Department of Molecular Biology University of Aarhus - Denmark Published by Department of Molecular Biology University of Aarhus Denmark

Printed by NAT Reprocenter,University of Aarhus

Layout and design Lisbeth Heilesen

Photos Frontpage: Department of Molecular Biology Science Park Unit (top) and Campus Unit - Lisbeth Heilesen Back page : University Campus - Erik W. Olsson Other photos: Lars Kruse, Jakob Mark, Jesper Buch Rais, Søren Kjeldgaard and Lisbeth Heilesen

Translation First part of ”40 Years with Molecular Biology in Aarhus” (Margaret Clark)

Editors Just Justesen Erik Østergaard Jensen Lisbeth Heilesen

September 2008

ii www.mb.au.dk Contents

Preface ...... 1 40 years with Molecular Biology in Aarhus ...... 3 Plant Molecular Biology ...... 11 Protein Function ...... 13 Cellular Signalling and Development ...... 17 DNA Processing ...... 19 RNA and Virus ...... 21 Molecular Nutrition ...... 23 Protein Interactions ...... 25 Molecular interventions ...... 27 Structural Biology ...... 29 PhD degrees ...... 32

Department of Molecular Biology iii MBI’s 40th Anniversary - 4 June 2008

iv www.mb.au.dk Preface

Characteristis of the 40 years old Department of Molecular Biology

Full of vitality Ready for new challenges A successful generation shift A few years ago it was decided has introduced many dynamic that engineering should be group leaders to the Depart- part of the Faculty of Science. ment with a pronounced The Department took up the tradition for collaboration and challenge and has launched a respect for each other. This has biotechnology bachelor study already proven successful for sustaining a highly respected programme, and at present we Department and will be im- are preparing an MSc degree portant for future challenges. programme in process techno- More than 120 PhD students logy to be offered in 2009 and and young post-docs also is in the process of establishing contribute significantly to the a new engineering-based re- by Erik Østergaard Jensen vitality of the Department search area. Head of Department Experienced The Department hosts a num- Calm he Department of Molecu- ber of senior scientists who During the recent years, seve- Tlar Biology can celebrate contribute with important ral new administrative systems its 40th anniversary. In many networks, a wealth of experi- have been imposed at the aspects, our Department shares mental and teaching experi- Department: a new accounting characteristics which could be ence, and they can tell the story system, a database for pub- found among forty-year-old of molecular biology, forming lications and activities, new persons. It is full of vitality, the foundation for young websites, electronic calendars, experienced, ready for new scientists. etc. The introduction of these challenges, calm, responsible, The support staff at the Depart- systems has been very stressful ment also has a lot experience. self-confident, open-minded and has required lot of pa- The technicians are the focal and ambitious. However, it is point of our laboratories and tience for all the users. Thanks important to realize that each they make sure that no valua- to a very dedicated support person at the Department con- ble information or material is staff, these systems are now tributes with her/his unique lost. The workshops keep all running and are in general qualities to this profile. our equipment up and going. very helpful.

Department of Molecular Biology 1 Responsible Open-minded financially strong groups can Last year, 165 students were The major part of the research also be the driving force for enrolled at the three study at the Department is related to core facilities that all groups programmes offered by the De- health issues. When Molecular can benefit from. A better infra- partment. Molecular Medicine Medicine was announced to be structure to support the pre- was launched in 2007, Biotech- a focus area at the University in paration of applications would nology in 2006 and Molecular 2005, the Department initiated also contribute to more and Biology in 2002. The establish- a collaboration with the Faculty high-quality applications. ment of these new study proof Health Sciences. It has pre- grammes with the large num- viously proven difficult to -in ber of students has only been tegrate these different research In conclusion, the Department possible because all teachers traditions in formal structures. Molecular Biology is a very including PhD students have However, we now have a new healthy and strong 40 years old shown responsibility for their study programme in Molecular Department with all the skills share of the teaching load, and Medicine with contributions and resources required to meet the overall work has been very from both Faculties and a PhD the challenges in a period of well coordinated, from indivi- field in Molecular Medicine time where competition is the dual courses to study program- mantra. mes. Ambitious The education of the 83 PhD Several groups at our Depart- students presently enrolled at ment are recognized world- the Department also requires wide for their research, we a dedicated contribution from have started three new study supervisors and committee programmes within the past members organizing the edu- six years and we educate PhD cation. students who are accepted as post-docs at high-ranking universities. Self-confident But we can get even better if we A number of our researchers work together for the same goal have applied for prestigious na- and take responsibility for each tional and international grants, other. It is important that all and with great success. The De- groups at the Department can partment is a partner in more benefit from the very succes- than 10 EU and NIH research sful groups. This could be done programmes; the Department is by strategic collaborations and heading three Centres of Excel- applications that can improve lence by the Danish National the general level of funding at Research Foundation and is a the Department, ensuring that major partner in two other Cen- all groups can afford to educate tres of Excellence out of a total Master and PhD students. The of 38 national centres.

2 www.mb.au.dk 40 years with Molecular Biology by Niels Ole Kjeldgaard at the 25th Anniversary of the Department (1968-1993) - and Erik Østergaard Jensen (1993-2008)

he Molecular Biology Depart- fessors, 15 Heads of Department and Tment was established during an 39 Associate Professors. Naturally especially favourable time for Da- there were also major building plans. nish research. Throughout Denmark it was recognized that research and In the autumn of 1965 the Faculty of education were central issues for Science set up a committee to study the country’s economic and cultural the requirements for expansion of future, and that the majority of the the Biology teaching at the Univer- population should have the opportu- sity of Aarhus. In addition to the nity to take an education to the high- Professor of Botany from Aarhus est possible level. During the 1950s University Dr. Kai Larsen, the com- it was decided to expand the existing mittee included four Professors from universities and departments of hig- the University of Copenhagen: Dr. C. Barker Joergensen ( Zoophysiology), her learning as well as to found new Niels Ole Kjeldgaard was the first Dr. Morten Lange (Botany), Dr. Ole universities. Professor to be appointed at the new Maaloe (Microbiology) and Dr. K. G. Department for Molecular Biology in An auspicious start Wingstrand (Zoology). The com- 1967 The University of Aarhus was part mittee unanimously supported the of this picture, and during 1960 it expansion plan and it was suggested culty recognized that it could be a was decided that its biology teaching that Professor-ships and Depart- catastrophic start if the new subjects should be broadened to include sub- ments be set up in the fields of Ge- were immediately overwhelmed by jects that were previously taught netics, Plant Physiology, Zoophysio- high student numbers. Therefore, an only at the University of Copenha- logy and Molecular Biology. It was a agreement was made that students, gen. At the beginning of the 1960s, time when the Ministry could meet even after the new departments were professorships in Zoology. Botany the financial demands so in 1966 a set up, could still, after selection, and Genetics were established so Professor of Genetics was appoin- continue to study in Copenhagen that teaching to Bachelor and Ma- ted, followed in June 1967 with the until satisfactory buildings could ac- ster levels in the Biological Sciences appointments of Professors of Plant commodate them in Aarhus. This could begin. At this time a typical Physiology and Molecular Biology. decision was an important basis for department’s personnel consisted of the successful expansion of our De- one Professor, one Head of Depart- Biology teaching began with se- partment in that attention was paid ment and two to three Associate lected students continuing to fol- to the development of the subject Professors. Thus, the faculty’s plan low courses in Copenhagen. It was matter rather than the pressure of in 1966 was that the biology depart- very important for securing a good teaching when it came to appointing ment as a whole should have 13 Pro- teaching base in Aarhus that the Fa- Department staff.

Department of Molecular Biology 3 The first steps The building plans for laboratories The middle of the 1960s saw huge and teaching facilities were complet- University building projects. The ed in 1967. They foresaw a chain of Mathematics Department was about buildings in the eastern part of what to be completed and from October then was a military parade ground 1968 it was able to provide space for and garages. The financing for the the Molecular Biology Department first link in this chain was in order, that was founded by the University the plan for the 3200 square meters Senate on the 5th of June 1968. The Biology 1 building was finalized and Department was housed in the H- the invitation to submit tenders took wing at one end of the attic, while place in December 1967. Micropalæontology was housed at the other end. During 1967 the Ge- It was originally planned that this neticists had likewise found housing building should house Plant Physio- with the Mathematicians while the logy, Genetics and Molecular Biolo- Department for Plant Physiology gy. In the meantime the Geneticists´ came under the wing of the Bota- primary interests had moved to- nists in the offshoot of the Natural wards population genetics and they History Museum.

Kjeld Marcker employed as Professor in Biochemistry in 1969

wished to have their own building attached to Mathematics. The Faculty had earmarked a Professorship for Biochemistry, and in May 1969, Kjeld Marcker was appointed to this position. It was obvious that a Biochemistry De- partment should be housed in the Biology I building which was completed in the summer of 1970. Kjeld Marcker and I agreed that there was no advantage in having two Depart- ments and that we should join forces in a Department for Molecular Bio- logy. In June 1970, Staffan Magnus- son came to be Head of Division for Protein Chemistry. The new Biology II building was built in 1973

4 www.mb.au.dk It was still a time for optimism, Scientific Activities situation regarding further buil- even though a student revolution Already during the first couple of dings in the biology complex was had shaken both the world and the years, research at the Department discouraging. University, resulting in a new kind was faring well. It was concentrated In connection with the general of governing body. A newly drawn on three main fields: Regulation of building fever, the University’s buil- up plan for the next building in the RNA synthesis in bacteria; control ding programme included a new ad- mechanisms for protein synthesis in dition to the Chemistry Department Biology complex was completed in eukaryotic cells; the amino acid se- on the allotments on the other side the summer of 1970 and the biology quence of prothrombin. The money of Langelandsgade. The Ministry of expansion prognosis for 1975 cal- for buying apparatus was included Education had acquired this land in led for a scientific staff of 17 Profes- in the money given for the building, 1968 and the Building Inspector for sorships, 17 Departmental Heads, 60 while the scientific positions that the locality had a drawn-up plan for Associate Professors, 8 Guest Profes- were earmarked for the Department Chemistry II already in the sum- sors and 70 Post Graduates as well allowed us not only to appoint Da- mer of 1971. In the spring of 1972, as buildings amounting to 31,000 nish researchers but also to invite the Faculty saw the possibility of square meters and an annual uptake foreign guests. In the summer of creating the necessary space for Bio- of 150 students. 1970, Professor Eugene Goldwasser logy by moving the Department for from the University of Chicago was Molecular Biology to Chemistry II. invited to hold a series of lectures This building should house teaching on cell differentiation, while in 1971 facilities as well as a the Group of Professor Masayasu Nomura from Biostructural Chemistry, which was the University of Wisconsin came to to be established at the Chemistry the Department as Guest Professor. Department. At the same time our international The Department’s acceptance of contacts were strengthened when the Faculty´s plan raised a storm of we organized the first Linderstroem- unforeseen problems. The other Lang conference on “Informational Biology Institutes protested strongly Structures” in August 1971 as well as against moving Molecular Biology two EMBO courses and symposia on from the planned complex. Even the “Mammalian Protein Synthesis” in Department for Genetics was against June 1972 and 1973. this plan. The good relations that existed between the Rector and some Problems build up Biologists meant that on several oc- The boundless optimism for expan- casions the Rector would override sion that had marked the Depart- the Faculty’s decisions. The demo- ment’s inauguration could not con- cratic conflict between the Faculty’s tinue. At the beginning of the 1970s majority and individual Biologists grants for staff positions and buil- resulted in the Rector cancelling the dings were no longer plentiful. planned building of Chemistry II Biology II had been planned and and sacrificing the relatively huge in- Staffan Magnusson employed as Head of the project went ahead more or less vestment in the project. This created Division for Protein Chemistry in 1970 according to plan but the financial a very tense atmosphere that also

