Cramped quarters create 'knotty' problem for genes
By Ruth SoRelle, M.P.H.
Imagine what happens when nature crams three or more feet of DNA into the nucleus of a cell too small to see with the naked eye.
The DNA twists, coils and compresses itself to fit into the tiny space. Inevitably, it forms knots. Until recently, no one knew what the consequences of those knots are.
However, recent work by Lynn Zechiedrich, Ph.D., associate professor of molecular virology and microbiology at Baylor College of Medicine, and her colleagues, shows that knotted DNA causes genes to malfunction. A report of her works appears in an online issue of the open access journal BMC Molecular Biology. Visit the Zechiedrich lab at http://www.bcm.edu//labs/zechiedrich/.
A genetic knotty problem
Knotting causes loss of genetic material by blocking DNA replication. The knotting also prevents the gene from being transcribed into the active template from which the cells makes a protein. Zechiedrich and her colleagues show that knots cause mutation at rates three to four orders of magnitude higher than those of unknotted DNA.
They concentrated their knot work on Escherichia coli, a common form of bacteria. Enzymes called topoisomerases (topoisomerases IV in E. coli) are charged with unknotting these tangles, but Zechiedrich's studies demonstrate that topoisomerase IV has to get to the knot quickly to prevent the toxic events that can lead to cell death.
Much of Zechiedrich's work focuses on elucidating the work of topoisomerases, which are enzymes critical to the work of cells.
"Cells have processes that make sure that newly replicated chromosomes segregate – become untangled from one another – and separate to make cell division possible," she said. "These processes hold up cell division until the DNA has been partitioned by the topoisomerases into each cell."
Some genes die before vital enzyme can untangle knots
"As a consequence, if, in the laboratory, we form more unsegregated DNA in a cell, the cell waits patiently and does not divide until topoisomerase IV catches up with the links we made. When this happens, the cells live. Knots, however, can block the function of a gene. If that gene is important for cell survival, then the cell dies or mutates before topoisomerase IV can catch up with the extra knots we tied.
"Therefore, DNA unknotting is a critically important role of the topoisomerases," she said. "Topoisomerases are the target for some of the most widely-prescribed antibiotics, the fluoroquinolones. Cipro, or ciprofloxacin, the antibiotic in demand during the 2001 anthrax scare, is one of these."
Study could improve fight against infection, cancer
"Topoisomerases are not just bacterial. Some of those made by human cells are important anti-cancer drug targets. Therefore, understanding what these enzymes do in a cell may help us better understand how these drugs stop infection and cancer."
"The DNA is not static within the cell," Zechiedrich said. "Its normal motion may pull the knot tight and maybe causes it to break or knots it so tightly that normal chemical reactions cannot occur. In either case, knots can lead to cell death."
Do knotted cells have evolutionary advantage?
"Maybe DNA knots help drive evolution," she says. "In the laboratory, most of the cells containing mutated DNA that resulted from knotting survived better than the starting cells that were not knotted—definitely an evolutionary advantage."
Others who took part in this research include former BCM graduate student Dr. Richard W. Deibler, now of Harvard Medical School; Dr. Jennifer K. Mann, of BCM and the Florida State University Department of Mathematics in Tallahassee, and Dr. De Witt L. Sumners, also of FSU.
Funding for this report came from the National Science Foundation, the National Institutes of Health, and the Burroughs Wellcome Fund.
The article can be found at http://www.biomedcentral.com/1471-2199/8/44
