scholarly journals Destabilization of the Tumor-Inducing Plasmid from an Octopine-Type Agrobacterium tumefaciens Lineage Drives a Large Deletion in the Co-resident At Megaplasmid

2019 ◽  
Vol 9 (10) ◽  
pp. 3489-3500
Author(s):  
Ian S. Barton ◽  
Thomas G. Platt ◽  
Douglas B. Rusch ◽  
Clay Fuqua
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Genetic Interaction ◽  
Large Deletion ◽  
Virulence Plasmid ◽  
Deletion Event ◽  
Fitness Consequences ◽  
Extrachromosomal Elements ◽  
The Family ◽  
Associated Functions ◽  
Large Plasmids

Bacteria with multi-replicon genome organizations, including members of the family Rhizobiaceae, often carry a variety of niche-associated functions on large plasmids. While evidence exists for cross-replicon interactions and co-evolution between replicons in many of these systems, remarkable strain-to-strain variation is also observed for extrachromosomal elements, suggesting increased genetic plasticity. Here, we show that curing of the tumor-inducing virulence plasmid (pTi) of an octopine-type Agrobacterium tumefaciens lineage leads to a large deletion in the co-resident At megaplasmid (pAt). The deletion event is mediated by a repetitive IS-element, IS66, and results in a variety of environment-dependent fitness consequences, including loss of independent conjugal transfer of the plasmid. Interestingly, a related and otherwise wild-type A. tumefaciens strain is missing exactly the same large pAt segment as the pAt deletion derivatives, suggesting a similar event over its natural history. Overall, the findings presented here uncover a novel genetic interaction between the two large plasmids of A. tumefaciens and provide evidence for cross-replicon integration and co-evolution of these plasmids.

scholarly journals Destabilization of the Tumor-Inducing Plasmid from an Octopine-TypeAgrobacterium tumefaciensLineage Drives a Large Deletion in the Co-Resident At Megaplasmid

2019 ◽  
Author(s):  
Ian S. Barton ◽  
Thomas G. Platt ◽  
Douglas B. Rusch ◽  
Clay Fuqua
Keyword(s):  
Genetic Interaction ◽  
Large Deletion ◽  
Virulence Plasmid ◽  
Wild Type ◽  
Deletion Event ◽  
Fitness Consequences ◽  
Extrachromosomal Elements ◽  
The Family ◽  
Associated Functions ◽  
Large Plasmids

ABSTRACTBacteria with multi-replicon genome organizations, including members of the familyRhizobiaceae, often carry a variety of niche-associated functions on large plasmids. While evidence exists for cross-replicon interactions and co-evolution between replicons in many of these systems, remarkable strain-to-strain variation is also observed for extrachromosomal elements, suggesting increased genetic plasticity. Here, we show that curing of the tumor-inducing virulence plasmid (pTi) of an octopine-typeAgrobacterium tumefacienslineage leads to a large deletion in the co-resident At megaplasmid (pAt). The deletion event is mediated by a repetitive IS-element, IS66, and results in a variety of environment-dependent fitness consequences, including loss of independent conjugal transfer of the plasmid. Interestingly, a related and otherwise wild-typeA. tumefaciensstrain is missing exactly the same large pAt segment as the pAt deletion derivatives, suggesting a similar event over its natural history. Overall, the findings presented here uncover a novel genetic interaction between the two large plasmids ofA. tumefaciensand provide evidence for cross-replicon integration and co-evolution of these plasmids.

scholarly journals The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity

2019 ◽  
Vol 21 (1) ◽  
pp. 3 ◽  
Author(s):  
Saura R. Silva ◽  
Ana Paula Moraes ◽  
Helen A. Penha ◽  
Maria H. M. Julião ◽  
Douglas S. Domingues ◽  
...  
Keyword(s):  
Life Form ◽  
Draft Genome ◽  
Innovation Process ◽  
Carnivorous Plant ◽  
Whole Genome Duplications ◽  
Go Enrichment ◽  
The Family ◽  
Genome Duplications ◽  
Terrestrial Life ◽  
Associated Functions

Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover, GO enrichment analyses suggest an ongoing gene birth–death–innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes.

Metschnikowia continentalisvar.borealis,Metschnikowia continentalisvar.continentalis, andMetschnikowia hibisci, new heterothallic haploid yeasts from ephemeral flowers and associated insects

1998 ◽  
Vol 44 (3) ◽  
pp. 279-288 ◽  
Author(s):  
Marc-André Lachance ◽  
Carlos A Rosa ◽  
William T Starmer ◽  
Birgit Schlag-Edler ◽  
J Stuart F. Baker ◽  
...  
Keyword(s):  
New South ◽  
Sequence Similarity ◽  
Large Deletion ◽  
Close Relative ◽  
North American Population ◽  
Central Brazil ◽  
South Wales ◽  
The Family ◽  
North And South America ◽  
North And South

Several strains of three new taxa of haploid heterothallic yeasts have been isolated from various ephemeral flowers and associated insects in North and South America and Australia. Metschnikowia continentalis comprises two varieties and is a close relative of Metschnikowia hawaiiensis. Like the latter, it produces giant ascospores and lives in association with the insects that colonize flowers of the family Convolvulaceae. These species exhibit an unusual asymmetrical mating, but their rare asci are sterile. The varieties of M. continentalis undergo unlimited mating, but ascospores are rarely formed. Metschnikowia continentalis var. continentalis was isolated in central Brazil and is thought to occur across South America.Metschnikowia continentalis var. borealis was recovered in the Great Lakes area and may represent a North American population. Metschnikowia hibisci was found in the flowers and insects of various Hibiscus species in the Australian states of New South Wales and Queensland but appeared to be absent in members of the Convolvulaceae growing in the same areas. The latter forms intermediate-sized ascospores and one of its mating types forms conjugation tubes in the presence of cells of other Metschnikowia species. The three taxa share with M. hawaiiensis a large deletion in the D2 region of their large ribosomal DNA subunit, but in M. hibisci, the variable domain of the D2 region shares little, if any, sequence similarity with others. The type cultures are as follows:M. continentalis var. continentalis strains UFMG96-173 (h+, CBS8429) and UFMG96-179 (h-, CBS8430); M. continentalis var. borealis strains UWO(PS)96-104.2 (h+, CBS 8431) and UWO(PS)96-101.1 (h-, CBS8432); and M. hibisci strains UWO(PS)95-797.2 (h+, CBS8433) and UWO(PS)95-805.1 (h-, CBS8434).Key words: Metschnikowia, yeast, Convolvulaceae, Hibiscus, geographic speciation.

scholarly journals Identification and Characterization of Rvs162/Rvs167-3, a Novel N-BAR Heterodimer in the Human Fungal Pathogen Candida albicans

2014 ◽  
Vol 14 (2) ◽  
pp. 182-193 ◽  
Author(s):  
Areti Gkourtsa ◽  
Janny van den Burg ◽  
Karin Strijbis ◽  
Teja Avula ◽  
Sietske Bijvoets ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Fluorescent Protein ◽  
Genetic Interaction ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Associated Functions ◽  
Increased Sensitivity ◽  
Green Fluorescent ◽  
And Function

ABSTRACT Membrane reshaping resides at the core of many important cellular processes, and among its mediators are the BAR (Bin, Amphiphysin, Rvs) domain-containing proteins. We have explored the diversity and function of the Rvs BAR proteins in Candida albicans and identified a novel family member, Rvs167-3 (orf19.1861). We show that Rvs167-3 specifically interacts with Rvs162 to form a stable BAR heterodimer able to bind liposomes in vitro . A second, distinct heterodimer is formed by the canonical BAR proteins Rvs161 and Rvs167. Purified Rvs161/Rvs167 complex also binds liposomes, indicating that C. albicans expresses two functional BAR heterodimers. We used live-cell imaging to localize green fluorescent protein (GFP)-tagged Rvs167-3 and Rvs167 and show that both proteins concentrate in small cortical spots. However, while Rvs167 strictly colocalizes with the endocytic marker protein Abp1, we do not observe any colocalization of Rvs167-3 with sites of endocytosis marked by Abp1. Furthermore, the rvs167-3 Δ/Δ mutant is not defective in endocytosis and strains lacking Rvs167-3 or its partner Rvs162 do not display increased sensitivity to high salt concentrations or decreased cell wall integrity, phenotypes which have been observed for rvs167 Δ/Δ and rvs161 Δ/Δ strains and which are linked to endocytosis defects. Taken together, our results indicate different roles for the two BAR heterodimers in C. albicans : the canonical Rvs161/Rvs167 heterodimer functions in endocytosis, whereas the novel Rvs162/Rvs167-3 heterodimer seems not to be involved in this process. Nevertheless, despite their different roles, our phenotypic analysis revealed a genetic interaction between the two BAR heterodimers, suggesting that they may have related but distinct membrane-associated functions.

