scholarly journals The Birth and Demise of the ISApl1-mcr-1-ISApl1 Composite Transposon: the Vehicle for Transferable Colistin Resistance

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Erik Snesrud ◽  
Patrick McGann ◽  
Michael Chandler
Keyword(s):  
Chromosomal Region ◽  
Novel Species ◽  
Single Copy ◽  
Comprehensive Analysis ◽  
Close Relative ◽  
Colistin Resistance ◽  
Software Suite ◽  
Sources Of Uncertainty ◽  
Transposition Mechanism ◽  
Cg Dinucleotides

ABSTRACT The origin and mobilization of the ~2,609-bp DNA segment containing the mobile colistin resistance gene mcr-1 continue to be sources of uncertainty, but recent evidence suggests that the gene originated in Moraxella species. Moreover mcr-1 can be mobilized as an ISApl1-flanked composite transposon (Tn6330), but many sequences have been identified without ISApl1 or with just a single copy (single ended). To further clarify the origins and mobilization of mcr-1, we employed the Geneious R8 software suite to comprehensively analyze the genetic environment of every complete mcr-1 structure deposited in GenBank as of this writing (September 2017) both with and without associated ISApl1 (n = 273). This revealed that the 2,609-bp mcr-1 structure was likely mobilized from a close relative of a novel species of Moraxella containing a chromosomal region sharing >96% nucleotide identity with the canonical sequence. This chromosomal region is bounded by AT and CG dinucleotides, which have been described on the inside ends (IE) of all intact Tn6330 described to date and represent the ancestral 2-bp target site duplications (TSDs) generated by ISApl1 transposition. We further demonstrate that all mcr-1 structures with just one ISApl1 copy or with no ISApl1 copies were formed by deletion of ISApl1 from the ancestral Tn6330, likely by a process related to the “copy-out–paste-in” transposition mechanism. Finally, we show that only the rare examples of single-ended structures that have retained a portion of the excised downstream ISApl1 including the entire inverted right repeat might be capable of mobilization. IMPORTANCE A comprehensive analysis of all intact mcr-1 sequences in GenBank was used to identify a region on the chromosome of a novel Moraxella species with remarkable homology to the canonical mcr-1 structure and that likely represents the origin of this important gene. These data also demonstrate that all mcr-1 structures lacking one or both flanking ISApl1 were formed from ancestral composite transposons that subsequently lost the insertion sequences by a process of abortive transposition. This observation conclusively shows that mobilization of mcr-1 occurs as part of a composite transposon and that structures lacking the downstream ISApl1 are not capable of mobilization.

scholarly journals Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Neža Čadež ◽  
Nicolas Bellora ◽  
Ricardo Ulloa ◽  
Miha Tome ◽  
Hrvoje Petković ◽  
...  
Keyword(s):  
Yeast Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Single Copy ◽  
The Novel ◽  
Orthologous Genes ◽  
Parasitic Fungi ◽  
Ethanol Yields ◽  
A New Species

During a survey of Nothofagus trees and their parasitic fungi in Andean Patagonia (Argentina), genetically distinct strains of Hanseniaspora were obtained from the sugar-containing stromata of parasitic Cyttaria spp. Phylogenetic analyses based on the single-gene sequences (encoding rRNA and actin) or on conserved, single-copy, orthologous genes from genome sequence assemblies revealed that these strains represent a new species closely related to Hanseniaspora valbyensis. Additionally, delimitation of this novel species was supported by genetic distance calculations using overall genome relatedness indices (OGRI) between the novel taxon and its closest relatives. To better understand the mode of speciation in Hanseniaspora, we examined genes that were retained or lost in the novel species in comparison to its closest relatives. These analyses show that, during diversification, this novel species and its closest relatives, H. valbyensis and Hanseniaspora jakobsenii, lost mitochondrial and other genes involved in the generation of precursor metabolites and energy, which could explain their slower growth and higher ethanol yields under aerobic conditions. Similarly, Hanseniaspora mollemarum lost the ability to sporulate, along with genes that are involved in meiosis and mating. Based on these findings, a formal description of the novel yeast species Hanseniaspora smithiae sp. nov. is proposed, with CRUB 1602H as the holotype.

scholarly journals Rhodotorula arctica sp. nov., a basidiomycetous yeast from Arctic soil

