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Analysis of the core genome and pangenome of Pseudomonas putida

Udaondo, Zulema ; Molina, Lázaro ; Segura, Ana ; Duque, Estrella ; Ramos, Juan L.

Environmental microbiology, 2016-10, Vol.18 (10), p.3268-3283 [Periódico revisado por pares]

England: Blackwell Publishing Ltd

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  • Título:
    Analysis of the core genome and pangenome of Pseudomonas putida
  • Autor: Udaondo, Zulema ; Molina, Lázaro ; Segura, Ana ; Duque, Estrella ; Ramos, Juan L.
  • Assuntos: Biological Transport - genetics ; Biosynthesis ; Carbon - metabolism ; Energy Metabolism - genetics ; Genome, Bacterial - genetics ; Genomes ; Membrane Transport Proteins - genetics ; Membrane Transport Proteins - metabolism ; Metabolism ; Open Reading Frames ; Pseudomonas aeruginosa ; Pseudomonas putida ; Pseudomonas putida - genetics ; Pseudomonas putida - metabolism
  • É parte de: Environmental microbiology, 2016-10, Vol.18 (10), p.3268-3283
  • Notas: istex:871162CF8A637F95C2CE6DFD954E93FE5C2BC745
    Fig. S1. Maximum likelihood phylogenetic tree of the core genes from nine Pseudomonas putida strains based on a multilocus sequence alignment of 3326 orthologous group of genes. Bootstrap values of 500 replication are shown at each node.Fig. S2. Flow diagram for glucose metabolism in Pseudomonas putida. Only enzymes belonging to the core gene set were used to prepare the diagram.Fig. S3. Representation of the tricarboxylic acid cycle (black line) and glyoxylate cycle (green line) in Pseudomonas putida core genome. Only enzymes belonging to the core genes set were used to prepare the flow diagram.Fig. S4. Representation of the GO 'Cellular component' core genome mutants. The pie chart shows the percentage of activities presents in the core genome mutant genes. The nonredundant GO terms were summarized with REVIGO system (Supek et al., 2011).Fig. S5. Representation of the GO 'Biological process' core genome mutants. The pie chart shows the percentage of activities presents in the core genome mutant genes. The nonredundant GO terms were summarized with REVIGO system (Supek et al., 2011).Table. S1. Complete list of mutated functions in P. putida KT2440. The table is divided in three sections: Mutants in the set of accessory genes of Pseudomonas putida KT2440; Mutants in the set of core genes of Pseudomonas putida KT2440; Mutants in the set of unique genes of Pseudomonas putida KT2440.
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  • Descrição: Summary Pseudomonas putida are strict aerobes that proliferate in a range of temperate niches and are of interest for environmental applications due to their capacity to degrade pollutants and ability to promote plant growth. Furthermore solvent‐tolerant strains are useful for biosynthesis of added‐value chemicals. We present a comprehensive comparative analysis of nine strains and the first characterization of the Pseudomonas putida pangenome. The core genome of P. putida comprises approximately 3386 genes. The most abundant genes within the core genome are those that encode nutrient transporters. Other conserved genes include those for central carbon metabolism through the Entner–Doudoroff pathway, the pentose phosphate cycle, arginine and proline metabolism, and pathways for degradation of aromatic chemicals. Genes that encode transporters, enzymes and regulators for amino acid metabolism (synthesis and degradation) are all part of the core genome, as well as various electron transporters, which enable aerobic metabolism under different oxygen regimes. Within the core genome are 30 genes for flagella biosynthesis and 12 key genes for biofilm formation. Pseudomonas putida strains share 85% of the coding regions with Pseudomonas aeruginosa; however, in P. putida, virulence factors such as exotoxins and type III secretion systems are absent.
  • Editor: England: Blackwell Publishing Ltd
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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