Featured Research

from universities, journals, and other organizations

How bacteria acquire immunity: First theoretical description of bacterial system to silence viral genes

Date:
September 16, 2010
Source:
Rice University
Summary:
In a new study, scientists have brought the latest tools of computational biology to bear in examining how the processes of natural selection and evolution influence the way bacteria acquire immunity from disease. The study builds upon one of the major discoveries made possible by molecular genetics in the past decade -- the revelation that bacteria and similar single-celled organisms have an acquired immune system.

In a new study, Rice University scientists bring the latest tools of computational biology to bear in examining how the processes of natural selection and evolution influence the way bacteria acquire immunity from disease.

The study is available online from Physical Review Letters. It builds upon one of the major discoveries made possible by molecular genetics in the past decade -- the revelation that bacteria and similar single-celled organisms have an acquired immune system.

"From a purely scientific perspective, this research is teaching us things we couldn't have imagined just a few years ago, but there's an applied interest in this work as well," said Michael Deem, the John W. Cox Professor in Biochemical and Genetic Engineering and professor of physics and astronomy at Rice. "It is believed, for instance, that the bacterial immune system uses a process akin to RNA interference to silence the disease genes it recognizes, and biotechnology companies may find it useful to develop this as a tool for silencing particular genes."

The new study by Deem and graduate student Jiankui He focused on a portion of the bacterial genome called the "CRISPR," which stands for "clustered regularly interspaced short palindromic repeats." The CRISPR contain two types of DNA sequences. One type -- short, repeating patterns that first attracted scientific interest -- is what led to the CRISPR name. But scientists more recently learned that the second type -- originally thought of as DNA "spacers" between the repeats -- is what the organism uses to recognize disease.

"Bacteria get attacked by viruses called phages, and the CRISPR contain genetic sequences from phages," Deem said. "The CRISPR system is both inheritable and programmable, meaning that some sequences may be there when the organism is first created, and new ones may also be added when new phages attack the organism during its life cycle."

The repeating sequences appear to be a kind of bookend or flag that the organism uses to determine where a snippet from a phage begins and ends. The CRISPR will often have between 30 and 50 of these snippets of phage sequences. Previous studies have found that once a bacteria has a phage sequence in its CRISPR, it has the ability to degrade any DNA or RNA that match that sequence -- meaning it can fend off attacks from any phages that have genes matching those in its CRISPR.

"What we wanted to explore was how the history of a bacterium's exposure to phages influences what's in the CRISPR," Deem said. "In other words, how is an organism's previous exposure to viruses reflected in its own genome?"

From earlier published studies, Deem and He knew that phage sequences were added to the CRISPR sequentially. So, in a CRISPR system containing 30 snippets, the newest one would be in position one, at the front of the line. In another study in 2007, researchers examining the CRISPR of whole populations of bacteria noticed some statistical irregularities. They found that the likelihood of two different organisms having the same snippet in their CRISPR increased exponentially as they progressed away from position one. So, in the organism with 30 snippets, the phage gene in position 30 was the most likely to be conserved time and again across all the bacteria in the population.

To use the power of computers to examine why this happens, Deem and He needed a mathematical description of what was happening over time to both the bacterial and phage populations. The equations they created reflect the way the bacterial and phage populations interact via the CRISPR.

"Each population is trying to expand, and selective pressure is constantly being applied on both sides," Deem said. "You can see how this plays out in the CRISPR over time. There's a diverse assortment of genes in the first spacer, but the second spacer has been in there longer, so there's been more selective pressure applied to that spacer. Because bacteria that contain the dominant viral strain in their CRISPR are more likely to survive than those that don't, they tend to squeeze out their neighbors that are more vulnerable. At position N, the farthest way from position one, selection has been at work the longest, so the genes we find there were the most common and the ones that tended to afford the most overall protection to the organism."

In addition to interest from biotechnology firms, Deem said the workings of the CRISPR are of interest to drugmakers who are investigating new types of antibiotics.

The research was supported by the Defense Advanced Research Projects Agency.


Story Source:

The above story is based on materials provided by Rice University. Note: Materials may be edited for content and length.


Journal Reference:

  1. Jiankui He, Michael Deem. Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). Physical Review Letters, 2010; 105 (12): 128102 DOI: 10.1103/PhysRevLett.105.128102

Cite This Page:

Rice University. "How bacteria acquire immunity: First theoretical description of bacterial system to silence viral genes." ScienceDaily. ScienceDaily, 16 September 2010. <www.sciencedaily.com/releases/2010/09/100915171531.htm>.
Rice University. (2010, September 16). How bacteria acquire immunity: First theoretical description of bacterial system to silence viral genes. ScienceDaily. Retrieved September 3, 2014 from www.sciencedaily.com/releases/2010/09/100915171531.htm
Rice University. "How bacteria acquire immunity: First theoretical description of bacterial system to silence viral genes." ScienceDaily. www.sciencedaily.com/releases/2010/09/100915171531.htm (accessed September 3, 2014).

Share This



More Plants & Animals News

Wednesday, September 3, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Snack Attack: Study Says Action Movies Make You Snack More

Snack Attack: Study Says Action Movies Make You Snack More

Newsy (Sep. 2, 2014) You're more likely to gain weight while watching action flicks than you are watching other types of programming, says a new study published in JAMA. Video provided by Newsy
Powered by NewsLook.com
Get A Mortgage, Receive A Cat — Only In Russia

Get A Mortgage, Receive A Cat — Only In Russia

Newsy (Sep. 2, 2014) The incentive is in keeping with a Russian superstition that it's good luck for a cat to be the first to cross the threshold of a new home. Video provided by Newsy
Powered by NewsLook.com
U.N. Says Ebola Travel Restrictions Will Cause Food Shortage

U.N. Says Ebola Travel Restrictions Will Cause Food Shortage

Newsy (Sep. 2, 2014) The U.N. says the problem is two-fold — quarantine zones and travel restrictions are limiting the movement of both people and food. Video provided by Newsy
Powered by NewsLook.com
Sharks Off the Menu and on the Tourist Trail in Palau

Sharks Off the Menu and on the Tourist Trail in Palau

AFP (Sep. 2, 2014) Tourists in Palau clamour to dive with sharks thanks to a pioneering conservation initiative -- as the island nation plans to completely ban commercial fishing in its vast ocean territory. 01:15 Video provided by AFP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins