Sanders M

References (26)

Title : Zealactones. Novel natural strigolactones from maize - Charnikhova_2017_Phytochemistry_137_123
Author(s) : Charnikhova TV , Gaus K , Lumbroso A , Sanders M , Vincken JP , De Mesmaeker A , Ruyter-Spira CP , Screpanti C , Bouwmeester HJ
Ref : Phytochemistry , 137 :123 , 2017
Abstract : In the root exudate and root extracts of maize hybrid cv NK Falkone seven putative strigolactones were detected using UPLC-TQ-MS-MS. All seven compounds displayed MS-MS-fragmentation common for strigolactones and particularly the presence of a fragment of m/z 97 Da, which may indicate the presence of the so-called D-ring, suggests they are strigolactones. The levels of all these putative strigolactones increased upon phosphate starvation and decreased upon fluridone (carotenoid biosynthesis inhibitor) treatment, both of which are a common response for strigolactones. All seven compounds were subsequently isolated with prep-HPLC-MS. They all exhibited Striga hermonthica seed germination inducing activity just as the synthetic strigolactone analog GR24. The structure of two of the seven compounds was elucidated by NMR spectroscopy as: methyl (2E,3E)-4-(3,3-dimethyl-5-oxo-2-(prop-1-en-2-yl)tetrahydrofuran-2-yl)-2-(((4-methyl-5-oxo-2,5-dihydrofuran-2-yl)oxy)methylene)but-3-enoate (two diastereomers 1a and 1b). Strigolactones (1a/b) are closely related to the methyl ester of carlactonoic acid (MeCLA) and heliolactone. However, they contain a unique 4,4-dimethyltetrahydrofuran-2-one motif as the "A-ring" instead of the classical (di)methylcyclohexene. Because these compounds were isolated from maize (Zea mays) we called them "zealactone 1a and 1b". The implications of this discovery for our view on strigolactones and their biosynthesis are discussed.
ESTHER : Charnikhova_2017_Phytochemistry_137_123
PubMedSearch : Charnikhova_2017_Phytochemistry_137_123
PubMedID: 28215609

Title : Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy - Reid_2012_PLoS.Pathog_8_e1002567
Author(s) : Reid AJ , Vermont SJ , Cotton JA , Harris D , Hill-Cawthorne GA , Konen-Waisman S , Latham SM , Mourier T , Norton R , Quail MA , Sanders M , Shanmugam D , Sohal A , Wasmuth JD , Brunk B , Grigg ME , Howard JC , Parkinson J , Roos DS , Trees AJ , Berriman M , Pain A , Wastling JM
Ref : PLoS Pathog , 8 :e1002567 , 2012
Abstract : Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.
ESTHER : Reid_2012_PLoS.Pathog_8_e1002567
PubMedSearch : Reid_2012_PLoS.Pathog_8_e1002567
PubMedID: 22457617
Gene_locus related to this paper: neocl-f0v9d7 , neocl-f0v729 , neocl-f0vc02 , neocl-f0vce2 , neocl-f0vq55

Title : Salmonella bongori provides insights into the evolution of the Salmonellae - Fookes_2011_PLoS.Pathog_7_e1002191
Author(s) : Fookes M , Schroeder GN , Langridge GC , Blondel CJ , Mammina C , Connor TR , Seth-Smith H , Vernikos GS , Robinson KS , Sanders M , Petty NK , Kingsley RA , Baumler AJ , Nuccio SP , Contreras I , Santiviago CA , Maskell D , Barrow P , Humphrey T , Nastasi A , Roberts M , Frankel G , Parkhill J , Dougan G , Thomson NR
Ref : PLoS Pathog , 7 :e1002191 , 2011
Abstract : The genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associated with cold-blooded animals, but it can infect humans. To define the phylogeny of this species, and compare it to S. enterica, we have sequenced 28 isolates representing most of the known diversity of S. bongori. This cross-species analysis allowed us to confidently differentiate ancestral functions from those acquired following speciation, which include both metabolic and virulence-associated capacities. We show that, although S. bongori inherited a basic set of Salmonella common virulence functions, it has subsequently elaborated on this in a different direction to S. enterica. It is an established feature of S. enterica evolution that the acquisition of the type III secretion systems (T3SS-1 and T3SS-2) has been followed by the sequential acquisition of genes encoding secreted targets, termed effectors proteins. We show that this is also true of S. bongori, which has acquired an array of novel effector proteins (sboA-L). All but two of these effectors have no significant S. enterica homologues and instead are highly similar to those found in enteropathogenic Escherichia coli (EPEC). Remarkably, SboH is found to be a chimeric effector protein, encoded by a fusion of the T3SS-1 effector gene sopA and a gene highly similar to the EPEC effector nleH from enteropathogenic E. coli. We demonstrate that representatives of these new effectors are translocated and that SboH, similarly to NleH, blocks intrinsic apoptotic pathways while being targeted to the mitochondria by the SopA part of the fusion. This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC.
ESTHER : Fookes_2011_PLoS.Pathog_7_e1002191
PubMedSearch : Fookes_2011_PLoS.Pathog_7_e1002191
PubMedID: 21876672
Gene_locus related to this paper: salbc-f8vhq9

Title : Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania - Rogers_2011_Genome.Res_21_2129
Author(s) : Rogers MB , Hilley JD , Dickens NJ , Wilkes J , Bates PA , Depledge DP , Harris D , Her Y , Herzyk P , Imamura H , Otto TD , Sanders M , Seeger K , Dujardin JC , Berriman M , Smith DF , Hertz-Fowler C , Mottram JC
Ref : Genome Res , 21 :2129 , 2011
Abstract : Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated a reference genome for Leishmania mexicana and refined the reference genomes for Leishmania major, Leishmania infantum, and Leishmania braziliensis. This has allowed the identification of a remarkably low number of genes or paralog groups (2, 14, 19, and 67, respectively) unique to one species. These were found to be conserved in additional isolates of the same species. We have predicted allelic variation and find that in these isolates, L. major and L. infantum have a surprisingly low number of predicted heterozygous SNPs compared with L. braziliensis and L. mexicana. We used short read coverage to infer ploidy and gene copy numbers, identifying large copy number variations between species, with 200 tandem gene arrays in L. major and 132 in L. mexicana. Chromosome copy number also varied significantly between species, with nine supernumerary chromosomes in L. infantum, four in L. mexicana, two in L. braziliensis, and one in L. major. A significant bias against gene arrays on supernumerary chromosomes was shown to exist, indicating that duplication events occur more frequently on disomic chromosomes. Taken together, our data demonstrate that there is little variation in unique gene content across Leishmania species, but large-scale genetic heterogeneity can result through gene amplification on disomic chromosomes and variation in chromosome number. Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression in response to environmental conditions in the host, providing a genetic basis for disease tropism.
ESTHER : Rogers_2011_Genome.Res_21_2129
PubMedSearch : Rogers_2011_Genome.Res_21_2129
PubMedID: 22038252

