mining bacterial genomes for laccases luka ausec , marko verce, miha Črnigoj, vesna jerman,
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University of Ljubljana, Biotechnical Faculty Dept. of Food Science and Technology, Chair of Microbiology. Mining bacterial genomes for laccases Luka Ausec , Marko Verce, Miha Črnigoj, Vesna Jerman, Ines Mandić-Mulec. The 2nd International Symposium “VERA JOHANIDES”, Zagreb, May 11 2013. - PowerPoint PPT PresentationTRANSCRIPT
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
Why care about laccases
What do they do? How do they do it?
Why care about laccases
What do they do? How do they do it?
Environmentally friendly
Fungal vs. Bacterial Laccases
Ease of pruduction Substrate range pH and temperature optimum Salt tolerance
Sources of novel bacterial laccases
DNA potential Activty
related cultured strains unknown known
metagenomics unknown unknown
bioinformatics known unknown
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
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
Mining the pool, #2: anaerobe
Laccase from Geobacter
metallireducens
pH optimum temperature optimum
Conclusions
Bacterial laccases are diverse Bioinformatic (HMM-based) approaches
successful Bacterial laccases have promissing traits for
biotechnological applications
Bioinformatic analysis of bacterial laccase-like genes
>2200 completed and draft bacterial genomes
METHODS: profile Hidden Markov Models (pHMM) 5 models constructed
2-domain laccases3-domain laccases
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