Mobile Genetic Elements in Pseudomonas stutzeri

Sousa, Leandro Pio de

doi:10.1007/s00284-019-01812-7

Cited by 10 publications

(8 citation statements)

References 33 publications

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“…Interestingly, OF001 region 2 and OF001 region 7 display putative site-specific integrases and excisionases, indicating site-specific recombination [ 100 ]. Multiple prophages have already been observed in other members of the genus Pseudomonas [ 101 – 104 ].…”

Section: Resultsmentioning

confidence: 96%

Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

et al. 2021

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Background Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. Results Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. Conclusions The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.

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Section: Resultsmentioning

confidence: 96%

Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

et al. 2021

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“…Case studies on the effects of TE on bacterial genomes have been published for a variety of bacteria, including Escherichia coli , 29 , 30 Acinetobacter baumannii , 31 , 32 Bacillus , 33 , 34 Klebsiella pneumoniae , 32 Mycobacterium , 12 , 35 , 36 Lactococcus garvieae , 37 Burkholderia multivorans, 38 Pseudomonas aeruginosa , 11 Pseudomonas stutzeri , 39 Thermus spp., 40 D. radiodurans , 14 - 16 , 41 and D. geothermalis . 17 …”

Section: Discussionmentioning

confidence: 99%

“…However, strain A1501 has 56 ISs. 39 A mobilome study of Thermus reported a significantly different number of IS copies per mega base pair genome size of 28 Thermus spp. In the 3 T. thermophilus strains HB27, HB8, and NAR1, many IS type elements distributed to rearrangement on genomes, including chromosomes and plasmids.…”

Section: Discussionmentioning

confidence: 99%

“…[8][9][10]28 These TE contribute to gene activation or inactivation through structural gene disruption and promoter disorder, resulting in genetic variation through plasticity and evolutional aspects of bacterial genomes. 1,3,6 Case studies on the effects of TE on bacterial genomes have been published for a variety of bacteria, including Escherichia coli, 29,30 Acinetobacter baumannii, 31,32 Bacillus, 33,34 Klebsiella pneumoniae, 32 Mycobacterium, 12,35,36 Lactococcus garvieae, 37 Burkholderia multivorans, 38 Pseudomonas aeruginosa, 11 Pseudomonas stutzeri, 39 Thermus spp., 40 D. radiodurans, [14][15][16]41 and D. geothermalis. 17 Taking L. garvieae as an example, 77 published genomes from 12 strains reveal 15 types of IS elements and 4 families of ISs (IS3, IS982, IS6, and IS21).…”

Section: Discussionmentioning

confidence: 99%

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Genome Plasticity by Insertion Sequences Learned From a Case of Radiation-Resistant Bacterium Deinococcus geothermalis

Lee

Bae

Choi

et al. 2021

Bioinform Biol Insights

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The genome of the radiation-resistant bacterium Deinococcus geothermalis contains 19 types of insertion sequences (ISs), including 93 total transposases (Tpases) in 73 full-length ISs from the main chromosome and 2 mega plasmids. In this study, 68 ISs from the D. geothermalis genome were extracted to implicate the earlier genome before its mutation by transposition of ISs. The total size of eliminated ISs from genome was 78.85 kb. From these in silico corrections of mutation by the ISs, we have become aware of some bioinformatics factualness as follows: (1) can reassemble the disrupted genes if the exact IS region was eliminated, (2) can configure the schematic clustering of major DDE type Tpases, (3) can determine IS integration order across multiple hot spots, and (4) can compare genetic relativeness by the partial synteny analysis between D. geothermalis and Deinococcus strain S9. Recently, we found that several IS elements actively transferred to other genomic sites under hydrogen peroxide-induced oxidative stress conditions, resulting in the inactivation of functional genes. Therefore, the single species genome’s mobilome study provides significant support to define bacterial genome plasticity and molecular evolution from past and present progressive transposition events.

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“…A degradative ICE containing a highly conserved core region almost identical to that of ICE bph-sal KF716 has been found in silico suggesting the existence of an ”ICE bph-sal subfamily”; they include ICE members located on the chromosome of naphthalene-degrading bacterium P. stutzeri AN10 and toluene/xylene and phenol-degrading bacterium P. stutzeri 2A20 [ 35 ]. All of these ICEs have been found in P. stutzeri , suggesting that P. stutzeri is the preferred host of the ICE bph-sal subfamily [ 39 ].…”

Section: Ice Clc Familymentioning

confidence: 99%

Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation

Hirose

2023

Microorganisms

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Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.

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Mobile Genetic Elements in Pseudomonas stutzeri

Cited by 10 publications

References 33 publications

Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

Genome Plasticity by Insertion Sequences Learned From a Case of Radiation-Resistant Bacterium Deinococcus geothermalis

Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation

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