2010 ◽  
Vol 60 (5) ◽  
pp. 1215-1218 ◽  
Author(s):  
H. S. Vishniac ◽  
M. Takashima
Keyword(s):  
Novel Species ◽  
Rdna Sequence ◽  
Basidiomycetous Yeast ◽  
Close Relative ◽  
Its Sequence ◽  
Arctic Soil

Three isolates, typified by Pro94 Y29T (=JCM 13290T =CBS 9278T =DBVPG 7841T), that represent a novel species, Rhodotorula arctica sp. nov., were studied. R. arctica differed from its only close relative, Bensingtonia yamatoana, by requiring thiamine and by failing to assimilate maltose and quinate, but strain Pro94 Y29T could be most readily identified using the rDNA sequence of the LSU D1/D2 region, which differed from that of B. yamatoana CBS 7423T at four positions, and the ITS sequence, which differed at nine positions. One R. arctica isolate, Pro94 Y56 (=JCM 13292 =CBS 9280 =DBVPG Y7843), was unique in requiring either l-arginine or l-citrulline as a source of nitrogen.

scholarly journals Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand’s high ultraviolet B radiation environment

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yanni Dong ◽  
Saurabh Gupta ◽  
Rixta Sievers ◽  
Jason J. Wargent ◽  
David Wheeler ◽  
...  
Keyword(s):  
Draft Genome ◽  
Single Copy ◽  
Ultraviolet B ◽  
Radiation Environment ◽  
Perennial Herb ◽  
Close Relative ◽  
Close Phylogenetic Relationship ◽  
Genome Draft ◽  
Relationship Of ◽  
Boechera Stricta

Abstract Background Pachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000 m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with UV-B stress, we sequenced its genome and compared the UV-B tolerance of two Pachycladon accessions with those of two A. thaliana accessions from different altitudes. Results A high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologs. Synteny analysis with genomes from other species of the Brassicaceae family found a close phylogenetic relationship of P. cheesemanii with Boechera stricta from Brassicaceae lineage I. While UV-B radiation caused a greater growth reduction in the A. thaliana accessions than in the P. cheesemanii accessions, growth was not reduced in one P. cheesemanii accession. The homologues of A. thaliana UV-B radiation response genes were duplicated in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii appears to differ from that in A. thaliana. Conclusion Although the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies allowing the plant to tolerate relatively high UV-B radiation.

scholarly journals pmcf.2-11, a single copy clone from chromosomal region 12q12–q13.1 [D12S32]

1988 ◽  
Vol 16 (17) ◽  
pp. 8749-8749
Author(s):  
J. Oberle ◽  
M.G. Mattei ◽  
T. Noguchi ◽  
D. Birnbaum
Keyword(s):  
Chromosomal Region ◽  
Single Copy

scholarly journals The Acquisition of Colistin Resistance Is Associated to the Amplification of a Large Chromosomal Region in Klebsiella pneumoniae kp52145

2021 ◽  
Vol 22 (2) ◽  
pp. 649
Author(s):  
María Blanca Sánchez ◽  
Alicia Sánchez-Gorostiaga ◽  
Trinidad Cuesta ◽  
José Luis Martínez
Keyword(s):  
Klebsiella Pneumoniae ◽  
Experimental Evolution ◽  
Chromosomal Region ◽  
Genetic Change ◽  
Cross Resistance ◽  
Common Mutation ◽  
Colistin Resistance ◽  
Mechanisms Of Resistance ◽  
Carbapenem Resistant ◽  
Resistant Strains

The appearance of carbapenem-resistant Klebsiella pneumoniae has increased the use of colistin as a last-resort antibiotic for treating infections by this pathogen. A consequence of its use has been the spread of colistin-resistant strains, in several cases carrying colistin resistance genes. In addition, when susceptible strains are confronted with colistin during treatment, mutation is a major cause of the acquisition of resistance. To analyze the mechanisms of resistance that might be selected during colistin treatment, an experimental evolution assay for 30 days using as a model the clinical K. pneumoniae kp52145 isolate in the presence of increasing amounts of colistin was performed. All evolved populations presented a decreased susceptibility to colistin, without showing cross-resistance to antibiotics belonging to other structural families. We did not find any common mutation in the evolved mutants, neither in already known genes, previously known to be associated with the resistance phenotype, nor in new ones. The only common genetic change observed in the strains that evolved in the presence of colistin was the amplification of a 34 Kb sequence, homologous to a prophage (Enterobacteria phage Fels-2). Our data support that gene amplification can be a driving force in the acquisition of colistin resistance by K. pneumoniae.

