For Immediate Release

Contact:
Lorinda Klein
Office of Communications
NYU Langone Medical Center
Tele: 212-404-3555
E-mail: Lorindaann.Klein@nyumc.org

Study Explains Mystery of Genetic Tolerance in E. coli
NYU Langone Researchers Use Combination of Genomics, Proteomics For Surprising Finding

NEW YORK, May 15, 2008 - A new study led by researchers at NYU Langone Medical Center is shedding new light on the action of key regulatory proteins in E. coli with far reaching implication for understanding bacterial evolution and virulence.  The study, published in the May 16, 2008 issue of the journal Science reveals a protein called Rho serves a global function in bacterial survival -- maintaining boundaries between genes and ensuring that bacterium produces enough RNA for immediate cellular functions. 

The study also found that Rho and its co-factors silence so-called foreign DNA in the bacterium, which had been acquired by swapping genes with other bacteria and viruses. E. coli is a common denizen of the human gut. While most strains are harmless, some can cause serious illness. 
           
Rho was the first termination factor discovered in bacteria. It act as red lights to gene transcription. However, it was not clear, until now, how many genes were affected by Rho and why it was so essential to bacterial survival. This study explains why when Rho is knocked out, bacterial cells die.

“Bacteria have a much tidier genome than humans,” said Evgeny Nudler, Ph.D., a Julie Wilson Anderson Professor of Biochemistry at NYU School of Medicine, who led the study.  “The tiny microorganisms pack their genes closely together, without a lot of so-called junk DNA.  For the E. coli bacteria, some 90 percent of the genome contains sequences that code for protein.”

“Our study shows that Rho is really pervasive, and it terminates transcription in nearly every gene,” says Dr. Nudler. “The first major role of Rho is to adjust the levels of transcription to the translational needs of the bacteria.  In other words, Rho makes sure the bacterium isn’t burdened with too much useless RNA. Rho is also needed for survival because it appears to keep potentially toxic genes at bay.” Transcription is the first step toward making a working protein and translation is the second step.

“Rho is an ancient protein and it is found throughout bacteria,” says Christopher J. Cardinale, an M.D.- Ph.D. student in Dr. Nudler’s laboratory and the first author on the paper. He speculates that Rho’s pervasive function as a genetic boundary keeper enables bacteria to grow quickly. “Bacteria are so small and they don’t carry around a lot of extra DNA. Throughout evolution Rho may have allowed genes to be packed close together, so that in turn enabled bacteria to grow quickly.” 
   
The elegant study combined the power of genomics, which allowed the researchers to assay the activity of the entire genomes of four strains of E. coli, and of proteomics, the genome-wide analysis of proteins. The NYU Langone Medical Center researchers and their colleagues at Columbia University Medical Center figured out what role Rho plays in the cell by evaluating the response of E. coli to the widely used animal antibiotic bicyclomycin, which specifically inhibits Rho. They could see which genes were switched on and off when Rho wasn’t functioning. In the second part of the study, they used a powerful robotic technique called DIGE (differential gene electrophoresis) to pluck out proteins produced by genes in E. coli in response to the antibiotic, and then employed mass spectrometry to identify these proteins.
           
The protein analysis showed that Rho, along with two co-factors, was silencing foreign DNA in E. coli. This foreign DNA, inserted into E. coli millions of years ago, was toxic to the cell. “It was really surprising that the genes that were the most actively regulated by Rho were those genes acquired by horizontal events [gene swapping], and not the genes belonging to the bacteria,” said Dr. Nudler.

Drs. Nudler and Cardinale said that there were no immediate clinical applications of their findings, but they speculated that their findings may be of use in the development of other antibiotics that target Rho. Most bacterial resistance to antibiotics is acquired through horizontal transfer, they point out.        

The authors of the study are Chrisopher J. Cardinale, Robert S. Washburn, Vasisht R. Tadigotta, Lewis M. Brown, Max E. Gottesman, and Evgeny Nudler.
                                               
###

ABOUT NYU LANGONE MEDICAL CENTER

One of the world’s premier academic medical institutions for more than 155 years, NYU Medical Center continues to be a leader in patient care, physician education and scientific research.  NYU Medical Center is internationally renowned for excellence in areas such as cardiovascular disease, pediatrics, skin care, neurosurgery, urology, cancer care, rehabilitation, plastic surgery, minimally invasive surgery, transplant surgery, infertility, women’s health and day surgery.

Below:
RNA polymerase moves along the DNA molecule, copying its sequence of letters into ribonucleic acid. A protein called Rho binds to the newly-synthesized RNA and blocks the polymerase, preventing it from expressing toxic genes.

###