Pseudomonas putida

Pseudomonas putida is a Gram-negative, rod-shaped, saprophytic soil 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.

Pseudomonas putida
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
Type strain
ATCC 12633

CCUG 12690
CFBP 2066
DSM 291
HAMBI 7
JCM 13063 and 20120
LMG 2257
NBRC 14164
NCAIM B.01634
NCCB 72006 and 68020
NCTC 10936

Synonyms

Bacillus fluorescens putidus" Flügge 1886
Bacillus putidus Trevisan 1889
Pseudomonas eisenbergii Migula 1900
Pseudomonas convexa Chester 1901
Pseudomonas incognita Chester 1901
Pseudomonas ovalis Chester 1901
Pseudomonas rugosa (Wright 1895) Chester 1901
Pseudomonas striata Chester 1901
Pseudomonas mildenbergii Bergey, et al.
Arthrobacter siderocapsulatus Dubinina and Zhdanov 1975
Pseudomonas arvilla O. Hayaishi
Pseudomonas barkeri Rhodes
Pseudomonas cyanogena Hammer

The Food and Drug Administration (FDA) has listed P. 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 of P. putida in many research labs is preferable to some other Pseudomonas species, such as Pseudomonas aeruginosa, for example, which is an opportunistic pathogen.[1]

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 not validly defined).[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 3748–6780 (average: 5197) and between 58.7–64.4% (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

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 pentanucleotide usage and the list of the most abundant octa- to tetradecanucleotides are useful measures of the bacterial 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. Whitman, William B; Rainey, Fred; Kämpfer, Peter; Trujillo, Martha; Chun, Jonsik; DeVos, Paul; Hedlund, Brian; Dedysh, Svetlana, eds. (2015-04-17). Bergey's Manual of Systematics of Archaea and Bacteria (1 ed.). Wiley. doi:10.1002/9781118960608.gbm01210. ISBN 978-1-118-96060-8.
  2. Kampers, Linde F. C.; Volkers, Rita J. M.; Martins dos Santos, Vitor A. P. (2019-06-14). "Pseudomonas putida <scp>KT</scp> 2440 is <scp>HV</scp> 1 certified, not <scp>GRAS</scp>". Microbial Biotechnology. 12 (5): 845–848. doi:10.1111/1751-7915.13443. ISSN 1751-7915. PMC 6680625. PMID 31199068.
  3. Anzai; Kim, H; Park, JY; Wakabayashi, H; Oyaizu, H; et al. (Jul 2000). "Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence". Int J Syst Evol Microbiol. 50 (4): 1563–89. doi:10.1099/00207713-50-4-1563. PMID 10939664.
  4. Keshavarz-Tohid, Vahid; Vacheron, Jordan; Dubost, Audrey; Prigent-Combaret, Claire; Taheri, Parissa; Tarighi, Saeed; Taghavi, Seyed Mohsen; Moënne-Loccoz, Yvan; Muller, Daniel (2019-07-01). "Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov". Systematic and Applied Microbiology. 42 (4): 468–480. doi:10.1016/j.syapm.2019.04.004. ISSN 0723-2020. PMID 31122691. S2CID 155282987.
  5. Nikolaidis, Marios; Mossialos, Dimitris; Oliver, Stephen G.; Amoutzias, Grigorios D. (2020-07-24). "Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis". Diversity. 12 (8): 289. doi:10.3390/d12080289. ISSN 1424-2818.
  6. Keshavarz-Tohid; Vacheron, J; Dubost, A; Prigent-Combaret, C; Taheri, P; Tarighi, S; Taghavi, SM; Moënne-Loccoz, Y; Muller, D; et al. (May 2019). "Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov". Syst Appl Microbiol. 42 (Pt 1): 468–480. doi:10.1016/j.syapm.2019.04.004. PMID 31122691. S2CID 155282987.
  7. Marqués, Silvia; Ramos, Juan L. (1993). "Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways". Molecular Microbiology. 9 (5): 923–9. doi:10.1111/j.1365-2958.1993.tb01222.x. PMID 7934920. S2CID 20663917.
  8. Gomes, NC; Kosheleva, IA; Abraham, WR; Smalla, K (2005). "Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community". FEMS Microbiology Ecology. 54 (1): 21–33. doi:10.1016/j.femsec.2005.02.005. 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. Ward, PG; Goff, M; Donner, M; Kaminsky, W; O'Connor, KE (2006). "A two step chemo-biotechnological conversion of polystyrene to a biodegradable thermoplastic". Environmental Science & Technology. 40 (7): 2433–7. Bibcode:2006EnST...40.2433W. doi:10.1021/es0517668. PMID 16649270.
  11. Amer, GA; Utkhede, RS (2000). "Development of formulations of biological agents for management of root rot of lettuce and cucumber". Canadian Journal of Microbiology. 46 (9): 809–16. doi:10.1139/w00-063. PMID 11006841.
  12. Validov, S; Kamilova, F; Qi, S; Stephan, D; Wang, JJ; Makarova, N; Lugtenberg, B (2007). "Selection of bacteria able to control Fusarium oxysporum f. Sp. Radicis-lycopersici in stonewool substrate". Journal of Applied Microbiology. 102 (2): 461–71. doi:10.1111/j.1365-2672.2006.03083.x. PMID 17241352. S2CID 3098008.
  13. Cornelis, Pierre, ed. (2008). Pseudomonas: Genomics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 978-1-904455-19-6. Archived from the original on 2016-09-12. Retrieved 2007-09-24.
  14. Poblete-Castro, Ignacio; Becker, Judith; Dohnt, Katrin; dos Santos, Vitor Martins; Wittmann, Christoph (March 2012). "Industrial biotechnology of Pseudomonas putida and related species". Applied Microbiology and Biotechnology. 93 (6): 2279–2290. doi:10.1007/s00253-012-3928-0. hdl:10033/246536. ISSN 0175-7598. PMID 22350258. 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. Summers, RM; Louie, TM; Yu, CL; Subramanian, M (2011). "Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source". Microbiology. 157 (Pt 2): 583–92. doi:10.1099/mic.0.043612-0. PMID 20966097.
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