scholarly journals A novel anti-dipteran Bacillus thuringiensis strain: Unusual Cry toxin genes in a highly dynamic plasmid environment

2020 ◽  
Author(s):  
Nancy Fayad ◽  
Zakaria Kambris ◽  
Laure El Chamy ◽  
Jacques Mahillon ◽  
Mireille Kallassy Awad
Keyword(s):  
Bacillus Thuringiensis ◽  
Mobile Genetic Elements ◽  
Global Market ◽  
Mobile Dna ◽  
Parasporal Crystal ◽  
Genetic Elements ◽  
Toxin Genes ◽  
Cry Toxin ◽  
Large Plasmids ◽  
Thuringiensis Strain

Bacillus thuringiensis emerged as a major bioinsecticide on the global market. It offers a valuable alternative to chemical products classically utilized to control pest insects. Despite the efficiency of several strains and products available on the market, the scientific community is always on the lookout for novel toxins that can replace or supplement the existing products. In this study, H3, a novel B. thuringiensis strain showing mosquitocidal activity, was isolated from Lebanese soil and characterized at an in vivo, genomic and proteomic levels. H3 parasporal crystal is toxic on its own but displays an unusual killing profile with a higher LC50 than the reference B. thuringiensis serovar israelensis crystal proteins. In addition, H3 has a different toxicity order: it is more toxic to Aedes albopictus and Anopheles gambiae than to Culex pipiens. Whole genome sequencing and crystal analysis revealed that H3 can produce eleven novel Cry proteins, eight of which are assembled in genes with an orf1-gap-orf2 organization, where orf2 is a potential Cry4-type crystallization domain. Moreover, pH3-180, the toxin-carrying plasmid, holds a wide repertoire of mobile genetic elements that amount to ca. 22% of its size., including novel insertion sequences and class II transposable elements Two other large plasmids present in H3 carry genetic determinants for the production of many interesting molecules - such as chitinase, cellulase and bacitracin - that may add up to H3 bioactive properties. This study therefore reports a novel mosquitocidal Bacillus thuringiensis strain with unusual Cry toxin genes in a rich mobile DNA environment. IMPORTANCE Bacillus thuringiensis, a soil entomopathogenic bacteria, is at the base of many sustainable eco-friendly bio-insecticides. Hence stems the need to continually characterize insecticidal toxins. H3 is an anti-dipteran B. thuringiensis strain, isolated from Lebanese soil, whose parasporal crystal contains eleven novel Cry toxins and no Cyt toxins. In addition to its individual activity, H3 showed potential as a co-formulant with classic commercialized B. thuringiensis products, to delay the emergence of resistance and to shorten the time required for killing. On a genomic level, H3 holds three large plasmids, one of which carries the toxin-coding genes, with four occurrences of the distinct orf1-gap-orf2 organization. Moreover, this plasmid is extremely rich in mobile genetic elements, unlike its two co-residents. This highlights the important underlying evolutionary traits between toxin-carrying plasmids and the adaptation of a B. thuringiensis strain to its environment and insect host spectrum.

scholarly journals Mobile Genetic Elements Related to the Diffusion of Plasmid-Mediated AmpC β-Lactamases or Carbapenemases from Enterobacteriaceae: Findings from a Multicenter Study in Spain

2015 ◽  
Vol 59 (9) ◽  
pp. 5260-5266 ◽  
Author(s):  
L. Zamorano ◽  
E. Miró ◽  
C. Juan ◽  
L. Gómez ◽  
G. Bou ◽  
...  
Keyword(s):  
Southern Hybridization ◽  
Mobile Genetic Elements ◽  
Pulsed Field Gel Electrophoresis ◽  
Content Type ◽  
Genetic Elements ◽  
Chromosomal Origin ◽  
Class 1 ◽  
Rapid Dissemination ◽  
Large Plasmids ◽  
Genetic Context

