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Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in Klebsiella pneumoniae

https://doi.org/10.1101/2020.11.02.365908

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Co-variation of tRNA Abundance and Codon Usage inEscherichia coliat Different Growth Rates

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Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

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Comparative genomics: the bacterial pan-genome

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Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

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Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.

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Transfer RNAs and pathogenicity islands

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Klebsiella pneumoniae liver abscess: a new invasive syndrome

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Fast gapped-read alignment with Bowtie 2

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Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

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Population genomics of Klebsiella pneumoniae

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Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

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Calibrating bacterial evolution

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A DNA segment encoding the anticodon stem/loop of tRNA determines the specific recombination of integrative-conjugative elements in Acidithiobacillus species

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Klebsiella pneumoniae Genotype K1: An Emerging Pathogen That Causes Septic Ocular or Central Nervous System Complications from Pyogenic Liver Abscess

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Clustal W and Clustal X version 2.0

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Biopython: freely available Python tools for computational molecular biology and bioinformatics

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Easyfig: a genome comparison visualizer

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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Prokka: rapid prokaryotic genome annotation

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Roary: rapid large-scale prokaryote pan genome analysis

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Complex heatmaps reveal patterns and correlations in multidimensional genomic data

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bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli

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PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

inferredcites →https://doi.org/10.1093/femsre/fuv004openalex-snapshot

Bacterial transfer RNAs

inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

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Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies

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PRODORIC: prokaryotic database of gene regulation

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ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

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Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

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tRNAdb 2009: compilation of tRNA sequences and tRNA genes

inferredcites →https://doi.org/10.1093/nar/gku1072openalex-snapshot

Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes

inferredcites →https://doi.org/10.1093/nar/gkv416openalex-snapshot

The MEME Suite

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The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

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PHASTER: a better, faster version of the PHAST phage search tool

inferredcites →https://doi.org/10.1093/nar/gkw413openalex-snapshot

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

inferredcites →https://doi.org/10.1093/nar/gky1080openalex-snapshot

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

inferredcites →https://doi.org/10.1093/nar/gky1085openalex-snapshot

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025834openalex-snapshot

Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040335openalex-snapshot

Codon usage and tRNA content in unicellular and multicellular organisms.

inferredcites →https://doi.org/10.1099/mgen.0.000102openalex-snapshot

Identification of Klebsiella capsule synthesis loci from whole genome data

inferredcites →https://doi.org/10.1099/mgen.0.000110openalex-snapshot

Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone

inferredcites →https://doi.org/10.1099/mgen.0.000196openalex-snapshot

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

inferredcites →https://doi.org/10.1101/gr.2896904openalex-snapshot

Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization

inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot

Matplotlib: A 2D Graphics Environment

inferredcites →https://doi.org/10.1111/1462-2920.13016openalex-snapshot

Deep transcriptome profiling of clinical K lebsiella pneumoniae isolates reveals strain and sequence type‐specific adaptation

inferredcites →https://doi.org/10.1111/1574-6976.12058openalex-snapshot

Conjugative and mobilizable genomic islands in bacteria: evolution and diversity

inferredcites →https://doi.org/10.1111/j.1462-5822.2006.00794.xopenalex-snapshot

Pathogenicity islands: a molecular toolbox for bacterial virulence

inferredcites →https://doi.org/10.1111/j.1574-6976.2008.00136.xopenalex-snapshot

Genomic islands: tools of bacterial horizontal gene transfer and evolution

inferredcites →https://doi.org/10.1128/cmr.11.4.589openalex-snapshot

Klebsiella spp. as Nosocomial Pathogens: Epidemiology, Taxonomy, Typing Methods, and Pathogenicity Factors

inferredcites →https://doi.org/10.1128/jb.01219-07openalex-snapshot

Characterization of Integrative and Conjugative Element ICEKp1-Associated Genomic Heterogeneity in aKlebsiella pneumoniaeStrain Isolated from a Primary Liver Abscess

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Standard reference strains of Escherichia coli from natural populations

inferredcites →https://doi.org/10.1128/jb.185.3.1059-1070.2003openalex-snapshot

Traffic at the tmRNA Gene

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Comparison of counterimmunoelectrophoresis and the capsular reaction test for typing of pneumococci

inferredcites →https://doi.org/10.1128/jcm.43.8.4178-4182.2005openalex-snapshot

Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates

inferredcites →https://doi.org/10.1128/mbio.00630-15openalex-snapshot

Mapping the Evolution of Hypervirulent Klebsiella pneumoniae

inferredcites →https://doi.org/10.1128/mra.01133-18openalex-snapshot

Draft Genome Sequences of the Escherichia coli Reference (ECOR) Collection

inferredcites →https://doi.org/10.1146/annurev.micro.62.081307.162948openalex-snapshot

Biology of trans-Translation

inferredcites →https://doi.org/10.1186/1741-7007-12-41openalex-snapshot

Comparative analysis of Klebsiella pneumoniae genomes identifies a phospholipase D family protein as a novel virulence factor

inferredcites →https://doi.org/10.1186/s12859-019-2669-9openalex-snapshot

ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments

inferredcites →https://doi.org/10.1186/s12859-019-2704-xopenalex-snapshot

RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases

inferredcites →https://doi.org/10.1371/journal.pgen.1008114openalex-snapshot

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

inferredcites →https://doi.org/10.1371/journal.pgen.1008465openalex-snapshot

Nitrate-responsive OBP4-XTH9 regulatory module controls lateral root development in Arabidopsis thaliana

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Virulent Clones of Klebsiella pneumoniae: Identification and Evolutionary Scenario Based on Genomic and Phenotypic Characterization

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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

inferredcites →https://doi.org/10.15252/emmm.201404767openalex-snapshot

A high‐resolution genomic analysis of multidrug‐resistant hospital outbreaks of Klebsiella pneumoniae

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Horizontal gene transfer in human pathogens

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rSeqTU—A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units

inferredcites →https://doi.org/10.3389/fgene.2019.00735openalex-snapshot

Identification of Cancer-Related Long Non-Coding RNAs Using XGBoost With High Accuracy

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Bovine Polymorphonuclear Neutrophils Cast Neutrophil Extracellular Traps against the Abortive Parasite Neospora caninum

inferredcites →https://doi.org/10.3389/fimmu.2017.01630openalex-snapshot

Potential Effects of Horizontal Gene Exchange in the Human Gut

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Klebsiella pneumoniae Asparagine tDNAs Are Integration Hotspots for Different Genomic Islands Encoding Microcin E492 Production Determinants and Other Putative Virulence Factors Present in Hypervirulent Strains

inferredcites →https://doi.org/10.3390/genes8110337openalex-snapshot

The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems

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Concepts for biocontrol in marine environments: is there a way forward?

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ARNold: A web tool for the prediction of Rho-independent transcription terminators

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1099/mgen.0.001138openalex-snapshot

Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258

inferred← citeshttps://doi.org/10.1101/2023.08.10.552780openalex-snapshot

Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae ST258

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