Identification of plasmids from Brazilian Chromobacterium violaceum strains

Chromobacterium violaceum is an opportunistic pathogen found in tropical and subtropical regions worldwide. Chromobacterium violaceum infections are difficult to treat, and many strains are resistant to antibiotics. Recently, a novel plasmid (pChV1) was discovered in the type strain ATCC 12472, suggesting that other C. violaceum strains may harbor extra-chromosomal DNA. The aim of the present study was to detect and compare new plasmids in Brazilian strains of C. violaceum using next-generation sequencing techniques. We obtained draft genomes of six plasmids from strains isolated from the Amazon region and aligned them with pChV1. At least three plasmids, CVAC05, CVACO2, and CVT8, were similar to pChV1. Phylogenetic analysis suggested that these new extra-chromosomal DNA sequences have a common origin with pChV1 but have diverged. Many of the ORFs detected were related to plasmid segregation/maintenance, viral structural proteins, and proteins with unknown functions. These findings may enable better genetic manipulation of C. violaceum, which will enhance our ability to exploit this valuable microorganism in industrial and clinical applications.

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Mab_3083c Is a Homologue of RNase J and Plays a Role in Colony Morphotype, Aggregation, and Sliding Motility of Mycobacterium abscessus

Microorganisms ◽

10.3390/microorganisms9040676 ◽

2021 ◽

Vol 9 (4) ◽

pp. 676

Author(s):

Ting-Yu Liu ◽

Sheng-Hui Tsai ◽

Jenn-Wei Chen ◽

Yu-Ching Wang ◽

Shiau-Ting Hu ◽

...

Keyword(s):

Type Strain ◽

Wild Type Strain ◽

Opportunistic Pathogen ◽

Mycobacterium Abscessus ◽

Colony Morphology ◽

Clinical Strain ◽

Immunocompromised Patients ◽

Clinical Infection ◽

Wild Type ◽

Sliding Motility

Mycobacterium abscessus is an opportunistic pathogen causing human diseases, especially in immunocompromised patients. M. abscessus strains with a rough morphotype are more virulent than those with a smooth morphotype. Morphotype switch may occur during a clinical infection. To investigate the genes involved in colony morphotype switching, we performed transposon mutagenesis in a rough clinical strain of M. abscessus. A morphotype switching mutant (smooth) named mab_3083c::Tn was obtained. This mutant was found to have a lower aggregative ability and a higher sliding motility than the wild type strain. However, its glycopeptidolipid (GPL) content remained the same as those of the wild type. Complementation of the mutant with a functional mab_3083c gene reverted its morphotype back to rough, indicating that mab_3083c is associated with colony morphology of M. abscessus. Bioinformatic analyses showed that mab_3083c has a 75.4% identity in amino acid sequence with the well-characterized ribonuclease J (RNase J) of M. smegmatis (RNase JMsmeg). Complementation of the mutant with the RNase J gene of M. smegmatis also switched its colony morphology from smooth back to rough. These results suggest that Mab_3083c is a homologue of RNase J and involved in regulating M. abscessus colony morphotype switching.

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Effect of tannic and gallic acids alone or in combination with carbenicillin or tetracycline on Chromobacterium violaceum CV026 growth, motility, and biofilm formation

Canadian Journal of Microbiology ◽

10.1139/cjm-2015-0101 ◽

2015 ◽

Vol 61 (7) ◽

pp. 487-494 ◽

Cited By ~ 4

Author(s):

Devendra H. Dusane ◽

Che O’May ◽

Nathalie Tufenkji

Keyword(s):

Antibacterial Activity ◽

Gallic Acid ◽

Tannic Acid ◽

Bacterial Growth ◽

Biofilm Formation ◽

Opportunistic Pathogen ◽

Chromobacterium Violaceum ◽

Minimum Inhibitory Concentrations

Chromobacterium violaceum is an opportunistic pathogen that causes infections that are difficult to treat. The goal of this research was to evaluate the effect of selected tannins (tannic acid (TA) and gallic acid (GA)) on bacterial growth, motility, antibiotic (carbenicillin, tetracycline) susceptibility, and biofilm formation. Both tannins, particularly TA, impaired bacterial growth levels and swimming motilities at sub-minimum inhibitory concentrations (sub-MICs). In combination with tannins, antibiotics showed increased MICs, suggesting that tannins interfered with antibacterial activity. Sub-MICs of tetracycline or TA alone enhanced biofilm formation of C. violaceum; however, in combination, these compounds inhibited biofilm formation. In contrast, carbenicillin at sub-MICs was effective in inhibiting C. violaceum biofilm formation; however, in combination with lower concentrations of TA or GA, biofilms were enhanced. These results provide insights into the effects of tannins on C. violaceum growth and their varying interaction with antibiotics used to target C. violaceum infections.

