Unity in variety--the pan-genome of the Chlamydiae

scientific article published on 20 June 2011

Unity in variety--the pan-genome of the Chlamydiae is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1093/MOLBEV/MSR161
P932PMC publication ID3247790
P698PubMed publication ID21690563
P5875ResearchGate publication ID51235900

P50authorMatthias HornQ38319169
Konrad SachseQ38330064
Garry MyersQ56535936
Astrid CollingroQ58095010
Thomas PenzQ114740036
Eva HeinzQ37374563
Thomas RatteiQ37374609
Thomas WeinmaierQ37374487
P2093author name stringTimothy D Read
Patrik M Bavoil
Robert C Brunham
Patrick Tischler
Maureen G Friedman
Simona Kahane
P2860cites workPlasmids and rickettsial evolution: insight from Rickettsia felisQ21092256
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approachQ21142687
The COG database: an updated version includes eukaryotesQ21284294
The Genome of the Amoeba Symbiont "Candidatus Amoebophilus asiaticus" Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated BacteriaQ22065482
Comparative Genomic Analysis of Chlamydia trachomatis Oculotropic and Genitotropic StrainsQ22065493
Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatisQ22065557
The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of ProtistsQ22065654
Illuminating the Evolutionary History of ChlamydiaeQ22065815
Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniaeQ22065841
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the ChlamydiaceaeQ22065992
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.Q22065998
Comparative genomes of Chlamydia pneumoniae and C. trachomatisQ22122313
Chlamydiae as Symbionts in EukaryotesQ22255610
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequenceQ24544402
Effective--a database of predicted secreted bacterial proteinsQ24611732
The Chlamydia trachomatis plasmid is a transcriptional regulator of chromosomal genes and a virulence factorQ24642084
InterPro: the integrative protein signature databaseQ24655685
Rfam: updates to the RNA families databaseQ24655855
Host cell-free growth of the Q fever bacterium Coxiella burnetiiQ24656253
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplastQ24671542
Analysis of proteins in Chlamydia trachomatis L2 outer membrane complex, COMC.Q37855589
Identification of human T cell targets recognized during Chlamydia trachomatis genital infectionQ37858681
Chlamydial CT441 is a PDZ domain-containing tail-specific protease that interferes with the NF-kappaB pathway of immune responseQ37859424
The temperature activated HtrA protease from pathogen Chlamydia trachomatis acts as both a chaperone and protease at 37 degrees C.Q37859510
Recovery of an environmental Chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp.Q37865810
Conservation of the biochemical properties of IncA from Chlamydia trachomatis and Chlamydia caviae: oligomerization of IncA mediates interaction between facing membranesQ37866611
Neospora caninum and Waddlia chondrophila strain 2032/99 in a septic stillborn calf.Q37872548
Infection of Acanthamoeba polyphaga with Simkania negevensis and S. negevensis survival within amoebal cystsQ37873365
A secondary structure motif predictive of protein localization to the chlamydial inclusion membraneQ37874933
The Chlamydia trachomatis IncA protein is required for homotypic vesicle fusionQ37874938
Simkania negevensis strain ZT: growth, antigenic and genome characteristicsQ37878448
Plasmid diversity in ChlamydiaQ37882713
Description and partial characterization of a new Chlamydia-like microorganismQ37890987
Comparison of proteins involved in pilus synthesis and mating pair stabilization from the related plasmids F and R100-1: insights into the mechanism of conjugation.Q39497030
Role for the Ankyrin eukaryotic-like genes of Legionella pneumophila in parasitism of protozoan hosts and human macrophagesQ40012620
PhyloGenie: automated phylome generation and analysisQ40157338
Indispensable role for the eukaryotic-like ankyrin domains of the ankyrin B effector of Legionella pneumophila within macrophages and amoebaeQ40332816
Functional and structural genomics using PEDANT.Q44495629
Eukaryotic and eubacterial contributions to the establishment of plastid proteome estimated by large-scale phylogenetic analyses.Q50577735
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.Q52040275
Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale.Q52674118
Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosusQ57007334
MacVector. Integrated sequence analysis for the MacintoshQ73147808
Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptorsQ24676085
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteinsQ24676525
WoLF PSORT: protein localization predictorQ24684530