ABSTRACTWe examined the genetic context of 74 acquiredampCgenes and 17 carbapenemase genes from 85 of 640Enterobacteriaceaeisolates collected in 2009. Using S1 pulsed-field gel electrophoresis and Southern hybridization, 37 of 74blaAmpCgenes were located on large plasmids of different sizes belonging to six incompatibility groups. We used sequencing and PCR mapping to investigate the regions flanking the acquiredampCgenes. TheblaCMY-2-like genes were associated with ISEcp1; the surroundingblaDHAgenes were similar toKlebsiella pneumoniaeplasmid pTN60013 associated with IS26and thepspandsapoperons; and theblaACC-1genes were associated with IS26elements inserted into ISEcp1. All of the carbapenemase genes (blaVIM-1,blaIMP-22, andblaIMP-28) were located in class 1 integrons. Therefore, although plasmids are the main cause of the rapid dissemination ofampCgenes amongEnterobacteriaceae, we need to be aware that other mobile genetic elements, such as insertion sequences, transposons, or integrons, can be involved in the mobilization of these genes of chromosomal origin. Additionally, three new integrons (In846 to In848) are described in this study.

Dual Insecticidal Activity of Spodoptera-Toxic Bacillus thuringiensis Strain Transformed with Lepidopteran-Specific Cry Toxin

2007 ◽  
Vol 10 (2) ◽  
pp. 137-143
Author(s):  
Joong Nam Kang ◽  
Jong Yul Roh ◽  
Sang Chul Shin ◽  
Sang-Hyun Koh ◽  
Yeong Jin Chung ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Insecticidal Activity ◽  
Cry Toxin ◽  
Thuringiensis Strain

scholarly journals A Novel and Direct Metamobilome Approach improves the Detection of Larger-sized Circular Elements across Kingdoms

2019 ◽  
Author(s):  
Katrine Skov Alanin ◽  
Tue Sparholt Jørgensen ◽  
Patrick Browne ◽  
Bent Petersen ◽  
Leise Riber ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Bacterial Species ◽  
Human Health Risk ◽  
Prokaryotic Genome ◽  
Mobile Genetic Elements ◽  
Wastewater Sample ◽  
Mobile Dna ◽  
Complex Samples ◽  
Genetic Elements ◽  
Dna Elements

AbstractMobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate immense genetic diversity. MGEs include DNA elements such as plasmids, transposons and Insertion Sequences (IS-elements), as well as bacteriophages (phages), and they serve as a vast communal gene pool. These mobile DNA elements represent a human health risk as they can add new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting circular MGEs, referred to as mobilomes, allows the expansion of our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomes from bacterial communities are not studied to the same extent as metagenomics, partly because of methodological biases arising from multiple displacement amplification (MDA), often used in previous metamobilome publications. In this study, we show that MDA is detrimental to the detection of larger-sized plasmids if small plasmids are present by comparing the abundances of reads mapping to plasmids in a wastewater sample spiked with a mock community of selected plasmids with and without MDA. Furthermore, we show that it is possible to produce samples consisting almost exclusively of circular MGEs and obtain a catalog of larger, complete, circular MGEs from complex samples without the use of MDA.ImportanceMobile genetic elements (MGEs) can transport genetic information between genomes in different bacterial species, adding new traits, potentially generating dangerous multidrug-resistant pathogens. In fact, plasmids and circular MGEs can encode bacterial genetic specializations such as virulence, resistance to metals, antimicrobial compounds, and bacteriophages, as well as the degradation of xenobiotics. For this reason, circular MGEs are crucial to investigate, but they are often missed in metagenomics and ecological studies. In this study, we present, for the first time, an improved method, which reduces the bias towards small MGEs and we demonstrate that this method can unveil larger, complete circular MGEs from complex samples without the use of multiple displacement amplification. This method may result in the detection of larger-sized plasmids that have hitherto remained unnoticed and therefore has the potential to reveal novel accessory genes, acting as possible targets in the development of preventive strategies directed at pathogens.

scholarly journals Mining New Crystal Protein Genes from Bacillus thuringiensis on the Basis of Mixed Plasmid-Enriched Genome Sequencing and a Computational Pipeline

2012 ◽  
Vol 78 (14) ◽  
pp. 4795-4801 ◽  
Author(s):  
Weixing Ye ◽  
Lei Zhu ◽  
Yingying Liu ◽  
Neil Crickmore ◽  
Donghai Peng ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Genomic Sequence ◽  
Crystal Protein ◽  
Support Vector ◽  
Computational Pipeline ◽  
Content Type ◽  
Toxin Genes ◽  
Protein Toxin ◽  
Cry Toxin ◽  
Crystal Protein Genes

