Pseudomonas putida

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Scientific classification
Kingdom: Eubacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: putida
Binomial name
Pseudomonas putida

Description and significance

Pseudomonas putida are Gram-negative rod-shaped bacteria. They are classified as Group 1 in Pseudomona. Other Pseudomonads are being re-evaluated to see if they truly fall into this category, while P. putida is firmly place in this group. P. putida are flourescent, aerobic, non sporeforming, oxidase positive bacteria. Having one or more polar flagella, they are motile organisms. They can be found in moist environments, such as soil and water, and grow optimally at room temperature. Certain strains have the ability to grow on and break down many dangerous pollutants and aromatic hydrocarbons such as toluene, benzene, and ethylbenzene. P. putida can also be used in petroleum plants to purify fuel. This bacterium is also capable of promoting plant growth after root colonization as well as simultaneously providing protection for the plant from pests and other harmful bacteria. Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated. Include a picture or two (with sources) if you can find them.

Genome structure

The genome of Pseudomonas putida was sequenced due to the many unique abilities that this bacterium possesses. Scientists are interested in which genes cause what function. So far, P. putida has the most genes of any microorganism that break down chemicals such as aromatic hydrocarbons. Research is being done on the difference in genome of P. putida and its relative Pseudomonas aeruginos in relation to cystic fibrosis. While P. aeruginos infects and kills those with the disease, P. putida lacks the genes that causes such destruction, like the genes that code for enzymes that digest cell membranes.

The Pseudomonas putida strain KT2440 genome was sequenced as a joint project between The Institute for Genomic Research and a German consortium in 1999. The way that they sequenced the genome was using the random shotgun method. They found that the one circular chromosome contains 6,181,863 base pairs. The total number of genes is 5,516, with 5,421 being protein coding. The total number of repeats, or stretches greater than 200 base pairs and almost identical, was 398. Interestingly, there was a high GC content in the genome, which created some difficulty in sequencing through the traditional methods. A significant amount of genes were found to code for enzymes that are used in the decomposition of matter. Most of the other genes are critical for Pseudomonas putida’s ability to recognize and react to external toxins and chemical signals. They also contain multiple accessory plasmids, including TOL and OCT plasmids, that aide the bacterium in breaking down environmental pollutants found in soil and water. Through sequencing the Pseudomonas putida genome, scientists were able to determine the biotechnological potential of the organism.

Cell structure and metabolism

Pseudomonas putida are aerobic oxidase positive bacteria, with one or more flagella. They can be found in moist environments, such as soil and water, and grow at a temperature of 25-30 degrees Celcius. Although Pseudomonas putida does not form spores, they are still able to withstand harsh environmental conditions. It is able to resist the severe effects of organic solvents that pollute the surrounding soil. In response to changes in its chemical surroundings and to help with membrane fluidity and cellular uptake, it can alter the degree of fatty acid saturation and even undergo cis-trans isomerization. P. putida are unique saprobes in that use a wide variety of non-living material as their source of nutrition, including multiple types of aromatic hydrocarbons. This allows them to be agents of bioremediation, one of the most differentiating and impressive features of Pseudomonas putida. Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.

Ecology

Pseudomonas putida has an incomparable effect on the environment. They are able to protect plants from pests, promote plant growth, and clean up organic pollutants found in soil and water.

The surface of the root and the soil that surrounds it are loaded with nutrients released by the plant. This environment is optimal for microbial growth. Pseudomonas putida is attracted to this area, and in turn promotes plant growth and even protects the root against pathogens. Two key elements that allow P. putida to attach in the first place is that they are motile and chemotactic towards the root output. After the initial attraction and migration toward the root, the bacteria immediately begins to grow and divide, forming multiple colonies around the root. The maximum population size is directly related to root weight, and once it is reached the number of colonies will stay constant. All of this can happen in less than 48 hours!

Pseudomonas putida play a huge role in bioremediation, or the removal or naturalization of soil or water contaminants. They can degrade toluene, xylene, and benzene, which are all toxic components of gasoline that leak into the soil by accidental spills. Other strains can convert styrene, better known as packing peanuts, which do not degrade naturally, into the biodegradable plastic polyhydroxyalkanoate (PHA). Methods used to get rid of styrene include incinerating it, spreading it on land, and injecting it underground, all of which release the toxins into the environment. Styrene can cause muscle weakness, lung irritation, and may even effect the brain and nervous system. Due to the fact that P. putida can use styrene as its only source of carbon and energy, it can completely remove this toxic chemical. P. putida can also turn Atrizine, an herbicide that is toxic to wildlife, into carbon dioxide and water.

Pathology

In genetic terms, Pseudomonas putida is very similar to strains of Pseudomonas aeruginosa, an opportunistic human pathogen. Although there is a considerable amount of genome conservation, P. putida seems to be missing the key virulent segments that P. aeroginosa has. Being a non-pathogenic bacteria, there has been only a handful of episodes where P. putida has infected humans. For the most part, it has been with immunocompromised patients, causing septicaemia, pneumonia, urinary tract infections, nosocomial bacteremia, septic arthritis, or peritonitis. P. putida is also closely related to Pseudomonas syringae, an abundant plant pathogen, but again it lacks the gene that causes such disease.

Several cases of disease caused by Pseudomonas putida have been investigated, being that the bacterium rarely colonizes mucosal surfaces or skin. One case was a 43-year-old female who was receiving nightly peritoneal dialysis treatments following a laparoscopic ovarian cyst operation. She developed peritonitis due to infection by Pseudomonas putida. Through this case and others, it was determined that risk factors for developing such an infection include the insertion of catheters, intubation, and/or intravascular devices following a recent course in antibiotics.

Another case of Pseudomonas putida infection was found in ten patients in and ear, nose, and throat outpatient clinic during the summer of 2000. All ten patients had chronic sinusitis, making them more susceptible to infection due to their challenged immune systems. Through investigation, it was discovered that all of the patients shared the same examination room. The source of the bacteria was from a contaminated bottle of StaKleer found in that room. StaKleer is an anti-fog solution used on mirrors and endoscopes to prevent condensation from occurring, allowing for the proper visualization of tissues. Other unopened bottles of the solution at the clinic were found to be contaminated with Pseudomonas putida as well.

Application to Biotechnology

Pseudomonas putida is being used in conjunction with Escherichia coli for developing new drugs. This study focuses on myxochromide S, a compound produced by Stigmatella aurantiaca, but the method is revolutionary in that there is unprecedented expression of gene clusters. The beginnings of many new drugs are from natural sources, such as plants and microorganisms, but they are too expensive to harvest from the origin. Combinatorial biosynthesis has revolutionized drug development by allowing the structure of certain molecules to be changed within an organism. With this metabolic engineering, where genes are introduced and their expressions are tightly controlled, successful production of drugs is possible. Pseudomonas putida is unique in that it allows the expression of a large biosynthetic cluster, producing five times as much myxochromide S as Stigmatella aurantiaca. This will also permit scientists to connect multiple clusters of genes onto a single DNA fragment.

Pseudomonas putida is able to purify fuel, a capability that the petroleum industry has taken great interest in. As previously mentioned, P. putida is able to convert styrene, a toxic waste product, into a biodegradable plastic. The strain CA-3 turns styrene into a stored energy source, in the form of a plastic polymer called polyhydroxyalkanoate (PHA). Using styrene its only source of carbon and energy, the styrene is completely used up, creating an elastic type of polymer. This polymer can then be used in the production of drug carriers, plastic coating of cardboard, and medical implants. Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

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