A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer systemQ24799946
Evolution and diversity of Rickettsia bacteriaQ24810316
Basic local alignment search toolQ25938991
MrBayes 3: Bayesian phylogenetic inference under mixed modelsQ26778438
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computingQ27860512
Improved prediction of signal peptides: SignalP 3.0Q27860548
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsQ27860746
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum LikelihoodQ27861000
Predicting coiled coils from protein sequencesQ27861097
The Kyoto Encyclopedia of Genes and Genomes—KEGGQ28109327
Divergence without difference: phylogenetics and taxonomy of Chlamydia resolvedQ28237926
The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevanceQ28240583
Chlamydia pneumoniae inclusion membrane protein Cpn0585 interacts with multiple Rab GTPasesQ28251473
Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational methodQ28297624
Chlamydia trachomatis-derived deubiquitinating enzymes in mammalian cells during infectionQ28484743
The Waddlia genome: a window into chlamydial biologyQ28751868
Massive comparative genomic analysis reveals convergent evolution of specialized bacteriaQ28752683
Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?Q28754450
An Ordination of the Upland Forest Communities of Southern WisconsinQ29030695
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic treesQ29547265
Locating proteins in the cell using TargetP, SignalP and related toolsQ29547300
ARB: a software environment for sequence dataQ29547354
Multiple alignment of DNA sequences with MAFFTQ29614386
Genomics and evolution of heritable bacterial symbiontsQ29615836
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regionsQ29617560
Novel bacterial endosymbionts of Acanthamoeba spp. related to the Paramecium caudatum symbiont Caedibacter caryophilus.Q30632845
Increasing diversity within ChlamydiaeQ30777291
Genomic BLAST: custom-defined virtual databases for complete and unfinished genomesQ33185176
Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogensQ33243561
The dps gene of symbiotic "Candidatus Legionella jeonii" in Amoeba proteus responds to hydrogen peroxide and phagocytosisQ33256247
Tackling the intractable - approaching the genetics of ChlamydialesQ33283134
SNARE protein mimicry by an intracellular bacteriumQ33325919
Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functionsQ33336587
Chemotaxis-like regulatory systems: unique roles in diverse bacteriaQ37451546
Conjugative plasmids: vessels of the communal gene poolQ37538155
Bacterial proteases from the intracellular vacuole niche; protease conservation and adaptation for pathogenic advantageQ37733692
Mobility of plasmids.Q37784107
Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodiesQ37851792
Identification of Chlamydia trachomatis outer membrane complex proteins by differential proteomicsQ37853351
Bacterial secretion systems with an emphasis on the chlamydial Type III secretion system.Q37854601
Chlamydial genes shed light on the evolution of photoautotrophic eukaryotesQ33351752
A novel inhibitor of Chlamydophila pneumoniae protein kinase D (PknD) inhibits phosphorylation of CdsD and suppresses bacterial replicationQ33510432
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the ChlamydiaeQ33521095
Interactions between flagellar and type III secretion proteins in Chlamydia pneumoniaeQ33526048
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clustersQ33600553
Raman microspectroscopy reveals long-term extracellular activity of ChlamydiaeQ33603497
Phylogenomics reveals a diverse Rickettsiales type IV secretion systemQ33826043
A protein secreted by the respiratory pathogen Chlamydia pneumoniae impairs IL-17 signalling via interaction with human Act1Q34082096
Inclusion membrane proteins of Protochlamydia amoebophila UWE25 reveal a conserved mechanism for host cell interaction among the ChlamydiaeQ34150817
F factor conjugation is a true type IV secretion system.Q34213377
Diversity in chemotaxis mechanisms among the bacteria and archaea.Q34349346
Cleavage of the NF-κB Family Protein p65/RelA by the Chlamydial Protease-like Activity Factor (CPAF) Impairs Proinflammatory Signaling in Cells Infected with ChlamydiaeQ34438726
Polymorphic proteins of Chlamydia spp.--autotransporters beyond the ProteobacteriaQ34453430
Proteins in the chlamydial inclusion membraneQ34574480
Parachlamydiaceae: potential emerging pathogensQ34650053
Toll-like receptor 2 activation by Chlamydia trachomatis is plasmid dependent, and plasmid-responsive chromosomal loci are coordinately regulated in response to glucose limitation by C. trachomatis but not by C. muridarumQ34739978
