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Ettamimi Sara Carlier Jorge D. Cox Cymon J. Elamine Youssef Hammani Khalil Ghazal Hassan Costa Maria C. 《Extremophiles : life under extreme conditions》2019,23(6):821-834
Extremophiles - The prokaryotic communities of water bodies contaminated by acid mine drainage from the São Domingos mining area in southern Portugal were analyzed using a meta-taxonomics... 相似文献
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Using a cDNA probe, two genomic clones were obtained encoding the human tissue inhibitor of metalloproteinases-3 (TIMP-3). Analysis of these clones showed that they contained four distal exons and three introns of the gene. Although the intron-exon structure is similar to that of the timpl gene, the first intron of the timp3 gene is much longer, being at least 17.5 kb in size. 相似文献
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Valentin Loux Mahendra Mariadassou Sintia Almeida Hélène Chiapello Amal Hammani Julien Buratti Annie Gendrault Valérie Barbe Jean-Marc Aury Stéphanie-Marie Deutsch Sandrine Parayre Marie-No?lle Madec Victoria Chuat Gwena?l Jan Pierre Peterlongo Vasco Azevedo Yves Le Loir Hélène Falentin 《BMC genomics》2015,16(1)
Background
Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties. PF is also extremely adaptable to several ecological niches and can grow on a variety of carbon and nitrogen sources. The aim of this work was to discover the genetic basis for strain-dependent traits related to its ability to use specific carbon sources. High-throughput sequencing technologies were ideal for this purpose as they have the potential to decipher genomic diversity at a moderate cost.Results
21 strains of PF were sequenced and the genomes were assembled de novo. Scaffolds were ordered by comparison with the complete reference genome CIRM-BIA1, obtained previously using traditional Sanger sequencing. Automatic functional annotation and manual curation were performed. Each gene was attributed to either the core genome or an accessory genome. The ability of the 21 strains to degrade 50 different sugars was evaluated. Thirty-three sugars were degraded by none of the sequenced strains whereas eight sugars were degraded by all of them. The corresponding genes were present in the core genome. Lactose, melibiose and xylitol were only used by some strains. In this case, the presence/absence of genes responsible for carbon uptake and degradation correlated well with the phenotypes, with the exception of xylitol. Furthermore, the simultaneous presence of these genes was in line the metabolic pathways described previously in other species. We also considered the genetic origin (transduction, rearrangement) of the corresponding genomic islands. Ribose and gluconate were degraded to a greater or lesser extent (quantitative phenotype) by some strains. For these sugars, the phenotypes could not be explained by the presence/absence of a gene but correlated with the premature appearance of a stop codon interrupting protein synthesis and preventing the catabolism of corresponding carbon sources.Conclusion
These results illustrate (i) the power of correlation studies to discover the genetic basis of binary strain-dependent traits, and (ii) the plasticity of PF chromosomes, probably resulting from horizontal transfers, duplications, transpositions and an accumulation of mutations. Knowledge of the genetic basis of nitrogen and sugar degradation opens up new strategies for the screening of PF strain collections to enable optimum cheese starter, probiotic and white biotechnology applications.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1467-7) contains supplementary material, which is available to authorized users. 相似文献9.
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