Title : The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions - Letek_2010_PLoS.Genet_6_e1001145
Author(s) : Letek M , Gonzalez P , Macarthur I , Rodriguez H , Freeman TC , Valero-Rello A , Blanco M , Buckley T , Cherevach I , Fahey R , Hapeshi A , Holdstock J , Leadon D , Navas J , Ocampo A , Quail MA , Sanders M , Scortti MM , Prescott JF , Fogarty U , Meijer WG , Parkhill J , Bentley SD , Vazquez-Boland JA
Ref : PLoS Genet , 6 :e1001145 , 2010
Abstract : We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid-rich intestine and manure of herbivores--two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche-adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi.
ESTHER : Letek_2010_PLoS.Genet_6_e1001145
PubMedSearch : Letek_2010_PLoS.Genet_6_e1001145
PubMedID: 20941392
Gene_locus related to this paper: coreq-e9sxw6 , coreq-e9t5k8 , coreq-e9t5k9 , coreq-e9t7v9 , rhoha-e9t397 , rhoe1-e4w8b9 , rhoe1-e4w8k3 , rhoe1-e4w8s0 , rhoe1-e4w9r2 , rhoe1-e4wah6 , rhoe1-e4wb26 , rhoe1-e4wb75 , rhoe1-e4wdz9 , rhoe1-e4wg39 , rhoe1-e4wg83 , rhoe1-e4whm4 , rhoe1-e4wih4 , rhoe1-e4wja5 , rhoe1-e4wjd9 , rhoe1-e4wjy2 , rhoe1-e4wat8 , coreq-e9t814 , rhoe1-e4wbp9 , coreq-e9t0s6 , coreq-e9swc5 , rhoe1-e4wix8 , rhoe1-e4wjy1

Title : The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis - Jackson_2010_PLoS.Negl.Trop.Dis_4_e658
Author(s) : Jackson AP , Sanders M , Berry A , McQuillan J , Aslett MA , Quail MA , Chukualim B , Capewell P , MacLeod A , Melville SE , Gibson W , Barry JD , Berriman M , Hertz-Fowler C
Ref : PLoS Negl Trop Dis , 4 :e658 , 2010
Abstract : BACKGROUND: Trypanosoma brucei gambiense is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a T. b. brucei isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between T. b. gambiense and the reference genome. We sought to identify features that were uniquely associated with T. b. gambiense and its ability to infect humans. METHODS AND FINDINGS: An improved high-quality draft genome sequence for the group 1 T. b. gambiense DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with T. b. brucei showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in T. b. gambiense DAL 972. A comparison of the variant surface glycoproteins (VSG) in T. b. brucei with all T. b. gambiense sequence reads showed that the essential structural repertoire of VSG domains is conserved across T. brucei.
CONCLUSIONS: This study provides the first estimate of intraspecific genomic variation within T. brucei, and so has important consequences for future population genomics studies. We have shown that the T. b. gambiense genome corresponds closely with the reference, which should therefore be an effective scaffold for any T. brucei genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in T. b. brucei, no T. b. gambiense-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.
ESTHER : Jackson_2010_PLoS.Negl.Trop.Dis_4_e658
PubMedSearch : Jackson_2010_PLoS.Negl.Trop.Dis_4_e658
PubMedID: 20404998
Gene_locus related to this paper: tryb2-q6h9e3 , tryb2-q38cd5 , tryb2-q57u20 , tryb2-q57u43 , tryb2-q57xb0 , tryb2-q57y40 , tryb2-q389w3 , tryb2-q582c7 , tryb2-q582c8 , tryb9-c9zpb9 , tryb9-c9zu35 , tryb9-d0a9w2 , trybr-PEPTB

Title : Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis - Holden_2009_PLoS.One_4_e6072
Author(s) : Holden MT , Hauser H , Sanders M , Ngo TH , Cherevach I , Cronin A , Goodhead I , Mungall K , Quail MA , Price C , Rabbinowitsch E , Sharp S , Croucher NJ , Chieu TB , Mai NT , Diep TS , Chinh NT , Kehoe M , Leigh JA , Ward PN , Dowson CG , Whatmore AM , Chanter N , Iversen P , Gottschalk M , Slater JD , Smith HE , Spratt BG , Xu J , Ye C , Bentley S , Barrell BG , Schultsz C , Maskell DJ , Parkhill J
Ref : PLoS ONE , 4 :e6072 , 2009
Abstract : BACKGROUND: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, approximately 40% of the approximately 2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three approximately 90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. CONCLUSIONS/SIGNIFICANCE: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.
ESTHER : Holden_2009_PLoS.One_4_e6072
PubMedSearch : Holden_2009_PLoS.One_4_e6072
PubMedID: 19603075
Gene_locus related to this paper: strsu-q302y4 , strsy-a4vus4 , strsy-a4vwf6

Title : Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens - Holden_2009_PLoS.Pathog_5_e1000346
Author(s) : Holden MT , Heather Z , Paillot R , Steward KF , Webb K , Ainslie F , Jourdan T , Bason NC , Holroyd NE , Mungall K , Quail MA , Sanders M , Simmonds M , Willey D , Brooks K , Aanensen DM , Spratt BG , Jolley KA , Maiden MC , Kehoe M , Chanter N , Bentley SD , Robinson C , Maskell DJ , Parkhill J , Waller AS
Ref : PLoS Pathog , 5 :e1000346 , 2009
Abstract : The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. Streptococcus equi subspecies equi (S. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A(2) toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.
ESTHER : Holden_2009_PLoS.Pathog_5_e1000346
PubMedSearch : Holden_2009_PLoS.Pathog_5_e1000346
PubMedID: 19325880
Gene_locus related to this paper: stre4-c0mbg3 , stre4-pepx , strem-b4u0u4 , strem-b4u3j8 , strs7-pepx

