Proteins Interacting with RNA and DNA Are Surprisingly SimilarChemists trying to produce new and more effective antibiotics have made a surprising discovery; a protein that attaches itself to RNA, making it possible for a certain antibiotic to fight bacterial infection, is remarkably similar to a class of proteins that bind to DNA.
The proteins have the same general shape, and they use a similar method to bind to RNA and DNA. Those similarities came as a surprise because the proteins have completely different functions, and they attach to different structures -- the double-stranded, ladder-like DNA, and the single-stranded RNA.
"You don't expect RNA-binding proteins to look like DNA-binding proteins because the structures in DNA and RNA are quite different," said David Draper, a Johns Hopkins University chemist who is heading the research team that made the discovery.
Draper's team discovered that the RNA- and DNA-binding proteins have the same shape, a configuration of three coils called alpha helices. Not only do they have the same shape, the proteins attach to RNA and DNA at precisely the same points along one of their coils.
A scientific paper detailing the findings was published in the January issue of a British science journal, Nature Structural Biology.
The discovery suggests that the RNA-binding protein, called L11, could be an ancient, ancestral form of other proteins that bind to DNA and are crucial to an embryo's development, turning on and off various genes needed to form specific anatomical features.
L11 has existed for at least 2 billion years, since the time when higher organisms began to diverge from bacteria. By comparison, the similar DNA- binding proteins, called homeodomain proteins, first emerged only about 400 million years ago, Draper said.
In the cells of living organisms, L11 attaches to ribosomes, particles that produce proteins. The L11 enables the ribosomes to make proteins twice as fast. When it attaches to the ribosomes in bacteria, the bacteria are able to multiply much faster than they ordinarily would because the rate of protein production is doubled.
An antibiotic called thiostrepton works by attaching to both the L11 protein and the ribosomal RNA of infection-causing bacteria, preventing the production of protein and controlling the bacterial infection.
But, although a nearly identical protein also is attached to the ribosomes of higher forms of life, the antibiotic will only bind to the bacterial RNA.
How the antibiotic distinguishes between the two types of RNA is a mystery, since the segment of RNA that the protein binds to is very similar in bacteria and higher organisms. There must be specific features that are only present in the bacterial RNA, Draper said.
"Those are very handy features because that means you can design drugs to target just bacteria and not kill the host," he said.
RNA, or ribonucleic acid, is essential in the manufacture of proteins ranging from vital enzymes and hormones to hemoglobin and structural components. DNA, or deoxyribonucleic acid, contains the huge library of genetic information organisms need to reproduce and to make RNA. Both RNA and DNA are made of molecules called nucleotides. But RNA is a single-stranded compound of the molecules and DNA has two strands, which are connected in a twisting structure called a double helix.
Learning why the RNA- and DNA-binding proteins are so similar could lead to insights specifically about the protein's interaction with RNA, which could shed light on how the antibiotic distinguishes between the two forms of RNA. Such insights could one day enable scientists to make better antibiotics.
In the search for more effective antibiotics, Draper is working with a biotechnology company to investigate compounds that bind to the same segment of RNA as thiostrepton. Thiostrepton is not water-soluble enough to be taken orally. Consequently, the antibiotic, which is used to treat ear infections in animals, can be administered only externally, as a salve.
"But you can't do that for an internal infection, such as tuberculosis," Draper said. A water-soluble antibiotic that worked the same way as thiostrepton could be administered orally. Also involved in the research were Hopkins graduate student Debraj GuhaThakurta and former graduate student Yanyan Xing.
Draper's work has earned him a prestigious MERIT award from the National Institutes of Health. MERIT stands for Method to Extend Research in Time. The 10-year awards are given only to scientists with a record of outstanding contributions and for work that has excellent future potential. The award was issued in September 1996 by the NIH's National Institute of General Medical Sciences, which has funded Draper's research since 1981.
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