scholarly journals Repression of YdaS Toxin is Mediated by Transcriptional Repressor RacR in the cryptic rac prophage of Escherichia coli-K12

2017 ◽  
Author(s):  
Revathy Krishnamurthi ◽  
Swagatha Ghosh ◽  
Supriya Khedkar ◽  
Aswin Sai Narain Seshasayee
Keyword(s):  
Escherichia Coli ◽  
Transcription Factor ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Driving Force ◽  
Transcriptional Repressor ◽  
Genomic Diversity ◽  
Toxin Gene ◽  
Escherichia Coli K12 ◽  
Putative Transcription Factor

AbstractHorizontal gene transfer is a major driving force behind the genomic diversity seen in prokaryotes. Theracprophage inE.coliK12 encodes a putative transcription factor RacR, whose deletion is lethal. We have shown that the essentiality ofracRinE.coliK12 is attributed to its role in transcriptionally repressing a toxin gene calledydaS, which is coded adjacent and divergently toracR.

scholarly journals Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic rac Prophage of Escherichia coli K-12

mSphere ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
Revathy Krishnamurthi ◽  
Swagatha Ghosh ◽  
Supriya Khedkar ◽  
Aswin Sai Narain Seshasayee
Keyword(s):  
Escherichia Coli ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Transcriptional Repressor ◽  
Type Ii ◽  
Content Type ◽  
E Coli ◽  
Putative Transcription Factor ◽  
K 12

ABSTRACT Transcription factors in the bacterium E. coli are rarely essential, and when they are essential, they are largely toxin-antitoxin systems. While studying transcription factors encoded in horizontally acquired regions in E. coli, we realized that the protein RacR, a putative transcription factor encoded by a gene on the rac prophage, is an essential protein. Here, using genetics, biochemistry, and bioinformatics, we show that its essentiality derives from its role as a transcriptional repressor of the ydaS and ydaT genes, whose products are toxic to the cell. Unlike type II toxin-antitoxin systems in which transcriptional regulation involves complexes of the toxin and antitoxin, repression by RacR is sufficient to keep ydaS transcriptionally silent. Horizontal gene transfer is a major driving force behind the genomic diversity seen in prokaryotes. The cryptic rac prophage in Escherichia coli K-12 carries the gene for a putative transcription factor RacR, whose deletion is lethal. We have shown that the essentiality of racR in E. coli K-12 is attributed to its role in transcriptionally repressing toxin gene(s) called ydaS and ydaT, which are adjacent to and coded divergently to racR. IMPORTANCE Transcription factors in the bacterium E. coli are rarely essential, and when they are essential, they are largely toxin-antitoxin systems. While studying transcription factors encoded in horizontally acquired regions in E. coli, we realized that the protein RacR, a putative transcription factor encoded by a gene on the rac prophage, is an essential protein. Here, using genetics, biochemistry, and bioinformatics, we show that its essentiality derives from its role as a transcriptional repressor of the ydaS and ydaT genes, whose products are toxic to the cell. Unlike type II toxin-antitoxin systems in which transcriptional regulation involves complexes of the toxin and antitoxin, repression by RacR is sufficient to keep ydaS transcriptionally silent.

scholarly journals panRGP: a pangenome-based method to predict genomic islands and explore their diversity

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i651-i658 ◽  
Author(s):  
Adelme Bazin ◽  
Guillaume Gautreau ◽  
Claudine Médigue ◽  
David Vallenet ◽  
Alexandra Calteau
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Species Level ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
Reference Dataset ◽  
Prokaryotic Genomes ◽  
Ideal Approach ◽  
Genomic Regions

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.

scholarly journals Horizontal Gene Transfer Involving Chloroplasts

2021 ◽  
Vol 22 (9) ◽  
pp. 4484
Author(s):  
Ewa Filip ◽  
Lidia Skuza
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Driving Force ◽  
Genetic Material ◽  
Adaptive Significance ◽  
Chloroplast Genomes ◽  
Organelle Genomes ◽  
Number Of Genes ◽  
Cellular Compartments

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

scholarly journals Stand-alone ClpG disaggregase confers superior heat tolerance to bacteria

2017 ◽  
Vol 115 (2) ◽  
pp. E273-E282 ◽  
Author(s):  
Changhan Lee ◽  
Kamila B. Franke ◽  
Shady Mansour Kamal ◽  
Hyunhee Kim ◽  
Heinrich Lünsdorf ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Atpase Activity ◽  
Stationary Phase ◽  
Virulence Factor ◽  
Heat Tolerance ◽  
Molecular Features ◽  
Partner Proteins

AAA+ disaggregases solubilize aggregated proteins and confer heat tolerance to cells. Their disaggregation activities crucially depend on partner proteins, which target the AAA+ disaggregases to protein aggregates while concurrently stimulating their ATPase activities. Here, we report on two potent ClpG disaggregase homologs acquired through horizontal gene transfer by the species Pseudomonas aeruginosa and subsequently abundant P. aeruginosa clone C. ClpG exhibits high, stand-alone disaggregation potential without involving any partner cooperation. Specific molecular features, including high basal ATPase activity, a unique aggregate binding domain, and almost exclusive expression in stationary phase distinguish ClpG from other AAA+ disaggregases. Consequently, ClpG largely contributes to heat tolerance of P. aeruginosa primarily in stationary phase and boosts heat resistance 100-fold when expressed in Escherichia coli. This qualifies ClpG as a potential persistence and virulence factor in P. aeruginosa.