Title : Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287\/91 provides insights into evolutionary and host adaptation pathways - Thomson_2008_Genome.Res_18_1624
Author(s) : Thomson NR , Clayton DJ , Windhorst D , Vernikos G , Davidson S , Churcher C , Quail MA , Stevens M , Jones MA , Watson M , Barron A , Layton A , Pickard D , Kingsley RA , Bignell A , Clark L , Harris B , Ormond D , Abdellah Z , Brooks K , Cherevach I , Chillingworth T , Woodward J , Norberczak H , Lord A , Arrowsmith C , Jagels K , Moule S , Mungall K , Sanders M , Whitehead S , Chabalgoity JA , Maskell D , Humphrey T , Roberts M , Barrow PA , Dougan G , Parkhill J
Ref : Genome Res , 18 :1624 , 2008
Abstract : We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis. Significantly, the genome of S. Gallinarum has undergone extensive degradation through deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those identified previously in other host-adapted bacteria reveals the loss of many common functional traits and provides insights into possible mechanisms of host and tissue adaptation. We propose that experimental analysis in chickens and mice of S. Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica.
ESTHER : Thomson_2008_Genome.Res_18_1624
PubMedSearch : Thomson_2008_Genome.Res_18_1624
PubMedID: 18583645
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-AES , salty-BIOH , salty-DLHH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-P74847 , salty-PLDB , salty-STM0332 , salty-STM4506 , salty-STY1441 , salty-STY2428 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YHET , salty-YQIA

Title : Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids - Letek_2008_J.Bacteriol_190_5797
Author(s) : Letek M , Ocampo-Sosa AA , Sanders M , Fogarty U , Buckley T , Leadon DP , Gonzalez P , Scortti M , Meijer WG , Parkhill J , Bentley S , Vazquez-Boland JA
Ref : Journal of Bacteriology , 190 :5797 , 2008
Abstract : The pathogenic actinomycete Rhodococcus equi harbors different types of virulence plasmids associated with specific nonhuman hosts. We determined the complete DNA sequence of a vapB(+) plasmid, typically associated with pig isolates, and compared it with that of the horse-specific vapA(+) plasmid type. pVAPB1593, a circular 79,251-bp element, had the same housekeeping backbone as the vapA(+) plasmid but differed over an approximately 22-kb region. This variable region encompassed the vap pathogenicity island (PAI), was clearly subject to selective pressures different from those affecting the backbone, and showed major genetic rearrangements involving the vap genes. The pVAPB1593 PAI harbored five different vap genes (vapB and vapJ to -M, with vapK present in two copies), which encoded products differing by 24 to 84% in amino acid sequence from the six full-length vapA(+) plasmid-encoded Vap proteins, consistent with a role for the specific vap gene complement in R. equi host tropism. Sequence analyses, including interpolated variable-order motifs for detection of alien DNA and reconstruction of Vap family phylogenetic relationships, suggested that the vap PAI was acquired by an ancestor plasmid via lateral gene transfer, subsequently evolving by vap gene duplication and sequence diversification to give different (host-adapted) plasmids. The R. equi virulence plasmids belong to a new family of actinobacterial circular replicons characterized by an ancient conjugative backbone and a horizontally acquired niche-adaptive plasticity region.
ESTHER : Letek_2008_J.Bacteriol_190_5797
PubMedSearch : Letek_2008_J.Bacteriol_190_5797
PubMedID: 18606735
Gene_locus related to this paper: coreq-e9sxw6 , coreq-e9t5k8 , coreq-e9t5k9 , coreq-e9t7v9 , coreq-d9i5p0

Title : The genome of the simian and human malaria parasite Plasmodium knowlesi - Pain_2008_Nature_455_799
Author(s) : Pain A , Bohme U , Berry AE , Mungall K , Finn RD , Jackson AP , Mourier T , Mistry J , Pasini EM , Aslett MA , Balasubrammaniam S , Borgwardt K , Brooks K , Carret C , Carver TJ , Cherevach I , Chillingworth T , Clark TG , Galinski MR , Hall N , Harper D , Harris D , Hauser H , Ivens A , Janssen CS , Keane T , Larke N , Lapp S , Marti M , Moule S , Meyer IM , Ormond D , Peters N , Sanders M , Sanders S , Sargeant TJ , Simmonds M , Smith F , Squares R , Thurston S , Tivey AR , Walker D , White B , Zuiderwijk E , Churcher C , Quail MA , Cowman AF , Turner CM , Rajandream MA , Kocken CH , Thomas AW , Newbold CI , Barrell BG , Berriman M
Ref : Nature , 455 :799 , 2008
Abstract : Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.
ESTHER : Pain_2008_Nature_455_799
PubMedSearch : Pain_2008_Nature_455_799
PubMedID: 18843368
Gene_locus related to this paper: plakh-b3kz42 , plakh-b3kz45 , plakh-b3l0y4 , plakh-b3l1r3 , plakh-b3l8u5 , plakh-b3l336 , plakh-b3l571 , plakh-b3la01 , plakh-b3lb44

Title : Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes - Sebaihia_2007_Genome.Res_17_1082
Author(s) : Sebaihia M , Peck MW , Minton NP , Thomson NR , Holden MT , Mitchell WJ , Carter AT , Bentley SD , Mason DR , Crossman L , Paul CJ , Ivens A , Wells-Bennik MH , Davis IJ , Cerdeno-Tarraga AM , Churcher C , Quail MA , Chillingworth T , Feltwell T , Fraser A , Goodhead I , Hance Z , Jagels K , Larke N , Maddison M , Moule S , Mungall K , Norbertczak H , Rabbinowitsch E , Sanders M , Simmonds M , White B , Whithead S , Parkhill J
Ref : Genome Res , 17 :1082 , 2007
Abstract : Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically and physiologically distinct groups of bacteria that share the ability to produce botulinum neurotoxin, the most poisonous toxin known to man, and the causative agent of botulism, a severe disease of humans and animals. We report here the complete genome sequence of a representative of Group I (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19 predicted genes, respectively. Consistent with the proteolytic phenotype of this strain, the genome harbors a large number of genes encoding secreted proteases and enzymes involved in uptake and metabolism of amino acids. The genome also reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a significant lack of recently acquired DNA, indicating a stable genomic content, in strong contrast to the fluid genome of Clostridium difficile, which can form longer-term relationships with its host. Overall, the genome indicates that C. botulinum is adapted to a saprophytic lifestyle both in soil and aquatic environments. This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues.
ESTHER : Sebaihia_2007_Genome.Res_17_1082
PubMedSearch : Sebaihia_2007_Genome.Res_17_1082
PubMedID: 17519437
Gene_locus related to this paper: clobh-A5I3I2 , clobh-A51055 , clob1-a7fqm2 , clob1-a7fv94 , clobl-a7gbn0 , clobh-pip , clobh-a5i3m0

