scholarly journals Isolation of Predation-Deficient Mutants of Bdellovibrio bacteriovorus by Using Transposon Mutagenesis

2008 ◽  
Vol 74 (17) ◽  
pp. 5436-5443 ◽  
Author(s):  
John J. Tudor ◽  
James J. Davis ◽  
Marissa Panichella ◽  
Adam Zwolak
Keyword(s):  
Dna Sequences ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The Other ◽  
Insertion Mutagenesis ◽  
Gene Products ◽  
Bdellovibrio Bacteriovorus ◽  
Transposon Insertion ◽  
Blast Analysis ◽  
Insertion Mutants

ABSTRACT The availability of the complete genome sequence of Bdellovibrio bacteriovorus provides an opportunity for investigating genes that play a significant role in predation. Using two independently derived facultatively predatory Bdellovibrio strains, we have designed a method to cultivate and screen transposon insertion mutants in 96-well microtiter dishes. Transposon insertion mutants were produced by introducing the plasposon pRL27, which carries a mini-Tn5. Mutants have been screened for predatory activity using 96-well plates. Seventeen independent nonpredatory mutants have been isolated, and DNA flanking the insertion has been sequenced. BLAST analysis revealed that most of these interrupted DNA sequences do not code for known proteins or functions. Two of the inactivated genes were analyzed further: one was found to code for a putative serine protease and the other a probable protein involved in secretion through the outer membrane. The methods described here are the first for the generation and isolation of predation-deficient mutants using random-transposon-insertion mutagenesis. As more mutants are isolated and their gene products analyzed, more light will be shed on how this predator carries out its exclusive life processes and perhaps how these products, or the organism itself, can be used for therapeutic, agricultural, and/or other purposes.

scholarly journals First Complete Genome Sequence of Brucella abortus 2308 isolated from an abortion storm in a dairy farm in India

2021 ◽  
Author(s):  
Amit Kumar ◽  
Malyaj R Prajapati ◽  
Surendra Upadhyay ◽  
Anamika Bhordia ◽  
Vinod Kumar Singh ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Sequences ◽  
Brucella Abortus ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Messenger Rna ◽  
Gc Content ◽  
Dairy Farm ◽  
Rrna Genes ◽  
Sequence Length

Abstract The present report communicates the first complete genome sequence of Brucella abortus 2308 strain isolated from a an abortion storm in a dairy farm located at Kanpur, Uttar Pradesh in India. It caused the last trimester abortions of 32 animals out of 100 cows in a dairy over a period of 60 days. The bacteria were isolated in pure culture from the placenta of aborted cows. The genome sequence length of isolated bacteria is 3,285,606 bp with a 57.25 % GC content, an N50 value of 296,426, L50 value of 4 containing 3,119 coding DNA sequences (CDSs), 49 tRNAs, 1 transfer messenger RNA (mRNA), and 3 rRNA genes. It is the first report of Brucella abortus 2308 isolation and complete genome sequence from Indian subcontinent.

scholarly journals Complete Genome Sequence of SMBL-WEM22, a Halotolerant Strain of Kosakonia cowanii Isolated from Hong Kong Seawater

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
W. E. Moore ◽  
G. K. K. Lai ◽  
S. D. J. Griffin ◽  
F. C. C. Leung
Keyword(s):  
Hong Kong ◽  
Dna Sequences ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Hybrid Assembly ◽  
Gram Negative ◽  
Content Type ◽  
Facultative Anaerobic ◽  
Long Read

Kosakonia cowanii is a Gram-negative, motile, facultative anaerobic enterobacterium that is found in soil, water, and sewage. K. cowanii SMBL-WEM22 is a halotolerant strain that was isolated from seawater in Hong Kong. The complete genome of SMBL-WEM22 (5,037,617 bp, with a GC content of 55.02%) was determined by hybrid assembly of short- and long-read DNA sequences.

scholarly journals Complete Genome Sequence of Lymphocystis Disease Virus Isolated from China

2004 ◽  
Vol 78 (13) ◽  
pp. 6982-6994 ◽  
Author(s):  
Qi-Ya Zhang ◽  
Feng Xiao ◽  
Jian Xie ◽  
Zheng-Qiu Li ◽  
Jian-Fang Gui
Keyword(s):  
Amino Acid ◽  
Disease Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Computer Assisted ◽  
Gene Products ◽  
Lymphocystis Disease Virus ◽  
C Genome ◽  
Lymphocystis Disease

