Featured Research

from universities, journals, and other organizations

First of its kind gene map of sulfate-reducing bacterium created

Date:
November 10, 2011
Source:
DOE/Lawrence Berkeley National Laboratory
Summary:
Critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment have been revealed in a new study. Researchers have created a first-of-its-kind gene map of Desulfovibrio vulgaris, which can be used to identify the genes that determine how these bacteria interact with their surrounding environment.

A first-of-its-kind gene map of the Desulfovibrio vulgaris bacterium could play an important role in future clean-ups of a wide range of contaminated environments.
Credit: Image courtesy of Berkeley Lab

Critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment have been revealed in a study by researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab). The researchers have provided the first ever map of the genes that determine how these bacteria interact with their surrounding environment.

"Knowing how bacteria respond to environmental changes is crucial to our understanding of how their physiology tracks with consequences that are both good, such as bioremediation, and bad, such as biofouling," says Aindrila Mukhopadhyay, a chemist with Berkeley Lab's Physical Biosciences Division, who led this research. "We have reported the first systematic mapping of the genes in a sulfate-reducing bacterium -- Desulfovibrio vulgaris - that regulate the mechanisms by which the bacteria perceive and respond to environmental signals."

Mukhopadhyay, who also holds an appointment with the Joint BioEnergy Institute (JBEI), a DOE Bioenergy Research Center, is the corresponding author of a paper that describes this research in the journal Genome Biology.

Desulfovibrio vulgaris is an anaerobic bacterium that is present in numerous ecological niches and serves as a model organism for the study of sulfate-reducing bacteria. The microbe has drawn much attention -- both good and bad -- for its unique ability to metabolize metals. On the good side, D. vulgaris can generate enzymes that reduce toxic heavy metals and radioactive nuclides into non-hazardous forms. On the bad side, D. vulgaris is also notorious as a pest that corrodes the metals used in oil drilling and storage operations.

"For all of these reasons, it is important that we understand the molecular signaling systems by which D. vulgaris interacts with and survives in its many different environments," says Mukhopadhyay. "Yet, after more than seven decades of study, not a single one of the approximately 70 known molecular signaling systems in D. vulgaris had been characterized."

As humans, it is customary to think of us interacting with our environment through the five senses -- sight, sound, smell, touch and taste. However, this information processing actually takes place through molecular signaling systems. Bacteria also process signals at the molecular level but they utilize a two-component system in which one protein -- a histidine kinase -- senses an environmental signal, which it then transfers to a second protein -- a response regulator -- that controls the reaction.

"These microbial systems are difficult to identify and study because they don't become active until they sense a specific environmental signal and we don't know what most of those signals are," Mukhopadhyay says. "We had to figure a way around this conundrum."

Mukhopadhyay and her co-authors were able to bypass the need to know the signal activation conditions and map virtually the entire D. vulgaris gene response network through genome-wide in vitro experimental determinations. They accomplished this using a "DNA-Affinity-Purified-chip (DAP-chip) strategy" they devised, in which purified response regulator proteins are incubated with genomicDNA and used to enrich DNA regions that bind to them. Both the enriched and the starting input DNA are amplified, pooled and hybridized in a customized D. vulgaris microarray to determine enriched gene targets.

"To our knowledge, this is the first extensive use of a genome-wide method to map all bacterial two component system response regulator binding sites in a single study," Mukhopadhyay says.

Mukhopadhyay and her colleagues have already used their new gene map to predict the functions of several response regulators in D. vulgaris that include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation. They have also predicted responses to stresses such as nitrite, low potassium and phosphate starvation.

"For several response regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study," Mukhopadhyay says. "In the future this gene map should help guide the development of bioremediation methods that do not exacerbate existing problems, and also help guide field practices that will enhance desirable outcomes."

The DAP-chip strategy used to create this regulatory gene map for D. vulgaris can also be used to create similar gene maps for any microbe whose genome has been sequenced. Given that the regulatory network of a microbe is often a reflection of the environments in which it thrives and the biogeochemical processes it can mediate, such gene maps should have an important role in future clean-ups of a wide range of contaminated environments.

"Our study is inherently foundational and the regulatory networks we discovered not only inform us about the bacterial response to heavy metals but also allows us to correlate microbial activity to other biofouling phenomena as well," says Mukhopadhyay.

Co-authoring the Genome Biology paper on this work, which was carried out through Berkeley Lab's ENIGMA program, were Lara Rajeev, Eric Luning, Paramvir Dehal, Morgan Price and Adam Arkin.

This research was funded by the DOE Office of Science.


Story Source:

The above story is based on materials provided by DOE/Lawrence Berkeley National Laboratory. Note: Materials may be edited for content and length.


Journal Reference:

  1. Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin and Aindrila Mukhopadhyay. Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biology, 2011, 12:R99 DOI: 10.1186/gb-2011-12-10-r99

Cite This Page:

DOE/Lawrence Berkeley National Laboratory. "First of its kind gene map of sulfate-reducing bacterium created." ScienceDaily. ScienceDaily, 10 November 2011. <www.sciencedaily.com/releases/2011/11/111109125735.htm>.
DOE/Lawrence Berkeley National Laboratory. (2011, November 10). First of its kind gene map of sulfate-reducing bacterium created. ScienceDaily. Retrieved September 15, 2014 from www.sciencedaily.com/releases/2011/11/111109125735.htm
DOE/Lawrence Berkeley National Laboratory. "First of its kind gene map of sulfate-reducing bacterium created." ScienceDaily. www.sciencedaily.com/releases/2011/11/111109125735.htm (accessed September 15, 2014).

Share This



More Plants & Animals News

Monday, September 15, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Conservationists Face Uphill PR Battle With New Shark Rules

Conservationists Face Uphill PR Battle With New Shark Rules

Newsy (Sep. 14, 2014) — New conservation measures for shark fishing face an uphill PR battle in the fight to slow shark extinction. Video provided by Newsy
Powered by NewsLook.com
Shocker: Journalists Are Utterly Addicted To Coffee

Shocker: Journalists Are Utterly Addicted To Coffee

Newsy (Sep. 13, 2014) — A U.K. survey found that journalists consumed the most amount of coffee, but that's only the tip of the coffee-related statistics iceberg. Video provided by Newsy
Powered by NewsLook.com
'Magic Mushrooms' Could Help Smokers Quit

'Magic Mushrooms' Could Help Smokers Quit

Newsy (Sep. 11, 2014) — In a small study, researchers found that the majority of long-time smokers quit after taking psilocybin pills and undergoing therapy sessions. Video provided by Newsy
Powered by NewsLook.com
Spinosaurus Could Be First Semi-Aquatic Dinosaur

Spinosaurus Could Be First Semi-Aquatic Dinosaur

Newsy (Sep. 11, 2014) — New research has shown that the Spinosaurus, the largest carnivorous dinosaur, might have been just as well suited for life in the water as on land. Video provided by Newsy
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