Title : The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081 - Thomson_2006_PLoS.Genet_2_e206
Author(s) : Thomson NR , Howard S , Wren BW , Holden MT , Crossman L , Challis GL , Churcher C , Mungall K , Brooks K , Chillingworth T , Feltwell T , Abdellah Z , Hauser H , Jagels K , Maddison M , Moule S , Sanders M , Whitehead S , Quail MA , Dougan G , Parkhill J , Prentice MB
Ref : PLoS Genet , 2 :e206 , 2006
Abstract : The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens.
ESTHER : Thomson_2006_PLoS.Genet_2_e206
PubMedSearch : Thomson_2006_PLoS.Genet_2_e206
PubMedID: 17173484
Gene_locus related to this paper: yere8-a1jik0 , yere8-a1jmx1 , yere8-a1jrp7 , yere8-bioh , yere8-menh , yere8-y3204 , yeren-fes , yeren-YPLA , yeren-YqiA , yermo-c4sfz7 , yerpe-y1616 , yerpe-YPO1501 , yerbe-c4rym7

Title : The genome of Rhizobium leguminosarum has recognizable core and accessory components - Young_2006_Genome.Biol_7_R34
Author(s) : Young JP , Crossman LC , Johnston AW , Thomson NR , Ghazoui ZF , Hull KH , Wexler M , Curson AR , Todd JD , Poole PS , Mauchline TH , East AK , Quail MA , Churcher C , Arrowsmith C , Cherevach I , Chillingworth T , Clarke K , Cronin A , Davis P , Fraser A , Hance Z , Hauser H , Jagels K , Moule S , Mungall K , Norbertczak H , Rabbinowitsch E , Sanders M , Simmonds M , Whitehead S , Parkhill J
Ref : Genome Biol , 7 :R34 , 2006
Abstract : BACKGROUND: Rhizobium leguminosarum is an alpha-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. RESULTS: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. CONCLUSION: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.
ESTHER : Young_2006_Genome.Biol_7_R34
PubMedSearch : Young_2006_Genome.Biol_7_R34
PubMedID: 16640791
Gene_locus related to this paper: rhiec-q2k7y0 , rhiec-q2k107 , rhiec-q2kav5 , rhiec-q2ke86 , rhil3-q1m3b7 , rhil3-q1m3u0 , rhil3-q1m4b4 , rhil3-q1m4e5 , rhil3-q1m4g3 , rhil3-q1m4h0 , rhil3-q1m5k0 , rhil3-q1m5s6 , rhil3-q1m6q0 , rhil3-q1m6u8 , rhil3-q1m6w8 , rhil3-q1m7c2 , rhil3-q1m7c3 , rhil3-q1m7i2 , rhil3-q1m7n3 , rhil3-q1m7q9 , rhil3-q1m7r8 , rhil3-q1m8d0 , rhil3-q1m8u4 , rhil3-q1m9d6 , rhil3-q1m9i6 , rhil3-q1m347 , rhil3-q1m571 , rhil3-q1m580 , rhil3-q1m672 , rhil3-q1m812 , rhil3-q1m841 , rhil3-q1m917 , rhil3-q1m919 , rhil3-q1mbv4 , rhil3-q1mbz5 , rhil3-q1mc48 , rhil3-q1mcr4 , rhil3-q1md19 , rhil3-q1mdd8 , rhil3-q1me05 , rhil3-q1mee4 , rhil3-q1mel6 , rhil3-q1men7 , rhil3-q1mf17 , rhil3-q1mf73 , rhil3-q1mf76 , rhil3-q1mfb0 , rhil3-q1mfp5 , rhil3-q1mg17 , rhil3-q1mg51 , rhil3-q1mg97 , rhil3-q1mgh3 , rhil3-q1mgh5 , rhil3-q1mgu7 , rhil3-q1mgx5 , rhil3-q1mh67 , rhil3-q1mhh7 , rhil3-q1mhz8 , rhil3-q1mi67 , rhil3-q1mi98 , rhil3-q1mia3 , rhil3-q1mig2 , rhil3-q1miz0 , rhil3-q1mj26 , rhil3-q1mj65 , rhil3-q1mjs2 , rhil3-q1mjx4 , rhil3-q1mk84 , rhil3-q1mkk8 , rhil3-q1mli7 , rhil3-q1mlj7 , rhil3-q1mm33 , rhil3-q1mmf9 , rhil3-q1mmp7 , rhil3-q1mmx0 , rhil3-q1mn42 , rhile-Q93EA8 , rhils-c6axl5 , rhils-c6b1w7 , rhilw-b5zrm4 , rhilw-b5zs97 , rhilv-j0vcs5

