similar extend. In this study mouse lines lacking LH3 or LH1 were created and analysed. Unexpectedly, the LH3 null mice died during the embryonal period due to fragmentation of basement membranes. Type IV collagen, one of the major components in basement membranes, aggregates on its way to extracellular space and is absent from the basement membranes making them fragile. This is most probably caused by abnormal processing of type IV collagen due to decreased glucosyltransferase activity of the LH3 null embryos. The first mouse model for human EDS VIA is presented here. The LH1 null mice did not have kyphoscoliosis characteristic of EDS VIA, but showed gait abnormalities due to muscular hypotonia and possible joint laxity, as also seen in EDS VIA patients. In addition, the null mice died occasionally from aortic ruptures. Ultra structural analysis revealed degradation of smooth muscle cells and abnormal collagen fibres even in non-ruptured aortas of LH1 null mice. The hydroxylation of lysine residues and crosslinking in LH1 null mice were also abnormal, as in human EDS VIA patients. The LH1 null mouse line provides an excellent tool for analysing several aspects of human EDS VIA, including muscular hypotonia, abnormalities in collagen fibres and their crosslinking.

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Metastasis is a major cause of cancer-related deaths and there is a great need for therapies aimed at preventing the spread of cancer, for which lysyl oxidase (LOX), an amino oxidase, plays a crucial role. The general aim of the thesis project was to screen and validate compounds with LOX inhibitory activities. To achieve this goal, we built a pharmacophore model of LOX inhibitors (LOXi) and screened a database of over 4400 compounds with known anti-tumoral activity in cell assays, the Biolab’s database. Top hits from the pharmacophore screening were docked to a LOX crystal structure to assess interactions between predicted inhibitors and the enzyme, and the methodology was implemented using MOE (Molecular Operating Environment) software. The pharmacophore model here developed had 5 features and produced an enrichment factor of 20 in our refinement stage. Biolab’s database screening resulted in the discovery of 344 hits. We docked the top 100 hits against a crystal structure of LOX and the results from the top 10 compounds, ranked by their interaction energy, were further analyzed. Using computer simulation software like MOE, increases the chances of finding a true inhibitor of LOX as compared to random testing of potential inhibitors, thus saving time and resources. / Metastaser är en viktig orsak till cancerrelaterade dödsfall och det finns ett stort behov av behandlingar som syftar till att förhindra spridning av cancer, där lysyloxidas (LOX), ett aminooxidas, spelar en avgörande roll. Det allmänna syftet med avhandlingsprojektet var att screena och validera föreningar med LOX-hämmande aktiviteter genom att konstruera en farmakofilmodell av LOX-hämmare (LOXi) för att screena en databas med föreningar med känd anti-tumoral aktivitet, Biolabs databas. De bästa träffarna från farmakoforscreeningen dockades till en LOX-kristallstruktur för att bedöma interaktioner mellan förutsedda hämmare och enzymet. Metoden implementerades med hjälp av programvaran MOE (Molecular Operating Environment). Den farmakospormodell som utvecklades här hade 5 funktioner och gav en anrikningsfaktor på 20 i vårt förfiningssteg. Biolabs databasscreening resulterade i upptäckten av 344 träffar. Vi dockade de 100 bästa träffarna mot en kristallstruktur av LOX och resultaten från de 10 bästa föreningarna, rangordnade efter deras interaktionsenergi, analyserades ytterligare. Genom att använda datorsimuleringsprogram som MOE ökar chansen att hitta en verklig hämmare av LOX jämfört med slumpmässiga tester av potentiella hämmare, vilket sparar tid och resurser.

