1 / 14

Bielen Ana

Scanning for genes encoding GDS(L) hydrolases in Actinobacteria from wide diversity of ecological niches. Bielen Ana. The 2 nd International Symposium “VERA JOHANIDES” Zagreb, May 10-11, 2013. Actinobacteria. various ecological niches. ... various benefits. Antibiotics

josiah
Download Presentation

Bielen Ana

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Scanning for genes encoding GDS(L) hydrolases in Actinobacteria from wide diversity of ecological niches Bielen Ana The 2ndInternational Symposium “VERA JOHANIDES” Zagreb, May 10-11, 2013

  2. Actinobacteria various ecological niches... ... various benefits • Antibiotics • Anticancer and other drugs • Probiotics • Hydrolytic enzymes for bioremediation and industrial applications GDS(L) family of hydrolytic enzymes

  3. Tween detergents glycerol esters Fats and oils GDS(L) enzymes from Streptomyces coelicolor (Sc1L) and S. rimosus (SrL) Multifunctionality, stability, broad substrate specificity! Classes of substrates... α/β-naphthyl esters p-nitrophenyl esters Activ(ated) in organic solvents (dioxane, THF, acetone...) Abramić et al, 1999; Bielen et al, 2009

  4. GDS(L) family of lipolytic enzymes GDS(L) esterase from S. scabies • conserved 3D structure • low overall sequence homology Block I Block II Block III Block V ... SEARCHING FOR NOVEL GDS(L) ENZYMES USING TRADITIONAL SEQUENCE SEARCH METHODS (e.g. Blast) IS NOT SUFFICIENT!

  5. Solution: HMM-based motif scanning techniques Step 1: Collect sequences of experimentally confirmed family members Etc.

  6. Solution: HMM-based motif scanning techniques Step 2: Construct multiple sequence alignment (e.g. seed alignment)

  7. Solution: HMM-based motif scanning techniques Step 3: Cut out conserved motifs

  8. Solution: HMM-based motif scanning techniques Step 4: Build model representing selected motifs (emission probabilities!) Step 5: Scan proteomes of selected organisms for desired motifs -> select best possible motifs in every sequence in proteome and assign ascore

  9. Solution: HMM-based motif scanning techniques Step 6: Combine different motif scanning methods for optimal results -> sharp cut-off discriminates between positive and negative hits Scores of A. thaliana proteome scanning for GDS(L) motifs - Viterbi and posterior decoding combined GDS(L) sequences – positive hits Other sequences – negative hits

  10. 52 actinobacterial proteomes cluster into several groups 257 GDS(L) enzymes great diversity, great potential

  11. Evidence for expansion of genes encoding for GDS(L) hydrolases in Actinobacteria by horizontal gene transfer • genes on plasmids • deviations in codon usage • incongruency between GDS(L) gene-phylogeny and species phylogeny • close homologues in distant organisms Actinobacteria Firmicutes Cyanobacteria Proteobacteria Fungi

  12. Previously unknown variations in motifs Block I Block V Block III Typical Variant Novel catalytic properties?

  13. Conclusions • Application of proper bioinformatic tools to explore sequence diversity present in the databases (more than blast is out there!) • Server for motif scanning -> under construction • Use natural diversity of hydrolitic enzymes for biotechnology

  14. Thankyou for your attention! Goldstein Pavle Paradžik Tina Vujaklija Dušica Bruvo-Mađarić Branka Vujaklija Ivan Pezer Željka

More Related