what makes the enterobacterial plant pathogen pectobacterium atrosepticum different to its animal ...
DESCRIPTION
Invited presentation from the 2007 IS-MPMI plant pathology meeting in Sorrento, Italy. Presentation delivered 26th July 2007.TRANSCRIPT
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Comparative genomics: What makes the enterobacterial plant pathogen Pectobacterium atrosepticum different to its animal pathogenic relatives? And other questions.
Leighton PritchardPaul BirchIan Toth
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Pectobacterium atrosepticum (Pba, formerly Erwinia carotovora subsp. atroseptica):•potato pathogen: blackleg (stem rot), rotting of stored tubers•major rot symptoms due to plant cell wall-degrading enzymes (PCWDEs)•also has T3SS and effectors, and phytotoxins•stealth (host manipulation) and brute force
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Pectobacterium atrosepticum (Pba, formerly Erwinia carotovora subsp. atroseptica):•plant, rather than animal-associated enterobacterium•soft-rot enterobacterium (with Dickeya spp., Pectobacterium carotovorum etc).•temperature/climate-related disease profiles•Pba-centric genomic and transcriptomic comparisons
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Genome sequenced 2004:
•SCRI/Sanger
•Lab strain SCRI1043
•5 Mb
•4472 CDS
•51% (G + C)
•17 putative horizontally-
acquired islands
Bell et al. (2004) Proc. Natl. Acad. Sci. USA 101 11105-11110
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Circular representation
Common sequence:similarity
Gaps :dissimilarity
Bell et al. (2004) Proc. Natl. Acad. Sci. USA 101 11105-11110
Reciprocal best hits(FASTA, 30% ID,
80% overlap)
Coloured by taxonomicgrouping
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Extended comparison to allavailable genomes
Colours indicate similarity:•red: high similarity•blue: low similarity
Most similar organisms onouter rings
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Extended comparison to allavailable genomes
Colours indicate similarity:•red: high similarity•blue: low similarity
Most similar organisms onouter rings
Radial gaps, with highly-similarsequences in less-similarorganisms indicate potential HGT or gene loss
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Selection pressure in allenvironments
Loss of functions important only in a former niche
Gain of function on adaptation to a novel niche
Acquisition from organismsinhabiting novel niche
What does Pba have that plant-associated bacteria have, but animal-associated enterobacteria do not?
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Marked features: more similar to PAB
than to AAE[>1.5X mean bit score](497, >10% of genome)
Plant-associated bacteria(PAB)
Animal-associated enterobacteria (AAE)
Toth et al. (2006) Ann. Rev. Phytopath. 44 305-336
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Attachment
Nitrogen fixation
Coronafacic acid
Type III Secretion System
Toth et al. (2006) Ann. Rev. Phytopath. 44 305-336
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AggA contributes to root adhesion in Pseudomonas putida
Pba ECA3266, aggA are similar to PAB, not AAE, and found in HAI
See Poster PS2-176 (Sonia HUMPHRIS)
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cfa synthesis genes similar to PAB, not AAE, and found in HAI
A series of cfa synthesisgene knockouts wasconstructed
Lesion length much reduced in the knockouts compared to WT
WT cfa-
Bell et al. (2004) Proc. Natl. Acad. Sci. USA 101 11105-11110
See Poster PS13-642 (Michael RAVENSDALE)
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11k Agilent arrays Pba, Dda
Challenge Pba array withDda and Pcc gDNA
(Complementary analysis to RBH of prepublication Dda genome)
Ravirala et al. (2007) Mol. Plant-Microbe Int. 20 313-320
See Poster PS13-637 (Hui LIU)
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Pba Pcc Dda Pba Pcc Dda Pba Pcc Dda
Pba Pcc Dda
Whole-genome Southern hybridisation
Exact match of 20 probes to Dda genome
Over 900 probes hybridise strongly to Dda gDNA (3200 total)
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PAB AAE
No RBH in Dda(1351)
No hyb to Pcc(1035)
30 selected islands of interest that don’t hyb to
Pcc, or make no RBH to Dda
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cfa synthesis genes
Pcc BAC spanning SPI-7/cfa genessequenced and annotated (Sanger)
Blue bars indicatematches (BLAST)
cfa gene probes do not hyb to Pcc; have no counterpart insyntenous SPI-7region
Pba
Pcc
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Region of Pba:•in HAI•no hyb to Pcc•RBH matches to Dda•RBHs to other PAB
nif: nitrogen fixation
•Prediction:•WT Pba fixes N•Pba nif knockouts do not fix N•WT Dda fixes N•WT Pcc does not fix N
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Pba Pcc Dda
•three WT Pba strains fix N•two WT Dickeya spp. Fix N•one of six tested Pcc WT strains fixes N•Pba nifA- mutant does notfix N
•Prediction:•WT Pba fixes N•Pba nif knockouts do not fix N•WT Dda fixes N•WT Pcc does not fix N
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What makes Pba different from animal-associated enterobacteria, andfrom other soft-rotting plant pathogens?
HGT activity
Putatively acquired functions:•coronafacic acid synthesis•root adhesion•nitrogen fixation
about 25% of genome also distinguishes Pba from close relatives…
What else to find out:
•What has Pba lost, in respect to animal-associated enterobacteria?
•(and closer relatives)?
•What do they all have in common?
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SCRIPaul BirchIan Toth
Hui LiuSonia HumphrisLucy MolelekiMichael RavensdalePete Hedley
Eduard VenterGunnhild TakleBeth HymanJennifer White
SangerPathogen Sequencing Unit
FundingSEERAD, BBSRC
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Comparisons against other bacterial genomes:
Reciprocal best hits(FASTA, 30% ID,
80% overlap)
linear representation
Coloured by taxonomicgrouping
Bell et al. (2004) Proc. Natl. Acad. Sci. USA 101 11105-11110
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database .gbk .crunch …
Python Script GenomeDiagram
Reportlab
database .gbk .crunch …
Python Script GenomeDiagram
Reportlab
229 bacterial comparisons
185970 RBH
23Gb of data
24h on 50-node cluster
Visualisation issues
Pritchard et al. (2006) Bioinformatics 22 616-617
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Failure to hybridise does notimply that the Pba gene isabsent
Dda: 2910 RBH to Pba; 949strongly hybridising probes(ca. 3200 total)
Weakly-hybridising probesare seen with > 90% aminoacid identity
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E. coli CFT073 Pasteurella multocida
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Salmonella entericasubsp. enterica
serovar Typhi LT2str. CT18
Plasmid hotspots
Toth et al. (2006) Ann. Rev. Phytopath. 44 305-336