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El remodelat vascular es un procés crític que present en el desenvolupament de patologies cardiovasculars com l’aterosclerosi i l’aneurisma d’aorta abdominal (AAA). La Lisil Oxidasa (LOX) i la Fibulina-5 (FBLN5) són dues proteïnes de matriu extracel•lular essencials en la formació i manteniment de les fibres elàstiques. Ambdues participen en processos fisiopatològics caracteritzats per l’alteració de l’equilibri síntesi/destrucció de la matriu extracel•lular i han estat involucrades en el remodelat vascular. Estudis en models experimentals han proporcionat indicis sobre la possible vinculació d’aquestes proteïnes en el desenvolupament d’aterosclerosi i d’AAA, si bé existeixen molts aspectes de la biologia d’aquestes proteïnes que haurien de ser analitzats en profunditat. Un aspecte crític en el remodelat vascular associat a la progressió de la lesió ateroscleròtica és l’aparició de regions d’hipòxia. L’estrès hipòxic és característic d’alguns processos fisiològics, però també de patologies com el càncer, els trastorns isquèmics, la inflamació crònica i l’aterosclerosi. Les cèl•lules endotelials són els sensors primaris d’aquest estrés hipòxic, i la seva adaptació a la hipòxia es produeix a través d’una complexa resposta finament regulada que afecta múltiples aspectes de la seva biologia, com la supervivència cel•lular, el control del to i la permeabilitat vascular, l’angiogènesi i el remodelat de la matriu extracel•lular. No obstant, no s’ha establert si la hipòxia pot regular la expressió de la LOX i la FBLN5 en cèl•lules endotelials ni la repercussió fisiològica que podria tenir. Les investigacions desenvolupades pel nostre grup indiquen que la LOX és un enzim clau en el manteniment de la integritat de l’endoteli i de la funció endotelial. La capacitat d’aquest enzim de controlar l’expressió gènica, en base a la seva activitat al nucli, així com l’activitat de factors de creixement fonamentals en l’homeòstasi vascular com el bFGF i el PDGF, suggereix que aquest enzim controla funcions cel•lulars que poden ser determinants en el desenvolupament de malalties cardiovasculars. En base a aquests antecedents, ens hem plantejat com a hipòtesis de treball que la LOX i la FBLN5 són proteïnes clau en l’homeòstasi vascular, que participen en la resposta adaptativa de les cèl•lules vasculars a la hipòxia, i que contribueixen al desenvolupament de patologies vasculars com l’aterosclerosi i l’aneurisma d’aorta abdominal. Els nostres resultats han demostrat que en artèries coronàries humanes, la LOX s’expressa principalment a l’endoteli i a l’adventícia, i que és la isoforma més expressada en cèl•lules vasculars, juntament amb la LOXL2. En cèl•lules endotelials, l’expressió de LOX i FBLN5 s’incrementa en resposta a hipòxia a través de mecanismes transcripcionals, si bé amb clares diferències entre ambdues proteïnes. Així, el factor HIF-1 juga un paper secundari en la regulació de la LOX per hipòxia en cèl•lules endotelials, una resposta en la que estan involucrades proteïnes de la família Smad i l’estrès oxidatiu. Per contra, HIF-1 és el principal responsable de la inducció de la FBLN5 en cèl•lules endotelials, en les quals hem demostrat que aquesta proteïna contribueix a la resposta adaptativa a l’estrès hipòxic. Finalment, hem observat que la sobre-expressió de LOX en cèl•lules endotelials mitjançant un sistema lentiviral indueix canvis en l’expressió gènica que afecten la senyalització i la comunicació cèl•lula-cèl•lula, d’entre els quals en destaca la inhibició de l’α2-macroglobulina. / Vascular remodeling is a critical process in the development of cardiovascular diseases such as atherosclerosis and abdominal aorta aneurysm (AAA). Lysyl oxidase (LOX) and Fibulin-5 (FBLN5) are two extracellular matrix proteins essential for the elastic fiber development and maintenance, and they both have an active role in physiological processes in which vascular remodeling is involved. By using different animal models, these proteins have been suggested to be involved with atherosclerosis and AAA. A critical aspect of the vascular remodeling in the atherosclerotic lesion is the apparition of hypoxic areas. Endothelial cells are primary sensors to the hypoxic stress, responding to it in a complex but subtly regulated way that affects multiple aspects of its biology. Nevertheless, it has not been established if the hypoxic stimulus can modulate LOX and FBLN5 expression, nor its possible physiological repercussions. Research made in our group shows the importance of LOX in the endothelial activity and vascular function. LOX can control the genetic expression as well as the activity of growth factors essential for the vascular homeostasis, suggesting that this enzyme may control cellular functions essential for the development of cardiovascular diseases. Based on these results, we have considered as working hypothesis that LOX and FBLN5 are key proteins in the vascular homeostasis, that they take part of the vascular response to hypoxia, and that they contribute to the development of vascular diseases like atherosclerosis and the AAA. Our results show that hypoxia transcriptionally induces LOX and FBLN5 in endothelial cells. While HIF-1 plays a secondary role in the regulation of LOX, being also involved in this modulation Smad proteins and oxidative stress, it is the main factor responsible for the FBLN5 induction. We also demonstrate that the modulation of FBLN5 in endothelial cells contributes to their adaptive response to hypoxia. Moreover, we have observed that overexpressing LOX in endothelial cells downregulates α2-macroglobulin expression.

