Hoede C

References (4)

Title : Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations - Rouxel_2011_Nat.Commun_2_202
Author(s) : Rouxel T , Grandaubert J , Hane JK , Hoede C , van de Wouw AP , Couloux A , Dominguez V , Anthouard V , Bally P , Bourras S , Cozijnsen AJ , Ciuffetti LM , Degrave A , Dilmaghani A , Duret L , Fudal I , Goodwin SB , Gout L , Glaser N , Linglin J , Kema GH , Lapalu N , Lawrence CB , May K , Meyer M , Ollivier B , Poulain J , Schoch CL , Simon A , Spatafora JW , Stachowiak A , Turgeon BG , Tyler BM , Vincent D , Weissenbach J , Amselem J , Quesneville H , Oliver RP , Wincker P , Balesdent MH , Howlett BJ
Ref : Nat Commun , 2 :202 , 2011
Abstract : Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
ESTHER : Rouxel_2011_Nat.Commun_2_202
PubMedSearch : Rouxel_2011_Nat.Commun_2_202
PubMedID: 21326234
Gene_locus related to this paper: lepmc-q6q891 , lepmj-e4zh04 , lepmj-e4ziv6 , lepmj-e4zju4 , lepmj-e4zqu4 , lepmj-e4zvh3 , lepmj-e4zvl4 , lepmj-e4zx66 , lepmj-e5a0i2 , lepmj-e5a510 , lepmj-e5aau5 , lepmj-e5acd1 , lepmj-e5a4g5 , lepmj-e4zhg2 , lepmj-e4zuw5 , lepmj-e5a2e0 , lepmj-e4zpv2 , lepmj-e4zxp4 , lepmj-e4zpy5 , lepmj-e5ae17 , lepmj-e4ziv2 , lepmj-e5a374 , lepmj-e5ab81 , lepmj-e4zgy1 , lepmj-e4zg43 , lepmj-kex1 , lepmj-cbpya

Title : Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism - Spanu_2010_Science_330_1543
Author(s) : Spanu PD , Abbott JC , Amselem J , Burgis TA , Soanes DM , Stuber K , Ver Loren van Themaat E , Brown JK , Butcher SA , Gurr SJ , Lebrun MH , Ridout CJ , Schulze-Lefert P , Talbot NJ , Ahmadinejad N , Ametz C , Barton GR , Benjdia M , Bidzinski P , Bindschedler LV , Both M , Brewer MT , Cadle-Davidson L , Cadle-Davidson MM , Collemare J , Cramer R , Frenkel O , Godfrey D , Harriman J , Hoede C , King BC , Klages S , Kleemann J , Knoll D , Koti PS , Kreplak J , Lopez-Ruiz FJ , Lu X , Maekawa T , Mahanil S , Micali C , Milgroom MG , Montana G , Noir S , O'Connell RJ , Oberhaensli S , Parlange F , Pedersen C , Quesneville H , Reinhardt R , Rott M , Sacristan S , Schmidt SM , Schon M , Skamnioti P , Sommer H , Stephens A , Takahara H , Thordal-Christensen H , Vigouroux M , Wessling R , Wicker T , Panstruga R
Ref : Science , 330 :1543 , 2010
Abstract : Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.
ESTHER : Spanu_2010_Science_330_1543
PubMedSearch : Spanu_2010_Science_330_1543
PubMedID: 21148392
Gene_locus related to this paper: blugr-d2cql4 , blug1-n1jlh9 , blug1-n1j5n4 , blug1-n1j9r9 , blug1-n1je34 , blug1-n1jkm5 , blug1-n1jhv6 , blug1-n1j8l0 , blug1-n1jqj7 , blug1-n1j543

Title : aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species - Lescat_2009_BMC.Microbiol_9_273
Author(s) : Lescat M , Hoede C , Clermont O , Garry L , Darlu P , Tuffery P , Denamur E , Picard B
Ref : BMC Microbiol , 9 :273 , 2009
Abstract : BACKGROUND: Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of Escherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B2 variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B1 variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene.
RESULTS: We identified the gene encoding esterase B as the acetyl-esterase gene (aes) using gene disruption. The analysis of aes nucleotide sequences in a panel of 78 reference strains, including the E. coli reference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed from aes sequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B1 and B2 by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link between aes and extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region of aes to be associated with virulence. CONCLUSION: Our findings suggest that aes does not play a direct role in the virulence of E. coli extraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.
ESTHER : Lescat_2009_BMC.Microbiol_9_273
PubMedSearch : Lescat_2009_BMC.Microbiol_9_273
PubMedID: 20040078
Gene_locus related to this paper: ecoli-Aes

Title : Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths - Touchon_2009_PLoS.Genet_5_e1000344
Author(s) : Touchon M , Hoede C , Tenaillon O , Barbe V , Baeriswyl S , Bidet P , Bingen E , Bonacorsi S , Bouchier C , Bouvet O , Calteau A , Chiapello H , Clermont O , Cruveiller S , Danchin A , Diard M , Dossat C , Karoui ME , Frapy E , Garry L , Ghigo JM , Gilles AM , Johnson J , Le Bouguenec C , Lescat M , Mangenot S , Martinez-Jehanne V , Matic I , Nassif X , Oztas S , Petit MA , Pichon C , Rouy Z , Ruf CS , Schneider D , Tourret J , Vacherie B , Vallenet D , Medigue C , Rocha EP , Denamur E
Ref : PLoS Genet , 5 :e1000344 , 2009
Abstract : The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.
ESTHER : Touchon_2009_PLoS.Genet_5_e1000344
PubMedSearch : Touchon_2009_PLoS.Genet_5_e1000344
PubMedID: 19165319
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C2429 , ecoli-C3633 , ecoli-C3636 , ecoli-C4836 , ecoli-d7xp23 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-IROD , ecoli-IROE , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-Z0347 , ecoli-Z1930 , ecoli-YfhR , ecout-q1r7l6 , escfe-e9z855 , yerpe-YBTT , ecolx-e0qx45