Department of Molecular Biology 5 caused a reduction in the amount of to Gustav Wieds Vej. Later, in 1992, pace. On the other hand, the Depart- space allotted to Molecular Biology one of the protein groups under the ment suffered a severe loss on the in Biology II. leadership of Torben Ellebæk Peter- death of Staffan Magnusson in 1990, Under the heated conflict, the ar- sen, also moved, supported by the and filling this vacancy is proving a chitect C.F. Moeller submitted a very food technology programme FØ- long drawn out affair. The optimi- optimistic time plan of under two TEK. These moves have naturally stic goal for the expansion of Biology, years for the completion of the Bio- served to ease the space problem for from 1975, is still along way from logy III building, though there was the Department but at the same time fulfilment. still a lack of funds and no teaching they have resulted in thinning out of Although until now I have named facilities for 2nd-part students of the research potential in the original only the scientific staff, it does not Biology. Therefore, in 1973, Copen- Department and a change in the re- mean that the allocation of technical hagen University confirmed that search environment. and administrative personnel was Aarhus students could continue in Therefore, on the occasion of the more generous. This has followed Copenhagen until 1975. Over the 25th anniversary of the founding of the same pattern with the desired entrance to Biology III, which houses the Department it must be a big wish number far from the reality. the teaching localities, is written that the old plans for the construc- “Built in the years 1977-1979”! tion of a new research and teaching The Department’s research and The move to Biology II took place building will soon be fulfilled. research funding in the spring of 1974. The Depart- Despite limited space and despite ment had its first graduate in 1973 Scientific staff much needed extra positions, the and its first PhD was given in 1974, Within the faculties that were Department’s research has fully and gradually all studies could be ta- created after 1972 there was a wish lived up to expectations and has at- ken in Aarhus. From about 1983, the to set up larger Department admini- tained much world recognition. For Department’s graduate production strative units. This led to the De- example, it is worth mentioning that reached a relatively constant level. partment of Plant Physiology amal- in 1973 the NOVO prize was given to gamating with the Department for Recent times Molecular Biology in the spring of Kjeld Marcker and in 1984 to Staffan Economic problems put a brake on 1976. Professor Poul Larsen died in Magnusson. the planned further expansion of the summer of 1976 and in keeping While the Department was being Biology though we still had time to with the desire to restrict spending, established, it was taken for granted dream. Biology IV, that also appea- this professorship was lost and that the financing of the University’s red in the overall building plans and has never been replaced. In 1983, a departments would also cover the had already had its own building group from the then Department for cost of research. However, during committee, is now a twenty-year old Genetics and Ecology moved across the recession, the funding from the dream that remains unfulfilled. to the Department for Molecular Bio- University was unable to keep up It was first when the Science Park logy. Even though, on paper, staff with demand and it became more was built that in 1991 with a contri- numbers were growing and the De- and more necessary to look for ex- bution from the Bioregulatory Re- partment gained new research fields, ternal funding. In the beginning of search Centre that it became possi- there was no dramatic change for the 1970s the funding system was ble to ease the rapidly accumulating Molecular Biology. gradually changed to what was cal- space problems in Biology I and II. A recruiting plan for research has Kjeld Marcker’s group was able to over the years brought the Depart- led a two-stringed system consisting secure satisfactory space by moving ment new staff positions at a slow of University and Research Council. 6 www.mb.au.dk While it has become more expensive ten. Originally it was The National MBI’s 25th Anniversary - 5 June 1993 to carry out research, the continuing Institutes of Health that provided financial depletion of the Universi- important support for protein che- ties and the increased demand from mistry research. Later, several of the the Research Council has meant that Institute´s research groups have ta- the two-stringed system has gra- ken part in a number of EU-research dually become multi-stringed – con- programmes. sisting of project grants as well as Dean Karl Pedersen Niels Ole Kjeldgaard private and international funding. Rector Henning Lehmann Funding requirements have natu- 25 years of Molecular Biology rally meant that researchers must In 1972, the first recombinant DNA take into consideration the research molecules were constructed at Stan- topics that are currently popular and ford University in California, and in 1973 a foreign DNA fragment was this has a tendency towards unifor- inserted in a plasmid and then trans- mity. The special project grants have ferred to Eschericia coli bacteria. become necessary for the continued These trials and the rapid techno- existence of the Department’s re- logical development in Molecular search. The Biotechnology Program- Biology that has occurred over the me of 1987-1990 supported many of past 20 years have had profound the Department’s groups after the consequences for the Department of establishment of the Bioregulatory Molecular Biology, not only that la- Research Centre just as the Biotech- boratory personnel must now wear nology Centre for Plants had. In ag- yellow lab coats to make believe that reement with the central administra- the work is dangerous. tion’s implicit belief that change also Some traditional researchers beli- improves the possibilities for good eve that Molecular Biology is a thing scientific collaboration, the earlier of the past, but the development that Centres, after a 5-year period, were started in the late 1970s has clearly replaced by the Centre for Human shown the importance of having de- Gene Research, the Centre for Bio- tailed knowledge of the cell’s mole- membrane Research, and the Centre cular mechanisms. for Plant Biotechnology, The Department for Molecular Special programmes for MD Biology has at all times been in the Foods and FØTEK have given impor- forefront of progress here in Den- tant general contributions to the fun- mark. The Department’s scientific production and the large number of ding of the Department’s research. graduates, post-graduates and PhDs Similarly, private funds, especially that have passed through have, to a The Cancer Society and The Carls- high degree, influenced the develop- berg Fund have given important ment of Molecular Biology in Den- contributions in the form of research mark, and have without doubt, reac- funding and stipends. Finally, inter- hed the goal that was set 25 national research must not be forgot- years ago.

Department of Molecular Biology 7 The past 15 years of the tal to Skejby in 10 years will be the only potential possibility to get one Department of Molecular address in the foreseeable future. Biology (MBI): However, during the recent years the A department on the move MBI has acquired some more space: a whole floor from Geology at Cam- by Erik Østergaard Jensen pus, a building from the Cancer So- ciety at the Science Park and a whole MBI at different locations floor at the Science Park. However, a The merger between the Biostructu- very recent investigation of the space ral Chemistry Group and the MBI distribution at the Faculty of Science in 1996 is one of the most important clearly demonstrated an urgent need events in the recent history of the De- for more space at the MBI, a conclu- MBI - Campus Unit partment. Brian F.C. Clark founded sion the research groups at the MBI the Biostructural Chemistry group have known for years. A take-over in 1974, and his group’s research has of the remaining part of the Science mistry Group and two additional Park by the Faculty of Science will be over the years been closely related to groups from the the MBI University the activities at the MBI with a strong the most obvious immediate solution Campus. Thus since 1996, the MBI to solve part of this problem. focus on the structural aspects of has been divided physically into two macromolecules. Three new wings equally sized units, the University were added to the Science Park in Campus unit with focus on molecu- 1996 hosting the Biostructural Che- lar biology and the Science Park unit with focus on proteins and plants. The structural biological research has now become an important and integrated part of many of the ongoing research projects at the MBI and is an example of a successful merger. Ever since the housing of the MBI’s research groups in different locati- Science Park - Pavilion 3 ons, it has been our dream to get one house for all MBI’s activities including the related study programmes. However, the successful expansion of the activities at the MBI has made the fulfilment of this dream almost impossible since the space available either at the Science Park or at Campus is not sufficient to house the more than 400 staff and students MBI - Science Park Unit working at the MBI. To be realistic, the move of the University Hospi- Science Park - Pavilion 12

8 www.mb.au.dk Several new study programmes Medicine. Several of our established is to keep the high standards with The Department has contributed to courses were remodelled to provide an increasing number of students the education of molecular biology the most relevant background for and to optimize all the new study students from the very beginning; the new study programme, and new programmes. however until recently the students courses were established. The study The number of PhD students has were enrolled either as biology or programme was offered for the first increased from 50 in 2000 to more chemistry students. In 2002 the De- time in 2007, and we got many more than 80 in 2008. More attention has partment became the master of its applications than the set limit of 60 been paid to the education of PhD own house by the introduction of a students. students over the recent years. Every new bachelor programme in mole- Very recently the MBI has contri- student is now associated with a cular biology with several different buted significantly to the establish- small committee of external and in- flavours, the human biology being ment of an MSc study programme ternal advisors that regularly gives the most popular. A total of 37 stu- in Molecular Nutrition and Food feed-back on their project. An ho- dents were enrolled in the molecular Technology, a study programme of- nours’ programme has been initiated biology study programme in 2003. fered by the Faculty of Agricultural to recruit highly qualified bachelor A recent initiative taken by the Sciences. students who can subsequently be Faculty of Science, the Engineering The recent years have been very enrolled as Phd students. College of Aarhus and the County busy setting up new study program- of Aarhus resulted in the establish- mes and courses with several diffe- Strong research groups at the MBI ment of the Aarhus Graduate School rent external partners – in 2007 we The tenured scientific staff has incre- of Engineering. The MBI decided to accepted 165 students in our three ased from 28 to 34 over the past 13 join the initiative and agreed to offer study programmes. Thus within a years (17 new appointments and 11 a technical bachelor in Biotechno- very short period of time, the MBI retirements). The appointed asso- logy in 2006 and a Master of Science has increased the production of stu- ciate and full professors have prima- in Engineering in process techno- dent study years from 180 in 2000 to rily consolidated and expanded the logy to be launched in 2009. A group 364 in 2007, the highest number at the established research fields. Howe- of teachers from the MBI took on the Faculty of Science! And we have only ver, one exception is the recruitment responsibility to develop the new seen the tip of the iceberg due to the of a professor in biotechnology to study programme, and in collabora- large number of new study program- support the new engineering stu- tion with the Engineering College of mes. The big challenge for the future dy programme. None of the four Aarhus, we could welcome 22 engi- founders of molecular biology and neering students in 2006. structural chemistry are employed at In 2005, the University announ- the Department any longer. Staffan ced Molecular Medicine to be a focus Magnusson died in 1990, Niels Ole area. A major part of the research at Kjeldgaard retired in 1994 and died the MBI is within the scope of mo- in 2006, Kjeld Marcker retired in lecular medicine. The MBI therefore 2002 and Brian F.C. Clark retired in decided to be an important player in 2007, but is still associated with the this initiative, and in collaboration Department. Another very important with the Faculty of Health Sciences, The MBI seminar programme with pro- person for the Department, Jens Ny- we established a bachelor and a ma- minent speakers including several Nobel borg, died in 2005. We all owe them a ster study programme in Molecular Prize Laureates is part of the study plan lot for what they started.

