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Gene annotation: Laccases and multicopper oxidases P.J. Hoegger 1, S. Kilaru 1, P.E. Courty 2, F. Martin 2, U. Kües 1 1 Georg-August-University Göttingen,

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Presentation on theme: "Gene annotation: Laccases and multicopper oxidases P.J. Hoegger 1, S. Kilaru 1, P.E. Courty 2, F. Martin 2, U. Kües 1 1 Georg-August-University Göttingen,"— Presentation transcript:

1 Gene annotation: Laccases and multicopper oxidases P.J. Hoegger 1, S. Kilaru 1, P.E. Courty 2, F. Martin 2, U. Kües 1 1 Georg-August-University Göttingen, Germany 2 INRA Nancy, France 4th Workshop of the Laccaria Genome Consortium Georg-August-Universität, Göttingen - November 16-17, 2006

2 Multi-copper oxidase family main members:- laccases - fungi - plants - insects - bacteria - ascorbate oxidases - plants - ferroxidases - fungi - ceruloplasmins - mammals

3 Laccase function and application Biological functions:- lignin degradation - lignification - pigment synthesis - fruiting body formation - melanin polymerization - detoxification - cuticle sclerotization - soil litter polymer degrad. Applications:- bleaching processes - bioremediation - composite wood production

4 Trametes versicolor laccase Lcc1 Piontek et al. 2002, JBC 277, type-1 Cu 1 type-2 Cu 2 type-3 Cu

5 Fungal laccase structure L1L2L4L3 Signal sequence signature sequences, including copper ligands HHHHHHHHCHH Substrate binding loops I II III IV

6 Scaffold 39 lcc11lcc1 262 kb222 kb25 kb lcc2 73 kb175 kb lcc3 112 kb3166 kb lcc4 194 kb904 kb lcc5 116 kb312 kb lcc6 429 kb lcc7lcc kb 569 kb lcc9 143 kb110 kb lcc kb65 kb Scaffold 69 Scaffold 2 Scaffold 13 Scaffold 47 Scaffold 67Scaffold 27 Scaffold 14 MCOs in the genome of L. bicolor SpeciesMCO members C. cinerea17 C. neoformans6 U. maydis6 P. chrysosporium5 F. graminearum13 M. grisea11 N. crassa10 A. nidulans7* C. globosum7 C. immitis2 R. oryzae5 yeasts3-5 S. pombe1

7 groupnr. sequences basidiomycetes146 ascomycetes108 zygomycetes5 plants62 animals12 bacteria29 total362 Multi-copper oxidase phylogenetic tree

8 L. bicolor MCOs in phylogenetic tree LbiLcc1 LbiLcc2 LbiLcc3 LbiLcc4 LbiLcc5 LbiLcc6 LbiLcc7 LbiLcc8 LbiLcc9 LbiLcc11 LbiLcc10

9 wood decaying species (Aphyllophorales, Agaricales) wood and litter decomposers (Agaricales)

10 Intron position conservation in basidiomycete laccase genes

11 Tree based on intron positions

12 Scaffold 39 lcc11lcc1 262 kb222 kb25 kb lcc2 73 kb175 kb lcc3 112 kb3166 kb lcc4 194 kb904 kb lcc5 116 kb312 kb lcc6 429 kb lcc7lcc kb 569 kb lcc9 143 kb110 kb lcc kb65 kb Scaffold 69 Scaffold 2 Scaffold 13 Scaffold 47 Scaffold 67Scaffold 27 Scaffold 14 L. bicolor MCO gene family

13 Syn. / non-syn. substitution rates

14 L. bicolor MCOs in phylogenetic tree LbiLcc1 LbiLcc2 LbiLcc3 LbiLcc4 LbiLcc5 LbiLcc6 LbiLcc7 LbiLcc8 LbiLcc9 LbiLcc11 LbiLcc10

15 Iron uptake in fungi Kosman 2003, Mol Microbiol, 47:

16 ftr1a ftr1blcc11 lcc10 lcc10 and lcc11 loci nucleotide id.89%86% aa id. / sim.91% / 95%84% / 88% 331 bp115 bp179 bp 205 bp iron permeaseferroxidase

17 observed syn. sub. potential syn. sub. ratio observed non-syn. sub. potential non-syn. sub. ratio ftr1a / ftr1b lcc10 / lcc Syn. / non-syn. substitution rates of lcc10/lcc11 and ftr1a/ftr1b

18 Intron position conservation in basidiomycete ferroxidase genes

19 MCO arsenal in basidiomycete species

20

21 MCO expression profile MCO geneL 0.5 %L 2 %W 0.1 %W 0.4 %FbM lcc11.60 ± ± ± ± ± ± 0.88 lcc21.97 ± ± ± ± ± ± 0.81 lcc lcc40.94 ± ± ± ± ± ± 0.08 lcc50.87 ± ± ± ± ± ± 0.24 lcc61.09 ± ± ± ± ± ± 0.03 lcc71.29 ± ± ± ± ± ± 0.09 lcc81.04 ± ± ± ± ± ± 0.04 lcc91.30 ± ± ± ± ± ± 0.12 lcc ± ± ± ± ± ± 0.09 lcc ± ± ± ± ± ± 0.28

22 Acknowledgements Molecular Wood Biotechnology, Institute of Forest Botany, Georg-August- University Göttingen, Germany Ursula Kües Patrik Hoegger Sreedhar Kilaru UMR 1136 Interactions Arbres Micro-organismes, Centre INRA de Nancy, Champenoux, France Francis Martin Marc Buée Pierre-Emmanuel Courty

23 MCO arsenal in fungal species basidiomyceteszfilamentous ascomycetesascomycetous yeasts

24 ftr1a ftr1blcc11 lcc10 lcc10 and lcc11 loci nucleotide id.89%86% aa id. / sim.91% / 95%84% / 88% frame- shift? A>G T/C>G G>A A/C>T 331 bp115 bp179 bp 205 bp


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