scholarly journals Proma Plasmids are Instrumental in the Dissemination of Linuron Catabolic Genes between Different Genera

2019 ◽  
Author(s):  
Johannes Werner ◽  
Eman Nour ◽  
Boyke Bunk ◽  
Cathrin Spröer ◽  
Kornelia Smalla ◽  
...  
Keyword(s):  
Krebs Cycle ◽  
Gene Clusters ◽  
Broad Host Range ◽  
Ecological Role ◽  
Catabolic Gene ◽  
Plasmid Copy ◽  
Catabolic Genes ◽  
Krebs Cycle Intermediates ◽  
On Farm ◽  
Broad Host Range Plasmids

ABSTRACTPromA plasmids are broad host range plasmids, which are often cryptic and hence have an uncertain ecological role. We present three novel PromA γ plasmids which carry genes associated with degradation of the phenylurea herbicide linuron, two (pPBL-H3-2 and pBPS33-2) of which originate from unrelated Hydrogenophaga hosts isolated from different environments, and one (pEN1) which was exogenously captured from an on-farm biopurification system. Both Hydrogenophaga plasmids carry all three necessary gene clusters determining the three main steps for conversion of linuron to Krebs cycle intermediates, while pEN1 only determines the initial linuron hydrolysis step. Linuron catabolic gene clusters that determine the same step were identical on all plasmids, encompassed in differently arranged constellations and characterized by the presence of multiple IS1071 elements. In all plasmids except pEN1, the insertion spot of the catabolic genes in the PromA γ plasmids was the same. Highly similar PromA plasmids carrying the linuron degrading gene cargo at the same insertion spot were were previously identified in linuron degrading Variovorax sp. Interestingly, in both Hydrogenophaga populations not every PromA plasmid copy carries catabolic genes. The results indicate that PromA plasmids are important vehicles of linuron catabolic gene dissemination, rather than being cryptic and only important for the mobilization of other plasmids.

scholarly journals Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax

2020 ◽  
Vol 12 (6) ◽  
pp. 827-841 ◽  
Author(s):  
Başak Öztürk ◽  
Johannes Werner ◽  
Jan P Meier-Kolthoff ◽  
Boyke Bunk ◽  
Cathrin Spröer ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Phylogenetic Position ◽  
Broad Host Range ◽  
Genetic Adaptation ◽  
Catabolic Gene ◽  
Array Configuration ◽  
Phenylurea Herbicide ◽  
Catabolic Genes ◽  
Clade 1

Abstract Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight into the mechanisms of genetic adaptation toward linuron metabolism. Whole-genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated that they unlikely originate from a common ancestral linuron degrader. The linuron degraders differentiated from Variovorax strains that do not degrade linuron by the presence of multiple plasmids of 20–839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed 1) high conservation and synteny and 2) strain-dependent distribution among the different plasmids. Most of them were bordered by IS1071 elements forming composite transposon structures, often in a multimeric array configuration, appointing IS1071 as a key element in the recruitment of linuron catabolic genes in Variovorax. Most of the strains carried at least one (catabolic) broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1 Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire regarding both catabolic functions and vehicles to acquire linuron biodegradation.

scholarly journals A Novel Hydrolase Identified by Genomic-Proteomic Analysis of Phenylurea Herbicide Mineralization by Variovorax sp. Strain SRS16

2011 ◽  
Vol 77 (24) ◽  
pp. 8754-8764 ◽  
Author(s):  
Karolien Bers ◽  
Baptiste Leroy ◽  
Philip Breugelmans ◽  
Pieter Albers ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Krebs Cycle ◽  
Divergent Evolution ◽  
Phenylurea Herbicides ◽  
Transcription Analysis ◽  
Content Type ◽  
First Report ◽  
Phenylurea Herbicide ◽  
Hydrolyzing Enzymes ◽  
Krebs Cycle Intermediates

ABSTRACTThe soil bacterial isolateVariovoraxsp. strain SRS16 mineralizes the phenylurea herbicide linuron. The proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (DCA) andN,O-dimethylhydroxylamine, followed by conversion of DCA to Krebs cycle intermediates. Differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (LibA), a multicomponent chloroaniline dioxygenase, and enzymes associated with a modified chlorocatecholortho-cleavage pathway. Purified LibA is a monomeric linuron hydrolase of ∼55 kDa with aKmand aVmaxfor linuron of 5.8 μM and 0.16 nmol min−1, respectively. This novel member of the amidase signature family is unrelated to phenylurea-hydrolyzing enzymes from Gram-positive bacteria and lacks activity toward other tested phenylurea herbicides. Orthologues oflibAare present in all other tested linuron-degradingVariovoraxstrains with the exception ofVariovoraxstrains WDL1 and PBS-H4, suggesting divergent evolution of the linuron catabolic pathway in differentVariovoraxstrains. The organization of the linuron degradation genes identified in the draft SRS16 genome sequence indicates that gene patchwork assembly is at the origin of the pathway. Transcription analysis suggests that a catabolic intermediate, rather than linuron itself, acts as effector in activation of the pathway. Our study provides the first report on the genetic organization of a bacterial pathway for complete mineralization of a phenylurea herbicide and the first report on a linuron hydrolase in Gram-negative bacteria.

