The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification

De Maayer P, Chan W-Y, Blom J, Venter SN, Duffy B, Smits THM, Coutinho TA (2012)
Bmc Genomics 13(1): 625.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
De Maayer, Pieter; Chan, Wai-Yin; Blom, JochenUniBi; Venter, Stephanus N.; Duffy, Brion; Smits, Theo H. M.; Coutinho, Teresa A.
Abstract / Bemerkung
Background: Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant and animal hosts. This suggests that members of this genus have undergone extensive genotypic diversification. One means by which this occurs among bacteria is through the acquisition and maintenance of plasmids. Here, we have analyzed and compared the sequences of a large plasmid common to all sequenced Pantoea spp. Results and discussion: The Large Pantoea Plasmids (LPP-1) of twenty strains encompassing seven different Pantoea species, including pathogens and endo-/epiphytes of a wide range of plant hosts as well as insect-associated strains, were compared. The LPP-1 plasmid sequences range in size from similar to 281 to 794 kb and carry between 238 and 750 protein coding sequences (CDS). A core set of 46 proteins, encompassing 2.2% of the total pan-plasmid (2,095 CDS), conserved among all LPP-1 plasmid sequences, includes those required for thiamine and pigment biosynthesis. Phylogenetic analysis reveals that these plasmids have arisen from an ancestral plasmid, which has undergone extensive diversification. Analysis of the proteins encoded on LPP-1 also showed that these plasmids contribute to a wide range of Pantoea phenotypes, including the transport and catabolism of various substrates, inorganic ion assimilation, resistance to antibiotics and heavy metals, colonization and persistence in the host and environment, pathogenesis and antibiosis. Conclusions: LPP-1 is universal to all Pantoea spp. whose genomes have been sequenced to date and is derived from an ancestral plasmid. LPP-1 encodes a large array of proteins that have played a major role in the adaptation of the different Pantoea spp. to their various ecological niches and their specialization as pathogens, biocontrol agents or benign saprophytes found in many diverse environments.
Bmc Genomics
Page URI


De Maayer P, Chan W-Y, Blom J, et al. The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. Bmc Genomics. 2012;13(1): 625.
De Maayer, P., Chan, W. - Y., Blom, J., Venter, S. N., Duffy, B., Smits, T. H. M., & Coutinho, T. A. (2012). The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. Bmc Genomics, 13(1), 625. doi:10.1186/1471-2164-13-625
De Maayer, Pieter, Chan, Wai-Yin, Blom, Jochen, Venter, Stephanus N., Duffy, Brion, Smits, Theo H. M., and Coutinho, Teresa A. 2012. “The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification”. Bmc Genomics 13 (1): 625.
De Maayer, P., Chan, W. - Y., Blom, J., Venter, S. N., Duffy, B., Smits, T. H. M., and Coutinho, T. A. (2012). The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. Bmc Genomics 13:625.
De Maayer, P., et al., 2012. The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. Bmc Genomics, 13(1): 625.
P. De Maayer, et al., “The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification”, Bmc Genomics, vol. 13, 2012, : 625.
De Maayer, P., Chan, W.-Y., Blom, J., Venter, S.N., Duffy, B., Smits, T.H.M., Coutinho, T.A.: The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. Bmc Genomics. 13, : 625 (2012).
De Maayer, Pieter, Chan, Wai-Yin, Blom, Jochen, Venter, Stephanus N., Duffy, Brion, Smits, Theo H. M., and Coutinho, Teresa A. “The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification”. Bmc Genomics 13.1 (2012): 625.