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Clinical Translation of Anti-aging Associated Genetics: Current Progress and Challenges

Current Aging Science ◽

10.2174/1874609814666210419104547 ◽

2021 ◽

Vol 14 ◽

Author(s):

Yi Wang

Keyword(s):

Genetic Manipulation ◽

Large Body ◽

Cost Effective ◽

Clinical Applications ◽

Biological Aging ◽

Aging Research ◽

Gene Therapies ◽

Molecular Approaches ◽

Gerontological Research ◽

Tremendous Challenge

Background: Currently, the focus of anti-aging research has been changed from geriatrics to biogerontology. This has taken anti-aging strategies from cost-effective but palliative therapeutics to active, molecular approaches. Outline: Over the years, a large body of basic gerontological research has indicated that the process of biological aging is closely associated with genetic factors. This leads to the development of various gene therapies such as RNA interference technology and results in a subsequent need of translating laboratory achievements into clinical applications. The translation has been a tremendous challenge at this stage with respect to practicality, safety and effectiveness of the genetic manipulation techniques. Objective: This review summarizes the current development of anti-aging strategies and the progress in the translation of laboratory achievements into clinical applications, highlights challenges encountered, and provides a prospective outlook for future anti-aging research.

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Recombination hotspots as a point process

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2005.1690 ◽

2005 ◽

Vol 360 (1460) ◽

pp. 1597-1603 ◽

Cited By ~ 4

Author(s):

Maria De Iorio ◽

Eric de Silva ◽

Michael P.H Stumpf

Keyword(s):

Point Process ◽

Dna Sequences ◽

Recombination Rate ◽

Population Genetic ◽

Process Model ◽

Chromosomal Dna ◽

New Approach ◽

Recombination Hotspots ◽

Minimum Number ◽

Fully Bayesian

The variation of the recombination rate along chromosomal DNA is one of the important determinants of the patterns of linkage disequilibrium. A number of inferential methods have been developed which estimate the recombination rate and its variation from population genetic data. The majority of these methods are based on modelling the genealogical process underlying a sample of DNA sequences and thus explicitly include a model of the demographic process. Here we propose a different inferential procedure based on a previously introduced framework where recombination is modelled as a point process along a DNA sequence. The approach infers regions containing putative hotspots based on the inferred minimum number of recombination events; it thus depends only indirectly on the underlying population demography. A Poisson point process model with local rates is then used to infer patterns of recombination rate estimation in a fully Bayesian framework. We illustrate this new approach by applying it to several population genetic datasets, including a region with an experimentally confirmed recombination hotspot.

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Triple-Helical DNA in Drosophila Heterochromatin

Cells ◽

10.3390/cells7120227 ◽

2018 ◽

Vol 7 (12) ◽

pp. 227 ◽

Cited By ~ 1

Author(s):

Eduardo Gorab

Keyword(s):

Nucleic Acids ◽

Dna Sequences ◽

Detection Methods ◽

Triplex Dna ◽

Thiazole Orange ◽

Chromosomal Dna ◽

Mitotic Chromosomes ◽

Satellite Repeats

Polynucleotide chains obeying Watson-Crick pairing are apt to form non-canonical complexes such as triple-helical nucleic acids. From early characterization in vitro, their occurrence in vivo has been strengthened by increasing evidence, although most remain circumstantial particularly for triplex DNA. Here, different approaches were employed to specify triple-stranded DNA sequences in the Drosophila melanogaster chromosomes. Antibodies to triplex nucleic acids, previously characterized, bind to centromeric regions of mitotic chromosomes and also to the polytene section 59E of mutant strains carrying the brown dominant allele, indicating that AAGAG tandem satellite repeats are triplex-forming sequences. The satellite probe hybridized to AAGAG-containing regions omitting chromosomal DNA denaturation, as expected, for the intra-molecular triplex DNA formation model in which single-stranded DNA coexists with triplexes. In addition, Thiazole Orange, previously described as capable of reproducing results obtained by antibodies to triple-helical DNA, binds to AAGAG repeats in situ thus validating both detection methods. Unusual phenotype and nuclear structure exhibited by Drosophila correlate with the non-canonical conformation of tandem satellite arrays. From the approaches that lead to the identification of triple-helical DNA in chromosomes, facilities particularly provided by Thiazole Orange use may broaden the investigation on the occurrence of triplex DNA in eukaryotic genomes.