scholarly journals The kfrA gene is the first in a tricistronic operon required for survival of IncP-1 plasmid R751

Microbiology ◽  
2006 ◽  
Vol 152 (6) ◽  
pp. 1621-1637 ◽  
Author(s):  
Malgorzata Adamczyk ◽  
Patrycja Dolowy ◽  
Michal Jonczyk ◽  
Christopher M. Thomas ◽  
Grazyna Jagura-Burdzy
Keyword(s):  
Coiled Coil ◽  
Broad Host Range ◽  
Gram Negative Bacteria ◽  
Bacterial Cells ◽  
Wild Type ◽  
C Terminus ◽  
Low Copy Number ◽  
And Control ◽  
Broad Host Range Plasmids

The kfrA gene of the IncP-1 broad-host-range plasmids is the best-studied member of a growing gene family that shows strong linkage to the minimal replicon of many low-copy-number plasmids. KfrA is a DNA binding protein with a long, alpha-helical, coiled-coil tail. Studying IncP-1β plasmid R751, evidence is presented that kfrA and its downstream genes upf54.8 and upf54.4 were organized in a tricistronic operon (renamed here kfrA kfrB kfrC), expressed from autoregulated kfrAp, that was also repressed by KorA and KorB. KfrA, KfrB and KfrC interacted and may have formed a multi-protein complex. Inactivation of either kfrA or kfrB in R751 resulted in long-term accumulation of plasmid-negative bacteria, whereas wild-type R751 itself persisted without selection. Immunofluorescence studies showed that KfrAR751 formed plasmid-associated foci, and deletion of the C terminus of KfrA caused plasmid R751ΔC 2 kfrA foci to disperse and mislocalize. Thus, the KfrABC complex may be an important component in the organization and control of the plasmid clusters that seem to form the segregating unit in bacterial cells. The studied operon is therefore part of the set of functions needed for R751 to function as an efficient vehicle for maintenance and spread of genes in Gram-negative bacteria.

scholarly journals Functional Redundancy of Linuron Degradation in Microbial Communities in Agricultural Soil and Biopurification Systems

2016 ◽  
Vol 82 (9) ◽  
pp. 2843-2853 ◽  
Author(s):  
Benjamin Horemans ◽  
Karolien Bers ◽  
Erick Ruiz Romero ◽  
Eva Pose Juan ◽  
Vincent Dunon ◽  
...  
Keyword(s):  
Agricultural Soil ◽  
Bacterial Consortium ◽  
Bacterial Degradation ◽  
Catabolic Gene ◽  
Bacterial Populations ◽  
Content Type ◽  
Respective Contribution ◽  
On Farm ◽  
Biopurification Systems

ABSTRACTThe abundance oflibA, encoding a hydrolase that initiates linuron degradation in the linuron-metabolizingVariovoraxsp. strain SRS16, was previously found to correlate well with linuron mineralization, but not in all tested environments. Recently, an alternative linuron hydrolase, HylA, was identified inVariovoraxsp. strain WDL1, a strain that initiates linuron degradation in a linuron-mineralizing commensal bacterial consortium. The discovery of alternative linuron hydrolases poses questions about the respective contribution and competitive character ofhylA- andlibA-carrying bacteria as well as the role of linuron-mineralizing consortia versus single strains in linuron-exposed settings. Therefore, dynamics ofhylAas well asdcaQas a marker for downstream catabolic functions involved in linuron mineralization, in response to linuron treatment in agricultural soil and on-farm biopurification systems (BPS), were compared with previously reportedlibAdynamics. The results suggest that (i) organisms containing eitherlibAorhylAcontribute simultaneously to linuron biodegradation in the same environment, albeit to various extents, (ii) environmental linuron mineralization depends on multispecies bacterial food webs, and (iii) initiation of linuron mineralization can be governed by currently unidentified enzymes.IMPORTANCEA limited set of different isofunctional catabolic gene functions is known for the bacterial degradation of the phenylurea herbicide linuron, but the role of this redundancy in linuron degradation in environmental settings is not known. In this study, the simultaneous involvement of bacteria carrying one of two isofunctional linuron hydrolysis genes in the degradation of linuron was shown in agricultural soil and on-farm biopurification systems, as was the involvement of other bacterial populations that mineralize the downstream metabolites of linuron hydrolysis. This study illustrates the importance of the synergistic metabolism of pesticides in environmental settings.

