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

• 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.

Subject headings

NATURVETENSKAP  -- Biologi -- Annan biologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Other Biological Topics (hsv//eng)

Keyword

Adaptation

Physiological

genetics

Bacterial Proteins

genetics

Biological Transport

Active

genetics

Cytochromes

genetics

DNA Transposable Elements

Dioxygenases

genetics

Energy Metabolism

genetics

Ferredoxins

genetics

Genes

Regulator

Genome

Bacterial

Genomic Islands

Genomics

Glutathione Transferase

genetics

Interspersed Repetitive Sequences

Mixed Function Oxygenases

genetics

Oxidoreductases

genetics

Pseudomonas putida

genetics

physiology

Sigma Factor

genetics

Signal Transduction

genetics

Soil Microbiology

Sulfur

metabolism

Publication and Content Type

ref (subject category)

art (subject category)