Aucun titre de diapositive

1
Pathway Tools Meeting - December 1, 2005, Geneva
(SIB)


Putting together synteny and metabolic
information to achieve relevant expert annotation
of microbial genomes
Dr Claudine Médigue
2
What is MaGe ? Yet another bacterial annotation
platform !

• Its development started in Oct. 2002

Context the Acinetobacter sp. ADP1
genome annotation (Summer 2004)
3
Introduction to the Prokaryotic Genome DataBase
(PkGDB)
Purpose storage of clean and complete
annotation data which are subsequently used in
the genomic comparative analysis.

• Relational SGBD (MySQL)

4
Simplified structure of PkGDB
Annotation project
Re-annotation project
Published genomes
Newly sequenced genomes
Reference annotation for model organisms
NCBIRefSeq
GenomeReviews
Gene prediction AMIGene
Subtilist
Ecogene
Geneprotec
Annotation management
Sequence updates and annotation transfer
Annotator management
Genomic ObjectsAutomatic and manual functional
assignations
Functional Classification
Annotation history
MultiFun
GeneOntology
Functional predictions
Specific regions
Protein similarities
? helixes and signal peptides
Enzymatic functions
Domains and motifs
Orthologs Paralogs
COG
Interpro
Uniprot
BioCyc
KEGG
Syntenies
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How to read the synteny maps ?
ACIAD0574
hutH
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A larger view of the previous Acinetobacter ADP1
region
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How are genes organized in a synteny group ?
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Synteny maps are useful to annotate gene
fusion/fission
Colored rectangles represent the part of the
protein which aligns with the corresponding
Acinetobacter protein.
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Simplified structure of PkGDB
Re-annotation project
Annotation project
Published genomes
Newly sequenced genomes
Reference annotation for model organisms
Reference annotation for model organisms
NCBIRefSeq
GenomeReviews
Gene prediction AMIGene
Geneprotec
Subtilist
Geneprotec
Subtilist
Ecogene
Ecogene
Annotation management
Sequence updates and annotation transfer
Annotator management
Annotator management
Genomic ObjectsAutomatic and manual functional
assignations
Functional Classification
Functional Classification
Annotation history
GeneOntology
GeneOntology
MultiFun
MultiFun
Functional predictions
Specific regions
Protein similarities
? helixes and signal peptides
Enzymatic functions
Domains and motifs
Orthologs Paralogs
COG
Interpro
Uniprot
KEGG
BioCyc
Syntenies
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Setting up a new annotation project an example
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Comparative Metabolic Capabilities an example
Reaction content comparisons between the 3
Bradyrhizobium organisms (BioWareHouse SQL query
on reactions having gene-gt protein-gtreaction
correspondences )
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Bradyrhizobium ORS278 region containing CDS
57715772
BRAOR5771-5772 - 5773
Cloning and Characterization of the Genes
Encoding Enzymes for the Protocatechuate
Meta-degradation Pathways of Pseudomonas
ochraceae NGJ1 Maruyama et al. (2004) Biosci.
Biotechnol. Biochem, 68, 1434-1441.
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AUTOmatic vs EXPert annotation of the region
Evidence
EC-number
Gene
PRODUCT
BRAOR5770
BLAST R. palus PRIAM (medium)
ligC
4-carboxy-2-hydroxymuconate-6-semialdehyde
dehydrogenase
1.1.1.18
AUTO
BLAST P. testosteroni Publication Enzyme
EXP
ligC
4-carboxy-2-hydroxymuconate-6-semialdehyde
dehydrogenase
1.2.1.45
BRAOR5771
BLAST R. palus PRIAM (high)
ligB
AUTO
EXP
Protochatechuate 4,5-dioxygenase, alpha subunit
1.13.11.8
BRAOR5772
BLAST R. palus PRIAM (high)
ligA
Protochatechuate 4,5-dioxygenase, beta subunit
1.13.11.8
AUTO
EXP
BRAOR5773
2-pyrone-4,6-dicarboxylic acid hydrolase
none
ligI
BLAST R. palus
AUTO
BLAST R. palus Publication Enzyme
EXP
2-pyrone-4,6-dicarboxylic acid hydrolase
ligI
3.1.1.57
BRAOR5774
Putative dehydrogenase
none
BLAST R. palus
none
AUTO
BLAST R. palus InterproScan
EXP
1.1.1.-
none
Putative dehydrogenase with NAD binding protein
BRAOR5775
Putative acyl transferase
none
BLAST R. palus
fidZ
AUTO
BLAST P. ochraceae Publication Enzyme
EXP
4.1.3.17
ligK
4-hydroxy-4-methyly-2-oxoglutarate aldolase
BRAOR5776
none
ligJ
BLAST R. palus
4-oxalomesaconate hydratase
AUTO
BLAST R. palus Publication Enzyme
EXP
ligJ
4-oxalomesaconate hydratase
4.2.1.83
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Bradyrhizobium ORS278 region after expert
annotation
BRAOR5771-72
BRAOR5777
BRAOR5778
BRAOR5770
BRAOR5773
BRAOR5776
BRAOR5775
4.2.1.83
1.2.1.45
1.13.11.8
3.1.1.57
ligJ
4.1.3.17
ligBA
ligI
ligC
ligK
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Connectivity to KEGG database
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Connectivity to KEGG database
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Bradyrhizobium ORS278 region after expert
annotation
ligR
The reactions catalyzed by 1.2.1.45 and 4.2.1.83
exist in MetaCyc but they are not involved in a
pathway.
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Enzymatic activity predictions (PRIAM) some
results

• Comparison of PRIAM predictions P and Expert
  annotations E

Pseudoalteromonas haloplanktis
Frankia alni
Pseudomonas entomophila
Acinetobacter ADP1
6861
5182
Total genes
3514
3325
1729 / 1498
Nb EC_P vs EC_E
927 / 993
1455 / 1232
1012 / 947
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PGDBs built at Genoscope
Tier 3 Computationally-Derived Databases
Subject to No Curation Tier 2
Computationally-Derived Databases Subject to
Moderate Curation
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Some Questions / Perspectives
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Metabolic Thesaurus project at Genoscope
Véronique de Berardiniss team
3325 Acinetobacter ADP1 annotated genes
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Metabolic Pathway Reconstruction / Experimental
Data
ColiScope
Metabolic Thesaurus
Sequencing of 2 commensal and 4 pathogenic E.
coli strains
Acinetobacter ADP1 KO collection
Phenotypic analysis growth essay on different
nutrient sources Metabolome analysis LC/MS and
CE/MS
Data Integration and Comparative Analysis
Evolution of metabolic capabilities gt adaptation
of microorganisms commensalism / virulence
emergence
Linked enzymatic activity to genes of unknown
function
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Participating teams

• AGC team

• Zoé Rouy

• David Vallenet

• Aurélie Lajus

• Stéphane Cruveiller

• Claudine Médigue

• Genoscope informatic system team

• Claude Scarpelli

• Laurent Sainte-Marthe

• Sylvain Bonneval

• and with the help of

• François Lefèvre (V. Schächter team)

• Mages users feedback helps in improving many
  functionalities of our system !