20 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Responses of phyllosphere microbiota and plant health to application of two different biocontrol agents.
Qin C, Tao J, Liu T, Liu Y, Xiao N, Li T, Gu Y, Yin H, Meng D., AMB Express 9(1), 2019
PMID: 30924016
Pantoea spp. Associated with Smooth Crabgrass (Digitaria ischaemum) Seed Inhibit Competitor Plant Species.
Elmore MT, White JF, Kingsley KL, Diehl KH, Verma SK., Microorganisms 7(5), 2019
PMID: 31117261
Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria.
Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN., Front Microbiol 9(), 2018
PMID: 29467735
Pantoea ananatis: genomic insights into a versatile pathogen.
Weller-Stuart T, De Maayer P, Coutinho T., Mol Plant Pathol 18(9), 2017
PMID: 27880983
Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.
De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits THM, Venter SN, Coutinho TA., Front Microbiol 8(), 2017
PMID: 28959245
Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees.
Rezzonico F, Smits THM, Born Y, Blom J, Frey JE, Goesmann A, Cleenwerck I, de Vos P, Bonaterra A, Duffy B, Montesinos E., Int J Syst Evol Microbiol 66(3), 2016
PMID: 26813696
Analysis of the effect of high hydrostatic pressure treatment and enterocin AS-48 addition on the bacterial communities of cherimoya pulp.
Pérez Pulido R, Toledo J, Grande MJ, Gálvez A, Lucas R., Int J Food Microbiol 196(), 2015
PMID: 25528726
Significant host jump of Xanthomonas vasicola from sugarcane to a Eucalyptus grandis clone in South Africa
Coutinho TA, Westhuizen L, Roux J, McFarlane SA, Venter SN., Plant Pathol 64(3), 2015
PMID: IND601328927
Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae.
Walterson AM, Stavrinides J., FEMS Microbiol Rev 39(6), 2015
PMID: 26109597
Pantoea intestinalis sp. nov., isolated from the human gut.
Prakash O, Nimonkar Y, Vaishampayan A, Mishra M, Kumbhare S, Josef N, Shouche YS., Int J Syst Evol Microbiol 65(10), 2015
PMID: 26297006
Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c.
Smits TH, Rezzonico F, Blom J, Goesmann A, Abelli A, Kron Morelli R, Vanneste JL, Duffy B., Genome Announc 3(6), 2015
PMID: 26659685
Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments.
Shyntum DY, Venter SN, Moleleki LN, Toth I, Coutinho TA., BMC Genomics 15(), 2014
PMID: 24571088
Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts.
De Maayer P, Chan WY, Rubagotti E, Venter SN, Toth IK, Birch PR, Coutinho TA., BMC Genomics 15(), 2014
PMID: 24884520
Response of phyllosphere bacterial communities to elevated CO2 during rice growing season.
Ren G, Zhang H, Lin X, Zhu J, Jia Z., Appl Microbiol Biotechnol 98(22), 2014
PMID: 25027571
Draft Genome Sequences of the Onion Center Rot Pathogen Pantoea ananatis PA4 and Maize Brown Stalk Rot Pathogen P. ananatis BD442.
Weller-Stuart T, Chan WY, Coutinho TA, Venter SN, Smits TH, Duffy B, Goszczynska T, Cowan DA, de Maayer P., Genome Announc 2(4), 2014
PMID: 25103759
Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R.
Remus-Emsermann MN, Kim EB, Marco ML, Tecon R, Leveau JH., Genome Announc 1(1), 2013
PMID: 23472227
Complete genome sequences of two feline leukemia virus subgroup B isolates with novel recombination sites.
Stewart H, Jarrett O, Hosie MJ, Willett BJ., Genome Announc 1(1), 2013
PMID: 23405366

70 References

Daten bereitgestellt von Europe PubMed Central.

Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus.
Brady CL, Cleenwerck I, van der Westhuizen L, Venter SN, Coutinho TA, De Vos P., Int. J. Syst. Evol. Microbiol. 62(Pt 7), 2011
PMID: 21841003
Genus XXIII Pantoea
Pantoea ananatis: an unconventional plant pathogen.
Coutinho TA, Venter SN., Mol. Plant Pathol. 10(3), 2009
PMID: 19400836
A putative new endophytic nitrogen-fixing bacterium Pantoea sp. from sugarcane.
Loiret FG, Ortega E, Kleiner D, Ortega-Rodes P, Rodes R, Dong Z., J. Appl. Microbiol. 97(3), 2004
PMID: 15281930
Pathogen aggressiveness and postharvest biocontrol efficiency in Pantoea agglomerans
Antibiosis activity of Pantoea agglomerans biocontrol strain E325 against Erwinia amylovora on apple flower stigmas.
Pusey PL, Stockwell VO, Reardon CL, Smits TH, Duffy B., Phytopathology 101(10), 2011
PMID: 21679036
Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1.
Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, Frey JE, Stockwell VO, Duffy B., PLoS ONE 6(7), 2011
PMID: 21789243
Recent evolution of bacterial pathogens: the gall-forming Pantoea agglomerans case.
Barash I, Manulis-Sasson S., Annu Rev Phytopathol 47(), 2009
PMID: 19400643
Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio.
Adams AS, Jordan MS, Adams SM, Suen G, Goodwin LA, Davenport KW, Currie CR, Raffa KF., ISME J 5(8), 2011
PMID: 21368904
An insect herbivore microbiome with high plant biomass-degrading capacity.
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomas AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR., PLoS Genet. 6(9), 2010
PMID: 20885794
The bacterium Pantoea stewartii uses two different type III secretion systems to colonize its plant host and insect vector.
Correa VR, Majerczak DR, Ammar el-D, Merighi M, Pratt RC, Hogenhout SA, Coplin DL, Redinbaugh MG., Appl. Environ. Microbiol. 78(17), 2012
PMID: 22773631
Pantoea agglomerans, a plant pathogen causing human disease.
Cruz AT, Cazacu AC, Allen CH., J. Clin. Microbiol. 45(6), 2007
PMID: 17442803
Genotypic comparison of Pantoea agglomerans plant and clinical strains.
Rezzonico F, Smits TH, Montesinos E, Frey JE, Duffy B., BMC Microbiol. 9(), 2009
PMID: 19772624
The roles of plasmids in phytopathogenic bacteria: mobile arsenals?
Vivian A, Murillo J, Jackson RW., Microbiology (Reading, Engl.) 147(Pt 4), 2001
PMID: 11283273
Origin and evolution of plasmids.
Kado CI., Antonie Van Leeuwenhoek 73(1), 1998
PMID: 9602285
Characterization of plasmids in Erwinia stewartii.
Coplin DL, Rowan RG, Chisholm DA, Whitmoyer RE., Appl. Environ. Microbiol. 42(4), 1981
PMID: 7337464
Characterization of the biosynthetic operon for the antibacterial peptide herbicolin in Pantoea vagans biocontrol strain C9-1 and incidence in Pantoea species.
Kamber T, Lansdell TA, Stockwell VO, Ishimaru CA, Smits TH, Duffy B., Appl. Environ. Microbiol. 78(12), 2012
PMID: 22504810
Plasmids of the epiphytic bacterium Erwinia ureduvora
Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3.
Smits TH, Rezzonico F, Pelludat C, Goesmann A, Frey JE, Duffy B., FEMS Microbiol. Lett. 308(1), 2010
PMID: 20487014
Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli.
Misawa N, Nakagawa M, Kobayashi K, Yamano S, Izawa Y, Nakamura K, Harashima K., J. Bacteriol. 172(12), 1990
PMID: 2254247
Carotenoids' influence on radiotolerance of Pantoea agglomerans, a plant pathogen.
