Science Current Events | Science News | Brightsurf.com
 
Email a Friend Send to a friend
Printer Friendly Print U.S.-German Research Consortium Sequences Genome of Versatile Soil Microbe

U.S.-German Research Consortium Sequences Genome of Versatile Soil Microbe

December 03, 2002

In a successful transatlantic collaboration, scientists at The Institute for Genomic Research (TIGR) in Rockville, MD, and at four research centers in Germany have deciphered and analyzed the complete genome of a bacterium, Pseudomonas putida, that has the potential to be used to remediate organic pollutants in soil as well as to help promote plant growth and fight plant diseases.

The genome analysis is published in the journal Environmental Microbiology, which devotes its entire December 2002 issue to articles about P. putida and related Pseudomonas species. The genome paper sheds light on the complex and versatile metabolism that gives P. putida an important role in laboratory research on soil bacteria and also gives the bacterium great potential for bioremediation and other uses.




TIGR's German collaborators in the sequencing project were the Medizinische Hochschule Hannover (MHH) medical college in Hannover; the Gesellschaft fuer Biotechnologische Forschung (GBF) national research center for biotechnology in Braunschweig; the Deutsches Krebsforschungszentrum (DKFZ) cancer research center n Heidelberg; and the sequencing and genomics center of QIAGEN GmbH in Hilden. Professor Burkhard Tuemmler from the MHH was the project's German coordinator. The P. putida project was supported by grants from the U.S. Department of Energy and from the German research ministry, the BMBF.

Associate Investigator Karen E. Nelson, who along with TIGR President Claire M. Fraser led TIGR's component of the sequencing and analysis project, said the availability of the complete genome sequence of P. putida strain KT2440 will make the organism more useful to a range of scientists who are developing new ways to use it and related microbes to clean up organic pollutants.

"This genome provides a great model for microorganisms that have tremendous potential in various areas of biotechnology, such as producing natural compounds, remediating polluted habitats, and fighting plant diseases," Nelson said.

P. putida is a fast-growing bacterium that is found in most temperate soil and water habitats where oxygen is present. Because the bacterium can colonize the root area of crop plants, researchers are trying to use P. putida strains in bioengineering research to develop biopesticides and plant growth promoters. The bacterium is also widely studied because of its diverse metabolism, which is capable of remediating toxic organic pollutants such as aliphatic or aromatic hydrocarbons.

P. putida was designated in 1982 by a National Institutes of Health advisory panel as the first "biosafety" host strain for gene cloning in Gram-negative soil bacteria. The KT2440 strain of P. putida is used by researchers for the analysis and manipulation of genes from soil bacteria.

Kenneth N. Timmis, who led the GBF's component of the project, described P. putida as "a nutritional opportunist par excellence" which plays an important role in maintaining environmental quality in soils and is useful in scientific studies. Timmis said, "Its fascinating biochemistry and physiology, its robustness, rapid growth and ease of handling in the laboratory, and its amenability to genetic analysis and manipulation have resulted in P. putida becoming a laboratory 'workhorse' for research on soil bacteria and bacteria-remediated soil processes."

TIGR, which in 1995 determined the first complete genome sequence of a free-living organism, is a world leader in microbial genomics. The institute has completed the full sequences of 30 organisms or microbial strains, and its scientists are now working on another 75 genome sequencing projects.

The genome analysis found that P. putida has a single circular chromosome with nearly 6.2 million DNA base pairs. An analysis by Nelson and Vitor Martins Dos Santos of the GBF found previously unidentified metabolic pathways in P. putida KT2440 that allow it to transform aromatic compounds, including phenylalkanoates, ferulate, vanillate, and coniferyl- and coumaryl alcohols, aldehydes and acids. TIGR Assistant Investigator Ian Paulsen, who explored the correlation of metabolic pathways with membrane transport capability, said P. putida has "lots of novel pathways and transport capabilities to break down aromatic and other unusual compounds."

The P. putida genome also was compared to that of other species to reveal details about the microbe's evolutionary history. Perhaps the most revealing comparison was with the genome of another member of the Pseudomonas genus - P. aeruginosa, which is an opportunistic pathogen and the leading cause of death for cystic fibrosis patients.

TIGR evolutionary biologist Jonathan Eisen said, "Such comparisons among closely related species with different biological properties are invaluable in learning about the biology of each species. In this case it allows us to better identify the features in the P. aeruginosa genome that contribute to making it a pathogen."

