Dutilh BE

References (4)

Title : Genome-wide study of the defective sucrose fermenter strain of Vibrio cholerae from the Latin American cholera epidemic - Garza_2012_PLoS.One_7_e37283
Author(s) : Garza DR , Thompson CC , Loureiro EC , Dutilh BE , Inada DT , Junior EC , Cardoso JF , Nunes MR , de Lima CP , Silvestre RV , Nunes KN , Santos EC , Edwards RA , Vicente AC , de Sa Morais LL
Ref : PLoS ONE , 7 :e37283 , 2012
Abstract : The 7th cholera pandemic reached Latin America in 1991, spreading from Peru to virtually all Latin American countries. During the late epidemic period, a strain that failed to ferment sucrose dominated cholera outbreaks in the Northern Brazilian Amazon region. In order to understand the genomic characteristics and the determinants of this altered sucrose fermenting phenotype, the genome of the strain IEC224 was sequenced. This paper reports a broad genomic study of this strain, showing its correlation with the major epidemic lineage. The potentially mobile genomic regions are shown to possess GC content deviation, and harbor the main V. cholera virulence genes. A novel bioinformatic approach was applied in order to identify the putative functions of hypothetical proteins, and was compared with the automatic annotation by RAST. The genome of a large bacteriophage was found to be integrated to the IEC224's alanine aminopeptidase gene. The presence of this phage is shown to be a common characteristic of the El Tor strains from the Latin American epidemic, as well as its putative ancestor from Angola. The defective sucrose fermenting phenotype is shown to be due to a single nucleotide insertion in the V. cholerae sucrose-specific transportation gene. This frame-shift mutation truncated a membrane protein, altering its structural pore-like conformation. Further, the identification of a common bacteriophage reinforces both the monophyletic and African-Origin hypotheses for the main causative agent of the 1991 Latin America cholera epidemics.
ESTHER : Garza_2012_PLoS.One_7_e37283
PubMedSearch : Garza_2012_PLoS.One_7_e37283
PubMedID: 22662140
Gene_locus related to this paper: vibch-VC1974 , vibch-y1892

Title : Nitrite-driven anaerobic methane oxidation by oxygenic bacteria - Ettwig_2010_Nature_464_543
Author(s) : Ettwig KF , Butler MK , Le Paslier D , Pelletier E , Mangenot S , Kuypers MM , Schreiber F , Dutilh BE , Zedelius J , de Beer D , Gloerich J , Wessels HJ , van Alen T , Luesken F , Wu ML , van de Pas-Schoonen KT , Op den Camp HJ , Janssen-Megens EM , Francoijs KJ , Stunnenberg H , Weissenbach J , Jetten MS , Strous M
Ref : Nature , 464 :543 , 2010
Abstract : Only three biological pathways are known to produce oxygen: photosynthesis, chlorate respiration and the detoxification of reactive oxygen species. Here we present evidence for a fourth pathway, possibly of considerable geochemical and evolutionary importance. The pathway was discovered after metagenomic sequencing of an enrichment culture that couples anaerobic oxidation of methane with the reduction of nitrite to dinitrogen. The complete genome of the dominant bacterium, named 'Candidatus Methylomirabilis oxyfera', was assembled. This apparently anaerobic, denitrifying bacterium encoded, transcribed and expressed the well-established aerobic pathway for methane oxidation, whereas it lacked known genes for dinitrogen production. Subsequent isotopic labelling indicated that 'M. oxyfera' bypassed the denitrification intermediate nitrous oxide by the conversion of two nitric oxide molecules to dinitrogen and oxygen, which was used to oxidize methane. These results extend our understanding of hydrocarbon degradation under anoxic conditions and explain the biochemical mechanism of a poorly understood freshwater methane sink. Because nitrogen oxides were already present on early Earth, our finding opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis.
ESTHER : Ettwig_2010_Nature_464_543
PubMedSearch : Ettwig_2010_Nature_464_543
PubMedID: 20336137
Gene_locus related to this paper: 9bact-d5mm47

Title : Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate - Datson_2007_BMC.Genomics_8_190
Author(s) : Datson NA , Morsink MC , Atanasova S , Armstrong VW , Zischler H , Schlumbohm C , Dutilh BE , Huynen MA , Waegele B , Ruepp A , de Kloet ER , Fuchs E
Ref : BMC Genomics , 8 :190 , 2007
Abstract : BACKGROUND: The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal model, the molecular tools for genetic analysis are extremely limited. RESULTS: Here we report the development of the first marmoset-specific oligonucleotide microarray (EUMAMA) containing probe sets targeting 1541 different marmoset transcripts expressed in hippocampus. These 1541 transcripts represent a wide variety of different functional gene classes. Hybridisation of the marmoset microarray with labelled RNA from hippocampus, cortex and a panel of 7 different peripheral tissues resulted in high detection rates of 85% in the neuronal tissues and on average 70% in the non-neuronal tissues. The expression profiles of the 2 neuronal tissues, hippocampus and cortex, were highly similar, as indicated by a correlation coefficient of 0.96. Several transcripts with a tissue-specific pattern of expression were identified. Besides the marmoset microarray we have generated 3215 ESTs derived from marmoset hippocampus, which have been annotated and submitted to GenBank [GenBank: EF214838-EF215447, EH380242-EH382846]. CONCLUSION: We have generated the first marmoset-specific DNA microarray and demonstrated its use to characterise large-scale gene expression profiles of hippocampus but also of other neuronal and non-neuronal tissues. In addition, we have generated a large collection of ESTs of marmoset origin, which are now available in the public domain. These new tools will facilitate molecular genetic research into this non-human primate animal model.
ESTHER : Datson_2007_BMC.Genomics_8_190
PubMedSearch : Datson_2007_BMC.Genomics_8_190
PubMedID: 17592630
Gene_locus related to this paper: calja-f7ia46

Title : Deciphering the evolution and metabolism of an anammox bacterium from a community genome - Strous_2006_Nature_440_790
Author(s) : Strous M , Pelletier E , Mangenot S , Rattei T , Lehner A , Taylor MW , Horn M , Daims H , Bartol-Mavel D , Wincker P , Barbe V , Fonknechten N , Vallenet D , Segurens B , Schenowitz-Truong C , Medigue C , Collingro A , Snel B , Dutilh BE , Op den Camp HJ , van der Drift C , Cirpus I , van de Pas-Schoonen KT , Harhangi HR , van Niftrik L , Schmid M , Keltjens J , van de Vossenberg J , Kartal B , Meier H , Frishman D , Huynen MA , Mewes HW , Weissenbach J , Jetten MS , Wagner M , Le Paslier D
Ref : Nature , 440 :790 , 2006
Abstract : Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.
ESTHER : Strous_2006_Nature_440_790
PubMedSearch : Strous_2006_Nature_440_790
PubMedID: 16598256
Gene_locus related to this paper: 9bact-q1py93 , 9bact-q1q3k9 , 9bact-q1q414