Department of Molecular Biology 9 The Department is presently di- Infrastructure vided into the following research On the administrative side we have fields: DNA Processing, RNA & been challenged by a new accounting Viruses, Cellular Signalling & De- system, a database to register pub- velopment, Plant Molecular Biology, lications and activities, and latest Structural Biology, Protein Function, an electronic calendar. However, Protein Interactions, and Molecu- after some years of running-in, the lar Nutrition. However, numerous benefits are now becoming evident, collaborative projects exist between and no doubt professional computer these research fields. The profiling of systems are required to manage the the Department towards the univer- The new iNano buildingbuilding increasing number of students, staff sity has been difficult, illustrated by and funding. the fact that until 2003, no professors ficulties in attracting venture capital, In 2003 the Danish Parliament had been appointed at the MBI ex- and thus only Cobento exists today. passed a new law concerning the cept for the founders. However, this The MBI is also one of the more ac- management of the universities. As has changed over the past five years tive Departments when it comes to a consequence, the Head of Depart- where seven professors have been invention disclosures, last year being ment was appointed by the Dean in appointed. The national awareness involved in 1/5 of all disclosures at 2004 and not as previously elected of the research at the MBI has also the University by the scientific staff. Another con- increased dramatically over the past External funding is the basis for sequence was a replacement of the few years. The research at the MBI all research at the MBI, and for the Departmental board with a Depart- has always been of high standards, past 15 years external funding has mental Council advising the Head of but for a period some 5-10 years ago, increased from 25 M DKK to 73 M Department. we had strong competition from DKK. Thus, as a whole the Depart- other universities in Denmark. The ment is doing excellently, but the fi- present state of our high research gures also hide large differences bet- quality is well illustrated by the fact ween the individual research groups. that the MBI is heading three Centres The national and international com- The past 15 years can best described of Excellence by the Danish National petition have become much more Research Foundation and is major tough, and even groups with a solid as the period where molecular bio- partners in two other Centres of Ex- publication record can have problems logy has become an integrated part cellence out of a total of 38 national in attracting money for their research of many different disciplines rather centres. and education of Master and PhD than being a specialized topic. At the The establishment of the iNA- students. This might have the conse- Department we have experienced a NO Centre at the Faculty of Science quence that some research program- successful generation shift, taking in 2002 has resulted in new - more mes must be terminated and new the best of - but not limited by - the technology-driven - research direc- have to be developed in areas with traditions at the MBI. There is a pro- tions at the MBI. The MBI has also better funding. On a small scale this fostered several spin-off companies is probably healthy, but we also face nouced collaborative spirit at our De- during the past 15 years like Borean the risk that some - less trendy pro- partment and this augers well for our Pharma, Cobento and Plantic; howe- jects - will die even if they scientifi- future when facing the increasing in- ver the survival rate is low due to dif- cally are potentially very interesting. ternational and national competition.

10 www.mb.au.dk Plant Molecular Biology

Professor Jens Stougaard Identification of a new class of LysM lipochitin- Associate Professor Bjarne Jochimsen oligosaccharide receptors in the rhizobium- legume interaction coupled with the ability to Our research in plant molecular biology focu- manipulate both the ligand and the individual ses on cellular mechanisms controlling organ domains of the receptor experimentally has ope- development, cellular communication systems ned new opportunities for functional analysis and mineral nutrition in the model plants Lotus of polysaccharide receptors. LysM domains are japonicus and Arabidopsis thaliana. For compara- widespread and appear to possess an unusual tive studies of regulatory and signal transduc- flexibility in ligand-binding specificity combined tion mechanisms, zebrafish has also been inclu- with a possible multi-domain mode of ligand ded among the experimental organisms. The binding. Structural and functional characte- research activities is embedded in the Centre risation of human, zebrafish and plant LysM for Carbohydrate Recognition and Signalling domains, their ligand-binding properties and (CARB) funded as a Centre of Excellence by the their mechanisms for converting recognition into signalling and cellular responses, is therefore of Danish National Research Foundation. CARB broad scientific interest and a central theme in includes collaborators at University of Otago, the Centre’s activities. Effective plant and bacte- Leiden University and University of Copenha- rial genetic methods are used to identify compo- gen and this international team applies interdi- nents recognising exo- and lipopolysaccharides sciplinary approaches such as molecular gene- exposed on cell surfaces. Cell response mecha- tics, biochemistry, crystallography, carbohydrate nisms related to plant hormone signalling and chemistry, nanobioscience and bioinformatics to control of the cell cycle is integrated into these investigate cellular processes from the level of cell-to-cell signalling studies. The interaction bet- molecules to the level of living organisms. ween cell cycle activation and cell differentiation The CARB Centre aims to understand interac- is of particular interest for understanding de- tions between cells and organisms by investi- velopment and cancer. Combining an assortment gating the role of carbohydrates exposed on of genome information and technologies availa- cell surfaces, and polysaccharide signal mole- ble in the model organisms, the aim is to take the cules secreted as part of a complex interaction analysis of signalling processes in multicellular between organisms. Characterisation of such organisms to a new level, distinguishing events cellular communication systems is important for in tissues, cells and nuclei and to establish an understanding factors determining pathogenesis understanding of fundamental life-processes in of microorganisms as well as immune responses, animals, humans and plants. symbiosis and cell-to-cell signalling involved in Adding colour and flavour to the activi- the development and functioning of multicellu- ties food related processes in seed development lar organisms. and plant uptake and deposition of iron are

Department of Molecular Biology 11 also investigated. A diverse set of physiological Tirichine L., Imaizumi-Anraku H., Yoshida S., Mura- methods, proteomics and genetics is used in kami Y., Madsen L.H., Miwa H., Nakagawa T., Sandal these studies aimed at improving the nutritional N., Albrektsen A., Kawaguchi M., Downie A., Sato quality of seeds and improving the content of S., Tabata S., Kouchi H.,Parniske M., Kawasaki S. and available iron and other minerals in plants. The Stougaard J. (2006) Deregulation of a Ca2+/calmodu- natural diversity in legumes like the model plant lin-dependent kinase leads to spontaneous nodule Lotus japonicus and common bean is one of the development. Nature 441, 1153-1156. sources investigated in an attempt to contribute towards breeding of better plants for food and Tirichine, L., Sandal, N., Madsen, L.H., Radutoiu, S., feed. Albrektsen, A., Sato, S., Asamizu, E., Tabata, S. and Radutoiu, S., Madsen, L.H, Madsen, E.B, Felle, H., Stougaard J. (2007) A gain of function mutation in a Umehara, Y., Grønlund, M., Kaneko, T., Sato, S., cytokinin receptor triggers spontaneous root nodule Tabata, S., Sandal N. and Stougaard, J. (2003) Plant organogenesis. Science 315, 104-107. recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature 425, 585-592. Radutoiu S., Madsen L.H, Esben Madsen B., Jur- Madsen, E.B., Madsen, L.H., Radutoiu, S., Olbryt, M., kiewicz A., Fukai E., Quistgaard EMH, Albrektsen Rakwalska, M., Szczyglowski, K., Kaneko, T., Sato, A.S., James E.K, Thirup S., and Stougaard J (2007. S., Tabata, S., Sandal, N. and Stougaard, J. (2003) A LysM domains mediate lipochitin-oligosaccharide receptor-like kinase gene involved in legume per- recognition and Nfr genes extend the symbiotic host ception of rhizobial signal molecules. Nature, 425, range. EMBO J 26, 3923- 3935. 637-640.

12 www.mb.au.dk Protein function

Professor Claus Oxvig Proteolytic regulation Associate Professor Peter Andreasen Approximately 2% of human genes encode Associate Professor Kim Kusk Mortensen proteolytic enzymes. The regulation by specific Associate Professor Lars Sottrup-Jensen proteolytic cleavage is common in biological Associate Professor Hans Chr. Thøgersen systems, emphasizing its importance. We have Associate Professor Hans Uffe Sperling-Petersen a longstanding interest in biological systems that function to regulate e.g. cellular growth Our current research programs focus on bio- and homeostasis, mainly systems that are rele- logical systems regulated by proteolysis, all vant in human reproduction and cardiovascular relevant to human physiology. We study fun- function, but also human disease such as cancer damental biochemical problems, but whenever and arteriosclerosis. Our general experimental possible, we make connections between basic strategy is 1) to connect knowledge of protein biochemistry and human disease. Protein design structure with biochemical function, 2) to ana- and combinatorial protein biochemistry is our lyze such function in cell-based model systems, second major research focus. We generate e.g. and 3) to explore its physiological role in animal monoclonal antibodies, useful in the develop- models. We seek to connect basic knowledge ment of diagnostic methods and novel therapeu- with human disease in order to understand pat- tic approaches. hological mechanisms, or to develop novel methods of diagnosis or novel therapeutic strategies. The problems we try to solve are approached Our research lies mainly within three biological experimentally using a wide variety of mo- systems: The insulin-like growth factor system dern biochemical methods. The area of exper- (CO), the plasminogen activator system (PA), tise covered by members of our laboratories is and the complement system (LSJ). broad, ranging from classical protein chemistry and biophysical analysis to modern techniques • The insulin-like growth factors (IGFs) are po- of molecular and cellular biology. Recently, we lypeptides with effects on cell proliferation and have implemented the zebrafish as a vertebrate differentiation. The IGFs bind to the IGF recep- model system of human physiology. We are tor, but six homologous binding proteins, IGF- actively engaged in national and international BP-1 to -6, have higher affinities for the IGFs and collaborative projects with other laboratories. therefore inhibit receptor stimulation. However, bioactive IGF can be released by specific proteolytic cleavage of the IGFBPs. By this mecha- Zebrafish nism, the metalloproteinase PAPP-A controls the activity of IGF in many normal tissues, and also

Department of Molecular Biology 13 in cardiovascular disease and cancer. We study sion; plasminogen activators in milk; uPA and how this system functions at the cell surface, and PAI-1 as prognostic markers in cancers; PAI-1 we are interested in several associated extra- inhibitory mechanism; molecular mechanisms cellular regulatory mechanisms. Knowledge of of endocytosis of serine protease-serpin comple- such principles can be used in the development xes; PAI-1 as a regulator of cell migration; PAI-1 of novel diagnostic methods and drugs. For expressing cell types in tumours; PAI-1 and uPA example, the direct inhibition of IGF signaling is inactivators. During its time in the department, a novel therapeutic strategy in cancer treatment. the group has published exactly 100 papers However, specific inhibition of growth promo- which have been quoted more than 5,500 times. ting proteolytic activity, i.e. inhibition of PAPP- A, represents a valuable alternative, in particular • The complement system is part of the effector because unintended interference with other branch of the immune system. Upon comple- signaling pathways, e.g. insulin signaling, is ment activation, targets such as invading micro- avoided by such approach. We therefore develop organisms become destined to destruction and inhibitors of PAPP-A as prototype protein drugs elimination. The system consists of more than to provide proof-of-concept in animal models 30 plasma and membrane proteins, several of (zebrafish and mouse) of human disease. which are proteinases or substrates. We are prin- cipally interested in understanding the relations- • Plasmin is an extracellular serine protease hip between structure and function of comple- which is able to degrade many extracellular ment proteins. Recently, we have contributed to proteins. Plasmin is important in turn-over of the determination of high resolution structures extracellular matrix. Plasmin is generated by of entire complement proteins. proteolytic activation of the ubiquitous zymogen plasminogen. The activation can be catalysed Protein design by either of two serine proteases. Tissue-type The primary aims of our protein engineering & plasminogen activator (tPA) catalyses plasmino- design efforts are 1) to provide tools for bio- gen activation in blood, whereas urokinase-type chemical analysis of protein synthesis (KKM, plasminogen activator (uPA) catalyses plasmino- HUSP), and 2) to develop tools for protein pro- gen activation in tissues. Plasmin as well as the duction and the utilization of recombinant prote- plasminogen activators are regulated by specific ins (HCT). As a blueprint in our engineering ef- proteinaceous inhibitors, i.e., alpha2-antiplasmin forts, we seek inspiration in the many cases were and plasminogen activator inhibitor-1 (PAI-1). established structural (and functional) protein uPA-catalysed plasminogen activation is par- modules are used repeatedly in the evolution of ticularly interesting in relation to invasive complex multifunctional proteins. growth and metastasis by malignant tumours. The group was established in Aarhus in 1989. • Many protein factors are involved in the pro- The main contributions have been in studies cess of translation in prokaryotes. The initiation of transcriptional regulation of PAI-1 expres- process involves mRNA, the ribosomal subunits,

14 www.mb.au.dk three initiation factors, IF1, IF2, and IF3, and are at the cutting edge worldwide. Other projects fMet-tRNAfMet. Although the three-dimensi- in the laboratory are focusing on design, produ- onal structures of most of the components are ction and characterization of designed enzymes known at the atomic level, many aspects of the and self-assembling protein structures. initiation process are still to be understood. We try to understand biochemical and structural • Early research in sequence-specific proteolysis details by means of several approaches. One (in blood coagulation) led to Factor Xa being re- approach involves the generation of antibo- cognized as the first usable tool for efficient clea- dies – mono- and polyclonal as well as phage vage of fusion proteins, and more recently even displayed single chain antibodies – against the more efficient proteases have been developed for initiation factors. Recently, we have also con- this purpose. Structural studies of other mosaic tributed with structural data using both NMR proteins (e.g. tetranectin) provided a starting and SAXS. Additionally, we exploit the process point for devising numerous new hybrid prote- of protein synthesis in our continuous effort to ins, multimerised, or armed with tetranectin-de- develop more efficient vectors for heterologous rived binding modules with new binding pro- expression in E. coli, a scientific field, where we perties rivaling those of antibodies in terms of

Figure Zebrafish embryo, 36 hours post fertilization. Development of the fertilized egg can be observed directly and progresses fast – segmentation begins at 10h and following 24h, the heart is beating. The zebrafish has many other advantages which makes is an attractive model organism in e.g. developmental studies and drug development.

