Transposable Modules Generated by a Single Copy of Insertion Sequence IS
            <i>Pme1</i>
            and Their Influence on Structure and Evolution of Natural Plasmids of
            <i>Paracoccus methylutens</i>
            DM12

Bartosik, Dariusz; Putyrski, Mateusz; Dziewit, Łukasz; Malewska, Edyta; Szymanik, Michal; Jagiełło, Ewa; Lukasik, Jacek; Baj, Jadwiga

doi:10.1128/jb.01878-07

Cited by 23 publications

(32 citation statements)

References 27 publications

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“…The former mobile genetic element flanked by 50-bp Aromatic catabolic pathways in microbial community H Suenaga et al IR sequences is located very close to the singlecomponent phenol hydroxylase gene and was thought to be ISPme1, an IS element from plasmid pMTH1 of Paracoccus methylutens DM12 (Bartosik et al, 2008). The latter element, designated Tn6032, has 25-bp IR sequences and carries three ORFs encoding polypeptides with moderate sequence identity to TniA (40%), TniB (35%) and an Nterminal portion of TniQ (23%) of Tn5053 from Xanthomonas sp.…”

Section: Aromatic Catabolic Pathways In Microbial Community H Suenagamentioning

confidence: 99%

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

et al. 2009

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Several types of environmental bacteria that can aerobically degrade various aromatic compounds have been identified. The catabolic genes in these bacteria have generally been found to form operons, which promote efficient and complete degradation. However, little is known about the degradation pathways in bacteria that are difficult to culture in the laboratory. By functionally screening a metagenomic library created from activated sludge, we had earlier identified 91 fosmid clones carrying genes for extradiol dioxygenase (EDO), a key enzyme in the degradation of aromatic compounds. In this study, we analyzed 38 of these fosmids for the presence and organization of novel genes for aromatics degradation. Only two of the metagenomic clones contained complete degradation pathways similar to those found in known aromatic compound-utilizing bacteria. The rest of the clones contained only subsets of the pathway genes, with novel gene arrangements. A circular 36.7-kb DNA form was assembled from the sequences of clones carrying genes belonging to a novel EDO subfamily. This plasmid-like DNA form, designated pSKYE1, possessed genes for DNA replication and stable maintenance as well as a small set of genes for phenol degradation; the encoded enzymes, phenol hydroxylase and EDO, are capable of the detoxification of aromatic compounds. This gene set was found in 20 of the 38 analyzed clones, suggesting that this 'detoxification apparatus' may be widespread in the environment.

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Section: Aromatic Catabolic Pathways In Microbial Community H Suenagamentioning

confidence: 99%

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

et al. 2009

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“…It has already been demonstrated that IS-related mutations occur in Escherichia coli (44), Lactococcus lactis (10), Mycobacterium tuberculosis (33), and Francisella tularensis (39). Their active role was also demonstrated in the evolution of Paracoccus methylutens DM12 plasmids (3). Early bioinformatic analysis of the L. helveticus DPC4571 genome sequence resulted in identification of IS-associated truncations in genes associated with cellobiose transport, acetaldehyde dehydrogenase and diacetyl reductase (6).…”

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confidence: 99%

Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison

Kaleta

O’Callaghan

Fitzgerald

et al. 2010

Appl Environ Microbiol

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Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous genotypes depending on the ecosystem from which it was isolated. The recently published genome sequence showed the remarkable flexibility of its structure, demonstrated by a substantial level of insertion sequence (IS) element expansion in association with massive gene decay. To assess this diversity and examine the level of genome plasticity within the L. helveticus species, an array-based comparative genome hybridization (aCGH) experiment was designed in which 10 strains were analyzed. The aCGH experiment revealed 16 clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered ISs were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65, and ISLhe63). These findings contribute to the overall viewpoint of the versatile character of IS elements and the role they may play in bacterial genome plasticity.Lactobacillus helveticus is a gram-positive, homofermentative lactic acid bacterium which is widely used in the manufacture of cheeses, such as Swiss cheese and some Cheddar-type cheeses (22,25). It is also commonly used in the production of different types of Italian cheeses, such as Parmigiano Reggiano (18) and Grana Padano, where it contributes to the formation of specific flavor compounds (42).Phylogenetic analysis of ribosomal protein sequences derived from lactobacilli and streptococci classified L. helveticus in the same group along with both gastrointestinal (GI) tract and dairy-specific species (14). Comparative analysis of the 16S rRNA of L. helveticus DPC4571 revealed 98.4% identity with Lactobacillus acidophilus NCFM and indicated that this probiotic strain was closely related to strain DPC4571, despite the different environments these two lactobacilli inhabit (4). The results of genomic analysis of L. helveticus suggested that two major events have occurred in the diversification process of L. helveticus from a common ancestor with L. acidophilus, selective gene loss and acquisition of a large number of insertion sequence (IS) elements (4). IS elements are DNA sequences capable of independent transposition within and between bacterial genomes (31). Their capacity for independent mobility demonstrates the parasitic nature of these elements (11); however, they can also be regarded as having a positive influence, as they assist in promoting genetic variation (1). Thus, even though the primal character of these elements remains unclear in that they may be considered simply as selfish DNA elements, their impact on the architecture of microbial genomes is undeniable. It has already been demonstrated that IS-related mutations occur in Escherichia coli (44), Lactococcus lactis (10)...

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“…The transposase of ISPme1 is very closely related (92% amino acid identity) to that of IS1247, which has previously been found upstream of the dhlB gene in mutants of Xanthobacter strain GJ10 with enhanced haloacid dehalogenase activity (36). A remarkable feature of the ISPme1 and IS1247 elements is that they are capable of mobilizing the 3= adjacent DNA regions in the absence of a composite transposon structure (36,52), so it seems very likely that ISPme1 was responsible for recruiting the dhlB2 gene into pDCA. ISPme1 is also likely to play a role in activating the tran- Table S1 in the supplemental material.…”

Section: Resultsmentioning

confidence: 88%

A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site

Munro

Liew

et al. 2016

Appl Environ Microbiol

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ABSTRACT1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1. Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination. IMPORTANCEEarlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes. O rganochlorine chemicals have been widely used as pesticides, solvents, and for plastic manufacture. Many of these compounds are xenobiotic, and, as a result, their environmental breakdown is often slow (1). The environmental persistence of organochlorines is a problem, since many of these chemicals are damaging to human and environmental health (2). One organochlorine of concern is 1,2-dichloroethane (DCA), which is often present as a groundwater contaminant (3, 4). DCA is not known to exi...

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Transposable Modules Generated by a Single Copy of Insertion Sequence IS Pme1 and Their Influence on Structure and Evolution of Natural Plasmids of Paracoccus methylutens DM12

Cited by 23 publications

References 27 publications

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison

A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site

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