Genomics and transcriptomics of Erwinia and Pantoea

At a glance

Project leader : Dr. Fabio Rezzonico, Dr. Theo Smits
Project team : Dr. Joël Pothier
Project status : completed
Funding partner : Internal
Contact person : Theo Smits

Description

We study the diversity, plasmid diversity and functionality, and evolution of the invasive bacterial pathogen Erwinia amylovora, cause of fire blight disease, and all related Erwinia species. Additionally, we investigate the biocontrol bacteria Pantoea agglomerans and Pantoea vagans using genomics and transcriptomics to elucidate mechanisms of action, increasing biocontrol activity and resolving biosafety concerns with these species. Working with collaborators in South Africa we are investigating the evolutionary genomics of beneficial and pathogenic Pantoea species.

Publications

Crosby, Katherine C.; Rojas, Mariah; Sharma, Parul; Johnson, Marcela A.; Mazloom, Reza; Kvitko, Brian H.; Smits, Theo H. M.; Venter, Stephanus N.; Coutinho, Teresa A.; Heath, Lenwood S.; Palmer, Marike; Vinatzer, Boris A.,

2023.

Genomic delineation and description of species and within-species lineages in the genus Pantoea.

Frontiers in Microbiology.

14(1254999).

Available from: https://doi.org/10.3389/fmicb.2023.1254999
Sulja, Arburon; Pothier, Joël F.; Blom, Jochen; Moretti, Chiaraluce; Buonaurio, Roberto; Rezzonico, Fabio; Smits, Theo H. M.,

2022.

Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734.

BMC Genomics.

23(742).

Available from: https://doi.org/10.1186/s12864-022-08966-y
Moretti, Chiaraluce; Rezzonico, Fabio; Orfei, Benedetta; Cortese, Chiara; Moreno‐Pérez, Alba; van den Burg, Harrold A.; Onofri, Andrea; Firrao, Giuseppe; Ramos, Cayo; Smits, Theo H.M.; Buonaurio, Roberto,

2021.

Synergistic interaction between the type III secretion system of the endophytic bacterium Pantoea agglomerans DAPP‐PG 734 and the virulence of the causal agent of olive knot Pseudomonas savastanoi pv. savastanoi DAPP‐PG 722.

Molecular Plant Pathology.

22(10), pp. 1209-1225.

Available from: https://doi.org/10.1111/mpp.13105
Smits, Theo H.M.; Duffy, Brion; Blom, Jochen; Ishimaru, Carol A.; Stockwell, Virginia O.,

2019.

Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species.

Archives of Microbiology.

201(6), pp. 713-722.

Available from: https://doi.org/10.1007/s00203-019-01647-7
Smits, Theo; Duffy, Brion; Sundin, George; Zhao, Youfu; Rezzonico, Fabio,

2017.

Erwinia amylovora in the genomics era : from genomes to pathogen virulence, regulation, and disease control strategies.

Journal of Plant Pathology.

99(Special issue), pp. 7-23.

Available from: https://doi.org/10.4454/jpp.v99i0.3917
Rezzonico, Fabio; Duffy, Brion; Smits, Theo H.M.; Pothier, Joël F.,

2017.

Erwinia species identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Journal of Plant Pathology.

99(Special issue), pp. 121-129.

Available from: https://doi.org/10.4454/jpp.v99i0.3916
Ishimaru, Carol; Lansdell, Teresa A.; Clardy, Jon; Duffy, Brion; Smits, Theo H.M.,

2017.

The histidine-reversible antibiotic herbicolin O produced by Pantoea vagans C9-1 is pantocin A.

Journal of Plant Pathology.

99(Special issue), pp. 91-97.

Available from: https://doi.org/10.4454/jpp.v99i0.3910
De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A.; Smits, Theo H.M.; Venter, Stephanus N.; Coutinho, Teresa A.,

2017.

Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii.

Frontiers in Microbiology.

8, pp. 1755.

Available from: https://doi.org/10.3389/fmicb.2017.01755
Kamber, Tim; Pothier, Joël; Pelludat, Cosima; Rezzonico, Fabio; Duffy, Brion; Smits, Theo,

2017.

Role of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host.

BMC Genomics.

16(628), pp. 1-12.

