Nearly all proteins are modified by covalent addition of complex oligosaccharides called glycans. Glycan parts are equally important for structure and function of proteins as polypeptide parts, but contrary to polypeptides, glycans are not defined by the firm genetic template. Instead, glycans are a product of complex dynamic interaction between environment and hundreds of genes. Due to their structural complexity and technological limitations the knowledge about glycans is lagging significantly behind the knowledge about proteins or DNA, but the situation is changing rapidly.
In 2009 we performed the first large population study of the human plasma glycome (Knezevic et al, J Proteome Res, 2009). This data enabled the first GWAS of the glycome (Lauc et al, PLoS Genet 2010) which (among others) identified HNF1A as master regulator of plasma protein antennary fucosylation. Further studies demonstrated the importance of this between HNF1A and glycosylation in HNF1A-MODY subtype of diabetes (Thnabalasingham et al, Diabetes, 2013). In collaboration with the team of Prof Zoldos we also showed that epigenetic silencing of HNF1A is important for plasma protein glycosylation (Zoldos et al, Epigenetics, 2012).
In 2011 we went a step further and performed the first large population study of the glycome of an individual protein (IgG, Pucic et al, Mol Cell Proteomics 2011). GWAS based on this data revealed a complex network of genes which regulate IgG glycosylation (Lauc et al, PLoS Genet, 2013). The majority of these genes were previously not associated with glycosylation, but were associated with a number of autoimmune and inflammatory diseases.
One of the main goals of this project will be to develop MS methods for the analysis of subclass specific IgG glycosylation and apply them for the analysis of IgG glycosylation in large cohorts. The analysis of multiple omics data will be performed in collaboration with the team of Prof. Vlahoviček. Epigenetic aspects of regulation of IgG glycosylation will be studied in collaboration with the team of Prof Zoldoš, and effects of alternatively glycosylation of plasma proteins on their interactions with drugs and other small molecules in collaboration with the team of Prof Weygand.
Dr. Gordan Lauc is a professor of biochemistry and molecular biology at the University of Zagreb and founder of private research laboratory Genos. He was born in Osijek in 1970, graduated molecular biology (1992) and obtained PhD in Biochemistry and the University of Zagreb in 1995. He got his postdoctoral training at the Institute for Medical Physics and Biophysics in Münster and Johns Hopkins University in Baltimore. He authored of over 100 research papers published in international journals and six international patents. He was invited to lecture at numerous international conferences, and was elected for visiting professor at the Johns Hopkins University in Baltimore, honorary professor at the University of Edinburgh and adjunct professor at Edith Cowan University in Perth. He is publishing in the field of glycobiology for over 20 years and his current work mostly focuses on the complex genetics of protein glycosylation and the role of alternative glycosylation in common diseases. His laboratory performed the first large scale studies of the human plasma glycome and human IgG glycome, which were the basis for the subsequent first GWAS of both IgG and total plasma glycomes. Professor Lauc was a chairman of the committee that prepared Croatian National Action plan for the increased investment in research in development, and is currently a member of the National Science Council and President of the National Council for Natural Sciences. He is a member of the Board of the International Glycoscience Organization and the Steering Committee of the European Glycoscience Forum.
1. Yu X, Wang Y, Krištić J, Dong J, Chu X, Ge S, Wang H, Fang H, Gao Q, Liu D, Zhao Z, Peng H, Pučić Baković M, Wu L, Song M, Stewart A, Rudan I, Campbell H, Lauc G, Wang W (2016) Profiling IgG N-glycans as potential biomarker of chronological and biological ages: a community-based study in a Han Chinese population. Medicine, in press (IF=5.723; Rank 15/153 – Medicine, General & Internal)
2. Theodoratou E, Thaçi K, Agakov F, Timofeeva MN, Štambuk J, Pučić-Baković M, Vučković F, Orchard P, Agakova A, Din FVN, Brown E, Rudd PM, Farrington SM, Dunlop MG, Campbell H and Lauc G (2016) Glycosylation of plasma IgG in colorectal cancer prognosis, Sci Rep 6, Article number: 28098 doi:10.1038/srep28098, (IF=5.578; Rank 5/56 – Multidisciplinary Science)
3. Freidin MB, Keser T, Gudelj I, Štambuk J, Vučenović D, Allegri M, Pavić T, Šimurina M, Fabiane SM, Lauc G (shared last author), Williams FMK (2015) The association between low back pain and composition of IgG glycome, Sci Rep 6, Article number: 26815 doi:10.1038/srep26815 (IF=5.578; Rank 5/56 – Multidisciplinary Science)
4. Wang Y, Klarić L, Yu X, Thaqi K, Dong J, Novokmet M, Wilson J, Polasek O, Liu Y, Krištić J, Ge S, Pučić-Baković M, Wu L, Zhou Y, Ugrina I, Song M, Zhang J, Guo X, Zeng Q, Rudan I, Campbell H, Aulchenko Y, Lauc G, and Wang W (2016) The associations between glycosylation of immunoglobulin G and blood pressures: a multiple ethnic cross-sectional study. Medicine, 95(17):e3379. doi: 10.1097/MD.0000000000003379 (IF=5.723; Rank 15/153 – Medicine, General & Internal)
