Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989

Pantoea vagans, a gram-negative bacterium from the genus Pantoea and family Enterobacteriaceae, is present in various natural environments and considered to be plant endophytes. We isolated the Pantoea vagans PV989 strain from the clinic and sequenced its whole genome. Besides a chromosome DNA molec...

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Bibliographic Details
Published in:International journal of genomics 2018-01, Vol.2018 (2018), p.1-9
Main Authors: Ni, Liyan, Bao, Qiyu, Lu, Shunfei, Ying, Jianchao, Lin, Chaoqing, Lu, Junwan, Ying, Yuanyuan, Liu, Yabo, Zhu, Tingyuan, Yin, Min, Xu, Lei, Xu, Teng
Format: Article
Language:English
Subjects:
Bacteria
Bacteriology
Chromosomes
Conjugation
Deoxyribonucleic acid
DNA
DNA repair
Endophytes
Environmental conditions
Erwinia amylovora
Fruit trees
Gene expression
Gene transfer
Genomes
Genomics
Integrase
Nucleotide sequence
Pantoea
Pantoea agglomerans
Phages
Plasmids
Recombinase
Variable region
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Summary:Pantoea vagans, a gram-negative bacterium from the genus Pantoea and family Enterobacteriaceae, is present in various natural environments and considered to be plant endophytes. We isolated the Pantoea vagans PV989 strain from the clinic and sequenced its whole genome. Besides a chromosome DNA molecule, it also harboured three large plasmids. A comparative genomics analysis was performed for the smallest plasmid, pPV989-94. It can be divided into four regions, including three conservative regions related to replication (R1), transfer conjugation (R2), and transfer leading (R3), and one variable region (R4). Further analysis showed that pPV989-94 is most similar to plasmids LA637P2 and pEA68 of Erwinia amylovora strains isolated from fruit trees. These three plasmids share three conservative regions (R1, R2, and R3). Interestingly, a fragment (R4′) in R4, mediated by phage integrase and phage integrase family site-specific recombinase and encoding 9 genes related to glycometabolism, resistance, and DNA repair, was unique in pPV989-94. Homologues of R4′ were found in other plasmids or chromosomes, suggesting that horizontal gene transfer (HGT) occurred among different bacteria of various species or genera. The acquired functional genes may play important roles in the adaptation of bacteria to different hosts or environmental conditions.
ISSN:2314-436X
2314-4378
DOI:10.1155/2018/1242819