Generation of targeted Chlamydia trachomatis null mutants.Q34879947
Chlamydial TARP is a bacterial nucleator of actinQ35108349
Golgi-dependent transport of cholesterol to the Chlamydia trachomatis inclusion.Q35144239
Infections with the chlamydia-like microorganism Simkania negevensis, a possible emerging pathogenQ35206867
The ferritin-like Dps protein is required for Salmonella enterica serovar Typhimurium oxidative stress resistance and virulenceQ35549402
Structural and functional analyses of the major outer membrane protein of Chlamydia trachomatisQ35949509
Parachlamydia acanthamoebae enters and multiplies within human macrophages and induces their apoptosis [corrected].Q36046355
Genome reduction in the alpha-ProteobacteriaQ36229163
Host origin of plastid solute transporters in the first photosynthetic eukaryotesQ36465609
Type III secretion à la ChlamydiaQ36812549
Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxisQ36879874
Emerging role of Chlamydia and Chlamydia-like organisms in adverse pregnancy outcomesQ37056121
Transformation and isolation of allelic exchange mutants of Chlamydia psittaci using recombinant DNA introduced by electroporationQ37068255
Cytokinesis is blocked in mammalian cells transfected with Chlamydia trachomatis gene CT223.Q37134011
Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes.Q37285967
The thermolysin family (M4) of enzymes: therapeutic and biotechnological potentialQ37371966
P433issue12
P304page(s)3253-3270
P577publication date2011-06-20
P1433published inMolecular Biology and EvolutionQ1992656
P1476titleUnity in variety--the pan-genome of the Chlamydiae
P478volume28

Reverse relations

cites work (P2860)
Q41290840A Rickettsiales symbiont of amoebae with ancient features.
Q91936123A SpoIID Homolog Cleaves Glycan Strands at the Chlamydial Division Septum
Q30829026A Zebrafish Model for Chlamydia Infection with the Obligate Intracellular Pathogen Waddlia chondrophila
Q28265122A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia
Q92163394A predation assay using amoebae to screen for virulence factors unearthed the first W. chondrophila inclusion membrane protein
Q44059216Advances and Obstacles in the Genetic Dissection of Chlamydial Virulence
Q27317343Amoebal endosymbiont Parachlamydia acanthamoebae Bn9 can grow in immortal human epithelial HEp-2 cells at low temperature; an in vitro model system to study chlamydial evolution
Q27316123Architecture and host interface of environmental chlamydiae revealed by electron cryotomography
Q46269762Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems
Q37834004Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont
Q28831366CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium
Q37002228CTL0511 from Chlamydia trachomatis Is a Type 2C Protein Phosphatase with Broad Substrate Specificity
Q34349905Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
Q34947890Candidatus Syngnamydia venezia, a novel member of the phylum Chlamydiae from the broad nosed pipefish, Syngnathus typhle
Q37608283Chlamydia exploit the mammalian tryptophan-depletion defense strategy as a counter-defensive cue to trigger a survival state of persistence
Q34545451Chlamydia induces anchorage independence in 3T3 cells and detrimental cytological defects in an infection model
Q90066010Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction
Q37035936Chlamydia trachomatis transports NAD via the Npt1 ATP/ADP translocase
Q27468863Chlamydia-Like Organisms (CLOs) in Finnish Ixodes ricinus Ticks and Human Skin
Q28829314Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans
Q27014662Chlamydiae interaction with the endoplasmic reticulum: contact, function and consequences
Q36786613Chlamydial intracellular survival strategies
Q36683752Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities
Q37838586Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake
Q36756597Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range.
Q37838935Comparative genomic analysis of human Chlamydia pneumoniae isolates from respiratory, brain and cardiac tissues
Q35805210Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer
Q37843592Conserved features and major differences in the outer membrane protein composition of chlamydiae
Q37846070Crescent and star shapes of members of the Chlamydiales order: impact of fixative methods
Q37843211Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance
Q28831333Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes
Q37834930Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria
Q37835599Deconstructing the Chlamydial Cell Wall
Q55261991Detection of Chlamydiaceae and Chlamydia-like organisms on the ocular surface of children and adults from a trachoma-endemic region.