Scheffersomyces parashehatae f.a., sp. nov., Scheffersomyces xylosifermentans f.a., sp. nov., Candida broadrunensis sp. nov. and Candida manassasensis sp. nov., novel yeasts associated with wood-ingesting insects, and their ecological and biofuel implications

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4330-4339 ◽  
Author(s):  
Sung-Oui Suh ◽  
Janice L. Houseknecht ◽  
Pushpa Gujjari ◽  
Jianlong J. Zhou
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Rrna Genes ◽  
Close Relative ◽  
Strain Atcc ◽  
Decayed Wood ◽  
Sequence Analyses ◽  
Sequence Comparisons ◽  
Protein Coding ◽  
Rotten Wood

During a survey of yeasts associated with wood-ingesting insects, 69 strains in the Scheffersomyces clade and related taxa were isolated from passalid and tenebrionid beetles and the decayed wood inhabited by them. The majority of these yeasts was found to be capable of fermenting xylose, and was recognized as Scheffersomyces stipitis or its close relative Scheffersomyces illinoinensis, which are known to be associated with wood-decaying beetles and rotten wood. Yeasts in ‘Scheffersomyces’ ( = Candida) ergatensis and ‘Scheffersomyces’ ( = Candida) coipomoensis were also frequently isolated. The remaining six strains were identified as representing four novel species in the genera Scheffersomyces and Candida based on multilocus sequence analyses of nuclear rRNA genes and four protein-coding genes, as well as other taxonomic characteristics. Two xylose-fermenting species, Scheffersomyces parashehatae f.a., sp. nov. (type strain ATCC MYA-4653T = CBS 12535T = EH045T; MycoBank MB805440) and Scheffersomyces xylosifermentans f.a., sp. nov. (type strain ATCC MYA-4859T = CBS 12540T = MY10-052T; MycoBank MB805441), formed a clade with Scheffersomyces shehatae and related Scheffersomyces species. Interestingly, S. xylosifermentans can survive at 40 °C, which is a rare property among xylose-fermenting yeasts. Candida broadrunensis sp. nov. (type strain ATCC MYA-4650T = CBS 11838T = EH019T; MycoBank MB805442) is a sister taxon of C. ergatensis, while Candida manassasensis sp. nov. (type strain ATCC MYA-4652T = CBS 12534T = EH030T; MycoBank MB805443) is closely related to Candida palmioleophila in the Candida glaebosa clade. The multilocus DNA sequence comparisons in this study suggest that the genus Scheffersomyces needs to be circumscribed to the species near S. stipitis (type species) and S. shehatae that can be characterized by the ability to ferment xylose.

scholarly journals Role of IncP-1β Plasmids pWDL7::rfpand pNB8c in Chloroaniline Catabolism as Determined by Genomic and Functional Analyses

2011 ◽  
Vol 78 (3) ◽  
pp. 828-838 ◽  
Author(s):  
J. E. Król ◽  
J. T. Penrod ◽  
H. McCaslin ◽  
L. M. Rogers ◽  
H. Yano ◽  
...  
Keyword(s):  
Single Copy ◽  
Degradation Pathway ◽  
Bacterial Degradation ◽  
Ring Cleavage ◽  
Close Relative ◽  
Broad Host Range ◽  
Content Type ◽  
Aromatic Ring Cleavage ◽  
Functional Analyses