ABSTRACT Lymphocystis diseases in fish throughout the world have been extensively described. Here we report the complete genome sequence of lymphocystis disease virus isolated in China (LCDV-C), an LCDV isolated from cultured flounder (Paralichthys olivaceus) with lymphocystis disease in China. The LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C. Computer-assisted analysis revealed 240 potential open reading frames (ORFs) and 176 nonoverlapping putative viral genes, which encode polypeptides ranging from 40 to 1,193 amino acids. The percent coding density is 67%, and the average length of each ORF is 702 bp. A search of the GenBank database using the 176 individual putative genes revealed 103 homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there are 8 genes that contain conserved domains of cellular genes and 65 novel genes that do not show any significant homology with the sequences in public databases. Although a certain extent of similarity between putative gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed, no colinearity was detected when their ORF arrangements and coding strategies were compared to each other, suggesting that a high degree of genetic rearrangements between them has occurred. And a large number of tandem and overlapping repeated sequences were observed in the LCDV-C genome. The deduced amino acid sequence of the major capsid protein (MCP) presents the highest identity to those of LCDV-1 and other iridoviruses among the LCDV-C gene products. Furthermore, a phylogenetic tree was constructed based on the multiple alignments of nine MCP amino acid sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but their amino acid identity is much less than that in other clusters. The unexpected levels of divergence between their genomes in size, gene organization, and gene product identity suggest that LCDV-C and LCDV-1 shouldn't belong to a same species and that LCDV-C should be considered a species different from LCDV-1.

scholarly journals Complete Genome Sequence of a Wild-Type Isolate of Caulobacter vibrioides Strain CB1

2018 ◽  
Vol 7 (12) ◽  
Author(s):  
Derrick C. Scott ◽  
Kiesha Wilson ◽  
Keshawn Ross ◽  
Damyen Ingram ◽  
Tajah Lewter ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Sequences ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genome Rearrangement ◽  
Gc Content ◽  
Wild Type ◽  
Content Type ◽  
Type Isolate

The complete genome sequence of Caulobacter vibrioides strain CB1 consists of a chromosome of 4,137,285 bp, with a GC content of 67.2% and 3,990 coding DNA sequences. This strain contains the typical genome rearrangement that is characteristic of the Caulobacter strains that are currently sequenced.

scholarly journals Complete Genome Sequence of Tessaracoccus sp. Strain T2.5-30 Isolated from 139.5 Meters Deep on the Subsurface of the Iberian Pyritic Belt

2017 ◽  
Vol 5 (17) ◽  
Author(s):  
Tânia Leandro ◽  
Milton S. da Costa ◽  
Jose L. Sanz ◽  
Ricardo Amils
Keyword(s):  
Genome Sequence ◽  
Dna Sequences ◽  
Complete Genome Sequence ◽  
Complete Genome

ABSTRACT Here, we report the complete genome sequence of Tessaracoccus sp. strain T2.5-30, which consists of a chromosome with 3.2 Mbp, 70.4% G+C content, and 3,005 coding DNA sequences. The strain was isolated from a rock core retrieved at a depth of 139.5 m in the subsurface of the Iberian Pyritic Belt (Spain).

scholarly journals Multiple Genes Encoding Pheromones and a Pheromone Receptor Define the Bβ1 Mating-Type Specificity in Schizophyllum commune

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 541-551 ◽  
Author(s):  
Lisa J Vaillancourt ◽  
Marjatta Raudaskoski ◽  
Charles A Specht ◽  
Carlene A Raper
Keyword(s):  
Dna Sequences ◽  
Transmembrane Domain ◽  
Receptor Gene ◽  
Schizophyllum Commune ◽  
The Other ◽  
Mating Types ◽  
Gene Products ◽  
Pheromone Receptor ◽  
Genes Encoding ◽  
Identical Series

The genes defining multiple B mating types in the wood-rotting mushroom Schizophyllum commune are predicted to encode multiple pheromones and pheromone receptors. These genes are clustered in each of two recombinable and independently functioning loci, Bα and Bβ. A difference in specificity at either locus between a mated pair of individuals initiates an identical series of events in sexual morphogenesis. The Bα1 locus was recently found to contain genes predicted to encode three lipopeptide pheromones and a pheromone receptor with a seven-transmembrane domain. These gene products interact in heterospecific pairs, the pheromone of one Bα specificity with the receptor of any one of the other eight Bα specificities, and are likely to activate a signaling cascade similar to that known for mating in Saccharomyces cerevisiae. We report here that the Bβ1 locus also contains at least three pheromone genes and one pheromone receptor gene, which function similarly to the genes in the Bα1 locus, but only within the series of Bβ specificities. A comparison of the DNA sequences of the Bα1 and Bβ1 loci suggests that each arose from a common ancestral sequence, allowing us to speculate about the evolution of this unique series of regulatory genes.