The import of yeast tRNALys (tRK1) into human mitochondria in the presence of cytosolic extract suggests that human cell possesses machinery for tRK1 import. Here, we show that precursor of mitochondrial lysyl-tRNA synthetase (preKARS2) interact with tRK1 and its derivatives containing tRK1 import determinants, and facilitates their import into isolated mitochondria and in vivo, when preKARS2 was overexpressed or downregulated. tRK1 import efficiency increased upon addition of glycolytic enzyme enolase, previously found as an actor of RNA import in yeast. We found that tRK1 and its derivatives translocate into mitochondrial matrix in polynucleotide phosphorylase (PNPase) dependent manner. Furthermore, a point mutation preventing trimerization of PNPase affect import of 5S rRNA and MRP RNA into mitochondria and subsequently mitochondrial translation. Overexpression of the wild-type PNPase induced an increase of 5S rRNA import into mitochondria and rescued translation.

Abstract Collagens are subject to extensive post-translational modifications, including the formation of 4-hydroxyproline, 3-hydroxyproline and hydroxylysine. These reactions are catalyzed by collagen prolyl 4-hydroxylases (C-P4Hs), prolyl 3-hydroxylases (P3Hs) and lysine hydroxylases (LHs), which belong to the 2-oxoglutarate-dependent dioxygenase family and require oxygen for their reaction. 4-Hydroxyproline residues have for a long time been known to be required for the stability of the collagen triple helix, but the role of prolyl 3-hydroxylation was revealed only a few years ago when mutations in P3H1 and the consequent loss of a single 3-hydroxyproline in collagen I was shown to cause recessive osteogenesis imperfecta. In this thesis the human P3H isoenzymes were expressed as recombinant enzymes, and analyses of their tissue expression and kinetic properties revealed that P3H2 is located in tissues rich in basement membranes and that it hydroxylates collagen IV, the major basement membrane collagen. The roles of the collagen hydroxylases and collagen IV in basement membrane formation were further studied using Madin-Darby canine kidney (MDCK) epithelial cells as an in vitro model for cell polarization. 4-Hydroxyproline also has a pivotal role in the system of cellular response to reduced oxygen levels (hypoxia). At a normal oxygen concentration, two proline residues in the α subunit of the hypoxia-inducible factor (HIF) are 4-hydroxylated by the HIF-P4Hs, which target HIF-α for proteasomal degradation. In hypoxia, the HIF-P4Hs are inactive, and the α subunit thus escapes degradation, dimerizes with a β subunit and after recruiting transcriptional coactivators induces the transcription of hypoxia-responsive genes in order to adapt the cell to hypoxia. Three human HIF-α subunits have been characterized to date, of which the third is known to be subject to extensive alternative splicing, with one of the splicing variants acting as a negative regulator of the hypoxia responsive system. Four novel splicing variants generated from the human HIF-3α locus are characterized here, and the expression of HIF-3α variants has been shown to be upregulated by hypoxia in a HIF-1 dependent manner. Further studies on the binding partners and transcriptional activity of HIF-3α revealed that this subunit has a more complex role in the adaptation of cells to hypoxia than had been expected. / Tiivistelmä Kollageenit ovat valkuaisaineita, joihin kohdistuu useita synteesin jälkeisiä muokkauksia kuten 4-hydroksiproliinin, 3-hydroksiproliinin ja hydroksilysiinin muodostuminen. Näitä reaktioita katalysoivat kollageeniprolyyli-4-hydroksylaasit (C-P4H:t), prolyyli-3-hydroksylaasit (P3H:t) ja lysyylihydroksylaasit (LH:t), jotka kuuluvat 2-oksoglutaraattidioksygenaasien entsyymiperheeseen ja tarvitsevat happea reaktioonsa. 