| Pseudomonas putida | |
|---|---|
 | |
| Pseudomonas putida onKing's B agar.Pyoverdine, producedto collect iron from the environment, glows under UV light. | |
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| DIC image ofPseudomonas putida culture wet mount, 400X | |
Scientific classification | |
| Domain: | Bacteria |
| Kingdom: | Pseudomonadati |
| Phylum: | Pseudomonadota |
| Class: | Gammaproteobacteria |
| Order: | Pseudomonadales |
| Family: | Pseudomonadaceae |
| Genus: | Pseudomonas |
| Species: | P. putida |
| Binomial name | |
| Pseudomonas putida Trevisan, 1889 | |
| Type strain | |
| ATCC 12633 CCUG 12690 | |
| Synonyms | |
Bacillus fluorescens putidus"Flügge 1886 | |
Pseudomonas putida is aGram-negative, rod-shaped,saprophyticsoilbacterium.[1] It has a versatile metabolism and is amenable to genetic manipulation, making it a common organism used in research, bioremediation, and synthesis of chemicals and other compounds.
TheFood and Drug Administration (FDA) has listedP. putida strain KT2440 as Host-vector system safety level 1 certified (HV-1), indicating that it is safe to use without any extra precautions.[2] Thus, use ofP. putida in many research labs is preferable to some otherPseudomonas species, such asPseudomonas aeruginosa, for example, which is anopportunistic pathogen.[1]
Based on 16SrRNA analysis,P. putida was taxonomically confirmed to be aPseudomonas species (sensu stricto) and placed, along with several other species, in theP. putida group, to which it lends its name.[3] However,phylogenomic analysis[4][5] of completegenomes from the entirePseudomonas genus clearly showed that the genomes that were named asP. putida did not form a monophyleticclade, but were dispersed and formed a wider evolutionary group (the putida group) that included other species as well, such asP. 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 not validly defined).[6]
A variety ofP. putida, called multiplasmid hydrocarbon-degradingPseudomonas, is the first patented organism in the world. Because it is a living organism, the patent was disputed and brought before theUnited States Supreme Court in the historic court caseDiamond v. Chakrabarty, which the inventor,Ananda Mohan Chakrabarty, won. It demonstrates a very diversemetabolism, including the ability to degrade organic solvents such astoluene.[7] This ability has been put to use inbioremediation, or the use of microorganisms to degrade environmental pollutants.
The protein count andGC content of the (63) genomes that belong to theP. putida wider evolutionary group (as defined by a phylogenomic analysis of 494 complete genomes from the entirePseudomonas genus) ranges between 3748–6780 (average: 5197) and between 58.7–64.4% (average: 62.3%), respectively.[5] The core proteome of the analyzed 63 genomes (of theP. putida group) comprised 1724 proteins, of which only 1 core protein was specific for this group, meaning that it was absent in all other analyzedPseudomonads.[5]
TheP. putidagenome specifies enzymes that repair oxidativeDNA damages (oxidizedguanine) during the stationary phase of growth thus avoidingmutagenesis.[8] Enzymes that participate in the removal of oxidized guanine in carbon-starvedP. putida DNA includeMutY glycosylase andMutM glycosylase.P. putida also specifies the enzyme MutT, apyrophosphohydrolase that converts 8-oxodGTP to 8-oxodGMP in order to prevent 8-oxodGTP from being used as a substrate by the replicative DNA polymerase.[8]
The diverse metabolism of wild-type strains ofP. putida may be exploited for bioremediation; for example, it has been shown in the laboratory to function as asoil inoculant to remedynaphthalene-contaminated soils.[9]
Pseudomonas putida is capable of convertingstyrene oil into thebiodegradable plasticPHA.[10][11] This may be of use in the effectiverecycling ofpolystyrene foam, otherwise thought to be not biodegradable.
Pseudomonas putida has demonstrated potentialbiocontrol properties, as an effective antagonist of plant pathogens such asPythium aphanidermatum[12] andFusarium oxysporum f.sp.radicis-lycopersici.[13]
Di- topentanucleotide usage and the list of the most abundant octa- to tetradecanucleotides are useful measures of the bacterialgenomic signature. TheP. 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 atypicaloligonucleotide 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 extragenicpalindromic sequence is the most common repeat in the genome that can be exploited for the typing ofP. putida strains. In the coding sequence ofP. putida, LLL is the most abundant tripeptide.[14] Phylogenomic analysis reclassified the strain KT2440 in a new speciesPseudomonas alloputida.[6]
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.[15] A new all-inclusive plasmid forP. putida KT2440, was introduced in 2024. This broad host range plasmid (pBBR1MCS2) enables fast iterative genome editing. The method is based on the instability of the vector plasmid combined with the CRISPR/Cas9 system. By manipulating the conditions to be optimal for curing,P. putida is able to cure the vector within 8h. This is significantly faster than with previous methods and this cuts the duration of one edit down to 1.5 days from 4-5 days. Curing speed is relevant because it directly effects when the next edit can take place.[16]
Pseudomonas putida CBB5, a nonengineered, wild-type variety found in soil, can live oncaffeine and has been observed to break caffeine down into carbon dioxide and ammonia.[17][18]