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

La gramática de ladiversidad microbiana

Víctor de LorenzoCentro Nal. Biotecnologia

CSIC, Madrid (Spain)

microorganisms

(156 k)

ecosystems

Known diversity

plant(270 k)

animal(1.230 k)

Existing diversity

animals

plants

microorganisms

microorganisms

200 k

ecosystems

plants(250k)

animal1500k

animalsplants

microbes

human

known existing

fungi80 k

protista100 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

nu

mber

of

new

gen

es

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 ofnew DNA sequence_________________________

Human DNA 1.3Average prokaryotes 172Xylella fastidiosa 377Borrelia burgdorferi 392

num

ber

of

item

sEnzymatic vs. Genetic diversity

Time/year00 30 70 90 00

Novel chemical reactions

Novel genes/Gene variants

Metagenomics

Accessing and exploiting the meta-genome

Cl Cl

Cl Cl

Cl Cl

Cl

Cl

OH

Substrate

Product(s)

XylR*XylR*

Inactive

Active

Pu-lacZPu-Km

Selectable phenotype

Colouredphenotype

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?

.

. .

.

.

.

. .

.

.

. ..

..

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?

Grammar Biological entity

Phoneme Gene/fold/functionWord Operon/complexSentence NetworkBook OrganismLibrary Ecosystem

2nd Question of the day:

How to predict biodegradation?

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

In silicobiodegradationof toluene:

Towards predictivebiodegradation

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 pol54

IHF

PtsN-PC source FtsH/DnaK

ppGpp

Anti-sigma?

Physiological control

Specificregulation

XylRXylR

CH3

R

Environmental signal

Environmental signal

Environmental signal

Environmental signal

Environmental signal