Analysis of the core genome and pangenome of Pseudomonas putida.
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.
Biotechnology Technological Area, Abengoa Research, Calle Energía Solar 1, Building E, Campus Palmas Altas, 41014, Sevilla, Spain.
Zulema
Z
Udaondo
Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, 18008, Granada, Spain.
Lázaro
L
Molina
Biotechnology Technological Area, Abengoa Research, Calle Energía Solar 1, Building E, Campus Palmas Altas, 41014, Sevilla, Spain.
Ana
A
Segura
Biotechnology Technological Area, Abengoa Research, Calle Energía Solar 1, Building E, Campus Palmas Altas, 41014, Sevilla, Spain.
Estrella
E
Duque
Biotechnology Technological Area, Abengoa Research, Calle Energía Solar 1, Building E, Campus Palmas Altas, 41014, Sevilla, Spain. juan.ramos@abengoa.com.
Juan L
JL
Ramos
D001692:Biological Transport / Q000235:genetics*; D002244:Carbon / Q000378:metabolism; D004734:Energy Metabolism / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D026901:Membrane Transport Proteins / Q000235:genetics* / Q000378:metabolism; D016366:Open Reading Frames; D016958:Pseudomonas putida / Q000235:genetics* / Q000378:metabolism
D026901:Membrane Transport Proteins; D002244:Carbon