User:Mroghair/Pputida sandbox

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This is the sandbox page in which I will draft my edits for the Pseudomonas putida Wikipedia page.


Mroghair/Pputida sandbox
Pseudomonas putida on King's B agar, which is glowing due to the production of pyoverdine. Image taken under UV light. Pyoverdine is produced by Pseudomonads to collect iron from the environment.
DIC image of Pseudomonas putida culture wet mount, 400X.
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Gammaproteobacteria
Order: Pseudomonadales
Family: Pseudomonadaceae
Genus: Pseudomonas
Species:
P. putida
Binomial name
Pseudomonas putida
Trevisan, 1889

Pseudomonas putida is a

bacterium.[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.

The

Pseudomonas aeruginosa, for example, which is an opportunistic pathogen.[1]

Metabolism and Environment

Siderophores

ISR induction

where found

History and Phylogeny

Based on 16S

rRNA analysis, P. putida was taxonomically confirmed to be a Pseudomonas species (sensu stricto) and placed, along with several other species, in the P. putida group, to which it lends its name.[3] However, phylogenomic analysis[4][5] 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, 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.[6]

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 in the historic court case Diamond v. Chakrabarty, which the inventor, Ananda Mohan Chakrabarty, won. It demonstrates a very diverse metabolism, including the ability to degrade organic solvents such as toluene.[7] This ability has been put to use in bioremediation, or the use of microorganisms to degrade environmental pollutants.

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 3748โ€“6780 (average: 5197) and between 58.7โ€“64.4% (average: 62.3%), respectively.[5] 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.[5]

Uses (in industry??)

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-contaminated soils.[8]

Pseudomonas putida is capable of converting styrene oil into the biodegradable plastic PHA.[9][10] This may be of use in the effective recycling of polystyrene foam, otherwise thought to be not biodegradable.

Biocontrol

Pseudomonas putida has demonstrated potential

biocontrol properties, as an effective antagonist of plant pathogens such as Pythium aphanidermatum[11] and Fusarium oxysporum f. sp. radicis-lycopersici.[12]

Oligonucleotide usage signatures of the P. alloputida KT2440 genome

Di- to

genomic 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 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.[13] Phylogenomic analysis reclassified the strain KT2440 in a new species Pseudomonas alloputida.[6]

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.[14]

CBB5 and caffeine consumption

Pseudomonas putida CBB5, a nonengineered, wild-type variety found in soil, can live on caffeine and has been observed to break caffeine down into carbon dioxide and ammonia.[15][16]

References

  1. ^
    ISBN 978-1-118-96060-8
    .
  2. ISSN 1751-7915. {{cite journal}}: line feed character in |title= at position 26 (help
    )
  3. PMID 10939664
    .
  4. S2CID 155282987
    .
  5. ^
    ISSN 1424-2818
    .
  6. ^
    S2CID 155282987
    .
  7. S2CID 20663917
    .
  8. PMID 16329969
    .
  9. ^ Britt, Robert Roy (March 7, 2006). "Immortal Polystyrene Foam Meets its Enemy". livescience.com. Archived from the original on November 4, 2021. Retrieved November 4, 2021.
  10. PMID 16649270
    .
  11. PMID 11006841
    .
  12. S2CID 3098008
    .
  13. ISBN 978-1-904455-19-6. Archived
    from the original on 2016-09-12. Retrieved 2007-09-24.
  14. S2CID 253775454. Archived
    from the original on 2023-03-15. Retrieved 2023-02-19.
  15. ^ Harmon, Katherine. "Newly Discovered Bacteria Lives on Caffeine". Scientific American Blog Network. Archived from the original on 2021-11-04. Retrieved 2021-11-04.
  16. PMID 20966097
    .

External links
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