Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,
description
Transcript of Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,
![Page 1: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/1.jpg)
Mining bacterial genomes for laccases
Luka Ausec, Marko Verce, Miha Črnigoj, Vesna Jerman, Ines Mandić-Mulec
University of Ljubljana, Biotechnical FacultyDept. of Food Science and Technology, Chair of Microbiology
The 2nd International Symposium “VERA JOHANIDES”, Zagreb, May 11 2013
![Page 2: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/2.jpg)
Why care about laccases
What do they do? How do they do it?
![Page 3: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/3.jpg)
Why care about laccases
What do they do? How do they do it?
Environmentally friendly
![Page 4: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/4.jpg)
Fungal vs. Bacterial Laccases
Ease of pruduction Substrate range pH and temperature optimum Salt tolerance
![Page 5: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/5.jpg)
Sources of novel bacterial laccases
DNA potential Activty
related cultured strains unknown known
metagenomics unknown unknown
bioinformatics known unknown
![Page 6: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/6.jpg)
From genomes to pool of potentials
Ausec, Zakrzewski et al., PLoS ONE 2011
6.5 %on plasmids
75% of genes encode signal peptides
2,200 draft and completed genomes
1,240 putative laccase genes
![Page 7: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/7.jpg)
Laccase from Thioalkalivibrio sp.
Mining the pool, #1: extremophile
pH
substrate optimal pH
ABTS 5
K4Fe(CN)6 5
pyrocatechol 8
pyrogallol 7
2,6-DMP 9.5
syringaldehyde 8
syringic acid N.A.
syringaldazine 8
guaiacol N.A.
Vanillic acid N.A.
ferulic acid N.A.
tyrosine N.A.
substrates
pH optima
![Page 8: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/8.jpg)
Mining the pool, #2: anaerobe
Laccase from Geobacter
metallireducens
pH optimum temperature optimum
![Page 9: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/9.jpg)
Conclusions
Bacterial laccases are diverse Bioinformatic (HMM-based) approaches
successful Bacterial laccases have promissing traits for
biotechnological applications
![Page 11: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/11.jpg)
Bioinformatic analysis of bacterial laccase-like genes
>2200 completed and draft bacterial genomes
METHODS: profile Hidden Markov Models (pHMM) 5 models constructed
![Page 12: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/12.jpg)
2-domain laccases3-domain laccases
![Page 13: Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman,](https://reader035.fdocuments.net/reader035/viewer/2022062322/568146c6550346895db40283/html5/thumbnails/13.jpg)
Figure 3 - List of species encoding laccase genes and possessing plasmids in their genomes. The bars represent the number of laccase genes in the genome (black) and the number of laccase genes on plasmids (gray). The length of the bar shows the total number of genes for each organism.
76 genes on plasmids of 46 organisms