scholarly journals Dissemination of the blaNDM-5 Gene via IncX3-Type Plasmid among Enterobacteriaceae in Children

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Dongxing Tian ◽  
Bingjie Wang ◽  
Hong Zhang ◽  
Fen Pan ◽  
Chun Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Klebsiella Pneumoniae ◽  
Pediatric Patients ◽  
Transmission Mechanism ◽  
Klebsiella Aerogenes ◽  
Content Type ◽  
E Coli

ABSTRACT The continuous emergence of novel New Delhi metallo-β-lactamase-5 (NDM-5)-producing Enterobacteriaceae isolates is receiving more and more public attention. Twenty-two NDM-5-producing strains were identified from 146 carbapenemase-producing Enterobacteriaceae (CRE) strains isolated from pediatric patients between January and March 2017, indicating that the blaNDM-5 gene has spread to children. All 22 isolates, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, showed significantly high resistance to β-lactam antibiotics (except aztreonam) but remained susceptible to tigecycline and colistin. K. pneumoniae and K. aerogenes strains were respectively defined as homologous clonal isolates by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) results confirmed the genetic relatedness with all K. pneumoniae strains belonging to sequence type (ST) 48. Two E. coli isolates (ST617 and ST1236) were considered genetically unrelated. Twenty-two blaNDM-5 plasmids were positive for the IncX3 amplicon and showed almost identical profiles after digestion with HindIII and EcoRI. Four representative strains (K. pneumoniae K725, K. aerogenes CR33, E. coli Z214, and E. coli Z244) were selected for further study. Plasmids harboring blaNDM-5 showed strong stability in both clinical isolates and transconjugants, without apparent plasmid loss after 100 serial generations. S1-PFGE followed by Southern blot analysis demonstrated that the blaNDM-5 gene was located on an ∼46-kb plasmid. Plasmid sequences of pNDM-K725, pNDM-CR33, and pNDM-Z214 were almost identical but were slightly different from that of pNDM-Z244. Compared with pNDM-Z244, ΔISAba125 and partial copies of IS3000 were missing. The genetic backgrounds of the blaNDM-5 gene in four strains were slightly different from that of the typical pNDM_MGR194. This study comprehensively characterized the horizontal gene transfer of the blaNDM-5 gene among different Enterobacteriaceae isolates in pediatric patients, and the IncX3-type plasmid was responsible for the spread. IMPORTANCE The emergence of CRE strains resistant to multiple antibiotics is considered a substantial threat to human health. Therefore, all the efforts to provide a detailed molecular transmission mechanism of specific drug resistance can contribute positively to prevent the further spread of multidrug-resistant bacteria. Although the new superbug harboring blaNDM-5 has been reported in many countries, it was mostly identified among E. coli strains, and the gene transfer mechanism has not been fully recognized and studied. In this work, we identified 22 blaNDM-5-positive strains in different species of Enterobacteriaceae, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, which indicated the horizontal gene transfer of blaNDM-5 among Enterobacteriaceae strains in pediatric patients. Moreover, blaNDM-5 was located on a 46-kb IncX3 plasmid, which is possibly responsible for this widespread horizontal gene transfer. The different genetic contexts of the blaNDM-5 gene indicated some minor evolutions of the plasmid, based on the complete sequences of the blaNDM-5 plasmids. These findings are of great significance to understand the transmission mechanism of drug resistance genes, develop anti-infection treatment, and take effective infection control measures.

scholarly journals Minimal and RNA-free RNase P in Aquifex aeolicus

2017 ◽  
Vol 114 (42) ◽  
pp. 11121-11126 ◽  
Author(s):  
Astrid I. Nickel ◽  
Nadine B. Wäber ◽  
Markus Gößringer ◽  
Marcus Lechner ◽  
Uwe Linne ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Rnase P ◽  
Aquifex Aeolicus ◽  
Trna Processing ◽  
Hyperthermophilic Bacterium ◽  
Domains Of Life

RNase P is an essential tRNA-processing enzyme in all domains of life. We identified an unknown type of protein-only RNase P in the hyperthermophilic bacterium Aquifex aeolicus: Without an RNA subunit and the smallest of its kind, the 23-kDa polypeptide comprises a metallonuclease domain only. The protein has RNase P activity in vitro and rescued the growth of Escherichia coli and Saccharomyces cerevisiae strains with inactivations of their more complex and larger endogenous ribonucleoprotein RNase P. Homologs of Aquifex RNase P (HARP) were identified in many Archaea and some Bacteria, of which all Archaea and most Bacteria also encode an RNA-based RNase P; activity of both RNase P forms from the same bacterium or archaeon could be verified in two selected cases. Bioinformatic analyses suggest that A. aeolicus and related Aquificaceae likely acquired HARP by horizontal gene transfer from an archaeon.

scholarly journals Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Karen V. Ambrose ◽  
Albrecht M. Koppenhöfer ◽  
Faith C. Belanger
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Toxin Gene ◽  
Insect Toxin
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