Q37124866Discovery of catalases in members of the Chlamydiales order
Q30558338Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ
Q34767506Distribution and diversity of bacterial secretion systems across metagenomic datasets
Q36902486Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen
Q52668358Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle.
Q37837034Environmental treasures: co-isolation of the first marine Chlamydiae and its protozoan host
Q90093540Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles?
Q37838898Following the Footsteps of Chlamydial Gene Regulation.
Q33565893Genetic variation in Chlamydia trachomatis and their hosts: impact on disease severity and tissue tropism
Q60930418Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp
Q49893062Genotyping of Candidatus Syngnamydia salmonis (chlamydiales; Simkaniaceae) co-cultured in Paramoeba perurans (amoebozoa; Paramoebidae).
Q111629317Horizontal gene transfer in the evolution of photosynthetic eukaryotes
Q52604616Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation.
Q37842912Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria
Q57466134Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida
Q34575947Identification and characterization of a novel porin family highlights a major difference in the outer membrane of chlamydial symbionts and pathogens
Q28740481Identification of immunogenic proteins of Waddlia chondrophila
Q27322698In contrast to Chlamydia trachomatis, Waddlia chondrophila grows in human cells without inhibiting apoptosis, fragmenting the Golgi apparatus, or diverting post-Golgi sphingomyelin transport
Q30661663Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae
Q37838397Interaction of Chlamydiae with human macrophages
Q34130460Lack of effective anti-apoptotic activities restricts growth of Parachlamydiaceae in insect cells
Q26827572Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms
Q34402710Massive expansion of Ubiquitination-related gene families within the Chlamydiae
Q34945481Metabolic features of Protochlamydia amoebophila elementary bodies--a link between activity and infectivity in Chlamydiae.
Q58758191Metagenomic Analysis of Fish-Associated Ca. Parilichlamydiaceae Reveals Striking Metabolic Similarities to the Terrestrial Chlamydiaceae
Q37546872Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats
Q21131135Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships
Q37836353One Face of Chlamydia trachomatis: The Infectious Elementary Body
Q35875539Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent.
Q37841537Plastid establishment did not require a chlamydial partner
Q37839078Proteomic analysis of the Simkania-containing vacuole: the central role of retrograde transport
Q28080622Purification and proteomics of pathogen-modified vacuoles and membranes
Q37837167Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum.
Q53035500Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine.
Q37841621Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights
Q64076450Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship
Q34708996Short and long-term genome stability analysis of prokaryotic genomes
Q37705096Simkania negevensis may produce long-lasting infections in human pneumocytes and endometrial cells
Q37834062Simkania negevensis, an Example of the Diversity of the Antimicrobial Susceptibility Pattern among Chlamydiales
Q37835486Simkania negevensis, an insight into the biology and clinical importance of a novel member of the Chlamydiales order
Q35082707Site-specific, insertional inactivation of incA in Chlamydia trachomatis using a group II intron
Q28078953Space: A Final Frontier for Vacuolar Pathogens
Q27925199Structural and biochemical characterization of Chlamydia trachomatis hypothetical protein CT263 supports that menaquinone synthesis occurs through the futalosine pathway.
Q28730662The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens
Q37525397The Impact of Protein Phosphorylation on Chlamydial Physiology
Q36004904The bacterial pangenome as a new tool for analysing pathogenic bacteria
Q37844907The chlamydial organism Simkania negevensis forms ER vacuole contact sites and inhibits ER-stress
Q37508088The chlamydiales pangenome revisited: structural stability and functional coherence
Q30152955The composition of the global and feature specific cyanobacterial core-genomes
Q50082618The effect of bacterial chemotaxis on host infection and pathogenicity
Q37846576The endosymbiont Amoebophilus asiaticus encodes an S-adenosylmethionine carrier that compensates for its missing methylation cycle
Q50026878The genome, microbiome and evolutionary medicine
Q37834388The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa
Q28276177The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems
Q27025555The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly
Q37841216Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae.
Q37833909Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae
Q37849961Unraveling the basic biology and clinical significance of the chlamydial plasmid
Q58803216Virulence-related comparative transcriptomics of infectious and non-infectious chlamydial particles
Q37028046Was the Chlamydial Adaptative Strategy to Tryptophan Starvation an Early Determinant of Plastid Endosymbiosis?

Search more.