Research graph
References from The host range of generalist and specialist phages in capsule-diverse Klebsiella hosts is driven by the evolvability of receptor-binding proteins. Local targets link to admitted publications; unresolved targets remain external evidence.
Understanding the impacts of bacteriophage viruses: from laboratory evolution to natural ecosystems
10.1146/annurev-virology-091919-075914 · 2022 · External reference
Phages in nature
10.4161/bact.1.1.14942 · 2011 · External reference
Molecular and evolutionary determinants of bacteriophage host range
10.1016/j.tim.2018.08.006 · 2019 · External reference
Isolation of polyvalent bacteriophages by sequential multiple-host approaches
10.1128/aem.02382-15 · 2016 · External reference
Host diversity slows bacteriophage adaptation by selecting generalists over specialists
10.1038/s41559-020-01364-1 · 2021 · External reference
Evolutionary rescue and the coexistence of generalist and specialist competitors: an experimental test
10.1098/rspb.2015.1932 · 2015 · External reference
Phage fibers and spikes: a nanoscale Swiss army knife for host infection
10.1016/j.mib.2024.102429 · 2024 · External reference
Targeting mechanisms of tailed bacteriophages
10.1038/s41579-018-0070-8 · 2018 · External reference
Trade-offs between receptor modification and fitness drive host-bacteriophage co-evolution leading to phage extinction or co-existence
10.1093/ismejo/wrae214 · 2024 · External reference
Prophages mediate defense against phage infection through diverse mechanisms
10.1038/ismej.2016.79 · 2016 · External reference
Bacteriophage resistance mechanisms
10.1038/nrmicro2315 · 2010 · External reference
Capturing the facets of evolvability in a mechanistic framework
10.1016/j.tree.2022.01.004 · 2022 · External reference
Viral receptor-binding protein evolves new function through mutations that cause trimer instability and functional heterogeneity
10.1093/molbev/msae056 · 2024 · External reference
A continuous evolution system for contracting the host range of bacteriophage T7
10.1038/s41598-019-57221-0 · 2020 · External reference
Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups
10.1186/s12985-023-02138-4 · 2023 · External reference
Abundance and co-occurrence of extracellular capsules increase environmental breadth: implications for the emergence of pathogens
10.1371/journal.ppat.1006525 · 2017 · External reference
Diversity-generating machines: genetics of bacterial sugar-coating
10.1016/j.tim.2018.06.006 · 2018 · External reference
Escherichia coli K1’s capsule is a barrier to bacteriophage T7
10.1128/aem.71.8.4872-4874.2005 · 2005 · External reference
Engineering the modular receptor-binding proteins of Klebsiella phages switches their capsule serotype specificity
10.1128/mbio.00455-21 · 2021 · External reference
Structural and functional studies of a Klebsiella phage capsule depolymerase tailspike: mechanistic insights into capsular degradation
10.1016/j.str.2020.04.015 · 2020 · External reference
Specific interaction of novel friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types
10.1128/jvi.01714-20 · 2021 · External reference
Genetic determinants of host tropism in Klebsiella phages
10.1016/j.celrep.2023.112048 · 2023 · External reference
Targeted phage hunting to specific Klebsiella pneumoniae clinical isolates is an efficient antibiotic resistance and infection control strategy
10.1128/spectrum.00254-24 · 2024 · External reference
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts
10.1093/nar/gku734 · 2014 · External reference
Phage abortive infection in lactococci: variations on a theme
10.1016/j.mib.2005.06.006 · 2005 · External reference
An updated evolutionary classification of CRISPR-Cas systems
10.1038/nrmicro3569 · 2015 · External reference
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements
2020 · External reference
Systematic discovery of antiphage defense systems in the microbial pangenome
10.1126/science.aar4120 · 2018 · External reference
Systematic and quantitative view of the antiviral arsenal of prokaryotes
10.1038/s41467-022-30269-9 · 2022 · External reference
Inhibitors of bacterial immune systems: discovery, mechanisms and applications
10.1038/s41576-023-00676-9 · 2024 · External reference
Gene-wide identification of episodic selection
10.1093/molbev/msv035 · 2015 · External reference
FUBAR: a fast, unconstrained Bayesian approximation for inferring selection
10.1093/molbev/mst030 · 2013 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
InterProScan 5: genome-scale protein function classification
10.1093/bioinformatics/btu031 · 2014 · External reference
Structure of the receptor-binding protein of bacteriophage det7: a podoviral tail spike in a myovirus
10.1128/jvi.01641-07 · 2008 · External reference
Crystal structure of ORF210 from E. coli O157:H1 phage CBA120 (TSP1), a putative tailspike protein
10.1371/journal.pone.0093156 · 2014 · External reference
Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer
10.1126/science.8023158 · 1994 · External reference
Tail assembly interference is a common strategy in bacterial antiviral defenses
10.1038/s41467-024-51915-4 · 2024 · External reference
Broad-range capsule-dependent lytic Sugarlandvirus against Klebsiella sp
10.1128/spectrum.04298-22 · 2023 · External reference