scholarly journals Cantharidin alters GPI-anchored protein sorting by targeting Cdc1 mediated remodeling in Endoplasmic Reticulum

2018 ◽  
Author(s):  
Pushpendra Kumar Sahu ◽  
Raghuvir Singh Tomar
Keyword(s):  
Endoplasmic Reticulum ◽  
Cell Wall ◽  
Genetic Interaction ◽  
Protein Sorting ◽  
Model Organism ◽  
Cell Wall Integrity ◽  
Yeast Cells ◽  
Growth Media ◽  
Gpi Anchor ◽  
Associated Functions

ABSTRACTCantharidin (CTD) is a potent anticancer small molecule produced by several species of blister beetle. It has been a traditional medicine for the treatment of warts and tumors for many decades. CTD suppresses the tumor growth by inducing apoptosis, cell cycle arrest, and DNA damage. It is a known inhibitor of PP2A and PP1. In this study, we identified new molecular targets of CTD usingSaccharomyces cerevisiaeas a model organism which expresses a Cantharidin Resistance Gene (CRG1).CRG1encodes a SAM-dependent methyltransferase that inactivates CTD by methylation. CTD alters lipid homeostasis, cell wall integrity, endocytosis, adhesion, and invasion in yeast cells. We found that CTD specifically affects the phosphatidylethanolamine (PE) associated functions which can be rescued by supplementation of ethanolamine (ETA) in the growth media. CTD also perturbed ER homeostasis and cell wall integrity by altering the GPI-anchored protein sorting. The CTD dependent genetic interaction profile ofCRG1revealed that Cdc1 activity in GPI-anchor remodeling is the key target of CTD, which we found to be independent of PP2A and PP1. Furthermore, our experiments with human cells suggest that CTD functions through a conserved mechanism in higher eukaryotes as well. Altogether, we conclude that CTD induces cytotoxicity by targeting Cdc1 activity in GPI-anchor remodeling in the endoplasmic reticulum (ER).

Agrobacterium tumefaciens. [Descriptions of Fungi and Bacteria].

1965 ◽  
Author(s):  
A. C. Hayward
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Geographical Distribution ◽  
Infected Plant ◽  
Distinct Species ◽  
Infested Soil ◽  
Abnormal Growth ◽  
Nursery Stock ◽  
Antibiotic Effect ◽  
The Family ◽  
Bacterial Plant Pathogen

Abstract A description is provided for Agrobacterium tumefaciens. Information is included on the disease caused by the organism, its transmission, geographical distribution, and hosts. HOSTS: Agrobacterium tumefaciens has the widest host range of any bacterial plant pathogen; Elliott (1951) lists 140 genera in 61 families of which only Liliaceae and Araceae are monocotyledons. No antibiotic effect has been found in the monocotyledons to explain their resistance (43, 2199), but sap from oats and barley has been shown to inhibit initiation of tumours in sunflower and to kill tumour cells (43, 3119). A distinct species, Agrobacterium rubi, is recognized as the cause of cane gall on Rubus spp. (34: 380, 138). DISEASE: Crown gall of apple, peach, rose and many other plants in the family Rosaceae, also on vine, hop, mulberry, beetroot, swede and mangold. The pathogen stimulate the cells of the host parenchyma to abnormal growth with the production of spherical or convoluted outgrowths. The galls may be subterranean on the roots at the collar or crown (on peach or rose) or they may be aerial on the stems (on willow or vine). GEOGRAPHICAL DISTRIBUTION: One of the most widely distributed bacterial pathogens which has been reported from all five continents (CMI Map 137, 1947). TRANSMISSION: A wound pathogen which is capable of saprophytic survival for long periods in the soil. Wounds may be caused by a variety of agencies including root-chewing insects (10: 505) and pruning instruments. Readily disseminated on nursery stock which may become infected by tools contaminated with the pathogen when cuttings or grafts are made. Reports of survival in soil vary widely depending on soil type (41: 277, 641; 32: 25; 20: 521, 292) and moisture content (3: 104). On hop, the pathogen is said to be transmitted on seed as well as by infected plant debris and infested soil (41: 52). It has also been shows to be disseminated by irrigation water in a peach nursery (24: 65; 23: 379).