scholarly journals Genomic and Functional Analysis of the IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Its Transposon Tn4655 Suggests Catabolic Gene Spread by a Tyrosine Recombinase

2006 ◽  
Vol 188 (11) ◽  
pp. 4057-4067 ◽  
Author(s):  
Masahiro Sota ◽  
Hirokazu Yano ◽  
Akira Ono ◽  
Ryo Miyazaki ◽  
Hidenori Ishii ◽  
...  
Keyword(s):  
Sequence Data ◽  
Gene Clusters ◽  
Catabolic Gene ◽  
Genetic Determinants ◽  
Tyrosine Recombinase ◽  
Site Specific ◽  
Recombination System ◽  
Catabolic Plasmid ◽  
Transmissible Plasmid ◽  
Catabolic Plasmids

ABSTRACT The naphthalene-catabolic (nah) genes on the incompatibility group P-9 (IncP-9) self-transmissible plasmid NAH7 from Pseudomonas putida G7 are some of the most extensively characterized genetic determinants for bacterial aerobic catabolism of aromatic hydrocarbons. In contrast to the detailed studies of its catabolic cascade and enzymatic functions, the biological characteristics of plasmid NAH7 have remained unclear. Our sequence determination in this study together with the previously deposited sequences revealed the entire structure of NAH7 (82,232 bp). Comparison of NAH7 with two other completely sequenced IncP-9 catabolic plasmids, pDTG1 and pWW0, revealed that the three plasmids share very high nucleotide similarities in a 39-kb region encoding the basic plasmid functions (the IncP-9 backbone). The backbone of NAH7 is phylogenetically more related to that of pDTG1 than that of pWW0. These three plasmids carry their catabolic gene clusters at different positions on the IncP-9 backbone. All of the NAH7-specified nah genes are located on a class II transposon, Tn4655. Our analysis of the Tn4655-encoded site-specific recombination system revealed that (i) a novel tyrosine recombinase, TnpI, catalyzed both the intra- and intermolecular recombination between two copies of the attI site, (ii) the functional attI site was located within a 119-bp segment, and (iii) the site-specific strand exchange occurred within a 30-bp segment in the 41-bp CORE site. Our results and the sequence data of other naphthalene-catabolic plasmids, pDTG1 and pND6-1, suggest a potential role of the TnpI-attI recombination system in the establishment of these catabolic plasmids.

scholarly journals Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field Trial

2003 ◽  
Vol 69 (1) ◽  
pp. 483-489 ◽  
Author(s):  
Steven D. Siciliano ◽  
James J. Germida ◽  
Kathy Banks ◽  
Charles W. Greer
Keyword(s):  
Microbial Community ◽  
Festuca Arundinacea ◽  
Rhizosphere Soil ◽  
Microbial Community Composition ◽  
Hydrocarbon Degradation ◽  
Bulk Soil ◽  
Catabolic Gene ◽  
Soil Microbial ◽  
Catabolic Genes ◽  
And Function

ABSTRACT The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.

scholarly journals Evolution of IncA/CblaCMY-2-Carrying Plasmids by Acquisition of theblaNDM-1Carbapenemase Gene

2011 ◽  
Vol 56 (2) ◽  
pp. 783-786 ◽  
Author(s):  
Alessandra Carattoli ◽  
Laura Villa ◽  
Laurent Poirel ◽  
Rémy A. Bonnin ◽  
Patrice Nordmann
Keyword(s):  
Host Range ◽  
Large Scale ◽  
The United States ◽  
Broad Host Range ◽  
New Delhi ◽  
Yersinia Ruckeri ◽  
Content Type ◽  
Photobacterium Damselae ◽  
Environmental Bacteria ◽  
Broad Host Range Plasmids

ABSTRACTTheblaNDM-1gene has been reported to be often located on broad-host-range plasmids of the IncA/C type in clinical but also environmental bacteria recovered from the New Delhi, India, area. IncA/C-type plasmids are the main vehicles for the spread of the cephalosporinase geneblaCMY-2, frequently identified in the United States, Canada, and Europe. In this study, we completed the sequence of IncA/C plasmid pNDM-KN carrying theblaNDM-1gene, recovered from aKlebsiella pneumoniaeisolate from Kenya. This sequence was compared with those of three IncA/C-type reference plasmids fromEscherichia coli,Yersinia ruckeri, andPhotobacterium damselae. Comparative analysis showed that theblaNDM-1gene was located on a widely diffused plasmid scaffold known to be responsible for the spread ofblaCMY-2-like genes and consequently for resistance to broad-spectrum cephalosporins. Considering that IncA/C plasmids possess a broad host range, this scaffold might support a large-scale diffusion of theblaNDM-1gene among Gram-negative rods.

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