Pseudomonas putida is a gram-negative

Gram-negative

Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color...

 rod-shaped saprotrophic soil

Soil

Soil is a natural body consisting of layers of mineral constituents of variable thicknesses, which differ from the parent materials in their morphological, physical, chemical, and mineralogical characteristics...

 bacterium. Based on 16S rRNA analysis, P. putida has been placed in the P. putida group, to which it lends its name.

It is the first patented organism in the world. Because it is a living organism the patent was disputed and brought before the United States Supreme Court in the historic court case Diamond v. Chakrabarty

Diamond v. Chakrabarty

Diamond v. Chakrabarty, , was a United States Supreme Court case dealing with whether genetically modified organisms can be patented.-Background:...

 which the inventor, Ananda M. Chakrabarty, won. It demonstrates a very diverse metabolism, including the ability to degrade organic solvents such as toluene

Toluene

Toluene, formerly known as toluol, is a clear, water-insoluble liquid with the typical smell of paint thinners. It is a mono-substituted benzene derivative, i.e., one in which a single hydrogen atom from the benzene molecule has been replaced by a univalent group, in this case CH3.It is an aromatic...

. This ability has been put to use in bioremediation

Bioremediation

Bioremediation is the use of microorganism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated...

, or the use of microorganisms to biodegrade oil. Use of P. putida is preferable to some other Pseudomonas

Pseudomonas

Pseudomonas is a genus of gammaproteobacteria, belonging to the family Pseudomonadaceae containing 191 validly described species.Recently, 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result, the genus Pseudomonas includes strains formerly classified in the...

species capable of such degradation as it is a safe species of bacteria, unlike P. aeruginosa for example, which is an opportunistic human pathogen.

Bioremediation

The diverse metabolism of P. putida may be exploited for bioremediation; for example, it is used as a soil inoculant

Soil inoculant

Soil inoculants are bacteria or fungi that are added to soils in order to improve plant growth by either:*Freeing up soil nutrients for plant use.*Entering into symbiotic relationships with plant root systems....

 to remedy naphthalene

Naphthalene

Naphthalene is an organic compound with formula . It is a white crystalline solid with a characteristic odor that is detectable at concentrations as low as 0.08 ppm by mass. As an aromatic hydrocarbon, naphthalene's structure consists of a fused pair of benzene rings...

 contaminated soils.

P. putida is capable of converting styrene oil into the biodegradable plastic

Biodegradable plastic

Biodegradable plastics are plastics that will decompose in natural aerobic and anaerobic environments. Biodegradation of plastics can be achieved by enabling microorganisms in the environment to metabolize the molecular structure of plastic films to produce an inert humus-like material that is...

 PHA

Polyhydroxyalkanoates

Polyhydroxyalkanoates or PHAs are linear polyesters produced in nature by bacterial fermentation of sugar or lipids. They are produced by the bacteria to store carbon and energy. More than 150 different monomers can be combined within this family to give materials with extremely different properties...

. This may be of use in the effective recycling

Recycling

Recycling is processing used materials into new products to prevent waste of potentially useful materials, reduce the consumption of fresh raw materials, reduce energy usage, reduce air pollution and water pollution by reducing the need for "conventional" waste disposal, and lower greenhouse...

 of Polystyrene

Polystyrene

Polystyrene ) also known as Thermocole, abbreviated following ISO Standard PS, is an aromatic polymer made from the monomer styrene, a liquid hydrocarbon that is manufactured from petroleum by the chemical industry...

 foam, otherwise thought to be non-biodegradable.

Biocontrol

P. putida has demonstrated potential biocontrol

BioControl

BioControl is a peer-reviewed scientific journal published by Springer Science+Business Media covering all aspects of basic and applied research in biological control of invertebrate, vertebrate, and weed pests, and plant diseases. The journal was established in 1956 as Entomophaga and published by...

 properties, as an effective antagonist of damping off diseases such as Pythium

Pythium

Pythium is a genus of parasitic oomycete. Most species are plant parasites, but Pythium insidiosum is an important pathogen of animals...

and Fusarium

Fusarium

Fusarium is a large genus of filamentous fungi widely distributed in soil and in association with plants. Most species are harmless saprobes, and are relatively abundant members of the soil microbial community. Some species produce mycotoxins in cereal crops that can affect human and animal health...

.

Oligonucleotide Usage Signatures of the Pseudomonas putida KT2440 Genome

Di- to pentanucleotide usage and the list of the most abundant octa- to tetradecanucleotides are useful measures of the bacterial genomic signature. The Pseudomonas putida KT2440 chromosome is characterized by strand symmetry and intra-strand parity of complementary oligonucleotides. Each tetranucleotide occurs with similar frequency on the two strands. Tetranucleotide usage is biased by G+C content and physicochemical constraints such as base stacking energy, dinucleotide propeller twist angle or trinucleotide bendability. The 105 regions with atypical oligonucleotide

Oligonucleotide

An oligonucleotide is a short nucleic acid polymer, typically with fifty or fewer bases. Although they can be formed by bond cleavage of longer segments, they are now more commonly synthesized, in a sequence-specific manner, from individual nucleoside phosphoramidites...

 composition can be differentiated by their patterns of oligonucleotide usage into categories of horizontally acquired gene islands, multidomain genes or ancient regions such as genes for ribosomal proteins and RNAs. A species-specific extragenic palindromic sequence

Palindromic sequence

A palindromic sequence is a nucleic acid sequence that is the same whether read 5' to 3' on one strand or 5' to 3' on the complementary strand with which it forms a double helix....

 is the most common repeat in the genome that can be exploited for the typing of P. putida strains. In the coding sequence of P. putida LLL is the most abundant tripeptide.

Organic Synthesis

Certain variants of P. putida have been used in organic synthesis

Organic synthesis

Organic synthesis is a special branch of chemical synthesis and is concerned with the construction of organic compounds via organic reactions. Organic molecules can often contain a higher level of complexity compared to purely inorganic compounds, so the synthesis of organic compounds has...

, the first example being the oxidation of benzene, employed by Prof. S. V. Ley in the synthesis of the cyclitol (+/-)pinitol

Pinitol

Pinitol is a cyclitol, a cyclic polyol. It is a known anti-diabetic agent isolated from Sutherlandia frutescens leaves. Gall plant tannins can be differentiated by their content of pinitol....

.

CBB5 and caffeine consumption

Pseudomonas putida CBB5 can live on pure caffeine, and has been observed to break caffeine down into carbon dioxide and ammonia.