scholarly journals Complete Genome Sequence of the Pokeweed Mosaic Virus (PkMV)-New Jersey Isolate and Its Comparison to PkMV-MD and PkMV-PA

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Rong Di
Keyword(s):  
New Jersey ◽  
Mosaic Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Sequence Comparison ◽  
Complete Genome ◽  
Sanger Sequencing ◽  
The Other ◽  
Phytolacca Americana ◽  
Sequencing Method

Pokeweed mosaic virus (PkMV) causes systemically mosaic symptoms on pokeweed ( Phytolacca americana L.) plants. The genome of the PkMV-NJ (New Jersey) isolate was cloned by PCR and sequenced by the Sanger sequencing method. The sequence comparison indicates that PkMV-NJ is more divergent from the other two sequenced isolates, PkMV-MD and PkMV-PA.

scholarly journals Genome Characterization of Lipid-Containing Marine Bacteriophage PM2 by Transposon Insertion Mutagenesis

2006 ◽  
Vol 80 (18) ◽  
pp. 9270-9278 ◽  
Author(s):  
Mart Krupovič ◽  
Heikki Vilen ◽  
Jaana K. H. Bamford ◽  
Hanna M. Kivelä ◽  
Juha-Matti Aalto ◽  
...  
Keyword(s):  
Lipid Vesicle ◽  
Insertion Mutagenesis ◽  
Transposon Insertion ◽  
New Genes ◽  
Double Stranded Dna ◽  
Marine Phage ◽  
Protein Rich ◽  
Insertion Mutants

ABSTRACT Bacteriophage PM2 presently is the only member of the Corticoviridae family. The virion consists of a protein-rich lipid vesicle, which is surrounded by an icosahedral protein capsid. The lipid vesicle encloses a supercoiled circular double-stranded DNA genome of 10,079 bp. PM2 belongs to the marine phage community and is known to infect two gram-negative Pseudoalteromonas species. In this study, we present a characterization of the PM2 genome made using the in vitro transposon insertion mutagenesis approach. Analysis of 101 insertion mutants yielded information on the essential and dispensable regions of the PM2 genome and led to the identification of several new genes. A number of lysis-deficient mutants as well as mutants displaying delayed- and/or incomplete-lysis phenotypes were identified. This enabled us to identify novel lysis-associated genes with no resemblance to those previously described from other bacteriophage systems. Nonessential genome regions are discussed in the context of PM2 genome evolution.

scholarly journals Analysis of the Complete Genome Sequence ofBacillus atrophaeusGQJK17 Reveals Its Biocontrol Characteristics as a Plant Growth-Promoting Rhizobacterium

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Jinjin Ma ◽  
Chengqiang Wang ◽  
Haide Wang ◽  
Kai Liu ◽  
Tongrui Zhang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Lycium Barbarum ◽  
Circular Chromosome ◽  
A Genome ◽  
Plant Growth Promoting ◽  
Growth Promoting

Bacillus atrophaeusGQJK17 was isolated from the rhizosphere ofLycium barbarumL. in China, which was shown to be a plant growth-promoting rhizobacterium as a new biological agent against pathogenic fungi and gram-positive bacteria. We present its biological characteristics and complete genome sequence, which contains a 4,325,818 bp circular chromosome with 4,181 coding DNA sequences and a G+C content of 43.3%. A genome analysis revealed a total of 8 candidate gene clusters for producing antimicrobial secondary metabolites, including surfactin, bacillaene, fengycin, and bacillibactin. Some other antimicrobial and plant growth-promoting genes were also discovered. Our results provide insights into the genetic and biological basis ofB. atrophaeusstrains as a biocontrol agent for application in agriculture.

scholarly journals Complete Genome Sequence of Raoultella electrica 1GB (DSM 102253T), Isolated from Anodic Biofilms of a Glucose-Fed Microbial Fuel Cell

2019 ◽  
Vol 8 (43) ◽  
Author(s):  
Simone Thiel ◽  
Boyke Bunk ◽  
Cathrin Spröer ◽  
Jörg Overmann ◽  
Dieter Jahn ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Fuel Cell ◽  
Microbial Fuel Cell ◽  
Dna Sequences ◽  
Plasmid Dna ◽  
Complete Genome Sequence ◽  
Microbial Fuel Cells ◽  
Complete Genome ◽  
Type Strain ◽  
Content Type

The type strain Raoultella electrica 1GB (DSM 102253T) was isolated from anodic biofilms of glucose-fed microbial fuel cells. The fully assembled, closed, circular 5.27-Mb genome and corresponding 0.52-Mb plasmid DNA sequences were elucidated. Potential electron transfer and pathogenicity mechanisms were deduced.

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