Department of Molecular Biology 15 specificity and affinity. Most of this exploitation Hansen, M, Wind, T, Blouse, GE, Christensen, A, research was carried out in a spin-out company Petersen, HH, Kjelgaard, S, Mathiasen, L, Holtet, (Borean A/S), which eventually was sold off in TL, Andreasen, PA (2005) A urokinase-type plas- bits, bringing in revenues in excess of 250 mil- minogen activator-inhibiting cyclic peptide with lion Danish kroner in toto. Future research will an unusual P2 residue and an extended protease seek to explore further ways of constructing new binding surface demonstrates new modalities for enhanced affinity tag / ligand systems that will enzyme inhibition. J. Biol. Chem. 280, 38424-37. further enhance the utility of the toolkit available Mikkelsen JH, Gyrup C, Kristensen P, Overga- to anyone with a need to manipulate recom- ard MT, Poulsen CB, Laursen LS, Oxvig C (2008) binant protein products in research or for any Selective inhibition of the proteolytic activity of other purpose. pregnancy-associated plasma protein-A by targeting substrate exosite binding. J. Biol. Chem., Fynbo CH, Lorentsen RH, Etzerodt M, Thøger- 283, 16772-80. sen HC, Holtet TL (2005) Characterization of a recombinant granzyme B derivative as a ”restric- Rasmussen LC, Oliveira CL, Jensen JM, Pedersen tion” protease. Protein Expr. Purif. 39, 209-18. JS, Sperling-Petersen HU, Mortensen KK (2008) Solution structure of C-terminal Escherichia coli Fredslund F, Jenner L, Husted LB, Nyborg J, translation initiation factor IF2 by small-angle Andersen GR, Sottrup-Jensen L (2006) The struc- X-ray scattering. Biochemistry 47, 5590-8. ture of bovine complement component 3 reveals the basis for thioester function. J. Mol. Biol. 361, 115-27.

16 www.mb.au.dk Cellular signalling and development

Associate Professor Ernst-Martin Füchtbauer mutated tumor suppressor genes and development of Associate Professor Just Justesen stem cell therapy in muscular dystrophy. Associate Professor Pia Møller Martensen Associate Professor Lene Pedersen The Protein Synthesis and Interferon Signalling Associate Professor Thomas Schmitt-John group (Just Justesen) is interested in interferon stimulated genes that are involved in regulation of Development and maintenance of multicellular orga- translation in protein synthesis. The 2-5A synthetases nisms requires a coordinate communication between are coded by the OAS genes. 2-5A synthetases make cells. This communication secures that cells behave 2’-5’ linked oligonucleotides that in turn activate appropriate according to their position in the body RNase L, which then acts on RNA, in particular of and maintain proper homeostasis. Disturbance of this viral origin, but also ribosomal RNA. The significance communication may result in aberrant differentiation, of having a number of OAS variants is studied by malformation, tumor development or cellular dege- looking at enzymatic properties and at how the OAS neration. Extracellular signalling molecules such as family has evolved from simple animals like marine interferons and inorganic phosphate activate cascades sponges, sea squirt, mussels and snails. Furthermore, of intracellular signal transduction pathways thus tryptophanyl tRNA synthetase (coded by WARS), regulating gene expression and thereby controlling which is strongly induced by immune interferon processes like growth, differentiation and/or anti- (gamma) is also investigated. Splice variants of WARS viral and immunological reactions. Intracellular traf- may play a role as an inhibitor of angiogenesis. It is ficking is equally important in these processes and for clear that the amino terminus of the human WARS is viral infection. Our groups are covering topics within associated with the interferon system whereas the ca- the fields of development and cell signalling, intra- nonical ligase activity resides in the carboxyterminus, cellular trafficking and virus-cell interactions through which is strongly conserved through evolution from a number of research projects. prokaryotes to eukaryotes.

The Molecular Embryology group (Ernst-Martin The Apoptosis and Interferon Signalling group Füchtbauer) is interested in the genetic regulation of (Pia Møller Martensen) is interested in the apoptotic embryonic development and cellular differentiation. properties and regulation of the ISG12 family of small The function of genes is investigated by mutatio- membrane proteins up-regulated by type 1 interferon. nal analysis in which the consequences of different This family of mitochondrial BH3-like proteins are mutations are investigated. The group has ample novel key players in the apoptotic pathway induced experience in different methods to generate gene- by interferon. Insights into the apoptotic pathways tically modified mice and therefore offers, within initiated by ISG12 proteins are based on putative int- the framework of the ’Danish Center for Transgenic eractions partners in the cell. Up-regulation of one of Mice’, collaboration possibilities to other researchers the ISG12 genes has been detected during pregnancy, interested in using these techniques. Organ develop- in several cancer types as well as in psoriasis. Endo- ment and cellular differentiation are complex proces- metriosis is a painful gynaecological disease defined ses which are related to many diseases. The research as the implantation of endometrium-like cells out- projects of the group cover many techniques like side their normal location in the uterus. Due to their histological and molecular analysis of murine em- regulation and apoptotic properties, the ISG12 family bryos, testing transcription control in tissue culture of proteins might be involved in the development of cells, investigating cancer development in mice with endometriosis. The research projects of this group

Department of Molecular Biology 17 tiation of human vascular smooth muscle cells to an osteoblast-like phenotype. The Pi transporters are receptors for retrovirus, which we exploit in our studies on function and regulation of the transporters. On the virus side, focus is on receptor and co-receptor interactions of retroviruses infecting human cells and on identification of entry routes and vesicle trafficking used by retroviruses and HIV-1 to infect cells and cross cellular barriers.

The Neurogenetics group (Tho- mas Schmitt-John) is interested in the genetic, biochemical- and cellular basis of neurodegenerative diseases of the neuromuscular system. Recently we identified a novel disease gene responsible for motor neuron degeneration in a mouse model for human motor neuron diseases. This gene encodes a vesicle traffic factor and thus, the intracellular vesicle traffic appears to play a critical role in motor neuron degeneration. Our group investigates the intracellular vesicle traffic in the context of neurodegeneration as well as disease associated gene regulation, using genetic, biochemical and cell biological techniques in vitro, in cover mammalian cell culture and in cellular signalling and normal mammalian cell culture, and in ge- baculovirus expression combi- and pathologic cellular processes, netically modified mice. Further- ned with molecular analyses of stem cells in cell therapy, and the more, the research projects of the proteins, RNA and DNA as well as interplay between retrovirus and Neurogenetics group comprise the analysis of tissue samples. their host cells with focus on cell analysis of murine spermatogene- entry and gene delivery/therapy. A sis defect, resembling the human Laboratory of Interdiciplinary recent interest is on the roles of Pi globozoospermia, a male infertili- Research (Lene Pedersen) is and Pi transporters in osteoblastic ty syndrome. The molecular cause interested in the role of inorga- differentiation of mesenchymal of this spermatogenesis defect is nic phosphate (Pi) and type III stem and preosteoblastic cells as also associated with factors of the sodium-dependent Pi transporters well as in the pathologic differen- retrograde vesicle traffic.

18 www.mb.au.dk DNA processing

Associate Professor Anni H. Andersen Common for all topoisomerases is that they relax Associate Professor Tinna V. Stevnsner supercoiled DNA by introducing transient breaks in Associate Professor Birgitta R. Knudsen the DNA double helix. Based on their mechanism of action they can be divided into two types, the type DNA topoisomerases I enzymes, which introduce single-stranded breaks The double helical nature of DNA leads to a number and the type II enzymes, which cleave both strands of topological problems in the form of under- or over- of the DNA helix. In our group, we are focusing on winding of the DNA helix, i.e. negative or positive the mechanistic and biological functions of both type I and II topoisomerases. By combining specialized supercoiling, whenever the DNA strands are sepa- in vitro methods and macromolecular visualization rated to expose the genetic code e.g. during replica- techniques (SAXS, Cryo-TEM and AFM) with in vivo tion and transcription (see Fig. 1). If such problems model systems in yeast S. cerevisiae or mammalian cell remain unsolved, the DNA metabolic processes of lines we have gained a detailed understanding of the the cell will stop and the cell will consequently die. multiple functions of the topoisomerases. It is therefore not surprising that all living organisms Some of our ongoing projects focus on the functions contain enzymes, the DNA topoisomerases, which of topoisomerases in DNA replication, transcription are specialized in regulating the DNA topology and, and post-transcriptional gene regulation. To study hence, are essential for the survival of all cells. In ad- the topoisomerase function in DNA replication we dition to the important biological functions of these are using yeast as a model to monitor replication in cells lacking the endogenous topoisomerase I and/ enzymes, the topoisomerases are the cellular targets or topoisomerase II gene. The replication process in for important anti-cancer chemotherapeutica, which these cells is analyzed by chromatin immunoprecipi- is why they are of great clinical interest. tation, qPCR, 2D gel-electrophoresis, FACS-analysis. Also, potential DNA damage caused by replication fork stalling is investigated. The functions of DNA topoisomerases in transcription and transcriptional regulation have been investigated by use of the microarray technology. We have examined global genome expression in cells lacking topoisomerase I, topoisomerase II or both enzymes and compared to the expression levels obtained in normal cells. One of the interesting observations in the microarray analysis is that lack of topoisomerase activity specifically affects genes which are located close to areas in the genome that are attached to the nuclear membrane and the nuclear pore complex. More detailed studies of the implications of this attachment for the effect of DNA topology on gene expression are now in progress. Figur 1. Exposition of the genetic code contained in DNA The functions of topoisomerase I in post-transcrip- leads to the accumulation of positive supercoils in front of, and tional gene regulation have been investigated in negative supercoils behind the polymerase. The supercoiling terms of its effect on pre-mRNA splicing. Previous needs to be removed by a DNA topoisomerase to allow com- studies have shown that topoisomerase I, in addi- pletion of the polymerase extension. tion to DNA relaxation, catalyzes SR-protein specific

Department of Molecular Biology 19 phosphorylation, whereby it may affect pre-mRNA Using different molecular biological techniques, splicing. To test this hypothesis we have compared including immuno-staining, immuno-precipitation, the splicing pattern in human cells as a function to repair activity assays and array-studies we are inve- topoisomerase I activity using splice-specific microar- stigating, how DNA repair mechanisms are regulated rays. These investigations have shown that the splice and altered by age. In particular, we are focusing on pattern of important cancer relevant transcripts such processes in different part of the brain and its synap- as p53 and BRCA1 are altered upon down regulation ses, which are essential for inter-neuron communica- of topoisomerase I expression. Presently, the exact tion. As model systems we are using premature aging function of topoisomerase I in p53 and BRCA1 spli- syndromes, as these are well suited for the investiga- cing is addressed in specialized assays. tions of aging related processes.

