by Keyword: Genomics

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Sanchez-Herrero, J. F., Bernabeu, M., Prieto, A., Hüttener, M., Juárez, A., (2020). Gene duplications in the genomes of staphylococci and enterococci Frontiers in Molecular Biosciences 7, 160

Gene duplications are a feature of bacterial genomes. In the present work we analyze the extent of gene duplications in the genomes of three microorganisms that belong to the Firmicutes phylum and that are etiologic agents of several nosocomial infections: Staphylococcus aureus, Enterococcus faecium, and Enterococcus faecalis. In all three groups, there is an irregular distribution of duplications in the genomes of the strains analyzed. Whereas in some of the strains duplications are scarce, hundreds of duplications are present in others. In all three species, mobile DNA accounts for a large percentage of the duplicated genes: phage DNA in S. aureus, and plasmid DNA in the enterococci. Duplicates also include core genes. In all three species, a reduced group of genes is duplicated in all strains analyzed. Duplication of the deoC and rpmG genes is a hallmark of S. aureus genomes. Duplication of the gene encoding the PTS IIB subunit is detected in all enterococci genomes. In E. faecalis it is remarkable that the genomes of some strains encode duplicates of the prgB and prgU genes. They belong to the prgABCU cluster, which responds to the presence of the peptide pheromone cCF10 by expressing the surface adhesins PrgA, PrgB, and PrgC.

Keywords: Bacterial genomics, Enterococcus faecalis, Enterococcus faecium, Gene duplication, Staphylococcus aureus

Said Al-Tawaha, A.R.M., Singh, S., Singh, V., Kafeel, U., Naikoo, M.I., Kumari, A., Amanullah, I., Al-Tawaha, A.R., Qaisi, A.M., Khanum, S., Thangadurai, D, Sangeetha, J., Islam, S., Etesami, H., Kerkoub, N., Amrani, A., Labidi, Z., Maaref, H., Nasri, H., Sanmukh, S.G., Torrents, E. , (2020). Improving water use efficiency and nitrogen use efficiency in rice through breeding and genomics approaches Rice Research for Quality Improvement: Genomics and Genetic Engineering (ed. Roychoudhury, A.), Springer (Singapore, Singapore) Volume 2: Nutrient Biofortification and Herbicide and Biotic Stress Resistance in Rice, 307-337

Rice is a staple food of more than half of the world’s population; more than 3.5 billion inhabitants depend on rice for obtaining 20% of their daily calorie intake. Nitrogen is the most important for crop growth and yield potential. Indeed, nitrogen is essential to stimulate tillering, leaf growth, photosynthesis, and protein synthesis. Significant achievements have recently been observed at the molecular level in nitrogen use efficiency and water use efficiency in plants. In this chapter we will discuss the following issue: (i) definition of both nitrogen use efficiency and water use efficiency, (ii) genes responsible for nitrogen use efficiency and water use efficiency, (iii) best ways for improving water and nutrient use efficiency in rice, and (iv) optimizing nitrogen options for improving water and nitrogen use efficiency of rice under different water regimes.

Keywords: Rice, Water use efficiency, Nitrogen use efficiency, Breeding, Genomics approaches

Bolognesi, Benedetta, Faure, Andre J., Seuma, Mireia, Schmiedel, Jörrn M., Tartaglia, Gian Gaetano, Lehner, Ben, (2019). The mutational landscape of a prion-like domain Nature Communications 10, (1), 4162

Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS). However, whether aggregates cause cellular toxicity is still not clear, even in simpler cellular systems. We reasoned that deep mutagenesis might be a powerful approach to disentangle the relationship between aggregation and toxicity. We generated >50,000 mutations in the prion-like domain (PRD) of TDP-43 and quantified their toxicity in yeast cells. Surprisingly, mutations that increase hydrophobicity and aggregation strongly decrease toxicity. In contrast, toxic variants promote the formation of dynamic liquid-like condensates. Mutations have their strongest effects in a hotspot that genetic interactions reveal to be structured in vivo, illustrating how mutagenesis can probe the in vivo structures of unstructured proteins. Our results show that aggregation of TDP-43 is not harmful but protects cells, most likely by titrating the protein away from a toxic liquid-like phase.

Keywords: Computational biology and bioinformatics, Genomics, Mechanisms of disease, Neurodegeneration, Systems biology