Genome British Columbia

Genome British Columbia

March 21, 2005 13:28 ET

Genome British Columbia: UBC Team Sequence Largest Bacterial Genome to Date; May Facilitate Clean up of Hazardous Waste and Development of New Antibiotics


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FOR: GENOME BRITISH COLUMBIA

MARCH 21, 2005 - 13:28 ET

Genome British Columbia: UBC Team Sequence Largest
Bacterial Genome to Date; May Facilitate Clean up of
Hazardous Waste and Development of New Antibiotics

VANCOUVER, BRITISH COLUMBIA--(CCNMatthews - March 21, 2005) - Genome
British Columbia

An international team led by three UBC microbiologists has completed the
sequencing and annotation of the genome of Rhodococcus sp. RHA1, a soil
bacterium, which is the largest bacterial genome sequenced to date. It
is the first genome of a Rhodococcus to be completely sequenced, and the
first bacterial genome to be entirely sequenced and annotated in Canada.

"We began this project expecting to learn more about how these bacteria
degrade toxic pollutants, but ended up also coming up with ideas on how
to cut costs in the production of antibiotics and other important
pharmaceuticals," enthused Prof. Lindsay Eltis, who together with Profs.
William Mohn and Julian Davies spearheaded the research effort.

The sequencing of the organism's genome has contributed to understanding
the physiological basis of its exceptional ability to break down PCB's
and other toxic wastes and its adaptation to environmental stresses.
According to Dr. Mohn, "This genome sequence is a powerful new tool for
advancing our understanding of how microorganisms degrade toxic
pollutants and how a group of important soil microorganisms function in
their natural environment."

Because of their strong catabolic capacities and genetic plasticity,
microorganisms such as Rhodococcus sp. RHA1 are capable of breaking down
complex organic compounds including environmental pollutants. The
organism was isolated from soil containing lindane, a highly toxic
insecticide, by Prof. Masao Fukuda, a collaborator in Nagaoka, Japan.
"We picked this organism because of its environmental and industrial
importance. The most commercially successful application of a bacterium
in an industrial process involves a strain of Rhodococcus," continued
Eltis.

Another important finding of the research shows just how similar
rhodococci are to streptomycetes, a family of bacteria that produce over
70% of the antibiotics in use today. "By making the genome sequence of
Rhodococcus RHA1 available to the scientific community worldwide we hope
that other research teams will build on this knowledge to develop new
antibiotics and other pharmaceutical products," said Dr. Michael McLeod,
head of annotation in the Microbial Envirogenomics Group (MEG) at UBC.

"Funding of this research by Genome Canada and Genome British Columbia
is another example of the Federal and Provincial Governments' commitment
to maintain Canada's leadership in science and to improve the
environment for people of all nations. This funding is especially vital
considering scientists south of the border are lamenting the lack of
funding (from the US government) for studying microbes which are not
seen as bioterrorism threats," continued Dr. McLeod.

The sequencing and assembly of the DNA was performed at the Michael
Smith Genome Sciences Center (GSC), while the sequence analysis and
subsequent experimental research was performed by the MEG. "The sequence
is of a very high quality, which means that the international scientific
community using the data can do so with a high degree of confidence,"
said Dr. Eltis.

The sequence and annotation of the Rhodococcus sp. RHA1 genome will be
formally presented to the scientific community at the International
Conference on Microbial Genomes on April 13-16, 2005 in Halifax, Nova
Scotia, Canada. For more information on this research visit the official
Rhodococcus Genome Project web site at http://www.rhodococcus.ca/.

The project involves collaborations with researchers from Japan,
Germany, England, Spain, Argentina, The Netherlands, Ireland and the
United States.

The focus of the BC Cancer Agency's Michael Smith Genome Sciences Centre
is to minimize the burden of cancer on individuals and society through
genomics research, and to advance life sciences research through the
development and application of genomics technologies. The GSC employs
more than 170 staff, and houses world-class DNA sequencing, BAC
fingerprint mapping and bioinformatics facilities. The GSC has sequenced
several genomes, and was the first lab in the world to sequence the
genome of the coronavirus associated with SARS.

Genome British Columbia is an organization that invests in and manages
19 large-scale genomics and proteomics research projects and science and
technology platforms focused on areas such as human health, forestry,
fisheries, agriculture and the environment. GBC is funded by Genome
Canada, the Province of BC and other private and public investors.

Genome Canada is the primary funding and information resource relating
to genomics and proteomics in Canada. Since its creation in 2000, it has
invested $855 million in research in Canada, from public and private
sector sources in Canada and abroad.

BACKGROUNDER ON RHODOCOCCUS SP. RHA1

The Rhodococcus sp. RHA1 genome contains over 9.7 million base pairs
(Mbp) making it the largest bacterial genome sequenced to date,
outpacing the next nearest sequenced genome by over 500 thousand base
pairs (Kbp). The genome is comprised of four linear genetic elements,
including a 7.8 Mbp chromosome, and 3 linear plasmids of 0.33 to 1.1
Mbp. Automated and manual analysis of the sequence has indicated the
presence of over 9,300 genes. These include genes encoding proteins that
break down a number of toxic substances including polychlorinated
biphenyls (PCBs), toluene and phthalates.

In total, the team has identified over 1,500 separate enzymes involved
in over 270 pathways. In addition to genes for degrading toxic waste,
Rhodococcus sp. RHA1 also contains a number of genes related to
antibiotic production including five genes that are larger than 25 Kbp.
Importantly, the annotation reveals that there is much more to learn
about this organism, as over half of the genes identified in each
plasmid and approximately 30% of the genes in the chromosome are of
unknown function.

Unlike most other genome projects, which stop after sequencing and
electronic annotation, this project is also using laboratory techniques
to study the function of this organism at a molecular level. The
Rhodococcus sp. RHA1 genome project is using high-throughput proteomics,
transcriptomics and gene disruption to investigate metabolic pathways,
regulatory networks and stress responses. To date, the team has verified
the expression of approximately 3,000 transcripts and approximately 250
proteins.

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Contact Information

  • FOR FURTHER INFORMATION PLEASE CONTACT:
    Genome British Columbia
    Linda Bartz
    Director, Communications
    (604) 637-4373
    lbartz@genomebc.ca
    or
    Genome British Columbia
    Rachael Froese Zamperini
    Communications Officer
    (604) 637-4378
    rfroesezamperini@genomebc.ca