La gramática de la diversidad microbiana Víctor de Lorenzo Centro Nal. Biotecnologia CSIC, Madrid...
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Transcript of La gramática de la diversidad microbiana Víctor de Lorenzo Centro Nal. Biotecnologia CSIC, Madrid...
La gramática de ladiversidad microbiana
Víctor de LorenzoCentro Nal. Biotecnologia
CSIC, Madrid (Spain)
microorganisms
200 k
ecosystems
plants(250k)
animal1500k
animalsplants
microbes
human
known existing
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
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 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
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