Title : The genome of the social amoeba Dictyostelium discoideum - Eichinger_2005_Nature_435_43
Author(s) : Eichinger L , Pachebat JA , Glockner G , Rajandream MA , Sucgang R , Berriman M , Song J , Olsen R , Szafranski K , Xu Q , Tunggal B , Kummerfeld S , Madera M , Konfortov BA , Rivero F , Bankier AT , Lehmann R , Hamlin N , Davies R , Gaudet P , Fey P , Pilcher K , Chen G , Saunders D , Sodergren E , Davis P , Kerhornou A , Nie X , Hall N , Anjard C , Hemphill L , Bason N , Farbrother P , Desany B , Just E , Morio T , Rost R , Churcher C , Cooper J , Haydock S , van Driessche N , Cronin A , Goodhead I , Muzny D , Mourier T , Pain A , Lu M , Harper D , Lindsay R , Hauser H , James K , Quiles M , Madan Babu M , Saito T , Buchrieser C , Wardroper A , Felder M , Thangavelu M , Johnson D , Knights A , Loulseged H , Mungall K , Oliver K , Price C , Quail MA , Urushihara H , Hernandez J , Rabbinowitsch E , Steffen D , Sanders M , Ma J , Kohara Y , Sharp S , Simmonds M , Spiegler S , Tivey A , Sugano S , White B , Walker D , Woodward J , Winckler T , Tanaka Y , Shaulsky G , Schleicher M , Weinstock G , Rosenthal A , Cox EC , Chisholm RL , Gibbs R , Loomis WF , Platzer M , Kay RR , Williams J , Dear PH , Noegel AA , Barrell B , Kuspa A
Ref : Nature , 435 :43 , 2005
Abstract : The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
ESTHER : Eichinger_2005_Nature_435_43
PubMedSearch : Eichinger_2005_Nature_435_43
PubMedID: 15875012
Gene_locus related to this paper: dicdi-abhd , dicdi-ACHE , dicdi-apra , dicdi-cinbp , dicdi-CMBL , dicdi-crysp , dicdi-DPOA , dicdi-P90528 , dicdi-ppme1 , dicdi-Q8MYE7 , dicdi-q54cf7 , dicdi-q54cl7 , dicdi-q54cm0 , dicdi-q54ct5 , dicdi-q54cu1 , dicdi-q54d54 , dicdi-q54d66 , dicdi-q54dj5 , dicdi-q54dy7 , dicdi-q54ek1 , dicdi-q54eq6 , dicdi-q54et1 , dicdi-q54et7 , dicdi-q54f01 , dicdi-q54g24 , dicdi-q54g47 , dicdi-q54gi7 , dicdi-q54gw5 , dicdi-q54gx3 , dicdi-q54h23 , dicdi-q54h73 , dicdi-q54i38 , dicdi-q54ie5 , dicdi-q54in4 , dicdi-q54kz1 , dicdi-q54l36 , dicdi-q54li1 , dicdi-q54m29 , dicdi-q54n21 , dicdi-q54n35 , dicdi-q54n85 , dicdi-q54qe7 , dicdi-q54qi3 , dicdi-q54qk2 , dicdi-q54rl3 , dicdi-q54rl8 , dicdi-q54sy6 , dicdi-q54sz3 , dicdi-q54t49 , dicdi-q54t91 , dicdi-q54th2 , dicdi-q54u01 , dicdi-q54vc2 , dicdi-q54vw1 , dicdi-q54xe3 , dicdi-q54xl3 , dicdi-q54xu1 , dicdi-q54xu2 , dicdi-q54y48 , dicdi-q54yd0 , dicdi-q54ye0 , dicdi-q54yl1 , dicdi-q54yr8 , dicdi-q54z90 , dicdi-q55bx3 , dicdi-q55d01 , dicdi-q55d81 , dicdi-q55du6 , dicdi-q55eu1 , dicdi-q55eu8 , dicdi-q55fk4 , dicdi-q55gk7 , dicdi-Q54ZA6 , dicdi-q86h82 , dicdi-Q86HC9 , dicdi-Q86HM5 , dicdi-Q86HM6 , dicdi-q86iz7 , dicdi-q86jb6 , dicdi-Q86KU7 , dicdi-q550s3 , dicdi-q552c0 , dicdi-q553t5 , dicdi-q555e5 , dicdi-q555h0 , dicdi-q555h1 , dicdi-q557k5 , dicdi-q558u2 , dicdi-Q869Q8 , dicdi-u554 , dicdi-y9086 , dicdi-q54r44 , dicdi-f172a

Title : The genome of the African trypanosome Trypanosoma brucei - Berriman_2005_Science_309_416
Author(s) : Berriman M , Ghedin E , Hertz-Fowler C , Blandin G , Renauld H , Bartholomeu DC , Lennard NJ , Caler E , Hamlin NE , Haas B , Bohme U , Hannick L , Aslett MA , Shallom J , Marcello L , Hou L , Wickstead B , Alsmark UC , Arrowsmith C , Atkin RJ , Barron AJ , Bringaud F , Brooks K , Carrington M , Cherevach I , Chillingworth TJ , Churcher C , Clark LN , Corton CH , Cronin A , Davies RM , Doggett J , Djikeng A , Feldblyum T , Field MC , Fraser A , Goodhead I , Hance Z , Harper D , Harris BR , Hauser H , Hostetler J , Ivens A , Jagels K , Johnson D , Johnson J , Jones K , Kerhornou AX , Koo H , Larke N , Landfear S , Larkin C , Leech V , Line A , Lord A , MacLeod A , Mooney PJ , Moule S , Martin DM , Morgan GW , Mungall K , Norbertczak H , Ormond D , Pai G , Peacock CS , Peterson J , Quail MA , Rabbinowitsch E , Rajandream MA , Reitter C , Salzberg SL , Sanders M , Schobel S , Sharp S , Simmonds M , Simpson AJ , Tallon L , Turner CM , Tait A , Tivey AR , Van Aken S , Walker D , Wanless D , Wang S , White B , White O , Whitehead S , Woodward J , Wortman J , Adams MD , Embley TM , Gull K , Ullu E , Barry JD , Fairlamb AH , Opperdoes F , Barrell BG , Donelson JE , Hall N , Fraser CM , Melville SE , El-Sayed NM
Ref : Science , 309 :416 , 2005
Abstract : African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.
ESTHER : Berriman_2005_Science_309_416
PubMedSearch : Berriman_2005_Science_309_416
PubMedID: 16020726
Gene_locus related to this paper: tryb2-q6h9e3 , tryb2-q6ha27 , tryb2-q38cd5 , tryb2-q38cd6 , tryb2-q38cd7 , tryb2-q38dc1 , tryb2-q38de4 , tryb2-q38ds6 , tryb2-q38dx1 , tryb2-q380z6 , tryb2-q382c1 , tryb2-q382l4 , tryb2-q383a9 , tryb2-q386e3 , tryb2-q387r7 , tryb2-q388n1 , tryb2-q389w3 , trybr-PEPTB , trycr-q4cq28 , trycr-q4cq94 , trycr-q4cq95 , trycr-q4cq96 , trycr-q4csm0 , trycr-q4cwv3 , trycr-q4cx66 , trycr-q4cxr6 , trycr-q4cyc5 , trycr-q4cyf6 , trycr-q4d3a2 , trycr-q4d3x3 , trycr-q4d3y4 , trycr-q4d6h1 , trycr-q4d8h8 , trycr-q4d8h9 , trycr-q4d8i0 , trycr-q4d786 , trycr-q4d975 , trycr-q4da08 , trycr-q4dap6 , trycr-q4dbm2 , trycr-q4dbn1 , trycr-q4ddw7 , trycr-q4de42 , trycr-q4dhn8 , trycr-q4dkk8 , trycr-q4dkk9 , trycr-q4dm56 , trycr-q4dqa6 , trycr-q4dt91 , trycr-q4dvp2 , trycr-q4dw34 , trycr-q4dwm3 , trycr-q4dy49 , trycr-q4dy82 , trycr-q4dzp6 , trycr-q4e3m8 , trycr-q4e4t5 , trycr-q4e5d1 , trycr-q4e5z2