5. Klasić M, Krištić J, Korać P, Horvat T, Markulin D, Vojta A, Reiding KR, Wuhrer M, Lauc G, Zoldoš V. (2016) DNA hypomethylation upregulates expression of MGAT3 gene in HepG2 cells and leads to changes in N-glycosylation of secreted proteins. Sci Rep 6, 24363, doi: 10.1038/srep24363 (IF=5.578; Rank 5/56 – Multidisciplinary Science)
6. Vučković F, Theodoratou E, Thaçi K, Timofeeva M, Vojta A, Štambuk J, Pučić-Baković M, Rudd P, Đerek L, Servis D, Wennerström A, Farrington SM, Perola M, Aulchenko Y, Dunlop M, Campbell H, Lauc G (2016) Immunoglobulin G Glycome in colorectal cancer. Clinical Cancer Research 22(12):3078-3086. DOI: 10.1158/1078-0432.CCR-15-1867 (IF=8,722; rank 12/211 – Oncology)
7. Barrios C, Zierer J, Gudelj I, Štambuk J, Ugrina I, Rodríguez E, Soler MJ, Pavić T, Šimurina M, Keser T, Pučić-Baković M, Mangino M, Pascual J, Spector TD, Lauc G (shared last author), Menni C (2016) Glycosylation profile of Immunoglobulin G in moderate kidney dysfunction. JASN, 27(3):933-41. doi: 10.1681/ASN.2015010109 (IF=9.466; rank 2/77 – Urology & Nephrology)
8. Vučković F, Krištić J, Gudelj I, Teruel Artacho M, Keser T, Pezer M, Pučić-Baković M,, Štambuk J, Trbojević-Akmačić I, Barrios C, Pavić T , Menni C, Wang Y, Zhou Y, Cui L, Song H, Zeng Q, Guo X, Pons-Estel BA, McKeigue P, Patrick AL, Gornik O, Spector TD, Harjaček M, Alarcon-Riquelme M, Molokhia M, Wang W, and Lauc G (2015) Systemic lupus erythematosus associates with the decreased immunosuppressive potential of the IgG glycome. Arthritis & Rheumatology 67(11):2978-89. (IF= 7,871; rank 3/30 – Rheumatology; 24/1955 – Clinical Medicine)
9. Jansen BC, Falck D, de Haan N, Hipgrave Ederveen AL, Razdorov G, Lauc G, and Wuhrer M (2016) LaCyTools – a targeted LC-MS data processing package for relative quantitation of glycopeptides. J. Proteome Res, published online Doi: 10.1021/acs.jproteome.6b00171 (IF=4.245; rank 14/79 – Biochemical Research Methods)
10. Lauc G (2016) Precision medicine that transcends genomics: Glycans as integrators of genes and environment (editorial), BBA Gen Subjects, published online, doi:10.1016/j.bbagen.2016.05.001 (IF=4,381; rank 68/290 – Biochem & Mol Biol, 14/73 Biophysics).
11. Kao D, Danzer H, Collin M, Gross A, Eichler J, Stambuk J, Lauc G, Lux A and Nimmerjahn F (2015) A monosaccharide residue is sufficient to maintain mouse and human IgG subclass activity and directs IgG effector functions to cellular Fc-receptors. Cell Reports 13(11):2376-85. doi: 10.1016/j.celrep.2015.11.027 (IF = 8,358; rank 27/184 – Cell Biology)
12. Lauc G, Pezer M, Rudan I, Campbell H (2015) Mechanisms of disease: The human N-glycome, BBA Gen Subjects, 1860:1574–1582, doi:10.1016/j.bbagen.2015.10.016 (IF=4,381; rank 68/290 – Biochem & Mol Biol, 14/73 Biophysics).
13. Trbojević-Akmačić, I, Ventham, NT, Theodoratou E, Vučković F, Kennedy NA, Krištić J, Nimmo ER, Drummond D, Štambuk J, Klarić L, Dunlop, MG, Novokmet M, Aulchenko Y, Gornik O, Kolarich D, Wuhrer M, McGovern D, Annese V, Kalla R, Pemberton I, Spencer D, Zoldoš V, Fernandes D, Campbell H, Pučić-Baković M, Satsangi J and Lauc G (2015) Inflammatory bowel disease associates with pro-inflammatory potential of the IgG glycome, IBD, 21:1237-47. PMID: 25895110, doi: 10.1097/MIB.0000000000000372. (IF=5,475; rank 9/75 – Gastroenterology & Hepatology)
14. Gudelj I, Keser T, Vučković F, Škaro V, Šupraha-Goreta S, Pavić T, Primorac D, Lauc G and Gornik O (2015) Estimation of human age using N-glycan profiles from bloodstains, Int J Leg Med, published online (IF=2.714; rank 2/15 – Medicine / Legal)
15. Trbojević-Akmačić I, Vilaj M and Lauc G (2016) High-throughput analysis of immunoglobulin G glycosylation, Exp Rev Proteomics, published online DOI: 10.1080/14789450.2016.1174584 (IF=2,896; rank 30/79 – Biochemical Research Methods)
16. Freidin BM, Lauc G, Allegri M, Primorac D, and Williams FMK (2016) Using omics in chronic pain conditions to delineate mechanisms and provide new therapeutic strategies. Pain Management, published online, doi:10.2217/pmt.16.2 (IF=2.646; rank 56/123 - Medicine, Research & Experimental)
17. Trbojević-Akmačić I, Nemec B, Vidic U, Malić S, Miklić K, Černigoj U, Vidič J, Lendero Krajnc N, Štrancar A, Lauc G, Lenac Roviš T, Pučić-Baković M (2016) Chromatographic monoliths for high-throughput immunoaffinity isolation of transferrin from human plasma, CCA, in press
18. Trbojević Akmačić I, Ugrina I, Štambuk J, Gudelj I, Vučković F, Lauc G, Pučić-Baković M. (2015) High-throughput glycomics: optimization of sample preparation. Biochemistry (Moscow) 80:934-942. DOI: 10.1134/S0006297915070123 (IF=1.303)
There is a continuous and urgent need to discover new antimicrobial compounds with diverse chemical structures and novel mechanism of action due to increase of incidence of new and re-emerging infectious diseases, appearance of undesirable side effects of certain antibiotics, as well as the increasing development of bacterial resistance to the antibiotics in current clinical use.