Dussault D, Caillet S, Le Tien C, Lacroix M., Lett. Appl. Microbiol. 47(3), 2008
PMID: 19552787
Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1).
Park JH, Dorrestein PC, Zhai H, Kinsland C, McLafferty FW, Begley TP., Biochemistry 42(42), 2003
PMID: 14567704
Structural and biochemical analysis of the asc operon encoding 6-phospho-beta-glucosidase in Pectobacterium carotovorum subsp. carotovorum LY34.
An CL, Lim WJ, Hong SY, Shin EC, Kim MK, Lee JR, Park SR, Woo JG, Lim YP, Yun HD., Res. Microbiol. 156(2), 2004
PMID: 15748978
Characterization of the Erwinia chrysanthemi Gan locus, involved in galactan catabolism.
Delangle A, Prouvost AF, Cogez V, Bohin JP, Lacroix JM, Cotte-Pattat NH., J. Bacteriol. 189(19), 2007
PMID: 17644603
Glucoamylases: structural and biotechnological aspects.
Marin-Navarro J, Polaina J., Appl. Microbiol. Biotechnol. 89(5), 2010
PMID: 21152915
Bordetella iron transport and virulence.
Brickman TJ, Anderson MT, Armstrong SK., Biometals 20(3-4), 2007
PMID: 17295050
The surprising Rut pathway: an unexpected way to derive nitrogen from pyrimidines.
Parales RE, Ingraham JL., J. Bacteriol. 192(16), 2010
PMID: 20562306
Resolving the contributions of the membrane-bound and periplasmic nitrate reductase systems to nitric oxide and nitrous oxide production in Salmonella enterica serovar Typhimurium.
Rowley G, Hensen D, Felgate H, Arkenberg A, Appia-Ayme C, Prior K, Harrington C, Field SJ, Butt JN, Baggs E, Richardson DJ., Biochem. J. 441(2), 2012
PMID: 22039967
Bacterial tellurite resistance.
Taylor DE., Trends Microbiol. 7(3), 1999
PMID: 10203839
A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-amino-4-deoxy-L-arabinose
Solution structure and dynamics of the outer membrane enzyme PagP by NMR.
Hwang PM, Choy WY, Lo EI, Chen L, Forman-Kay JD, Raetz CR, Prive GG, Bishop RE, Kay LE., Proc. Natl. Acad. Sci. U.S.A. 99(21), 2002
PMID: 12357033
Cable pili and the associated 22 kDa adhesin contribute to Burkholderia cenocepacia persistence in vivo.
Goldberg JB, Ganesan S, Comstock AT, Zhao Y, Sajjan US., PLoS ONE 6(7), 2011
PMID: 21811611
Flagellar phase variation of Salmonella enterica serovar Typhimurium contributes to virulence in the murine typhoid infection model but does not influence Salmonella-induced enteropathogenesis.
Ikeda JS, Schmitt CK, Darnell SC, Watson PR, Bispham J, Wallis TS, Weinstein DL, Metcalf ES, Adams P, O'Connor CD, O'Brien AD., Infect. Immun. 69(5), 2001
PMID: 11292720
A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation.
Liu B, Hu B, Zhou Z, Guo D, Guo X, Ding P, Feng L, Wang L., Nucleic Acids Res. 40(10), 2012
PMID: 22287625
Bacterial cyclic beta-(1,2)-glucan acts in systemic suppression of plant immune responses.
Rigano LA, Payette C, Brouillard G, Marano MR, Abramowicz L, Torres PS, Yun M, Castagnaro AP, Oirdi ME, Dufour V, Malamud F, Dow JM, Bouarab K, Vojnov AA., Plant Cell 19(6), 2007
PMID: 17601826
Characterization of the genes of the 2,3-butanediol operons from Klebsiella terrigena and Enterobacter aerogenes.
Blomqvist K, Nikkola M, Lehtovaara P, Suihko ML, Airaksinen U, Straby KB, Knowles JK, Penttila ME., J. Bacteriol. 175(5), 1993
PMID: 8444801
Bacterial volatiles induce systemic resistance in Arabidopsis.
Ryu CM, Farag MA, Hu CH, Reddy MS, Kloepper JW, Pare PW., Plant Physiol. 134(3), 2004