4-hydroksiproliinitähteiden on kauan tiedetty stabiloivan kollageeninrakenteen, kun taas 3-hydroksiproliinitähteiden merkitys on selvinnyt vasta viime vuosina. Mutaatiot P3H1-isoentsyymiä koodittavassa geenissä ja sen seurauksena yhden ainoan 3-hydroksiproliinitähteen puuttuminen kollageenissa I johtavat vaikeaan luustosairauteen, osteogenesis imperfectaan. Tässä väitöskirjassa ihmisen P3H:t tuotettiin rekombinanttiproteiineina. Tulokset paljastivat, että P3H2 ilmentyy erityisesti kudoksissa, joissa on paljon tyvikalvorakenteita ja että P3H2 hydroksyloi tehokkaasti kollageeni IV:n kaltaisia synteettisiä peptidejä. Lisäksi koiran munuaisten epiteelisoluihin pohjautuvaa in vitro-mallia käytettiin apuna tutkiessamme kollageeneja hydroksyloivien entsyymien ja kollageenin IV roolia tyvikalvon muodostumisessa sekä solujen polarisaatiossa. Kollageenia stabiloivan tehtävänsä lisäksi 4-hydroksiproliinilla on myös merkittävä rooli solujen vasteessa vähähappisille olosuhteille (hypoksia). Normaalissa happiosapaineessa (normoksia), hypoksiaindusoituvan tekijän (HIF) α-alayksikköön muodostuu HIF-P4H entsyymien katalysoimana kaksi 4-hydroksiproliinitähdettä, jotka kohdistavat α-alayksikön proteasomaaliseen hajotukseen. Hypoksiassa HIF-P4H:t eivät kykene toimimaan, jolloin α-alayksikkö säästyy hajotukselta, muodostaa kompleksin β-alayksikön kanssa ja sitoo transkriptiokofaktoreita. HIF-kompleksi kykenee tällöin lisäämään hypoksiassa tarvittavien geenien luentaa. Tänä päivänä tunnetaan kolme HIF α-alayksikköä, joista HIF-3α:sta tiedetään esiintyvän useita erilaisia silmukointimuotoja ja yhden näistä muodoista tiedetään toimivan negatiivisena säätelijänä hypoksiavasteessa. Tässä väitöskirjatyössä on tunnistettu neljä uutta HIF-3α:n silmukointimuotoa ja osoitettu että HIF-3α:n määrä kasvaa hypoksiassa HIF-1:n säätelemänä. Lisäksi sitoutumis- ja transkriptiokokeet paljastivat, että HIF-3α:n rooli hypoksiavasteessa on monimutkaisempi kuin aikaisemmin kuviteltiin.

Abstract The extracellular matrix is not just a scaffold for cells and tissues, but rather a dynamic part of the human body. Characteristics of collagens, the major protein components of the extracellular matrix, are determined already during synthesis and mutations in genes encoding collagens, unbalance of regulators or dysfunction of collagen modifying enzymes, for instance, can lead to severe clinical complications. Certain hydroxylysine residues formed by lysyl hydroxylases (LHs) function in collagens as precursors of collagen cross-links that stabilize collagenous structures and thereby tissues. In humans, a deficiency of LH1, which is known to hydroxylate lysines in the helical regions of collagen polypeptides, causes Ehlers-Danlos syndrome VIA (EDS VIA). It is characterized e.g. by progressive kyphoscoliosis and hypermobile joints. Mutations in LH2, which is known to hydroxylate lysines in the telopeptides of collagen polypeptides, cause Bruck syndrome type 2 (BS2). BS2 patients suffer from fragile bones and congenital joint contractures, for instance, but the syndrome is usually not lethal. In this work we have generated and analyzed genetically modified LH1 and LH2 null mouse lines to study the in vivo functions and roles of these enzymes. Analyses concentrated also on collagen cross-links that were determined from several null or heterozygous mouse tissues. In the present work we also studied the effects of known BS2 mutations on recombinant human LH2 polypeptides to understand the molecular pathology of the syndrome. As an animal model for human EDS VIA, LH1 null mice had certain characteristics typical for EDS VIA, such as muscular hypotonia, but generally the symptoms were milder. Like EDS VIA patients, the mice have an increased risk of arterial ruptures and ultrastructural