La gramática de la diversidad microbiana Víctor de Lorenzo Centro Nal. Biotecnologia CSIC, Madrid (Spain)

microorganisms (156 k) ecosystems Known diversity plant (270 k) animal (1.230 k)

Existing diversity animals plants micro organisms

micro organisms 200 k ecosystems plants (250k) animal 1500k animals plants microbes human known existing

fungi 80 k protista 100 k known eubacteria & archaea existing nonculturable culturable 10 k

True vs. False Diversity.. TV sets Human languages

1st Question of the day: How to access Microbial diversity?

The problem of the global genome

genomes sequenced number of new genes 100% 0% How many genomes do we need to access microbial diversity Bioinformatics Genomics/sequencing Gene mining Predictions from number of niches number of genes

New protein folds/megabase of new DNA sequence _________________________ Human DNA1.3 Average prokaryotes 172 Xylella fastidiosa 377 Borrelia burgdorferi 392

number of items Enzymatic vs. Genetic diversity Time/year Novel chemical reactions Novel genes/ Gene variants

Metagenomics

Accessing and exploiting the meta-genome

Cl OH Substrate Product(s) XylR* Inactive Active Pu-lacZPu-Km Selectable phenotype Coloured phenotype Expression Library a b c d +

What is a gene? One gene-one enzyme? One gene-one protein? One gene-one function? One gene-one protein fold?

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The gene landscape

The grammar of Biodiversity... The minimal biological diversity unit? Phonemes (F. de Saussure) Generative Grammar (N. Chomsky) Words, sentences, languages Alphabets, books, editions, libraries How many books?

GrammarBiological entity PhonemeGene/fold/function WordOperon/complex SentenceNetwork Book Organism LibraryEcosystem

2nd Question of the day: How to predict biodegradation?

~ 320 strains ~ 650 compounds ~ 470 catabolic enzymes ~ 730 reactions of environmental interest

In silico biodegradation of toluene: Towards predictive biodegradation

3rd Question of the day: Can bioinformatics reveal features of regulatory networks which are opaque to experimentation?

Levels of regulation in the Pu promoter RNA pol  54 IHF PtsN-P C source FtsH/DnaK ppGpp Anti-sigma? Physiological control Specific regulation XylR CH 3 R

Environmental signal