Novel Klebsiella pneumoniae K23-specific bacteriophages from different families: similarity of depolymerases and their therapeutic potential
10.3389/fmicb.2021.669618 · 2021 · External reference
Unresolved reference
2024 · External reference
MacSyFinder v2: improved modelling and search engine to identify molecular systems in genomes
10.24072/pcjournal.250 · 2023 · External reference
Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI
10.1016/j.str.2010.07.006 · 2010 · External reference
Experimental evolution of the TolC-receptor phage U136B functionally identifies a tail fiber protein involved in adsorption through strong parallel adaptation
10.1128/aem.00079-23 · 2023 · External reference
Parallel evolution of host-attachment proteins in phage PP01 populations adapting to Escherichia coli O157:H7
10.3390/ph11020060 · 2018 · External reference
Local migration promotes competitive restraint in a host-pathogen “tragedy of the commons”
10.1038/nature04864 · 2006 · External reference
Phage and bacteria support mutual diversity in a narrowing staircase of coexistence
10.1038/ismej.2014.80 · 2014 · External reference
Modeling the directed evolution of broad host range phages
10.3390/antibiotics11121709 · 2022 · External reference
Competition and the origins of novelty: experimental evolution of niche-width expansion in a virus
10.1098/rsbl.2012.0616 · 2013 · External reference
The generalism–specialism debate: the role of generalists in the life and death of species
10.1111/j.1095-8312.2011.01789.x · 2011 · External reference
Localised genetic heterogeneity provides a novel mode of evolution in dsDNA phages
10.1038/s41598-017-14285-0 · 2017 · External reference
Expansion of the plaquing host range and improvement of the absorption rate of a T5-like Salmonella phage by altering the long tail fibers
10.1128/aem.00895-22 · 2022 · External reference
Virus population extinction via ecological traps
10.1111/j.1461-0248.2006.01013.x · 2007 · External reference
Practical methods for determining phage growth parameters.
2009 · External reference
DepoScope: accurate phage depolymerase annotation and domain delineation using large language models
10.1371/journal.pcbi.1011831 · 2024 · External reference
Structural insights into the chaperone-assisted assembly of a simplified tail fiber of the myocyanophage Pam3
10.3390/v14102260 · 2022 · External reference
Morphogenesis of the T4 tail and tail fibers
10.1186/1743-422x-7-355 · 2010 · External reference
Structure of the receptor-binding carboxy-terminal domain of the bacteriophage T5 L-shaped tail fibre with and without its intra-molecular chaperone
10.3390/v7122946 · 2015 · External reference
Protein dynamism and evolvability
10.1126/science.1169375 · 2009 · External reference
Destabilizing mutations encode nongenetic variation that drives evolutionary innovation
10.1126/science.aar1954 · 2018 · External reference
Small proteins in bacteria - Big challenges in prediction and identification
10.1002/pmic.202200421 · 2023 · External reference
Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification
10.1016/j.str.2010.12.003 · 2011 · External reference
Unicycler: resolving bacterial genome assemblies from short and long sequencing reads
2017 · External reference
Pharokka: a fast scalable bacteriophage annotation tool
10.1093/bioinformatics/btac776 · 2023 · External reference
Unresolved reference
External reference
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
10.1089/cmb.2012.0021 · 2012 · External reference
metaSPAdes: a new versatile metagenomic assembler
10.1101/gr.213959.116 · 2017 · External reference
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement
10.1371/journal.pone.0112963 · 2014 · External reference
Unresolved reference
External reference
VIRIDIC-a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses
10.3390/v12111268 · 2020 · External reference
Fast and accurate short read alignment with Burrows-Wheeler transform
10.1093/bioinformatics/btp324 · 2009 · External reference
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
10.1093/nar/gks918 · 2012 · External reference
igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
10.1093/bioinformatics/btac830 · 2023 · External reference
MEGA X: molecular evolutionary genetics analysis across computing platforms
10.1093/molbev/msy096 · 2018 · External reference
10.32614/cran.package.gggenomes
10.32614/cran.package.gggenomes · External reference
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
10.1186/s40168-020-00990-y · 2021 · External reference
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
10.1038/s41587-020-00774-7 · 2021 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
PHASTEST: faster than PHASTER, better than PHAST
10.1093/nar/gkad382 · 2023 · External reference
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
10.1093/nar/gkf436 · 2002 · External reference
HyPhy 2.5—a customizable platform for evolutionary hypothesis testing using phylogenies
10.1093/molbev/msz197 · 2020 · External reference
Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes
10.1093/molbev/msx335 · 2018 · External reference
RDP4: detection and analysis of recombination patterns in virus genomes
10.1093/ve/vev003 · 2015 · External reference
Unresolved reference
2020 · External reference
The HHpred interactive server for protein homology detection and structure prediction
10.1093/nar/gki408 · 2005 · External reference
