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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Wiley
2018-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2018/1242819 |
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| author | Lei Xu Min Yin Tingyuan Zhu Yabo Liu Yuanyuan Ying Junwan Lu Chaoqing Lin Jianchao Ying Teng Xu Liyan Ni Qiyu Bao Shunfei Lu |
| author_facet | Lei Xu Min Yin Tingyuan Zhu Yabo Liu Yuanyuan Ying Junwan Lu Chaoqing Lin Jianchao Ying Teng Xu Liyan Ni Qiyu Bao Shunfei Lu |
| author_sort | Lei Xu |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-ab7825081ddb4cf68d11a9a8ff78f910 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Wiley |
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| series | International Journal of Genomics |
| spelling | doaj-art-ab7825081ddb4cf68d11a9a8ff78f9102025-02-03T01:02:37ZengWileyInternational Journal of Genomics2314-436X2314-43782018-01-01201810.1155/2018/12428191242819Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989Lei Xu0Min Yin1Tingyuan Zhu2Yabo Liu3Yuanyuan Ying4Junwan Lu5Chaoqing Lin6Jianchao Ying7Teng Xu8Liyan Ni9Qiyu Bao10Shunfei Lu11School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaSchool of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaSchool of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaSchool of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaSchool of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaSchool of Medicine, Lishui College, Lishui 323000, ChinaThe Second Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, ChinaSchool of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaSchool of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaThe Second Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, ChinaSchool of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, ChinaSchool of Medicine, Lishui College, Lishui 323000, ChinaPantoea 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.http://dx.doi.org/10.1155/2018/1242819 |
| spellingShingle | Lei Xu Min Yin Tingyuan Zhu Yabo Liu Yuanyuan Ying Junwan Lu Chaoqing Lin Jianchao Ying Teng Xu Liyan Ni Qiyu Bao Shunfei Lu Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989 International Journal of Genomics |
| title | Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989 |
| title_full | Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989 |
| title_fullStr | Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989 |
| title_full_unstemmed | Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989 |
| title_short | Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989 |
| title_sort | comparative genomics analysis of plasmid ppv989 94 from a clinical isolate of pantoea vagans pv989 |
| url | http://dx.doi.org/10.1155/2018/1242819 |
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