Title : The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation - Thomson_2005_Genome.Res_15_629
Author(s) : Thomson NR , Yeats C , Bell K , Holden MT , Bentley SD , Livingstone M , Cerdeno-Tarraga AM , Harris B , Doggett J , Ormond D , Mungall K , Clarke K , Feltwell T , Hance Z , Sanders M , Quail MA , Price C , Barrell BG , Parkhill J , Longbottom D
Ref : Genome Res , 15 :629 , 2005
Abstract : The obligate intracellular bacterial pathogen Chlamydophila abortus strain S26/3 (formerly the abortion subtype of Chlamydia psittaci) is an important cause of late gestation abortions in ruminants and pigs. Furthermore, although relatively rare, zoonotic infection can result in acute illness and miscarriage in pregnant women. The complete genome sequence was determined and shows a high level of conservation in both sequence and overall gene content in comparison to other Chlamydiaceae. The 1,144,377-bp genome contains 961 predicted coding sequences, 842 of which are conserved with those of Chlamydophila caviae and Chlamydophila pneumoniae. Within this conserved Cp. abortus core genome we have identified the major regions of variation and have focused our analysis on these loci, several of which were found to encode highly variable protein families, such as TMH/Inc and Pmp families, which are strong candidates for the source of diversity in host tropism and disease causation in this group of organisms. Significantly, Cp. abortus lacks any toxin genes, and also lacks genes involved in tryptophan metabolism and nucleotide salvaging (guaB is present as a pseudogene), suggesting that the genetic basis of niche adaptation of this species is distinct from those previously proposed for other chlamydial species.
ESTHER : Thomson_2005_Genome.Res_15_629
PubMedSearch : Thomson_2005_Genome.Res_15_629
PubMedID: 15837807
Gene_locus related to this paper: chlab-q5l5y2 , chlab-q5l6t6

Title : Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance - Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
Author(s) : Holden MT , Feil EJ , Lindsay JA , Peacock SJ , Day NP , Enright MC , Foster TJ , Moore CE , Hurst L , Atkin R , Barron A , Bason N , Bentley SD , Chillingworth C , Chillingworth T , Churcher C , Clark L , Corton C , Cronin A , Doggett J , Dowd L , Feltwell T , Hance Z , Harris B , Hauser H , Holroyd S , Jagels K , James KD , Lennard N , Line A , Mayes R , Moule S , Mungall K , Ormond D , Quail MA , Rabbinowitsch E , Rutherford K , Sanders M , Sharp S , Simmonds M , Stevens K , Whitehead S , Barrell BG , Spratt BG , Parkhill J
Ref : Proc Natl Acad Sci U S A , 101 :9786 , 2004
Abstract : Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent and drug-resistant strains, presenting a major and constantly changing clinical challenge. We sequenced the approximately 2.8-Mbp genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a representative of an invasive community-acquired methicillin-susceptible S. aureus clone (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of clinically important S. aureus genomes and to identify regions affecting virulence and drug resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse S. aureus strain sequenced to date: approximately 6% of the genome is novel compared with other published genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible, but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated SCC(476)), which is integrated at the same site on the chromosome as SCCmec elements in MRSA strains but encodes a putative fusidic acid resistance protein. The crucial role that accessory elements play in the rapid evolution of S. aureus is clearly illustrated by comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired strain; the differential distribution of large mobile elements carrying virulence and drug-resistance determinants may be responsible for the clinically important phenotypic differences in these strains.
ESTHER : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
PubMedSearch : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_9786
PubMedID: 15213324
Gene_locus related to this paper: staau-d2feb3 , staau-d2uin3 , staau-LIP , staau-lipas , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0011 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2367 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2594

Title : Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors - Bell_2004_Proc.Natl.Acad.Sci.U.S.A_101_11105
Author(s) : Bell KS , Sebaihia M , Pritchard L , Holden MT , Hyman LJ , Holeva MC , Thomson NR , Bentley SD , Churcher LJ , Mungall K , Atkin R , Bason N , Brooks K , Chillingworth T , Clark K , Doggett J , Fraser A , Hance Z , Hauser H , Jagels K , Moule S , Norbertczak H , Ormond D , Price C , Quail MA , Sanders M , Walker D , Whitehead S , Salmond GP , Birch PR , Parkhill J , Toth IK
Ref : Proc Natl Acad Sci U S A , 101 :11105 , 2004
Abstract : The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains an overrepresentation of pathogenicity determinants, including possible horizontally acquired gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To investigate whether these gene clusters play a role in the disease process, an arrayed set of insertional mutants was generated, and mutations were identified. Plant bioassays showed that these mutants were significantly reduced in virulence, demonstrating both the presence of novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding our understanding of phytopathogenicity in the Enterobacteriaceae.
ESTHER : Bell_2004_Proc.Natl.Acad.Sci.U.S.A_101_11105
PubMedSearch : Bell_2004_Proc.Natl.Acad.Sci.U.S.A_101_11105
PubMedID: 15263089
Gene_locus related to this paper: erwct-q6czi2 , erwct-q6czl9 , erwct-q6czu1 , erwct-q6d0l3 , erwct-q6d1e3 , erwct-q6d1l9 , erwct-q6d2k4 , erwct-q6d2x2 , erwct-q6d3m9 , erwct-q6d4b7 , erwct-q6d6t8 , erwct-q6d7j1 , erwct-q6d7p5 , erwct-q6d7w3 , erwct-q6d8k2 , erwct-q6d8q7 , erwct-q6d9l2 , erwct-q6d041 , erwct-q6d134 , erwct-q6d207 , erwct-q6d508 , erwct-q6d615 , erwct-q6d673 , erwct-q6d739.1 , erwct-q6d739.2 , erwct-q6d884 , erwct-q6da42 , erwct-q6da66 , erwct-q6dac1 , erwct-q6dar9 , erwct-Y3465