PMID: 14976231
Respiratory hydrogen use by Salmonella enterica serovar Typhimurium is essential for virulence.
Maier RJ, Olczak A, Maier S, Soni S, Gunn J., Infect. Immun. 72(11), 2004
PMID: 15501756
Biological activity of harpin produced by Pantoea stewartii subsp. stewartii.
Ahmad M, Majerczak DR, Pike S, Hoyos ME, Novacky A, Coplin DL., Mol. Plant Microbe Interact. 14(10), 2001
PMID: 11605962
What is type VI secretion doing in all those bugs?
Schwarz S, Hood RD, Mougous JD., Trends Microbiol. 18(12), 2010
PMID: 20961764
Molecular characterization of the klebicin B plasmid of Klebsiella pneumoniae.
Riley MA, Pinou T, Wertz JE, Tan Y, Valletta CM., Plasmid 45(3), 2001
PMID: 11407916
A nonribosomal system of peptide biosynthesis.
Kleinkauf H, Von Dohren H., Eur. J. Biochem. 236(2), 1996
PMID: 8612601
Complete genome sequence of the rice pathogen Pantoea ananatis strain PA13.
Choi O, Lim JY, Seo YS, Hwang I, Kim J., J. Bacteriol. 194(2), 2012
PMID: 22207741
Genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback.
De Maayer P, Chan WY, Venter SN, Toth IK, Birch PR, Joubert F, Coutinho TA., J. Bacteriol. 192(11), 2010
PMID: 20348253
Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342.
De Maayer P, Chan WY, Rezzonico F, Buhlmann A, Venter SN, Blom J, Goesmann A, Frey JE, Smits TH, Duffy B, Coutinho TA., J. Bacteriol. 194(6), 2012
PMID: 22374951
The complete genome sequence of Pantoea ananatis AJ13355, an organism with great biotechnological potential.
Hara Y, Kadotani N, Izui H, Katashkina JI, Kuvaeva TM, Andreeva IG, Golubeva LI, Malko DB, Makeev VJ, Mashko SV, Kozlov YI., Appl. Microbiol. Biotechnol. 93(1), 2011
PMID: 22159605
Draft genome sequence of Pantoea ananatis B1-9, a nonpathogenic plant growth-promoting bacterium.
Kim HJ, Lee JH, Kang BR, Rong X, McSpadden Gardener BB, Ji HJ, Park CS, Kim YC., J. Bacteriol. 194(3), 2012
PMID: 22247529
Genome sequence of Pantoea agglomerans strain IG1.
Matsuzawa T, Mori K, Kadowaki T, Shimada M, Tashiro K, Kuhara S, Inagawa H, Soma G, Takegawa K., J. Bacteriol. 194(5), 2012
PMID: 22328756
Genome sequence of Pantoea sp. strain Sc 1, an opportunistic cotton pathogen.
Medrano EG, Bell AA., J. Bacteriol. 194(11), 2012
PMID: 22582377
Genome sequence of the biocontrol agent Pantoea vagans strain C9-1.
Smits TH, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, Stockwell VO, Frey JE, Duffy B., J. Bacteriol. 192(24), 2010
PMID: 20952567
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT


Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
TCDB: the Transporter Classification Database for membrane transport protein analyses and information.
Saier MH Jr, Tran CV, Barabote RD., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381841
GenomeDiagram: a python package for the visualization of large-scale genomic data.
Pritchard L, White JA, Birch PR, Toth IK., Bioinformatics 22(5), 2005
PMID: 16377612
Choosing BLAST options for better detection of orthologs as reciprocal best hits.
Moreno-Hagelsieb G, Latimer K., Bioinformatics 24(3), 2007
PMID: 18042555
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences.
Kumar S, Nei M, Dudley J, Tamura K., Brief. Bioinformatics 9(4), 2008
PMID: 18417537

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 23151240
PubMed | Europe PMC

Suchen in

Google Scholar