We will direct our efforts towards combating microbial resistance to clinically important and efficient ribosomal antibiotics based on the action of methyltransferases from Erm, Arm and Kam family. In our previous research we defined sequence-structure-function relationships of several representatives of these families. We will define the details of the interactions of antibiotic resistance methyltransferases with the ribosome and establish the core binding motifs and corresponding RNA-binding modules. This will complete the collection of essential data that will enable us to combine computational and experimental approach to identify specific inhibitors of ribosomal methyltransferases that cause antibiotic resistance and thus keep the existing macrolide and aminoglycoside antibiotics functional.
A great number of natural active compounds from plant extracts and essential oils should be examined in order to determine their antibacterial, anti quorum sensing and antibiofilm activity. In collaboration with the Weygand group we will also functionally characterise peptide-derived compounds found in several antibiotic producing streptomyces and plant symbionts by assessing their antimicrobial and quorum sensing properties.
Metagenomic approach to combating antibiotic resistance in collaboration with the Vlahoviček group will encompass bioinformatics analysis of metagenomic data for new biosynthetic pathways responsible for the production of secondary metabolites with possible antimicrobial activity and for the natural diversity and evolution of antibiotic resistance determinants. This will enable formation of the large data set that will provide the new insight into emergence and spreading of antibiotic resistance and set the basis for the screening of corresponding environmental samples for antimicrobial activity.
Dr. Gordana Maravić, a professor of molecular biology at the University of Zagreb, graduated molecular biology in 1996 and obtained PhD in Molecular Biology and the University of Zagreb in 2002. She was an International Centre for Genetic Engineering and Bioctechnology fellow (Trieste, Italy) for the period of two years. For over 10 years she has been involved in research of mechanisms of antibiotic resistance and functional studies of antibiotic resistance determinants, including interaction of antibiotics and antibiotic resistance enzymes with ribosome, functional studies of antibiotic resistance rRNA methyltransferases, antibiotic modulation of quorum sensing, as well as screening of specific inhibitors in vivo and in vitro by relevant molecular assays. In 2009 and 2012 she was a president of the scientific committee of 3rd and 4th Central European Symposium on Antimicrobials and Antimicrobial Resistance. She is a vice-president of the national Committee for the contained use of GMO’s. In the period from 2007-2012 she served as a head of Department of Biochemistry and Molecular Biology at University of Zagreb Faculty of Pharmacy and Biochemistry.
1. Jakšić Despot, Daniela; Kocsubé, Sandor; Bencsik, Ottó; Kecskeméti, Anita; Szekeres, András; Vágvölgyi, Csaba; Varga, Janos; Šegvić Klarić, Maja. Species diversity and cytotoxic potency of airborne sterigmatocystin-producing Aspergilli from the section Versicolores. Science of the total environment. 562 (2016); 269-30 (IF=4.099; rank 18/223 – Environmental Sciences, median IF 1.606)
2. Šamec D, Durgo K, Grúz J, Kremer D, Kosalec I, Piljac-Žegarac J, Salopek-Sondi B. Genetic and phytochemical variability of six Teucrium arduini L. populations and their antioxidant/prooxidant behaviour examined by biochemical, macromolecule- and cell-based approaches. Food Chem. 2015 Nov 1;186:298-305. (IF = 3.391; rank 8/123 – Food Science & Technology, median IF 1.222)
3. Mura P, Mennini N, Kosalec I, Furlanetto S, Orlandini S, Jug M. Amidated pectin-based wafers for econazole buccal delivery: formulation optimization and antimicrobial efficacy estimation. Carbohydr Polym. 2015 May 5;121:231-40 (IF = 4.074; rank 4/72- Chemistry, Applied, median IF 1.256)
4. Dunkić V, Kosalec I, Kosir IJ, Potocnik T, Cerenak A, Koncic MZ, Vitali D, Muller ID, Kopricanec M, Bezic N, Srecec S, Kremer D. Antioxidant and Antimicrobial Properties of Veronica spicata L. (Plantaginaceae). Curr Drug Targets. 2015; 16(14):1660-70. (IF = 3.597; rank 52/256 – Pharmacology & Pharmacy, median IF = 2.205)
5. Kremer D, Bolarić S, Ballian D, Bogunić F, Stešević D, Karlović K, Kosalec I, Vokurka A, Vuković Rodríguez J, Randić M, Bezić N, Dunkić V. Morphological, genetic and phytochemical variation of the endemic Teucrium arduini L. (Lamiaceae). Phytochemistry. 2015 Aug; 116:111-9. (IF = 3.350; rank 28/199 – Plant Sciences, median IF = 1.337)
6. Kremer D, Košir IJ, Končić MZ, Čerenak A, Potočnik T, Srečec S, Randić M, Kosalec I. Antimicrobial and Antioxidant Properties of Satureja Montana L. and S. Subspicata Vis. (Lamiaceae). Curr Drug Targets. 2015;16(14):1623-33. (IF = 3.597; rank 52/256 – Pharmacology & Pharmacy, median IF = 2.205)