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SirR, a Novel Iron-Dependent Repressor inStaphylococcus epidermidis

Infection and Immunity ◽

10.1128/iai.66.9.4123-4129.1998 ◽

1998 ◽

Vol 66 (9) ◽

pp. 4123-4129 ◽

Cited By ~ 63

Author(s):

Philip J. Hill ◽

Alan Cockayne ◽

Patrick Landers ◽

Julie A. Morrissey ◽

Catriona M. Sims ◽

...

Keyword(s):

Binding Site ◽

Dna Sequences ◽

Blot Analysis ◽

Target Genes ◽

Consensus Sequence ◽

Dependent Manner ◽

Chromosomal Dna ◽

Iron Starvation ◽

Mobility Shift ◽

Western Blots

ABSTRACT In Staphylococcus epidermidis and Staphylococcus aureus, a number of cell wall- and cytoplasmic membrane-associated lipoproteins are induced in response to iron starvation. To gain insights into the molecular basis of iron-dependent gene regulation in the staphylococci, we sequenced the DNA upstream of the 3-kb S. epidermidis sitABC operon, which Northern blot analysis indicates is transcriptionally regulated by the growth medium iron content. We identified two DNA sequences which are homologous to elements of the Corynebacterium diphtheriae DtxR regulon, which controls, in response to iron stress, for example, production of diphtheria toxin, siderophore, and a heme oxygenase. Upstream of thesitABC operon and divergently transcribed lies a 645-bp open reading frame (ORF), which codes for a polypeptide of approximately 25 kDa with homology to the DtxR family of metal-dependent repressor proteins. This ORF has been designated SirR (staphylococcal iron regulator repressor). Within thesitABC promoter/operator region, we also located a region of dyad symmetry overlapping the transcriptional start ofsitABC which shows high homology to the DtxR operator consensus sequence, suggesting that this region, termed the Sir box, is the SirR-binding site. The SirR protein was overexpressed, purified, and used in DNA mobility shift assays; SirR retarded the migration of a synthetic oligonucleotide based on the Sir box in a metal (Fe2+ or Mn2+)-dependent manner, providing confirmatory evidence that this motif is the SirR-binding site. Furthermore, Southern blot analysis of staphylococcal chromosomal DNA with the synthetic Sir box as a probe confirmed that there are at least five Sir boxes in the S. epidermidis genome and at least three in the genome of S. aureus, suggesting that SirR controls the expression of multiple target genes. Using a monospecific polyclonal antibody raised against SirR to probe Western blots of whole-cell lysates of S. aureus, S. carnosus,S. epidermidis, S. hominis, S. cohnii, S. lugdunensis, and S. haemolyticus, we identified an approximately 25-kDa cross-reactive protein in each of the staphylococcal species examined. Taken together, these data suggest that SirR functions as a divalent metal cation-dependent transcriptional repressor which is widespread among the staphylococci.

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Fuzzysplit: demultiplexing and trimming sequenced DNA with a declarative language

PeerJ ◽

10.7717/peerj.7170 ◽

2019 ◽

Vol 7 ◽

pp. e7170

Author(s):

Daniel Liu

Keyword(s):

Next Generation Sequencing ◽

Dna Sequences ◽

Use Cases ◽

Next Generation ◽

Declarative Language ◽

Matching Accuracy ◽

Sequencing Technologies ◽

Preliminary Comparison ◽

Generation Sequencing

Next-generation sequencing technologies create large, multiplexed DNA sequences that require preprocessing before any further analysis. Part of this preprocessing includes demultiplexing and trimming sequences. Although there are many existing tools that can handle these preprocessing steps, they cannot be easily extended to new sequence schematics when new pipelines are developed. We present Fuzzysplit, a tool that relies on a simple declarative language to describe the schematics of sequences, which makes it incredibly adaptable to different use cases. In this paper, we explain the matching algorithms behind Fuzzysplit and we provide a preliminary comparison of its performance with other well-established tools. Overall, we find that its matching accuracy is comparable to previous tools.

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A systematic comparison of eight new plastome sequences from Ipomoea L

PeerJ ◽

10.7717/peerj.6563 ◽

2019 ◽

Vol 7 ◽

pp. e6563

Author(s):

Jianying Sun ◽

Xiaofeng Dong ◽

Qinghe Cao ◽

Tao Xu ◽

Mingku Zhu ◽

...

Keyword(s):

Comparative Analysis ◽

Next Generation Sequencing ◽

Chloroplast Genome ◽

Dna Sequences ◽

Repetitive Sequences ◽

Single Copy ◽

Next Generation ◽

Variable Regions ◽

Chloroplast Genomes ◽

Generation Sequencing

Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.

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