The Molecular Biology of Aging - Andersen, FF, Knudsen, B, Frøhlich, RF, Krüger, D, Bun- Statistically, old age is associated with at marked in- gert, J, Agbandje-McKenna, M, McKenna, R, Juul, S, Koch, crease in a number of diseases, the so-called age-re- J, Rubinstein, J, Guldbrandtsen, B, Hede, MS, Karlsson, G, lated diseases. These include cancer, diabetes, cardio- Andersen, AH, Knudsen, BR (2008) Assembly and struc- vascular diseases and neurodegenerative diseases. tural analysis of a covalently closed nano-scale DNA cage. Nucleic Acids Res. 36, 1113-9. The molecular biological causes for aging are as yet - Frøhlich, RF, Veigaard, C, Andersen, FF, McClenton, unknown but several theories have been put forward AK, Gentry, AC, Andersen, AH, Osheroff, N, Stevnsner, T, to explain the phenomenon of aging. Knudsen, BR (2007) Tryptophane-205 of human topoisome- One of these theories involves certain cellular rase I is essential for camptothecin inhibition of negative organelles – the mitochondria. The last steps of the but not positive supercoil removal. Nucleic Acids Res. 35, cellular energy production are performed in the mito- 6170-80. chondria via oxidative phosphorylation. As a conse- - Oestergaard VH, Giangiacomo L, Bjergbaek L, Knudsen quence of this process, highly reactive by-products BR, Andersen AH. Hindering the strand passage reaction the so-called free radicals are formed. Free radicals of human topoisomerase IIalpha without disturbing DNA cleavage, ATP hydrolysis, or the operation of the N-termi- may damage the DNA of mitochondria, leading to a nal clamp. J Biol Chem. 2004 279, 28093-9. decrease in the essential mitochondria functioning - Oestergaard, VH, Knudsen, BR, Andersen, AH (2004) (see Fig. 2). DNA repair mechanisms, which can re- Dissecting the cell-killing mechanism of the topoisomerase cognize and remove DNA damage, are found both in II-targeting drug ICRF-193. J Biol Chem. 279, 28100-5. the cell nucleus and in the mitochondria. - Weissman, L, de Souza-Pinto, NC, Stevnsner, T, Bohr, VA (2007) DNA repair, mitochondria and neurodegeneration. Neuroscience 145, 1318-1329.

Figure 2. The mitochondrial aging theory. Free radicals are generated as a by-product of the cellular energy production and can cause oxidative stress in the mitochondria. Hereby, macromolecules in the mitochondria may be damaged and their function inhibited. The cell will age and ultimately die. The cellular defense against free radicals are shown as yellow arrows.

20 www.mb.au.dk RNA and virus

Professor Jørgen Kjems trafficking and in vivo delivery. We have also used Professor Finn Skou Pedersen SELEX to select 2’F-modified RNA aptamers that Associate Professor Bjarne Bonvén bind strongly and highly specifically to human onco- Associate Professor Torben Heick Jensen proteins with very high affinity and block processes Associate Professor Poul Jørgensen implicated in formation of metastases. Associate Professor Jan Egebjerg Jensen Professor Finn S. Pedersen’s group work with vari- The laboratory of Associate Professor Torben Heick ous aspects of retrovirus-host interactions. One line Jensen, who is also the director of the Danish Natio- of research concerns the induction of lymphomas and nal Research Foundation ”Centre for mRNP Bioge- leukemias in mice by proviral insertional mutagene- nesis and Metabolism”, investigates effects on gene sis, where we have developed novel mouse models expression occurring at the co- and post-transcripti- of altered disease specificity, identified novel target onal levels. During transcription mRNA is processed genes for multi-step oncogenesis, and investigated by enzymes and packaged with proteins into mRNP how proviral insertion may deregulate such genes. particles. These are the entities undergoing nuclear A second line of research concerns the interaction of export and cytoplasmic translation. Improper mRNP the virus with the host cell during specific steps of formation leads to nuclear retention and subsequent the replication cycle such as for example the produc- nuclear degradation of the mRNA in a process invol- tion and packaging of viral genomes into particles or ving the 3’-5’ exonucleolytic RNA exosome. Using viral entry into target cells. Part of this work exploits both yeast and human cells, the laboratory studies knowledge of viral replication for gene technological the “molecular battle” between productive events of purposes. A third line of research concerns the iden- mRNP formation and destruction by mRNP quality tification of endogenous retroviruses inherent to the control. Lately, these analyses have led to the disco- human genome and analysis of the possible role of very of new degradation pathways as well as a whole those in human physiology. new class of RNAs. Selected References Professor Jørgem Kjems’ group has developed novel Saguez C., Schmid M., Olesen J.R., Ghazy M., Poulsen types of RNA based therapeutics including in vivo M.B., Nasser T., Moore C. and Jensen T.H.: Nuclear stabilized siRNA with decreased off-target effects, mRNA surveillance in THO/sub2 mutants is trig- aptamers and bifunctional RNA oligonucleotides. gered by inefficient polyadenylation. Molecular Cell Using mice as model systems we can deliver siRNAs (2008), 31(1):91-103. to the lung by the means of various nanocarriers Damgaard C.K., Kahns S., Lykke-Andersen S., designs and consequently down regulate cellular and Nielsen A.L., Jensen T.H. and Kjems J.: A 5’ splice viral genes or reach inflamed tissue as a treatment for site enhances the recruitment of basal transcription rheumatoid arthritis. Another active area we are focu- initiation factors in vivo. Molecular Cell (2008) 29(2): sing on is the incorporation of drugs into biodegrada- 271-278. ble polymeric nanoparticles to be use in 3D scaffolds for tissue engineering. The inclusion of cell specific Rougemaille M., Olesen J.R., Thomsen R., Seraphin ligands and “biological triggers” into the nanocar- B., Libri D. and Jensen T.H.: Dissecting mechanisms rier design are used for modulation of cellular drug of mRNA surveillance in THO/sub2 complex mutants. EMBO J. (2007) 26(9): 2317-2326.

Department of Molecular Biology 21 Bramsen, J.B., Lauersen, M.B., Damgaard, C.K., Will- Torarinsson, E., Yao, Z. , Wiklund E.D. , Bramsen, sen, S.L., Wengel, J., and Kjems, J.: Improved silencing J.B. , Hansen, C., Kjems, J., Tommerup, N., Ruzzo, properties of small interfering RNAs with segmented W.L.and Gorodkin, J.: Comparative genomics beyond sense strand. Nucleic Acids Res. 35:5886-97, 2007. sequence based alignments: RNA structures in the ENCODE regions. Genome Res. 18:242-51, 2008. Rahbek, U.L., Howard. K.A., Oupicky, D., Dong,M., Nielsen, A.F., Raarup, M-R., Besenbacher,F. , Kjems, J.: Glud SZ, Sørensen AB, Andrulis M, Wang B, Kondo Intracellular siRNA and precursor miRNA trafficking E, Jessen R, Krenacs L, Stelkovics E, Wabl M, Ser- using Bioresponsive Copolypeptides. J. Gene Med. fling E, Palmetshofer A, Pedersen FS.: A tumor- 10:81-93, 2008. suppressor function for NFATc3 in T-cell lympho- Odadzica, D., Bramsen, J.B., Bus; C., Kjems, J., and magenesis by murine leukemia virus. Blood. Nov Engels, J.W.: Synthesis of 2`-O-modified Adenosine 15;106(10):3546-52, 2005. Building Blocks and application for RNA Interferen- ce. Bioorg. Med. Chem. 16:518-29, 2008. Figure: Processes removing unwanted RNA from the cell

22 www.mb.au.dk Molecular nutrition

Professor Xuebing Xu associated carbohydrates and lipid-related pharma- Associate Professor Torben Ellebæk Petersen ceuticals, with strong consideration of sustainability Associate Professor Esben Skipper Sørensen and environmental impact.

Agro-Biotechnology Science The group’s vision is to conduct and foster interdisci- Agro-Biotechnology Science Group (Xuebing Xu) has plinary research to offer a knowledge foundation for long strong research in enzyme technology and lipid the production of value-enhanced secondary agricul- product/process development. The research involves tural products and food ingredients by means of mo- in enzymatic technology development for functionali- dern biotechnology. The basic objective is to explore sation of traditional fat stuffs as well as tailor-making practical technology that contributes to a sustainable of structured lipids for health and nutrition. Physical growth of agricultural products and food industry in characterization of lipids and products as well as the Danish society, based on high-quality basic and process monitoring technology represents another applied research. focused area. Sustainable enzymology and green solvent technology become a recent focus in research, The group’s research can be highlighted with follo- including pioneering research concerning ionic wing phrases such as (1) Lipid processing and new liquid-mediated enzymatic modification of bulky oils utilization of lipid resource; (2) Industrial biotechno- and fats for ingredients or biofuels processing. The logy for designing lipids; (3) Sustainable enzymology research profile covers model-assisted design of task- and green solvent technology; (4) Quality control and specific ionic liquids, protocol design, separation and characterization of food lipids; (5) Polar lipids and scale-up technology. The new opportunity for value- lipid-associated carbohydrates; (6) Innovative utili- added utilisation of lipids and agricultural products zation of agricultural products; (7) Food nanotechno- from green solvents (SCCO2 and ionic liquids) has logy; (8) Food ingredients and lipid-related pharma- greatly expanded the research into polar lipids, lipid- ceuticals; and (9) biobased products and biofuels.

Guo Z., Lue B.-M, Thomasen K., Meyer A.S. and Xu X. Pre- dictions of flavonoid solubility in ionic liquids by COSMO- RS: experimental verification, structural elucidation, and solvation characterization, Green Chem. 9: 1362-1373 (2007).

Marianne L. Damstrup, Jens Abildskov, Søren Kiil, Anker D. Jensen, Flemming V. Sparsø and Xuebing Xu. Process Development of Continuous Glycerolysis in Immobilized Enzyme Packed Reactor for industrial applied Monoacyl- glycerol Production, J. Agric. Food Chem. 55 (19): 7786-7792 (2007).

Zhang H., Mu H., Xu X. Monitoring lipase-catalyzed butterfat interesterification with rapeseed oil by Fourier transform near-infrared spectroscopy, Anal. Bioanal. Chem. 386:1889–1897 (2006).