7. Vladimir-Knežević S, Cvijanović O, Blažeković B, Kindl M, Štefan MB, Domitrović R. Hepatoprotective effects of Micromeria croatica ethanolic extract against CCl4-induced liver injury in mice. BMC Complement Altern Med. 2015 doi: 10.1186/s12906-015-0763-8. (IF = 2.020; rank 6/24 – Integrative & Complementary Medicine, median IF = 1.361)
8. Ulm L, Krivohlavek A, Jurašin D, Ljubojević M, Šinko G, Crnković T, Žuntar I, Šikić S, Vinković Vrček I. Response of biochemical biomarkers in the aquatic crustacean Daphnia magna exposed to silver nanoparticles. Environ Sci Pollut Res Int. 2015 Dec;22(24):19990-9. (IF = 2.828; rank 54/223 – Environmental Sciences, median IF = 1.606)
9. Vrček IV, Žuntar I, Petlevski R, Pavičić I, Dutour Sikirić M, Ćurlin M, Goessler W. Comparison of in vitro toxicity of silver ions and silver nanoparticles on human hepatoma cells. Environ Toxicol. 2016 Jun;31(6):679-92. (IF = 3.197; rank 54/223 – Environmental Sciences, median IF = 1.606)
10. Milevoj Kopčinović L, Domijan AM, Posavac K, Čepelak I, Žanić Grubišić T, Rumora L. Systemic redox imbalance in stable chronic obstructive pulmonary disease. Biomarkers. 2016 Apr 28:1-7. (IF = 2.260; rank 78/163 – Biotechnology & Applied microbiology, median IF = 2.125)
11. Šegvić Klarić M, Jakšić Despot D, Kopjar N, Rašić D, Kocsubé S, Varga J, Peraica M (2015) Cytotoxic and genotoxic potencies of single and combined spore extracts of airborne OTA-producing and OTA-non-producing Aspergilli in Human lung A549 cells. Ecotoxicol Environ Saf. 120 (2015); 206-214 (IF = 2.762; rank 56/223 – Environmental Sciences, median IF 1.606)
12. Kovačić, Sanja; Rumora, Lada; Gjurcevic, Emil; Šegvić Klarić, Maja. Effects of nitric oxide on blood-brain barrier permeability in common carp (Cyprinus carpio L.). American journal of veterinary research. 76 (2015); 615-624. (IF = 1.335; rank 39/133 – Veterinary Sciences, median IF = 0.889)
13. Kindl M, Blažeković B, Bucar F, Vladimir-Knežević S. Antioxidant and Anticholinesterase Potential of Six Thymus Species. Evid Based Complement Alternat Med. 2015; doi: 10.1155/2015/403950 (IF = 1.880; rank 7/24 – Integrative & Complementary Medicine, median IF = 1.361)
14. Domitrović R, Rashed K, Cvijanović O, Vladimir-Knežević S, Škoda M, Višnić A. Myricitrin exhibits antioxidant, anti-inflammatory and antifibrotic activity in carbon tetrachloride-intoxicated mice. Chem Biol Interact. 2015 Mar 25;230:21-9. (IF = 2.577; rank 110/255 Pharmacology & Pharmacy, median IF = 2.205)
15. Gabričević M, Lente G, Fábián I. Hydrogen Isotope Exchange of Chlorinated Ethylenes in Aqueous Solution: Possibly a Termolecular Liquid Phase Reaction. J Phys Chem A. 2015 Dec 24;119(51):12627-34. (IF = 2.693; rank 52/139 Chemistry, Physical, median IF = 2.167)
We use computational tools and methods to discover knowledge in processes of life at the level of entire biological systems – systems biology.
Currently, several projects are active in the group:
Computational analysis of human glycan profiles
This project analyzes glycan profiles of human blood plasma. We have a variety of high-throughput experimental methods available today which can encompass and create a lot of data from whole biological systems. In parallel, there is a need for efficient data processing to gain as much useful information as possible from these analyses. An example of such a high-throughput experimental method is HPLC analysis of human blood plasma glycan profiles. This project is developing a system of methods based on machine learning which can search through HPLC data and discover patterns of glycolysation within large groups of the population.
Computational analysis of the relationship between histone modifications and gene expression
This project studies histone modifications, or modifications of proteins which participate in packing of DNA and are closely linked to gene regulation. There is evidence that histone modifications are in fact a mean for coding for certain processes downstream of genes. Quantative models for predictions of gene expression levels through histone modification have shown thus far that gene expression and histone modification have a high correlation and that a relatively small number of histone modifications are necessary to predict gene expression levels, as well as that their relationship is general and valid in many cell types.
Codon usage in metagenomes
Metagenomics, the study of bacterial communities isolated straight from the environment, is a field which investigates bacterial populations in their natural environments. We identify functional adaptations of whole bacterial communities which enable them to survive in diverse environmental conditions such as animal digestive tracts, where bacteria degrade food into forms which can be harvested by the animal and where changes in bacterial composition can lead to obesity and disease. The method we are developing can not only identify the functions bacteria posses but also predict how much they are used and therefore offer a more accurate description of life in bacterial communities.