ABSTRACTWe have designed a high-throughput system for the identification of novel crystal protein genes (cry) fromBacillus thuringiensisstrains. The system was developed with two goals: (i) to acquire the mixed plasmid-enriched genomic sequence ofB. thuringiensisusing next-generation sequencing biotechnology, and (ii) to identifycrygenes with a computational pipeline (using BtToxin_scanner). In our pipeline method, we employed three different kinds of well-developed prediction methods, BLAST, hidden Markov model (HMM), and support vector machine (SVM), to predict the presence of Cry toxin genes. The pipeline proved to be fast (average speed, 1.02 Mb/min for proteins and open reading frames [ORFs] and 1.80 Mb/min for nucleotide sequences), sensitive (it detected 40% more protein toxin genes than a keyword extraction method using genomic sequences downloaded from GenBank), and highly specific. Twenty-one strains from our laboratory's collection were selected based on their plasmid pattern and/or crystal morphology. The plasmid-enriched genomic DNA was extracted from these strains and mixed for Illumina sequencing. The sequencing data werede novoassembled, and a total of 113 candidatecrysequences were identified using the computational pipeline. Twenty-seven candidate sequences were selected on the basis of their low level of sequence identity to knowncrygenes, and eight full-length genes were obtained with PCR. Finally, three newcry-type genes (primary ranks) and fivecryholotypes, which were designatedcry8Ac1,cry7Ha1,cry21Ca1,cry32Fa1, andcry21Da1by theB. thuringiensisToxin Nomenclature Committee, were identified. The system described here is both efficient and cost-effective and can greatly accelerate the discovery of novelcrygenes.

scholarly journals Comparative prevalence of superantigenic toxin genes in meticillin-resistant and meticillin-susceptible Staphylococcus aureus isolates

2008 ◽  
Vol 57 (9) ◽  
pp. 1106-1112 ◽  
Author(s):  
Dong-Liang Hu ◽  
Katsuhiko Omoe ◽  
Fumio Inoue ◽  
Takesi Kasai ◽  
Minoru Yasujima ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Mobile Genetic Elements ◽  
Toxin Gene ◽  
Type I ◽  
Gene Encoding ◽  
Genetic Elements ◽  
Toxin Genes ◽  
Time Period ◽  
Enterotoxin Genes ◽  
Toxic Shock Syndrome Toxin

A total of 118 meticillin-resistant Staphylococcus aureus (MRSA) and 140 meticillin-susceptible S. aureus (MSSA) isolates from different patients in the same time period were comprehensively searched using a multiplex PCR for the classical and recently described superantigenic toxin gene family comprising the staphylococcal enterotoxin genes sea to ser and the toxic shock syndrome toxin 1 gene, tst-1. Both MRSA and MSSA isolates carried a number of superantigenic toxin genes, but the MRSA isolates harboured more superantigenic toxin genes than the MSSA isolates. The most frequent genotype of the MRSA isolates was sec, sell and tst-1 together with the gene combination seg, sei, selm, seln and selo, which was found strictly in combination in 69.5 % of the isolates tested. In contrast, possession of the sec, sell and tst-1 genes in MSSA isolates was significantly less than in MRSA (2.1 vs 77.1 %, respectively), although they also often contained the combination genes (25.0 %). This notable higher prevalence in MRSA isolates indicated that possession of the sec, sell and tst-1 genes in particular appeared to be a habitual feature of MRSA. Moreover, these were mainly due to the fixed combinations of the mobile genetic elements type I νSa4 encoding sec, sell and tst-1, and type I νSaβ encoding seg, sei, selm, seln and selo. Analysis of the relationship between toxin genotypes and the toxin gene-encoding profiles of mobile genetic elements has a possible role in determining superantigenic toxin genotypes in S. aureus.

scholarly journals Bacillus cytotoxicus Genomics: Chromosomal Diversity and Plasmidome Versatility

