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

AbstractBiodegradation 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 in the mechanisms of genetic adaptation towards linuron metabolism in Variovorax. Whole genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed (i) high conservation and synteny and (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071 elements forming composite transposon structures appointing IS1071 as key for catabolic gene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation.ImportanceThe genus Variovorax and especially a clade of strains that phylogenetically separates from the majority of Variovorax species, appears to be a specialist in the biodegradation of the phenyl urea herbicide linuron. Horizontal gene transfer (HGT) likely played an essential role in the genetic adaptation of those strain to acquire the linuron catabolic genotype. However, we do not know the genetic repertoire involved in this adaptation both regarding catabolic gene functions as well as gene functions that promote HGT neither do we know how this varies between the different strains. These questions are addressed in this paper by analyzing the full genome sequences of six linuron degrading Variovorax strains. This knowledge is important for understanding the mechanisms that steer world-wide genetic adaptation in a particular species and this for a particular phenotypic trait as linuron biodegradation.

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

10.1101/831255 ◽

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.

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A plant endophyte Staphylococcus hominis strain MBL_AB63 produces a novel lantibiotic, homicorcin and a position one variant

Scientific Reports ◽

10.1038/s41598-021-90613-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Aftab Uddin ◽

Shammi Akter ◽

Mahbuba Ferdous ◽

Badrul Haidar ◽

Al Amin ◽

...

Keyword(s):

Gene Clusters ◽

Antimicrobial Activities ◽

Whole Genome Sequence ◽

Antimicrobial Substances ◽

The Core ◽

Rp Hplc ◽

Ring Structures ◽

Core Peptide ◽

Staphylococcus Hominis ◽

Epilancin 15X

AbstractHere we report a jute endophyte Staphylococcus hominis strain MBL_AB63 isolated from jute seeds which showed promising antimicrobial activity against Staphylococcus aureus SG511 when screening for antimicrobial substances. The whole genome sequence of this strain, annotated using BAGEL4 and antiSMASH 5.0 to predict the gene clusters for antimicrobial substances identified a novel antimicrobial peptide cluster that belongs to the class I lantibiotic group. The predicted lantibiotic (homicorcin) was found to be 82% similar to a reported peptide epicidin 280 having a difference of seven amino acids at several positions of the core peptide. Two distinct peaks obtained at close retention times from a RP-HPLC purified fraction have comparable antimicrobial activities and LC–MS revealed the molecular mass of these peaks to be 3046.5 and 3043.2 Da. The presence of an oxidoreductase (homO) similar to that of epicidin 280- associated eciO or epilancin 15X- associated elxO in the homicorcin gene cluster is predicted to be responsible for the reduction of the first dehydrated residue dehydroalanine (Dha) to 2-hydroxypropionate that causes an increase of 3 Da mass of homicorcin 1. Trypsin digestion of the core peptide and its variant followed by ESI–MS analysis suggests the presence of three ring structures, one in the N-terminal and other two interlocking rings at the C-terminal region that remain undigested. Homicorcin exerts bactericidal activity against susceptible cells by disrupting the integrity of the cytoplasmic membrane through pore formation as observed under FE-SEM.

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

Journal of Bacteriology ◽

10.1128/jb.00185-06 ◽

2006 ◽

Vol 188 (11) ◽

pp. 4057-4067 ◽

Cited By ~ 69

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.69.1.483-489.2003 ◽

2003 ◽

Vol 69 (1) ◽

pp. 483-489 ◽

Cited By ~ 208

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.

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Whole-Genome Sequencing Reveals a New Genospecies ofMethylobacteriumsp. GXS13, Isolated fromVitis viniferaL. Xylem Sap

Genome Announcements ◽

10.1128/genomea.01695-15 ◽

2016 ◽

Vol 4 (1) ◽

Cited By ~ 1

Author(s):

Wan Xin Lai ◽

Han Ming Gan ◽

André O. Hudson ◽

Michael A. Savka

Keyword(s):

Xylem Sap ◽

Gene Clusters ◽

Homoserine Lactone ◽

Whole Genome Sequence ◽

Whole Genome ◽

Acyl Homoserine Lactone ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Cell Wall Modification ◽

Cytokinin Synthesis

The whole-genome sequence of a new genospecies ofMethylobacteriumsp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server.

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Identification of A Novel Arsenic Resistance Transposon Nested in A Mercury Resistance Transposon of Bacillus sp. MB24

Microorganisms ◽

10.3390/microorganisms7110566 ◽

2019 ◽

Vol 7 (11) ◽

pp. 566 ◽

Cited By ~ 1

Author(s):

Mei-Fang Chien ◽

Ying-Ning Ho ◽

Hui-Erh Yang ◽

Masaru Narita ◽

Keisuke Miyauchi ◽

...

Keyword(s):

Gene Clusters ◽

Whole Genome Sequence ◽

Mercury Resistance ◽

Bacillus Sp ◽

Arsenic Resistance ◽

First Case ◽

Arsenite Resistance ◽

Ars Operon ◽

Minamata Bay ◽

Bacterium Bacillus

A novel TnMERI1-like transposon designated as TnMARS1 was identified from mercury resistant Bacilli isolated from Minamata Bay sediment. Two adjacent ars operon-like gene clusters, ars1 and ars2, flanked by a pair of 78-bp inverted repeat sequences, which resulted in a 13.8-kbp transposon-like fragment, were found to be sandwiched between two transposable genes of the TnMERI1-like transposon of a mercury resistant bacterium, Bacillus sp. MB24. The presence of a single transcription start site in each cluster determined by 5′-RACE suggested that both are operons. Quantitative real time RT-PCR showed that the transcription of the arsR genes contained in each operon was induced by arsenite, while arsR2 responded to arsenite more sensitively and strikingly than arsR1 did. Further, arsenic resistance complementary experiments showed that the ars2 operon conferred arsenate and arsenite resistance to an arsB-knocked out Bacillus host, while the ars1 operon only raised arsenite resistance slightly. This transposon nested in TnMARS1 was designated as TnARS1. Multi-gene cluster blast against bacteria and Bacilli whole genome sequence databases suggested that TnMARS1 is the first case of a TnMERI1-like transposon combined with an arsenic resistance transposon. The findings of this study suggested that TnMERI1-like transposons could recruit other mobile elements into its genetic structure, and subsequently cause horizontal dissemination of both mercury and arsenic resistances among Bacilli in Minamata Bay.