Genomic complexity of the simplest Metazoa, the sponge
Sponges are living fossils, inhabiting the plant for 580 million years, and the closest living species to the first multicellular animal. Therefore, by researching sponges we are also investigating our own evolutionary past. Our research of sponge genomes has shown that, despite the morphological simplicity of sponges, their genetic repertoire is surprisingly complex. This shows that even ancient ancestors of animals already had the potential for more complex life functions.
Prof. Vlahoviček studied molecular biology at the University of Zagreb, Croatia and obtained his PhD in Bioinformatics, working on a prediction of physicochemical properties of DNA. He spent 10 years as a research fellow at the International Center for Genetic Engineering and Biotechnology in Trieste, Italy. He established a computational biology group at the Zagreb University in 2002, where he moved permanently in 2006 with the EMBO Young Investigators Programme installation grant. His group develops computational tools and uses machine learning techniques to tackle open questions in developmental genomics and metagenomics.
1. Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence M, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos J, Sunyaev SR, Cell-of-origin chromatin organization shapes the mutational landscape of cancerNature, 10.1038/nature14221 (IF = 42.351; rank 1/55 Multidisciplinary Sciences, median IF = 0.786)
2. Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller, Viren Amin, John W Whitaker, Matthew D Schultz, Lucas D Ward, Abhishek Sarkar, Gerald Quon, Richard S Sandstrom, Matthew L Eaton, Yi-Chieh Wu, Andreas R Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R Alan Harris, Noam Shoresh, Charles B Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R Mercer, Shane J Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C Sallari, Kyle T Siebenthall, Nicholas A Sinnott-Armstrong, Michael Stevens, Robert E Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E Beaudet, Laurie A Boyer, Philip L De Jager, Peggy J Farnham, Susan J Fisher, David Haussler, Steven J M Jones, Wei Li, Marco A Marra, Michael T McManus, Shamil Sunyaev, James A Thomson, Thea D Tlsty, Li-Huei Tsai, Wei Wang, Robert A Waterland, Michael Q Zhang, Lisa H Chadwick, Bradley E Bernstein, Joseph F Costello, Joseph R Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis, and Roadmap Epigenomics Consortium. Integrative Analysis of 111 Reference Human Epigenomes. Nature. 518 (2015) (IF = 42.351; rank 1/55 Multidisciplinary Sciences, median IF = 0.786)
3. Koren, A., Handsaker, R. E., Kamitaki, N., Karlić, R., Ghosh, S., Polak, P., Eggan, K., McCarroll, S. A. (2014). Genetic variation in human DNA replication timing. Cell, 159(5), 1015–26. (IF = 33.116; rank 1/291 Biochemistry and Molecular Biology, median IF =2.861)
4. Flemr, M., Malik, R., Franke, V., Nejepinska, J., Sedlacek, R., Vlahoviček, K., and Svoboda, P. A retrotransposon-driven Dicer isoform directs endogenous siRNA production in mouse oocytes, Cell 2013. 155(4):807-16. (IF = 33.116; rank 1/291 Biochemistry and Molecular Biology, median IF =2.861)
5. Abe K-I, Yamamoto R, Franke V, Cao M, Suzuki Y, Suzuki MG, Vlahoviček K, Svoboda P, Schultz R M, and Aoki F. The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3’ processing. EMBO J. 2015 Jun 3; 10.15252/embj.201490648. (IF=10.434, rank 11/270 Biochemistry and Molecular Biology, median IF = 2.861)
6. Akalin, A., Franke, V., Vlahoviček, K., Mason, C. E., & Schübeler, D. (2014). Genomation: a toolkit to summarize, annotate and visualize genomic intervals. Bioinformatics, doi:10.1093/bioinformatics/btu775 (IF = 4.621; rank 4/52 Mathematical and Computational Biology, median IF = 1.503)
7. Godinic-Mikulcic, V., Jaric, J., Greber, B. J., Franke, V., Hodnik, V., Anderluh, G., … Weygand-Durasevic, I. (2014). Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs. Nucleic Acids Research, 42(8), 5191–201. (IF = 8.808; rank 22/291 Biochemistry and Molecular Biology, median IF =2.861)
8. Falanga A, Stojanovic O, Kiffer-Moreira T, Pinto S, Millan JL, Vlahoviček K, Baralle M (2014) Exonic splicing signals impose constraints upon the evolution of enzymatic activity. Nucleic acids research 42: 5790-5798 (IF = 8.808; rank 22/291 Biochemistry and Molecular Biology, median IF =2.861)
9. Roller M, Lucić V, Nagy I, Perica T, and Vlahoviček, K. Environmental shaping of codon usage and functional adaptation across microbial communities, Nucleic Acids Res, 2013 41(19):8842-52. (IF = 8.808; rank 22/291 Biochemistry and Molecular Biology, median IF =2.861)
10. Yukawa M, Akiyama T, Franke V, Mise N, Isagawa T, Suzuki Y, Suzuki MG, Vlahoviček K, Abe K, Aburatani H, Aoki F Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. PLoS One 2014 9: e92689 (IF = 3.534; rank 8/55 Multidisciplinary Sciences, median IF = 0.786)
Our research is directed towards understanding the mechanisms that determine how cells ensure accurate and efficient translation of the genetic code to produce functional proteins. Protein synthesis proceeds by delivery to the ribosome of aminoacyl-tRNAs, which pair with the corresponding mRNA sequences. The formation of aminoacyl-tRNAs is catalyzed by the aminoacyl-tRNA synthetases (aaRSs), a family of enzymes that link amino acids with correct tRNAs. Accurate aminoacyl-tRNA synthesis often requires an additional editing activity intrinsic to many aaRSs. The association of aminoacyl-tRNA synthetases into larger complexes, including those with elongation factors and other non-synthetase proteins, may promote aminoacylation, especially at certain environmental conditions. The quality of protein products are further controlled at other stages during ribosomal translation and depends on a series of macromolecular interactions, enabling the association of components of the protein synthesis machinery with the ribosome. These assemblies can increase translation efficiency by limiting substrate diffusion away from the ribosome thereby allowing rapid recycling of tRNAs. Our current research interests are focused on aminoacyl-tRNA synthetase higher-order complexes and their interactions with the ribosome.