Title : Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei - Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
Author(s) : Holden MT , Titball RW , Peacock SJ , Cerdeno-Tarraga AM , Atkins T , Crossman LC , Pitt T , Churcher C , Mungall K , Bentley SD , Sebaihia M , Thomson NR , Bason N , Beacham IR , Brooks K , Brown KA , Brown NF , Challis GL , Cherevach I , Chillingworth T , Cronin A , Crossett B , Davis P , DeShazer D , Feltwell T , Fraser A , Hance Z , Hauser H , Holroyd S , Jagels K , Keith KE , Maddison M , Moule S , Price C , Quail MA , Rabbinowitsch E , Rutherford K , Sanders M , Simmonds M , Songsivilai S , Stevens K , Tumapa S , Vesaratchavest M , Whitehead S , Yeats C , Barrell BG , Oyston PC , Parkhill J
Ref : Proc Natl Acad Sci U S A , 101 :14240 , 2004
Abstract : Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species.
ESTHER : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
PubMedSearch : Holden_2004_Proc.Natl.Acad.Sci.U.S.A_101_14240
PubMedID: 15377794
Gene_locus related to this paper: burma-a5j5w8 , burma-a5tj72 , burma-a5tq93 , burma-metx , burma-q62a61 , burma-q62ar2.1 , burma-q62ar2.2 , burma-q62ax8 , burma-q62b60 , burma-q62b79 , burma-q62bh9 , burma-q62bl4 , burma-q62bl7 , burma-q62c00 , burma-q62cg5 , burma-q62d41 , burma-q62d56 , burma-q62d83 , burma-q62dg2 , burma-q62du7 , burma-q62e67 , burma-q62eb8 , burma-q62ed8 , burma-q62f28 , burma-q62fx7 , burma-q62g26 , burma-q62gx9 , burma-q62gy2 , burma-q62hq2 , burma-q62i62 , burma-q62ib8 , burma-q62ie8 , burma-q62j07 , burma-q62j15 , burma-q62jn5 , burma-q62jy7 , burma-q62kb7 , burma-q62kg0 , burma-q62kh9 , burma-q62lp7 , burma-q62m40 , burma-q62mc3 , burma-q62mf4 , burma-q62mq7 , burma-q629m1 , burma-q629p4 , burma-q629u0 , burp1-q3jvq2 , burps-a4lm41 , burps-q3v7s4 , burps-q63hx2 , burps-q63i95 , burps-q63im5 , burps-q63is4 , burps-q63ja6 , burps-q63ja9 , burps-q63jh5 , burps-q63l17 , burps-q63l41 , burps-q63l44 , burps-q63lt9 , burps-q63me1 , burps-q63mj7 , burps-q63mj8 , burps-q63mn8 , burps-q63mr2 , burps-q63n52 , burps-q63p18 , burps-q63p99 , burps-q63ug2 , burps-q63ug5 , burps-q63xf9 , burps-q63y36 , burps-q63y45 , burps-q63y52 , burps-q63y59 , burta-q2t474 , burps-hboh

Title : Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica - Parkhill_2003_Nat.Genet_35_32
Author(s) : Parkhill J , Sebaihia M , Preston A , Murphy LD , Thomson N , Harris DE , Holden MT , Churcher CM , Bentley SD , Mungall KL , Cerdeno-Tarraga AM , Temple L , James K , Harris B , Quail MA , Achtman M , Atkin R , Baker S , Basham D , Bason N , Cherevach I , Chillingworth T , Collins M , Cronin A , Davis P , Doggett J , Feltwell T , Goble A , Hamlin N , Hauser H , Holroyd S , Jagels K , Leather S , Moule S , Norberczak H , O'Neil S , Ormond D , Price C , Rabbinowitsch E , Rutter S , Sanders M , Saunders D , Seeger K , Sharp S , Simmonds M , Skelton J , Squares R , Squares S , Stevens K , Unwin L , Whitehead S , Barrell BG , Maskell DJ
Ref : Nat Genet , 35 :32 , 2003
Abstract : Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica are closely related Gram-negative beta-proteobacteria that colonize the respiratory tracts of mammals. B. pertussis is a strict human pathogen of recent evolutionary origin and is the primary etiologic agent of whooping cough. B. parapertussis can also cause whooping cough, and B. bronchiseptica causes chronic respiratory infections in a wide range of animals. We sequenced the genomes of B. bronchiseptica RB50 (5,338,400 bp; 5,007 predicted genes), B. parapertussis 12822 (4,773,551 bp; 4,404 genes) and B. pertussis Tohama I (4,086,186 bp; 3,816 genes). Our analysis indicates that B. parapertussis and B. pertussis are independent derivatives of B. bronchiseptica-like ancestors. During the evolution of these two host-restricted species there was large-scale gene loss and inactivation; host adaptation seems to be a consequence of loss, not gain, of function, and differences in virulence may be related to loss of regulatory or control functions.
ESTHER : Parkhill_2003_Nat.Genet_35_32
PubMedSearch : Parkhill_2003_Nat.Genet_35_32
PubMedID: 12910271
Gene_locus related to this paper: borbr-BB0273 , borbr-BB0570 , borbr-BB0670 , borbr-BB1064 , borbr-BB1079 , borbr-BB1247 , borbr-BB1498 , borbr-BB2718 , borbr-BB4129 , borbr-BB4247 , borbr-MHPC , borbr-q7wdw1 , borbr-q7wiz8 , borbr-q7wk25 , borbr-q7wmc2 , borbr-q7wpd9 , borpa-q7w3f3 , borpa-q7w9v8 , borpe-BIOH , borpe-BP0300 , borpe-BP2114 , borpe-BP2146 , borpe-BP2511 , borpe-BP3096 , borpe-BP3623 , borpe-BP3691 , borpe-CATD2 , borpe-METX , borpe-O30449 , borpe-PHBC , borpe-q7vsl4 , borpe-q7vt07 , borpe-q7vtg0 , borpe-q7vtv2 , borpe-q7vus4 , borpe-q7vuv4 , borpe-q7vv11 , borpe-q7vv48 , borpe-q7vvf6 , borpe-q7vwu4 , borpe-q7vyn0 , borpe-q7vyq4 , borpe-q7vz26 , borpe-q7vzb4 , borpe-q7vzj6 , borpe-q7w073

