Paracoccus methylutens sp. nov. — a New Aerobic Facultatively Methylotrophic Bacterium Utilizing Dichloromethane

Доронина, Н. В.; Trotsenko, Yu. A.; Krausova, Valentina I.; Сузина, Н. Е.

doi:10.1016/s0723-2020(98)80027-1

Cited by 46 publications

(21 citation statements)

References 17 publications

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“…In order to define the TMos of pMTH1, the complete nucleotide sequence of this plasmid was determined. It consisted of 31,999 bp with an average GC content of 64.1%, which is close to that of the P. methylutens chromosome (67%) (10). pMTH1 was predicted to encode 27 putative open reading frames (ORFs) (Fig.…”

Section: Resultsmentioning

confidence: 91%

“…These are convenient tools, enabling the direct identification of even phenotypically silent elements (4,16,23). In this report, we present the characterization of "atypical" transposable elements "captured" by entrapment vector pMEC1 (4) in a methylotrophic bacterium utilizing dichloromethane, Paracoccus methylutens DM12 (Alphaproteobacteria) (10). We also show that these elements are generated frequently and that their activity is able to significantly shape the structures of genomes of plasmids naturally occurring in this strain.…”

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confidence: 89%

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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

et al. 2008

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We demonstrated that a single copy of insertion sequence ISPme1 can mobilize adjacent segments of genomic DNA of Paracoccus methylutens DM12, which leads to the generation of diverse transposable elements of various size and DNA contents. All elements (named transposable modules [TMos]) contain ISPme1 (placed at the 5 ends of the elements) and have variable 3-end regions of between 0.5 and 5 kb. ISPme1 was shown to encode an outwardly oriented promoter, which may activate the transcription of genes transposed within TMos in evolutionarily distinct hosts. TMos may therefore be considered to be natural systems enabling gene capture, expression, and spread. However, unless these elements have been inserted into a highly conserved genetic context to enable a precise definition of their termini, it is extremely difficult or even impossible to identify them in bacterial genomes by in silico sequence analysis. We showed that TMos are present in the chromosome and plasmids of strain DM12. Sequence analysis of plasmid pMTH1 (32 kb) revealed that four TMos, previously identified with a trap vector, pMEC1, comprise 87% of its genome. Repeated TMos within pMTH1 may stimulate other structural rearrangements resulting from homologous recombination between long repeat sequences. This illustrates that TMos may play a significant role in shaping the structure of natural plasmids, which consequently may have a great impact on the evolution of plasmid genomes.Sequencing projects have revealed that bacterial genomes are not static, monolithic structures. They can contain a number of different kinds of integrated mobile genetic elements (e.g., transposable elements, plasmids, bacteriophages, and integrative and conjugative elements) acquired by lateral gene transfer.Insertion sequences (ISs), which are the simplest forms of transposable elements (TEs), are components of nearly all bacterial genomes. To date, more than 1,500 ISs have been identified in over 295 bacterial and archaeal species (21). The transposition of ISs promotes structural changes in DNA that lead to the formation of various mutations (insertions, deletions, inversions, translocations, and replicon fusion). These elements are therefore considered to be the major recombinogenic factors in bacterial genomes. Their activity results in the shuffling of genetic information among various replicons present in a bacterial cell (chromosomes, plasmids, and bacteriophages), which may ultimately enable its spread by lateral gene transfer. These elements thus play the role of a factor that significantly enhances variability and, consequently, the adaptive and evolutionary capacities of their hosts.ISs have a very simple structure, since they carry only the genetic information necessary for their own transposition.

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Section: Resultsmentioning

confidence: 91%

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confidence: 89%

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

et al. 2008

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“…Extensive phenotypic and genotypic characterization of the 14 aerobic DCM utilizers has led to the classification of seven representatives (strains DM1, DM3 and DM5-DM9 T ) as Methylopila helvetica (Doronina et al, 2000). Four further representatives were classified as Methylobacterium dichloromethanicum DM4 T (Doronina et al, 2000), Methylorhabdus multivorans DM13 T (Doronina et al, 1995), Methylophilus leisingeri DM11 T N. V. Doronina and others (Doronina & Trotsenko, 1994) and Paracoccus methylutens DM12 T (Doronina et al, 1998a). Like the latter organism, one of the remaining unidentified isolates (strain DM10 T ) had the ribulose bisphosphate (RuBP) pathway for C " assimilation (Doronina et al, 1992), but differed from known facultatively autotrophic methylotrophic bacteria in some other properties.…”

Section: Introductionmentioning

confidence: 99%

Albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane.