2021 ◽  
Vol 12 ◽  
Author(s):  
Nancy Fayad ◽  
Klèma Marcel Koné ◽  
Annika Gillis ◽  
Jacques Mahillon
Keyword(s):  
Bacillus Cereus ◽  
Potential Role ◽  
Random Amplified Polymorphic Dna ◽  
Mobile Genetic Elements ◽  
Genomic Diversity ◽  
Genome Plasticity ◽  
Genetic Elements ◽  
Gene Coding ◽  
Group Members ◽  
Large Plasmids

Bacillus cytotoxicus is the thermotolerant representative of the Bacillus cereus group. This group, also known as B. cereus sensu lato, comprises both beneficial and pathogenic members and includes psychrotolerant and thermotolerant species. Bacillus cytotoxicus was originally recovered from a fatal outbreak in France in 1998. This species forms a remote cluster from the B. cereus group members and reliably contains the cytk-1 gene, coding for a cytotoxic variant of cytotoxin K. Although this species was originally thought to be homogenous, intra-species diversity has been recently described with four clades, six random amplified polymorphic DNA (RAPD) patterns, and 11 plasmids profiles. This study aimed to get new insights into the genomic diversity of B. cytotoxicus and to decipher the underlying chromosomal and plasmidial variations among six representative isolates through whole genome sequencing (WGS). Among the six sequenced strains, four fitted the previously described genomic clades A and D, while the remaining two constituted new distinct branches. As for the plasmid content of these strains, three large plasmids were putatively conjugative and three small ones potentially mobilizable, harboring coding genes for putative leaderless bacteriocins. Mobile genetic elements, such as prophages, Insertion Sequences (IS), and Bacillus cereus repeats (bcr) greatly contributed to the B. cytotoxicus diversity. As for IS elements and bcr, IS3 and bcr1 were the most abundant elements and, along with the group II intron B.c.I8, were found in all analyzed B. cytotoxicus strains. When compared to other B. cytotoxicus strains, the type-strain NVH 391-98 displayed a relatively low number of IS. Our results shed new light on the contribution of mobile genetic elements to the genome plasticity of B. cytotoxicus and their potential role in horizontal gene transfer.

scholarly journals SpoOA represses transcription of the cry toxin genes in Bacillus thuringiensis

Microbiology ◽  
1997 ◽  
Vol 143 (8) ◽  
pp. 2743-2751 ◽  
Author(s):  
S. Poncet ◽  
E. Dervyn ◽  
A. Klier ◽  
G. Rapoport
Keyword(s):  
Bacillus Thuringiensis ◽  
Toxin Genes ◽  
Cry Toxin

scholarly journals Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensis

2018 ◽  
Vol 42 (6) ◽  
pp. 829-856 ◽  
Author(s):  
Annika Gillis ◽  
Nancy Fayad ◽  
Lionel Makart ◽  
Alexander Bolotin ◽  
Alexei Sorokin ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Mobile Genetic Elements ◽  
Genetic Elements

scholarly journals Omics-based comparative analysis of putative mobile genetic elements in Lactococcus lactis

2019 ◽  
Vol 366 (Supplement_1) ◽  
pp. i105-i113
Author(s):  
Joakim Mark Andersen ◽  
Christine Møller Pedersen ◽  
Claus Heiner Bang-Berthelsen
Keyword(s):  
Genetic Variation ◽  
Lactococcus Lactis ◽  
Mobile Genetic Elements ◽  
Chromosome Size ◽  
Chromosomal Variation ◽  
Mobile Dna ◽  
Important Species ◽  
Genetic Elements ◽  
Gene Functions ◽  
Transcriptomics Data

ABSTRACT Lactococcus lactis is globally used in food fermentation. Genomics is useful to investigate speciation and differential occurrence of (un)desired gene functions, often related to mobile DNA. This study investigates L. lactis for putative chromosomal mobile genetic elements through comparative genomics, and analyses how they contribute to chromosomal variation at strain level. Our work identified 95 loci that may range over 10% of the chromosome size when including prophages, and the loci display a marked differential occurrence in the analysed strains. Analysis of differential transcriptomics data revealed how mobile genetic elements may impact the host physiology in response to conditional changes. This insight in the genetic variation of mobile genetic elements in L. lactis holds potential to further identify important functions related to food and biotechnology applications within this important species.

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