We also study aaRS-homologs and macromolecular complexes they are involved in. We have recently discovered a new group enzymes named amino acid:[carrier protein] ligases that are structurally similar to class II aminoacyl-tRNA synthetases. They do not aminoacylate tRNA, but transfer activated amino acids to the phosphopantetheine group of small carrier proteins. The ultimate cellular fate of these activated amino acids is currently unknown. They may be required for non-ribosomal synthesis of peptides and/or other natural compounds. Our goal is to determine the roles of newly discovered cellular pathways comprising aaRS-like proteins. To explore structural and functional parallels between ribosomal and non-ribosomal peptide synthesis we combine biochemical and biophysical approaches with crystallographic, computational and genetic studies (in collaboration with other teams within the project and with foreign partners).
Dr. Ivana Weygand-Durasevic was a professor of biochemistry at the Department of Chemistry, Faculty of Science, University of Zagreb. She obtained PhD in Chemistry from University of Zagreb in 1981 and then had a postdoctoral training at the Department of Molecular Biophysics and Biochemistry, Yale University (with professor Dieter Söll). She returned at Yale as visiting scientist, where she spent several years and was elected visiting associate professor in 1995. Dr. Weygand-Durasevic was visiting researcher at several other institutions: Aarhus University (Denmark), Institute for Molecular and Cellular biology (IBMC, Strasbourg), European Molecular Biology Laboratory, (EMBL, Grenoble). The focus of her research has been on protein biosynthesis, protein:RNA and protein:protein interactions, and translation quality control mechanisms, with specific emphasis on the structure and function of aminoacyl-tRNA synthetases and synthetase-like proteins. In 2006 she received the National Annual Science Award of the Republic of Croatia for the achievement in aminoacyl-tRNA synthetase research. In 2012 she became a member of Croatian Academy of Science. She has published more than seventy papers, mostly related to protein biosynthesis.
During the past several years her group has been investigating unusual, phylogenetically diverged methanogenic-type seryl-tRNA synthetases (SerRSs). Biochemical and structural studies (performed in collaboration with crystallographers) revealed a number of idiosyncratic structural and mechanistic features of that ancient atypical synthetase (Bilokapic et al, EMBO J. 2006; Bilokapic et al, J. Biol. Chem. 2008; Jaric et al, J. Biol. Chem. 2009), clarifying some evolutionary related questions. They found that the specificity and the efficiency of serylation both in eukaryotes and in archaea can be modulated by interactions between seryl-tRNA synthetases and other proteins (Godinic et al, FEBS J, 2008; Mocibob and Weygand-Durasevic, Arch. Biochem. Biophys. 2008; (Godinic-Mikulcic et al, J. Biol. Chem. 2011). The most diverged members of SerRS super-family are SerRS-like proteins, which function in numerous bacteria. They structurally resemble catalytic domain of methanogenic type SerRSs (Mocibob et al, Proc. Natl. Acad. Sci. USA, 2010), but their enzymatic activity is reminiscent of adenylation domains in nonribosomal peptide synthesis. Based on biochemical experiments and recently solved crystal structure of an SerRS-homolg in the complex with its macromolecular substrate (a carrier protein), the mechanisam of specific protein aminoacylation by newly discovered synthetase-like enzyme has been revealed (Mocibob et al, Structure 2013).