An analysis by Tuemmler and Christian Weinel of the MHH identified numerous chemosensory systems, cell attachment factors, and transport systems in P. putida that had been thought to be involved in virulence in P. aeruginosa. For example the KT2440 (P. putida) genome contains a chromosomal region that is present in 85% of P. aeruginosa clinical isolates from sepsis and urinary tract infections. "That suggests that those genes many not be specific for virulence," said Eisen. The researchers did, however, find many genes in P. aeruginosa and not P. putida that had not previously been identified as candidates for being involved in pathogenicity. The identification of such genes may help biomedical researchers pinpoint potential targets for developing drugs or vaccines against this pathogen.

The Institute for Genomic Research (TIGR)



Related Bacteria Current Events and Bacteria News Articles Bacteria Current Events and Bacteria News RSS Bacteria Current Events and Bacteria News RSS
Factors from common human bacteria may trigger multiple sclerosis
Current research suggests that a common oral bacterium may exacerbate autoimmune disease. The related report by Nichols et al, "Unique Lipids from a Common Human Bacterium Represent a New Class of TLR2 Ligands Capable of Enhancing Autoimmunity," appears in the December 2009 issue of The American Journal of Pathology.

Exposure to both traffic, indoor pollutants puts some kids at higher risk for asthma later
New research presents strong evidence that the "synergistic" effect of early-life exposure to both outdoor traffic-related pollution and indoor endotoxin causes more harm to developing lungs than one or the other exposure alone.

New study finds MRSA on the rise in hospital outpatients
The community-associated strain of the deadly superbug MRSA-an infection-causing bacteria resistant to most common antibiotics-poses a far greater health threat than previously known and is making its way into hospitals, according to a study in the December issue of Emerging Infectious Diseases.

Researchers establish common seasonal pattern among bacterial communities in Arctic rivers
New research on bacterial communities throughout six large Arctic river ecosystems reveals predictable temporal patterns, suggesting that scientists could use these communities as markers for monitoring climate change in the polar regions.

Biologists discover bacterial defense mechanism against aggressive oxygen
Bacteria possess an ingenious mechanism for preventing oxygen from harming the building blocks of the cell.

Saving the single cysteine: new antioxidant system found
We've all read studies about the health benefits of having a life partner. The same thing is true at the molecular level, where amino acids known as cysteines are much more vulnerable to damage when single than when paired up with other cysteines.

Beyond sunlight: Explorers census 17,650 ocean species between edge of darkness and black abyss
Census of Marine Life scientists have inventoried an astonishing abundance, diversity and distribution of deep sea species that have never known sunlight - creatures that somehow manage a living in a frigid black world down to 5,000 meters (~3 miles) below the ocean waves.

Surface bacteria maintain skin's healthy balance
On the skin's surface, bacteria are abundant, diverse and constant, but inflammation is undesirable. Research at the University of California, San Diego School of Medicine now shows that the normal bacteria living on the skin surface trigger a pathway that prevents excessive inflammation after injury.

On the Trail of a Vaccine for Lyme Disease: Yale Researchers Target Tick Saliva
A protein found in the saliva of ticks helps protect mice from developing Lyme disease, Yale researchers have discovered. The findings, published in the November 19 issue of Cell Host & Microbe, may spur development of a new vaccine against infection from Lyme disease, which is spread through tick bites.

Cigarettes Harbor Many Bacteria Harmful to Human Health
Cigarettes are "widely contaminated" with bacteria, including some known to cause disease in people, concludes a new international study conducted by a University of Maryland environmental health researcher and microbial ecologists at the Ecole Centrale de Lyon in France.
More Bacteria Current Events and Bacteria News Articles
A Field Guide to Bacteria (Comstock Book)

A Field Guide to Bacteria (Comstock Book)
by Betsey Dexter Dyer (Author)

Pocket-guide to observing bacteria without a laboratory or fancy equipment. Presents all the major taxonomic groups of bacteria in a useable, accessible format for amateur naturalists who may or may not have access to a microscope. Includes ideas for planning field trips to explore bacteria in their natural environments. Illustrated, some color. Softcover, hardcover available.