scholarly journals Tn5386, a Novel Tn916-Like Mobile Element in Enterococcus faecium D344R That Interacts with Tn916 To Yield a Large Genomic Deletion

2005 ◽  
Vol 187 (19) ◽  
pp. 6668-6677 ◽  
Author(s):  
Louis B. Rice ◽  
Lenore L. Carias ◽  
Steven Marshall ◽  
Susan D. Rudin ◽  
Rebecca Hutton-Thomas
Keyword(s):  
Enterococcus Faecium ◽  
Pcr Amplification ◽  
Mobile Element ◽  
Large Deletion ◽  
The Other ◽  
Deletion Event ◽  
Site Analysis ◽  
Genomic Deletions ◽  
Pcr Product ◽  
Spontaneous Conversion

ABSTRACT We describe Tn5386, a novel ca.-29-kb Tn916-like mobile element discovered to occur in ampicillin-resistant, Tn916-containing Enterococcus faecium D344R. PCR amplification experiments after overnight growth with or without tetracycline revealed “joint” regions of circularized Tn5386 composed of 6-bp sequences linking different transposon termini. In one case (no tetracycline), the termini were consistent with those derived by target site analysis of the integrated element. In the other case, the termini were virtually identical in distance from the integrase binding regions, as seen with Tn916. These data are consistent with a model in which one PCR product results from the action of Tn5386 integrase, whereas the other results from the action of the Tn916 integrase on Tn5386. Spontaneous conversion of D344R to an ampicillin-susceptible phenotype (D344SRF) was associated with a 178-kb deletion extending from the left end of Tn5386 to the left end of Tn916. Examination of the Tn5386 junction after the large deletion event suggests that the deletion resulted from an interaction between the nonintegrase ends of Tn5386 and Tn916. The terminus of Tn5386 identified in this reaction suggested that it may have resulted from the activity of the Tn916 integrase (IntTn916 ). The “joint” of the circular element resulting from this excision was amplifiable from D344R, the sequence of which revealed a heteroduplex consistent with IntTn916 -mediated excision. In contrast, Tn5386 joints amplified from ampicillin-susceptible D344SRF revealed ends consistent with Tn5386 integrase activity, reflecting the absence of Tn916 from this strain. Tn5386 represents a new member of the Tn916 transposon family. Our data suggest that excision of Tn5386 can be catalyzed by the Tn916 integrase and that large genomic deletions may result from the interaction between these heterologous elements.

scholarly journals Pathogenomics of the Virulence Plasmids of Escherichia coli

2009 ◽  
Vol 73 (4) ◽  
pp. 750-774 ◽  
Author(s):  
Timothy J. Johnson ◽  
Lisa K. Nolan
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Antimicrobial Agents ◽  
Microbial Populations ◽  
Virulence Plasmid ◽  
E Coli ◽  
Virulence Plasmids ◽  
Bacterial Plasmids ◽  
Extrachromosomal Elements ◽  
Agents Of Change

SUMMARY Bacterial plasmids are self-replicating, extrachromosomal elements that are key agents of change in microbial populations. They promote the dissemination of a variety of traits, including virulence, enhanced fitness, resistance to antimicrobial agents, and metabolism of rare substances. Escherichia coli, perhaps the most studied of microorganisms, has been found to possess a variety of plasmid types. Included among these are plasmids associated with virulence. Several types of E. coli virulence plasmids exist, including those essential for the virulence of enterotoxigenic E. coli, enteroinvasive E. coli, enteropathogenic E. coli, enterohemorrhagic E. coli, enteroaggregative E. coli, and extraintestinal pathogenic E. coli. Despite their diversity, these plasmids belong to a few plasmid backbones that present themselves in a conserved and syntenic manner. Thanks to some recent research, including sequence analysis of several representative plasmid genomes and molecular pathogenesis studies, the evolution of these virulence plasmids and the implications of their acquisition by E. coli are now better understood and appreciated. Here, work involving each of the E. coli virulence plasmid types is summarized, with the available plasmid genomic sequences for several E. coli pathotypes being compared in an effort to understand the evolution of these plasmid types and define their core and accessory components.