Доронина¹,

Trotsenko²,

Tourova³

et al. 2001

International Journal of Systematic and Evolutionary Microbiology

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“…Some members of this genus are able to oxidize reduced sulfur compounds such as thiosulfate, thiocyanate, carbonyl sulfide and carbon disulfide to gain energy for autotrophic growth (Katayama et al, 1995 ;Siller et al, 1996 ;Lipski et al, 1998 ;Rainey et al, 1999). Most Paracoccus species are able to grow on carbon dioxide by using hydrogen oxidation as the source of metabolic energy ; some species can also grow methylotrophically with methanol, methylamine (Urakami et al, 1990 ;Ohara et al, 1990 ; Van Verseveld & Stouthamer, 1992), dichloromethane (Doronina et al, 1998), or with more complex substances such as N,N-dimethylformamide (Urakami et al, 1990) or methylated sulfides (Rainey et al, 1999). Phylogenetic analyses have demonstrated that all of the described species of the genus Paracoccus form a coherent cluster within the α-3 subclass of the Proteobacteria (Kelly et al, 2000).…”

Section: Abstract : Methylotroph Chemolithotroph Thermotolerant Almentioning

confidence: 99%

“…As follows from the phylogenetic tree ( Fig. 1 Doronina et al (1998), Doronina & Trotsenko (2000) and Kelly et al (2000). k, Absent ; j, present, , not reported.…”

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confidence: 94%

Emended description of Paracoccus kondratievae.

Доронина¹,

Trotsenko²,

Kuznetzov³

et al. 2002

International Journal of Systematic and Evolutionary Microbiology

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An aerobic, facultatively chemolithotrophic and methylotrophic strain, GB, was isolated from a maize rhizosphere. On the basis of comparative analysis of its phenotypic and genotypic properties, it is proposed that strain GB T (l VKM B-2222 T l NCIMB 13773 T ) be assigned to the genus Paracoccus as Paracoccus kondratievae sp. nov. Keywords : methylotroph, chemolithotroph, thermotolerant, alkaliphilic, ParacoccusUntil recently, the genus Paracoccus contained only two species, namely Paracoccus denitrificans and Paracoccus halodenitrificans (Van Verseveld & Stouthamer, 1992). At present, the genus Paracoccus includes 13 validated species and has become the focus of many studies on its physiological versatility, and on the ability to degrade unusual and potentially polluting compounds, as extensively reviewed by Kelly et al. (2000). Some members of this genus are able to oxidize reduced sulfur compounds such as thiosulfate, thiocyanate, carbonyl sulfide and carbon disulfide to gain energy for autotrophic growth (Katayama et al., 1995 ;Siller et al., 1996 ;Lipski et al., 1998 ;Rainey et al., 1999). Most Paracoccus species are able to grow on carbon dioxide by using hydrogen oxidation as the source of metabolic energy ; some species can also grow methylotrophically with methanol, methylamine (Urakami et al., 1990 ;Ohara et al., 1990 ; Van Verseveld & Stouthamer, 1992), dichloromethane (Doronina et al., 1998), or with more complex substances such as N,N-dimethylformamide (Urakami et al., 1990) or methylated sulfides (Rainey et al., 1999). Phylogenetic analyses have demonstrated that all of the described species of the genus Paracoccus form a coherent cluster within the α-3 subclass of the Proteobacteria (Kelly et al., 2000).Very recently, we isolated (and made a preliminary description of ) a colourless, methanol-utilizing Paracoccus-like strain -strain GB T -that possessed the ribulose bisphosphate pathway. Based on analysis of cytophysiological and metabolic properties, cellular The GenBank/EMBL/DDBJ accession number for the 16S rRNA sequence of strain GB T is AF250332.ubiquinones, phospholipids and fatty acids, the DNA base composition and DNA-DNA hybridization, isolate GB was preliminarily classified as Paracoccus kondratievae (Doronina & Trotsenko, 2000, 2001. This paper reports on the phylogenetic analysis and further taxonomic characterization of Paracoccus kondratievae sp. nov. The 16S rRNA gene was amplified and sequenced according to Lane (1991). The almost complete 16S rRNA gene sequence from strain GB T was aligned, using the  program for sequence alignment to the representative paracocci. The positions of sequence uncertainties were omitted ; in total, 1290 nucleotides were used in the analysis. Their phylogenetic relationships were determined by the neighbour-joining method and the programs of the  package ( Van de Peer & De Wachter, 1994), by maximum-likelihood by using the  program (Strimmer & von Haeseler, 1996), and by maximumparsimony by using the program  from the ...

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Paracoccus methylutens sp. nov. — a New Aerobic Facultatively Methylotrophic Bacterium Utilizing Dichloromethane

Cited by 46 publications

References 17 publications

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

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

Albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane.

Emended description of Paracoccus kondratievae.

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