ABSTRACTBroad-host-range catabolic plasmids play an important role in bacterial degradation of man-made compounds. To gain insight into the role of these plasmids in chloroaniline degradation, we determined the first complete nucleotide sequences of an IncP-1 chloroaniline degradation plasmid, pWDL7::rfpand its close relative pNB8c, as well as the expression pattern, function, and bioaugmentation potential of the putative 3-chloroaniline (3-CA) oxidation genes. Based on phylogenetic analysis of backbone proteins, both plasmids are members of a distinct clade within the IncP-1β subgroup. The plasmids are almost identical, but whereas pWDL7::rfpcarries a duplicate inverted catabolic transposon, Tn6063, containing a putative 3-CA oxidation gene cluster,dcaQTA1A2BR, pNB8c contains only a single copy of the transposon. No genes for an aromatic ring cleavage pathway were detected on either plasmid, suggesting that only the upper 3-CA degradation pathway was present. ThedcaA1A2Bgene products expressed from a high-copy-number vector were shown to convert 3-CA to 4-chlorocatechol inEscherichia coli. Slight differences in thedcapromoter region between the plasmids and lack of induction of transcription of the pNB8cdcagenes by 3-CA may explain previous findings that pNB8C does not confer 3-CA transformation. Bioaugmentation of activated sludge with pWDL7::rfpaccelerated removal of 3-CA, but only in the presence of an additional carbon source. Successful bioaugmentation requires complementation of the upper pathway genes with chlorocatechol cleavage genes in indigenous bacteria. The genome sequences of these plasmids thus help explain the molecular basis of their catabolic activities.

scholarly journals Description of Paenibacillus albicerus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup.

2021 ◽  
Author(s):  
Vipool Thorat ◽  
Kiran Kirdat ◽  
Bhavesh Tiwarekar ◽  
Priyanka Dhanavade ◽  
Prachi Karodi ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Close Relative ◽  
Rrna Gene ◽  
Carbon Utilization ◽  
Gene Sequence Analysis ◽  
Close Relatives

Abstract Two aerobic, Gram-stain variable, catalase and oxidase-positive, spore-forming, motile rods of strain UniB2T and UniB3T, were isolated from digestive syrup containing fungal diastase (10 mg/ml), pepsin (2 mg/ml) and sugar base containing polyethene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2T has the highest sequence similarity with Paenibacillus humicus NBRC 102415T (98.30 %) and strain UniB3T showed the highest sequence similarity with Niallia circulans DSM 11T (98.95 %). The DNA G+C content of UniB2T was 63.74 mol %. The dDDH and ANI values between the strain UniB2T and its phylogenetically close relative were <38.3 % and <89.55 %, respectively. The major fatty acids of the strain UniB2T were C16:00 (13.9 %), C15:0 anteiso (39.7 %), C17:0 anteiso (15.5 %). The DNA G+C content of UniB3T was 35.6 mol%. The dDDH and ANI values between the strain UniB3T and its close relatives were <29.1 % and 84.62%, respectively. The major fatty acids of strain UniB3T were C16:0 (13.54 %), C15:0 anteiso (40.09 %) and C17:0 anteiso (16.03 %). Major polar lipids for both strains were Diphosphotidylglycerol and Phosphatidylethanolamine. Additionally, both the strains showed unique carbon utilization and assimilation pattern that differentiated them from their phylogenetically related neighbours. These phenotypic, genotypic and chemotaxonomic characters indicated the strains UniB2T and UniB3T represent two novel species for which the names Paenibacillus albicerus sp. nov. (Type strain UniB2T =MCC 3997T =KCTC 43095T =JCM34513T) and Niallia alba sp. nov. (Type strain UniB3T = MCC 3998T =KCTC 43235T =JCM 34492T) are proposed.

scholarly journals Gluconacetobacter dulcium sp. nov., a novel Gluconacetobacter species from sugar-rich environments

2020 ◽  
Author(s):  
Atena Sadat Sombolestani ◽  
Ilse Cleenwerck ◽  
Margo Cnockaert ◽  
Wim Borremans ◽  
Anneleen D. Wieme ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Single Copy ◽  
Phylogenomic Analysis ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Maldi Tof Mass Spectra ◽  
Type Strains ◽  
Core Genes

A phylogenomic analysis based on 107 single-copy core genes revealed that three strains from sugar-rich environments, i.e. LMG 1728T, LMG 1731 and LMG 22058, represented a single, novel Gluconacetobacter lineage with Gluconacetobacter liquefaciens as nearest validly named neighbour. OrthoANIu and digital DNA–DNA hybridization analyses among these strains and Gluconacetobacter type strains confirmed that the three strains represented a novel Gluconacetobacter species. Biochemical characteristics and MALDI-TOF mass spectra allowed differentiation of this novel species from the type strains of G. liquefaciens and other closely related Gluconacetobacter species. We therefore propose to classify strains LMG 1728T, LMG 1731 and LMG 22058 in the novel species Gluconacetobacter dulcium sp. nov., with LMG 1728T (=CECT 30142T) as the type strain.

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