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Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis

Genome Biology and Evolution ◽

10.1093/gbe/evaa218 ◽

2020 ◽

Vol 12 (12) ◽

pp. 2491-2507

Author(s):

Claudio A Valero-Jiménez ◽

Maikel B F Steentjes ◽

Jason C Slot ◽

Xiaoqian Shi-Kunne ◽

Olga E Scholten ◽

...

Keyword(s):

Secondary Metabolite ◽

Gene Clusters ◽

Single Species ◽

White Rot ◽

White Rot Fungus ◽

Broad Host Range ◽

Allium Species ◽

Sclerotium Cepivorum ◽

Single Host ◽

Long Read

Abstract Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8–39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.

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Draft Whole Genome Sequence Analyses on Pseudomonas syringae pv. actinidiae Hypersensitive Response Negative Strains Detected from Kiwifruit Bleeding Sap Samples

Phytopathology ◽

10.1094/phyto-08-17-0278-r ◽

2018 ◽

Vol 108 (5) ◽

pp. 552-560 ◽

Cited By ~ 3

Author(s):

Enrico Biondi ◽

Alan Zamorano ◽

Ernesto Vega ◽

Stefano Ardizzi ◽

Davide Sitta ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Genome Sequence ◽

Hypersensitive Response ◽

Time Window ◽

Gene Clusters ◽

Whole Genome Sequence ◽

Optimal Time ◽

Whole Genome ◽

Isolation And Identification ◽

The Difference

Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring in both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then through its direct isolation and identification. The results of molecular analyses showed more effectiveness in the P. syringae pv. actinidiae detection when compared with those of microbiological analyses through the pathogen isolation on the nutritive and semiselective media selected. The bleeding sap analyses allowed the isolation and identification of two hypersensitive response (HR) negative and hypovirulent P. syringae pv. actinidiae strains from different regions in Italy. Moreover, multilocus sequence analysis (MLSA) and whole genome sequence (WGS) were carried out on selected Italian and Chilean P. syringae pv. actinidiae virulent strains to verify the presence of genetic variability compared with the HR negative strains and to compare the variability of selected gene clusters between strains isolated in both countries. All the strains showed the lack of argK and coronatine gene clusters as reported for the biovar 3 P. syringae pv. actinidiae strains. Despite the biologic differences obtained in the tobacco bioassays and in pathogenicity assays, the MLSA and WGS analyses did not show significant differences between the WGS of the HR negative and HR positive strains; the difference, on the other hand, between PAC_ICE sequences of Italian and Chilean P. syringae pv. actinidiae strains was confirmed. The inability of the hypovirulent strains IPV-BO 8893 and IPV-BO 9286 to provoke HR in tobacco and the low virulence shown in this host could not be associated with mutations or recombinations in T3SS island.

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Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics

Applied and Environmental Microbiology ◽

10.1128/aem.02930-15 ◽

2015 ◽

Vol 82 (5) ◽

pp. 1401-1411 ◽

Cited By ~ 9

Author(s):

Kai Chen ◽

Xihui Xu ◽

Long Zhang ◽

Zhenjiu Gou ◽

Shunpeng Li ◽

...

Keyword(s):

Receptor Gene ◽

Genetic Load ◽

Gene Clusters ◽

Evolutionary Strategy ◽

Evolutionary Strategies ◽

Adaptation Mechanism ◽

Content Type ◽

Catabolic Genes ◽

Catabolic Plasmids ◽

Dehalogenase Gene

ABSTRACTComamonasplasmids play important roles in shaping the phenotypes of their hosts and the adaptation of these hosts to changing environments, and understanding the evolutionary strategy of these plasmids is thus of great concern. In this study, the sequence of the 119-kb 3,5-dibromo-4-hydroxybenzonitrile-catabolizing plasmid pBHB fromComamonassp. strain 7D-2 was studied and compared with those of three otherComamonashaloaromatic catabolic plasmids. Incompatibility group determination based on a phylogenetic analysis of 24 backbone gene proteins, as well as TrfA, revealed that these four plasmids all belong to the IncP-1β subgroup. Comparison of the four plasmids revealed a conserved backbone region and diverse genetic-load regions. The four plasmids share a core genome consisting of 40 genes (>50% similarities) and contain 12 to 50 unique genes each, most of which are xenobiotic-catabolic genes. Two functional reductive dehalogenase gene clusters are specifically located on pBHB, showing distinctive evolution of pBHB for haloaromatics. The higher catabolic ability of thebhbA2B2cluster than thebhbABcluster may be due to the transcription levels and the character of the dehalogenase gene itself rather than that of its extracytoplasmic binding receptor gene. The plasmid pBHB is riddled with transposons and insertion sequence (IS) elements, and ISs play important roles in the evolution of pBHB. The analysis of the origin of thebhbgenes on pBHB suggested that these accessory genes evolved independently. Our work provides insights into the evolutionary strategies ofComamonasplasmids, especially into the adaptation mechanism employed by pBHB for haloaromatics.

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