''Pseudomonas putida'' is a

Gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wa ...

, rod-shaped,

saprotrophic Saprotrophic nutrition or lysotrophic nutrition is a process of chemoheterotrophic extracellular digestion involved in the processing of decayed (dead or waste) organic matter. It occurs in saprotrophs, and is most often associated with fungi ...

soil Soil, also commonly referred to as earth or dirt, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life. Some scientific definitions distinguish ''dirt'' from ''soil'' by restricting the former ...

bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

. Based on 16S

rRNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribos ...

analysis, ''P. putida'' was taxonomically confirmed to be a ''

Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able t ...

'' species (''sensu stricto'') and placed, along with several other species, in the ''P. putida'' group, to which it lends its name. However, phylogenomic analysis of complete genomes from the entire ''Pseudomonas'' genus clearly showed that the genomes that were named as ''P. putida'' did not form a monophyletic

clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English ter ...

, but were dispersed and formed a wider evolutionary group (the putida group) that included other species as well, such as ''P. alkylphenolia, P. alloputida, P. monteilii, P. cremoricolorata, P. fulva, P. parafulva, P. entomophila, P. mosselii, P. plecoglossicida'' and several genomic species (new species which are currentely not validely defined as new species. A variety of ''P. putida'', called multiplasmid hydrocarbon-degrading ''Pseudomonas'', 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 The Supreme Court of the United States (SCOTUS) is the highest court in the federal judiciary of the United States. It has ultimate appellate jurisdiction over all U.S. federal court cases, and over state court cases that involve a point o ...

in the historic court case ''

Diamond v. Chakrabarty ''Diamond v. Chakrabarty'', 447 U.S. 303 (1980), was a United States Supreme Court case dealing with whether living organisms can be patented. Writing for a five-justice majority, Chief Justice Warren E. Burger held that human-made bacteria could ...

'', which the inventor, Ananda Mohan Chakrabarty, won. It demonstrates a very diverse

metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run ...

, including the ability to degrade organic solvents such as

toluene Toluene (), also known as toluol (), is a substituted aromatic hydrocarbon. It is a colorless, water-insoluble liquid with the smell associated with paint thinners. It is a mono-substituted benzene derivative, consisting of a methyl group (CH3) ...

. This ability has been put to use in

bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi, and plants), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluent ...

, or the use of microorganisms to degrade environmental pollutants. Use of ''P. putida'' is preferable to some other ''

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

Genomics

The protein count and GC content of the (63) genomes that belong to the ''P. putida'' wider evolutionary group (as defined by a phylogenomic analysis of 494 complete genomes from the entire ''Pseudomonas'' genus) ranges between 3748–6780 (average: 5197) and between 58.7–64.4% (average: 62.3%), respectively. The core proteome of the analyzed 63 genomes (of the ''P. putida'' group) comprised 1724 proteins, of which only 1 core protein was specific for this group, meaning that it was absent in all other analyzed ''Pseudomonads''.

Uses

Bioremediation

The diverse metabolism of wild-type strains of ''P. putida'' may be exploited for bioremediation; for example, it has been shown in the laboratory to function as a soil inoculant to remedy

naphthalene Naphthalene is an organic compound with formula . It is the simplest polycyclic aromatic hydrocarbon, and is a white crystalline solid with a characteristic odor that is detectable at concentrations as low as 0.08 ppm by mass. As an aromat ...

-contaminated soils. ''Pseudomonas putida'' is capable of converting

styrene Styrene () is an organic compound with the chemical formula C6H5CH=CH2. This derivative of benzene is a colorless oily liquid, although aged samples can appear yellowish. The compound evaporates easily and has a sweet smell, although high concen ...

oil into the

biodegradable plastic Biodegradable plastics are plastics that can be decomposed by the action of living organisms, usually microbes, into water, carbon dioxide, and biomass. Biodegradable plastics are commonly produced with renewable raw materials, micro-organisms ...

PHA. This may be of use in the effective

recycling Recycling is the process of converting waste materials into new materials and objects. The Energy recycling, recovery of energy from waste materials is often included in this concept. The recyclability of a material depends on its ability t ...

polystyrene Polystyrene (PS) is a synthetic polymer made from monomers of the Aromatic hydrocarbon, aromatic hydrocarbon styrene. Polystyrene can be solid or foamed. General-purpose polystyrene is clear, hard, and brittle. It is an inexpensive resin pe ...

foam, otherwise thought to be not biodegradable.

Biocontrol

''Pseudomonas putida'' has demonstrated potential

biocontrol Biological control or biocontrol is a method of controlling pests, such as insects, mites, weeds, and plant diseases, using other organisms. It relies on predation, parasitism, herbivory, or other natural mechanisms, but typically also in ...

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

Pythium ''Pythium'' is a genus of parasitic oomycetes. They were formerly classified as fungi. Most species are plant parasites, but ''Pythium insidiosum'' is an important pathogen of animals, causing pythiosis. The feet of the fungus gnat are frequen ...

'' and ''

Fusarium ''Fusarium'' is a large genus of filamentous fungi, part of a group often referred to as hyphomycetes, widely distributed in soil and associated with plants. Most species are harmless saprobes, and are relatively abundant members of the soil mi ...

''.

Oligonucleotide usage signatures of the ''P. alloputida'' KT2440 genome

Di- to pentanucleotide usage and the list of the most abundant octa- to tetradecanucleotides are useful measures of the bacterial

genomic Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...

signature. The ''P. putida'' KT2440 chromosome is characterized by strand symmetry and intrastrand 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 Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids ...

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 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. Phylogenomic analysis reclassified the strain KT2440 in a new species ''Pseudomonas alloputida''.

Organic synthesis

''Pseudomonas putida's'' amenability to genetic manipulation has allowed it to be used in the synthesis of numerous organic pharmaceutical and agricultural compounds from various substrates.

CBB5 and caffeine consumption

''Pseudomonas putida'' CBB5, a nonengineered, wild-type variety found in soil, can live on

caffeine Caffeine is a central nervous system (CNS) stimulant of the methylxanthine chemical classification, class. It is mainly recreational drug use, used recreationally as a Nootropic, cognitive enhancer, increasing alertness and attentional perfor ...

and has been observed to break caffeine down into carbon dioxide and ammonia.

References

External links

* Risk Assessment Summary, CEPA 1999
''Pseudomonas putida'' CR30RNSLL(pADPTel)
*Pseudomonas putida is an example for plant growth promoting Rhizobacterium, which produces iron chelating substances.
Type strain of ''Pseudomonas putida'' at Bac''Dive'' - the Bacterial Diversity Metadatabase
{{Taxonbar, from=Q2738168 Pseudomonadales Oil spill remediation technologies Bacteria described in 1889