BACKGROUND: Researchers at the Scripps Institution of Oceanography have discovered bacteria in mud from the Bahamas with the potential to help fight cancer. Now that the bacteria's genome has been successfully sequenced, that information is now being used by a pharmaceutical company to treat bone marrow cancer patients.
ABOUT THE BACTERIA: The bacteria known as Salinispora tropica is related to the Streptomyces genus, a land-based group of bacteria considered to be the kinds of antibiotic-producing organisms. First discovered in 1991 in shallow ocean sediment off the Bahamas, it took several years to successfully sequence Salinispora's genome, revealing that this mud-dwelling bacteria produces natural antibiotics and anti-cancer products. Researchers found that 10% of the bacteria's genome is dedicated to producing molecules for antibiotics and anti-cancer agents, compared to only 6% to 8% of most organisms' genomes. The decoding opens the door to a broad range of possibilities for isolating and adapting potent molecules the marine organism naturally employs for chemical defense, scavenging for nutrients, and communication in its ocean environment. One compound, salinosporamide A, is currently in human clinical trials for treating multiple myeloma, a cancer of plasma cells in bone marrow, as well as for treating solid tumors.
SEQUENCING ABCS: Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome: the building blocks that make up an organism's DNA. The entire genome can't be sequenced at once because DNA sequencing methods can only handle short stretches of DNA at a time. So scientists break the DNA into small pieces, sequence those, and then reassemble the pieces into the proper order to sequence the entire genome. There are two ways of doing this. The 'clone-by-clone' approach involves breaking the genome into chunks, called clones, each about 150,000 base pairs long, then using genome mapping techniques to figure where each belongs in the genome. Next they cut the clones into smaller, overlapping pieces of about 500 base pairs each, sequence those pieces, and use the overlaps to reconstruct the sequence of the entire clone.
An alternative strategy, called the 'whole-genome shotgun method', involves breaking the genome into small pieces, sequencing them, and then reassembling the pieces into the full genome. The clone-by-clone approach is more reliable, but slow and time-consuming. The shotgun method is faster, but it can be extremely difficult to accurately put together so many tiny pieces of sequence all at once. Neither of these approaches proved sufficient to completely solve the Salinispora tropica genomic puzzle, however. Instead, information about the natural chemistry of the organism helped close the sequencing gap.
The American Geophysical Union contributed to the information contained in the TV portion of this report.