Ein-O Science BioSigns Bacteria

Ein-O Science BioSigns Bacteria
by Tedco

The hands on cell and microbiology models provide magnified and cross section details. The set includes Virus, Bacteria, Plant Cell, White Blood Cell, Red Blood Cell and Animal Cell. Ein-O's I Know Guides and storage box are included. Consider using these models with a display of your own making - featuring the intricacies of cell structure, comparing and contrasting differences, investigating functions & interactions, or describing the efforts of modern medicine... a neat Science Fair Project. Virus - This hands-on interactive model provides magnified and cross-sectioned detailing of a Virus. Animal Cell - This hands-on interactive model provides magnified and cross-sectioned detailing of an Animal Cell. White Blood Cell - This hands-on interactive model provides...

Bacteria (Discovery Channel School Science)

Bacteria (Discovery Channel School Science)
by Lynn Brunelle (Author), Barbara Ravage (Author), Lynn Brunelle (Editor), Barbara Ravage (Editor), Gareth Stevens Publishing (Editor)



Good Germs, Bad Germs: Health and Survival in a Bacterial World

Good Germs, Bad Germs: Health and Survival in a Bacterial World
by Jessica Snyder Sachs (Author)

Making Peace with Microbes
 
Public sanitation and antibiotic drugs have brought about historic increases in the human life span; they have also unintentionally produced new health crises by disrupting the intimate, age-old balance between humans and the microorganisms that inhabit our bodies and our environment. As a result, antibiotic resistance now ranks among the gravest medical problems of modern times. Good Germs, Bad Germs addresses not only this issue but also what has become known as the “hygiene hypothesis”—  an argument that links the over-sanitation of modern life to now-epidemic increases in immune and other disorders. In telling the story of what went terribly wrong in our war on germs, Jessica Snyder Sachs explores our emerging understanding of the symbiotic...

60 Minutes - Superbug (November 11, 2007)

60 Minutes - Superbug (November 11, 2007)

Airdate 11/11/07 MRSA is a superbug, a staff infection that has moved out of hospitals and nursing homes and is now infecting healthy people, sometimes killing them. That's because once the MRSA infection gets into the blood stream, it is largely resistant to antibiotics. For now, the best medicine is prevention. What does this mean? Scrubbing down school desks? Hosing down team locker rooms? Sending infected kids home? Lesley Stahl reports.

This product is manufactured on demand using DVD-R recordable media. Amazon.com's standard return policy will apply.

Molecular Genetics of Bacteria (Snyder, Molecular Genetics of Bacteria)

Molecular Genetics of Bacteria (Snyder, Molecular Genetics of Bacteria)
by Larry Snyder (Author), Wendy Champness (Author)

This landmark volume provides the single most comprehensive and authoritative textbook on bacterial molecular genetics. Perfect for advanced undergraduate and graduate-level courses, the text presents the latest research on the subject in a clearly written and well-illustrated style. It provides descriptive background information, detailed experimental methods, examples of genetic analyses, and advanced material relevant to current applications of molecular genetics. While providing a deep understanding of bacterial molecular genetics, the material is integrated with biochemical, genomic, and structural information to broaden understanding.

The approach centers on the most-studied bacteria, Escherichia coli and Bacillus subtilis. In addition, examples from other bacteria with...

Magic School Bus World of Germs Science Kit

Magic School Bus World of Germs Science Kit
by Young Scientist Club

The World of Germs- Magic School Bus Science Kit FUN

Disposable EARLOOP Face MASK, Filters Bacteria 3 Ply - (Box of 50)

Disposable EARLOOP Face MASK, Filters Bacteria 3 Ply - (Box of 50)
by EVERREADY FIRST AID

Tie-on surgical face mask with high bacterial filtration efficiency (BFE), low breathing resistance, soft, odorless, non-irritating, comfortable superior fit, fiberglass free.

Essick Air #1970 Quart Bacteria Treatment

Essick Air #1970 Quart Bacteria Treatment
by ESSICK AIR PRODUCTS

QT, Humidifier Bacteria Treatment, Helps Fight Bacteria & Algae Build Up, Keeps Water Smelling Clean, EPA Registered, For Use In All Evaporative Console & Room Size Humidifiers.

Enzymatic Therapy Acidophilus Pearls (90 Pearls)

Enzymatic Therapy Acidophilus Pearls (90 Pearls)
by Enzymatic

This formula provides a combination of Acidophilus and Bididiobacterium species to support the overall health of the intestinal tract.

© 2009 BrightSurf.com