Department of Molecular Biology 23 Bioactive Milk Proteins characterization. Hence a number of projects on these The Protein Chemistry Laboratory (Torben Ellebæk membrane proteins (mucins, lactadherin, CD36 etc.) Petersen & Esben Skipper Sørensen), which houses are ongoing in the group. E.g. a study aims at charac- the bioactive milk protein research group, was estab- terizing the inhibiting effect these membrane proteins lished in 1992 as a result of a series of grants from the have on the infectivity of virus and bacteria in the Danish Dairy Research Foundation and the national intestinal system. FØTEK research program. At present the group con- Another protein characterized at the laboratory, sists of five senior researchers, three post-docs, four EPV20, was found to be homologous with the human Ph.D.-students, three technicians and a number of NPC-2 protein, which is a pivotal factor in intra- master and project students. cellular cholesterol transport. Studies are ongoing The major research theme of the group is structu- to elucidate whether this milk protein can influence ral and functional characterization of bioactive milk cholesterol transport in cellular systems and animal proteins - and several for milk hitherto unknown models. proteins have been identified and characterized at the Another project at the laboratory under the theme laboratory in the past 15 years. of molecular nutrition, but not directly linked to The laboratory hosts a number of basic science re- milk research, is the investigation of vitamin B12 search projects on milk and mammary gland biology. and its binding proteins and receptors. This project Likewise the group is also leading and conducting is another example of research from the laboratory more applied research projects which aim at develo- which has been led to commercialization through the ping food ingredients, functional foods, nutraceu- establishment of the biotech company Cobento A/S. ticals and other products based on bioactive milk proteins. In that connection the group has a long and strong record of collaboration with industrial part- Bojsen A, Buesa J, Montava R, Kvistgaard AS, Kongs- ners in taking basic science all the way to patenting bak MB, Petersen TE, Heegaard CW, Rasmussen JT. and commercial product. Inhibitory activities of bovine macromolecular whey The research group has published more than proteins on rotavirus infections in vitro and in vivo. hundred articles in internationally peer-reviewed Journal of Dairy Science 90:66-74 (2007). journals and several patents have been filled on the purification and utilization of bioactive milk proteins. Agnholt, J., Kelsen, J., Schack, L., Hvas, C.L., Dahle- rup, J.F., and Sørensen, E.S. Osteopontin, a protein A series of patents on the purification and function of with cytokine-like properties, associated with inflam- the cytokine osteopontin, which can be purified from mation and stimulation of T cell cytokine production milk in relatively large quantities, have been filed. in Crohn’s disease. Scandinavian Journal of Immuno- Several projects on the industrial scale production of logy. 65: 453-60 (2007). osteopontin and its role and potential use in products stimulating the immune response, wound healing Christensen B, Nielsen MS, Haselmann KF, Peter- processes and inhibition of bacterial growth are cur- sen TE, Sørensen ES. Post-translationally modified rently undertaken at the laboratory. Osteopontin is residues of native human osteopontin are located in now a commercial product and is marketed by Arla clusters: identification of 36 phosphorylation and five Foods for use in e.g. infant formulas and oral hygiene O-glycosylation sites and their biological implicati- applications. ons. Biochemical Journal 390:285-92 (2005). The milk fat membrane fraction of milk is an excellent source for purification of membrane proteins which are otherwise very difficult to obtain in sufficient amounts for structural and functional

24 www.mb.au.dk Protein interactions

Professor Jan Johannes Enghild • Functional genomics and proteomics. Professor Daniel Otzen • Extracellular matrix homeostasis. Lektor Torsten Kristensen • Proteases and inhibitors. • Free radicals and antioxidant enzymes. The research combines modern analytical methods • Formation of plaques or fibrils. with classical protein chemistry techniques methods • Protein aggregation. to characterize covalent and non-covalent changes • Insoluble proteins and their interactions with to proteins and the consequences for their biological other proteins. functions. We use a dual approach in our hypothe- • Characterization of post-translational modificati- sis driven research. Firstly, we characterize protein ons. structure and function to reveal the mechanisms behind observed protein-protein and protein-ligand Conformational transitions in proteins interactions. This research is geared towards answe- ring important basic questions of protein structure Our aim is to understand the structural transitions and mechanism. Secondly, we study perturbations of that accompany protein binding to membranes (both normal physiology in order to investigate the signi- integral or peripheral membrane proteins, including ficance of our structural observations. In addition, antimicrobial peptides and protein-detergent comple- we employ proteomics methods aimed at discovery xes) and pathological/functional protein aggregation. science research to tease apart more complex que- Using state-of-the-art spectroscopic techniques we stions. Discovery science is characterized by non- quantify the energetics, stoichiometry and kinetics of selective gathering of information characterizing a the associated conformational changes to understand particular biological system. The gathered results are how the conformational landscapes of proteins, and subsequently analyzed with the hope that significant thus the formation of different structures, can be characteristics will emerge to provide insight into “tuned” by the environment and vice versa. Ultim- the mechanism and function of the system. This ap- ately we want to be able to prevent the physiological proach contrasts significantly with hypothesis-driven accumulation of harmful protein aggregates of the science, but we believe that discovery- and hypothe- types seen in Parkinson’s and Alzheimer’s Disease. sis-driven sciences are complementary approaches Headlines include: that, when used in combination, can advance the speed of knowledge generation. • Structure and stability of states along the aggregation pathway of proteins involved in neurode- Protein modifications generative diseases • Understanding and harnessing beneficial protein This research team focuses on proteolysis, post-trans- aggregation, e.g. bacterial amyloid lational modifications and, evaluation of protein fol- • Characterization of the mode of action of antimi- ding/stability, oxidation, the role that particular prote- crobial peptides ins play in the formation of plaques or fibrils and the • Understanding how lipids and detergents modu- interactions between soluble and insoluble proteins. late the folding and stability of integral mem- Some of the headlines for the research include: brane proteins

Department of Molecular Biology 25 which form aggregates in the cornea. These studies will support the development of compounds that can inhibit the aggregation and thus hopefully prohibit the impairment of sight of individuals affected by the mutations in TGBIp. • The corneal proteome has been described by 2D gel electrophoresis and liquid mass spectrometry. These studies have generated a map of proteins present in the corneal tissue which can be applied in further research project and have shown that a number of Figure: Aggregates of the Fas4 domain of TGFBIP with the plasma proteins are transported actively into the tis- mutation causing lattice corneal dystrophy formed in vitro (left) sue. resemble the “needle-like” structures formed by the full-length TGFBIP protein as seen in the cornea of a patient suffering from • Using a special laser-mediated dissection lattice corneal dystrophy (right). technique, we have isolated deposit-rich sections of the corneal tissue, which we will analyze by mass Topic: Ocular transparency spectrometryto elucidate the composition of the protein aggregates. The research group is part of the Center for Inso- luble Protein Structures (inSPIN) supported by the • With Professor Søren Keiding we are developing Danish National Research Foundation (Danmarks techniques to study the structure of proteins in vivo Grundforskningsfond). One research area is ocular using non-invasive Coherent Anti-Raman Scattering transparency with special focus on the cornea, a spe- microscopy. This can be applied both to TGFBIp de- cialized tissue in the front part of the eye. This tissue posits and benign amyloid deposits in bacteria. is normally transparent. However, a range of diseases compromise transparency and results in significant Pedersen, J. S., and Otzen, D. E. Amyloid - A state in many impairment of sight or even blindness, including guises: survival of the fittest fibril fold, Protein Science 17, corneal dystrophies established by the aggregation of 1-9 (2008). the protein transforming growth-growth factor beta- Otzen, D. E., and Nielsen, P. H. We find them here, we find induced protein (TGFBIp) in the tissue. We currently them there: Functional bacterial amyloid, Cell. Mol. Life Sci. study this system by bottom-up (protein analyses) 65, 910-927 (2008). and top-down (proteomics) approaches: Pedersen, J. S., Dikov, D., Flink, J. L., Hjuler, H. A., Christi- ansen, G., and Otzen, D. E. The changing face of glucagon • We have characterized TGFBIp purified from the fibrillation: Structural polymorphism and conformational cornea and generated a range of recombinant prote- imprinting, Journal of Molecular Biology 355, 501-523 ins representing natural variants which mediates the (2006). aggregation of the protein in the cornea. Our studies Mogensen, J. E., Tapadar, D., Schmidt, M. A., and Otzen, D. link “test tube” properties measured by spectroscopic E. Barriers to folding of the Transmembrane Domain of the approaches with observed physiological features. Escherichia coli Autotransporter Adhesin involved in diffuse adherence, Biochemistry 44, 4533-4545 (2005). • Together with Professor Jan Skov Pedersen we Valnickova Z, Petersen S.V., Nielsen S.B., Otzen D.E., have shown that wildtype and mutant TGFBIp have Enghild J.J. Heparin binding induces a conformational different tendencies to form higher order structures change in pigment epithelium-derived factor. J Biol Chem. in solution. 2;282(9):6661-7 (2007). Valnickova Z, Sanglas L, Arolas J.L, Pallarés I., Guevara T., • In collaboration with Professor Niels Christian Solà M., Kristensen T., Enghild J. J., Avilés F. X., Gomis- Nielsen we have determined the three dimensional Rüth F. X. Structure of activated thrombin-activatable fibri- structure of TGFBIp with solution NMR and initi- nolysis inhibitor, a molecular link between coagulation and ated studies by solid-state NMR to analyze mutants fibrinolysis. Molecular Cell 22;31(4):598-606 (2008).

26 www.mb.au.dk Molecular interventions

Suresh Rattan, PhD, Dr.scient. interventions include testing the effects of synthetic Peter Kristensen, PhD and natural compounds (for example, cytokinins, po- Anders Olsen, PhD lyphenols and spices), and establishing the beneficial effects of mild stress, termed hormesis, on preventing Cellular processes are regulated by interactions bet- or slowing down the accumulation of molecular da- ween different macromolecules. Basic understanding mage. Other hormetic interventions such as nutritio- of normal and pathological processes can be gained nal components, mechanical stretching and exercise by manipulation of such molecular interactions, are being investigated to elucidate the effects and me- which also provide a point of intervention. Occur- chanisms of mild stress on cellular lifespan, wound rence of damage in macromolecules is intrinsic to healing, angiogenesis, and sugar-induced accelerated the basic molecular processes of life. Alterations in molecular damage accumulation. gene expression levels and the degree of molecular damage are often causative events leading to unique Phage display group (Peter Kristensen) The central phenotypes. These include muscular, skeletal and dogma in molecular biology states that it is impos- neuronal degenerative diseases, cancer, failure of sible to derive a unique gene sequence from a protein the immune system, altered angiogenesis, metabolic sequence due to the degeneracy of the genetic code. disorders and hormonal deficiencies. Since studies of However, the technique of phage display is one the molecular events are often hampered by the com- example of a technique where it is possible to link plexity of the human body, much basic knowledge genotype and phenotype. The application of phage can be best obtained by taking advantage of various display opens up the possibility of creating large li- model systems, followed by validation in higher sy- braries of different proteins (for example, antibodies). stems or organisms. Additionally, single cell analyses We are utilising such antibody-generating systems in complex systems can assist further advancement as a discovery tool, to identify important biological in this respect. Within our groups, the focus is mainly networks and biomarkers. We are isolating antibo- at elucidating the molecular mechanisms leading to dies which are capable of modulating blood vessel ageing and age-related malfunctions, such as vascu- formation. By intervention in the process of forma- lar and mental impairments. Development of novel tion of new blood vessels, we have in mice models technologies and biotechnological reagents combined demonstrated that tumor development is delayed. with experimental model systems to address questi- Also we are aiming to increase our understanding ons regarding the occurrence and accumulation of of the age-related decline in the ability to form new molecular damage, and interventions are integral to blood vessels. An important area of our research is to this research. develop tools which are capable of analysing gene expression at the single cell level, again this mainly rely Cellular Ageing group (Suresh Rattan) is using the on the application of the phage display technology. experimental model system, the “Hayflick system” of The last area of interest covers the development of long-term serially subculturing of normal diploid hu- methods which can be applied in areas of industrial man cells which have a limited proliferative capacity. importance, such as the development of proteins Cell types used are epidermal fibroblasts and kera- with novel catalytic properties or changed stabilities. tinocytes, bone marrow stem cells and osteoblasts, Thus we have been able to devise methods relying of and vascular- and micro-vascular endothelial cells. Darwinian selection of enzymes with higher thermo- Macromolecular damages, specially the oxidative stability. damage to proteins, alterations in proteasomes and lysosomes), and alterations in cellular responses to C. elegans group (Anders Olsen) The main focus stress through heat shock proteins, hemeoxygenase, of the C. elegans research group is to investigate the and antioxidant pathways are being studied. Various mechanistic relationship between cancer and ageing