Available from: https://doi.org/10.1186/s12864-017-4010-1
Palmer, Marike; Steenkamp, Emma T.; Coetzee, Martin P.A.; Chan, Wai-Yin; van Zyl, Elritha; De Maayer, Pieter; Coutinho, Teresa A.; Blom, Jochen; Smits, Theo; Duffy, Brion; Venter, Stephanus N.,

2017.

Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella.

Antonie van Leeuwenhoek.

110(10), pp. 1287-1309.

Available from: https://doi.org/10.1007/s10482-017-0852-4
Rezzonico, Fabio; Smits, Theo; Born, Yannick; Blom, Jochen; Frey, Jürg E.; Goesmann, Alexander; Cleenwerck, Ilse; de Vos, Paul; Bonaterra, Anna; Duffy, Brion; Montesinos, Emilio,

2016.

Erwinia gerundensis sp. nov. : a cosmopolitan epiphyte originally isolated from pome fruit trees.

International Journal of Systematic and Evolutionary Microbiology.

66, pp. 1583-1592.

Available from: https://doi.org/10.1099/ijsem.0.000920
Kamber, Tim; Buchmann, Jan P.; Pothier, Joël; Smits, Theo; Wicker, Thomas; Duffy, Brion,

2016.

Fire blight disease reactome : RNA-seq transcriptional profile of apple host plant defence responses to Erwinia amylovora pathogen infection.

Scientific Reports.

6(21600).

Available from: https://doi.org/10.1038/srep21600
Smits, Theo H.M.; Rezzonico, Fabio; Blom, Jochen; Goesmann, Alexander; Abelli, Azzurra; Kron Morelli, Roberto; Vanneste, Joël L.; Duffy, Brion,

2015.

Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c.

Genome Announcements.

3(6).

Available from: https://doi.org/10.1128/genomeA.01448-15
De Maayer, Pieter; Chan, Wai-Yin; Martin, Douglas A.; Blom, Jochen; Venter, Stephanus N.; Duffy, Brion; Cowan, Don A.; Smits, Theo H. M.; Coutinho, Teresa A.,

2015.

Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis.

Frontiers in Microbiology.

6(576).

Available from: https://doi.org/10.3389/fmicb.2015.00576
Ismail, Emadeldeen; Blom, Jochen; Bultreys, Alain; Ivanovic, Milan; Obradovic, Aleksa; van Doorn, Joop; Bergsma-Vlami, Maria; Maes, Martine; Willems, Anne; Duffy, Brion; Stockwell, Virginia O.; Smits, Theo H.M.; Pulawska, Joanna,

2014.

A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids.

Archives of Microbiology.

196(12), pp. 891-899.

Available from: https://doi.org/10.1007/s00203-014-1028-5
Weller-Stuart, Tania; Chan, Wai-Yin; Coutinho, Teresa A.; Venter, Stephanus N.; Smits, Theo H.M.; Duffy, Brion; Goszczynska, Teresa; Cowan, Don A.; de Maayer, Pieter,

2014.

Draft genome sequences for the onion center roth pathogen Pantoea ananatis PA4 and maize brown stalk rot pathogen P. ananatis BD442.

Genome Announcements.

2(4).

Available from: https://doi.org/10.1128/genomeA.00750-14
Rezzonico, Fabio; Smits, Theo H.M.; Holliger, Eduard, eds.,

2014.

Proceedings of the 13th international workshop on fire blight.

13th International Workshop on Fire Blight, Zürich, 2-5 July 2013.

Leuven:

International Society for Horticultural Sciences.

.

ISBN 9789462610460.
Barbé, Silva; Llop, Pablo; Blom, Jochen; Cabrefiga, Jose; Goesmann, Alexander; Duffy, Brion; Montesinos, E.; Smits, Theo H.M.; López, M. M.,

2013.

Complete sequence of Erwinia piriflorinigrans plasmids pEPIR37 and pEPIR5 and role of pEPIR37 in pathogen virulence.

Plant Pathology.

62(4), pp. 786-798.

Available from: https://doi.org/10.1111/ppa.12002
Mann, Rachel A.; Smits, Theo H.M.; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E.; Plummer, Kim M.; Beer, Steven V.; Luck, Joanne; Duffy, Brion; Rodoni, Brendan,

2013.

Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

PLOS ONE.

8(2).

Available from: https://doi.org/10.1371/journal.pone.0055644

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