Title : Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13 - Hall_2002_Nature_419_527
Author(s) : Hall N , Pain A , Berriman M , Churcher C , Harris B , Harris D , Mungall K , Bowman S , Atkin R , Baker S , Barron A , Brooks K , Buckee CO , Burrows C , Cherevach I , Chillingworth C , Chillingworth T , Christodoulou Z , Clark L , Clark R , Corton C , Cronin A , Davies R , Davis P , Dear P , Dearden F , Doggett J , Feltwell T , Goble A , Goodhead I , Gwilliam R , Hamlin N , Hance Z , Harper D , Hauser H , Hornsby T , Holroyd S , Horrocks P , Humphray S , Jagels K , James KD , Johnson D , Kerhornou A , Knights A , Konfortov B , Kyes S , Larke N , Lawson D , Lennard N , Line A , Maddison M , McLean J , Mooney P , Moule S , Murphy L , Oliver K , Ormond D , Price C , Quail MA , Rabbinowitsch E , Rajandream MA , Rutter S , Rutherford KM , Sanders M , Simmonds M , Seeger K , Sharp S , Smith R , Squares R , Squares S , Stevens K , Taylor K , Tivey A , Unwin L , Whitehead S , Woodward J , Sulston JE , Craig A , Newbold C , Barrell BG
Ref : Nature , 419 :527 , 2002
Abstract : Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.
ESTHER : Hall_2002_Nature_419_527
PubMedSearch : Hall_2002_Nature_419_527
PubMedID: 12368867
Gene_locus related to this paper: plaf7-c0h4q4 , plafa-MAL6P1.135 , plafa-PFD0185C , plafa-PFI1775W , plafa-PFI1800W

Title : Structure and Function of Cholinesterases from Agnathans and Cephalochordates -
Author(s) : Pezzementi L , Sutherland D , Sanders M , Soong W , Milner D , McClellan JS , Sapp M , Coblentz WB , Rulewicz G , Merritt S
Ref : In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases , (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp. :105 , 1998

Title : Two cholinesterase activities and genes are present in amphioxus - Sutherland_1997_J.Exp.Zool_277_213
Author(s) : Sutherland D , McClellan JS , Milner D , Soong W , Axon N , Sanders M , Hester A , Kao YH , Poczatek T , Routt S , Pezzementi L
Ref : Journal of Experimental Zoology , 277 :213 , 1997
Abstract : To obtain information about the evolution of the cholinesterases, acetylcholinesterase (AChE) and butyrylcholinesterase (BCHE) in the vertebrates, we investigated the cholinesterase (ChE) activity of the cephalochordate amphioxus (Branchiostoma floridae and Branchiostoma lanceolatum). On the basis of evidence from enzymology, pharmacology, and molecular biology, we conclude that amphioxus possesses two ChE activities and two ChE genes. Two covalent inhibitors of cholinesterases were able to pharmacologically isolate the two activities as drug-sensitive ChE and drug-resistant ChE. Kinetically, in terms of substrate specificity, the drug-sensitive ChE resembles vertebrate AChE, and the drug-resistant ChE resembles the BCHE of cartilaginous and bony fish or the intermediate ChE of protostome invertebrates. We also used the polymerase chain reaction with degenerate oligonucleotide primers and genomic DNA to obtain clones of 1,574 and 1,011 bp corresponding to two cholinesterase genes from amphioxus, which we designated as ChE1 and ChE2. ChE2 codes for an enzyme with an acyl-binding pocket sequence, a portion of the protein that plays an important role in determining substrate specificity, typical of invertebrate ChE. ChE1, which contains a 503-bp intron, encodes a protein with a novel acyl binding site. Phylogenetic analysis of the sequences suggests that the two genes are a result of a duplication event in the lineage leading to amphioxus. We discuss the relevance of our results to the evolution of the cholinesterases in the chordates. Previously, we reported that amphioxus contained a single cholinesterase activity with properties intermediate to AChE and BCHE (Pezzementi et al. [1991] In: Cholinesterases: Structure, Function, Mechanism, Genetics and Cell Biology. J. Massouli et al., eds. ACS: Washington, D.C., pp. 24-31).
ESTHER : Sutherland_1997_J.Exp.Zool_277_213
PubMedSearch : Sutherland_1997_J.Exp.Zool_277_213
PubMedID: 9062997

Title : Biochemical and molecular characterization of acetylcholinesterase from the hagfish Myxine glutinosa - Sanders_1996_Comp.Biochem.Physiol.B.Biochem.Mol.Biol_115_97
Author(s) : Sanders M , Mathews B , Sutherland D , Soong W , Giles H , Pezzementi L
Ref : Comparative Biochemistry & Physiology B Biochem Mol Biol , 115 :97 , 1996
Abstract : To obtain information about the evolution of the cholinesterases, we investigated the cholinesterase activity of an agnathan vertebrate, the hagfish Myxine glutinosa. On the basis of evidence from enzymology, pharmacology, and molecular biology, we conclude that the cholinesterase activity is due to acetylcholinesterase (AChE). The enzyme hydrolyzes acetylthiocholine preferentially and exhibits substrate inhibition. The hydrolysis of both acetylthiocholine and butyrylthiocholine are inhibited in parallel by cholinesterase inhibitors, with the AChE-specific drug BW284c51 being the most potent; however, this drug and propidium, a peripheral anionic site ligand, are much weaker inhibitors of the hagfish enzyme than of Torpedo AChE. We used sequential extraction, collagenase digestion, and velocity sedimentation on sucrose gradients to determine that the AChE from the skeletal muscle of the hagfish is present in both globular and asymmetric forms. We also used the polymerase chain reaction with degenerate oligonucleotide probes and genomic DNA to obtain a 1 kb gene fragment for hagfish AChE. The enzyme has an acyl binding site typical of other vertebrate AChE, but lacks two aromatic residues implicated in the function of the peripheral anionic subsite. We discuss the relevance of our findings to the evolution of the cholinesterases in the vertebrates.
ESTHER : Sanders_1996_Comp.Biochem.Physiol.B.Biochem.Mol.Biol_115_97
PubMedSearch : Sanders_1996_Comp.Biochem.Physiol.B.Biochem.Mol.Biol_115_97
PubMedID: 8896335

Title : Structure and Function of Cholinesterase from Amphioxus -
Author(s) : Pezzementi L , Sanders M , Jenkins T , Holliman D , Toutant JP , Bradley RJ
Ref : In: Cholinesterases: Structure, Function, Mechanism, Genetics, and Cell Biology , (Massoulie J, Barnard EA, Chatonnet A, Bacou F, Doctor BP, Quinn DM) American Chemical Society, Washington, DC :24 , 1991