changes can be seen in the wall of the aorta, explained by inadequate helical lysine hydroxylation accompanied by a changed cross-linking state of tissues. Similarly, analysis of the LH2 null mouse line demonstrated the importance of the enzyme in cross-link formation. We showed that even a reduced amount of LH2 in adult mice changes the cross-linking pattern in tissues and a total lack of the enzyme leads to embryonic lethality. Furthermore, we demonstrated that LH2 is particularly important in tissue structures supporting blood vessels in the developing mouse embryo or in extraembryonic tissues. Finally, our in vitro studies with recombinant human LH2 polypeptides revealed that the known BS2 mutations severely affect the activity of the enzyme thus explaining the clinical symptoms of the patients, but the mutations do not lead to a total inactivation of the enzyme, which may be critical for the survival of patients. / Tiivistelmä Solunulkoinen matriksi ei ole ainoastaan soluja ja kudoksia tukeva rakenne, vaan se on dynaaminen osa ihmiskehoa. Kollageenien, solunulkoisen matriksin yleisimpien proteiinien ominaisuudet määräytyvät jo kollageenien synteesivaiheessa ja mutaatiot kollageeneja koodittavissa geeneissä, säätelytekijöiden epätasapaino tai esimerkiksi kollageeneja muokkaavien entsyymien toimintahäiriöt voivat johtaa vaikeisiin kliinisiin komplikaatioihin. Tietyt lysyylihydroksylaasien (LH) muodostamat hydroksilysiinitähteet toimivat kollageeneissa kollageeniristisidosten esiasteina. Ristisidokset vakauttavat kollageenirakenteita ja siten myös kudoksia. LH1 hydroksyloi lysiinejä kollageenipolypeptidien kolmoiskierteisellä alueella ja ihmisellä entsyymin puutos aiheuttaa tyypin VIA Ehlers-Danlosin syndrooman (EDS VIA), jossa potilailla on esimerkiksi etenevää kyfoskolioosia ja yliliikkuvat nivelet. Mutaatiot LH2-entsyymissä, joka hydroksyloi lysiinejä kollageenipolypeptidien telopeptidialueilla, aiheuttavat tyypin 2 Bruckin syndrooman (BS2). BS2-potilaat kärsivät mm. luiden hauraudesta ja niveljäykkyydestä, mutta syndrooma ei yleensä ole letaali. Tässä työssä loimme ja analysoimme geneettisesti muunnellut LH1 ja LH2 hiirilinjat, joiden kyseinen LH-geeniaktiivisuus on hiljennetty. Linjojen avulla halusimme tutkia näiden entsyymien toimintaa ja merkitystä in vivo. Analyysit keskittyivät myös kollageeniristisidoksiin, joita tutkittiin useista poistogeenisten tai heterotsygoottisten hiirten kudoksista. Ymmärtääksemme BS2:n molekyylipatologiaa, tutkimme tässä työssä myös tunnettujen BS2-mutaatioiden vaikutuksia ihmisen LH2-rekombinanttiproteiinissa. EDS VIA:n eläinmallina LH1 poistogeenisillä hiirillä on joitakin ominaisuuksia, kuten lihashypotonia, jotka ovat tyypillisiä EDS VIA:lle, mutta yleisesti oireet ovat lievempiä. Kuten EDS VIA-potilailla, hiirillä on kohonnut valtimoiden repeytymisriski ja aortan seinämän ultrarakenteessa voidaankin havaita muutoksia. Oireita voidaan selittää riittämättömällä kollageenien kolmoiskierteisen alueen lysiinien hydroksylaatiolla, joka muuttaa kollageenien ristisidostilaa kudoksissa. Myös LH2-hiirilinjan analysointi osoitti kyseisen entsyymin tärkeyden ristisidosten muodostamisessa. Jo alentunut LH2:n määrä aikuisissa hiirissä muuttaa kudosten kollageeniristisidoksia ja täydellinen entsyymin puuttuminen johtaa sikiön kuolemaan. Lisäksi osoitimme, että LH2 on erityisen tärkeä kudosrakenteissa, jotka tukevat kehittyvän hiiren sikiön tai sikiön ulkopuolisten kudosten verisuonia. In vitro-tutkimukset ihmisen LH2-rekombinanttiproteiinilla paljastivat, että tunnetut BS2-mutaatiot vaikuttavat erittäin haitallisesti entsyymin toimintaan, mikä selittää potilaiden kliiniset oireet, mutta mutaatiot eivät kuitenkaan aiheuta entsyymin täydellistä inaktivaatiota, mikä voi olla kriittistä potilaiden selviytymisen kannalta.