1. Cvetešić N, Šemanjski M, Soufi B, Krug K, Gruić-Sovulj I, Maček B (2016) Proteome-wide Measurement of Non-canonical Bacterial Mistranslation by Quantitative Mass Spectrometry of Protein Modifications. Sci Rep. 6, Article number: 28631 doi:10.1038/srep28631 Full text (IF= 5.228 rank 7/63 – Multidisciplinary Sciences)
2. Cvetešić N, Biluš M, Gruić-Sovulj I (2015) The tRNA A76 Hydroxyl Groups Control Partitioning of the tRNA-dependent Pre- and Post-transfer Editing Pathways in Class I tRNA Synthetase. J Biol Chem. 290, 22; 1398-1391. doi: 10.1074/jbc.M115.648568. PMID: 25873392 Full text (IF=4.573 rank 61/290 - Biochemistry & Molecular Biology)
3. Maršavelski A, Močibob M, Gruić-Sovulj I & Vianello R. (2015) The origin of specificity and insight into recognition between aminoacyl carrier protein and its protein partner Phys Chem Chem Phys. 17, 19030-8. doi: 10.1039/c5cp03066h. PMID: 26129823 Full text (IF=4.493 rank 6/34 – Physics, atomic, molecular & chemical and rank 32/139 – Chemistry, physical)
4. Cvetešić N, Dulić M, Bilus M, Šoštarić N, Lenhard B, Gruić-Sovulj I. (2016) Naturally Occurring Isoleucyl-tRNA Synthetase without tRNA-dependent Pre-transfer Editing. J Biol Chem. 291, 8618-31. doi: 10.1074/jbc.M115.698225. PMID: 26921320 Full text (IF= 4.573 rank 61/290 - Biochemistry & Molecular Biology)
5. Kekez M, Bauer N, Šarić E, Rokov Plavec J. (2016) Exclusive cytosolic localization and broad tRNASer specificity of Arabidopsis thaliana seryl-tRNA synthetase, J Plant Biol 59(1): 44-54. doi:10.1007/s12374-016-0370-3 Full text (IF=1.2018; rank 114/204 – Plant sciences)
Posttranslational modification to proteins by glycosylation is an important source of variability in human populations. Large-scale studies performed by group of prof. Lauc demonstrated this for both human plasma glycome (Knežević et al., J Prot Res, 2009) and IgG glycome (Pučić et al., Mol Cell Prot, 2011). In addition to genetic predetermination of the individual glycome composition, the environment plays an important role in changing the glycome during a life-time. Glycophenotypes have been associated with many pathophysiological conditions and diseases such as diabetes, cardiovascular, inflammatory, autoimmune diseases, and cancer. The heritability of glycans is generally below 50% indicating that the temporal stability of the glycome is the result of regulatory mechanisms, which maintain stable regulation of protein glycosylation with time, but are not necessarily heritable. Stable epigenetic regulation of glyco-gene expression is an important mechanism, which can explain both the temporal stability of the glycome in homeostasis and specific changes which occur in various diseases (Horvat et al., Clinical Epigenetics, 2011).
We demonstrated the importance of epigenetic deregulation of genes involved in protein glycosylation in several recent studies. We have shown that epigenetic silencing by cytosine methylation in HNF1A promoter, a transcription factor previously shown to be master regulator of plasma protein antennary fucosylation, changes the composition of the human plasma N-glycome (Zoldoš et al., Epigenetics, 2012). In collaboration with the team of prof. Lauc, we also shown that hypermethylation of HNF1A promoter induces the same type of changes (increase in highly branched glycans) in plasma glycome as the inactivating mutation in this gene, which causes HNF1A-MODY subtype of monogenic diabetes.
We further demonstrated that epigenetic changes, induced by DNA methylation and histone deacetylation inhibitors, affect membrane N-glycome of HeLa cells (Horvat et al., BBA General Subjects, 2012), and that the N-glycome profiles can be reverted after the removal of the same inhibitors (Horvat et al., PLoS One, 2013). Glycans on the cell membrane are essential elements of tumor cell's metastatic potential and are also an entry point for nearly all pathogenic microorganisms. Since epigenetic inhibitors used in this work are registered drugs, the study provides a new line of research in the application of these drugs as anticancer and antimicrobial agents. We are currently investigating the effects of epigenetic inhibitors on the N-glycome of HepG2 cells, a suitable in vitro model system for studies of human liver, an organ where HNF1A is highly expressed and is involved in regulation of many liver-specific genes.
The main goal of the epigenetic group on INTEGRA-Life project are:
. To develop chromatin immunoprecipitation methods (ChiP-qPCR) for analysis of histone modifications
. To develop qPCR assays for analysis of glyco-gene expression in plasma, specific cell lines, as well as in paraffin embedded liver and pancreatic tissues
. To develop pyrosequencing assays for CpG methylation of key glyco-genes and apply them to study large case/control and population cohorts
. To perform analyses expression and cytosine methylation of specific glyco-genes from microdissected tissues (in studies involving hepatocellular carcinoma, diabetes, inflammatory bowel disease)
Dr. Vlatka Zoldoš is an associate professor of Genetics and Epigenetics at the Faculty of Science University of Zagreb. She was born in Zagreb in 1968, graduated Biology in 1992, and obtained PhD in Molecular Biology at the University of Paris XI and University of Zagreb in 2000 within the program of dual mentorships. She was working for 15 years in the field of plant biology. In 2008, she established epigenetic group at the Department of Molecular Biology, Faculty of Science, and changed the research field. Her group is currently working on epigenetic regulation of N-glycosylation of human proteins. She has also introduced the technique of microdissection using Zeiss-Palm laser microdissector, at the Department of Molecular Biology, which enables separation of individual cells or parts of tissue sections.