Department of Molecular Biology 27 using the soil nematode Caenorhabditis elegans. Rattan, S.I.S. Increased molecular damage and hetero- C. elegans is an excellent model system for ageing geneity as the basis of aging. Biochemical Journal, 389: studies. More than 100 gene mutations have been 267-272 (2008). shown to influence the nematode lifespan and a large Berge, U., Kristensen, P. and Rattan, S.I.S. Hormetic modulation of differentiation of normal human epidermal fraction of these “Age genes” share identity with keratinocytes undergoing replicative senescence in vitro. genes of known function in other species. We are Experimental Gerontology, 43(7):658-62 (2008). particularly interested in the role of tumor suppres- Rattan, S.I.S., Sejersen, H, Fernandes, R.A. and Luo, W. sors and checkpoint proteins in the ageing process. To Stress mediated hormetic modulation of wound healing prevent cancer, cells are equipped with surveillance and angiogenesis in human cells. Annals of the New York systems that detect damage and stop cells from divi- Academy of Sciences, 1119: 112-121, (2007). ding. These surveillance systems are collectively cal- Kim Bak Jensen, Ole Nørregaard Jensen, Peter Ravn, led cellular checkpoints. We have made the discovery Brian.F.C.Clark and Peter Kristensen. Identification of Ke- that inactivation of some checkpoint proteins can in- ratinocyte Specific Markers using Phage Display and Mass Spectrometry. Molecular and Cellular Proteomics, 2, 61-69 crease stress resistance and lifespan of C. elegans. It is (2003). currently unknown how checkpoint proteins mecha- Jesper S. Pedersen, Daniel E. Otzen and Peter Kristensen. nistically determine lifespan. Therefore, to further our Directed evolution of barnase stability using proteolytic understanding of this phenomenon we completed a selection. Journal of Molecular Biology, 323, 115-123 (2002). C. elegans whole genome RNAi screen for checkpoint Olsen, A., Vantipalli, M. C., and Lithgow, G. L. . Checkpoint defects which returned 50 genes that cause resistance Proteins Regulate Survival of the Post-Mitotic Adult Soma to the chemo therapeutic drug hydroxyurea when in Caenorhabditis elegans. Science, 312(5778):1381-5 (2006). inactivated. A detailed analysis of these genes will (B) (C) help us understand how checkpoints determine lifespan. Importantly, by taking a comparative biology approach in our analysis we will be able to address how well these findings translate to higher organisms such as humans. Our group also uses C. elegans to study other age-related diseases such as Alzheimer’s disease.

(A)

A. The Hayflick system of cellular ageing in vitro, which is used to test potential anti-ageing interventions. Pictures show young, middle-aged and senescent human skin fibroblasts.

B. (Top) Human endothelial cells forming tubes in vitro (blood vessels). Recom- binant antibodies can be tested for the ability to inhibit tube formation – anti- angiogenic effect. (Bottom) subpopulation of blood cells recognised by antibodies (arrows point at red antigen staining, blue nuclear stain) generated using only one single cell as antigenic material – single cell analysis.

C. (Top) The soil nematode C. elegans is a powerful model organism for studying the genetics of ageing. (Bottom) Transgenic nematode showing localisation of the FOXO transcription factor fused to GFP.

28 www.mb.au.dk Structural Biology

Professor Poul Nissen Disease (www.pumpkin.au.dk). The Na+,K+-ATPase Associate Professor Søren Skou Thirup maintains the steep Na+ and K+ gradients across Associate Professor Morten Kjeldgaard the cell membrane that are critical for secondary Associate Professor Charlotte Rohde Knudsen transport schemes and the action potential used in Associate Professor Gregers Rom Andersen neurotransmission (see figure 1a). The first structure Associate Professor Ditlev Egeskov Brodersen of this pump was recently determined (Morth et al.). The pumps represent very promising targets for the Cartography of the molecules of life development of new antibiotics, and drugs against In the visual culture of the 21st century, scientific cancer and cardiovascular diseases. Also, Ribosome imagery has become increasingly important in po- complexes are being studied to elucidate the mecha- pularising and communicating scientific knowledge. nisms of protein synthesis in eukaryotes. Complexes Moreover, in analysing the structure and function with the translation factor eEF2 have been studied of the large molecules of the cell at the atomic level by single-particle cryo-EM in a collaboration with a visualisation becomes more than just a matter of cryo-EM group. These studies showed large confor- communicating scientific insight, it is an integral part mational changes on the ribosome to be associated of the production of scientific knowledge in the field with hydrolysis of GTP. of structural biology. At the Centre for Structural Biology we explore Neuroreceptors and mitochondrial translation nature on the atomic level analysing the processes of In Søren Thirup’s group the Vps10p family of recep- decoding genetic information, cell to cell signalling, tors is the subject of structural studies. These recep- the immune system, and transport in and out of the tors are primarily expressed in neuronal tissue and cell. they have been shown to be involved in the signalling The Centre for Structural Biology (www.bioxray. of neuronal cell death, alzheimers disease and type au.dk) was founded by Jens Nyborg and represents 2 diabetes. In sortilin the 680 amino acid Vps10p over 30 years of experience with structure determina- domain, the common denominator of the family, tion of macromolecules. The Centre consists of eight constitutes the entire extracellular part, whereas addi- independent but closely connected research groups tional domains are found in the other four members; at the Department of Molecular Biology, University SorLA, SorCS1-3 (see figure 1b). The receptors have of Aarhus. Common to the groups is the use of X-ray a single transmembrane helix and a short cytosolic crystallography to elucidate the three-dimensional C-terminal tail containing sequence motifs recognised structure of biological macromolecules. In addition to by sorting adaptor proteins such as GGA1. The group the crystallographic analysis, a wide range of molecu- has recently determined the crystal structure of the lar biological, biochemical, biophysical, and analytical Vps10p domain of sortilin in complex with neuroten- techniques are used at the Centre. sin (Quistgaard et al.). Also structures of fragments of the sortilin and SorLA cytoplasmic tails have been de- Ion pumps and ribosomes termined in complex with the VHS domain of GGA1. The group of Poul Nissen studies ion pumps like The group is also studying elements of mitochondrial Na+,K+-ATPase, Ca2+-ATPase and H+-ATPase. Ion protein synthesis, where the non-canonical structure pumps are key enzymes in cell biology, physiology of mitochondrial tRNA’s are of special interest. and medicine. The pumps transform the chemical energy from ATP hyrolysis to the powersource of Structural bioinformatics and termination of trans- electrochemical gradients and voltage across bio- lation membranes. They are fascinating examples of bio- In the research group of Morten Kjeldgaard release logical nanomachines. These studies are organised factors involved in translation termination are studi- in the Center for Membrane Pumps in Cells and ed. We have determined the structure of release factor

Department of Molecular Biology 29 aRF1 from Halobacterium sp. to a resolution of 2.1Å. molecule approach. Another theme in the laboratory The structure is superficially similar to the human is the identification and analysis of novel interaction release factor eRF1, but with some important diffe- partners of eEF1A which shed new light on some of rences. For example, one domain which is not visible the noncanonical roles that have been ascribed to this in the human factor is visible in the archeal structure, factor including cytoskeletal organisation, apoptosis and the structure is generally more accurate. Another and signal transduction. Furthermore, the group fo- effort concerns the development of new methods in cuses on the role of various eEF1A isoforms in cancer. the processing of crystallographic diffraction data. Other projects focus on methods in structural bioin- Eukaryotic translation and the complement system formatics, in particular of calcium ATPase membrane The research group of Gregers R. Andersen studies proteins. We have developed methods to determine protein synthesis in eukaryotes with crystallography, flexible regions in these molecules, defining areas small angle scattering and cryo-EM in collaboration. of significance in the conformational changes they In particular, the translation elongation factor eEF2 undergo. We are involved in the development of a with its toxin sensitive diphthamide modification has comprehensive database that will enable researchers been investigated. Also, the fungi specific translation to overview a wide range data on the calcium AT- factor eEF3 have been studied both in isolation and Pase family of structures. Finally, a research area in a variety of complexes revealing important features development is focussed on molecular shape analysis. of tRNA translocation and release from ribosomes. Furthermore, the group has determined the structure Elongation factors in translation of the mRNA associated exon junction complex (see The laboratory of Charlotte R. Knudsen studies the figure 1c). This is deposited upstream of splice sites functionalities of translation elongation factors EF-Tu and provides a binding platform for a variety of peri- from E. coli and eEF1A from humans with special pheral proteins. The complex functions during mRNP emphasis on the relationship between structure and export, cytoplasmatic localization and nonsense function. These elongation factors belong to the family of guanine-nucleotide binding proteins and play mediated decay of aberrant mRNA during transla- a prominent role during the assembly of amino acids tion (Andersen et al.). Finally, the research group is into proteins upon decoding of the genetic message. engaged in structural studies of complement system The multifunctionality of EF-Tu is scrutinized using a being part of the the innate immune defense. We have protein engineering protocol. Recently, the group has determined the structures of complement C3 and C5, studied aspects of the guanine nucleotide exchange which after proteolytic cleavage by specific conver- mechanism (Dahl et al.). In addition, studies of the tases elicit the proximal and terminal complement dynamic nature of EF-Tu was initiated using a single- response, respectively.

a b c d

Figure 1. a: The crystal structure of the Na+,K+-ATPase showing the a (blue), b (gold) and g (red) subunits and bound ions as spheres. The membrane is indicated as the grey box. b: Surface representation of the neuroreceptor Sortilin with structural features indicated by different colours. c: Electron density of RNA bound in the exon junction complex. d: RNA degradation assay, crystals, and structure of the Schizosaccharomyces pombe Pop2p deadenylation subunit.

