Projects / Programmes source: ARRS

Primerjalna genomika za ciljne izboljšave industrijskih sevov (Slovene)

Research activity

Code Science Field Subfield
4.06.01  Biotechnical sciences  Biotechnology  Recombinant DNA technology 
Evaluation (rules)
source: COBISS
Researchers (12)
no. Code Name and surname Research area Role Period No. of publications
1.  30761  PhD Marko Blažič  Biochemistry and molecular biology  Junior researcher  2009 - 2011  26 
2.  18332  PhD Neža Čadež  Biotechnology  Researcher  2011  306 
3.  25518  PhD Miha Črnigoj  Pharmacy  Researcher  2009 - 2011  42 
4.  32502  PhD Dušan Goranovič  Biotechnology  Researcher  2010 - 2011  30 
5.  25519  PhD Jaka Horvat  Biotechnology  Researcher  2009 - 2011  49 
6.  23483  PhD Enej Kuščer  Biotechnology  Researcher  2009 - 2011  36 
7.  25521  PhD Urška Lešnik  Biotechnology  Researcher  2009 - 2010  31 
8.  05993  PhD Ines Mandić-Mulec  Biotechnology  Researcher  2009  590 
9.  21244  PhD Jan Mavri  Pharmacy  Researcher  2009  57 
10.  13542  PhD Hrvoje Petković  Biotechnology  Principal Researcher  2009 - 2011  289 
11.  10873  PhD Nataša Poklar Ulrih  Chemistry  Researcher  2009 - 2011  792 
12.  04001  PhD Peter Raspor  Microbiology and immunology  Researcher  2009  1,877 
Organisations (2)
no. Code Research organisation City Registration number No. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  64,462 
2.  2592  ACIES BIO, biotehnološke raziskave in razvoj, d.o.o. (Slovene)  Ljubljana  2226391  472 
Significance for science
“Comparative genomics for targeted industrial strain improvement” was a collaborative project of three institutions, the Biotechnical Faculty (BF) of the University of Ljubljana, Lek/Sandoz pharmaceutical company and a biotech SME Acies Bio. The three were joined in the effort to increase understanding and expertise in the field of novel methods, technologies and approaches for improvement of industrial strains and technologies. The main focus of researchers from BF and Acies Bio has been the collaboration in R&D activities carried out by Lek/Sandoz. The results of this project are aimed towards application, especially in development of the industrial bioprocess for production of FK506 strain and evaluation of the technology by comparative genomics approach. Novel improved, economical and rapid methods for DNA sequencing have opened new horizons in the field of research of industrially important metabolites. Whole-genome-based metabolic engineering has become a realistic approach in improvement of medicinally and industrially important microbial strains. In the course of our project we have obtained whole genome sequences of wild type and industrial overproducing strain of the immunosuppressive compound FK506 producing organism Streptomyces tsukubaensis. Taking advantage of the genomic sequences, obtained in 2009, we have already identified a novel biosynthetic pathway for provision of allylmalonyl-CoA extender unit. This pathway opened new opportunities in the field of metabolic and biosynthetic engineering and enabled the development of a novel approach for production of FK506 without impurities. In addition, new regulatory pathways have been identified which contribute to higher yield of FK506. We have also identified gene clusters encoding undesired parallel pathways which lead to the biosynthesis of “competitive” compounds which consume the same precursors as FK506.. Based on the results of this project two (2) articles were published in high impact factor journals. The first one describes the novel biosynthetic pathway in the highly rated Journal of Biological Chemistry and the second one describes a novel biosynthetic approach for FK506, based on the inactivation of one of the genes of this metabolic pathway. This article was published in the journal “Metabolic engineering”. Two additional articles are expected to be published in 2012, covering the identified gene clusters for “competitive” compounds and the regulatory pathways involved in FK506 biosynthesis
Significance for the country
Two larger and successful pharmaceutical companies with fermentation production facilities are located in Slovenia. Production bioprocesses and microbial strains are being continuously improved due to economic demands for increased yield and strict legislation on product quality and impurity profile. Classical random mutagenesis (chemical mutagens, UV-light) and selection as well as genetic engineering are being used. Classical mutagenesis has been proven to be a very successful method, as many industrial strains have had target metabolite yields increased by several hundred-fold than the corresponding wild type strain. Unfortunately, no information about the reasons for improved properties are obtained using classical approach. In the scope of this project a comparative genomics approach has been used to determine which metabolic pathways influence the increase of FK506 yield. Several previously unknown metabolic pathways have already been found to have key importance for FK506 yield increase and novel approaches have been designed that may enable significant reduction of production cost for the industrial partner Lek/Sandoz. Classical as well as genetic approach of microbial strain improvement are also among most important activities of Acies Bio, a young biotech company located in Ljubljana Technology Park and actively participating in implementation of the project. Based also on the results of this project researchers of Acies Bio and Lek/Sandoz have filed a patent application covering the improved production process of FK506 (EP2272963 A1). This has increased the expertise of Acies Bio researchers as well as established the reputation of Acies Bio as a competent R&D partner. Successful collaboration with a big pharmaceutical company Lek/Sandoz is expected to have a big impact on the company in the future. Undergraduate and graduate students of the Biotechnical faculty of the University of Ljubljana are also involved in some aspects of this project, and are thus able to obtain important knowledge about research in industrial environment. In the first year, they mainly focused on processing of data obtained by the sequencing of S. tsukubaensis genome. The students introduced themselves to modern bioinformatic methods and programs used for processing whole genomes, already used by researchers in industrial environment. In 2010 and 2011 two diploma theses have been carried out and defended by students of the Biotechnical faculty of the University of Ljubljana. Currently, two PhD students and one undergraduate student from the Biotechnical faculty and one undergraduate student from the Faculty of chemistry and chemical technology are finalizing their theses, related to the activities of this project.
Most important scientific results Annual report 2009, 2010, final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Annual report 2009, 2010, final report, complete report on dLib.si
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