Several projects are currently active in the group:
. Chromatin dynamics and genome plasticity (MZOS grant)
. Diagnostic and prognostic biomarkers for inflammatory bowel disease (FP7 grant)
. Epigenetic vs. genetic diversity of natural plant populations: A case study of Croatian endemic Salvia species (HrZZ grant)
1. Vojta A, Dobrinić P, Tadić V, Bočkor L, Korać P, Julg B, Klasić M, Zoldoš V (2016) Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Research, March 2016, 1 – 14. doi: 10.1093/nar/gkw159; izvorni znanstveni članakIF = 9.112; časopis rangiran u 10% (20/290) najboljih časopisa u području Biochemisty & Molecular Biology
2. Theodoratou E, Campbell H, Ventham NT, Kolarich D, Pučić-Baković M, Zoldoš V, Fernandes D, Pemberton IK, Rudan I, Kennedy NA, Wuhrer M, Nimmo E, Annese V, McGovern DPB, Satsangi J, and Lauc G (2014) The role of glycosylation in IBD, Nature Reviews Gastroenterology and Hepatology, 11 (10): 588 – 600. doi: 10.1038/ngastro; revijalni članak IF=12,610; rank 3/76 – Gastroenterology & Hepatology; Q1 (Gastroenterology)
3. Zoldoš V, Horvat T, Lauc G (2013) Glycomics meets genomics, epigenomics and other high throughput omics for system biology studies. Curr Opin Chem Biol 17:34-40. doi:10.1016/j.cbpa.2012.12.007;IF=9,850; rank 16/289 – Biochemistry & Molecular Biology, Q1 (Biochemistry)
4. Krištić J, Vučković F, Menni C, Klarić L, Keser T, Beceheli I, Pučić-Baković M, Novokmet M, Mangino M, Thaqi K, Rudan P, Novokmet N, Šarac J, Missoni S, Kolčić I, Polašek O, Rudan I, Campbell H, Hayward C, Aulchenko Y, Valdes A, Wilson JF, Gornik O, Primorac D, Zoldoš V, Spector T and Lauc G (2014) Glycans are a novel biomarker of chronological and biological age. J Gerontol A Biol Sci Med Sci, 69(7): 779 – 789. doi:10.1093/gerona/glt190 ; izvorni znanstveni članakIF=5.416; rank 2/50 Geriatrics & Gerontology; Q1 (Geriatrics & Gerontology)
5. Lauc G, Vojta A, Zoldoš V (2013) Epigenetic regulation of glycosylation is the quantum mechanics of biology. BBA General Subjects, 1840(1): 65-70. doi:10.1016/j.bbagen.2013.08.017. revijalni članakIF=4,381; rank 68/289 – Biochemisty & Molecular Biology; Q1 (Biochemistry)
6. Vičić V, Barišić D, Horvat T, Biruš I, Zoldoš V (2013) Epigenetic characterization of chromatin in cycling cells of pedunculate oak, Quercus robur L. Tree Genetics & Genomes, 9: 1247-1256, doi: 10.1007/sl1295-013-0632; izvorni znanstveni članakIF 2.435; Q1 (Forestry)
7. Vojta A, Samaržija I, Bočkor I, Zoldoš V (2016) Glyco-genes change expression in cancer through aberrant methylation. BBA General Subjects. doi: 10.1016/j.bbagen.2016.01.002; izvorni znanstveni članakIF = 4.381; rank 89/290 – Biochemisty & Molecular Biology; Q1 (Biochemistry)
8. Vičić Bočkor V, Barišić D, Horvat T, Maglica Ž, Vojta A. Zoldoš V (2014) Inhibition of DNA Methylation Alters Chromatin Organization, Nuclear Positioning and Activity of 45S rDNA Loci in Cycling Cells of Q. robur. //PLoS One 5;9(8):e103954 ; izvorni znanstveni članakIF=4,092; rank 12/85 – Biology, Q1 (Biology)
9. Vojta A & Zoldoš V (2013) Adaptation or Malignant Transformation: the Two Faces of Epigenetically Mediated Response to Stress. BioMed Research International, article ID 954060,doi:10.1155/2013/954060. ; izvorni znanstveni članakIF = 2.88; Q1 (Biochemistry, Genetics and Molecular Biology – miscellaneous)
10. Menni C, Keser T, Mangino M, Bell JT, Erte I, Akmačić I, Vučković F, Pučić Baković M, Gornik O, McCarthy MI, Zoldoš V (shared last author), Spector TD, Lauc G, Valdes A (2013) Glycosylation of Immunoglobulin G: Role of genetic and epigenetic influences. PLoS ONE, 8(12): e82558; izvorni znanstveni članakIF=4,092; rank 12/85 – Biology, Q1 (Biology)
11. Horvat T, Deželjin M, Redžić I, Barišić D, Herak-Bosnar M, Lauc G, Zoldoš V (2013) Reversibility of Membrane N-Glycome of HeLa Cells upon Treatment with Epigenetic Inhibitors. PLoS ONE 8(1): e54672. doi:10.1371/journal.pone.0054672; izvorni znanstveni članak IF=4,092; rank 12/85 – Biology, Q1 (Biology)
12. Zoldoš V, Novokmet M, Beceheli I, Lauc G (2013) Genomics and epigenomics of the human glycome. Glycoconjugate J, 30:41-50. IF=3,747; rank 148/286 – Biochemistry & Molecular Biology, Q2 (Biochemistry & Molecular Biology)
13. Dobrinić P, Tadić V, Bočkor L, Markulin D, Tremski M, Zoldoš V, Vojta A (2016) Genome editing tools for functional analysis of HNF1A and IL6ST genes. Croatica Chemica Acta, 89(2) doi:10.5562/cca2859
14. Klasić M, Krištić J, Korać P, Horvat T, Markulin D, Vojta A, Reiding KR, Wuhrer M, Lauc G, Zoldoš V (2016) DNA hypomethylation upregulates expression of MGAT3 gene in HepG2 cells and leads to changes in N-glycosylation of secreted proteins. Scientific Reports 6, 24363, doi: 10.1038/srep 24363 (2016). IF = 5.578
15. Lauc G, Krištić J, Zoldoš V (2014) Glycans – the third revolution on evolution. Frontiers in Genetics. (perspective article). 5(145): 1 -7; doi: 10.3389/fgene.2014.00145; revijalni članak