Post on 19-Dec-2015
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