scholarly journals Characterisation of a new megaplasmid family associated with the spread of multidrug resistance in Pseudomonas aeruginosa

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Adrian Cazares ◽  
James P.J. Hall ◽  
Laura L. Wright ◽  
Macauley Grimes ◽  
Jean-Guillaume Emond-Rhéault ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistance ◽  
Global Scale ◽  
Experimental Characterization ◽  
Bioinformatics Analyses ◽  
Multiple Datasets ◽  
The Family ◽  
Long Read ◽  
Large Plasmids

Unlike in other important pathogens, the role of plasmids in the emergence of antimicrobial resistance (AMR) in Pseudomonas aeruginosa (Pa) has remained largely unaddressed. Previous work on AMR in Pa has mostly used genome sequencing methods that are limited because of the difficulty of using short-read data to detect and reconstruct complex plasmids. Here, using superior long-read sequencing, comprehensive bioinformatics analyses, and experimental characterization, we uncover an emerging family of important Pseudomonas megaplasmids and report its contribution to dissemination of multidrug resistance (MDR) on a global scale. Firstly, we identified large plasmids with a key role in the spread of MDR in a hospital in Thailand, and characterised their resistance regions revealing evidence of duplication, recombination and shared repeats, indicative of dynamic adaptation. Applying phylogenomics and pangenomics approaches we linked related megaplasmids and defined a core and pangenome for the family, exposing wide variations in AMR genes carriage. We then surveyed thousands of publicly available genomes, leading to discovery of dozens of megaplasmid relatives overlooked in multiple datasets, including already published studies. By integrating all this information and looking beyond the pathogenic species we gained valuable insights into the evolution of the megaplasmid family and revealed its widespread and multispecies distribution. We also showed that members of this family are stable in the absence of antibiotic pressure, bear no fitness cost to their host, and can be readily transferred between different Pseudomonas species. Our findings expand the bacterial plasmidome and provide insights on how MDR plasmids emerge from environmental reservoirs.

scholarly journals Positive Selection for Mutations Affecting Bioconversion of Aromatic Compounds in Agrobacterium tumefaciens: Analysis of Spontaneous Mutations in the Protocatechuate 3,4-Dioxygenase Gene

2000 ◽  
Vol 182 (21) ◽  
pp. 6145-6153 ◽  
Author(s):  
Donna Parke
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Positive Selection ◽  
Aromatic Compounds ◽  
Spontaneous Mutation ◽  
Carbon Sources ◽  
Large Deletion ◽  
Missense Mutations ◽  
Amino Acid Residues ◽  
Selection For ◽  
Intradiol Dioxygenase

ABSTRACT A positive selection method for mutations affecting bioconversion of aromatic compounds was applied to a mutant strain ofAgrobacterium tumefaciens A348. The nucleotide sequence of the A348 pcaHGB genes, which encode protocatechuate 3,4-dioxygenase (PcaHG) and β-carboxy-cis,cis-muconate cycloisomerase (PcaB) for the first two steps in catabolism of the diphenolic protocatechuate, was determined. An omega element was introduced into the pcaB gene of A348, creating strain ADO2077. In the presence of phenolic compounds that can serve as carbon sources, growth of ADO2077 is inhibited due to accumulation of the tricarboxylate intermediate. The toxic effect, previously described forAcinetobacter sp., affords a powerful selection for suppressor mutations in genes required for upstream catabolic steps. By monitoring loss of the marker in pcaB, it was possible to determine that the formation of deletions was minimal compared to results obtained with Acinetobacter sp. Thus, the tricarboxylic acid trick in and of itself does not appear to select for large deletion mutations. The power of the selection was demonstrated by targeting the pcaHG genes of A. tumefaciensfor spontaneous mutation. Sixteen strains carrying putative second-site mutations in pcaH or -G were subjected to sequence analysis. All single-site events, their mutations revealed no particular bias toward multibase deletions or unusual patterns: five (−1) frameshifts, one (+1) frameshift, one tandem duplication of 88 bp, one deletion of 92 bp, one nonsense mutation, and seven missense mutations. PcaHG is considered to be the prototypical ferric intradiol dioxygenase. The missense mutations served to corroborate the significance of active site amino acid residues deduced from crystal structures of PcaHG from Pseudomonas putida andAcinetobacter sp. as well as of residues in other parts of the enzyme.

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