Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440

Abstract

A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.

Genome‐wide identification of tolerance mechanisms toward p‐coumaric acid in Pseudomonas putida

“…Most of them are described to be transcribed divergently of the genes they regulate. Here, the operon PP_1263 to PP_1266, which is divergently transcribed, has been annotated as an efflux system for the export of fusaric acid, a fungal toxin released by phytopathogenes (Martins Dos Santos, Heim, Moore, Strätz, & Timmis, 2004). Further studies are required to elucidate the effect of this regulator and the genes that it possibly regulates for the tolerance.…”

The Crc Global Regulator Inhibits the Pseudomonas putida pWW0 Toluene/Xylene Assimilation Pathway by Repressing the Translation of Regulatory and Structural Genes

“…Pseudomonas putida is a ubiquitous soil bacterium that shows great metabolic versatility and the ability to live under a wide range of environmental conditions (1). Its biotechnological potential and its ability to degrade many aromatic compounds that generate pollution problems have led to the detailed study of its metabolism.…”

Molecular Characterization of the Gallate Dioxygenase from Pseudomonas putida KT2440

“…Pseudomonas putida is one of the best studied species of the genus and many aspects of its biology have been unraveled (2,3). P. putida strain KT2440 is a paradigm of a metabolically versatile bacterium used as a workhorse for genetic and physiological studies as well as for the development of biotechnological applications (3). This strain is particularly renowned for its ability to metabolize aromatic compounds (4).…”

“…Among bacteria, Pseudomonas species constitute a large diverse group of ubiquitous ␥-proteobacteria that are well known for their broad metabolic versatility and genetic plasticity. Pseudomonas putida is one of the best studied species of the genus and many aspects of its biology have been unraveled (2,3). P. putida strain KT2440 is a paradigm of a metabolically versatile bacterium used as a workhorse for genetic and physiological studies as well as for the development of biotechnological applications (3).…”