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).

Journal Article | Published | English

No fulltext has been uploaded

Author
; ; ; ; ; ;
Abstract
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.
Publishing Year
ISSN
PUB-ID

Cite this

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).
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).
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.
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).
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.
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, (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).
This data publication is cited in the following publications:
This publication cites the following data publications:

11 Citations in Europe PMC

Data provided by Europe PubMed Central.

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
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
Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae.
Walterson AM, Stavrinides J., FEMS Microbiol. Rev. 39(6), 2015
PMID: 26109597
Analysis of the effect of high hydrostatic pressure treatment and enterocin AS-48 addition on the bacterial communities of cherimoya pulp.
Perez Pulido R, Toledo J, Grande MJ, Galvez A, Lucas R., Int. J. Food Microbiol. 196(), 2015
PMID: 25528726
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
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
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
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
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

Data provided by Europe PubMed Central.

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), 2012
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
AUTHOR UNKNOWN, 1999

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
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), 2006
PMID: 16377612
Choosing BLAST options for better detection of orthologs as reciprocal best hits.
Moreno-Hagelsieb G, Latimer K., Bioinformatics 24(3), 2008
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

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 23151240
PubMed | Europe PMC

Search this title in

Google Scholar