30 www.mb.au.dk RNA metabolism and decay crobes. Based on the wealth of genomic information The laboratory of Ditlev E. Brodersen studies the available today a large family of LysM (Lysin Motif) controlled turnover of nuclear and cytoplasmic RNAs containing proteins can be identified in bacteria, - fundamental processes which are essential for main- plants and mammals. The functions of these proteins taining the quality and quantity of all transcripts. are diverse. For bacterial LysM proteins the func- In the eukaryotic nucleus, elaborate quality control tions range from peptidoglycan degradation during mechanisms are in place that guarantee that mRNAs division to involvement in pathogenesis. In higher exported to the cytoplasm for translation into prote- eukaryotes the LysM proteins functions in signal ins are intact and fully functional. Aberrant molecules perception pathways implicated in immune defence are quickly intercepted and targeted for destruction and development. We study the structural basis for via a large complex known as the RNA exosome. The the interaction between LysM proteins and carbohy- group has determined the crystal structure of the nu- drates and the implication on the function af these clear 3’-5’ exonuclease Rrp6p responsible for this re- complexes in e.g. signalling process initiating sym- moval (Midtgaard et al.). The group also studies RNA biosis between legumes and rhizobia bacteria. Also, turnover pathways in the cytosol, such as the removal the group focuses on a range of bacterial toxins and of the poly-A tail found in the 3’ end of eukaryotic their interaction with host cell receptors or substrates mRNAs (deadenylation). One of the active subunits (Jørgensen et al.). The aim is to obtain an understan- of the mega-Dalton Ccr4-Not complex responsible for ding of the molecular details and chemical basis for this process, Pop2p, has been characterised both bio- microbiol pathogenesis. This knowledge can be used chemically and structurally (see figure 1d), detailing for designing new, highly specific anti-microbial the specificity and activity of the enzyme (Jonstrupet drugs. al.). Selected publications Innate immunity Andersen CBF, Ballut L, Johansen JS, Chamieh H, Niel- In the research group of Rune Hartmann the inter- sen KH, Oliveira CLP, Pedersen JS, Seraphin B, Le Hir H, feron cytokines (small hormone like proteins) are Andersen GR. (2006). Structure of the exon junction core studied. These control the innate immune response complex with a trapped DEAD-box ATPase bound to RNA. to viral infections, and are popularly speaking the Science 313: 1968-72. body’s alarm system. If a cell is infected by a virus, Dahl LD, Wieden H-J, Rodnina M, Knudsen CR. (2006). The the cell will start to produce interferon within one importance of P-loop and domain movements in EF-Tu for to two hours. The newly produced interferon will guanine nucleotide exchange. J Biol Chem 281: 21139-46. bind to receptor complexes found on the cell sur- Jonstrup AT, Andersen KR, Van LB, Brodersen DE. (2007). face of neighbouring cells and activate this receptor. The 1.4 Å crystal structure of the S. pombe Pop2p dea- The activation of the receptor leads to activation of denylase subunit unveils the configuration of an active transcription factors which induce the synthesis of a enzyme. Nucleic Acids Res 35: 3153-64. number of antiviral genes. Thus, in effect interferon Jørgensen R, Merrill AR, Yates SP, Marquez VE, Schwan AL, is warning the cell of the coming virus and initiates Boesen T, Andersen GR. (2005). Exotoxin A-eEF2 complex the defensive mechanism. Our prime interest is Type structure indicates ADP-ribosylation by ribosome mimicry. III Interferon’s. We study how interferon binds to its Nature 18: 979-84. receptor and induces signalling. Through determina- Midtgaard SF, Assenholt J, Jonstrup AT, Van LB, Jensen tion of the crystal structure of interferon bound to the TH, Brodersen DE. (2006). Structure of the nuclear exo- receptor we hope to gain novel insight in the receptor some component Rrp6p reveals an interplay between the interaction. We are using the knowledge gained from active site and the HRDC domain. Proc Natl Acad Sci USA, structural biology to design in vivo experiments that 103(32): 11898-903. can further illuminate the role of Type III interferon Morth JP, Pedersen BP, Toustrup-Jensen MS, Sørensen TL, in the innate immune response. Petersen J, Andersen JP, Vilsen B, Nissen P. (2007). Crystal structure of the sodium-potassium pump. Nature 450: Microbial symbiosis and pathogenesis 1111-4. In the laboratory of Thomas Boesen research is cen- Quistgaard EM, Madsen P, Grøftehauge MK, Nissen P, Pe- tered around the interplay between host cells and mi- tersen CM, Thirup S. (2008). Ligands bind to Sortilin in the tunnel of a 10 bladed b-propeller domain. in prep.

Department of Molecular Biology 31 PhD degrees

1974 1987 Norbert Wolf Christian Würtz Heegaard Elsebet Lund Robyn van Heeswijck Eva C. B. Jørgensen Kurt Jensen Handberg Torsten Kristensen Tinna V. Stevnsner Niels Bech Laursen 1976 Michael Etzerodt Poul Hunniche Madsen Esben Skipper Sørensen Frode Engbæk Jane Frydenberg Lene Heegaard Madsen Claus Oxvig

1977 1989 1993 1996 Torben Ellebæk Petersen Lis Rosendahl Jens Østergaard Peter Kristoffersen Finn Skou Pedersen Ove Wiborg Jesper Q. Svejstrup Lene Pedersen Niels Aagaard Jensen Bodil Theilade Peter Birk Rasmussen 1978 Kent Christiansen Thor Las Holtet Lars Sottrup-Jensen 1990 Hans-Jürgen H. Hoffmann Annette Balle Sørensen Torben Lund Jørgen Christiansen Jan-Elo Jørgensen Henning Christiansen Just Justesen Kirsten Paludan Kaare Lund Steen Mollerup Karen Skriver Peder Søndergaard Mad- Galina Polekhina 1980 Henrik Dalbøge sen Ann Lund Hans-Henrik M. Dahl Henrik Steen Olsen Qunxin She Søren Borg Niels N. Sandal George Aboagye-Mathie- Anders Lade Nielsen 1981 sen Lars Høllund Jensen Johan Chr. Leer 1991 Anders Henrik Lund Tove Christensen 1994 Anne-Sofie Thøger Ander- 1982 Bent Karsten Jakobsen Uffe H. Mortensen sen Hans Christian Thøgersen Morten Jørsboe Christian Bendixen Klavs Dolmer Jytte Mollerup Andersen Knud Larsen Belinda A. Phillipson Kåre Lehmann Nielsen Bo Thomsen Jan Alsner Lotte Bang Pedersen 1983 Ole Olsen Søren Christensen Birgitta Ruth Knudsen Leif Skøt Anni Hangaard Andersen Peter J. Lauridsen Mette Østergaard Kirsten A. Nielsen Birgitte S. Wulff Peter Reinholt Nielsen 1984 Lars Erik Berglund Karin Jacobsen-Lyon Jens Kildsgaard Carsten Herskind Lisbeth Høj Johansen Niels Jørgen Larsen Karl Kristian Thomsen Jan Enghild Marianne Hjøllund Mad- 1997 Nils Goltermann Gitte Steen Jensen sen Niels Kirk Thomsen Torben Halkier Jonna Hvas John Oskær Rasmussen 1985 Niels Stampe Rüdiger Hans Jakob Larsen Birgitte Nauerby Steen Bennike Mortensen Peter Stein Nielsen Charlotte G. Frederiksen Jette Fjeldsted Lovmand Karna Skorstengaard Anne B. Tolstrup Thomas Thykjær Andersen Erik Østergaard Jensen 1992 Ove Damgaard Hansen Karen Vibe-Pedersen Poul Erik Hyldgaard 1995 Bente Larsen Esper Boel Jensen Mogens Duch Susanne Krogh Devine Bjarne Juul Bonven Frédéric Jullien Lars Eyde Theill Sanne Jensen Grete Mørch Sørensen Lone Kjær Rasmussen Boe Sandahl Sørensen Anne Dam Jensen Hong Yan Dai Emøke Bendixen Birgitte Østergaard Peter- 1986 Erik Østergaard Lotte Bach Larsen sen Ole Dragsbæk Madsen Knud Poulsen Mogens Kruhøffer Ole Kristensen Arne Villy Jensen Peter Brams Liselotte Elgaard Jensen 32 www.mb.au.dk Helene Krogh-Pedersen Mette Grønlund Henrik Uffe Holst Astrid Colding Sivertsen Poul Nissen Yong Wang Jeannette H.F. Justesen Vibe Hallundbæk Øster- Peter Kresten Nielsen Lotte Bjergbæk gaard Helle Moving Morten Sunesen 2003 Henning Bünsow Boldt Pia Svendsen Niels Jonas H. Graversen Kim Bak Jensen Rikke Christina Nielsen Helle Dyhr-Mikkelsen Helle Færk Jørgensen Lars Aagaard Jens Preben Morth Thomas Juhl Kristensen Berit Olsen Krogh Mads Breum Larsen Lars Ellgaard Larsen Marie Kveiborg Hanne Poulsen 2006 Jesper Laursen Michael Toft Overgaard Louise Vagner Laursen Mads Gravers Jeppesen Jesper Haaning Mortensen Michael Lisby Victor G. Stepanov Jan Kristian Jensen Steen Ethelberg Søren Riis Paludan Karina Dalsgaard Sørensen Esben Bjørn Madsen Linda Jabobsen Janne Lytoft Simonsen Trine Elkjær Larsen Cro- Line Hummelshøj Mogen- Peder Lisby Nørby Søren Warming vato sen Lars Kjøller Mikkel Holmen Andersen Charlotte Georgi Jakobsen Lone Tjener Pallesen Tommy Byskov Lund Helle Heibroch Petersen Kim H. Hebelstrup Torben Heick Jensen Kristian Hobolt Jensen 2004 Kristian Wejse Sanggaard Vibeke Diness Jakobsen Jesper Bøje Andersen 1998 2001 Steen Günther Nielbo Ebbe S. Andersen MichaelSchandorf Søren- Charlotte Modin Søren Vestergaard Rasmus- Christian B.F. Andersen sen Michael Adam Dabrowski sen Morten Muhlig Nielsen Søren Jensby Nielsen Agnieszka Danielewicz Katrine Egelund Pedersen Marianne S. Hede Connie Benfeldt Rikke Egelund Olsen Félicie F. Andersen Rikke F. Hougaard Anette Chemnitz Hansen Lene Krusell Shervin Bahrami Leif Schauser Thomas Østergaard Tange Esben Lorentzen 2007 Lise-Lotte Guldmann Mikkel Steen Petersen Brian Søgaard Laursen Jesper Bertram Bramsen Allan Jensen Rune Hartmann Martin Larsen Niels Høgslund Jørgensen Jacob Giehm Mikkelsen Kasper Dreyer Engkilde Rolf Bo Andersen Claus Gyrup Nielsen Susan K. Lindtner Hans Peter Sørensen Julie Støve Bødker 1999 Mette K. Lund Stig Uggerhøj Andersen Brian Christensen Morten Dunø Iben Anne Hansen Signe E. Larsen Louise C.V. Rasmussen Svend Kjær Lone Bæk Anne Ahlmann Nielsen Birgit K. Hougaard Hanne Norsgaard Rikke Høegh Lorentsen Trine Kastrup Dalsgaard Palle Gørtler Laustsen 2002 Thomas Egebjerg Rasmus- Signe Jensen 2005 sen Jesper Hansen Bonde Mai Marie Holm 2008 (until mid-September Troels Wind Francisco Mansilla Castaño Charlotte Harkjær Fynbo 2008) Thomas Jespersen Olav Michael Andersen Stefan Borre-Gude Simon Glerup Ole Valente Mortensen Annette M.G. Dirac Anette Thyssen Jonstrup Lotte Schack Søren Kahns Steen Vang Petersen Rene Jørgensen Daniel M. Dupont Anne Birgitte N. Pedersen Camilla Skouboe Søren Peter Jonstrup 2000 Lise Bjerre Husted Søren Lykke-Andersen Svend Haaning Peter Askjær Bente Vestergaard Nielsen Karen Colbjørn Larsen Esben M.H. Quistgaard Laust B. Johnsen Mette Christiansen Steffen Sinning Per Larsen Ditlev E. Brodersen Dereck E.W. Chatterton Morten Bjerring Henrik Hornshøj Jensen Mikkel D. Lundorf Susanne E. Hede Kasper Thorsen Joachim Silber Cristina Cvitanich Jakob Nilsson Jens Raabjerg Olesen Jesper Pallesen Guilaine Bouteiller Christian K. Damgaard Kristian B. Laursen Ulrik Lytt Rahbek Morten Præstegaard Karin Stenderup Nielsen Tina Thorslund Lasse Bohl Jenner Henrik Karring Lisbeth S. Laursen Department of Molecular Biology 33 34 www.mb.au.dk Staff and students at the Annual Meeting and 40th Anniversary Meeting of the Department of Molecular Biology - 4 June 2008

Department of Molecular Biology 35